Patent Publication Number: US-2019194683-A1

Title: Methods and compositions for resistance to cyst nematode in plants

Description:
This application claims priority to U.S. Provisional Application Nos. 62/544,856 and 62/544,824, the disclosures of which are explicitly incorporated by reference herein. 
    
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH 
     This invention was made with government support under 17-CRHF-0-6055 awarded by the USDA/NIFA. The government has certain rights in the invention. 
    
    
     BACKGROUND 
     Field of the Invention 
     The present disclosure provides methods and compositions for conferring or producing nematode resistance in a plant or plant cells, and nematode resistant plants or plant cells. The disclosure further provides methods for improving growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance. 
     Description of Related Art 
     Soybean cyst nematode ( Heterodera glycines ; SCN) is consistently the most damaging disease or pest of U.S. soybeans, one of the world&#39;s most important crops (Niblack et al., 2006, Annu Rev Phytopathol 44, 283-303; Jones et al., 2013, Mol Plant Pathol 14, 946-961; Mitchum, 2016, Mol Plant Pathol 5, 175-181; T. W. Allen, 2017, Soybean Yield Loss Estimates Due to Diseases in the United States and Ontario, Canada, from 2010 to 2014. Plant Health Research. doi:10.1094/PHP-RS-16-0066). Plant parasitic nematodes, including cyst nematodes, infest the roots of many valuable crops and establish elaborate feeding structures (Kyndt et al., 2013, Planta 238, 807-818). Cyst nematodes secrete a complex arsenal of effector molecules that modulate the host&#39;s physiology and promote fusion of neighboring host cells into a large unicellular feeding site, termed a syncytium (Gheysen and Mitchum, 2011, Curr Opin Plant Biol 14, 415-421; Hewezi and Baum, 2013, Mol Plant Microbe Interact 26, 9-16; Mitchum et al., 2013, New Phytologist 199, 879-894), with negative effects on the health and propagation of the involved plants. 
     A soybean locus, Rhg1 (Resistance to  Heterodera glycines ), has been widely used by soybean breeders and growers as the best available disease resistance locus to reduce damage caused by SCN (Concibido et al., 2004, Crop Science 44, 1121-1131; Mitchum, 2016, Id.). The complex Rhg1 locus on soybean chromosome 18 is a tandemly repeated block of four genes: Glyma.18G022400 (formerly Glyma18g02580), Glyma.18G022500 (formerly Glyma18g02590), Glyma.18G022600 (formerly Glyma18g02600) and Glyma.18G022700 (formerly Glyma18g02610), as well as the adjacent nucleotides that comprise the chromosomal segment containing the above genes, which is tandemly repeated in haplotypes that confer increased SCN resistance (Cook et al., 2012, Science 338, 1206-1209; U.S. Patent Application Publ. No. 2013-0305410 A1). (The 13-character gene names are from the Wm82.a1 genome assembly and Glyma 1.0 gene models (Schmutz et al., 2010, Nature 463, 178-183) and the more recent 15-character gene names are from the U.S. Department of Energy Joint Genome Institute Wm82.a2 soybean genome assembly and Glyma 2.0 gene model naming revision.) The relevant genes at the Rhg1 locus do not encode proteins widely associated with plant disease resistance. Instead, resistance is mediated by copy number variation of three disparate genes at the Rhg1 locus, one of which (Glyma.18G022500) encodes proteins with high similarity to known α-SNAP proteins (U.S. Patent Application Publ. No. 2013-0305410 A1; Mitchum et al., 2004, Mol Plant Pathol 5, 175-181; Jones and Dangl, 2006, Nature 444, 323-329; Dodds and Rathjen, 2010, Nat Rev Genet 11, 539-548; Cook et al., 2012, Science 338, 1206-1209; Cook et al., 2014, Plant Physiol 165, 630-647; Lee et al., 2015, Mol Ecol 24, 1774-1791). 
     Alpha-Soluble NSF Attachment Protein (α-SNAP or α-SNAP herein) is a ubiquitous housekeeping protein in plants and animals that facilitates cellular vesicular trafficking by mediating the disassembly and reuse of the four-protein bundles of SNARE proteins (soluble NSF attachment protein receptor proteins) that form when t-SNARE and v-SNARE proteins anneal during vesicle docking to target membranes (Jahn and Scheller, 2006, Nat Rev Mol Cell Biol 7, 631-643; Baker and Hughson, 2016, Nat Rev Mol Cell Biol 17, 465-479; Zhao and Brunger, 2016, J Mol Biol 428, 1912-1926). α-SNAP functions together with the ATPase N-ethylmaleimide Sensitive Factor (NSF) to carry out this SNARE bundle disassembly (Zhao and Brunger, 2015, J Mol Biol 428: 1912-1926). 
     NSF is an ATPases Associated with various cellular Activities (AAA) family protein containing three well defined domains: the N-domain, which mediates interactions with one or more α-SNAP polypeptides, the D1 ATPase domains, which couple ATP hydrolysis to force-generating conformational changes that remodel SNARE complexes, and the D2 ATPase domain, which mediates NSF hexamerization (Whiteheart et al., 2001, Int Rev Cytol 207, 71-112; Hanson and Whiteheart, 2005, Nat Rev Mol Cell Biol 6, 519-529; Zhao et al., 2010, J. Biol. Chem. 285, 761-772). 
     The soybean resistance-associated Rhg1 α-SNAPs comprise polymorphic variant sequences of Glyma.18G022500 that encode variant α-SNAP proteins (U.S. patent application Ser. No. 13/843,447). Rhg1 resistance-associated α-SNAPs have lower binding affinity for NSF and SNARE/NSF complexes, and disrupt vesicle trafficking in planta (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). The relative abundance of Rhg1-encoded defective α-SNAP variants increases substantially within host syncytium cells at the nematode feeding site (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA Proc. Natl. Acad. Sci. USA 113, E7375-E7382, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). 
