Patent Publication Number: US-2021171971-A1

Title: Interactors and targets for improving plant agronomic characteristics

Description:
REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY 
     The official copy of the sequence listing is submitted electronically via EFS-Web as an ASCII formatted sequence listing with a file named 7841_ST25.txt created on Dec. 7, 2018 and having a size of 1897 kilobytes and is filed concurrently with the specification. The sequence listing comprised in this ASCII formatted document is part of the specification and is herein incorporated by reference in its entirety. 
     FIELD 
     This disclosure relates to compositions and methods for improving yield in plants. 
     BACKGROUND 
     Global demand and consumption of agricultural crops is increasing at a rapid pace. Accordingly, there is a need to develop new compositions and methods to increase yield in plants. This invention provides such compositions and methods. 
     SUMMARY 
     Provided herein are polynucleotides encoding a polypeptide comprising an amino acid sequence that is at least 90%, 92%, 95%, 96%, 97%, 98%, 99% or 100% identical to a full length amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. Provided herein are polynucleotides that are at least 85% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NOS: 12-22, 32-39, and 300-561. 
     Provided herein are SEQ ID NOS: 1-11 (Interactor Polypeptides); SEQ ID NOS: 12-22 (polynucleotides encoding Interactor Polypeptides); SEQ ID NOS: 23-31, 563, and 567-572 (Direct Target Polypeptides); SEQ ID NOS: 32-39, 564, and 573-579 (polynucleotides encoding Direct Target Polypeptides); SEQ ID NOS: 40-299 (Differentially Expressed Polypeptides); SEQ ID NOS: 300-561 (polynucleotides encoding Differentially Expressed Polupeptides); SEQ ID NOS: 223-284 (Down Regulated Polypeptides); SEQ ID NOS: 485-547 (polynucleotides encoding Down Regulated Polypeptides). 
     Also provided are recombinant DNA constructs comprising a regulatory element operably linked to a polynucleotide encoding a polypeptide comprising an amino acid sequence that is at least 80% to 100% identical to a full length amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. In certain embodiments the regulatory element is a heterologous promoter. 
     Also provided are recombinant DNA constructs comprising a genetic element that suppresses or reduces expression of a polynucleotide encoding a polypeptide comprising an amino acid sequence that is at least 80% to about 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 223-284 (Down Regulated Polypeptides). In certain embodiments the reduction in expression is performed by RNAi mechanism. 
     Provided are plant cells, plants, and seeds comprising the polynucleotide encoding a polypeptide or the recombinant DNA construct comprising a regulatory element operably linked to the polynucleotide encoding a polypeptide. In certain embodiments, the regulatory element is a heterologous promoter. In certain embodiments, the plant and/or seed is from a monocot plant. In certain embodiments, the plant is a monocot plant. In certain embodiments, the monocot plant is maize. 
     Further provided are plant cells, plants, and seeds comprising a targeted genetic modification at a genomic locus that encodes a polypeptide comprising an amino acid sequence that is at least 80% to about 100% identical to a full length amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573, wherein the genetic modification increases the level and/or activity of the encoded polypeptide. In certain embodiments, the genetic modification is selected from the group consisting of an insertion, deletion, single nucleotide polymorphism (SNP), and a polynucleotide modification. In certain embodiments the targeted genetic modification is present in (a) the coding region; (b) a non-coding region; (c) a regulatory sequence; (d) an untranslated region; or (e) any combination of (a)-(d) of the genomic locus that encodes the polypeptide. In certain embodiments, the plant and/or seed is from a monocot plant. In certain embodiments, the plant is a monocot plant. In certain embodiments, the monocot plant is maize. 
     Provided are methods for increasing yield in a plant by expressing in a regenerable plant cell a recombinant DNA construct comprising a regulatory element operably linked to a polynucleotide encoding a polypeptide comprising an amino acid sequence that is at least 80% to about 100% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573; and generating the plant, wherein the plant comprises in its genome the recombinant DNA construct. In certain embodiments, the regulatory element is a heterologous promoter. In certain embodiments, the plant is a monocot plant. In certain embodiments, the monocot plant is maize. In certain embodiments, the yield is grain yield. 
     Further provided are methods for increasing yield in a plant by introducing in a regenerable plant cell a targeted genetic modification at a genomic locus that encodes a polypeptide comprising an amino acid sequence that is at least 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573; and generating the plant, wherein the level and/or activity of the encoded polypeptide is increased in the plant. In certain embodiments, the genetic modification is introduced using a genome modification technique selected from the group consisting of a polynucleotide-guided endonuclease, CRISPR-Cas endonucleases, base editing deaminases, a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an engineered site-specific meganucleases, or an Argonaute. In certain embodiments, the targeted genetic modification is present in (a) the coding region; (b) a non-coding region; (c) a regulatory sequence; (d) an untranslated region; or (e) any combination of (a)-(d) of the genomic locus that encodes the polypeptide. In certain embodiments, the plant cell is from a monocot plant. In certain embodiments, the monocot plant is maize. In certain embodiments, the yield is grain yield. 
     Provided are methods for increasing photosynthetic activity in a plant by expressing in a regenerable plant cell a recombinant DNA construct comprising a regulatory element operably linked to a polynucleotide encoding a polypeptide comprising an amino acid sequence that is at least 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573; and generating the plant, wherein the plant comprises in its genome the recombinant DNA construct. In certain embodiments, the regulatory element is a heterologous promoter. In certain embodiments, the plant is a monocot plant. In certain embodiments, the monocot plant is maize. 
     Also provided are methods for increasing photosynthetic activity in a plant by introducing in a regenerable plant cell a targeted genetic modification at a genomic locus that encodes a polypeptide comprising an amino acid sequence that is at least 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573; and generating the plant, wherein the level and/or activity of the encoded polypeptide is increased in the plant. In certain embodiments, the genetic modification is introduced using a genome modification technique selected from the group consisting of a polynucleotide-guided endonuclease, CRISPR-Cas endonucleases, base editing deaminases, a zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), an engineered site-specific meganucleases, or an Argonaute. In certain embodiments, the targeted genetic modification is present in (a) the coding region; (b) a non-coding region; (c) a regulatory sequence; (d) an untranslated region; or (e) any combination of (a)-(d) of the genomic locus that encodes the polypeptide. In certain embodiments, the plant cell is from a monocot plant. In certain embodiments, the monocot plant is maize. 
     BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE LISTING 
     The disclosure can be more fully understood from the following detailed description and the accompanying drawings and Sequence Listing, which form a part of this application. 
     The sequence descriptions and sequence listing attached hereto comply with the rules governing nucleotide and amino acid sequence disclosures in patent applications as set forth in 37 C.F.R. §§ 1.821 and 1.825. The sequence descriptions comprise the three letter codes for amino acids as defined in 37 C.F.R. §§ 1.821 and 1.825, which are incorporated herein by reference. 
     
       
         
           
               
             
               
                 TABLE 1A 
               
             
            
               
                   
               
               
                 Sequence Listing Description- Interactors and Direct Targets 
               
            
           
           
               
               
            
               
                   
                 Functional Annotation 
               
               
                   
                   
               
            
           
           
               
               
            
               
                 Interactors 
                   
               
            
           
           
               
               
               
            
               
                 SEQ ID NO: 1 
                 GRMZM2G160687 (zag2 - Zea AGAMOUS 
                 DNA-binding transcription factor 
               
               
                   
                 homolog2) 
                 activity 
               
               
                 SEQ ID NO: 2 
                 GRMZM2G160565 (bde1 - bearded-ear1; 
                 DNA-binding transcription factor 
               
               
                   
                 ZmMADS56) 
                 activity 
               
               
                 SEQ ID NO: 3 
                 GRMZM2G072582 (mads3 - MADS3; 
                 DNA-binding transcription factor 
               
               
                   
                 ZmZAPL) 
                 activity 
               
               
                 SEQ ID NO: 4 
                 GRMZM2G099522 (zmm14 -  Zea mays   
                 DNA-binding transcription factor 
               
               
                   
                 MADS14; ZmM5) 
                 activity 
               
               
                 SEQ ID NO: 5 
                 GRMZM2G159397 (zmm6 -  Zea mays   
                 DNA-binding transcription factor 
               
               
                   
                 MADS6) 
                 activity 
               
               
                 SEQ ID NO: 6 
                 GRMZM2G097059 (zmm7 -  Zea mays   
                 DNA-binding transcription factor 
               
               
                   
                 MADS7) 
                 activity 
               
               
                 SEQ ID NO: 7 
                 GRMZM2G087095 (zmm24 -  Zea mays   
                 DNA-binding transcription factor 
               
               
                   
                 MADS24) 
                 activity 
               
               
                 SEQ ID NO: 8 
                 GRMZM5G814279 (mads74 - MADS- 
                 DNA-binding transcription factor 
               
               
                   
                 transcription factor 74, ZmMADS47-like) 
                 activity 
               
               
                 SEQ ID NO: 9 
                 GRMZM2G059102 (mads68 - MADS- 
                 DNA-binding transcription factor 
               
               
                   
                 transcription factor 68; ZmM47) 
                 activity 
               
               
                 SEQ ID NO: 10 
                 GRMZM2G170365 (ZmSF2 -  Zea mays   
                 mRNA splicing 
               
               
                   
                 splicing factor 2) 
               
               
                 SEQ ID NO: 11 
                 GRMZM2G086779 (ZmSFT-like -  Zea mays   
                 mRNA splicing 
               
               
                   
                 mRNA splicing factor thioredoxin-like U5 
               
               
                   
                 snRNP) 
               
               
                 SEQ ID NO: 12 
                 GRMZM2G160687 genomic (zag2 - Zea 
                 DNA-binding transcription factor 
               
               
                   
                 AGAMOUS homolog2) 
                 activity 
               
               
                 SEQ ID NO: 13 
                 GRMZM2G160565 genomic (bde1 - 
                 DNA-binding transcription factor 
               
               
                   
                 bearded-ear1; ZmMADS56) 
                 activity 
               
               
                 SEQ ID NO: 14 
                 GRMZM2G072582 genomic (mads3 - 
                 DNA-binding transcription factor 
               
               
                   
                 MADS3; ZmZAPL) 
                 activity 
               
               
                 SEQ ID NO: 15 
                 GRMZM2G099522 genomic (zmm14 -  Zea   
                 DNA-binding transcription factor 
               
               
                   
                   mays  MADS14; ZmM5) 
                 activity 
               
               
                 SEQ ID NO: 16 
                 GRMZM2G159397 genomic (zmm6 -  Zea   
                 DNA-binding transcription factor 
               
               
                   
                   mays  MADS6) 
                 activity 
               
               
                 SEQ ID NO: 17 
                 GRMZM2G097059 genomic (zmm7 -  Zea   
                 DNA-binding transcription factor 
               
               
                   
                   mays  MADS7) 
                 activity 
               
               
                 SEQ ID NO: 18 
                 GRMZM2G087095 genomic (zmm24 -  Zea   
                 DNA-binding transcription factor 
               
               
                   
                   mays  MADS24) 
                 activity 
               
               
                 SEQ ID NO: 19 
                 GRMZM5G814279 genomic (mads74 - 
                 DNA-binding transcription factor 
               
               
                   
                 MADS-transcription factor 74, 
                 activity 
               
               
                   
                 ZmMADS47-like) 
               
               
                 SEQ ID NO: 20 
                 GRMZM2G059102 genomic (mads68 - 
                 DNA-binding transcription factor 
               
               
                   
                 MADS-transcription factor 68; ZmM47) 
                 activity 
               
               
                 SEQ ID NO: 21 
                 GRMZM2G170365 genomic (ZmSF2 -  Zea   
                 mRNA splicing 
               
               
                   
                   mays  splicing factor 2) 
               
               
                 SEQ ID NO: 22 
                 GRMZM2G086779 genomic (ZmSFT-like - 
                 mRNA splicing 
               
               
                   
                   Zea mays  mRNA splicing factor 
               
               
                   
                 thioredoxin-like U5 snRNP) 
               
            
           
           
               
               
            
               
                 Direct Targets 
                   
               
            
           
           
               
               
               
            
               
                 SEQ ID NO: 23 
                 GRMZM2G036880 (light-harvesting 
                 integral component of thylakoid 
               
               
                   
                 complex I chlorophyll a/b binding protein 
                 membrane 
               
               
                   
                 1 (LHCA1) like) 
               
               
                 SEQ ID NO: 24 
                 GRMZM2G117412 (Chlorophyll a-b 
                 photosynthesis 
               
               
                   
                 binding protein) 
               
               
                 SEQ ID NO: 25 
                 GRMZM2G176840 (PSBP-like protein 1, 
                 photosynthesis 
               
               
                   
                 chloroplastic) 
               
               
                 SEQ ID NO: 26 
                 GRMZM2G149428 (Ihcb5 - light 
                 photosynthesis 
               
               
                   
                 harvesting chlorophyll a/b binding 
               
               
                   
                 protein5) 
               
               
                 SEQ ID NO: 27 
                 GRMZM2G112728 (all-trans-nonaprenyl- 
                 photosynthesis 
               
               
                   
                 diphosphate synthase) 
               
               
                 SEQ ID NO: 28 
                 GRMZM2G306345 (pdk1 - pyruvate, 
                 photosynthesis 
               
               
                   
                 orthophosphate dikinase1) 
               
               
                 SEQ ID NO: 29 
                 GRMZM2G306345 (pdk1 - pyruvate, 
                 photosynthesis 
               
               
                   
                 orthophosphate dikinase1) 
               
               
                 SEQ ID NO: 30 
                 GRMZM2G459166 (F-box protein GID2 
                 giberellin signaling 
               
               
                   
                 (GID2, SLY1)) 
               
               
                 SEQ ID NO: 31 
                 GRMZM2G073427 (bzip111 - bZIP- 
                 DNA-binding transcription factor 
               
               
                   
                 transcription factor 111) 
                 activity 
               
               
                 SEQ ID NO: 32 
                 GRMZM2G036880 genomic (light- 
                 integral component of thylakoid 
               
               
                   
                 harvesting complex I chlorophyll a/b 
                 membrane 
               
               
                   
                 binding protein 1 (LHCA1) like) 
               
               
                 SEQ ID NO: 33 
                 GRMZM2G117412 genomic (Chlorophyll 
                 photosynthesis 
               
               
                   
                 a-b binding protein) 
               
               
                 SEQ ID NO: 34 
                 GRMZM2G176840 genomic (PSBP-like 
                 photosynthesis 
               
               
                   
                 protein 1, chloroplastic) 
               
               
                 SEQ ID NO: 35 
                 GRMZM2G149428 genomic (Ihcb5 - light 
                 photosynthesis 
               
               
                   
                 harvesting chlorophyll a/b binding 
               
               
                   
                 protein5) 
               
               
                 SEQ ID NO: 36 
                 GRMZM2G112728 genomic (all-trans- 
                 photosynthesis 
               
               
                   
                 nonaprenyl-diphosphate synthase) 
               
               
                 SEQ ID NO: 37 
                 GRMZM2G306345 genomic (pdk1 - 
                 photosynthesis 
               
               
                   
                 pyruvate, orthophosphate dikinase1) 
               
               
                 SEQ ID NO: 38 
                 GRMZM2G459166 genomic (F-box 
                 giberellin signaling 
               
               
                   
                 protein GID2 (GID2, SLY1)) 
               
               
                 SEQ ID NO: 39 
                 GRMZM2G073427 genomic (bzip111 - 
                 DNA-binding transcription factor 
               
               
                   
                 bZIP-transcription factor 111) 
                 activity 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 1B 
               
             
            
               
                   
               
               
                 Sequence Listing Description- Differentially Expressed Genes 
               
            
           
           
               
               
            
               
                 Differentially Expressed Genes 
                 Functional Annotation 
               
               
                   
               
            
           
           
               
               
               
            
               
                 SEQ ID NO: 40 
                 Zm00001d022088 Protein Agamous-like 
                 DNA-binding transcription factor 
               
               
                   
                 MADS-box protein AGL8 
                 activity 
               
               
                 SEQ ID NO: 41 
                 Zm00001d023455 Protein Transcription 
                 DNA-binding transcription factor 
               
               
                   
                 repressor OFP13 
                 activity 
               
               
                 SEQ ID NO: 42 
                 Zm00001d023456 Protein Transcription 
                 DNA-binding transcription factor 
               
               
                   
                 repressor OFP6 
                 activity 
               
               
                 SEQ ID NO: 43 
                 Zm00001d038273 Protein Coronatine- 
                 shade avoidance 
               
               
                   
                 insensitive protein 1 
               
               
                 SEQ ID NO: 44 
                 Zm00001d004053 Protein hypothetical 
                 None identified 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 45 
                 Zm00001d029183 Protein cytochrome 
                 isoflavone 2′-hydroxylase activity 
               
               
                   
                 P450 family 81 subfamily D 
               
               
                   
                 polypeptide 8 
               
               
                 SEQ ID NO: 46 
                 Zm00001d051194 Protein Arginine 
                 arginine decarboxylase activity 
               
               
                   
                 decarboxylase 
               
               
                 SEQ ID NO: 47 
                 Zm00001d033132 Protein photosystem II 
                 photosynthesis 
               
               
                   
                 light harvesting complex gene 2.1 
               
               
                 SEQ ID NO: 48 
                 Zm00001d029215 Protein Villin-2 
                 actin filament bundle assembly 
               
               
                 SEQ ID NO: 49 
                 Zm00001d033543 Protein Integral 
                 cellular carbohydrate metabolic 
               
               
                   
                 membrane HPP family protein 
                 process 
               
               
                 SEQ ID NO: 50 
                 Zm00001d053925 Protein hypothetical 
                 chlorophyll biosynthetic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 51 
                 Zm00001d028269 Protein hypothetical 
                 DNA-binding transcription factor 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 52 
                 Zm00001d033544 Protein 
                 transferase activity, transferring 
               
               
                   
                 Glycosyltransferase family protein 64 
                 hexosyl groups 
               
               
                   
                 protein C5 
               
               
                 SEQ ID NO: 53 
                 Zm00001d034015 Protein exoglucanasel 
                 glucan exo-1,3-beta-glucosidase 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 54 
                 Zm00001d027743 Protein 
                 sugar mediated signaling pathway 
               
               
                   
                 Serine/threonine-protein kinase EDR1 
               
               
                 SEQ ID NO: 55 
                 Zm00001d048311 Protein Sucrose 
                 sucrose transmembrane transporter 
               
               
                   
                 transport protein SUC3 
                 activity 
               
               
                 SEQ ID NO: 56 
                 Zm00001d047256 Protein Protein kinase 
                 signal transduction 
               
               
                   
                 domain superfamily protein 
               
               
                 SEQ ID NO: 57 
                 Zm00001d048720 Protein Glutaredoxin- 
                 electron transport chain 
               
               
                   
                 C13 
               
               
                 SEQ ID NO: 58 
                 Zm00001d023426 Protein hypothetical 
                 chlorophyll biosynthetic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 59 
                 Zm00001d004331 Protein hypothetical 
                 regulation of transcription, DNA- 
               
               
                   
                 protein 
                 templated 
               
               
                 SEQ ID NO: 60 
                 Zm00001d050748 Protein proline-rich 
                 ATPase activity, coupled to 
               
               
                   
                 family protein 
                 transmembrane movement of 
               
               
                   
                   
                 substances 
               
               
                 SEQ ID NO: 61 
                 Zm00001d010321 Protein pyruvate 
                 pyruvate, phosphate dikinase 
               
               
                   
                 orthophosphate dikinase2 
                 activity 
               
               
                 SEQ ID NO: 62 
                 Zm00001d004894 Protein ribulose 
                 ribulose-bisphosphate carboxylase 
               
               
                   
                 bisphosphate carboxylase small subunit2 
                 activity 
               
               
                 SEQ ID NO: 63 
                 Zm00001d042346 Protein alpha/beta- 
                 haloalkane dehalogenase activity 
               
               
                   
                 Hydrolases superfamily protein 
               
               
                 SEQ ID NO: 64 
                 Zm00001d031657 Protein putative 
                 acid phosphatase activity 
               
               
                   
                 inactive purple acid phosphatase 27 
               
               
                 SEQ ID NO: 65 
                 Zm00001d008178 Protein ABC 
                 basipetal auxin transport 
               
               
                   
                 transporter B family member 21 
               
               
                 SEQ ID NO: 66 
                 Zm00001d043044 Protein Sec1/munc18- 
                 kinase activity 
               
               
                   
                 like (SM) proteins superfamily 
               
               
                 SEQ ID NO: 67 
                 Zm00001d018623 Protein Photosynthetic 
                 electron transporter, transferring 
               
               
                   
                 NDH subunit of lumenal location 3 
                 electrons within the cyclic electron 
               
               
                   
                 chloroplastic 
                 transport pathway of 
               
               
                   
                   
                 photosynthesis activity 
               
               
                 SEQ ID NO: 68 
                 Zm00001d043095 Protein Zinc finger 
                 chloroplast organization 
               
               
                   
                 protein VAR3 chloroplastic 
               
               
                 SEQ ID NO: 69 
                 Zm00001d029062 Protein Vicilin-like 
                 nutrient reservoir activity 
               
               
                   
                 seed storage protein 
               
               
                 SEQ ID NO: 70 
                 Zm00001d011900 Protein RNA-binding 
                 RNA binding 
               
               
                   
                 protein BRN1 
               
               
                 SEQ ID NO: 71 
                 Zm00001d010672 Protein Metacaspase 
                 phosphoglycerate kinase activity 
               
               
                   
                 type II 
               
               
                 SEQ ID NO: 72 
                 Zm00001d011183 Protein thiamine 
                 thiazole biosynthetic process 
               
               
                   
                 biosynthesis1 
               
               
                 SEQ ID NO: 73 
                 Zm00001d037103 Protein Peroxiredoxin 
                 peroxiredoxin activity 
               
               
                   
                 Q chloroplastic 
               
               
                 SEQ ID NO: 74 
                 Zm00001d009028 Protein Triose 
                 transporter activity 
               
               
                   
                 phosphate/phosphate translocator, 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 75 
                 Zm00001d013937 Protein 
                 chlorophyll biosynthetic process 
               
               
                   
                 Protochlorophyllide reductase C 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 76 
                 Zm00001d002873 Protein UPF0426 
                 plastoglobule 
               
               
                   
                 protein chloroplastic 
               
               
                 SEQ ID NO: 77 
                 Zm00001d037362 Protein DNA 
                 DNA topoisomerase activity 
               
               
                   
                 topoisomerase type IA core 
               
               
                 SEQ ID NO: 78 
                 Zm00001d026404 Protein hypothetical 
                 arginine catabolic process to 
               
               
                   
                 protein 
                 glutamate 
               
               
                 SEQ ID NO: 79 
                 Zm00001d047255 Protein 3-oxoacyl- 
                 3-oxoacyl-[acyl-carrier-protein] 
               
               
                   
                 [acyl-carrier-protein] synthase II 
                 synthase activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 80 
                 Zm00001d031253 Protein dicarboxylic 
                 transporter activity 
               
               
                   
                 acid transporter2 
               
               
                 SEQ ID NO: 81 
                 Zm00001d027576 Protein hypothetical 
                 voltage-gated anion channel 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 82 
                 Zm00001d052595 Protein Ribulose 
                 ribulose-bisphosphate carboxylase 
               
               
                   
                 bisphosphate carboxylase small chain, 
                 activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 83 
                 Zm00001d013367 Protein Tubulin alpha- 
                 structural molecule activity 
               
               
                   
                 4 chain 
               
               
                 SEQ ID NO: 84 
                 Zm00001d046001 Protein Triose 
                 transmembrane transporter activity 
               
               
                   
                 phosphate/phosphate translocator TPT 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 85 
                 Zm00001d008963 Protein GDT1-like 
                 chloroplast membrane 
               
               
                   
                 protein 1 chloroplastic 
               
               
                 SEQ ID NO: 86 
                 Zm00001d048515 Protein Stress 
                 gene silencing 
               
               
                   
                 responsive alpha-beta barrel domain 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 87 
                 Zm00001d052595 Protein Ribulose 
                 ribulose-bisphosphate carboxylase 
               
               
                   
                 bisphosphate carboxylase small chain, 
                 activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 88 
                 Zm00001d042049 Protein Ferredoxin 
                 photosynthetic electron transport 
               
               
                   
                   
                 in photosystem I 
               
               
                 SEQ ID NO: 89 
                 Zm00001d040242 Protein Nuclear 
                 cellular macromolecule metabolic 
               
               
                   
                 transport factor 2 (NTF2) family protein 
                 process 
               
               
                 SEQ ID NO: 90 
                 Zm00001d042697 Protein photosystem II 
                 PSII associated light-harvesting 
               
               
                   
                 subunit PsbS1 
                 complex II 
               
               
                 SEQ ID NO: 91 
                 Zm00001d019518 Protein Photosystem I 
                 photosystem I reaction center 
               
               
                   
                 reaction center subunit IV A 
               
               
                 SEQ ID NO: 92 
                 Zm00001d048313 Protein NAD(P)-linked 
                 photosystem II assembly 
               
               
                   
                 oxidoreductase superfamily protein 
               
               
                 SEQ ID NO: 93 
                 Zm00001d033150 Protein hypothetical 
                 transcription regulatory region 
               
               
                   
                 protein 
                 sequence-specific DNA binding 
               
               
                 SEQ ID NO: 94 
                 Zm00001d007858 Protein Pyridoxal 
                 oxidoreductase activity 
               
               
                   
                 reductase chloroplastic 
               
               
                 SEQ ID NO: 95 
                 Zm00001d003588 Protein Ras-related 
                 protein binding 
               
               
                   
                 protein RABD1 
               
               
                 SEQ ID NO: 96 
                 Zm00001d036903 Protein Plant Tudor- 
                 RNA binding 
               
               
                   
                 like RNA-binding protein 
               
               
                 SEQ ID NO: 97 
                 Zm00001d031484 Protein PsbP domain- 
                 photosystem II oxygen evolving 
               
               
                   
                 containing protein 3 chloroplastic 
                 complex 
               
               
                 SEQ ID NO: 98 
                 Zm00001d018157 Protein light harvesting 
                 photosynthesis, light harvesting in 
               
               
                   
                 complex a/b protein4 
                 photosystem I 
               
               
                 SEQ ID NO: 99 
                 Zm00001d005814 Protein Photosystem I 
                 photosynthesis, light harvesting in 
               
               
                   
                 chlorophyll a/b-binding protein 6 
                 photosystem I 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 100 
                 Zm00001d033338 Protein NAD(P)-linked 
                 oxidoreductase activity 
               
               
                   
                 oxidoreductase superfamily protein 
               
               
                 SEQ ID NO: 101 
                 Zm00001d053446 Protein potassium 
                 voltage-gated potassium channel 
               
               
                   
                 channel3 
                 activity 
               
               
                 SEQ ID NO: 102 
                 Zm00001d026603 Protein Magnesium- 
                 photosynthesis, light reaction 
               
               
                   
                 chelatase subunit ChlH chloroplastic 
               
               
                 SEQ ID NO: 103 
                 Zm00001d027841 Protein Ribulose- 
                 pentose-phosphate shunt, non- 
               
               
                   
                 phosphate 3-epimerase 
                 oxidative branch 
               
               
                 SEQ ID NO: 104 
                 Zm00001d030048 Protein pfkB-like 
                 isopentenyl diphosphate 
               