     Resistance-associated Rhg1 haplotypes group into structural classes based on the type of α-SNAP polymorphisms that they encode, which also correlates with the copy-number of Rhg1 repeats that are present across hundreds of soybean accessions (Cook et al., 2014, Plant Physiol 165, 630-647; Lee et al., 2015).). Rhg1 HC  (high copy) loci carry four or more and frequently nine or ten Rhg1 repeats, and Rhg1 LC  (low-copy) loci carry three or fewer Rhg1 repeats. Rhg1 LC  is also known as rhg1-a and Rhg HC  is also known as rhg1-b (Mitchum 2016 and Liu 2017 Nat. Commun. 8, 14822). Rhg1 HC  and Rhg1 LC  encode similar yet distinct α-SNAP variants that are impaired in normal α-SNAP/NSF interactions (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). All Rhg1 HC  loci examined to date also have one Rhg1 repeat that encodes a wildtype (WT) α-SNAP along with multiple repeats encoding a resistance-type α-SNAP, while Rhg1 LC  loci encode only resistance-type α-SNAPs and no WT α-SNAP (Cook et al., 2012, Science 338, 1206-1209; Cook et al., 2014, Plant Physiol 165, 630-647; Lee et al., 2015). Plants carrying Rhg1 HC  or Rhg1 LC  loci exhibit elevated transcript abundance that correlates approximately with copy number for the repeat genes, including the Rhg1 α-SNAP gene, and variants thereof (U.S. Patent Application Publ. No. 2013-0305410 A1; Cook et al., 2012, Science 338, 1206-1209; Cook et al., 2014, Plant Physiol 165, 630-647). 
     In experiments performed in  N. benthamiana  leaves, high expression of these resistance-conferring α-SNAPs hindered vesicular trafficking and eventually elicited cell death, but co-expression of wild type soybean α-SNAPs diminished this cytotoxicity (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). 
     Therefore, there is a need in the art for methods and compositions that enable the generation and propagation of SCN-resistant plant cells that harbor Rhg1 resistance-associated genes, including Rhg1 resistance-associated α-SNAPs. 
     SUMMARY OF THE INVENTION 
     The present disclosure provides methods for producing plant cells resistant to nematodes. The disclosure further provides methods for improving the growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance. The present disclosure also provides compositions for producing plant cells resistant to nematodes, or for improving the growth or survival of a plant cell containing one or more Rhg1 genes conferring nematode resistance. In further aspects, the disclosure provides plant cells and plants with increased resistance to nematodes, without or preferably with improved growth or survival. 
     In some embodiments, the disclosure provides methods and compositions for producing plant cells resistant to nematodes, or for improving the growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance, comprising increasing expression of, altering an expression pattern of, altering a polynucleotide sequence of, altering abundance or localization of a polypeptide product of, or increasing copy number of, one or more polynucleotides encoding α-SNAP proteins, or homologs or variants thereof, and/or one or more polynucleotides encoding NSF proteins, or homologs or variants thereof, wherein said plant cells are resistant to nematodes relative to native plant cells. 
     In certain embodiments, the disclosure provides methods of producing plant cells resistant to nematodes, or for improving the growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance, comprising increasing expression of, altering an expression pattern of, altering a polynucleotide sequence of, altering abundance or localization of a polypeptide product of, or increasing copy number of a polynucleotide encoding one or more α-SNAP proteins with at least 95% identity to a polynucleotide identified by SEQ ID NOs: 5 or 6, or an encoded polypeptide with at least 95% identity to a polypeptide identified by SEQ ID NOs: 14 or 15, or homologs or variants thereof. 
     In further embodiments, the disclosure provides methods of producing plant cells resistant to nematodes, or for improving the growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance, comprising increasing expression of, altering an expression pattern of, altering a polynucleotide sequence of, altering abundance or localization of a polypeptide product of, or increasing copy number of a polynucleotide encoding and a polynucleotide encoding one or more NSF proteins with at least 95% identity to a polynucleotide identified by SEQ ID NOS: 8 or 9, or an encoded polypeptide with at least 95% identity to a polypeptide identified by SEQ ID NOs 17 or 18, or homologs or variants thereof. 
     In still further embodiments, the disclosure provides methods of producing plant cells resistant to nematodes, or for improving the growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance, comprising increasing expression of, altering an expression pattern of, altering a polynucleotide sequence of, altering abundance or localization of a polypeptide product of, or increasing copy number of both (a) a polynucleotide encoding one or more α-SNAP proteins encoded by a polynucleotide with at least 95% identity to SEQ ID NO: 5 or SEQ ID NO: 6, and (b) a polynucleotide encoding one or more NSF proteins encoded by a polynucleotide with at least 95% identity to SEQ ID NO: 9, or homologs or functionally conserved variants of any of the aforementioned SEQ ID NOs. 
     In embodiments, the methods of the disclosure produce plant cells or plants resistant to nematodes. In certain embodiments, the plant cells or plants provided herein are soybean, sugar beets, potatoes, corn, wheat, pea or beans or those plants listed in Tables 6 and 7. 
     In embodiments, the methods of the disclosure comprise increasing expression of, altering an expression pattern of, altering a polynucleotide sequence of, altering abundance or localization of a polypeptide product of, or increasing copy number of a polynucleotide cells in the root of the plant. In some embodiments, the one or more polynucleotides encoding α-SNAP proteins or NSF proteins, or homologs or variants thereof, is increased by incorporation of a construct comprising a promoter operably linked to one or more of said polynucleotides in the plant cells. In embodiments, the disclosure provides a method of increasing nematode resistance in a plant, wherein at least two of the polynucleotides recited herein have increased expression, an altered expression pattern, or increased copy number. 
     In one aspect, the disclosure provides a method of altering the abundance of one or more α-SNAP proteins in a plant cell. In certain embodiments of the disclosed methods, an amount of an α-SNAP encoded by the sequence identified in SEQ ID NO: 2, or a polynucleotide with at least 95% identity thereof, is reduced relative to an amount of an α-SNAP encoded by either of the sequences identified in SEQ ID NO: 5 and SEQ ID NO: 6, or polynucleotides with at least 95% 75% identity, or homologs or functionally conserved variants of the SEQ ID NO: 2, SEQ ID NO: 5, or SEQ ID NO: 6. 