               
                   
                 carbohydrate kinase family protein 
                 biosynthetic process, 
               
               
                   
                   
                 methylerythritol 4-phosphate 
               
               
                   
                   
                 pathway 
               
               
                 SEQ ID NO: 105 
                 Zm00001d005346 Protein Aldo-keto 
                 oxidoreductase activity 
               
               
                   
                 reductase/oxidoreductase 
               
               
                 SEQ ID NO: 106 
                 Zm00001d023706 Protein thioredoxin M1 
                 transcription coregulator activity 
               
               
                 SEQ ID NO: 107 
                 Zm00001d042050 Protein Protein 
                 chlorophyll biosynthetic process 
               
               
                   
                 RETICULATA-RELATED 4 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 108 
                 Zm00001d042533 Protein Trigger factor 
                 protein transport 
               
               
                 SEQ ID NO: 109 
                 Zm00001d022590 Protein hypothetical 
                 transcription, DNA-templated 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 110 
                 Zm00001d045431 Protein Enolase 1 
                 phosphopyruvate hydratase 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 111 
                 Zm00001d047743 Protein fatty acid 
                 oxidoreductase activity, acting on 
               
               
                   
                 desaturase7 
                 paired donors, with oxidation of a 
               
               
                   
                   
                 pair of donors resulting in the 
               
               
                   
                   
                 reduction of molecular oxygen to 
               
               
                   
                   
                 two molecules of water 
               
               
                 SEQ ID NO: 112 
                 Zm00001d036738 Protein S-adenosyl-L- 
                 methyltransferase activity 
               
               
                   
                 methionine-dependent methyltransferase 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 113 
                 Zm00001d018274 Protein Isoleucine-- 
                 valyl-tRNA aminoacylation 
               
               
                   
                 tRNA ligase chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 114 
                 Zm00001d035003 Protein ferredoxin2 
                 electron transfer activity 
               
               
                 SEQ ID NO: 115 
                 Zm00001d027321 Protein hypothetical 
                 peptidyl-prolyl cis-trans isomerase 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 116 
                 Zm00001d014284 Protein CMV 1a 
                 methyltransferase activity 
               
               
                   
                 interacting protein 1 
               
               
                 SEQ ID NO: 117 
                 Zm00001d036340 Protein photosystem 
                 photosystem II 
               
               
                   
                 II1 
               
               
                 SEQ ID NO: 118 
                 Zm00001d003767 Protein Photosystem I 
                 photosynthesis, light harvesting in 
               
               
                   
                 subunit O 
                 photosystem I 
               
               
                 SEQ ID NO: 119 
                 Zm00001d031997 Protein NAD(P)- 
                 nucleotide binding 
               
               
                   
                 binding Rossmann-fold superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 120 
                 Zm00001d019479 Protein granule-bound 
                 NDP-glucose-starch 
               
               
                   
                 starch synthase 1b 
                 glucosyltransferase activity 
               
               
                 SEQ ID NO: 121 
                 Zm00001d024148 Protein Photosynthetic 
                 photosynthetic electron transport 
               
               
                   
                 NDH subunit of subcomplex B 1 
                 in photosystem I 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 122 
                 Zm00001d038579 Protein 
                 photosynthesis, light reaction 
               
               
                   
                 Phosphoglycerate kinase 
               
               
                 SEQ ID NO: 123 
                 Zm00001d037273 Protein Peptide 
                 electron transport chain 
               
               
                   
                 methionine sulfoxide reductase msrB 
               
               
                 SEQ ID NO: 124 
                 Zm00001d025845 Protein hypothetical 
                 chloroplast thylakoid membrane 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 125 
                 Zm00001d027422 Protein PsbP-like 
                 chloroplast photosystem II 
               
               
                   
                 protein 1 chloroplastic 
               
               
                 SEQ ID NO: 126 
                 Zm00001d024519 Protein rubredoxin 
                 iron ion binding 
               
               
                   
                 family protein 
               
               
                 SEQ ID NO: 127 
                 Zm00001d040163 Protein deoxy xylulose 
                 1-deoxy-D-xylulose-5-phosphate 
               
               
                   
                 reductoisomerase1 
                 reductoisomerase activity 
               
               
                 SEQ ID NO: 128 
                 Zm00001d012868 Protein carotene 
                 oxidoreductase activity 
               
               
                   
                 isomerase3 
               
               
                 SEQ ID NO: 129 
                 Zm00001d021763 Protein photosystem II 
                 photosynthesis, light harvesting in 
               
               
                   
                 subunit29 
                 photosystem I 
               
               
                 SEQ ID NO: 130 
                 Zm00001d035761 Protein Peptidyl-prolyl 
                 peptidyl-prolyl cis-trans isomerase 
               
               
                   
                 cis-trans isomerase 
                 activity 
               
               
                 SEQ ID NO: 131 
                 Zm00001d032301 Protein S-adenosyl-L- 
                 methyltransferase activity 
               
               
                   
                 methionine-dependent methyltransferase 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 132 
                 Zm00001d028562 Protein Fructose-1,6- 
                 photosynthetic electron transport 
               
               
                   
                 bisphosphatase 
                 in photosystem I 
               
               
                 SEQ ID NO: 133 
                 Zm00001d034538 Protein Rubredoxin- 
                 iron ion binding 
               
               
                   
                 like superfamily protein 
               
               
                 SEQ ID NO: 134 
                 Zm00001d048116 Protein hypothetical 
                 isopentenyl diphosphate 
               
               
                   
                 protein 
                 biosynthetic process, 
               
               
                   
                   
                 methylerythritol 4-phosphate 
               
               
                   
                   
                 pathway 
               
               
                 SEQ ID NO: 135 
                 Zm00001d048998 Protein Chlorophyll a- 
                 photosynthesis 
               
               
                   
                 b binding protein CP26 chloroplastic 
               
               
                 SEQ ID NO: 136 
                 Zm00001d049490 Protein Protein 
                 translation initiation factor activity 
               
               
                   
                 CHLORORESPIRATORY REDUCTION 
               
               
                   
                 6 chloroplastic 
               
               
                 SEQ ID NO: 137 
                 Zm00001d015975 Protein putative 
                 lactoylglutathione lyase activity 
               
               
                   
                 lactoylglutathione lyase chloroplastic 
               
               
                 SEQ ID NO: 138 
                 Zm00001d015613 Protein Protein TIC 21 
                 protein import into chloroplast 
               
               
                   
                 chloroplastic 
                 stroma 
               
               
                 SEQ ID NO: 139 
                 Zm00001d039258 Protein Triose 
                 glucose-6-phosphate 
               
               
                   
                 phosphate/phosphate translocator TPT 
                 transmembrane transporter activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 140 
                 Zm00001d007267 Protein light harvesting 
                 photosynthesis, light harvesting in 
               
               
                   
                 chlorophyll a/b binding protein5 
                 photosystem I 
               
               
                 SEQ ID NO: 141 
                 Zm00001d033383 Protein 
                 thiamine biosynthetic process 
               
               
                   
                 hydroxymethylpyrimidine phosphate 
               
               
                   
                 synthase1 
               
               
                 SEQ ID NO: 142 
                 Zm00001d026645 Protein K(+) efflux 
                 solute: proton antiporter activity 
               
               
                   
                 antiporter 2 chloroplastic 
               
               
                 SEQ ID NO: 143 
                 Zm00001d023757 Protein NAD(P)H- 
                 heat shock protein binding 
               
               
                   
                 quinone oxidoreductase subunit U 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 144 
                 Zm00001d034005 Protein evolutionarily 
                 oxidation-reduction process 
               
               
                   
                 conserved C-terminal region 2 
               
               
                 SEQ ID NO: 145 
                 Zm00001d022381 Protein NADPH- 
                 hydrogen peroxide catabolic 
               
               
                   
                 dependent thioredoxin reductase 3 
                 process 
               
               
                 SEQ ID NO: 146 
                 Zm00001d031962 Protein hypothetical 
                 protein dephosphorylation 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 147 
                 Zm00001d005446 Protein Photosystem I 
                 photosystem I reaction center 
               
               
                   
                 reaction center subunit IV A 
               
               
                 SEQ ID NO: 148 
                 Zm00001d027511 Protein Catalase 
                 hydrogen peroxide catabolic 
               
               
                   
                 isozyme 2 
                 process 
               
               
                 SEQ ID NO: 149 
                 Zm00001d017178 Protein hypothetical 
                 primary metabolic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 150 
                 Zm00001d038947 Protein putative 
                 electron transfer activity 
               
               
                   
                 galacturonosyltransferase-like 9 
               
               
                 SEQ ID NO: 151 
                 Zm00001d034739 Protein 
                 acetylpyruvate hydrolase activity 
               
               
                   
                 Fumarylacetoacetate (FAA) hydrolase 
               
               
                   
                 family 
               
               
                 SEQ ID NO: 152 
                 Zm00001d044745 Protein Alanine--tRNA 
                 alanyl-tRNA aminoacylation 
               
               
                   
                 ligase chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 153 
                 Zm00001d038491 Protein 
                 N-acetyltransferase activity 
               
               
                   
                 Acetyltransferase NSI 
               
               
                 SEQ ID NO: 154 
                 Zm00001d014445 Protein Protein kinase 
                 kinase activity 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 155 
                 Zm00001d039745 Protein Protein 
                 phosphoprotein phosphatase 
               
               
                   
                 phosphatase 2C 
                 activity 
               
               
                 SEQ ID NO: 156 
                 Zm00001d038485 Protein 
                 photosystem II stabilization 
               
               
                   
                 Serine/threonine-protein kinase STN8 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 157 
                 Zm00001d012287 Protein hypothetical 
                 starch biosynthetic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 158 
                 Zm00001d027694 Protein Solanesyl 
                 plastoquinone biosynthetic process 
               
               
                   
                 diphosphate synthase 2 chloroplastic 
               
               
                 SEQ ID NO: 159 
                 Zm00001d003470 Protein putative 
                 response to abscisic acid 
               
               
                   
                 plastid-lipid-associated protein 2 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 160 
                 Zm00001d019180 Protein Nudix 
                 hydrolase activity 
               
               
                   
                 hydrolase 16 mitochondrial 
               
               
                 SEQ ID NO: 161 
                 Zm00001d007394 Protein Rubredoxin- 
                 iron ion binding 
               
               
                   
                 like superfamily protein 
               
               
                 SEQ ID NO: 162 
                 Zm00001d053432 Protein iron-sulfur 
                 electron transporter, transferring 
               
               
                   
                 protein2 
                 electrons within cytochrome b6/f 
               
               
                   
                   
                 complex of photosystem II activity 
               
               
                 SEQ ID NO: 163 
                 Zm00001d039900 Protein putative zinc 
                 metalloendopeptidase activity 
               
               
                   
                 metalloprotease EGY2 chloroplastic 
               
               
                 SEQ ID NO: 164 
                 Zm00001d050810 Protein 2-hydroxy-3- 
                 pentose-phosphate shunt 
               
               
                   
                 oxopropionate reductase 
               
               
                 SEQ ID NO: 165 
                 Zm00001d016802 Protein L-ascorbate 
                 L-ascorbate peroxidase activity 
               
               
                   
                 peroxidase S chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 166 
                 Zm00001d004978 Protein Saccharopine 
                 oxidoreductase activity 
               
               
                   
                 dehydrogenase 
               
               
                 SEQ ID NO: 167 
                 Zm00001d028924 Protein NifU-like 
                 iron-sulfur cluster assembly 
               
               
                   
                 protein 1 chloroplastic 
               
               
                 SEQ ID NO: 168 
                 Zm00001d002815 Protein NAD(P)H- 
                 oxidoreductase activity, acting on 
               
               
                   
                 quinone oxidoreductase subunit M 
                 NAD(P)H, quinone or similar 
               
               
                   
                 chloroplastic 
                 compound as acceptor 
               
               
                 SEQ ID NO: 169 
                 Zm00001d029065 Protein Protein LRP16 
                 regulation of transcription, DNA- 
               
               
                   
                   
                 templated 
               
               
                 SEQ ID NO: 170 
                 Zm00001d052184 Protein Protein 
                 chloroplast envelope 
               
               
                   
                 CURVATURE THYLAKOID ID 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 171 
                 Zm00001d038337 Protein DAR GTPase 3 
                 GTP binding 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 172 
                 Zm00001d003713 Protein Exocyst 
                 pollen tube growth 
               
               
                   
                 complex component SEC5A 
               
               
                 SEQ ID NO: 173 
                 Zm00001d031953 Protein Thioredoxin 
                 protein disulfide oxidoreductase 
               
               
                   
                 family protein 
                 activity 
               
               
                 SEQ ID NO: 174 
                 Zm00001d053576 Protein putative 
                 eukaryotic translation elongation 
               
               
                   
                 elongation factor 1-gamma 2 
                 factor 1 complex 
               
               
                 SEQ ID NO: 175 
                 Zm00001d000123 Protein NAD(P)- 
                 response to oxidative stress 
               
               
                   
                 binding Rossmann-fold superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 176 
                 Zm00001d045431 Protein Enolase 1 
                 phosphopyruvate hydratase 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 177 
                 Zm00001d036630 Protein Filamentation 
                 metalloendopeptidase activity 
               
               
                   
                 temperature-sensitive H 2B 
               
               
                 SEQ ID NO: 178 
                 Zm00001d048515 Protein Stress 
                 gene silencing 
               
               
                   
                 responsive alpha-beta barrel domain 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 179 
                 Zm00001d021310 Protein 
                 reductive pentose-phosphate cycle 
               
               
                   
                 Triosephosphate isomerase 
               
               
                 SEQ ID NO: 180 
                 Zm00001d042353 Protein sucrose 
                 sucrose synthase activity 
               
               
                   
                 phosphate synthase2 
               
               
                 SEQ ID NO: 181 
                 Zm00001d050150 Protein Adenylate 
                 adenylate kinase activity 
               
               
                   
                 kinase 5 chloroplastic 
               
               
                 SEQ ID NO: 182 
                 Zm00001d025545 Protein zeaxanthin 
                 abscisic acid biosynthetic process 
               
               
                   
                 epoxidase2 
               
               
                 SEQ ID NO: 183 
                 Zm00001d012168 Protein Membrane- 
                 chloroplast thylakoid membrane 
               
               
                   
                 associated protein VIPP1 chloroplastic 
               
               
                 SEQ ID NO: 184 
                 Zm00001d011581 Protein Peroxiredoxin- 
                 peroxiredoxin activity 
               
               
                   
                 2B 
               
               
                 SEQ ID NO: 185 
                 Zm00001d018030 Protein Photosynthetic 
                 regulation of transcription by RNA 
               
               
                   
                 NDH subunit of subcomplex B 4 
                 polymerase II 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 186 
                 Zm00001d018145 Protein Presequence 
                 protein processing 
               
               
                   
                 protease 2 chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 187 
                 Zm00001d040221 Protein Peptidase 
                 metalloendopeptidase activity 
               
               
                   
                 family M48 family protein 
               
               
                 SEQ ID NO: 188 
                 Zm00001d033594 Protein Myelin- 
                 phosphorus metabolic process 
               
               
                   
                 associated oligodendrocyte basic protein 
               
               
                   
                 isoform 1 
               
               
                 SEQ ID NO: 189 
                 Zm00001d008625 Protein Inner 
                 thylakoid membrane organization 
               
               
                   
                 membrane protein ALBINO3 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 190 
                 Zm00001d032380 Protein acclimation of 
                 photosystem II assembly 
               
               
                   
                 photosynthesis to environment 
               
               
                 SEQ ID NO: 191 
                 Zm00001d045575 Protein Ferredoxin- 
                 photosynthetic electron transport 
               
               
                   
                 NADP reductase leaf isozyme 1 
                 in photosystem I 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 192 
                 Zm00001d042526 Protein 
                 regulation of stomatai closure 
               
               
                   
                 Rhodanese/Cell cycle control phosphatase 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 193 
                 Zm00001d043168 Protein MAR-binding 
                 photosystem II assembly 
               
               
                   
                 filament-like protein 1-1 isoform 2 
               
               
                 SEQ ID NO: 194 
                 Zm00001d053545 Protein NAD(P)- 
                 nucleotide binding 
               
               
                   
                 binding Rossmann-fold superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 195 
                 Zm00001d053981 Protein putative 
                 pyridoxal phosphate biosynthetic 
               
               
                   
                 pyridoxal 5′-phosphate synthase subunit 
                 process 
               
               
                   
                 PDX2 
               
               
                 SEQ ID NO: 196 
                 Zm00001d017746 Protein vitamin E 
                 tocopherol O-methyltransferase 
               
               
                   
                 synthesis4 
                 activity 
               
               
                 SEQ ID NO: 197 
                 Zm00001d012083 Protein Thioredoxin F- 
                 pentose-phosphate shunt 
               
               
                   
                 type chloroplastic 
               
               
                 SEQ ID NO: 198 
                 Zm00001d024718 Protein Beta-carotene 
                 strigolactone biosynthetic process 
               
               
                   
                 isomerase D27 chloroplastic 
               
               
                 SEQ ID NO: 199 
                 Zm00001d021621 Protein 
                 3′-5′ exonuclease activity 
               
               
                   
                 Polynucleotidyl transferase ribonuclease 
               
               
                   
                 H fold protein with HRDC domain 
               
               
                 SEQ ID NO: 200 
                 Zm00001d015004 Protein Protein LOW 
                 aromatic amino acid family 
               
               
                   
                 PSII ACCUMULATION 3 chloroplastic 
                 biosynthetic process 
               
               
                 SEQ ID NO: 201 
                 Zm00001d039131 Protein ADP glucose 
                 glucose-1-phosphate 
               
               
                   
                 pyrophosphorylase2 
                 adenylyltransferase activity 
               
               
                 SEQ ID NO: 202 
                 Zm00001d044970 Protein putative 
                 protein tyrosine phosphatase 
               
               
                   
                 tyrosine-protein phosphatase 
                 activity 
               
               
                 SEQ ID NO: 203 
                 Zm00001d018401 Protein plastid 
                 positive regulation of ubiquitin 
               
               
                   
                 transcriptionally active 17 
                 protein ligase activity 
               
               
                 SEQ ID NO: 204 
                 Zm00001d015975 Protein putative 
                 lactoylglutathione lyase activity 
               
               
                   
                 lactoylglutathione lyase chloroplastic 
               
               
                 SEQ ID NO: 205 
                 Zm00001d013428 Protein 
                 phosphoglucomutase activity 
               
               
                   
                 phosphoglucomutase2 
               
               
                 SEQ ID NO: 206 
                 Zm00001d021246 Protein Ras-related 
                 chloroplast thylakoid membrane 
               
               
                   
                 protein RABA3 
               
               
                 SEQ ID NO: 207 
                 Zm00001d007921 Protein Tic62 protein 
                 oxidation-reduction process 
               
               
                 SEQ ID NO: 208 
                 Zm00001d027511 Protein Catalase 
                 hydrogen peroxide catabolic 
               
               
                   
                 isozyme 2 
                 process 
               
               
                 SEQ ID NO: 209 
                 Zm00001d027309 Protein Phosphoglucan 
                 intracellular signal transduction 
               
               
                   
                 phosphatase DSP4 chloroplastic 
               
               
                 SEQ ID NO: 210 
                 Zm00001d025544 Protein Zeaxanthin 
                 zeaxanthin epoxidase [overall] 
               
               
                   
                 epoxidase chloroplastic 
                 activity 
               
               
                 SEQ ID NO: 211 
                 Zm00001d039276 Protein Ubiquitin 
                 cellular metabolic process 
               
               
                   
                 ligase SINAT3 
               
               
                 SEQ ID NO: 212 
                 Zm00001d003512 Protein Zeaxanthin 
                 zeaxanthin epoxidase [overall] 
               
               
                   
                 epoxidase chloroplastic 
                 activity 
               
               
                 SEQ ID NO: 213 
                 Zm00001d053861 Protein Putative 
                 GTP binding 
               
               
                   
                 translation elongation factor family 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 214 
                 Zm00001d038894 Protein 
                 circadian rhythm 
               
               
                   
                 Serine/threonine-protein kinase STN7 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 215 
                 Zm00001d051321 Protein ATP- 
                 metalloendopeptidase activity 
               
               
                   
                 dependent zinc metalloprotease FTSH 7 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 216 
                 Zm00001d016826 Protein proline-rich 
                 anatomical structure 
               
               
                   
                 family protein 
                 morphogenesis 
               
               
                 SEQ ID NO: 217 
                 Zm00001d016854 Protein Ferrochelatase 
                 starch biosynthetic process 
               
               
                 SEQ ID NO: 218 
                 Zm00001d017435 Protein hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 219 
                 Zm00001d048373 Protein Carotenoid 
                 oxidoreductase activity, acting on 
               
               
                   
                 910(9′10′)-cleavage dioxygenase 1 
                 single donors with incorporation of 
               
               
                   
                   
                 molecular oxygen, incorporation 
               
               
                   
                   
                 of two atoms of oxygen 
               
               
                 SEQ ID NO: 220 
                 Zm00001d018901 Protein protein 
                 protein binding 
               
               
                   
                 containing PDZ domain a K-box domain 
               
               
                   
                 and a TPR region 
               
               
                 SEQ ID NO: 221 
                 Zm00001d019454 Protein PGR5-like 
                 photosynthetic electron transport 
               
               
                   
                 protein 1B chloroplastic 
                 in photosystem I 
               
               
                 SEQ ID NO: 222 
                 Zm00001d031899 Protein malate 
                 malate dehydrogenase (NADP+) 
               
               
                   
                 dehydrogenase6 
                 activity 
               
               
                 SEQ ID NO: 223 
                 Zm00001d045706 Protein Restorer of 
                 aldehyde dehydrogenase (NAD) 
               
               
                   
                 fertility2 
                 activity 
               
               
                 SEQ ID NO: 224 
                 Zm00001d035869 Protein Protein MEI2- 
                 nucleotide binding 
               
               
                   
                 like 5 
               
               
                 SEQ ID NO: 225 
                 Zm00001d053262 Protein calcium- 
                 protein localization 
               
               
                   
                 dependent lipid-binding family protein 
               
               
                 SEQ ID NO: 226 
                 Zm00001d017958 Protein Glutamine 
                 glutamine biosynthetic process 
               
               
                   
                 synthetase root isozyme 3 
               
               
                 SEQ ID NO: 227 
                 Zm00001d007113 Protein Xylose 
                 xylose isomerase activity 
               
               
                   
                 isomerase 
               
               
                 SEQ ID NO: 228 
                 Zm00001d051650 Protein Sucrose 
                 transcription, DNA-templated 
               
               
                   
                 cleavage protein-like protein 
               
               
                 SEQ ID NO: 229 
                 Zm00001d015138 Protein hypothetical 
                 nuclear pore 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 230 
                 Zm00001d030103 Protein putative 
                 xyloglucan: xyloglucosyl 
               
               
                   
                 xyloglucan endotransglucosylase/ 
                 transferase activity 
               
               
                   
                 hydrolase protein 30 
               
               
                 SEQ ID NO: 231 
                 Zm00001d021846 Protein Insulin- 
                 metalloendopeptidase activity 
               
               
                   
                 degrading enzyme-like 1 peroxisomal 
               
               
                 SEQ ID NO: 232 
                 Zm00001d041576 Protein Transcription 
                 regulation of transcription, DNA- 
               
               
                   
                 factor MYB48 
                 templated 
               
               
                 SEQ ID NO: 233 
                 Zm00001d005391 Protein Cysteine 
                 cysteine-type endopeptidase 
               
               
                   
                 proteinases superfamily protein 
                 activity 
               
               
                 SEQ ID NO: 234 
                 Zm00001d009022 Protein NmrA-like 
                 166 nucleotide binding 
               
               
                   
                 negative transcriptional regulator family 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 235 
                 Zm00001d041343 Protein putative 
                 defense response 
               
               
                   
                 disease resistance protein 
               
               
                 SEQ ID NO: 236 
                 Zm00001d039965 Protein Delta(7)-sterol- 
                 fatty acid biosynthetic process 
               
               
                   
                 C5(6)-desaturase 1 
               
               
                 SEQ ID NO: 237 
                 Zm00001d029047 Protein Receptor-like 
                 signaling receptor activity 
               
               
                   
                 protein kinase FERONIA 
               
               
                 SEQ ID NO: 238 
                 Zm00001d028230 Protein Sugar transport 
                 sucrose transport 
               
               
                   
                 protein 13 
               
               
                 SEQ ID NO: 239 
                 Zm00001d013243 Protein Cyclic 
                 plant-type hypersensitive response 
               
               
                   
                 nucleotide-gated ion channel 2 
               
               
                 SEQ ID NO: 240 
                 Zm00001d032926 Protein 
                 chlorophyll catabolic process 
               
               
                   
                 chlorophyllase2 
               
               
                 SEQ ID NO: 241 
                 Zm00001d045667 Protein Protein NRT1/ 
                 nitrate assimilation 
               
               
                   
                 PTR FAMILY 3.1 
               
               
                 SEQ ID NO: 242 
                 Zm00001d021846 Protein Insulin- 
                 metalloendopeptidase activity 
               
               
                   
                 degrading enzyme-like 1 peroxisomal 
               
               
                 SEQ ID NO: 243 
                 Zm00001d033469 Protein Ferredoxin 
                 electron transfer activity 
               
               
                 SEQ ID NO: 244 
                 Zm00001d019563 Protein Aquaporin 
                 transporter activity 
               
               
                   
                 PIP2-1 
               
               
                 SEQ ID NO: 245 
                 Zm00001d003866 Protein hypothetical 
                 cell wall organization 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 246 
                 Zm00001d039325 Protein Putative 
                 signaling receptor activity 
               
               
                   
                 inactive receptor-like protein kinase 
               
               
                 SEQ ID NO: 247 
                 Zm00001d023516 Protein Salt stress- 
                 mannose binding 
               
               
                   
                 induced protein 
               
               
                 SEQ ID NO: 248 
                 Zm00001d050918 Protein hypothetical 
                 aldehyde dehydrogenase (NAD) 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 249 
                 Zm00001d025253 Protein hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 250 
                 Zm00001d024499 Protein Nuclear factor 
                 aminoacyl-tRNA hydrolase 
               
               
                   
                 1 A-type isoform 2 
                 activity 
               
               
                 SEQ ID NO: 251 
                 Zm00001d045948 Protein Protein 
                 drug transmembrane transporter 
               
               
                   
                 DETOXIFICATION 16 
                 activity 
               
               
                 SEQ ID NO: 252 
                 Zm00001d021569 Protein Transparent 
                 drug transmembrane transporter 
               
               
                   
                 testa 12 protein 
                 activity 
               
               
                 SEQ ID NO: 253 
                 Zm00001d053327 Protein Galactoside 2- 
                 xyloglucan biosynthetic process 
               
               
                   
                 alpha-L-fucosyltransferase 
               
               
                 SEQ ID NO: 254 
                 Zm00001d047208 Protein WAT1-related 
                 auxin-activated signaling pathway 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 255 
                 Zm00001d007687 Protein Tropinone 
                 response to karrikin 
               
               
                   
                 reductase-like protein 
               
               
                 SEQ ID NO: 256 
                 Zm00001d015126 Protein response to low 
                 pyridoxamine-phosphate oxidase 
               