     In a further aspect, this disclosure provides compositions for producing plant cells resistant to nematodes, or for improving the growth or survival of a plant cell containing one or more Rhg1 genes capable of conferring nematode resistance. In some embodiments, the disclosure provides constructs comprising a promoter operably linked to one or more polynucleotides encoding α-SNAP proteins, one or more polynucleotides encoding NSF proteins, or homologs or variants thereof. In further embodiments, the disclosure provides a construct comprising a polynucleotide with at least 95% identity to SEQ ID NO: 5 or SEQ ID NO: 6, and/or a polynucleotide with at least 95% identity to SEQ ID NO: 9, or homologs or functionally conserved variants of the SEQ ID NOs identified herein. In certain embodiments, a construct of the disclosure comprises a plant promoter. 
     In still another aspect, the disclosure provides a nematode resistant transgenic plant cell, or a transgenic plant cell containing one or more Rhg1 genes capable of conferring nematode resistance comprising with improved growth or survival. In embodiments, a transgenic plant cell of the disclosure comprises one or more polynucleotides encoding α-SNAP proteins, or one or more polynucleotides encoding NSF proteins, or homologs or variants thereof. In certain embodiments, a transgenic plant or plant cells of the disclosure comprises one or more α-SNAP proteins encoded by polynucleotides with at least 95% identity to the polynucleotides identified by SEQ ID NOS: 1-7, or polypeptides with at least 95% identity to polypeptides identified by SEQ ID NOs 10-16, or homologs or variants thereof. In further embodiments, a transgenic plant cell of the disclosure comprises one or more NSF proteins encoded by polynucleotides with at least 95% identity to the polynucleotides identified by SEQ ID NOS: 8 and 9, or comprise polypeptides with at least 95% identity to polypeptides identified by SEQ ID NOs 17 and 18, or homologs or variants thereof. 
     Embodiments of the disclosure also provide seeds comprising the transgenic plant cells described herein, plants grown from the seeds described herein, parts, progeny or asexual propagates of the transgenic plant cells disclosed herein. In some embodiments, the transgenic plant, plant cell or seed, or part, progeny or asexual propagate thereof of the disclosure are soybeans, sugar beets, potatoes, corn, wheat, peas or beans, or a wide variety of plant species as listed in Tables 6 and 7. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The following detailed description can be best understood when read in conjunction with the following drawings in which: 
         FIG. 1A  shows an immunoblot of wild-type α-SNAPs, Rhg1 resistance-type α-SNAPs and NSF in HG type test soybean roots. Rhg1 LC  varieties: PI 548402 (Peking), PI 89772, PI 437654, PI 90763; Rhg1 HC  varieties: PI 88788, PI 209332, PI 548316 (7 copy). PonceauS staining shows total protein loaded per lane.  FIG. 1B  illustrates densitometry indicating total NSF expression in HG type test lines.  FIG. 1C , shows immunoblots from trifoliate leaves or roots of Williams 82 (Wm82) and modern Rhg1 LC  and Rhg1 HC  varieties Forrest and Fayette (labeling as described for  FIG. 1A ).  FIG. 1D  shows immunoblots for total WT α-SNAPs and α-SNAP Rhg1 LC in “Forrest” (Rhg1 LC ) transgenic roots transformed with an empty vector (EV) or the native Williams 82 α-SNAP Rhg1 WT locus, or in Williams 82 roots transformed with empty vector. 
         FIG. 2A  is an alignment of soybean NSF Ch07 , NSF Ch13 , and NSF RAN07  N-terminal domains (SEQ ID NOs:20, 22, and 21, respectively). Large identical regions are omitted. N-domain residues that bind α-SNAP are shaded dark grey (N 21 , RR 82-83 , KK 117-118 ). NSF RAN07  polymorphisms R 4 Q, N 21 Y, S 25 N,  116 F, M 181 I are shaded light grey.  FIG. 2B  shows NSF RAN07  modeled to NSF CHO  cryo-EM structure (3J97A, State II). NSF residue patches implicated in α-SNAP binding are labeled I, II or III, respectively.  FIG. 2C  shows NSF RAN07  polymorphisms (N 21 Y), with zoomed in view of polymorphic N-domain region.  FIG. 2D  shows that NSF N-domain R 4  is conserved in most model eukaryotes. Frequency logo of first 10 NSF N-domain residues of the following organisms:  Homo sapiens, Bos taurus, Mus musculus, Cricetulus griseus  (Chinese hamster),  Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Xenopus laevis, Gallus gallus, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharyomyces pombe, Chlamydomonas reinhardtii, Physcomitrella patens, Zea mays, Oryza sativa, Solanum tuberosum, Cucumis sativa, Arabidopsis thaliana, Medicago truncatula, Nicotiana benthamiana , and  Glycine max.    
         FIG. 3A  is a ribbon diagram showing cryo-EM structure of mammalian 20S supercomplex, masked to show only SNARE bundle (right, “SNARE complex”), one α-SNAP (middle, “α-SNAP”) and two NSF N-domains (left and middle behind, “NSF N-Domain”). Conserved NSF N-domain patches (I, R10; II, RK67-68; III, KK104-105) and α-SNAP C-terminal contacts (D217DEED290-293) are shown extending from the ribbon depiction (see also, FIG.  3 B).  FIG. 3B  is a ribbon diagram showing NSF RAN07  polymorphisms; RAN07 residues are labeled (shown black), and arrows point out the α-SNAP interacting residues (light grey).  FIG. 3C  is a photograph of silver-stained SDS/PAGE of recombinant NSF Ch07  or NSF RAN07  bound in vitro by the recombinant proteins indicated on second line: no-α-SNAP control (No) or wild-type (WT), low-copy (LC), or high copy (HC) Rhg1 α-SNAP. BSA: bovine serum albumin.  FIG. 3D  shows densitometric quantification of NSF Ch07  or NSF RAN07  bound by Rhg1 α-SNAPs in  FIG. 3C ; data are from three independent experiments and error bars show SEM. 