               
                   
                 sulfur 3 
                 activity 
               
               
                 SEQ ID NO: 257 
                 Zm00001d034781 Protein G-type lectin 
                 multicellular organism 
               
               
                   
                 S-receptor-like serine/threonine-protein 
                 development 
               
               
                   
                 kinase 
               
               
                 SEQ ID NO: 258 
                 Zm00001d016655 Protein hypothetical 
                 voltage-gated potassium channel 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 259 
                 Zm00001d043517 Protein Peptidase M28 
                 regulation of inflorescence 
               
               
                   
                 family protein 
                 meristem growth 
               
               
                 SEQ ID NO: 260 
                 Zm00001d045667 Protein Protein NRT1/ 
                 nitrate assimilation 
               
               
                   
                 PTR FAMILY 3.1 
               
               
                 SEQ ID NO: 261 
                 Zm00001d000126 Function unknown 
                 voltage-gated potassium channel 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 262 
                 Zm00001d029706 Glutathione S- 
                 glutathione transferase activity 
               
               
                   
                 transferase GSTU6-like protein 
               
               
                 SEQ ID NO: 263 
                 Zm00001d029321 Cationic amino acid 
                 amino acid transmembrane 
               
               
                   
                 transporter 
                 transporter activity 
               
               
                 SEQ ID NO: 264 
                 Zm00001d014701 Transcription regulator 
                 regulation of transcription, DNA- 
               
               
                   
                 HTH, Myb-type, DNA-binding protein 
                 templated 
               
               
                 SEQ ID NO: 265 
                 Zm00001d049624 Glutamate-rich WD 
                 zinc ion transmembrane transport 
               
               
                   
                 repeat-containing protein 1-like protein 
               
               
                 SEQ ID NO: 266 
                 Zm00001d034359 Zinc finger, C2H2- 
                 nucleic acid binding 
               
               
                   
                 type/integrase, DNA-binding protein 
               
               
                 SEQ ID NO: 267 
                 Zm00001d033924 Cell wall protein 
                 proton-transporting ATP synthase 
               
               
                   
                 pherophorin-C10 (PHC10) 
                 activity, rotational mechanism 
               
               
                 SEQ ID NO: 268 
                 Zm00001d032222 UDP- 
                 glucuronosyltransferase activity 
               
               
                   
                 glycosyltransferase 85A2-like protein 
               
               
                 SEQ ID NO: 269 
                 Zm00001d018155 Galactoside 2-alpha-L- 
                 cell wall biogenesis 
               
               
                   
                 fucosyltransferase-like protein 
               
               
                 SEQ ID NO: 270 
                 Zm00001d036263 Receptor protein 
                 protein serine/threonine kinase 
               
               
                   
                 serine/threonine kinase 
                 activity 
               
               
                 SEQ ID NO: 271 
                 Zm00001d044043 Acetylajmaline 
                 lipid catabolic process 
               
               
                   
                 esterase 
               
               
                 SEQ ID NO: 272 
                 Zm00001d027425 MADS-box 
                 transcription, DNA-templated 
               
               
                   
                 transcription factor 56-like protein 
               
               
                 SEQ ID NO: 273 
                 Zm00001d048635 Putative disease 
                 plant-type hypersensitive response 
               
               
                   
                 resistance RPP13-like protein 3-like 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 274 
                 Zm00001d006795 Omega- 
                 transferase activity, transferring 
               
               
                   
                 hydroxypalmitate O-feruloyl transferase 
                 acyl groups other than amino-acyl 
               
               
                   
                   
                 groups 
               
               
                 SEQ ID NO: 275 
                 Zm00001d041972 Cellulose synthase-like 
                 ellulose biosynthetic process 
               
               
                   
                 protein G2-like protein 
               
               
                 SEQ ID NO: 276 
                 Zm00001d000183 Hexose carrier protein 
                 carbohydrate transport 
               
               
                   
                 HEX6-like sugar transport protein 
               
               
                 SEQ ID NO: 277 
                 Zm00001d039575 1-aminocyclopropane- 
                 oxidoreductase activity, acting on 
               
               
                   
                 1-carboxylate oxidase 
                 paired donors, with incorporation 
               
               
                   
                   
                 or reduction of molecular oxygen, 
               
               
                   
                   
                 2-oxoglutarate as one donor, and 
               
               
                   
                   
                 incorporation of one atom each of 
               
               
                   
                   
                 oxygen into both donors 
               
               
                 SEQ ID NO: 278 
                 Zm00001d046202 Transposase, 
                 sequence-specific DNA binding 
               
               
                   
                 Ptta/En/Spm, plant 
               
               
                 SEQ ID NO: 279 
                 Zm00001d013571 Ubiquitin-protein 
                 protein binding 
               
               
                   
                 ligase/zinc ion binding protein 
               
               
                 SEQ ID NO: 280 
                 Zm00001d015470 GDU1 
                 multicellular organism 
               
               
                   
                   
                 development 
               
               
                 SEQ ID NO: 281 
                 Zm00001d053965 16.9 kDa class I heat 
                 response to stress 
               
               
                   
                 shock protein 1 
               
               
                 SEQ ID NO: 282 
                 Zm00001d029164 Inactive beta-amylase 
                 ellular polysaccharide catabolic 
               
               
                   
                 9-like protein 
                 process 
               
               
                 SEQ ID NO: 283 
                 Zm00001d031717 Transcription factor 
                 transcription, DNA-templated 
               
               
                   
                 MYC4-like protein 
               
               
                 SEQ ID NO: 284 
                 Zm00001d035767 Jasmonate O- 
                 jasmonic acid metabolic process 
               
               
                   
                 methyltransferase 
               
               
                 SEQ ID NO: 285 
                 Zm00001d004279 Myrcene synthase, 
                 monoterpenoid biosynthetic 
               
               
                   
                 chloroplastic-like protein 
                 process 
               
               
                 SEQ ID NO: 286 
                 Zm00001d003462 Lipoyl synthase 2, 
                 lipoate synthase activity 
               
               
                   
                 mitochondrial-like protein 
               
               
                 SEQ ID NO: 287 
                 Zm00001d026360 Cyclin PHO80-like 
                 protein kinase binding 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 288 
                 Zm00001d013984 Protein EXECUTER 1 
                 3′-5′-exoribonuclease activity 
               
               
                   
                 (EXI) 
               
               
                 SEQ ID NO: 289 
                 Zm00001d047207 Copper-transporting 
                 calcium-transporting ATPase 
               
               
                   
                 ATPase (CTATP) 
                 activity 
               
               
                 SEQ ID NO: 290 
                 Zm00001d030381 Deoxyribodipyrimidine 
                 protein-chromophore linkage 
               
               
                   
                 photo-lyase; Photoreactivating enzyme 
               
               
                   
                 CPD photolyase 
               
               
                 SEQ ID NO: 291 
                 Zm00001d046755 Two-component 
                 phosphorelay response regulator 
               
               
                   
                 response regulator ARR12-like protein 
                 activity 
               
               
                 SEQ ID NO: 292 
                 Zm00001d007167 CBL-interacting 
                 peptidyl-serine phosphorylation 
               
               
                   
                 protein kinase 07 
               
               
                 SEQ ID NO: 293 
                 Zm00001d039392 High affinity cationic 
                 L-alpha-amino acid 
               
               
                   
                 amino acid transporter 
                 transmembrane transport 
               
               
                 SEQ ID NO: 294 
                 Zm00001d013627 Retinoblastoma- 
                 chromatin silencing by small RNA 
               
               
                   
                 binding protein 
               
               
                 SEQ ID NO: 295 
                 Zm00001d044717 Cyclic nucleotide 
                 ion gated channel activity 
               
               
                   
                 binding/inward rectifier potassium 
               
               
                   
                 channel 
               
               
                 SEQ ID NO: 296 
                 Zm00001d032933 KIP1-like protein 
                 N-acetyltransferase activity 
               
               
                 SEQ ID NO: 297 
                 Zm00001d034467 Transcription regulator 
                 cell differentiation 
               
               
                   
                 HTH, Myb-type, DNA-binding protein 
               
               
                 SEQ ID NO: 298 
                 Zm00001d018797 Photosystem I reaction 
                 photosynthesis 
               
               
                   
                 center subunit psaK, chloroplast precursor 
               
               
                 SEQ ID NO: 299 
                 Zm00001d002934 Secondary wall NAC 
                 sequence-specific DNA binding 
               
               
                   
                 transcription factor 4 
               
               
                 SEQ ID NO: 300 
                 Zm00001d022088 cDNA Agamous-like 
                 DNA-binding transcription factor 
               
               
                   
                 MADS-box protein AGL8 
                 activity 
               
               
                 SEQ ID NO: 301 
                 Zm00001d023455 cDNA Transcription 
                 DNA-binding transcription factor 
               
               
                   
                 repressor OFP13 
                 activity 
               
               
                 SEQ ID NO: 302 
                 Zm00001d023456 cDNA Transcription 
                 DNA-binding transcription factor 
               
               
                   
                 repressor OFP6 
                 activity 
               
               
                 SEQ ID NO: 303 
                 Zm00001d038273 cDNA Coronatine- 
                 shade avoidance 
               
               
                   
                 insensitive protein 1 
               
               
                 SEQ ID NO: 304 
                 Zm00001d004053 cDNA hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 305 
                 Zm00001d029183 cDNA cytochrome 
                 isoflavone 2′-hydroxylase activity 
               
               
                   
                 P450 family 81 subfamily D 
               
               
                   
                 polypeptide 8 
               
               
                 SEQ ID NO: 306 
                 Zm00001d051194 cDNA Arginine 
                 arginine decarboxylase activity 
               
               
                   
                 decarboxylase 
               
               
                 SEQ ID NO: 307 
                 Zm00001d033132 cDNA photosystem II 
                 photosynthesis 
               
               
                   
                 light harvesting complex gene 2.1 
               
               
                 SEQ ID NO: 308 
                 Zm00001d029215 cDNA Villin-2 
                 actin filament bundle assembly 
               
               
                 SEQ ID NO: 309 
                 Zm00001d033543 cDNA Integral 
                 cellular carbohydrate metabolic 
               
               
                   
                 membrane HPP family protein 
                 process 
               
               
                 SEQ ID NO: 310 
                 Zm00001d053925 cDNA hypothetical 
                 chlorophyll biosynthetic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 311 
                 Zm00001d028269 cDNA hypothetical 
                 DNA-binding transcription factor 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 312 
                 Zm00001d033544 cDNA 
                 transferase activity, transferring 
               
               
                   
                 Glycosyltransferase family protein 64 
                 hexosyl groups 
               
               
                   
                 protein C5 
               
               
                 SEQ ID NO: 313 
                 Zm00001d034015 cDNA exoglucanase1 
                 glucan exo-1,3-beta-glucosidase 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 314 
                 Zm00001d027743 cDNA 
                 sugar mediated signaling pathway 
               
               
                   
                 Serine/threonine-protein kinase EDR1 
               
               
                 SEQ ID NO: 315 
                 Zm00001d048311 cDNA Sucrose 
                 sucrose transmembrane transporter 
               
               
                   
                 transport protein SUC3 
                 activity 
               
               
                 SEQ ID NO: 316 
                 Zm00001d047256 cDNA Protein kinase 
                 signal transduction 
               
               
                   
                 domain superfamily protein 
               
               
                 SEQ ID NO: 317 
                 Zm00001d048720 cDNA Glutaredoxin- 
                 electron transport chain 
               
               
                   
                 C13 
               
               
                 SEQ ID NO: 318 
                 Zm00001d023426 cDNA hypothetical 
                 chlorophyll biosynthetic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 319 
                 Zm00001d004331 cDNA hypothetical 
                 regulation of transcription, DNA- 
               
               
                   
                 protein 
                 templated 
               
               
                 SEQ ID NO: 320 
                 Zm00001d050748 cDNA proline-rich 
                 ATPase activity, coupled to 
               
               
                   
                 family protein 
                 transmembrane movement of 
               
               
                   
                   
                 substances 
               
               
                 SEQ ID NO: 321 
                 Zm00001d010321 cDNA pyruvate 
                 pyruvate, phosphate dikinase 
               
               
                   
                 orthophosphate dikinase2 
                 activity 
               
               
                 SEQ ID NO: 322 
                 Zm00001d004894 cDNA ribulose 
                 ribulose-bisphosphate carboxylase 
               
               
                   
                 bisphosphate carboxylase small subunit2 
                 activity 
               
               
                 SEQ ID NO: 323 
                 Zm00001d042346 cDNA alpha/beta- 
                 haloalkane dehalogenase activity 
               
               
                   
                 Hydrolases superfamily protein 
               
               
                 SEQ ID NO: 324 
                 Zm00001d031657 cDNA putative 
                 acid phosphatase activity 
               
               
                   
                 inactive purple acid phosphatase 27 
               
               
                 SEQ ID NO: 325 
                 Zm00001d008178 cDNA ABC 
                 basipetal auxin transport 
               
               
                   
                 transporter B family member 21 
               
               
                 SEQ ID NO: 326 
                 Zm00001d043044 cDNA Secl/munc18- 
                 kinase activity 
               
               
                   
                 like (SM) proteins superfamily 
               
               
                 SEQ ID NO: 327 
                 Zm00001d018623 cDNA Photosynthetic 
                 electron transporter, transferring 
               
               
                   
                 NDH subunit of lumenal location 3 
                 electrons within the cyclic electron 
               
               
                   
                 chloroplastic 
                 transport pathway of 
               
               
                   
                   
                 photosynthesis activity 
               
               
                 SEQ ID NO: 328 
                 Zm00001d043095 cDNA Zinc finger 
                 chloroplast organization 
               
               
                   
                 protein VAR3 chloroplastic 
               
               
                 SEQ ID NO: 329 
                 Zm00001d029062 cDNA Vicilin-like 
                 nutrient reservoir activity 
               
               
                   
                 seed storage protein 
               
               
                 SEQ ID NO: 330 
                 Zm00001d011900 cDNA RNA-binding 
                 RNA binding 
               
               
                   
                 protein BRN1 
               
               
                 SEQ ID NO: 331 
                 Zm00001d010672 cDNA Metacaspase 
                 phosphoglycerate kinase activity 
               
               
                   
                 type II 
               
               
                 SEQ ID NO: 332 
                 Zm00001d011183 cDNA thiamine 
                 thiazole biosynthetic process 
               
               
                   
                 biosynthesis1 
               
               
                 SEQ ID NO: 333 
                 Zm00001d037103 cDNA Peroxiredoxin 
                 peroxiredoxin activity 
               
               
                   
                 Q chloroplastic 
               
               
                 SEQ ID NO: 334 
                 Zm00001d009028 cDNA Triose 
                 transporter activity 
               
               
                   
                 phosphate/phosphate translocator, 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 335 
                 Zm00001d013937 cDNA 
                 chlorophyll biosynthetic process 
               
               
                   
                 Protochlorophyllide reductase C 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 336 
                 Zm00001d002873 cDNA UPF0426 
                 plastoglobule 
               
               
                   
                 protein chloroplastic 
               
               
                 SEQ ID NO: 337 
                 Zm00001d037362 cDNA DNA 
                 DNA topoisomerase activity 
               
               
                   
                 topoisomerase type IA core 
               
               
                 SEQ ID NO: 338 
                 Zm00001d026404 cDNA hypothetical 
                 arginine catabolic process to 
               
               
                   
                 protein 
                 glutamate 
               
               
                 SEQ ID NO: 339 
                 Zm00001d047255 cDNA 3-oxoacyl- 
                 3-oxoacyl-[acyl-carrier-protein] 
               
               
                   
                 [acyl-carrier-protein] synthase II 
                 synthase activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 340 
                 Zm00001d031253 cDNA dicarboxylic 
                 transporter activity 
               
               
                   
                 acid transported 
               
               
                 SEQ ID NO: 341 
                 Zm00001d027576 cDNA hypothetical 
                 voltage-gated anion channel 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 342 
                 Zm00001d052595 cDNA Ribulose 
                 ribulose-bisphosphate carboxylase 
               
               
                   
                 bisphosphate carboxylase small chain, 
                 activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 343 
                 Zm00001d013367 cDNA Tubulin alpha-4 
                 structural molecule activity 
               
               
                   
                 chain 
               
               
                 SEQ ID NO: 344 
                 Zm00001d046001 cDNA Triose 
                 transmembrane transporter activity 
               
               
                   
                 phosphate/phosphate translocator TPT 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 345 
                 Zm00001d008963 cDNA GDT1-like 
                 chloroplast membrane 
               
               
                   
                 protein 1 chloroplastic 
               
               
                 SEQ ID NO: 346 
                 Zm00001d048515 cDNA Stress 
                 gene silencing 
               
               
                   
                 responsive alpha-beta barrel domain 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 347 
                 Zm00001d018779 cDNA hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 348 
                 Zm00001d052595 cDNA Ribulose 
                 ribulose-bisphosphate carboxylase 
               
               
                   
                 bisphosphate carboxylase small chain, 
                 activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 349 
                 Zm00001d042049 cDNA Ferredoxin 
                 photosynthetic electron transport 
               
               
                   
                   
                 in photosystem I 
               
               
                 SEQ ID NO: 350 
                 Zm00001d040242 cDNA Nuclear 
                 cellular macromolecule metabolic 
               
               
                   
                 transport factor 2 (NTF2) family protein 
                 process 
               
               
                 SEQ ID NO: 351 
                 Zm00001d042697 cDNA photosystem II 
                 PSII associated light-harvesting 
               
               
                   
                 subunit PsbS1 
                 complex II 
               
               
                 SEQ ID NO: 352 
                 Zm00001d019518 cDNA Photosystem I 
                 photosystem I reaction center 
               
               
                   
                 reaction center subunit IV A 
               
               
                 SEQ ID NO: 353 
                 Zm00001d048313 cDNA NAD(P)-linked 
                 photosystem II assembly 
               
               
                   
                 oxidoreductase superfamily protein 
               
               
                 SEQ ID NO: 354 
                 Zm00001d033150 cDNA hypothetical 
                 transcription regulatory region 
               
               
                   
                 protein 
                 sequence-specific DNA binding 
               
               
                 SEQ ID NO: 355 
                 Zm00001d007858 cDNA Pyridoxal 
                 oxidoreductase activity 
               
               
                   
                 reductase chloroplastic 
               
               
                 SEQ ID NO: 356 
                 Zm00001d003588 cDNA Ras-related 
                 protein binding 
               
               
                   
                 protein RABD1 
               
               
                 SEQ ID NO: 357 
                 Zm00001d036903 cDNA Plant Tudor-like 
                 RNA binding 
               
               
                   
                 RNA-binding protein 
               
               
                 SEQ ID NO: 358 
                 Zm00001d031484 cDNA PsbP domain- 
                 photosystem II oxygen evolving 
               
               
                   
                 containing protein 3 chloroplastic 
                 complex 
               
               
                 SEQ ID NO: 359 
                 Zm00001d018157 cDNA light harvesting 
                 photosynthesis, light harvesting in 
               
               
                   
                 complex a/b protein4 
                 photosystem I 
               
               
                 SEQ ID NO: 360 
                 Zm00001d005814 cDNA Photosystem I 
                 photosynthesis, light harvesting in 
               
               
                   
                 chlorophyll a/b-binding protein 6 
                 photosystem I 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 361 
                 Zm00001d033338 cDNA NAD(P)-linked 
                 oxidoreductase activity 
               
               
                   
                 oxidoreductase superfamily protein 
               
               
                 SEQ ID NO: 362 
                 Zm00001d053446 cDNA potassium 
                 voltage-gated potassium channel 
               
               
                   
                 channel3 
                 activity 
               
               
                 SEQ ID NO: 363 
                 Zm00001d026603 cDNA Magnesium- 
                 photosynthesis, light reaction 
               
               
                   
                 chelatase subunit ChlH chloroplastic 
               
               
                 SEQ ID NO: 364 
                 Zm00001d027841 cDNA Ribulose- 
                 pentose-phosphate shunt, non- 
               
               
                   
                 phosphate 3-epimerase 
                 oxidative branch 
               
               
                 SEQ ID NO: 365 
                 Zm00001d030048 cDNA pfkB-like 
                 isopentenyl diphosphate 
               
               
                   
                 carbohydrate kinase family protein 
                 biosynthetic process, 
               
               
                   
                   
                 methylerythritol 4-phosphate 
               
               
                   
                   
                 pathway 
               
               
                 SEQ ID NO: 366 
                 Zm00001d005346 cDNA Aldo-keto 
                 oxidoreductase activity 
               
               
                   
                 reductase/oxidoreductase 
               
               
                 SEQ ID NO: 367 
                 Zm00001d023706 cDNA thioredoxin M1 
                 transcription coregulator activity 
               
               
                 SEQ ID NO: 368 
                 Zm00001d042050 cDNA Protein 
                 chlorophyll biosynthetic process 
               
               
                   
                 RETICULATA-RELATED 4 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 369 
                 Zm00001d042533 cDNA Trigger factor 
                 protein transport 
               
               
                 SEQ ID NO: 370 
                 Zm00001d022590 cDNA hypothetical 
                 transcription, DNA-templated 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 371 
                 Zm00001d045431 cDNA Enolase 1 
                 phosphopyruvate hydratase 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 372 
                 Zm00001d047743 cDNA fatty acid 
                 oxidoreductase activity, acting on 
               
               
                   
                 desaturase7 
                 paired donors, with oxidation of a 
               
               
                   
                   
                 pair of donors resulting in the 
               
               
                   
                   
                 reduction of molecular oxygen to 
               
               
                   
                   
                 two molecules of water 
               
               
                 SEQ ID NO: 373 
                 Zm00001d036738 cDNA S-adenosyl-L- 
                 methyltransferase activity 
               
               
                   
                 methionine-dependent methyltransferase 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 374 
                 Zm00001d018274 cDNA Isoleucine- 
                 valyl-tRNA aminoacylation 
               
               
                   
                 tRNA ligase chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 375 
                 Zm00001d035003 cDNA ferredoxin2 
                 electron transfer activity 
               
               
                 SEQ ID NO: 376 
                 Zm00001d027321 cDNA hypothetical 
                 peptidyl-prolyl cis-trans isomerase 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 377 
                 Zm00001d014284 cDNA CMV 1a 
                 methyltransferase activity 
               
               
                   
                 interacting protein 1 
               
               
                 SEQ ID NO: 378 
                 Zm00001d036340 cDNA photosystem III 
                 photosystem II 
               
               
                 SEQ ID NO: 379 
                 Zm00001d003767 cDNA Photosystem I 
                 photosynthesis, light harvesting in 
               
               
                   
                 subunit O 
                 photosystem I 
               
               
                 SEQ ID NO: 380 
                 Zm00001d031997 cDNA NAD(P)- 
                 nucleotide binding 
               
               
                   
                 binding Rossmann-fold superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 381 
                 Zm00001d019479 cDNA granule-bound 
                 NDP-glucose-starch 
               
               
                   
                 starch synthase1b 
                 glucosyltransferase activity 
               
               
                 SEQ ID NO: 382 
                 Zm00001d024148 cDNA Photosynthetic 
                 photosynthetic electron transport 
               
               
                   
                 NDH subunit of subcomplex B 1 
                 in photosystem I 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 383 
                 Zm00001d038579 cDNA 
                 photosynthesis, light reaction 
               
               
                   
                 Phosphoglycerate kinase 
               
               
                 SEQ ID NO: 384 
                 Zm00001d037273 cDNA Peptide 
                 electron transport chain 
               
               
                   
                 methionine sulfoxide reductase msrB 
               
               
                 SEQ ID NO: 385 
                 Zm00001d025845 cDNA hypothetical 
                 chloroplast thylakoid membrane 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 386 
                 Zm00001d027422 cDNA PsbP-like 
                 chloroplast photosystem II 
               
               
                   
                 protein 1 chloroplastic 
               
               
                 SEQ ID NO: 387 
                 Zm00001d024519 cDNA rubredoxin 
                 iron ion binding 
               
               
                   
                 family protein 
               
               
                 SEQ ID NO: 388 
                 Zm00001d040163 cDNA deoxy xylulose 
                 1-deoxy-D-xylulose-5-phosphate 
               
               
                   
                 reductoisomerase1 
                 reductoisomerase activity 
               
               
                 SEQ ID NO: 389 
                 Zm00001d012868 cDNA carotene 
                 oxidoreductase activity 
               
               
                   
                 isomerase3 
               
               
                 SEQ ID NO: 390 
                 Zm00001d021763 cDNA photosystem II 
                 photosynthesis, light harvesting in 
               
               
                   
                 subunit29 
                 photosystem I 
               
               
                 SEQ ID NO: 391 
                 Zm00001d035761 cDNA Peptidyl-prolyl 
                 peptidyl-prolyl cis-trans isomerase 
               
               
                   
                 cis-trans isomerase 
                 activity 
               
               
                 SEQ ID NO: 392 
                 Zm00001d032301 cDNA S-adenosyl-L- 
                 methyltransferase activity 
               
               
                   
                 methionine-dependent methyltransferase 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 393 
                 Zm00001d028562 cDNA Fructose-1,6- 
                 photosynthetic electron transport 
               
               
                   
                 bisphosphatase 
                 in photosystem I 
               
               
                 SEQ ID NO: 394 
                 Zm00001d034538 cDNA Rubredoxin-like 
                 iron ion binding 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 395 
                 Zm00001d048116 cDNA hypothetical 
                 isopentenyl diphosphate 
               
               
                   
                 protein 
                 biosynthetic process, 
               
               
                   
                   
                 methylerythritol 4-phosphate 
               
               
                   
                   
                 pathway 
               
               
                 SEQ ID NO: 396 
                 Zm00001d048998 cDNA Chlorophyll a-b 
                 photosynthesis 
               
               
                   
                 binding protein CP26 chloroplastic 
               
               
                 SEQ ID NO: 397 
                 Zm00001d049490 cDNA Protein 
                 translation initiation factor activity 
               
               
                   
                 CHLORORESPIRATORY REDUCTION 
               
               
                   
                 6 chloroplastic 
               
               
                 SEQ ID NO: 398 
                 Zm00001d015975 cDNA putative 
                 lactoylglutathione lyase activity 
               
               
                   
                 lactoylglutathione lyase chloroplastic 
               
               
                 SEQ ID NO: 399 
                 Zm00001d021435 cDNA hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 400 
                 Zm00001d015613 cDNA Protein TIC 21 
                 protein import into chloroplast 
               
               
                   
                 chloroplastic 
                 stroma 
               
               
                 SEQ ID NO: 401 
                 Zm00001d039258 cDNA Triose 
                 glucose-6-phosphate 
               
               
                   
                 phosphate/phosphate translocator TPT 
                 transmembrane transporter activity 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 402 
                 Zm00001d007267 cDNA light harvesting 
                 photosynthesis, light harvesting in 
               
               
                   
                 chlorophyll a/b binding protein5 
                 photosystem I 
               
               
                 SEQ ID NO: 403 
                 Zm00001d033383 cDNA 
                 thiamine biosynthetic process 
               
               
                   
                 hydroxymethylpyrimidine phosphate 
               
               
                   
                 synthase1 
               
               
                 SEQ ID NO: 404 
                 Zm00001d026645 cDNA K(+) efflux 
                 solute: proton antiporter activity 
               
               
                   
                 antiporter 2 chloroplastic 
               
               
                 SEQ ID NO: 405 
                 Zm00001d023757 cDNA NAD(P)H- 
                 heat shock protein binding 
               
               
                   
                 quinone oxidoreductase subunit U 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 406 
                 Zm00001d034005 cDNA evolutionarily 
                 oxidation-reduction process 
               
               
                   
                 conserved C-terminal region 2 
               
               
                 SEQ ID NO: 407 
                 Zm00001d022381 cDNA NADPH- 
                 hydrogen peroxide catabolic 
               
               
                   
                 dependent thioredoxin reductase 3 
                 process 
               
               
                 SEQ ID NO: 408 
                 Zm00001d031962 cDNA hypothetical 
                 protein dephosphorylation 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 409 
                 Zm00001d005446 cDNA Photosystem I 
                 photosystem I reaction center 
               
               
                   
                 reaction center subunit IV A 
               
               
                 SEQ ID NO: 410 
                 Zm00001d027511 cDNA Catalase 
                 hydrogen peroxide catabolic 
               
               
                   
                 isozyme 2 
                 process 
               
               
                 SEQ ID NO: 411 
                 Zm00001d017178 cDNA hypothetical 
                 primary metabolic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 412 
                 Zm00001d03 8947 cDNA putative 
                 electron transfer activity 
               
               
                   
                 galacturonosyltransferase-like 9 
               
               
                 SEQ ID NO: 413 
                 Zm00001d034739 cDNA 
                 acetylpyruvate hydrolase activity 
               
               
                   
                 Fumarylacetoacetate (FAA) hydrolase 
               
               
                   
                 family 
               
               
                 SEQ ID NO: 414 
                 Zm00001d044745 cDNA Alanine--tRNA 
                 alanyl-tRNA aminoacylation 
               
               
                   
                 ligase chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 415 
                 Zm00001d038491 cDNA 
                 N-acetyltransferase activity 
               
               
                   
                 Acetyltransferase NSI 
               
               
                 SEQ ID NO: 416 
                 Zm00001d014445 cDNA Protein kinase 
                 kinase activity 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 417 
                 Zm00001d039745 cDNA Protein 
                 phosphoprotein phosphatase 
               
               
                   
                 phosphatase 2C 
                 activity 
               
               
                 SEQ ID NO: 418 
                 Zm00001d038485 cDNA 
                 photosystem II stabilization 
               
               
                   
                 Serine/threonine-protein kinase STN8 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 419 
                 Zm00001d012287 cDNA hypothetical 
                 starch biosynthetic process 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 420 
                 Zm00001d027694 cDNA Solanesyl 
                 plastoquinone biosynthetic process 
               
               
                   
                 diphosphate synthase 2 chloroplastic 
               
               
                 SEQ ID NO: 421 
                 Zm00001d003470 cDNA putative plastid- 
                 response to abscisic acid 
               
               
                   
                 lipid-associated protein 2 chloroplastic 
               
               
                 SEQ ID NO: 422 
                 Zm00001d019180 cDNA Nudix 
                 hydrolase activity 
               
               
                   
                 hydrolase 16 mitochondrial 
               
               
                 SEQ ID NO: 423 
                 Zm00001d007394 cDNA Rubredoxin-like 
                 iron ion binding 
               
               
                   
                 superfamily protein 
               
               
                 SEQ ID NO: 424 
                 Zm00001d053432 cDNA iron-sulfur 
                 electron transporter, transferring 
               
               
                   
                 protein2 
                 electrons within cytochrome b6/f 
               
               
                   
                   
                 complex of photosystem II activity 
               
               
                 SEQ ID NO: 425 
                 Zm00001d039900 cDNA putative zinc 
                 metalloendopeptidase activity 
               
               
                   
                 metalloprotease EGY2 chloroplastic 
               
               
                 SEQ ID NO: 426 
                 Zm00001d050810 cDNA 2-hydroxy-3- 
                 pentose-phosphate shunt 
               
               
                   
                 oxopropionate reductase 
               
               
                 SEQ ID NO: 427 
                 Zm00001d016802 cDNA L-ascorbate 
                 L-ascorbate peroxidase activity 
               
               
                   
                 peroxidase S chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 428 
                 Zm00001d004978 cDNA Saccharopine 
                 oxidoreductase activity 
               
               
                   
                 dehydrogenase 
               
               
                 SEQ ID NO: 429 
                 Zm00001d028924 cDNA NifU-like 
                 iron-sulfur cluster assembly 
               
               
                   
                 protein 1 chloroplastic 
               
               
                 SEQ ID NO: 430 
                 Zm00001d002815 cDNA NAD(P)H- 
                 oxidoreductase activity, acting on 
               
               
                   
                 quinone oxidoreductase subunit M 
                 NAD(P)H, quinone or similar 
               
               
                   
                 chloroplastic 
                 compound as acceptor 
               
               
                 SEQ ID NO: 431 
                 Zm00001d029065 cDNA Protein LRP16 
                 regulation of transcription, DNA- 
               
               
                   
                   
                 templated 
               
               
                 SEQ ID NO: 432 
                 Zm00001d052184 cDNA Protein 
                 chloroplast envelope 
               
               
                   
                 CURVATURE THYLAKOID 1D 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 433 
                 Zm00001d038337 cDNA DAR GTPase 3 
                 GTP binding 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 434 
                 Zm00001d003713 cDNA Exocyst 
                 pollen tube growth 
               
               
                   
                 complex component SEC5A 
               
               
                 SEQ ID NO: 435 
                 Zm00001d031953 cDNA Thioredoxin 
                 protein disulfide oxidoreductase 
               
               
                   
                 family protein 
                 activity 
               
               
                 SEQ ID NO: 436 
                 Zm00001d053576 cDNA putative 
                 eukaryotic translation elongation 
               
               
                   
                 elongation factor 1-gamma 2 
                 factor 1 complex 
               
               
                 SEQ ID NO: 437 
                 Zm00001d000123 cDNA NAD(P)- 
                 response to oxidative stress 
               
               
                   
                 binding Rossmann-fold superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 438 
                 Zm00001d045431 cDNA Enolase 1 
                 phosphopyruvate hydratase 
               
               
                   
                   
                 activity 
               
               
                 SEQ ID NO: 439 
                 Zm00001d036630 cDNA Filamentation 
                 metalloendopeptidase activity 
               
               
                   
                 temperature-sensitive H 2B 
               
               
                 SEQ ID NO: 440 
                 Zm00001d048515 cDNA Stress 
                 gene silencing 
               
               
                   
                 responsive alpha-beta barrel domain 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 441 
                 Zm00001d021310 cDNA 
                 reductive pentose-phosphate cycle 
               
               
                   
                 Triosephosphate isomerase 
               
               
                 SEQ ID NO: 442 
                 Zm00001d042353 cDNA sucrose 
                 sucrose synthase activity 
               
               
                   
                 phosphate synthase2 
               
               
                 SEQ ID NO: 443 
                 Zm00001d050150 cDNA Adenylate 
                 adenylate kinase activity 
               
               
                   
                 kinase 5 chloroplastic 
               
               
                 SEQ ID NO: 444 
                 Zm00001d025545 cDNA zeaxanthin 
                 abscisic acid biosynthetic process 
               
               
                   
                 epoxidase2 
               
               
                 SEQ ID NO: 445 
                 Zm00001d012168 cDNA Membrane- 
                 chloroplast thylakoid membrane 
               
               
                   
                 associated protein VIPP1 chloroplastic 
               
               
                 SEQ ID NO: 446 
                 Zm00001d011581 cDNA Peroxiredoxin- 
                 peroxiredoxin activity 
               
               
                   
                 2B 
               
               
                 SEQ ID NO: 447 
                 Zm00001d018030 cDNA Photosynthetic 
                 regulation of transcription by RNA 
               
               
                   
                 NDH subunit of subcomplex B 4 
                 polymerase II 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 448 
                 Zm00001d018145 cDNA Presequence 
                 protein processing 
               
               
                   
                 protease 2 chloroplastic/mitochondrial 
               
               
                 SEQ ID NO: 449 
                 Zm00001d040221 cDNA Peptidase 
                 metalloendopeptidase activity 
               
               
                   
                 family M48 family protein 
               
               
                 SEQ ID NO: 450 
                 Zm00001d033594 cDNA Myelin- 
                 phosphorus metabolic process 
               
               
                   
                 associated oligodendrocyte basic protein 
               
               
                   
                 isoform 1 
               
               
                 SEQ ID NO: 451 
                 Zm00001d008625 cDNA Inner membrane 
                 thylakoid membrane organization 
               
               
                   
                 protein ALBINO3 chloroplastic 
               
               
                 SEQ ID NO: 452 
                 Zm00001d032380 cDNA acclimation of 
                 photosystem II assembly 
               
               
                   
                 photosynthesis to environment 
               
               
                 SEQ ID NO: 453 
                 Zm00001d045575 cDNA Ferredoxin- 
                 photosynthetic electron transport 
               
               
                   
                 NADP reductase leaf isozyme 1 
                 in photosystem I 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 454 
                 Zm00001d042526 cDNA Rhodanese/Cell 
                 regulation of stomatai closure 
               
               
                   
                 cycle control phosphatase superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 455 
                 Zm00001d043168 cDNA MAR-binding 
                 photosystem II assembly 
               
               
                   
                 filament-like protein 1-1 isoform 2 
               
               
                 SEQ ID NO: 456 
                 Zm00001d053545 cDNA NAD(P)- 
                 nucleotide binding 
               
               
                   
                 binding Rossmann-fold superfamily 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 457 
                 Zm00001d053981 cDNA putative 
                 pyridoxal phosphate biosynthetic 
               
               
                   
                 pyridoxal 5′-phosphate synthase subunit 
                 process 
               
               
                   
                 PDX2 
               
               
                 SEQ ID NO: 458 
                 Zm00001d017746 cDNA vitamin E 
                 tocopherol O-methyltransferase 
               
               
                   
                 synthesis4 
                 activity 
               
               
                 SEQ ID NO: 459 
                 Zm00001d012083 cDNA Thioredoxin F- 
                 pentose-phosphate shunt 
               
               
                   
                 type chloroplastic 
               
               
                 SEQ ID NO: 460 
                 Zm00001d024718 cDNA Beta-carotene 
                 strigolactone biosynthetic process 
               
               
                   
                 isomerase D27 chloroplastic 
               
               
                 SEQ ID NO: 461 
                 Zm00001d021621 cDNA Polynucleotidyl 
                 3′-5′ exonuclease activity 
               
               
                   
                 transferase ribonuclease H fold protein 
               
               
                   
                 with HRDC domain 
               
               
                 SEQ ID NO: 462 
                 Zm00001d015004 cDNA Protein LOW 
                 aromatic amino acid family 
               
               
                   
                 PSII ACCUMULATION 3 chloroplastic 
                 biosynthetic process 
               
               
                 SEQ ID NO: 463 
                 Zm00001d039131 cDNA ADP glucose 
                 glucose-1-phosphate 
               
               
                   
                 pyrophosphorylase2 
                 adenylyltransferase activity 
               
               
                 SEQ ID NO: 464 
                 Zm00001d044970 cDNA putative 
                 protein tyrosine phosphatase 
               
               
                   
                 tyrosine-protein phosphatase 
                 activity 
               
               
                 SEQ ID NO: 465 
                 Zm00001d018401 cDNA plastid 
                 positive regulation of ubiquitin 
               
               
                   
                 transcriptionally active 17 
                 protein ligase activity 
               
               
                 SEQ ID NO: 466 
                 Zm00001d015975 cDNA putative 
                 lactoylglutathione lyase activity 
               
               
                   
                 lactoylglutathione lyase chloroplastic 
               
               
                 SEQ ID NO: 467 
                 Zm00001d013428 cDNA 
                 phosphoglucomutase activity 
               
               
                   
                 phosphoglucomutase2 
               
               
                 SEQ ID NO: 468 
                 Zm00001d021246 cDNA Ras-related 
                 chloroplast thylakoid membrane 
               
               
                   
                 protein RABA3 
               
               
                 SEQ ID NO: 469 
                 Zm00001d007921 cDNA Tic62 protein 
                 oxidation-reduction process 
               
               
                 SEQ ID NO: 470 
                 Zm00001d027511 cDNA Catalase 
                 hydrogen peroxide catabolic 
               
               
                   
                 isozyme 2 
                 process 
               
               
                 SEQ ID NO: 471 
                 Zm00001d027309 cDNA Phosphoglucan 
                 intracellular signal transduction 
               
               
                   
                 phosphatase DSP4 chloroplastic 
               
               
                 SEQ ID NO: 472 
                 Zm00001d025544 cDNA Zeaxanthin 
                 zeaxanthin epoxidase [overall] 
               
               
                   
                 epoxidase chloroplastic 
                 activity 
               
               
                 SEQ ID NO: 473 
                 Zm00001d039276 cDNA Ubiquitin ligase 
                 cellular metabolic process 
               
               
                   
                 SINAT3 
               
               
                 SEQ ID NO: 474 
                 Zm00001d003512 cDNA Zeaxanthin 
                 zeaxanthin epoxidase [overall] 
               
               
                   
                 epoxidase chloroplastic 
                 activity 
               
               
                 SEQ ID NO: 475 
                 Zm00001d053861 cDNA Putative 
                 GTP binding 
               
               
                   
                 translation elongation factor family 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 476 
                 Zm00001d038894 cDNA 
                 circadian rhythm 
               
               
                   
                 Serine/threonine-protein kinase STN7 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 477 
                 Zm00001d051321 cDNA ATP-dependent 
                 metalloendopeptidase activity 
               
               
                   
                 zinc metalloprotease FTSH 7 
               
               
                   
                 chloroplastic 
               
               
                 SEQ ID NO: 478 
                 Zm00001d016826 cDNA proline-rich 
                 anatomical structure 
               
               
                   
                 family protein 
                 morphogenesis 
               
               
                 SEQ ID NO: 479 
                 Zm00001d016854 cDNA Ferrochelatase 
                 starch biosynthetic process 
               
               
                 SEQ ID NO: 480 
                 Zm00001d017435 cDNA hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 481 
                 Zm00001d048373 cDNA Carotenoid 
                 oxidoreductase activity, acting on 
               
               
                   
                 910(9′10′)-cleavage dioxygenase 1 
                 single donors with incorporation of 
               
               
                   
                   
                 molecular oxygen, incorporation 
               
               
                   
                   
                 of two atoms of oxygen 
               
               
                 SEQ ID NO: 482 
                 Zm00001d018901 cDNA protein 
                 protein binding 
               
               
                   
                 containing PDZ domain a K-box domain 
               
               
                   
                 and a TPR region 
               
               
                 SEQ ID NO: 483 
                 Zm00001d019454 cDNA PGR5-like 
                 photosynthetic electron transport 
               
               
                   
                 protein 1B chloroplastic 
                 in photosystem I 
               
               
                 SEQ ID NO: 484 
                 Zm00001d031899 cDNA malate 
                 malate dehydrogenase (NADP+) 
               
               
                   
                 dehydrogenase6 
                 activity 
               
               
                 SEQ ID NO: 485 
                 Zm00001d045706 cDNA Restorer of 
                 aldehyde dehydrogenase (NAD) 
               
               
                   
                 fertility2 
                 activity 
               
               
                 SEQ ID NO: 486 
                 Zm00001d035869 cDNA Protein MEI2- 
                 nucleotide binding 
               
               
                   
                 like 5 
               
               
                 SEQ ID NO: 487 
                 Zm00001d053262 cDNA calcium- 
                 protein localization 
               
               
                   
                 dependent lipid-binding family protein 
               
               
                 SEQ ID NO: 488 
                 Zm00001d017958 cDNA Glutamine 
                 glutamine biosynthetic process 
               
               
                   
                 synthetase root isozyme 3 
               
               
                 SEQ ID NO: 489 
                 Zm00001d007113 cDNA Xylose 
                 xylose isomerase activity 
               
               
                   
                 isomerase 
               
               
                 SEQ ID NO: 490 
                 Zm00001d051650 cDNA Sucrose 
                 transcription, DNA-templated 
               
               
                   
                 cleavage protein-like protein 
               
               
                 SEQ ID NO: 491 
                 Zm00001d015138 cDNA hypothetical 
                 nuclear pore 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 492 
                 Zm00001d030103 cDNA putative 
                 xyloglucamxyloglucosyl 
               
               
                   
                 xyloglucan endotransglucosylase/ 
                 transferase activity 
               
               
                   
                 hydrolase protein 30 
               
               
                 SEQ ID NO: 493 
                 Zm00001d021846 cDNA Insulin- 
                 metalloendopeptidase activity 
               
               
                   
                 degrading enzyme-like 1 peroxisomal 
               
               
                 SEQ ID NO: 494 
                 Zm00001d041576 cDNA Transcription 
                 regulation of transcription, DNA- 
               
               
                   
                 factor MYB48 
                 templated 
               
               
                 SEQ ID NO: 495 
                 Zm00001d005391 cDNA Cysteine 
                 cysteine-type endopeptidase 
               
               
                   
                 proteinases superfamily protein 
                 activity 
               
               
                 SEQ ID NO: 496 
                 Zm00001d009022 cDNA NmrA-like 
                 166 nucleotide binding 
               
               
                   
                 negative transcriptional regulator family 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 497 
                 Zm00001d041343 cDNA putative disease 
                 defense response 
               
               
                   
                 resistance protein 
               
               
                 SEQ ID NO: 498 
                 Zm00001d039965 cDNA Delta(7)-sterol- 
                 fatty acid biosynthetic process 
               
               
                   
                 C5(6)-desaturase 1 
               
               
                 SEQ ID NO: 499 
                 Zm00001d029047 cDNA Receptor-like 
                 signaling receptor activity 
               
               
                   
                 protein kinase FERONIA 
               
               
                 SEQ ID NO: 500 
                 Zm00001d028230 cDNA Sugar transport 
                 sucrose transport 
               
               
                   
                 protein 13 
               
               
                 SEQ ID NO: 501 
                 Zm00001d013243 cDNA Cyclic 
                 plant-type hypersensitive response 
               
               
                   
                 nucleotide-gated ion channel 2 
               
               
                 SEQ ID NO: 502 
                 Zm00001d032926 cDNA chlorophyllase2 
                 chlorophyll catabolic process 
               
               
                 SEQ ID NO: 503 
                 Zm00001d045667 cDNA Protein NRT1/ 
                 nitrate assimilation 
               
               
                   
                 PTR FAMILY 3.1 
               
               
                 SEQ ID NO: 504 
                 Zm00001d021846 cDNA Insulin- 
                 metalloendopeptidase activity 
               
               
                   
                 degrading enzyme-like 1 peroxisomal 
               
               
                 SEQ ID NO: 505 
                 Zm00001d033469 cDNA Ferredoxin 
                 electron transfer activity 
               
               
                 SEQ ID NO: 506 
                 Zm00001d019563 cDNA Aquaporin 
                 transporter activity 
               
               
                   
                 PIP2-1 
               
               
                 SEQ ID NO: 507 
                 Zm00001d003866 cDNA hypothetical 
                 cell wall organization 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 508 
                 Zm00001d039325 cDNA Putative 
                 signaling receptor activity 
               
               
                   
                 inactive receptor-like protein kinase 
               
               
                 SEQ ID NO: 509 
                 Zm00001d023516 cDNA Salt stress- 
                 mannose binding 
               
               
                   
                 induced protein 
               
               
                 SEQ ID NO: 510 
                 Zm00001d050918 cDNA hypothetical 
                 aldehyde dehydrogenase (NAD) 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 511 
                 Zm00001d025253 cDNA hypothetical 
                 none 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 512 
                 Zm00001d024499 cDNA Nuclear factor 1 
                 aminoacyl-tRNA hydrolase 
               
               
                   
                 A-type isoform 2 
                 activity 
               
               
                 SEQ ID NO: 513 
                 Zm00001d045948 cDNA Protein 
                 drug transmembrane transporter 
               
               
                   
                 DETOXIFICATION 16 
                 activity 
               
               
                 SEQ ID NO: 514 
                 Zm00001d021569 cDNA Transparent 
                 drug transmembrane transporter 
               
               
                   
                 testa 12 protein 
                 activity 
               
               
                 SEQ ID NO: 515 
                 Zm00001d053327 cDNA Galactoside 2- 
                 xyloglucan biosynthetic process 
               
               
                   
                 alpha-L-fucosyltransferase 
               
               
                 SEQ ID NO: 516 
                 Zm00001d047208 cDNA WAT1-related 
                 auxin-activated signaling pathway 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 517 
                 Zm00001d007687 cDNA Tropinone 
                 response to karrikin 
               
               
                   
                 reductase-like protein 
               
               
                 SEQ ID NO: 518 
                 Zm00001d015126 cDNA response to low 
                 pyridoxamine-phosphate oxidase 
               
               
                   
                 sulfur 3 
                 activity 
               
               
                 SEQ ID NO: 519 
                 Zm00001d034781 cDNA G-type lectin S- 
                 multicellular organism 
               
               
                   
                 receptor-like serine/threonine-protein 
                 development 
               
               
                   
                 kinase 
               
               
                 SEQ ID NO: 520 
                 Zm00001d016655 cDNA hypothetical 
                 voltage-gated potassium channel 
               
               
                   
                 protein 
                 activity 
               
               
                 SEQ ID NO: 521 
                 Zm00001d043517 cDNA Peptidase M28 
                 regulation of inflorescence 
               
               
                   
                 family protein 
                 meristem growth 
               
               
                 SEQ ID NO: 522 
                 Zm00001d045667 cDNA Protein NRT1/ 
                 nitrate assimilation 
               
               
                   
                 PTR FAMILY 3.1 
               
               
                 SEQ ID NO: 523 
                 Zm00001d000126 cDNA Function 
                 voltage-gated potassium channel 
               
               
                   
                 unknown 
                 activity 
               
               
                 SEQ ID NO: 524 
                 Zm00001d029706 cDNA Glutathione S- 
                 glutathione transferase activity 
               
               
                   
                 transferase GSTU6-like protein 
               
               
                 SEQ ID NO: 525 
                 Zm00001d029321 cDNA Cationic amino 
                 amino acid transmembrane 
               
               
                   
                 acid transporter 
                 transporter activity 
               
               
                 SEQ ID NO: 526 
                 Zm00001d014701 cDNA Transcription 
                 regulation of transcription, DNA- 
               
               
                   
                 regulator HTH, Myb-type, DNA-binding 
                 templated 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 527 
                 Zm00001d049624 cDNA Glutamate-rich 
                 zinc ion transmembrane transport 
               
               
                   
                 WD repeat-containing protein 1-like 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 528 
                 Zm00001d034359 cDNA Zinc finger, 
                 nucleic acid binding 
               
               
                   
                 C2H2-type/integrase, DNA-binding 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 529 
                 Zm00001d033924 cDNA Cell wall 
                 proton-transporting ATP synthase 
               
               
                   
                 protein pherophorin-C10 (PHC10) 
                 activity, rotational mechanism 
               
               
                 SEQ ID NO: 530 
                 Zm00001d032222 cDNA UDP- 
                 glucuronosyltransferase activity 
               
               
                   
                 glycosyltransferase 85A2-like protein 
               
               
                 SEQ ID NO: 531 
                 Zm00001d018155 cDNA Galactoside 2- 
                 cell wall biogenesis 
               
               
                   
                 alpha-L-fucosyltransferase-like protein 
               
               
                 SEQ ID NO: 532 
                 Zm00001d036263 cDNA Receptor 
                 protein serine/threonine kinase 
               
               
                   
                 protein serine/threonine kinase 
                 activity 
               
               
                 SEQ ID NO: 533 
                 Zm00001d044043 cDNA Acetylajmaline 
                 lipid catabolic process 
               
               
                   
                 esterase 
               
               
                 SEQ ID NO: 534 
                 Zm00001d027425 cDNA MADS-box 
                 transcription, DNA-templated 
               
               
                   
                 transcription factor 56-like protein 
               
               
                 SEQ ID NO: 535 
                 Zm00001d048635 cDNA Putative disease 
                 plant-type hypersensitive response 
               
               
                   
                 resistance RPP13-like protein 3-like 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 536 
                 Zm00001d006795 cDNA Omega- 
                 transferase activity, transferring 
               
               
                   
                 hydroxypalmitate O-feruloyl transferase 
                 acyl groups other than amino-acyl 
               
               
                   
                   
                 groups 
               
               
                 SEQ ID NO: 537 
                 Zm00001d041972 cDNA Cellulose 
                 ellulose biosynthetic process 
               
               
                   
                 synthase-like protein G2-like protein 
               
               
                 SEQ ID NO: 538 
                 Zm00001d000183 cDNA Hexose carrier 
                 carbohydrate transport 
               
               
                   
                 protein HEX6-like sugar transport protein 
               
               
                 SEQ ID NO: 539 
                 Zm00001d039575 cDNA 1- 
                 oxidoreductase activity, acting on 
               
               
                   
                 aminocyclopropane-1-carboxylate oxidase 
                 paired donors, with incorporation 
               
               
                   
                   
                 or reduction of molecular oxygen, 
               
               
                   
                   
                 2-oxoglutarate as one donor, and 
               
               
                   
                   
                 incorporation of one atom each of 
               
               
                   
                   
                 oxygen into both donors 
               
               
                 SEQ ID NO: 540 
                 Zm00001d046202 cDNA Transposase, 
                 sequence-specific DNA binding 
               
               
                   
                 Ptta/En/Spm, plant 
               
               
                 SEQ ID NO: 541 
                 Zm00001d013571 cDNA Ubiquitin- 
                 protein binding 
               
               
                   
                 protein ligase/zinc ion binding protein 
               
               
                 SEQ ID NO: 542 
                 Zm00001d015470 cDNA GDU1 
                 multicellular organism 
               
               
                   
                   
                 development 
               
               
                 SEQ ID NO: 543 
                 Zm00001d053965 cDNA 16.9 kDa class I 
                 response to stress 
               
               
                   
                 heat shock protein 1 
               
               
                 SEQ ID NO: 544 
                 Zm00001d029164 cDNA Inactive beta- 
                 ellular polysaccharide catabolic 
               
               
                   
                 amylase 9-like protein 
                 process 
               
               
                 SEQ ID NO: 545 
                 Zm00001d031717 cDNA Transcription 
                 transcription, DNA-templated 
               
               
                   
                 factor MYC4-like protein 
               
               
                 SEQ ID NO: 546 
                 Zm00001d035767 cDNA Jasmonate O- 
                 jasmonic acid metabolic process 
               
               
                   
                 methyltransferase 
               
               
                 SEQ ID NO: 547 
                 Zm00001d004279 cDNA Myrcene 
                 monoterpenoid biosynthetic 
               
               
                   
                 synthase, chloroplastic-like protein 
                 process 
               
               
                 SEQ ID NO: 548 
                 Zm00001d003462 cDNA Lipoyl synthase 
                 lipoate synthase activity 
               
               
                   
                 2, mitochondrial-like protein 
               
               
                 SEQ ID NO: 549 
                 Zm00001d026360 cDNA Cyclin PHO80- 
                 protein kinase binding 
               
               
                   
                 like protein 
               
               
                 SEQ ID NO: 550 
                 Zm00001d013984 cDNA Protein 
                 3′-5′-exoribonuclease activity 
               
               
                   
                 EXECUTER 1 (EX1) 
               
               
                 SEQ ID NO: 551 
                 Zm00001d047207 cDNA Copper- 
                 calcium-transporting ATPase 
               