         FIG. 4A  is a photograph of  N. benthamiana  leaves ˜6 days post agro-infiltration with 9:1 or 14:1 mixed cultures of α-SNAP Rhg1  LC and NSF Ch07  or NSF Ch13  or NSF RAN07  or empty vector (nine or fourteen parts  Agrobacterium tumefaciens  that delivers α-SNAP Rhg1 LC to one part  Agrobacterium  that delivers soybean NSF or empty vector control).  FIG. 4B , same as in  FIG. 4A , but 7:1 or 11:1 mixed cultures of α-SNAP Rhg1  LC co-expressed with NSF N.benth  or NSF Ch13  or NSF RAN07  or empty vector.  FIG. 4C  is a photograph of silver-stained SDS/PAGE of recombinant NSF N.benth  bound in vitro by recombinant wild-type, low-copy (LC), or high copy (HC) Rhg1 α-SNAP proteins or WT α-SNAP lacking the final 10 C-terminal residues (α-SNAP1-279). BSA, bovine serum albumin.  FIG. 4D , same as in  FIG. 4A  and  FIG. 4B , but 4:1 or 9:1 mixed cultures of α-SNAP Rhg1 LC or α-SNAP Rhg1 LC-1289A co-expressed with NSF Ch07  or NSF RAN07 . 
         FIG. 5A  shows frequency of SoySNP50K SNP ss715597431 (corresponding to NSF RAN07  R 4 Q) in all 19,645 SoySNP50K-genotyped  Glycine max  accessions.  FIG. 5B  shows frequency of ss715597431 in all USDA  G. max  with Rhg1 LC  or Rhg1 HC  haplotype signatures or in remainder of SoySNP50K-genotyped  G. max  from USDA collection.  FIG. 5C  and  FIG. 5D  show SNP mapping of the NSF RAN07  candidate gene interval for low copy Rhg1 and high copy Rhg1 respectively, indicating relative SNP frequencies. HG type and SoyNAM populations used for SNP mapping. 
         FIG. 6A  is an anti-HA immunoblot of  N. benthamiana  leaves agroinfiltrated to express empty vector, N-HA-α-SNAP Ch11  or N-HA-α-SNAP Ch11 -IR (intron-retention). PonceauS staining indicates relative total protein levels.  FIG. 6B  illustrates modeling of α-SNAP Ch11 -IR to sec17 crystal structure (yeast α-SNAP, PDB ID 1QQE) suggests early termination of alpha-helix 12.  FIG. 6C  shows immunoblots for total WT α-SNAP and α-SNAP Rhg1 LC levels in Forrest (Rhg1 LC ) transgenic roots transformed with an empty vector (EV) or the native WT α-SNAP Ch11  locus from Williams 82.  FIG. 6D , as described in  FIG. 5A , except frequency of SoySNP50K SNP ss715610416 allele that is closest marker for α-SNAP Ch11 -IR, in all 19,645 USDA accessions.  FIG. 6E  illustrates the frequency of ss715610416 in all USDA  Glycine max  with Rhg1 LC  or Rhg1 HC  haplotype signatures vs. remainder of SoySNP50K-genotyped USDA collection. 
         FIG. 7A  shows immunoblot of wild-type α-SNAPs and NSF expression in HG type test soybean roots. Rhg1 LC  varieties: PI 548402 (Peking), PI 89772, PI 437654, PI 90763; Rhg1 HC  varieties: PI 88788, PI 209332, PI 548316 (7 copy). PonceauS staining shows total protein loaded per lane.  FIG. 7B  shows densitometry data on the ratio of WT α-SNAPs to Rhg1 resistance type α-SNAPs. Ratios calculated using Image J densitometry as in  FIG. 1B .  FIG. 7C  is an agarose gel showing PCR amplicons generated with RAN07 or NSF Ch 07 WT specific primers on HG type soybeans and soybean genome reference variety Williams82 (Wm82). Rhg1 LC  varieties: “Forrest” (PI 548402-derived), PI 89772, PI 437654, PI 90763; Rhg1 HC  varieties: PI 88788, PI 209332, PI 548316 (7 copy). 
         FIG. 8A  and  FIG. 8B  show NSF RAN07  (SEQ ID NO:18) amino acid alignment with NSF Ch07  of soybean reference genome Williams82 (SEQ ID NO:17). N-domain amino acid polymorphisms unique to RAN07 are indicated by boldface in the corresponding residues in Wm82 NSFCh07. 
         FIG. 9A  shows NSF RAN07  modeled to an NSF CHO  cryo-EM structure (as described in  FIG. 2A ), but rotated 90° on the X-axis. NSF residue patches implicated in α-SNAP binding are indicated.  FIG. 9B  shows that NSF N-domain R 4  is conserved in most model eukaryotes. Frequency logo of first 10 NSF N-domain residues of the following organisms:  Homo sapiens, Bos taurus, Mus musculus, Cricetulus griseus  (Chinese hamster),  Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Xenopus laevis, Gallus gallus, Neurospora crassa, Saccharomyces cerevisiae, Schizosaccharyomyces pombe, Chlamydomonas reinhardtii, Physcomitrella patens, Zea mays, Oryza sativa, Solanum tuberosum, Cucumis sativa, Arabidopsis thaliana, Medicago truncatula, Nicotiana benthamiana , and  Glycine max .  FIG. 9C  is an alignment of NSF N-domain using available plant NSF amino acid sequences from Phytozome.org (SEQ ID NOs:23-52). The alignment was generated with Jalview starting at a conserved methionine residue corresponding to RAN07 met 17. Residues polymorphic in RAN07 are outlined with a box with the corresponding position labeled above. 