               
                   
                 transporting ATPase (CTATP) 
                 activity 
               
               
                 SEQ ID NO: 552 
                 Zm00001d030381 
                 protein-chromophore linkage 
               
               
                   
                 cDNA Deoxyribodipyrimidine photo- 
               
               
                   
                 lyase; Photoreactivating enzyme CPD 
               
               
                   
                 photolyase 
               
               
                 SEQ ID NO: 553 
                 Zm00001d046755 cDNA Two- 
                 phosphorelay response regulator 
               
               
                   
                 component response regulator ARR12- 
                 activity 
               
               
                   
                 like protein 
               
               
                 SEQ ID NO: 554 
                 Zm00001d007167 cDNA CBL-interacting 
                 peptidyl-serine phosphorylation 
               
               
                   
                 protein kinase 07 
               
               
                 SEQ ID NO: 555 
                 Zm00001d039392 cDNA High affinity 
                 L-alpha-amino acid 
               
               
                   
                 cationic amino acid transporter 
                 transmembrane transport 
               
               
                 SEQ ID NO: 556 
                 Zm00001d013627 
                 chromatin silencing by small RNA 
               
               
                   
                 cDNA Retinoblastoma-binding protein 
               
               
                 SEQ ID NO: 557 
                 Zm00001d044717 cDNA Cyclic 
                 ion gated channel activity 
               
               
                   
                 nucleotide binding/inward rectifier 
               
               
                   
                 potassium channel 
               
               
                 SEQ ID NO: 558 
                 Zm00001d032933 cDNA KIP1-like 
                 N-acetyltransferase activity 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 559 
                 Zm00001d034467 cDNA Transcription 
                 cell differentiation 
               
               
                   
                 regulator HTH, Myb-type, DNA-binding 
               
               
                   
                 protein 
               
               
                 SEQ ID NO: 560 
                 Zm00001d018797 cDNA Photosystem I 
                 photosynthesis 
               
               
                   
                 reaction center subunit psaK, chloroplast 
               
               
                   
                 precursor 
               
               
                 SEQ ID NO: 561 
                 Zm00001d002934 cDNA Secondary wall 
                 sequence-specific DNA binding 
               
               
                   
                 NAC transcription factor 4 
               
               
                 SEQ ID NO: 562 
                 Zmm28 
                 Transcription factor 
               
               
                 SEQ ID NO: 563 
                 Zm00001d003911 (AFB2-like/TIR1-like 
                 Auxin receptor 
               
               
                   
                 (afb2)) 
               
               
                 SEQ ID NO: 564 
                 Zm00001d003911 genomic (AFB2- 
                 Auxin receptor 
               
               
                   
                 like/TIR1-like (afb2)) 
               
               
                 SEQ ID NO: 565 
                 AT5G24800.1, BASIC LEUCINE 
                 Transcription factor 
               
               
                   
                 ZIPPER 9 
               
               
                 SEQ ID NO: 566 
                 AT5G24800.1, BASIC LEUCINE 
                 Transcription factor 
               
               
                   
                 ZIPPER 9 
               
               
                 SEQ ID NO: 567 
                 Zm00001d051684, CONSTANS gene 
                 Transcription factor 
               
               
                   
                 family like 14 
               
               
                 SEQ ID NO: 568 
                 Zm00001d044194, MYB-LIKE DNA- 
                 Transcription factor 
               
               
                   
                 BINDING PROTEIN, mybr97 - MYB- 
               
               
                   
                 related-transcription factor 97 
               
               
                 SEQ ID NO: 569 
                 Zm00001d028974, ETHYLENE 
                 Transcription factor 
               
               
                   
                 INSENSITIVE 3-LIKE 1 
               
               
                 SEQ ID NO: 570 
                 Zm00001d044301, PROTEIN 
                 Signal transduction 
               
               
                   
                 PHOSPHATASE 2C 
               
               
                 SEQ ID NO: 571 
                 Zm00001d015239, LANOSTEROL 
                 Steroid biosynthetic process 
               
               
                   
                 SYNTHASE 
               
               
                 SEQ ID NO: 573 
                 Zm00001d023933, 2,4-dihydroxy-1,4- 
                 Response to wounding 
               
               
                   
                 benzoxazin-3-one-glucoside dioxygenase/ 
               
               
                   
                 DIBOA-Glc dioxygenase 
               
               
                 SEQ ID NO: 573 
                 Zm00001d029875, ZmMYBR43, Myb- 
                 Transcription factor 
               
               
                   
                 like DNA-binding domain (Myb_DNA- 
               
               
                   
                 binding) 
               
               
                 SEQ ID NO: 574 
                 Zm00001d051684, CONSTANS gene 
                 Transcription factor 
               
               
                   
                 family like 14 
               
               
                 SEQ ID NO: 575 
                 Zm00001d044194, MYB-LIKE DNA- 
                 Transcription factor 
               
               
                   
                 BINDING PROTEIN, mybr97 - MYB- 
               
               
                   
                 related-transcription factor 97 
               
               
                 SEQ ID NO: 576 
                 Zm00001d028974, ETHYLENE 
                 Transcription factor 
               
               
                   
                 INSENSITIVE 3-LIKE 1 
               
               
                 SEQ ID NO: 577 
                 Zm00001d044301, PROTEIN 
                 Signal transduction 
               
               
                   
                 PHOSPHATASE 2C 
               
               
                 SEQ ID NO: 578 
                 Zm00001d015239, LANOSTEROL 
                 Steroid biosynthetic process 
               
               
                   
                 SYNTHASE 
               
               
                 SEQ ID NO: 579 
                 Zm00001d023933, 2,4-dihydroxy-1,4- 
                 Response to wounding 
               
               
                   
                 benzoxazin-3-one-glucoside dioxygenase/ 
               
               
                   
                 DIBOA-Glc dioxygenase 
               
               
                   
               
            
           
         
       
     
    
    