         FIG. 10A  shows cryo-EM structure of mammalian 20S supercomplex showing SNARE bundle similar to that of  FIG. 4A .  FIG. 10B  depicts that same as  FIG. 10A  but rotated 90° on Y-axis.  FIG. 10C  is the same as  FIG. 3C , except the recombinant NSF Ch07  or NSF RAN07  is bound in vitro by no-α-SNAP control (No) or wild-type (WT), low-copy (LC), or high copy (HC) Rhg1 α-SNAP, or WT α-SNAP truncated at final 10 residues (WT1-279). BSA: bovine serum albumin. 
         FIG. 11A  shows  N. benthamiana  leaves −6 days post agro-infiltration with 1:4 or 4:1 mixed cultures of α-SNAP Rhg1 LC and NSF Ch07  or NSF RAN07  or α-SNAP Rhg1 WT or empty vector (one or three parts  Agrobacterium  that delivers α-SNAP Rhg1 LC to one part  Agrobacterium  that delivers soybean NSF, or α-SNAP Rhg1WT  or empty vector control) as in  FIG. 4A .  FIG. 11B  shows  N. benthamiana  leaves like those shown in  FIG. 4A , but with a 9:1 or 19:1 mixed culture of α-SNAP Rhg1 LC co-expressed with NSF Ch07  or NSF RAN07  or empty vector.  FIG. 11C  shows  N. benthamiana  leaves as shown in  FIG. 4A , but using α-SNAP Rhg1HC  instead of α-SNAP Rhg1 LC in the corresponding mixture cultures of NSF Ch07  or NSF RAN07  or empty vector. 
         FIG. 11D  depicts  N. benthamiana  leaves −6 days post agro-infiltration with 1:9 mixed cultures of NSF Ch07  or NSF RAN07  or NSF Ch13  or NSF Nbenth  to empty vector (9 parts empty vector cultures to 1part NSF expressing  Agrobacterium  culture).  FIG. 11E  shows  N. benthamiana  leaves similar to those shown in  FIG. 4A , but with a 11:1 mixed culture of α-SNAP Rhg1LC  or α-SNAPRhg1Lc1-2soα-SNAP Rhg1LC1-280  (lacks the final 10 C-terminal residues) co-expressed with NSF Ch07  or NSF RAN07  or empty vector. 
         FIG. 12A  and  FIG. 12B  show an amino acid alignment with NSF  N. benthamiana  (SEQ ID NO:53) and NSF Ch07  (SEQ ID NO:18) of soybean reference genome Williams82. NSF N-domain residues are conserved in α-SNAP binding and are shown in boldface. 
         FIG. 13A  (SEQ ID NOs:54-88) and  FIG. 13B  (SEQ ID NOs:89-123) show an alignment of NSF N-domain starting from position 1 and depicts general conservation of R4. The alignment was generated with Jalview and includes all reliable Angiosperm NSF sequences available from Phytozome.org. 
         FIG. 14  is an immunoblot showing expression results for α-SNAP Rhg1 LC in independent soybean lines transformed with genes encoding α-SNAP Rhg1 LC and either wild-type NSF Ch07  or NSF RAN07 . Only one transformed plant was obtained for the α-SNAP Rhg1 LC+wild-type NSF Ch07  DNA construct and that plant did not actually express α-SNAP Rhg1 LC protein. 
     
    
    
     DETAILED DESCRIPTION 
     All publications, patents and patent applications cited herein are hereby expressly incorporated by reference for all purposes. 
     Before describing the disclosed methods and compositions in detail, a number of terms will be defined. As used herein, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly dictates otherwise. 
     It is noted that terms like “preferably,” “commonly,” and “typically” are not utilized herein to limit the scope of the claimed invention or to imply that certain features are critical, essential, or even important to the structure or function of the claimed invention. Rather, these terms are merely intended to highlight alternative or additional features that can or cannot be utilized in a particular embodiment of this invention. 
     For the purposes of describing and defining this invention it is noted that the term “substantially” is utilized herein to represent the inherent degree of uncertainty that can be attributed to any quantitative comparison, value, measurement, or other representation. The term “substantially” is also utilized herein to represent the degree by which a quantitative representation can vary from a stated reference without resulting in a change in the basic function of the subject matter at issue. 
     In addition to the methods that are more specifically described herein and/or described by reference to literature citations, methods well known to those skilled in the art (e.g., Ausubel, F., et al. (Eds.),  Current Protocols in Molecular Biology,  2017; Acquaah, G. (Ed.),  Principles of Plant Genetics and Breeding,  2 nd  Edition 2012) can be used to carry out many of the manipulations disclosed herein. 
     As used herein, a “plant” includes any portion of the plant, including but not limited to, a whole plant, a portion of a plant such as a part of a root, leaf, stem, seed, pod, flower, cell, tissue or plant germplasm or any progeny thereof. 
     As used herein, soybean refers to whole soybean plant or portions thereof including, but not limited to, soybean plant cells, soybean plant protoplasts, soybean plant tissue culture cells or calli. 
     As used herein, a plant cell refers to cells harvested or derived from any portion of the plant or plant tissue, germplasm, cultured cells or calli. 
     As used herein “substantially equivalent” in terms of amino acid modification is intended to mean an amino acid that imparts, confers, or results in the substantially same function as the substituted amino acid. 
     As used herein, “germplasm” refers to genetic material from an individual or group of individuals or a clone derived from a line, cultivar, variety or culture, and the cells or tissues containing said genetic material. In the plural sense, “germ plasm” refers to collections of multiple lines, cultivars, varieties or cultures. 
     As used herein, “native polynucleotide” or “native polypeptide” refer to an endogenous polynucleotide or polypeptide in a naturally occurring chromosomal context. In contrast, an “exogenous” or “ectopic” polynucleotide or polypeptide refers to expression of a transgenic gene, or expression controlled by a non-native chromosomal context (e.g., by introduction of non-native promoters or enhancer elements). 
     As used herein, “nematode” is intended to mean any roundworm or unsegmented worm belonging to the phylum Nematoda 
     As used herein, “enhanced resistance” is intended to mean increased resistance to nematodes compared to native plants of the same species. 
     As used herein, “altering the expression pattern of” a gene or polypeptide comprises increasing its expression, decreasing its expression, or altering the location of its expression. As used herein, increasing, decreasing, or altering expression of a gene or polypeptide can be at the nucleotide or polypeptide level, and can comprise alterations in native or exogenous polynucleotide or polypeptide. Altering the location of expression of a gene product or polypeptide means altering the location or relative abundance in different parts of a plant. Alternatively, in some embodiments described herein, altering the location of expression means altering the sub-cellular localization of expression in a cell. 
     As used herein, “modification” as it refers to an amino acid, polypeptide and/or nucleotide is intended mean for example missense mutation, nonsense mutation, insertion, deletion, duplication, frameshift mutation and repeat expansion. 
     The Rhg1 locus is a chromosomal region identified as a region important for resistance to SCN. When used in reference to a protein, the term Rhg1 typically is not italicized, and refers to the protein products of one or more genes that are located at the Rhg1 locus. As used herein, a locus is a chromosomal region where one or more trait determinants, genes, polymorphic nucleic acids, or markers are located. A quantitative trait locus (QTL) refers to a polymorphic genetic locus where one or more underlying genes controls a trait that is quantitatively measured and contains at least two alleles that differentially affect expression of a phenotype or genotype in at least one genetic background, with said locus accounting for part but not all the observed variation in the overall phenotypic trait that is being assessed. A genetic marker is a nucleotide sequence or amino acid sequence that can be used to identify a genetically linked locus, such as a QTL. Examples of genetic markers include, but are not limited to, single nucleotide polymorphisms (SNP), simple sequence repeats (SSR; or microsatellite), a restriction enzyme recognition site change, genomic copy number of specific genes or target sequences or other sequence-based differences between a susceptible and resistant plant. 
     A “linked” genetic locus describes a situation in which a genetic marker and a trait are closely linked chromosomally such that the genetic marker and the trait do not independently segregate and recombination between the genetic marker and the trait does not occur during meiosis with a readily detectable frequency. The genetic marker and the trait can segregate independently, but generally do not. For example, a genetic marker for a trait can only segregate independently from the trait 5% of the time; suitably only 5%, 4%, 3%, 2%, 1%, 0.75%, 0.5%, 0.25%, or less of the time. Genetic markers with closer linkage to the trait-producing locus will serve as better markers because they segregate independently from the trait less often because the genetic marker is more closely linked to the trait. Genetic markers that directly detect polymorphic nucleotide sites that cause variation in the trait of interest are particularly useful for their accuracy in marker-assisted plant breeding. Thus, the methods of screening provided herein can be used in traditional breeding, recombinant biology or transgenic breeding programs or any hybrid thereof to select or screen for resistant varieties. 
     A linked locus can also describe two loci that do not reside close to each other on a chromosome, and therefore are not physically linked, but exhibit lack of independent segregation (i.e. they co-segregate). In the formal genetic sense, such a pair of co-segregating loci exhibit genetic linkage. As used herein, the terms “linked locus” and “co-segregating locus” are used interchangeably, and thus refer to physical linkage (on the same chromosome) or genetic linkage (either on the same chromosome or co-segregating on different chromosomes). A gene or locus is “associated” with another gene or locus when they are linked or co-segregate with one another. For example, a gene, allele, or locus is “associated” with Rhg1 if it co-segregates or is physically linked to the Rhg1 locus. 
     As used herein, Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 refer to the soybean genomic nomenclature describing those genes, the proteins or polypeptides they encode, and include any polynucleotide or polypeptide variants, naturally occurring or otherwise, and any homologues or conserved portions in other plant species. In some embodiments, Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 refer to the genes or polypeptides, and any polynucleotide or polypeptide variants, naturally occurring or otherwise, in plants of the genus Glycine, and encompass any homologues or conserved portions in other plant species. The 13-character gene names are from the Wm82.a1 genome assembly and Glyma 1.0 gene models (Schmutz et al., 2010) and the more recent 15-character gene names are from the U.S. Department of Energy Joint Genome Institute Wm82.a2 soybean genome assembly and Glyma 2.0 gene model naming revision. 
     The present disclosure provides methods and compositions for increasing resistance of a plant or plant cells to cyst nematodes. In some embodiments, the disclosure provides methods and compositions for generating transgenic plant materials, including transgenic cells and plants. In additional embodiments, the disclosure provides compositions comprising nucleotide constructs useful for generating transgenic cells and plants resistant to nematodes. In still further embodiments, the disclosure provides nucleotide constructs encoding Rhg1 resistance-type polypeptides, or homologs or variants thereof. In certain embodiments, Rhg1 resistance-type α-SNAPs are provided. In further embodiments, the disclosure provides Rhg1 resistance-type α-SNAPs encoded by SEQ ID NO: 5 or SEQ ID NO: 6, or homologs or variants thereof. 
     In some embodiments, the disclosure provides alleles associated with the Rhg1 locus due to lack of independent segregation from the locus. In certain embodiments, the disclosure provides alleles that co-segregate with Rhg1 genes despite residing on a different chromosome (i.e., despite lack of physical linkage on the same chromosome). In one aspect, alleles associated with the Rhg1 locus comprise genes that improve the growth, reproduction and/or SCN resistance of plant cells, plants, or germplasm, that carry Rhg1 SCN resistance-conferring alleles. In certain embodiments, the disclosure provides alleles of an NSF gene, wherein the alleles of an NSF gene are associated with Rhg1. In some embodiments, the disclosure provides alleles of an NSF gene, wherein the alleles of an NSF gene are associated with improved growth, or completion of the life cycle, of plants that carry SCN resistance-conferring alleles of the Rhg1 locus. In particular embodiments, the NSF gene of the disclosure is Glyma.07G195900, or variants thereof. In an exemplary embodiment, the disclosure provides alleles of NSF associated with Rhg1 encoded by SEQ ID NO: 8, a protein corresponding to SEQ ID NO: 17, or homologs or variants thereof. In other exemplary embodiments, the disclosure provides alleles of NSF encoded by SEQ ID NO: 9, a protein corresponding to SEQ ID NO: 18, or homologs or variants thereof. 