     DETAILED DESCRIPTION 
     I. Compositions 
     A. Polynucleotides and Polypeptides 
     The present disclosure provides polynucleotides encoding polypeptides. Accordingly, as used herein “polypeptide,” “protein,” or the like, refers to a protein represented by a SEQ ID NO. 
     One aspect of the disclosure provides a polynucleotide encoding a polypeptide comprising an amino acid sequence that is at least 80-99% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573). 
     As used herein “encoding,” “encoded,” or the like, with respect to a specified nucleic acid, is meant comprising the information for translation into the specified protein. A nucleic acid encoding a protein may comprise non-translated sequences (e.g., introns) within translated regions of the nucleic acid, or may lack such intervening non-translated sequences (e.g., as in cDNA). The information by which a protein is encoded is specified by the use of codons. Typically, the amino acid sequence is encoded by the nucleic acid using the “universal” genetic code. However, variants of the universal code, such as is present in some plant, animal and fungal mitochondria, the bacterium  Mycoplasma capricolum  (Yamao, et al., (1985) Proc. Natl. Acad. Sci. USA 82:2306-9) or the ciliate Macronucleus, may be used when the nucleic acid is expressed using these organisms. 
     When the nucleic acid is prepared or altered synthetically, advantage can be taken of known codon preferences of the intended host where the nucleic acid is to be expressed. For example, although nucleic acid sequences of the present invention may be expressed in both monocotyledonous and dicotyledonous plant species, sequences can be modified to account for the specific codon preferences and GC content preferences of monocotyledonous plants or dicotyledonous plants as these preferences have been shown to differ (Murray, et al., (1989) Nucleic Acids Res. 17:477-98). 
     As used herein, “polynucleotide” includes reference to a deoxyribopolynucleotide, ribopolynucleotide or analogs thereof that have the essential nature of a natural ribonucleotide in that they hybridize, under stringent hybridization conditions, to substantially the same nucleotide sequence as naturally occurring nucleotides and/or allow translation into the same amino acid(s) as the naturally occurring nucleotide(s). A polynucleotide can be full-length or a subsequence of a structural or regulatory gene. Unless otherwise indicated, the term includes reference to the specified sequence as well as the complementary sequence thereof. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including inter alia, simple and complex cells. 
     The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residues is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. 
     As used herein, “sequence identity” or “identity” in the context of two nucleic acid or polypeptide sequences includes reference to the residues in the two sequences, which are the same when aligned for maximum correspondence over a specified comparison window. When percentage of sequence identity is used in reference to proteins it is recognized that residue positions which are not identical often differ by conservative amino acid substitutions, where amino acid residues are substituted for other amino acid residues with similar chemical properties (e.g., charge or hydrophobicity) and therefore do not change the functional properties of the molecule. Where sequences differ in conservative substitutions, the percent sequence identity may be adjusted upwards to correct for the conservative nature of the substitution. Sequences, which differ by such conservative substitutions, are said to have “sequence similarity” or “similarity.” Means for making this adjustment are well known to those of skill in the art. Typically, this involves scoring a conservative substitution as a partial rather than a full mismatch, thereby increasing the percentage sequence identity. Thus, for example, where an identical amino acid is given a score of 1 and a non-conservative substitution is given a score of zero, a conservative substitution is given a score between zero and 1. The scoring of conservative substitutions is calculated, e.g., according to the algorithm of Meyers and Miller, (1988) Computer Applic. Biol. Sci. 4:11-17, e.g., as implemented in the program PC/GENE (Intelligenetics, Mountain View, Calif., USA). 
     As used herein, “percentage of sequence identity” means the value determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The percentage is calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. 
     As used herein, “reference sequence” is a defined sequence used as a basis for sequence comparison. A reference sequence may be a subset or the entirety of a specified sequence; for example, as a segment of a full-length cDNA or gene sequence or the complete cDNA or gene sequence. 
     As used herein, “comparison window” means includes reference to a contiguous and specified segment of a polynucleotide sequence, wherein the polynucleotide sequence may be compared to a reference sequence and wherein the portion of the polynucleotide sequence in the comparison window may comprise additions or deletions (i.e., gaps) compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. Generally, the comparison window is at least 20 contiguous nucleotides in length, and optionally can be 30, 40, 50, 100 or longer. Those of skill in the art understand that to avoid a high similarity to a reference sequence due to inclusion of gaps in the polynucleotide sequence a gap penalty is typically introduced and is subtracted from the number of matches. 
     Methods of alignment of nucleotide and amino acid sequences for comparison are well known in the art. The local homology algorithm (BESTFIT) of Smith and Waterman, (1981) Adv. Appl. Math 2:482, may conduct optimal alignment of sequences for comparison; by the homology alignment algorithm (GAP) of Needleman and Wunsch, (1970) J. Mol. Biol. 48:443-53; by the search for similarity method (Tfasta and Fasta) of Pearson and Lipman, (1988) Proc. Natl. Acad. Sci. USA 85:2444; by computerized implementations of these algorithms, including, but not limited to: CLUSTAL in the PC/Gene program by Intelligenetics, Mountain View, California, GAP, BESTFIT, BLAST, FASTA and TFASTA in the Wisconsin Genetics Software Package®, Version 8 (available from Genetics Computer Group (GCG® programs (Accelrys, Inc., San Diego, Calif.)). The CLUSTAL program is well described by Higgins and Sharp, (1988) Gene 73:237 44; Higgins and Sharp, (1989) CABIOS 5:151 3; Corpet, et al., (1988) Nucleic Acids Res. 16:10881-90; Huang, et al., (1992) Computer Applications in the Biosciences 8:155-65, and Pearson, et al., (1994) Meth. Mol. Biol. 24:307-31. The preferred program to use for optimal global alignment of multiple sequences is PileUp (Feng and Doolittle, (1987) J. Mol. Evol., 25:351-60 which is similar to the method described by Higgins and Sharp, (1989) CABIOS 5:151-53 and hereby incorporated by reference). The BLAST family of programs which can be used for database similarity searches includes: BLASTN for nucleotide query sequences against nucleotide database sequences; BLASTX for nucleotide query sequences against protein database sequences; BLASTP for protein query sequences against protein database sequences; TBLASTN for protein query sequences against nucleotide database sequences; and TBLASTX for nucleotide query sequences against nucleotide database sequences. See, CURRENT PROTOCOLS IN MOLECULAR BIOLOGY, Chapter 19, Ausubel, et al., eds., Greene Publishing and Wiley-Interscience, New York (1995). 
     GAP uses the algorithm of Needleman and Wunsch, supra, to find the alignment of two complete sequences that maximizes the number of matches and minimizes the number of gaps. GAP considers all possible alignments and gap positions and creates the alignment with the largest number of matched bases and the fewest gaps. It allows for the provision of a gap creation penalty and a gap extension penalty in units of matched bases. GAP must make a profit of gap creation penalty number of matches for each gap it inserts. If a gap extension penalty greater than zero is chosen, GAP must, in addition, make a profit for each gap inserted of the length of the gap times the gap extension penalty. Default gap creation penalty values and gap extension penalty values in Version 10 of the Wisconsin Genetics Software Package® are 8 and 2, respectively. The gap creation and gap extension penalties can be expressed as an integer selected from the group of integers consisting of from 0 to 100. Thus, for example, the gap creation and gap extension penalties can be 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50 or greater. 
     GAP presents one member of the family of best alignments. There may be many members of this family, but no other member has a better quality. GAP displays four figures of merit for alignments: Quality, Ratio, Identity and Similarity. The Quality is the metric maximized in order to align the sequences. Ratio is the quality divided by the number of bases in the shorter segment. Percent Identity is the percent of the symbols that actually match. Percent Similarity is the percent of the symbols that are similar. Symbols that are across from gaps are ignored. A similarity is scored when the scoring matrix value for a pair of symbols is greater than or equal to 0.50, the similarity threshold. The scoring matrix used in Version 10 of the Wisconsin Genetics Software Package® is BLOSUM62 (see, Henikoff and Henikoff, (1989) Proc. Natl. Acad. Sci. USA 89:10915). 
     Unless otherwise stated, sequence identity/similarity values provided herein refer to the value obtained using the BLAST 2.0 suite of programs using default parameters (Altschul, et al., (1997) Nucleic Acids Res. 25:3389-402). 
     As those of ordinary skill in the art will understand, BLAST searches assume that proteins can be modeled as random sequences. However, many real proteins comprise regions of nonrandom sequences, which may be homopolymeric tracts, short-period repeats, or regions enriched in one or more amino acids. Such low-complexity regions may be aligned between unrelated proteins even though other regions of the protein are entirely dissimilar. A number of low-complexity filter programs can be employed to reduce such low-complexity alignments. For example, the SEG (Wooten and Federhen, (1993) Comput. Chem. 17:149-63) and XNU (Claverie and States, (1993) Comput. Chem. 17:191-201) low-complexity filters can be employed alone or in combination. 
     Accordingly, in any of the embodiments described herein, the polynucleotide may encode a polypeptide that is at least 80% identical to any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. For example, the polynucleotide may encode a polypeptide that is at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, or at least 99% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. 
     B. Recombinant DNA Construct 
     Also provided is a recombinant DNA construct comprising any of the polynucleotides described herein. In certain embodiments, the recombinant DNA construct further comprises at least one regulatory element. In certain embodiments, the at least one regulatory element of the recombinant DNA construct comprises a promoter. In certain embodiments, the promoter is a heterologous promoter. 
     As used herein, a “recombinant DNA construct” comprises two or more operably linked DNA segments, preferably DNA segments that are not operably linked in nature (i.e., heterologous). Non-limiting examples of recombinant DNA constructs include a polynucleotide of interest operably linked to heterologous sequences, also referred to as “regulatory elements,” which aid in the expression, autologous replication, and/or genomic insertion of the sequence of interest. Such regulatory elements include, for example, promoters, termination sequences, enhancers, etc., or any component of an expression cassette; a plasmid, cosmid, virus, autonomously replicating sequence, phage, or linear or circular single-stranded or double-stranded DNA or RNA nucleotide sequence; and/or sequences that encode heterologous polypeptides. 
     The polynucleotides described herein can be provided in expression cassettes for expression in a plant of interest or any organism of interest. The cassette can include 5′ and 3′ regulatory sequences operably linked to a polynucleotide. “Operably linked” is intended to mean a functional linkage between two or more elements. For, example, an operable linkage between a polynucleotide of interest and a regulatory sequence (e.g., a promoter) is a functional link that allows for expression of the polynucleotide of interest. Operably linked elements may be contiguous or non-contiguous. When used to refer to the joining of two protein coding regions, operably linked is intended that the coding regions are in the same reading frame. The cassette may additionally contain at least one additional gene to be cotransformed into the organism. Alternatively, the additional gene(s) can be provided on multiple expression cassettes. Such an expression cassette is provided with a plurality of restriction sites and/or recombination sites for insertion of the polynucleotide to be under the transcriptional regulation of the regulatory regions. The expression cassette may additionally contain selectable marker genes. 
     The expression cassette can include in the 5′-3′ direction of transcription, a transcriptional and translational initiation region (e.g., a promoter), a polynucleotide, and a transcriptional and translational termination region (e.g., termination region) functional in plants. The regulatory regions (e.g., promoters, transcriptional regulatory regions, and translational termination regions) and/or the polynucleotide may be native/analogous to the host cell or to each other. Alternatively, the regulatory regions and/or the polynucleotide may be heterologous to the host cell or to each other. 
     As used herein, “heterologous” in reference to a sequence is a sequence that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous polynucleotide that is from a species different from the species from which the polynucleotide was derived, or, if from the same/analogous species, one or both are substantially modified from their original form and/or genomic locus, or the promoter is not the native promoter for the operably linked polynucleotide. 
     The termination region may be native with the transcriptional initiation region, with the plant host, or may be derived from another source (i.e., foreign or heterologous) than the promoter, the polynucleotide, the plant host, or any combination thereof. 
     The expression cassette may additionally contain a 5′ leader sequences. Such leader sequences can act to enhance translation. Translation leaders are known in the art and include viral translational leader sequences. 
     In preparing the expression cassette, the various DNA fragments may be manipulated, to provide for the DNA sequences in the proper orientation and, as appropriate, in the proper reading frame. Toward this end, adapters or linkers may be employed to join the DNA fragments or other manipulations may be involved to provide for convenient restriction sites, removal of superfluous DNA, removal of restriction sites, or the like. For this purpose, in vitro mutagenesis, primer repair, restriction, annealing, resubstitutions, e.g., transitions and transversions, may be involved. 
     As used herein “promoter” refers to a region of DNA upstream from the start of transcription and involved in recognition and binding of RNA polymerase and other proteins to initiate transcription. A “plant promoter” is a promoter capable of initiating transcription in plant cells. Exemplary plant promoters include, but are not limited to, those that are obtained from plants, plant viruses and bacteria which comprise genes expressed in plant cells such  Agrobacterium  or  Rhizobium . Certain types of promoters preferentially initiate transcription in certain tissues, such as leaves, roots, seeds, fibers, xylem vessels, tracheids or sclerenchyma. Such promoters are referred to as “tissue preferred.” A “cell type” specific promoter primarily drives expression in certain cell types in one or more organs, for example, vascular cells in roots or leaves. An “inducible” or “regulatable” promoter is a promoter, which is under environmental control. Examples of environmental conditions that may affect transcription by inducible promoters include anaerobic conditions or the presence of light. Another type of promoter is a developmentally regulated promoter, for example, a promoter that drives expression during pollen development. Tissue preferred, cell type specific, developmentally regulated and inducible promoters constitute the class of “non-constitutive” promoters. A “constitutive” promoter is a promoter, which is active under most environmental conditions. Constitutive promoters include, for example, the core promoter of the Rsyn7 promoter and other constitutive promoters disclosed in WO 99/43838 and U.S. Pat. No. 6,072,050; the core CaMV 35S promoter (Odell et al. (1985) Nature 313:810-812); rice actin (McElroy et al. (1990) Plant Cell 2:163-171); ubiquitin (Christensen et al. (1989) Plant Mol. Biol. 12:619-632 and Christensen et al. (1992) Plant Mol. Biol. 18:675-689); pEMU (Last et al. (1991) Theor. Appl. Genet. 81:581-588); MAS (Velten et al. (1984) EMBO J. 3:2723-2730); ALS promoter (U.S. Pat. No. 5,659,026); GOS2 (U.S. Pat. No. 6,504,083), and the like. Other constitutive promoters include, for example, U.S. Pat. Nos. 5,608,149; 5,608,144; 5,604,121; 5,569,597; 5,466,785; 5,399,680; 5,268,463; 5,608,142; and 6,177,611. 
     Also contemplated are synthetic promoters which include a combination of one or more heterologous regulatory elements. 
     C. Plants and Plant Cells 
     Provided are plants, plant cells, plant parts, seed, and grain comprising a polynucleotide sequence described herein or a recombinant DNA construct described herein, so that the plants, plant cells, plant parts, seed, and/or grain have increased expression of a polypeptide. In certain embodiments, the plants, plant cells, plant parts, seeds, and/or grain have stably incorporated an exogenous polynucleotide described herein into its genome. In certain embodiments, the plants, plant cells, plant parts, seeds, and/or grain can comprise multiple polynucleotides (i.e., at least 1, 2, 3, 4, 5, 6 or more). 
     In specific embodiments, the polynucleotide(s) in the plants, plant cells, plant parts, seeds, and/or grain are operably linked to a heterologous regulatory element, such as, but not limited to, a constitutive promoter, a tissue-preferred promoter, or a synthetic promoter for expression in plants or a constitutive enhancer. For example, in certain embodiments the heterologous regulatory element is the maize GOS2 promoter. 
     Also provided herein are plants, plant cells, plant parts, seeds, and grain comprising an introduced genetic modification at a genomic locus that encodes a polypeptide comprising an amino acid sequence that is at least 80% identical to an amino acid sequence selected from the group consisting of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. 
     In certain embodiments, the genetic modification increases the activity of the protein. In certain embodiments, the genetic modification increases the level of the protein. In certain embodiments, the genetic modification increases both the level and activity of the protein. 
     A “genomic locus” as used herein, generally refers to the location on a chromosome of the plant where a gene, such as a polynucleotide encoding a polypeptide, is found. As used herein, “gene” includes a nucleic acid fragment that expresses a functional molecule such as, but not limited to, a specific protein coding sequence and regulatory elements, such as those preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. 
     A “regulatory element” generally refers to a transcriptional regulatory element involved in regulating the transcription of a nucleic acid molecule such as a gene or a target gene. The regulatory element is a nucleic acid and may include a promoter, an enhancer, an intron, a 5′-untranslated region (5′-UTR, also known as a leader sequence), or a 3′-UTR or a combination thereof. A regulatory element may act in “cis” or “trans”, and generally it acts in “cis”, i.e. it activates expression of genes located on the same nucleic acid molecule, e.g. a chromosome, where the regulatory element is located. 
     An “enhancer” element is any nucleic acid molecule that increases transcription of a nucleic acid molecule when functionally linked to a promoter regardless of its relative position. 
     A “repressor” (also sometimes called herein silencer) is defined as any nucleic acid molecule which inhibits the transcription when functionally linked to a promoter regardless of relative position. 
     The term “cis-element” generally refers to transcriptional regulatory element that affects or modulates expression of an operably linked transcribable polynucleotide, where the transcribable polynucleotide is present in the same DNA sequence. A cis-element may function to bind transcription factors, which are trans-acting polypeptides that regulate transcription. 
     An “intron” is an intervening sequence in a gene that is transcribed into RNA but is then excised in the process of generating the mature mRNA. The term is also used for the excised RNA sequences. An “exon” is a portion of the sequence of a gene that is transcribed and is found in the mature messenger RNA derived from the gene but is not necessarily a part of the sequence that encodes the final gene product. 
     The 5′ untranslated region (5′UTR) (also known as a translational leader sequence or leader RNA) is the region of an mRNA that is directly upstream from the initiation codon. This region is involved in the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. 
     The “3′ non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. 
     “Genetic modification,” “DNA modification,” and the like refers to a site-specific modification that alters or changes the nucleotide sequence at a specific genomic locus of the plant. The genetic modification of the compositions and methods described herein may be any modification known in the art such as, for example, insertion, deletion, single nucleotide polymorphism (SNP), and or a polynucleotide modification. Additionally, the targeted DNA modification in the genomic locus may be located anywhere in the genomic locus, such as, for example, a coding region of the encoded polypeptide (e.g., exon), a non-coding region (e.g., intron), a regulatory element, or untranslated region. 
     As used herein, a “targeted” genetic modification or “targeted” DNA modification, refers to the direct manipulation of an organism&#39;s genes. The targeted modification may be introduced using any technique known in the art, such as, for example, plant breeding, genome editing, or single locus conversion. 
     The type and location of the DNA modification of the polynucleotide is not particularly limited so long as the DNA modification results in increased expression and/or activity of the protein encoded by the corresponding polynucleotide. 
     In certain embodiments, the plant, plant cells, plant parts, seeds, and/or grain comprise one or more nucleotide modifications present within (a) the coding region; (b) non-coding region; (c) regulatory sequence; (d) untranslated region, or (e) any combination of (a)-(d) of an endogenous polynucleotide encoding a polypeptide. 
     In certain embodiments the DNA modification is an insertion of one or more nucleotides, preferably contiguous, in the genomic locus. For example, the insertion of an expression modulating element (EME), such as an EME described in PCT/US2018/025446, in operable linkage with the gene of interest described herein. In certain embodiments, the targeted DNA modification may be the replacement of an endogenous promoter with another promoter known in the art to have higher expression, such as, for example, the maize GOS2 promoter. In certain embodiments, the targeted DNA modification may be the insertion of a promoter known in the art to have higher expression, such as, for example, the maize GOS2 promoter, into the 5′UTR so that expression of the endogenous polypeptide is controlled by the inserted promoter. In certain embodiments, the DNA modification is a modification to optimize Kozak context to increase expression. In certain embodiments, the DNA modification is a polynucleotide modification or SNP at a site that regulates the stability of the expressed protein. 
     As used herein “increased,” “increase,” or the like refers to any detectable increase in an experimental group (e.g., plant with a DNA modification described herein) as compared to a control group (e.g., wild-type plant that does not comprise the DNA modification). Accordingly, increased expression of a protein comprises any detectable increase in the total level of the protein in a sample and can be determined using routine methods in the art such as, for example, Western blotting and ELISA. 
     In certain embodiments, the genomic locus has more than one (e.g., 2, 3, 4, 5, 6, 7, 8, 9, or 10) DNA modification. For example, the translated region and a regulatory element of a genomic locus may each comprise a targeted DNA modification. In certain embodiments, more than one genomic locus of the plant may comprise a DNA modification. 
     The DNA modification of the genomic locus may be done using any genome modification technique known in the art or described herein. In certain embodiments the targeted DNA modification is through a genome modification technique selected from the group consisting of a polynucleotide-guided endonuclease, CRISPR-Cas endonucleases, base editing deaminases, zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), engineered site-specific meganuclease, or Argonaute. 
     In certain embodiments, the genome modification may be facilitated through the induction of a double-stranded break (DSB) or single-strand break, in a defined position in the genome near the desired alteration. DSBs can be induced using any DSB-inducing agent available, including, but not limited to, TALENs, meganucleases, zinc finger nucleases, Cas9-gRNA systems (based on bacterial CRISPR-Cas systems), guided cpfl endonuclease systems, and the like. In some embodiments, the introduction of a DSB can be combined with the introduction of a polynucleotide modification template. 
     The polynucleotides or recombinant DNA constructs disclosed herein may be used for transformation of any plant species, including, but not limited to, monocots and dicots. Additionally, the genetic modifications described herein may be used to modify any plant species, including, but not limited to, monocots and dicots. 
     In specific embodiments, plants of the present disclosure are crop plants (for example, corn, alfalfa, sunflower,  Brassica , soybean, cotton, safflower, peanut, sorghum, wheat, millet, tobacco, etc.). In other embodiments, corn and soybean plants are optimal, and in yet other embodiments corn plants are optimal. 
     Other plants of interest include, for example, grain plants that provide seeds of interest, oil-seed plants, and leguminous plants. Seeds of interest include, for example, grain seeds, such as corn, wheat, barley, rice, sorghum, rye, etc. Oil-seed plants include, for example, cotton, soybean, safflower, sunflower,  Brassica , maize, alfalfa, palm, coconut, etc. Leguminous plants include beans and peas. Beans include guar, locust bean, fenugreek, soybean, garden beans, cowpea, mungbean, lima bean, fava bean, lentils, chickpea. 
     For example, in certain embodiments, maize plants are provided that comprise, in their genome, a recombinant DNA construct comprising a polynucleotide that encodes a polypeptide comprising an amino acid sequence that is at least 80% to about 100% identical to any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. In certain embodiments, the polypeptide comprising an amino acid sequence that is at least 80% to about 100% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573 comprises the amino acid sequence set forth in SEQ ID NO: 28. In certain embodiments, the polypeptide comprising an amino acid sequence that is at least 80% to about 100% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. 
     In other embodiments, maize plants are provided that comprise a genetic modification at a genomic locus that encodes a polypeptide comprising an amino acid sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. In certain embodiments, the polypeptide comprising an amino acid sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573 comprises the amino acid sequence set forth in SEQ ID NO: 28. In certain embodiments, the polypeptide comprising an amino acid sequence that is at least 80% identical to the amino acid sequence of any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. 
     D. Stacking Other Traits of Interest 
     In some embodiments, the polynucleotides disclosed herein are engineered into a molecular stack. Thus, the various host cells, plants, plant cells, plant parts, seeds, and/or grain disclosed herein can further comprise one or more traits of interest. In certain embodiments, the host cell, plant, plant part, plant cell, seed, and/or grain is stacked with any combination of polynucleotide sequences of interest in order to create plants with a desired combination of traits. As used herein, the term “stacked” refers to having multiple traits present in the same plant or organism of interest. For example, “stacked traits” may comprise a molecular stack where the sequences are physically adjacent to each other. A trait, as used herein, refers to the phenotype derived from a particular sequence or groups of sequences. In one embodiment, the molecular stack comprises at least one polynucleotide that confers tolerance to glyphosate. Polynucleotides that confer glyphosate tolerance are known in the art. 
     In certain embodiments, the molecular stack comprises at least one polynucleotide that confers tolerance to glyphosate and at least one additional polynucleotide that confers tolerance to a second herbicide. 
     In certain embodiments, the plant, plant cell, seed, and/or grain having an inventive polynucleotide sequence may be stacked with, for example, one or more sequences that confer tolerance to: an ALS inhibitor; an HPPD inhibitor; 2,4-D; other phenoxy auxin herbicides; aryloxyphenoxypropionate herbicides; dicamba; glufosinate herbicides; herbicides which target the protox enzyme (also referred to as “protox inhibitors”). 
     The plant, plant cell, plant part, seed, and/or grain having an inventive polynucleotide sequence can also be combined with at least one other trait to produce plants that further comprise a variety of desired trait combinations. For instance, the plant, plant cell, plant part, seed, and/or grain having an inventive polynucleotide sequence may be stacked with polynucleotides encoding polypeptides having pesticidal and/or insecticidal activity, or a plant, plant cell, plant part, seed, and/or grain having an inventive polynucleotide sequence may be combined with a plant disease resistance gene. 
     These stacked combinations can be created by any method including, but not limited to, breeding plants by any conventional methodology, or genetic transformation. If the sequences are stacked by genetically transforming the plants, the polynucleotide sequences of interest can be combined at any time and in any order. The traits can be introduced simultaneously in a co-transformation protocol with the polynucleotides of interest provided by any combination of transformation cassettes. For example, if two sequences will be introduced, the two sequences can be contained in separate transformation cassettes (trans) or contained on the same transformation cassette (cis). Expression of the sequences can be driven by the same promoter or by different promoters. In certain cases, it may be desirable to introduce a transformation cassette that will suppress the expression of the polynucleotide of interest. This may be combined with any combination of other suppression cassettes or overexpression cassettes to generate the desired combination of traits in the plant. It is further recognized that polynucleotide sequences can be stacked at a desired genomic location using a site-specific recombination system. See, for example, WO99/25821, WO99/25854, WO99/25840, WO99/25855, and WO99/25853, all of which are herein incorporated by reference. Any plant having an inventive polynucleotide sequence disclosed herein can be used to make a food or a feed product. Such methods comprise obtaining a plant, explant, seed, plant cell, or cell comprising the polynucleotide sequence and processing the plant, explant, seed, plant cell, or cell to produce a food or feed product. 
     II. Methods of Use 
     A. Methods for Increasing Yield, and/or Increasing the Activity of Polynucleotides in a Plant 
     Provided are methods for increasing yield in a plant, modifying flowering time of a plant, and/or increasing the activity of one or more polynucleotides disclosed herein in a plant comprising introducing into a plant, plant cell, plant part, seed, and/or grain a recombinant DNA construct comprising any of the inventive polynucleotides described herein, whereby the polypeptide is expressed in the plant. Also provided are methods for increasing yield in a plant, modifying flowering time of a plant, and/or increasing the activity in a plant comprising introducing a genetic modification at a genomic locus of a plant that encodes a polypeptide comprising an amino acid sequence that is at least 80%-99% or 100% identical to the amino acid sequence set for in any one of SEQ ID NOS: 1-11, 23-31, 40-299, 563, 565, and 567-573. 
     The plant for use in the inventive methods can be any plant species described herein. In certain embodiments, the plant is a grain plant, an oil-seed plant, or leguminous plant. In certain embodiments, the plant is a grain plant such as maize. 
     As used herein, “yield” refers to the amount of agricultural production harvested per unit of land and may include reference to bushels per acre of a crop at harvest, as adjusted for grain moisture (e.g., typically 15% for maize). Grain moisture is measured in the grain at harvest. The adjusted test weight of grain is determined to be the weight in pounds per bushel, adjusted for grain moisture level at harvest. 
     In certain embodiments yield is measured in plants grown under optimal growth conditions. As used herein, “optimal conditions” refers to plants that are grown under well-watered or non-drought conditions. In certain embodiments, optimal growth conditions are determined based on the yield of the wild-type control plants in the experiment. As used herein, plants are considered to be grown under optimal conditions when the wild-type plant provides at least 75% of the predicted grain yield. 
     As used herein, “modifying flowering time” refers to a change in the number of days or growth heat units required for a plant to flower. In certain embodiments, the flowering time of the plant is delayed upon increased expression of the polypeptide. Also contemplated are embodiments in which flowering time is decreased (i.e., less days or growth heat units required for a plant to flower) upon decreased expression of the polypeptide. 
     As used herein, increase in photosynthetic activity, refers to any detectable increase in the functional activity of the protein compared to a suitable control. The functional activity may be any known biological property of one or more of the polypeptides disclosed herein and includes, for example, increased formation of protein complexes, modulation of biochemical pathways, and/or increased grain yield. 
     Various methods can be used to introduce a sequence of interest into a plant, plant part, plant cell, seed, and/or grain. “Introducing” is intended to mean presenting to the plant, plant cell, seed, and/or grain the inventive polynucleotide or resulting polypeptide in such a manner that the sequence gains access to the interior of a cell of the plant. The methods of the disclosure do not depend on a particular method for introducing a sequence into a plant, plant cell, seed, and/or grain, only that the polynucleotide or polypeptide gains access to the interior of at least one cell of the plant. 
     “Stable transformation” is intended to mean that the polynucleotide introduced into a plant integrates into the genome of the plant of interest and is capable of being inherited by the progeny thereof. “Transient transformation” is intended to mean that a polynucleotide is introduced into the plant of interest and does not integrate into the genome of the plant or organism or a polypeptide is introduced into a plant or organism. 
     Transformation protocols as well as protocols for introducing polypeptides or polynucleotide sequences into plants may vary depending on the type of plant or plant cell, i.e., monocot or dicot, targeted for transformation. 
     In specific embodiments, the polynucleotide sequences disclosed herein can be provided to a plant using a variety of transient transformation methods. Such transient transformation methods include, but are not limited to, the introduction of the encoded protein directly into the plant. Such methods include, for example, microinjection or particle bombardment. See, for example, Crossway et al. (1986)  Mol Gen. Genet.  202:179-185; Nomura et al. (1986)  Plant Sci.  44:53-58; Hepler et al. (1994)  Proc. Natl. Acad. Sci.  91: 2176-2180 and Hush et al. (1994)  The Journal of Cell Science  107:775-784, all of which are herein incorporated by reference. 
     In other embodiments, the inventive polynucleotides disclosed herein may be introduced into plants by contacting plants with a virus or viral nucleic acids. Generally, such methods involve incorporating a nucleotide construct of the disclosure within a DNA or RNA molecule. It is recognized that the inventive polynucleotide sequence may be initially synthesized as part of a viral polyprotein, which later may be processed by proteolysis in vivo or in vitro to produce the desired recombinant protein. Further, it is recognized that promoters disclosed herein also encompass promoters utilized for transcription by viral RNA polymerases. Methods for introducing polynucleotides into plants and expressing a protein encoded therein, involving viral DNA or RNA molecules, are known in the art. See, for example, U.S. Pat. Nos. 5,889,191, 5,889,190, 5,866,785, 5,589,367, 5,316,931, and Porta et al. (1996)  Molecular Biotechnology  5:209-221; herein incorporated by reference. 
     Various methods can be used to introduce a genetic modification at a genomic locus that encodes and polypeptide into the plant, plant part, plant cell, seed, and/or grain. In certain embodiments the targeted DNA modification is through a genome modification technique selected from the group consisting of a polynucleotide-guided endonuclease, CRISPR-Cas endonucleases, base editing deaminases, zinc finger nuclease, a transcription activator-like effector nuclease (TALEN), engineered site-specific meganuclease, or Argonaute. 
     In some embodiments, the genome modification may be facilitated through the induction of a double-stranded break (DSB) or single-strand break, in a defined position in the genome near the desired alteration. DSBs can be induced using any DSB-inducing agent available, including, but not limited to, TALENs, meganucleases, zinc finger nucleases, Cas9-gRNA systems (based on bacterial CRISPR-Cas systems), guided cpfl endonuclease systems, and the like. In some embodiments, the introduction of a DSB can be combined with the introduction of a polynucleotide modification template. 
     A polynucleotide modification template can be introduced into a cell by any method known in the art, such as, but not limited to, transient introduction methods, transfection, electroporation, microinjection, particle mediated delivery, topical application, whiskers mediated delivery, delivery via cell-penetrating peptides, or mesoporous silica nanoparticle (MSN)-mediated direct delivery. 
     The polynucleotide modification template can be introduced into a cell as a single stranded polynucleotide molecule, a double stranded polynucleotide molecule, or as part of a circular DNA (vector DNA). The polynucleotide modification template can also be tethered to the guide RNA and/or the Cas endonuclease. Tethered DNAs can allow for co-localizing target and template DNA, useful in genome editing and targeted genome regulation, and can also be useful in targeting post-mitotic cells where function of endogenous HR machinery is expected to be highly diminished (Mali et al. 2013 Nature Methods Vol. 10: 957-963.) The polynucleotide modification template may be present transiently in the cell or it can be introduced via a viral replicon. 
     A “modified nucleotide” or “edited nucleotide” refers to a nucleotide sequence of interest that comprises at least one alteration when compared to its non-modified nucleotide sequence. Such “alterations” include, for example: (i) replacement of at least one nucleotide, (ii) a deletion of at least one nucleotide, (iii) an insertion of at least one nucleotide, or (iv) any combination of (i)-(iii). 
     The term “polynucleotide modification template” includes a polynucleotide that comprises at least one nucleotide modification when compared to the nucleotide sequence to be edited. A nucleotide modification can be at least one nucleotide substitution, addition or deletion. Optionally, the polynucleotide modification template can further comprise homologous nucleotide sequences flanking the at least one nucleotide modification, wherein the flanking homologous nucleotide sequences provide sufficient homology to the desired nucleotide sequence to be edited. 
     The process for editing a genomic sequence combining DSB and modification templates generally comprises: providing to a host cell, a DSB-inducing agent, or a nucleic acid encoding a DSB-inducing agent, that recognizes a target sequence in the chromosomal sequence and is able to induce a DSB in the genomic sequence, and at least one polynucleotide modification template comprising at least one nucleotide alteration when compared to the nucleotide sequence to be edited. The polynucleotide modification template can further comprise nucleotide sequences flanking the at least one nucleotide alteration, in which the flanking sequences are substantially homologous to the chromosomal region flanking the DSB. 
     The endonuclease can be provided to a cell by any method known in the art, for example, but not limited to, transient introduction methods, transfection, microinjection, and/or topical application or indirectly via recombination constructs. The endonuclease can be provided as a protein or as a guided polynucleotide complex directly to a cell or indirectly via recombination constructs. The endonuclease can be introduced into a cell transiently or can be incorporated into the genome of the host cell using any method known in the art. In the case of a CRISPR-Cas system, uptake of the endonuclease and/or the guided polynucleotide into the cell can be facilitated with a Cell Penetrating Peptide (CPP) as described in WO2016073433 published May 12, 2016. 
     In addition to modification by a double strand break technology, modification of one or more bases without such double strand break are achieved using base editing technology, see e.g., Gaudelli et al., (2017) Programmable base editing of A*T to G*C in genomic DNA without DNA cleavage. Nature 551(7681):464-471; Komor et al., (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature 533(7603):420-4. 
     These fusions contain dCas9 or Cas9 nickase and a suitable deaminase, and they can convert e.g., cytosine to uracil without inducing double-strand break of the target DNA. Uracil is then converted to thymine through DNA replication or repair. Improved base editors that have targeting flexibility and specificity are used to edit endogenous locus to create target variations and improve grain yield. Similarly, adenine base editors enable adenine to inosine change, which is then converted to guanine through repair or replication. Thus, targeted base changes i.e., C⋅G to T⋅A conversion and A⋅T to G⋅C conversion at one more locations made using appropriate site-specific base editors. 
     In an embodiment, base editing is a genome editing method that enables direct conversion of one base pair to another at a target genomic locus without requiring double-stranded DNA breaks (DSBs), homology-directed repair (HDR) processes, or external donor DNA templates. In an embodiment, base editors include (i) a catalytically impaired CRISPR-Cas9 mutant that are mutated such that one of their nuclease domains cannot make DSBs; (ii) a single-strand-specific cytidine/adenine deaminase that converts C to U or A to G within an appropriate nucleotide window in the single-stranded DNA bubble created by Cas9; (iii) a uracil glycosylase inhibitor (UGI) that impedes uracil excision and downstream processes that decrease base editing efficiency and product purity; and (iv) nickase activity to cleave the non-edited DNA strand, followed by cellular DNA repair processes to replace the G-containing DNA strand. 
     As used herein, a “genomic region” is a segment of a chromosome in the genome of a cell that is present on either side of the target site or, alternatively, also comprises a portion of the target site. The genomic region can comprise at least 5-10, 5-15, 5-20, 5-25, 5-30, 5-35, 5-40, 5-45, 5-50, 5-55, 5-60, 5-65, 5-70, 5-75, 5-80, 5-85, 5-90, 5-95, 5-100, 5-200, 5-300, 5-400, 5-500, 5-600, 5-700, 5-800, 5-900, 5-1000, 5-1100, 5-1200, 5-1300, 5-1400, 5-1500, 5-1600, 5-1700, 5-1800, 5-1900, 5-2000, 5-2100, 5-2200, 5-2300, 5-2400, 5-2500, 5-2600, 5-2700, 5-2800. 5-2900, 5-3000, 5-3100 or more bases such that the genomic region has sufficient homology to undergo homologous recombination with the corresponding region of homology. 
     TAL effector nucleases (TALEN) are a class of sequence-specific nucleases that can be used to make double-strand breaks at specific target sequences in the genome of a plant or other organism. (Miller et al. (2011) Nature Biotechnology 29:143-148). 
     Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Endonucleases include restriction endonucleases, which cleave DNA at specific sites without damaging the bases, and meganucleases, also known as homing endonucleases (HEases), which like restriction endonucleases, bind and cut at a specific recognition site, however the recognition sites for meganucleases are typically longer, about 18 bp or more (patent application PCT/US12/30061, filed on Mar. 22, 2012). Meganucleases have been classified into four families based on conserved sequence motifs, the families are the LAGLIDADG, GIY-YIG, H—N—H, and His-Cys box families. These motifs participate in the coordination of metal ions and hydrolysis of phosphodiester bonds. HEases are notable for their long recognition sites, and for tolerating some sequence polymorphisms in their DNA substrates. The naming convention for meganuclease is similar to the convention for other restriction endonuclease. Meganucleases are also characterized by prefix F-, I-, or PI- for enzymes encoded by free-standing ORFs, introns, and inteins, respectively. One step in the recombination process involves polynucleotide cleavage at or near the recognition site. The cleaving activity can be used to produce a double-strand break. For reviews of site-specific recombinases and their recognition sites, see, Sauer (1994) Curr Op Biotechnol 5:521-7; and Sadowski (1993) FASEB 7:760-7. In some examples the recombinase is from the Integrase or Resolvase families. 
     Zinc finger nucleases (ZFNs) are engineered double-strand break inducing agents comprised of a zinc finger DNA binding domain and a double-strand-break-inducing agent domain. Recognition site specificity is conferred by the zinc finger domain, which typically comprising two, three, or four zinc fingers, for example having a C2H2 structure, however other zinc finger structures are known and have been engineered. Zinc finger domains are amenable for designing polypeptides which specifically bind a selected polynucleotide recognition sequence. ZFNs include an engineered DNA-binding zinc finger domain linked to a non-specific endonuclease domain, for example nuclease domain from a Type IIs endonuclease such as FokI. Additional functionalities can be fused to the zinc-finger binding domain, including transcriptional activator domains, transcription repressor domains, and methylases. In some examples, dimerization of nuclease domain is required for cleavage activity. Each zinc finger recognizes three consecutive base pairs in the target DNA. For example, a 3 finger domain recognized a sequence of 9 contiguous nucleotides, with a dimerization requirement of the nuclease, two sets of zinc finger triplets are used to bind an 18 nucleotide recognition sequence. 
     Genome editing using DSB-inducing agents, such as Cas9-gRNA complexes, has been described, for example in U.S. Patent Application US 2015-0082478 A1, published on Mar. 19, 2015, WO2015/026886 A1, published on Feb. 26, 2015, WO2016007347, published on Jan. 14, 2016, and WO201625131, published on Feb. 18, 2016, all of which are incorporated by reference herein. 
     A guide polynucleotide/Cas endonuclease complex can cleave one or both strands of a DNA target sequence. A guide polynucleotide/Cas endonuclease complex that can cleave both strands of a DNA target sequence typically comprise a Cas protein that has all of its endonuclease domains in a functional state (e.g., wild type endonuclease domains or variants thereof retaining some or all activity in each endonuclease domain). Non-limiting examples of Cas9 nickases suitable for use herein are disclosed in U.S. Patent Appl. Publ. No. 2014/0189896, which is incorporated herein by reference. 
     Other Cas endonuclease systems have been described in PCT patent applications PCT/US16/32073, filed May 12, 2016 and PCT/US16/32028 filed May 12, 2016, both applications incorporated herein by reference. 
     The terms “target site”, “target sequence”, “target site sequence, “target DNA”, “target locus”, “genomic target site”, “genomic target sequence”, “genomic target locus” and “protospacer”, are used interchangeably herein and refer to a polynucleotide sequence such as, but not limited to, a nucleotide sequence on a chromosome, episome, or any other DNA molecule in the genome (including chromosomal, choloroplastic, mitochondrial DNA, plasmid DNA) of a cell, at which a guide polynucleotide/Cas endonuclease complex can recognize, bind to, and optionally nick or cleave. The target site can be an endogenous site in the genome of a cell, or alternatively, the target site can be heterologous to the cell and thereby not be naturally occurring in the genome of the cell, or the target site can be found in a heterologous genomic location compared to where it occurs in nature. As used herein, terms “endogenous target sequence” and “native target sequence” are used interchangeable herein to refer to a target sequence that is endogenous or native to the genome of a cell and is at the endogenous or native position of that target sequence in the genome of the cell. Cells include, but are not limited to, human, non-human, animal, bacterial, fungal, insect, yeast, non-conventional yeast, and plant cells as well as plants and seeds produced by the methods described herein. An “artificial target site” or “artificial target sequence” are used interchangeably herein and refer to a target sequence that has been introduced into the genome of a cell. Such an artificial target sequence can be identical in sequence to an endogenous or native target sequence in the genome of a cell but be located in a different position (i.e., a non-endogenous or non-native position) in the genome of a cell. 
     An “altered target site”, “altered target sequence”, “modified target site”, “modified target sequence” are used interchangeably herein and refer to a target sequence as disclosed herein that comprises at least one alteration when compared to non-altered target sequence. Such “alterations” include, for example: (i) replacement of at least one nucleotide, (ii) a deletion of at least one nucleotide, (iii) an insertion of at least one nucleotide, or (iv) any combination of (i)-(iii). 
     Methods for “modifying a target site” and “altering a target site” are used interchangeably herein and refer to methods for producing an altered target site. 
     The length of the target DNA sequence (target site) can vary, and includes, for example, target sites that are at least 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more nucleotides in length. It is further possible that the target site can be palindromic, that is, the sequence on one strand reads the same in the opposite direction on the complementary strand. The nick/cleavage site can be within the target sequence or the nick/cleavage site could be outside of the target sequence. In another variation, the cleavage could occur at nucleotide positions immediately opposite each other to produce a blunt end cut or, in other Cases, the incisions could be staggered to produce single-stranded overhangs, also called “sticky ends”, which can be either 5′ overhangs, or 3′ overhangs. Active variants of genomic target sites can also be used. Such active variants can comprise at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more sequence identity to the given target site, wherein the active variants retain biological activity and hence are capable of being recognized and cleaved by an Cas endonuclease. Assays to measure the single or double-strand break of a target site by an endonuclease are known in the art and generally measure the overall activity and specificity of the agent on DNA substrates containing recognition sites. 
     A “protospacer adjacent motif” (PAM) herein refers to a short nucleotide sequence adjacent to a target sequence (protospacer) that is recognized (targeted) by a guide polynucleotide/Cas endonuclease system described herein. The Cas endonuclease may not successfully recognize a target DNA sequence if the target DNA sequence is not followed by a PAM sequence. The sequence and length of a PAM herein can differ depending on the Cas protein or Cas protein complex used. The PAM sequence can be of any length but is typically 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 nucleotides long. 
     The terms “targeting”, “gene targeting” and “DNA targeting” are used interchangeably herein. DNA targeting herein may be the specific introduction of a knock-out, edit, or knock-in at a particular DNA sequence, such as in a chromosome or plasmid of a cell. In general, DNA targeting can be performed herein by cleaving one or both strands at a specific DNA sequence in a cell with an endonuclease associated with a suitable polynucleotide component. Such DNA cleavage, if a double-strand break (DSB), can prompt NHEJ or HDR processes which can lead to modifications at the target site. 
     A targeting method herein can be performed in such a way that two or more DNA target sites are targeted in the method, for example. Such a method can optionally be characterized as a multiplex method. Two, three, four, five, six, seven, eight, nine, ten, or more target sites can be targeted at the same time in certain embodiments. A multiplex method is typically performed by a targeting method herein in which multiple different RNA components are provided, each designed to guide an guidepolynucleotide/Cas endonuclease complex to a unique DNA target site. 
     The terms “knock-out”, “gene knock-out” and “genetic knock-out” are used interchangeably herein. A knock-out represents a DNA sequence of a cell that has been rendered partially or completely inoperative by targeting with a Cas protein; such a DNA sequence prior to knock-out could have encoded an amino acid sequence, or could have had a regulatory function (e.g., promoter), for example. A knock-out may be produced by an indel (insertion or deletion of nucleotide bases in a target DNA sequence through NHEJ), or by specific removal of sequence that reduces or completely destroys the function of sequence at or near the targeting site. 
     The guide polynucleotide/Cas endonuclease system can be used in combination with a co-delivered polynucleotide modification template to allow for editing (modification) of a genomic nucleotide sequence of interest. (See also U.S. Patent Application US 2015-0082478 A1, published on Mar. 19, 2015 and WO2015/026886 A1, published on Feb. 26, 2015, both are hereby incorporated in its entirety by reference.) 
     The terms “knock-in”, “gene knock-in, “gene insertion” and “genetic knock-in” are used interchangeably herein. A knock-in represents the replacement or insertion of a DNA sequence at a specific DNA sequence in cell by targeting with a Cas protein (by HR, wherein a suitable donor DNA polynucleotide is also used). Examples of knock-ins are a specific insertion of a heterologous amino acid coding sequence in a coding region of a gene, or a specific insertion of a transcriptional regulatory element in a genetic locus. 
     The following are examples of specific embodiments of some aspects of the invention. The examples are offered for illustrative purposes only and are not intended to limit the scope of the invention in any way. 
     Example 1 
     Protein-Protein Interactions with ZMM28 
     This example demonstrates the interaction of other polypeptides with Zmm28 transcription factor (SEQ ID NO: 562). MADS-box transcription factors associate as homo- or hetero-dimers to bind CArG box elements and subsequently modulate target gene expression. To identify protein-protein interaction partners that potentially interact with native ZMM28 protein, Yeast Two-Hybrid (Y2H) screening was performed with a B73 immature ear library resulting in the identification of six potential MADS box protein-protein interaction partners (Table 2a). 
     Since native zmm28 does not express at early growth stages, protein-protein interaction partners contributing to the transgenic maize events phenotypes in seedlings and young leaves were assayed using Y2H screening of a PH184C seedling (V2-V3) library and a B73 V3-V7 leaf library. Nine total interacting proteins, none of which are MADS box proteins, were identified from the two libraries. 
     Potential interaction partners of ZMM28 were further tested in vivo with a bimolecular fluorescence complementation (BiFC) assay. Following transfection of maize protoplasts, fluorescence was measured indicating interaction between nGFP-Prey and cGFP-ZMM28 (Bait). As BiFC is prone to false-positive self-assembly independent of protein-protein interaction, flow cytometry was used to quantify the BiFC signal and reduce the occurrence of false positives. All signal comparisons were made to a negative control providing a baseline for self-assembly. The control was created by deleting 47 amino acids from the leucine zipper-like K-domain of ZMMADSL6, a protein interaction partner of ZMM28 identified from bioinformatics prediction and Y2H experiment. Truncated ZMMADSL6 (ZMMADSL6-MUT) had significantly reduced interaction with ZMM28 relative to WT ZMMADSL6 while still maintaining nuclear localization. Of the 12 tested protein interactions, eight were confirmed via the BiFC assay with almost half the interactions confirmed positive in both BiFC and Y2H assays (Table 2a). Table 2: ZMM28 protein-protein interactions, transcription, direct targets. 
     