     Also provided are Rhg1 genes that contribute to SCN resistance (SEQ ID NOS: 1-7) and the proteins they encode (SEQ ID NOs 10-16) located within a tandem repeat present in the genomes of soybeans exhibiting resistance to cyst nematodes, including, but not limited to, P188788, Peking, Hartwig, Fayette, and Forrest. Embodiments of the Rhg1 genes that contribute to SCN resistance of the present disclosure are as described in U.S. patent application Ser. No. 13/843,447, and also as described in Cook, D. E., et al. 2012, Science 338:1206-1209, and the associated Supporting Online Material, which are incorporated herein by reference in their entirety. 
     In certain embodiments, the Rhg1 genes that contribute to SCN are located on a tandemly repeated segment of chromosome 18 in resistant soybeans, and silencing of one or more of three genes in the segment leads to increased susceptibility to SCN in an otherwise resistant variety. In certain embodiments, the tandemly repeated segment comprises four genes, along with part of a fifth gene, and other DNA sequences in a chromosome segment that in some described soybean accessions (Cook et al., 2012, Science 338, 1206-1209) is approximately 31 kb in length. The tandemly repeated Rhg1 chromosome segment is found in at least two copies in the SCN-resistant varieties that have been characterized to have SCN resistance due in part to the Rhg1 locus. Various resistant varieties carry three, seven or ten copies, or other numbers of copies. In the published examples the higher copy number versions of Rhg1 express higher levels of transcripts for the three genes. Higher copy number versions of Rhg1 also confer more resistance to SCN on their own (exhibit less reliance on the simultaneous presence of desirable alleles of other SCN resistance QTL such as Rhg4 in order to effectively confer resistance to HG Type 0 SCN populations), relative to Rhg1 haplotypes with lower Rhg1 repeat copy numbers. 
     In certain aspects, the disclosure provides transgenic plants or transgenic plant cells with increased resistance to cyst nematodes, particularly SCN, carrying one or a plurality of transgenes encoding a non-native or exogenous Rhg1 derived, or Rhg1 associated, polynucleotide encoding one or more of the polynucleotides of SEQ ID NOs:1-9 or the polypeptides of SEQ ID NOs:10-18. Non-transgenic plants carrying these polypeptides, or bred or otherwise engineered to express increased levels of these polypeptides or the polynucleotides encoding these polypeptides, are also provided. 
     In some aspects, the disclosure provides methods and compositions for increasing resistance of a plant or plant cell to cyst nematodes, including but not limited to SCN, by increasing expression of, or altering an expression pattern of, or increasing copy number of one or more Rhg1 genes corresponding to the  Glycine max  genes designated Glyma.18G022700 (SEQ ID NO:3), Glyma.18G022500 (SEQ ID NO: 2), variants of Glyma.18G022500 (SEQ ID NO:5 or SEQ ID NO:6), and/or Glyma.18G022400 (SEQ ID NO: 1), polypeptides or functional fragments or variants thereof in cells of the plant are also provided. In another aspect, the disclosure provides methods and compositions for producing a plant or plant cell with increased resistance to cyst nematodes, including but not limited to SCN, by increasing expression of, or altering an expression pattern of, or increasing copy number of one or more Rhg1 associated genes corresponding to Glyma.07G195900 (SEQ ID NO: 8 or SEQ ID NO: 9). In embodiments, the methods and compositions of the disclosure further comprise increasing the expression of, or altering the expression pattern of, or increasing the copy number of, a polynucleotide encoding an NSF allele or a polypeptide product of said allele, in combination with one or more of the Rhg1, or Rhg1 associated, genes above. The polynucleotides of the disclosure can be 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the sequences provided. 
     In another aspect, the disclosure provides methods and compositions for increasing plant growth, seed production, or completion of the life cycle of plants in which resistance to SCN has been manipulated by increasing expression of, or altering an expression pattern of, or increasing copy number of Rhg1 genes. In certain embodiments, methods for increasing plant growth, seed production or completion of the life cycle of plants in which resistance to SCN has been manipulated comprise increasing expression of, altering expression pattern of, or increasing copy number of one or more polynucleotides encoding an NSF protein. In some embodiments, methods for increasing plant growth, seed production or completion of the life cycle of plants in which resistance to SCN has been manipulated comprise increasing expression of, altering an expression pattern of, or increasing copy number of a polynucleotide corresponding to Glyma.07G195900. In particular embodiments of the disclosure, a polynucleotide corresponding to Glyma.07G195900 comprises a polynucleotide identified in SEQ ID NO: 8 or SEQ ID NO: 9, polypeptides or functional fragments or variants thereof. The polynucleotide can be 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the sequences provided. In embodiments, the methods and compositions of the disclosure further comprise increasing the expression of, or altering the expression pattern of, or increasing the copy number of, a polynucleotide encoding an NSF allele or a polypeptide product of said allele, in combination with one or more of the Rhg1, or Rhg1 associated, genes above. 
     In still another aspect, the disclosure provides methods and compositions for increasing plant growth, seed production or completion of the life cycle of plants that contain Rhg1 alleles that contribute to SCN resistance by increasing expression of, or altering an expression pattern of, or increasing copy number of genes associated with, or linked with, Rhg1 genes that contribute to SCN resistance. In certain embodiments, the disclosure provides methods of increasing expression of, or altering an expression pattern of, or increasing copy number of a gene or protein corresponding to the  Glycine max  gene designated Glyma.07G195900. In still further embodiments, the disclosure provides methods and compositions for increasing plant growth, seed production, or completion of the life cycle of plants that contain Rhg1 alleles that contribute to SCN resistance, by increasing expression of, or altering an expression pattern of, or increasing copy number of one or more polynucleotides identified by SEQ ID NO: 8 or SEQ ID NO:9, a polypeptide sequence identified by SEQ ID NO: 17 or SEQ ID NO:18, or homologues, or variants thereof. 