       
         
           
               
             
               
                 TABLE 2a 
               
             
            
               
                   
               
               
                 Transgenic protein-protein interaction partners. 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 ID 
                 Description 
                 Clade 
                 Expression 
                 Y2H 
                 BiFC 
                 HY1H 
                 Sum 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Zm00001d041781 
                 ZmZAG2 
                 AG 
                 0.001 
                 + 
                 − 
                 − 
                 + 
               
               
                 Zm00001d017614 
                 ZmMADS6 
                 AGL6 
                 0.002 
                 + 
                 + 
                 + 
                 +++ 
               
               
                 Zm00001d018667 
                 ZmZAPL 
                 AP1-FULL 
                 0.001 
                 + 
                 + 
                 + 
                 +++ 
               
               
                 Zm00001d022088 
                 ZMM28 
                 AP1 FULL 
                 1.000 
                 − 
                 + 
                 − 
                 + 
               
               
                 Zm00001d028217 
                 ZmM5 
                 SEP 
                 0.005 
                 + 
                 + 
                 − 
                 ++ 
               
               
                 Zm00001d031620 
                 ZmMADSL6 
                 SEP 
                 0.007 
                 + 
                 + 
                 + 
                 +++ 
               
               
                 Zm00001d021057 
                 ZmMADS7-LIKE 
                 SEP 
                 0.002 
                 + 
                 − 
                 − 
                 + 
               
               
                 Zm00001d034047 
                 ZmMADS24 
                 SEP 
                 0.007 
                 − 
                 + 
                 − 
                 + 
               
               
                 Zm00001d044899 
                 ZmMADS47-LIKE 
                 SVP 
                 0.240 
                 − 
                 − 
                 + 
                 + 
               
               
                 Zm00001d027957 
                 ZmM47 
                 SVP 
                 1.862 
                 − 
                 + 
                 + 
                 ++ 
               
               
                 Zm00001d037925 
                 ZmSF2 
                 N/A 
                 0.534 
                 + 
                 − 
                 + 
                 ++ 
               
               
                 Zm00001d022164 
                 ZmSFT-LIKE 
                 N/A 
                 0.788 
                 + 
                 + 
                 + 
                 +++ 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2b 
               
             
            
               
                   
               
               
                 Gene ontology enrichment from RNA-seq data 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                 DEG V6 
                 Number 
                   
                   
               
               
                 GO terms 
                 Ontology 1   
                 Description 
                 Leaf 2   
                 in Ref. 3   
                 p-value 4   
                 FDR 5   
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
            
               
                 GO:0015979 
                 P 
                 photosynthesis 
                 12 
                 94 
                 3.10E−10 
                 1.40E−07 
               
               
                 GO:0009765 
                 P 
                 photosynthesis, light harvesting 
                 7 
                 25 
                 4.50E−09 
                 1.10E−06 
               
               
                 GO:0019684 
                 P 
                 photosynthesis, light reaction 
                 7 
                 40 
                 1.50E−07 
                 2.40E−05 
               
               
                 GO:0033013 
                 P 
                 tetrapyrrole metabolic process 
                 5 
                 39 
                 4.50E−05 
                 0.0042 
               
               
                 GO:0034357 
                 C 
                 photosynthetic membrane 
                 7 
                 57 
                 1.90E−06 
                 7.20E−05 
               
               
                 GO:0044436 
                 C 
                 thylakoid part 
                 6 
                 34 
                 1.10E−06 
                 7.20E−05 
               
               
                 GO:0009579 
                 C 
                 thylakoid 
                 7 
                 60 
                 2.70E−06 
                 7.20E−05 
               
               
                 GO:0004222 
                 F 
                 metalloendopeptidase activity 
                 5 
                 48 
                 0.00012 
                 0.038 
               
               
                 GO:0006091 
                 P 
                 generation of precursor metabolites 
                 14 
                 315 
                 6.70E−06 
                  0.00078 
               
               
                   
                   
                 and energy 
               
               
                 GO:0005975 
                 P 
                 carbohydrate metabolic process 
                 20 
                 788 
                 0.00028 
                 0.022 
               
               
                 GO:0018130 
                 P 
                 heterocycle biosynthetic process 
                 6 
                 95 
                 0.00043 
                 0.028 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2d 
               
             
            
               
                   
               
               
                 Summary results demonstrating ZMM28 interaction with direct target promoters. 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                   
                 Pathway 
                   
                 Bound in 
                 Log 2   
               
               
                 ID 
                 Description 
                 (Discovery) 
                 CArG 
                 (assay) 
                 Expression   
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Zm00001d053787 
                 lhca1l, photosystem I light 
                 photosynthesis, 
                 3 
                 Protoplast 
                 0.51* 
               
               
                   
                 harvesting complex 
                 light harvesting 
               
               
                   
                 gene 1-like 
                 (RNAseq) 
               
               
                 Zm00001d005814 
                 lhca5l, photosystem I light 
                 photosynthesis, 
                 3 
                 Protoplast 
                 0.28* 
               
               
                   
                 harvesting complex 
                 light harvesting 
               
               
                   
                 gene 6-like 
                 (RNAseq) 
               
               
                 Zm00001d027422 
                 Photosystem II PsbP, oxygen 
                 Photosynthesis 
                 3 
                 Protoplast 
                 0.24* 
               
               
                   
                 evolving complex member 
                 (RNAseq) 
               
               
                   
                 (ps2oe) 
               
               
                 Zm00001d007267 
                 lhcb5, light-harvesting 
                 photosynthesis, 
                 3 
                 HY1H 
                 0.22* 
               
               
                   
                 complex II chlorophyll a/b 
                 light harvesting 
               
               
                   
                 binding protein S 
                 (RNAseq) 
               
               
                 Zm00001d027694 
                 Solanesyl diphosphate 
                 Photosynthesis 
                 3 
                 Protoplast 
                 0.2* 
               
               
                   
                 synthase 2 chloroplastic 
                 (RNAseq) 
               
               
                   
                 (sds) 
               
               
                 Zm00001d038163 
                 Pyruvate, phosphate 
                 Photosynthesis/ 
                 2 
                 Protoplast 
                 0.04 
               
               
                   
                 dikinase 
                 pyruvate 
               
               
                   
                 (chloroplastic/cytoplasmic) 
                 metabolism 
               
               
                   
                 (ppdk) 
                 (RNAseq) 
               
               
                 Zm00001d016973 
                 GID2-like F-box protein 
                 hormone signaling 
                 2 
                 HY1H 
                 0.12 
               
               
                   
                 (gid2) 
                 (ChIPseq) 
               
               
                 Zm00001d003911 
                 AFB2-like/TIR1-like (ofb2) 
                 hormone signaling 
                 5 
                 HY1H 
                 0.00 
               
               
                   
                   
                 (ChIPseq) 
               
               
                 Zm00001d030995 
                 b2IP111, CAMP-response 
                 transcription 
                 5 
                 Protoplast 
                 0.23 
               
               
                   
                 element binding protein- 
                 factor activity 
               
               
                   
                 related   
                 (ChIPseq) 
               
               
                   
               
               
                     indicates data missing or illegible when filed 
               
            
           
         
       
     
     Table 2(a) provides a summary of protein-protein interactions with potential contribution to transgenically expressed zmm28. Expression values are from RNA-seq from transgenic V6 maize leaves and are normalized to zmm28. A “+” was listed for protein-interaction predictions based on yeast two-hybrid (Y2H); maize protoplast BiFC; and in heterodimer yeast one-hybrid (HY1H). (b) GO-term enrichment for transcriptomic analysis of DP202216 V6 leaf tissue. Photosynthesis related includes GO Terms 0015979, 0009765, 0019684, 0006091, 0033013, 0034357, 0044436, and 0009579. (d) Summary of promoter direct target analysis and expression in V6 leaves of event DP202216. 1 P=biological process, F=molecular function, C=cellular component.  2  Number of genes associated with each GO term that are differentially expressed between control and event DP202216 V6 leaf, DEG=differentially expressed gene.  3  Total number of genes in each GO category expressed in V6 leaf total detected transcripts.  4  Fisher&#39;s exact test for GO term enrichment.  5  False discovery rate.  6  V6 Leaf. * Statistically significant (adjusted p&lt;0.05). 
     
       
         
           
               
             
               
                 TABLE 2(c) 
               
             
            
               
                   
               
               
                 Differential Expression Values for Genes Involved 
               
            
           
           
               
               
            
               
                   
                 log2 fold 
               
               
                   
                 change 
               
               
                   
                   
               
            
           
           
               
            
               
                 Photosynthesis related 
               
            
           
           
               
               
               
            
               
                   
                 lhcb9 
                 0.7188 
               
               
                   
                 lhca1l 
                 0.5080 
               
               
                   
                 GRMZM2G436986 
                 0.3699 
               
               
                   
                 GRMZM2G005433 
                 0.3474 
               
               
                   
                 GRMZM2G083016 
                 0.3327 
               
               
                   
                 lhac6l 
                 0.3099 
               
               
                   
                 GRMZM2G059083 
                 0.2878 
               
               
                   
                 psbs1 
                 0.2849 
               
               
                   
                 GRMZM2G103101 
                 0.2754 
               
               
                   
                 GRMZM2G117412 
                 0.2752 
               
               
                   
                 chlh1 
                 0.2710 
               
               
                   
                 fdx2 
                 0.2506 
               
               
                   
                 GRMZM2G089136 
                 0.2431 
               
               
                   
                 ps2oe 
                 0.2386 
               
               
                   
                 GRMZM2G033885 
                 0.2353 
               
               
                   
                 lhcb5 
                 0.2200 
               
               
                   
                 GRMZM2G016066 
                 0.2139 
               
               
                   
                 sds 
                 0.2042 
               
               
                   
                 ris2 
                 0.2018 
               
               
                   
                 GRMZM2G064302 
                 0.1902 
               
               
                   
                 GRMZM2G168143 
                 0.1652 
               
               
                   
                 GRMZM2G023528 
                 0.1622 
               
               
                   
                 GRMZM2G027955 
                 0.1579 
               
               
                   
                 GRMZM2G113325 
                 0.1219 
               
               
                   
                 GRMZM2G127421 
                 −0.2992 
               
               
                   
                 GRMZM2G359127 
                 −0.3116 
               
            
           
           
               
            
               
                 Carbohydrate metabolic process 
               
            
           
           
               
               
               
            
               
                   
                 GRMZM2G017186 
                 0.6168 
               
               
                   
                 GRMZM2G083016 
                 0.2431 
               
               
                   
                 GRMZM2G026807 
                 0.2701 
               
               
                   
                 GRMZM2G121128 
                 0.2688 
               
               
                   
                 gbss1b 
                 0.2450 
               
               
                   
                 GRMZM2G089136 
                 0.2431 
               
               
                   
                 GRMZM2G306732 
                 0.2312 
               
               
                   
                 GRMZM2G064302 
                 0.1902 
               
               
                   
                 sps2 
                 0.1834 
               
               
                   
                 GRMZM2G023528 
                 0.1622 
               
               
                   
                 GRMZM2G125977 
                 0.1599 
               
               
                   
                 GRMZM2G027955 
                 0.1579 
               
               
                   
                 pgm2 
                 0.1495 
               
               
                   
                 GRMZM2G052546 
                 0.1399 
               
               
                   
                 mdh6 
                 0.0968 
               
               
                   
                 GRMZM2G005493 
                 −0.1821 
               
               
                   
                 umc2230 
                 −0.2250 
               
               
                   
                 GRMZM2G122431 
                 −0.6249 
               
               
                   
                 GRMZM2G082034 
                 −0.8355 
               
               
                   
                 GRMZM2G347708 
                 −0.9058 
               
            
           
           
               
            
               
                 Heterocycle biosynthetic process 
               
            
           
           
               
               
               
            
               
                   
                 thi1 
                 0.3236 
               
               
                   
                 GRMZM2G177412 
                 0.3099 
               
               
                   
                 chlh1 
                 0.2710 
               
               
                   
                 GRMZM2G027663 
                 0.2200 
               
               
                   
                 GRMZM2G023528 
                 0.1622 
               
               
                   
                 GRMZM2G113325 
                 0.1219 
               
            
           
           
               
            
               
                 Metalloendopeptidase activity 
               
            
           
           
               
               
               
            
               
                   
                 GRMZM2G044697 
                 0.2005 
               
               
                   
                 GRMZM2G087598 
                 0.1873 
               
               
                   
                 prep2 
                 0.1714 
               
               
                   
                 GRMZM2G111200 
                 0.1703 
               
               
                   
                 GRMZM2G163193 
                 0.1281 
               
               
                   
                   
               
            
           
         
       
     
     Pathway analysis of differentially expressed gene transcripts are shown above. Log 2 fold change heat maps of differentially expressed genes functioning in enriched pathways in event DP202216 V6 leaf tissue. 
     Example 2 
     Identification of Direct Interacting Partners 
     Yeast two-hybrid assay. A commercially available yeast two-hybrid system (Clontech (USA)/Takara (Japan) was used to discover and test for potential protein interaction partners with ZMM28. Three maize cDNA prey libraries were constructed from B73 V12-V14 immature ear, PH184C V2-V3 whole seedling, and B73 V3-V7 leaf RNA. The cDNA libraries were generated using SMART technology and co-transformed with linearized pGADT7-Rec into Yeast Strain Y187. At least one million prey clones from each library were mated to a ZMM28 bait strain. Mating was continued until zygotes could be observed using a light microscope and then plated on QDO/-Ade/-His/-Leu/-Trp and incubated at 30° C. for 5 days. Identified protein interaction partners were re-transformed into the Y2H system for confirmation testing. 
     Bimolecular fluorescence complementation (BiFC). Coding sequences for candidate protein-protein interaction partners to ZMM28 were synthesized by GenScript (USA) and placed under the control of the ZmGos2 promoter with a ZmUbi intron 1. The coding sequences were translationally fused to the C-terminal or N-terminal part of the monomeric Ac-GFP1 (Clontech, USA/Takara, Japan) with a 30× Glutamine linker. ZMMADSL6 was selected as a positive control in the BiFC assay as it was confirmed to interact with ZMM28 by Y2H. A truncated version of ZMMADSL6 without the protein interaction domain (a leucine zipper like region in the K-domain) was generated as a negative control. 
     Maize seedlings were germinated and grown in Fafard Super Fine Germination Mix for 6 days in a lighted growth chamber (30° C., 60% RH, 24 h light) and were transferred to a dark growth chamber (30° C., 60% RH, 0 h light) and grown for an additional 4 days to V1. Seedlings were sub-irrigated with deionized water. Maize protoplasts were isolated from these seedlings and were transiently transformed by PEG-mediated transfection as described by Yoo et al.63 with the addition of 0.6 M mannitol in the enzyme, WI, W5 and MMG solutions. Protoplasts were transfected with 10 pmol bait+10 pmol prey plasmid DNA per 3×104 cells. Protoplasts were incubated on a 12-well (1 mL WI) plate for 20 hours at RT before samples were analyzed. 
     BiFC signals were detected by flow cytometry performed using an Attune™ Flow Cytometer (Thermo Fisher Scientific, Waltham, Mass., USA) with a Blue/Violet configuration (488 nm, 20 mW laser and a 405 nm, 50 mW laser). Protoplasts were first gated (R1) by forward scatter (FSC) and side scatter (SCC) to identify 10,000 intact cells (events) and subsequently analyzed for fluorescence emission measured on BL1 (530/30 nm band pass filter) and BL2 (574/26 nm band pass filter) to distinguish between cells exhibiting the BiFC signal (R2) and auto-fluorescence. At least two independent experiments were performed for each protein interaction test with the positive and negative controls present in every experiment. All experiments were designed and analyzed as single factor randomized complete blocks with n=4. Significant differences were determined by analysis of variance with P&lt;0.05 comparing protein interaction partners to the truncated ZMMADSL6 (ZMMADSL6-MUT) negative control. Western blots were used to confirm expression in cells transfected with the negative control ZMMADSL6-MUT (prey) and ZMM28 (bait). 
     RNA-Seq of ZmGos2-zmm28 and control and data analysis. DP202216 was selected for in-depth molecular analysis due to its more favorable insertion region. RNA-Seq libraries were constructed from four biological replicates of control and DP202216 youngest fully expanded leaves at V6 stage. Sequencing was performed on an Illumina HiSeq2500 (Illumina, Inc., USA) with a total read count of 154 million, and a minimum of 12 million reads per sample. RNA-Seq data were aligned to a proprietary maize B73 reference genome using Bowtie 2. Overall loci abundances were estimated using the expected fragment counts metric computed by RSEM65. Samples were vetted for quality by “Robust Principal Components based on Projection Pursuit (PP): GRID search Algorithm” in the “Scalable Robust Estimators with High Breakdown Point” R package [https://cran.r-project.org/package=rrcov]. Fold change was computed and hypothesis tests for differential expression were run using DESeq2, which fits the following model:
         K ij ˜NB (p ij , α i )=   μ ij =s j g ij      log 2  q ij =x j. β t          

     Where K ij  is the observed count for gene i in sample j following a Negative Binomial distribution, (μ ij , α i , s j , q ij ) are all parameters fit to the data (see citation), x j.  is 1 if sample j is transgenic and 0 if it is control and β i  contains the log 2  fold changes for gene i across all high-nitrogen leaf samples. 
     All genes in the proprietary reference genome were converted to public gene model identifiers. The DEGs were then annotated with Gene Ontology terms and differential gene set enrichment was done comparing to the total publicly mapped transcript set for the entire V6 leaf data set using AgriGO. 
     Chromatin immunoprecipitation and sequencing (ChIP-seq) data analysis. Chromatin immunoprecipitation (ChIP) was performed in duplicate on the youngest fully expanded leaf from V4 control and DP202216 maize plants using an anti-ZMM28 antibody (R743); ChIP without antibody was included as a control for each sample. Sequencing was performed on an Illumina HiSeq2500 (Illumina, Inc., USA) with a total read count of 461 million, with a minimum of 26 million reads per sample. ChIP-Seq reads were aligned to a proprietary maize B73 reference genome using Bowtie 2. Alignments were then fed to MACS 2.071 in order to detect differential binding in the transgenic samples. Reproducible peaks were then selected using Irreproducible Discovery Rate (IDR) analysis. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Maize protoplast Bimolecular Fluorescence Complementation assay summary 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                 Positive 
                   
                   
                   
               
               
                   
                   
                   
                 control cell 
                 GOI cell 
               
               
                   
                   
                 Negative 
                 count 
                 count 
               
               
                   
                   
                 control 
                 (Positive vs. 
                 (GOI vs. 
                 GOI vs. 
               
               
                   
                 Protein 
                 cell 
                 negative p 
                 negative p 
                 positive 
               
               
                 GOI ID 
                 description 
                 count 
                 value) 
                 value) 
                 (p-value) 
                 Summary 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                 Zm00001d041781 
                 ZmZAG2 
                 65 
                 155 
                 (0.027) 
                 125 
                 (0.053) 
                 0.195 
                 − 
               
               
                 Zm00001d017614 
                 ZmMADS6 
                 375 
                 1589 
                 (0.002) 
                 1899 
                 (0.002) 
                 0.146 
                 + 
               
               
                 Zm00001d018667 
                 ZmZAPL 
                 491 
                 1538 
                 (0.037) 
                 2161 
                 (0.010) 
                 0.285 
                 + 
               
               
                 Zm00001d022088 
                 ZMM28 
                 483 
                 878 
                 (0.010) 
                 1014 
                 (0.034) 
                 0.429 
                 + 
               
               
                 Zm00001d028217 
                 ZmM5 
                 2085 
                 4728 
                 (0.007) 
                 4512 
                 (0.004) 
                 0.675 
                 + 
               
               
                 Zm00001d031620 
                 ZmMADSL6 
                 2396 
                 N/A 
                 (N/A) 
                 4059 
                 (0.002) 
                 N/A 
                 + 
               
               
                 Zm00001d021057 
                 ZmMADS7- 
                 421 
                 1321 
                 (0.006) 
                 438 
                 (0.427) 
                 0.010 
                 − 
               
               
                   
                 LIKE 
               
               
                 Zm00001d034047 
                 ZmMADS24 
                 586 
                 2024 
                 (0.044) 
                 2099 
                 (0.035) 
                 0.764 
                 + 
               
               
                 Zm00001d044899 
                 ZmMADS47- 
                 483 
                 878 
                 (0.010) 
                 254 
                 (0.047) 
                 0.006 
                 − 
               
               
                   
                 LIKE 
               
               
                 Zm00001d027957 
                 ZmM47 
                 483 
                 878 
                 (0.010) 
                 1085 
                 (0.005) 
                 0.107 
                 + 
               
               
                 Zm00001d037925 
                 ZmSF2 
                 483 
                 878 
                 (0.010) 
                 715 
                 (0.077) 
                 0.363 
                 − 
               
               
                 Zm00001d022164 
                 ZmSFT-LIKE 
                 421 
                 1321 
                 (0.006) 
                 2328 
                 (0.016) 
                 0.016 
                 + 
               
               
                   
               
            
           
         
       
     
     Values represent BiFC positive cell counts from selected gate strategies out of 10,000 cells in representative flow cytometry experiments. Negative- and positive-control cell counts represent fluorescent cells in protoplast populations co-transfected with BiFC fusion constructs of truncated ZmMADSL6 and ZMM28 or full length ZmMADSL6 and ZMM28, respectively. GOI=gene of interest. +/− indicates whether the BiFC assay was concluded to be positive (+) or negative (−) based on the p-value calculations. 
     Example 3 
     Direct-Target Analysis 
     This example demonstrates the analysis behind identification of the direct targets of Zmm28. To identify genes directly modulated by transgenic ZMM28 and their associated pathways, genomic sequences directly bound by ZMM28 were recovered from leaves of control and DP202216 plants at the V4 stage, at which time no detectable native ZMM28 protein is produced, and analyzed by chromatin immunoprecipitation and sequencing (ChIP-Seq). In addition, putative direct targets of the transgenic ZMM28 were identified from CArG-motif enrichment of the promoters from the strong differentially regulated DEGs in the transcriptome experiment. 
     Two in-cell assays were used to collectively validate candidate direct target promoters identified from above two experiments. A heterodimer Yeast One-Hybrid (HY1H) assay analyzed the capability of ZMM28 and one of its protein-protein interaction partners to directly bind a promoter. Additionally, V2 etiolated maize protoplast cells were used in a protoplast direct-target assay using a ZsGreen1 reporter to detect ZMM28 interactions with promoters. The HY1H assay provided predetermined heterodimer interaction partners while the maize protoplast direct-target assay potentially tested ZMM28 homodimers or heterodimers, forming between native protein-protein interaction partners. Promoters of key photosynthetic pathway components were bound by ZMM28, as were promoters of gibberellin and auxin receptor genes which are responsible for sensing these phytohormones (Table 2d). 
     Potential direct target genes (directly bound by the ZMM28 transcription factor) in V4 leaf ChIP-Seq data and select RNA-seq DEG candidates which contain CArG-boxes in the 3 kb upstream of the coding sequence were then screened based on potential function. Promoters of genes with known functional relevance and identifiable CArG sequences were synthesized (Genscript, USA) for direct target assays. Synthesized sequences were cloned into pAbAi (Clontech, USA/TAKARA, Japan) for inclusion in Yeast One-Hybrid assays with ZMM28 and Heterodimer Yeast One-Hybrid assays with ZMM28 and ZMM28 protein-protein interaction partners. Promoter sequences were integrated into the Yeast One-Hybrid Gold strain and individually transformed with a ZMM28-prey plasmid to test for protein-DNA interactions per the Yeast One-Hybrid manual. Heterodimer Yeast One-Hybrid was similarly performed, but including ZMM28 encoded on a Yeast Two-Hybrid bait plasmid (pGBK-T7) and ZMM28 protein-protein interaction partners encoded on a prey (pGAD-T7) plasmid. 
     Plant cell-based direct target assays were conducted in maize protoplasts. Protoplasts were isolated and transfected as described above. Reporter constructs consisted of the synthesized promoter sequences identified above transcriptionally fused to a ZsGreen1 (Clontech, USA/TAKARA, Japan) coding sequence followed by a pinII terminator. Effector constructs comprised a maize Gos2 promoter followed by a maize ZmUbi intron driving an effector protein coding sequence. Effector proteins were ZMM28, ZMM28 translationally fused to a 5×VP16 transcriptional activation domain, or β-glucuronidase as a negative control. Protoplasts were evaluated with flow cytometry with similar methodology to above. 
     Example 4 
     Transcriptome Analysis to Identify Differentially Expressed Genes 
     This example demonstrates identification of several differentially expressed genes in plants expressing Zmm28 transgenically. Transcriptome analysis was conducted to identify differentially-expressed genes (DEGs) and their associated pathways that could provide a possible molecular basis for the previously described increased photosynthesis, N uptake, and plant growth. For simplicity, RNA-seq analysis was focused on V6 leaves from DP202216 and control plants. Results of this analysis identified 192 up-regulated and 64 down-regulated transcripts in DP202216 leaves as compared to the control leaf data (Table 3). CArG box sequences were contained within 3 kb upstream of their promoters in 76% of the DEGs, relative to 26-28% of DEGs from two over-expressed non-MADS transcription factors over a total of four experiments. These results suggest that many of the DEGs may be directly regulated by transgenic ZMM28 binding to their promoters at the V6 stage. 
     To further gain a global view of the differentially-expressed gene (DEG) function, Gene Ontology (GO) enrichment analysis was conducted and 11 GO terms were identified in the V6 leaf DEG dataset (Table 2b,c). Photosynthesis, generation of precursor metabolites and energy, as well as carbohydrate metabolic processes were the three main GO terms identified, all of which could contribute to promote plant growth and development. These results are consistent with the measured phenotypes of ZmGos2-zmm28 plants and suggest that photosynthesis and carbon assimilation-related genes expression are responsible for the measured grain yield increase. 
     Polynucleotide sequences encoding a polypeptide represented by one of SEQ ID NOS: 40-222 and polynucleotide sequences represented by one of SEQ ID NOS: 285-484 and 548-561 exhibit increased expression in plants that have increased and extended expression of Zmm28, compared to a control maize plant. Therefore, these sequences and their allelic variants representing about 95% sequence identity to one of SEQ ID NOS: 40-222, 285-484 and 548-561 are suitable for expression modulation and/or activity modulation to improve agronomic characteristics of maize. This can be achieved by a variety of means, transgenic up-regulation, marker-assisted breeding that selects for increased expression alleles, genome editing or genome engineering that employ site-specific DNA modification, screening for naturally occurring variants or induced mutagenized populations or a combination thereof 
     Polynucleotide sequences encoding a polypeptide represented by one of SEQ ID NOS: 223-284 and polynucleotide sequences represented by one of SEQ ID NOS: 485-547 exhibit reduced expression in plants that have increased and extended expression of Zmm28. Therefore, these sequences and their allelic variants representing about 95% sequence identity to one of SEQ ID NOS: 223-284 and 485-547 are suitable for expression modulation and/or activity modulation to improve agronomic characteristics of maize. This can be achieved by a variety of means, transgenic down-regulation, marker-assisted breeding that selects for reduced expression alleles, genome editing or genome engineering that employ site-specific DNA modification, screening for naturally occurring variants or induced mutagenized populations or a combination thereof. 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 List of differentially expressed genes at a 95% confidence 
               
               
                 interval in DP202216 vs control V6 leaf tissue 
               
            
           
           
               
               
               
               
               
            
               
                   
                   
                 Base 
                 log 2  fold 
                 adjusted 
               
               
                   
                 ID 
                 mean 
                 change 
                 p-value 
               
               
                   
                   
               
            
           
           
               
               
               
               
               
            
               
                   
                 Zm00001d022088 
                 366.7 
                 2.161 
                 0.000 
               
               
                   
                 Zm00001d023455 
                 399.2 
                 1.309 
                 0.000 
               
               
                   
                 Zm00001d023456 
                 775.4 
                 1.175 
                 0.000 
               
               
                   
                 Zm00001d038273 
                 268.1 
                 1.056 
                 0.000 
               
               
                   
                 Zm00001d004053 
                 788.2 
                 1.054 
                 0.000 
               
               
                   
                 Zm00001d029183 
                 467.1 
                 0.885 
                 0.018 
               
               
                   
                 Zm00001d051194 
                 422.1 
                 0.735 
                 0.006 
               
               
                   
                 Zm00001d033132 
                 1007.7 
                 0.719 
                 0.000 
               
               
                   
                 Zm00001d029215 
                 401.8 
                 0.710 
                 0.049 
               
               
                   
                 Zm00001d033543 
                 949.1 
                 0.710 
                 0.010 
               
               
                   
                 Zm00001d053925 
                 887.4 
                 0.695 
                 0.003 
               
               
                   
                 Zm00001d028269 
                 226.6 
                 0.651 
                 0.000 
               
               
                   
                 Zm00001d033544 
                 255.6 
                 0.643 
                 0.000 
               
               
                   
                 Zm00001d034015 
                 844.9 
                 0.617 
                 0.000 
               
               
                   
                 Zm00001d027743 
                 384.8 
                 0.601 
                 0.000 
               
               
                   
                 Zm00001d048311 
                 698.4 
                 0.565 
                 0.000 
               
               
                   
                 Zm00001d053787 
                 4263.0 
                 0.508 
                 0.019 
               
               
                   
                 Zm00001d047256 
                 331.2 
                 0.490 
                 0.000 
               
               
                   
                 Zm00001d048720 
                 258.8 
                 0.440 
                 0.017 
               
               
                   
                 Zm00001d023426 
                 2247.4 
                 0.436 
                 0.004 
               
               
                   
                 Zm00001d004331 
                 771.7 
                 0.430 
                 0.049 
               
               
                   
                 Zm00001d050748 
                 566.4 
                 0.424 
                 0.000 
               
               
                   
                 Zm00001d010321 
                 1082.7 
                 0.416 
                 0.008 
               
               
                   
                 Zm00001d004894 
                 15128.1 
                 0.403 
                 0.000 
               
               
                   
                 Zm00001d042346 
                 506.7 
                 0.401 
                 0.045 
               
               
                   
                 Zm00001d031657 
                 1064.8 
                 0.393 
                 0.002 
               
               
                   
                 Zm00001d008178 
                 262.0 
                 0.377 
                 0.042 
               
               
                   
                 Zm00001d043044 
                 3741.8 
                 0.371 
                 0.001 
               
               
                   
                 Zm00001d018623 
                 374.5 
                 0.370 
                 0.002 
               
               
                   
                 Zm00001d043095 
                 820.2 
                 0.369 
                 0.000 
               
               
                   
                 Zm00001d029062 
                 448.4 
                 0.354 
                 0.018 
               
               
                   
                 Zm00001d011900 
                 1851.3 
                 0.347 
                 0.001 
               
               
                   
                 Zm00001d010672 
                 3578.8 
                 0.333 
                 0.003 
               
               
                   
                 Zm00001d011183 
                 6346.0 
                 0.324 
                 0.049 
               
               
                   
                 Zm00001d037103 
                 1178.1 
                 0.322 
                 0.039 
               
               
                   
                 Zm00001d009028 
                 28412.8 
                 0.318 
                 0.038 
               
               
                   
                 Zm00001d013937 
                 3658.0 
                 0.318 
                 0.008 
               
               
                   
                 Zm00001d002873 
                 412.1 
                 0.315 
                 0.010 
               
               
                   
                 Zm00001d037362 
                 731.7 
                 0.311 
                 0.039 
               
               
                   
                 Zm00001d026404 
                 8690.7 
                 0.310 
                 0.028 
               
               
                   
                 Zm00001d047255 
                 2253.8 
                 0.309 
                 0.024 
               
               
                   
                 Zm00001d031253 
                 5805.9 
                 0.309 
                 0.000 
               
               
                   
                 Zm00001d027576 
                 856.8 
                 0.306 
                 0.011 
               
               
                   
                 Zm00001d052595 
                 12058.5 
                 0.304 
                 0.002 
               
               
                   
                 Zm00001d013367 
                 1046.5 
                 0.301 
                 0.007 
               
               
                   
                 Zm00001d046001 
                 2845.8 
                 0.297 
                 0.049 
               
               
                   
                 Zm00001d008963 
                 418.8 
                 0.296 
                 0.049 
               
               
                   
                 Zm00001d048515 
                 366.0 
                 0.290 
                 0.043 
               
               
                   
                 Zm00001d018779 
                 5833.9 
                 0.289 
                 0.028 
               
               
                   
                 Zm00001d052595 
                 5155.7 
                 0.289 
                 0.020 
               
               
                   
                 Zm00001d042049 
                 5095.7 
                 0.288 
                 0.016 
               
               
                   
                 Zm00001d040242 
                 573.1 
                 0.287 
                 0.022 
               
               
                   
                 Zm00001d042697 
                 29924.1 
                 0.285 
                 0.000 
               
               
                   
                 Zm00001d019518 
                 2389.6 
                 0.283 
                 0.004 
               
               
                   
                 Zm00001d048313 
                 568.8 
                 0.283 
                 0.034 
               
               
                   
                 Zm00001d033150 
                 2844.8 
                 0.281 
                 0.000 
               
               
                   
                 Zm00001d007858 
                 4471.7 
                 0.280 
                 0.000 
               
               
                   
                 Zm00001d003588 
                 1202.7 
                 0.280 
                 0.005 
               
               
                   
                 Zm00001d036903 
                 1562.2 
                 0.279 
                 0.019 
               
               
                   
                 Zm00001d031484 
                 3091.2 
                 0.276 
                 0.000 
               
               
                   
                 Zm00001d018157 
                 2066.8 
                 0.275 
                 0.012 
               
               
                   
                 Zm00001d005814 
                 3964.9 
                 0.275 
                 0.000 
               
               
                   
                 Zm00001d033338 
                 1889.2 
                 0.275 
                 0.028 
               
               
                   
                 Zm00001d053446 
                 1126.3 
                 0.272 
                 0.027 
               
               
                   
                 Zm00001d026603 
                 26238.1 
                 0.271 
                 0.000 
               
               
                   
                 Zm00001d027841 
                 19250.6 
                 0.270 
                 0.016 
               
               
                   
                 Zm00001d030048 
                 4061.0 
                 0.269 
                 0.001 
               
               
                   
                 Zm00001d005346 
                 4426.3 
                 0.267 
                 0.025 
               
               
                   
                 Zm00001d023706 
                 4737.6 
                 0.267 
                 0.000 
               
               
                   
                 Zm00001d042050 
                 13900.2 
                 0.266 
                 0.013 
               
               
                   
                 Zm00001d042533 
                 870.8 
                 0.262 
                 0.019 
               
               
                   
                 Zm00001d022590 
                 756.8 
                 0.261 
                 0.024 
               
               
                   
                 Zm00001d045431 
                 3088.4 
                 0.260 
                 0.045 
               
               
                   
                 Zm00001d047743 
                 2167.9 
                 0.260 
                 0.000 
               
               
                   
                 Zm00001d036738 
                 4088.9 
                 0.251 
                 0.000 
               
               
                   
                 Zm00001d018274 
                 2320.0 
                 0.251 
                 0.020 
               
               
                   
                 Zm00001d035003 
                 9178.4 
                 0.251 
                 0.028 
               
               
                   
                 Zm00001d027321 
                 906.8 
                 0.250 
                 0.013 
               
               
                   
                 Zm00001d014284 
                 2863.7 
                 0.249 
                 0.000 
               
               
                   
                 Zm00001d036340 
                 3635.8 
                 0.248 
                 0.039 
               
               
                   
                 Zm00001d003767 
                 684.3 
                 0.248 
                 0.021 
               
               
                   
                 Zm00001d031997 
                 2770.7 
                 0.246 
                 0.022 
               
               
                   
                 Zm00001d019479 
                 7547.5 
                 0.245 
                 0.000 
               
               
                   
                 Zm00001d024148 
                 10915.4 
                 0.244 
                 0.013 
               
               
                   
                 Zm00001d038579 
                 22011.0 
                 0.243 
                 0.000 
               
               
                   
                 Zm00001d037273 
                 2559.2 
                 0.240 
                 0.028 
               
               
                   
                 Zm00001d025845 
                 682.1 
                 0.239 
                 0.033 
               
               
                   
                 Zm00001d027422 
                 1300.4 
                 0.239 
                 0.049 
               
               
                   
                 Zm00001d024519 
                 15382.2 
                 0.238 
                 0.000 
               
               
                   
                 Zm00001d040163 
                 4199.3 
                 0.238 
                 0.000 
               
               
                   
                 Zm00001d012868 
                 2451.1 
                 0.237 
                 0.001 
               
               
                   
                 Zm00001d021763 
                 46089.8 
                 0.235 
                 0.049 
               
               
                   
                 Zm00001d035761 
                 2876.1 
                 0.232 
                 0.028 
               
               
                   
                 Zm00001d032301 
                 1829.9 
                 0.231 
                 0.003 
               
               
                   
                 Zm00001d028562 
                 7597.8 
                 0.231 
                 0.048 
               
               
                   
                 Zm00001d034538 
                 1219.9 
                 0.231 
                 0.042 
               
               
                   
                 Zm00001d048116 
                 1310.7 
                 0.230 
                 0.003 
               
               
                   
                 Zm00001d048998 
                 33243.0 
                 0.226 
                 0.003 
               
               
                   
                 Zm00001d049490 
                 896.9 
                 0.225 
                 0.049 
               
               
                   
                 Zm00001d015975 
                 1389.6 
                 0.224 
                 0.030 
               
               
                   
                 Zm00001d021435 
                 101585.8 
                 0.223 
                 0.001 
               
               
                   
                 Zm00001d015613 
                 1517.4 
                 0.221 
                 0.049 
               
               
                   
                 Zm00001d039258 
                 45911.3 
                 0.221 
                 0.023 
               
               
                   
                 Zm00001d007267 
                 22445.6 
                 0.220 
                 0.000 
               
               
                   
                 Zm00001d033383 
                 8820.9 
                 0.220 
                 0.040 
               
               
                   
                 Zm00001d026645 
                 774.2 
                 0.220 
                 0.028 
               
               
                   
                 Zm00001d023757 
                 3788.0 
                 0.219 
                 0.026 
               
               
                   
                 Zm00001d034005 
                 1328.0 
                 0.218 
                 0.017 
               
               
                   
                 Zm00001d022381 
                 1437.7 
                 0.215 
                 0.028 
               
               
                   
                 Zm00001d031962 
                 1481.3 
                 0.214 
                 0.012 
               
               
                   
                 Zm00001d005446 
                 17349.9 
                 0.214 
                 0.017 
               
               
                   
                 Zm00001d027511 
                 1065.8 
                 0.211 
                 0.034 
               
               
                   
                 Zm00001d017178 
                 1469.3 
                 0.210 
                 0.020 
               
               
                   
                 Zm00001d038947 
                 2902.2 
                 0.209 
                 0.007 
               
               
                   
                 Zm00001d009982 
                 2640.8 
                 0.209 
                 0.006 
               
               
                   
                 Zm00001d034739 
                 1282.4 
                 0.208 
                 0.033 
               
               
                   
                 Zm00001d044745 
                 2078.9 
                 0.208 
                 0.002 
               
               
                   
                 Zm00001d038491 
                 1871.3 
                 0.208 
                 0.007 
               
               
                   
                 Zm00001d014445 
                 2012.3 
                 0.207 
                 0.029 
               
               
                   
                 Zm00001d039745 
                 2541.4 
                 0.207 
                 0.049 
               
               
                   
                 Zm00001d038485 
                 2954.2 
                 0.207 
                 0.020 
               
               
                   
                 Zm00001d012287 
                 3196.9 
                 0.205 
                 0.042 
               
               
                   
                 Zm00001d027694 
                 4079.0 
                 0.204 
                 0.002 
               
               
                   
                 Zm00001d003470 
                 2149.7 
                 0.204 
                 0.049 
               
               
                   
                 Zm00001d019180 
                 1691.1 
                 0.203 
                 0.001 
               
               
                   
                 Zm00001d007394 
                 2809.7 
                 0.203 
                 0.046 
               
               
                   
                 Zm00001d053432 
                 14717.4 
                 0.202 
                 0.000 
               
               
                   
                 Zm00001d039900 
                 3507.8 
                 0.200 
                 0.004 
               
               
                   
                 Zm00001d050810 
                 2267.9 
                 0.200 
                 0.013 
               
               
                   
                 Zm00001d016802 
                 3694.7 
                 0.200 
                 0.024 
               
               
                   
                 Zm00001d004978 
                 1355.2 
                 0.199 
                 0.049 
               
               
                   
                 Zm00001d028924 
                 2314.7 
                 0.199 
                 0.017 
               
               
                   
                 Zm00001d002815 
                 6335.2 
                 0.198 
                 0.034 
               
               
                   
                 Zm00001d029065 
                 1335.9 
                 0.198 
                 0.033 
               
               
                   
                 Zm00001d052184 
                 1429.5 
                 0.197 
                 0.005 
               
               
                   
                 Zm00001d038337 
                 1709.0 
                 0.193 
                 0.049 
               
               
                   
                 Zm00001d003713 
                 843.8 
                 0.193 
                 0.049 
               
               
                   
                 Zm00001d031953 
                 2062.3 
                 0.193 
                 0.049 
               
               
                   
                 Zm00001d053576 
                 1070.5 
                 0.191 
                 0.036 
               
               
                   
                 Zm00001d000123 
                 4446.2 
                 0.191 
                 0.010 
               
               
                   
                 Zm00001d045431 
                 12598.3 
                 0.190 
                 0.039 
               
               
                   
                 Zm00001d036630 
                 26955.9 
                 0.187 
                 0.000 
               
               
                   
                 Zm00001d048515 
                 4138.4 
                 0.186 
                 0.044 
               
               
                   
                 Zm00001d021310 
                 10622.2 
                 0.185 
                 0.009 
               
               
                   
                 Zm00001d038037 
                 13570.3 
                 0.184 
                 0.005 
               
               
                   
                 Zm00001d042353 
                 1578.4 
                 0.183 
                 0.029 
               
               
                   
                 Zm00001d050150 
                 1799.2 
                 0.183 
                 0.014 
               
               
                   
                 Zm00001d025545 
                 10158.4 
                 0.182 
                 0.000 
               
               
                   
                 Zm00001d012168 
                 1918.6 
                 0.182 
                 0.006 
               
               
                   
                 Zm00001d011581 
                 2421.3 
                 0.176 
                 0.013 
               
               
                   
                 Zm00001d018030 
                 12550.6 
                 0.173 
                 0.012 
               
               
                   
                 Zm00001d018145 
                 15856.7 
                 0.171 
                 0.012 
               
               
                   
                 Zm00001d040221 
                 4822.7 
                 0.170 
                 0.001 
               
               
                   
                 Zm00001d033594 
                 4970.0 
                 0.170 
                 0.006 
               
               
                   
                 Zm00001d008625 
                 3404.2 
                 0.170 
                 0.015 
               
               
                   
                 Zm00001d032380 
                 6439.8 
                 0.169 
                 0.042 
               
               
                   
                 Zm00001d045575 
                 9388.9 
                 0.165 
                 0.012 
               
               
                   
                 Zm00001d042526 
                 12885.2 
                 0.164 
                 0.024 
               
               
                   
                 Zm00001d043168 
                 9130.5 
                 0.164 
                 0.014 
               
               
                   
                 Zm00001d053545 
                 13321.4 
                 0.162 
                 0.012 
               
               
                   
                 Zm00001d053981 
                 2247.8 
                 0.162 
                 0.031 
               
               
                   
                 Zm00001d017746 
                 3272.3 
                 0.162 
                 0.023 
               
               
                   
                 Zm00001d012083 
                 3531.8 
                 0.161 
                 0.002 
               
               
                   
                 Zm00001d024718 
                 1276.1 
                 0.160 
                 0.039 
               
               
                   
                 Zm00001d021621 
                 29252.0 
                 0.160 
                 0.033 
               
               
                   
                 Zm00001d015004 
                 3642.0 
                 0.159 
                 0.031 
               
               
                   
                 Zm00001d039131 
                 6755.2 
                 0.158 
                 0.013 
               
               
                   
                 Zm00001d044970 
                 11313.1 
                 0.158 
                 0.015 
               
               
                   
                 Zm00001d018401 
                 3854.9 
                 0.156 
                 0.007 
               
               
                   
                 Zm00001d015975 
                 2687.4 
                 0.150 
                 0.024 
               
               
                   
                 Zm00001d013428 
                 6916.2 
                 0.150 
                 0.002 
               
               
                   
                 Zm00001d021246 
                 8907.5 
                 0.148 
                 0.041 
               
               
                   
                 Zm00001d007921 
                 1700.3 
                 0.146 
                 0.045 
               
               
                   
                 Zm00001d027511 
                 11194.0 
                 0.144 
                 0.039 
               
               
                   
                 Zm00001d027309 
                 2776.5 
                 0.140 
                 0.031 
               
               
                   
                 Zm00001d025544 
                 4067.6 
                 0.138 
                 0.040 
               
               
                   
                 Zm00001d039276 
                 2421.5 
                 0.137 
                 0.049 
               
               
                   
                 Zm00001d003512 
                 7940.7 
                 0.134 
                 0.016 
               
               
                   
                 Zm00001d053861 
                 4328.4 
                 0.130 
                 0.048 
               
               
                   
                 Zm00001d038894 
                 18625.0 
                 0.129 
                 0.007 
               
               
                   
                 Zm00001d051321 
                 5842.9 
                 0.128 
                 0.039 
               
               
                   
                 Zm00001d016826 
                 6846.9 
                 0.126 
                 0.031 
               
               
                   
                 Zm00001d016854 
                 3875.9 
                 0.122 
                 0.032 
               
               
                   
                 Zm00001d017435 
                 4798.8 
                 0.121 
                 0.018 
               
               
                   
                 Zm00001d048373 
                 16010.1 
                 0.109 
                 0.019 
               
               
                   
                 Zm00001d018901 
                 18599.9 
                 0.104 
                 0.043 
               
               
                   
                 Zm00001d019454 
                 18340.3 
                 0.100 
                 0.046 
               
               
                   
                 Zm00001d031899 
                 38207.2 
                 0.097 
                 0.036 
               
               
                   
                 Zm00001d045706 
                 13660.8 
                 −0.114 
                 0.003 
               
               
                   
                 Zm00001d035869 
                 3703.4 
                 −0.169 
                 0.035 
               
               
                   
                 Zm00001d053262 
                 2715.0 
                 −0.177 
                 0.034 
               
               
                   
                 Zm00001d017958 
                 1986.1 
                 −0.179 
                 0.042 
               
               
                   
                 Zm00001d007113 
                 2081.6 
                 −0.182 
                 0.007 
               
               
                   
                 Zm00001d051650 
                 1133.1 
                 −0.205 
                 0.025 
               
               
                   
                 Zm00001d015138 
                 60518.8 
                 −0.222 
                 0.000 
               
               
                   
                 Zm00001d030103 
                 1549.1 
                 −0.225 
                 0.034 
               
               
                   
                 Zm00001d021846 
                 1819.7 
                 −0.226 
                 0.000 
               
               
                   
                 Zm00001d041576 
                 849.3 
                 −0.252 
                 0.039 
               
               
                   
                 Zm00001d005391 
                 618.2 
                 −0.255 
                 0.019 
               
               
                   
                 Zm00001d009022 
                 4240.0 
                 −0.264 
                 0.023 
               
               
                   
                 Zm00001d041343 
                 1309.4 
                 −0.268 
                 0.045 
               
               
                   
                 Zm00001d039965 
                 528.6 
                 −0.274 
                 0.025 
               
               
                   
                 Zm00001d029047 
                 509.7 
                 −0.275 
                 0.021 
               
               
                   
                 Zm00001d028230 
                 2507.9 
                 −0.284 
                 0.012 
               
               
                   
                 Zm00001d013243 
                 725.6 
                 −0.286 
                 0.040 
               
               
                   
                 Zm00001d032926 
                 458.9 
                 −0.299 
                 0.034 
               
               
                   
                 Zm00001d045667 
                 1861.6 
                 −0.302 
                 0.000 
               
               
                   
                 Zm00001d021846 
                 701.7 
                 −0.303 
                 0.025 
               
               
                   
                 Zm00001d033469 
                 934.7 
                 −0.312 
                 0.032 
               
               
                   
                 Zm00001d019563 
                 3360.0 
                 −0.314 
                 0.007 
               
               
                   
                 Zm00001d003866 
                 945.1 
                 −0.316 
                 0.008 
               
               
                   
                 Zm00001d039325 
                 1802.7 
                 −0.321 
                 0.000 
               
               
                   
                 Zm00001d023516 
                 69804.9 
                 −0.324 
                 0.036 
               
               
                   
                 Zm00001d050918 
                 301.0 
                 −0.325 
                 0.029 
               
               
                   
                 Zm00001d025253 
                 331.5 
                 −0.346 
                 0.040 
               
               
                   
                 Zm00001d024499 
                 1459.3 
                 −0.364 
                 0.029 
               
               
                   
                 Zm00001d045948 
                 478.6 
                 −0.374 
                 0.013 
               
               
                   
                 Zm00001d021569 
                 473.1 
                 −0.376 
                 0.024 
               
               
                   
                 Zm00001d053327 
                 601.3 
                 −0.377 
                 0.002 
               
               
                   
                 Zm00001d047208 
                 736.1 
                 −0.379 
                 0.000 
               
               
                   
                 Zm00001d007687 
                 1551.8 
                 −0.385 
                 0.001 
               
               
                   
                 Zm00001d015126 
                 1333.7 
                 −0.395 
                 0.005 
               
               
                   
                 Zm00001d034781 
                 288.2 
                 −0.403 
                 0.006 
               
               
                   
                 Zm00001d016655 
                 1486.6 
                 −0.412 
                 0.049 
               
               
                   
                 Zm00001d043517 
                 322.3 
                 −0.426 
                 0.013 
               
               
                   
                 Zm00001d045667 
                 288.4 
                 −0.427 
                 0.049 
               
               
                   
                   
               
               
                   
                 Base Mean = the mean of counts of all samples, normalized for sequencing depth. 
               
            
           
         
       
     
     Example 5 
     Transcriptome Analysis to Identify Differentially Expressed Genes 
     This example demonstrates identification of several differentially expressed genes in plants expressing Zmm28 transgenically. Transcriptome analysis was conducted to identify differentially-expressed genes (DEGs) and their associated pathways that could provide a possible molecular basis for the previously described increased photosynthesis, N uptake, and plant growth. For simplicity, RNA-seq analysis was focused on V6 leaves from DP202216 and control plants. Results of this analysis identified 192 up-regulated and 64 down-regulated transcripts in DP202216 leaves as compared to the control leaf data (Table 4). CArG box sequences were contained within 3 kb upstream of their promoters in 76% of the DEGs, relative to 26-28% of DEGs from two over-expressed non-MADS transcription factors over a total of four experiments. 
     Example 6 
     Increasing Photosynthetic Flux Through Gene Expression Alteration of One or More Sequences 
     In some embodiments, altering expression levels of direct target genes or their protein products/activities thereof (e.g., polypeptides represented by SEQ ID NOS: 23-31 or polynucleotides represented by SEQ ID NOS: 32-39)) may positively affect grain yield. In particular embodiments, altering expression or gene product amounts may change photosynthetic flux. For example, increasing expression of polypeptides represented by SEQ ID NOS: 23-31 may lead to increases in photosynthesis as measured by increased CO 2  exchange rate (CER) or electron transport rate. In other examples, expression changes may lead to positive feedback resulting in both increased leaf area with increased light interception and increased photosynthetic rate per leaf area. In yet other examples, expression changes in polypeptides represented by SEQ ID NOS: 23-31 may lead to increased photosynthate and enhanced uptake and assimilation of nitrogen. Increases or decreases in gene expression levels is achieved by introducing a targeted genetic modification or through expression of a recombinant DNA construct. Targeted genetic modifications include for example, removing a repressor element from the regulatory region of the gene or by mutating one or more motifs to increase expression levels of the gene. Enhancer elements can also be introduced to increase gene expression. 
     Example 6 
     Increasing Plant Growth and/or N-Assimilation Through Gene Expression Alteration 
     In some embodiments, altering gene expression of direct target genes may enhance plant growth. In particular embodiments, altering gene expression may lead to enhanced early vigor or enhanced grain yield. In some embodiments, changes in expression of SEQ ID NO: 30, 38, 563 and/or 564 lead to enhancement of phytohormone reception response leading to increased plant growth or enhanced grain yield. 
     In some embodiments, altering gene expression of direct target genes may enhance nitrogen uptake or assimilation. In particular embodiments, changes in expression of SEQ ID NO: 39 or related genes such as SEQ ID NO: 566 lead to improvements in nitrogen uptake or assimilation. Such improvements may further lead to enhanced plant growth and/or grain yield. 
     Increases or decreases in gene expression levels is achieved by introducing a targeted genetic modification or through expression of a recombinant DNA construct. Targeted genetic modifications include for example, removing a repressor element from the regulatory region of the gene or by mutating one or more motifs to increase expression levels of the gene. Enhancer elements can also be introduced to increase gene expression 
     Example 7 
     Increasing Plant Stress Tolerance 
     In some embodiments, altering gene expression of direct target genes may enhance plant stress or disease tolerance. In particular embodiments, changes in expression of SEQ ID NOS: 574-579 results in improvements in biotic or abiotic stress tolerance. In particular embodiments, such expression changes and stress tolerance may lead to enhanced plant vigor, enhanced biomass accumulation and/or enhanced grain yield. 
     Increases or decreases in gene expression levels to improve plant stress tolerance is achieved by introducing a targeted genetic modification or through expression of a recombinant DNA construct. Targeted genetic modifications include for example, removing a repressor element from the regulatory region of the gene or by mutating one or more motifs to increase expression levels of the gene. Enhancer elements can also be introduced to increase gene expression 
     Terms used in the claims and specification are defined as set forth below unless otherwise specified. It must be noted that, as used in the specification and the appended claims, the singular forms “a,” “an” and “the” include plural referents unless the context clearly dictates otherwise. 
     All publications and patent applications in this specification are indicative of the level of ordinary skill in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated by reference. 
     Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Unless mentioned otherwise, the techniques employed or contemplated herein are standard methodologies well known to one of ordinary skill in the art. The materials, methods and examples are illustrative only and not limiting. 
     Many modifications and other embodiments of the inventions set forth herein will come to mind to one skilled in the art to which these inventions pertain having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the inventions are not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation. 
     Units, prefixes and symbols may be denoted in their SI accepted form. Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively. Numeric ranges are inclusive of the numbers defining the range. Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.