     In certain embodiments, the disclosure provides transgenic plants or transgenic plant cells comprising one or more polynucleotides encoding an α-SNAP protein variant. In particular embodiments, the α-SNAP protein variant or variants confer reduced or substantially disrupted cellular vesicular trafficking in cells. In some embodiments, the α-SNAP protein variant or variants exhibit disrupted disassembly and reuse of the four-protein bundles of SNARE proteins that form when t-SNARE and v-SNARE proteins anneal during vesicle docking to target membranes. 
     Certain embodiments of the disclosure provide an α-SNAP protein variant corresponding to the gene designated Glyma.18G022500. In some embodiments, an α-SNAP protein variant of the disclosure corresponds to the Glyma.18G022500 from Fayette or Peking soybean lines. In particular embodiments, the α-SNAP protein variant (or variants) of the disclosure are encoded by polynucleotides identified by SEQ ID NO:5 or SEQ ID NO:6, polypeptides identified by SEQ ID NO: 14 or SEQ ID NO: 15, or functional fragments or variants thereof. 
     In some embodiments, the α-SNAPs of the disclosure exhibit reduced or substantially disrupted binding to wild-type NSF and to SNARE/NSF complexes. For example, in certain embodiments, the α-SNAPs of the present disclosure harbor point mutations, substitutions, deletions, or other mutagenic sequence variants. In particular embodiments, the point mutations, substitutions, deletions, or other mutagenic sequence variants of the α-SNAPs disclosed herein are localized to the C-terminus of the protein. In specific particular embodiments, the α-SNAPs of the present disclosure comprise a soybean α-SNAP sequence with one or more variant C-terminal residues in the polypeptide sequence at conserved residues Q 203 , D 208 , DEED 243-246  (SEQ ID NO:124), or EEDD 284-287  (SEQ ID NO:125). In other embodiments, the α-SNAPs of the present disclosure comprises one or more variant c-terminal residues in the polypeptide sequence at conserved residues in rat α-SNAP at D 217 , E 249 , EE 252 -253, or DEED 290-293  (SEQ ID NO:126). 
     In some embodiments, the α-SNAP proteins are modified by amino acids modification at positions corresponding to positions 203, 208, 284, 285, 286, and 287 by α-SNAP numbering as set forth in SEQ ID NOS: 11, 14, or 15. Positions 203 208, 284, 285, 286, and 287 correspond to the C-terminal of the Rhg1 haplotype. In one aspect modifications present in the low copy (LC) of Glyma.18G022500 is critical to nematode resistance. The modifications D208E and expression of EEDD 284-287  (SEQ ID NO:125), confer enhanced resistance of the soybean against the nematode. 
     In another embodiment, the modified polynucleotides encode a modified α-SNAP polypeptide, wherein the modified α-SNAP polypeptide comprises: a replacement at position D286 that is D286F, or D286W, or D286Y; and a replacement at position D287 that is D287E or remains D287; and an insertion after position 287 that is (ins)288A, (ins)288G, (ins)2881, (ins)288L, (ins)288M, or (ins)288V; and a replacement at position L288 that is L288A, L288G, L2881, L2881, L288M, or L288V, or a functional equivalent amino acid to the WT amino acid expressed at position 285, 286, 287, or 288, each by α-SNAP numbering relative to the positions set for in SEQ ID NO: 11. 
     In yet other embodiments the encoded modified α-SNAP has one or more polynucleotides that encode a modified an α-SNAP polypeptide wherein the modified polypeptide comprises other amino acids in the same family. In one aspect D208E can be modified to any functional equivalent amino acid. In another aspect, any or both E284 and E285 can also be modified to E284D or E285D or any functionally equivalent amino acid. In yet another aspect, any or both of D286 and D287 can be also be modified to D286E or D287E or any functional equivalent amino acid. The numbering presented herein is relative to the positions in SEQ ID NO: 11. In some embodiments the encoded modified α-SNAP polypeptides comprises amino acid modifications selected from a combination of wild type amino acids or functional equivalent amino acid substitutions at positions 208, 284, 285, 286, and 287 or adjacent residues. The number presented herein is relative to the positions in SEQ ID. NO: 11. 
     In some embodiments, the NSF variants of the disclosure exhibit reduced or substantially disrupted binding to α-SNAP proteins. In certain embodiments, the NSF variants of the disclosure exhibit reduced or substantially disrupted binding to “wild-type” α-SNAP proteins, such as an α-SNAP protein encoded by Glyma.18G022500 haplotype of soybean accession Williams 82 (SEQ ID NO: 2), homologues, or functionally conserved variants thereof. For example, in certain embodiments, the NSF variants of the present disclosure harbor point mutations, substitutions, deletions, or other mutagenic sequence variants. In embodiments, the point mutations, substitutions, deletions, or other mutagenic sequence variants of NSF are localized to regions near the N-terminus of the protein. In particular embodiments, the NSF variants of the present disclosure comprise an NSF protein with one or more variant N-terminal residues at conserved residues corresponding to R 10  or RK 114-115  in the Chinese hamster NSF protein sequence. In some embodiments, the NSF of the present disclosure comprises a soybean NSF protein with one or both of an N 21 Y mutation or a A 116F  mutation in the soybean NSF protein sequence. The A 116F  notation refers to an insertion of an additional amino acid, in this case “F” or phenylalanine, as the one hundred sixteenth amino acid of the protein. 
     In some embodiments, the NSF variants of the disclosure exhibit enhanced or substantially improved binding to α-SNAP proteins associated with improved plant resistance to cyst nematodes. For example, in certain embodiments, the NSF variants of the present disclosure harbor point mutations, substitutions, deletions, or other mutagenic sequence variants that facilitate binding to, or functionally interacting with, a variant α-SNAP protein that is less capable of binding to a “wild-type” NSF protein. In embodiments, the point mutations, substitutions, deletions, or other mutagenic sequence variants of NSF that facilitate binding to, or functionally interacting with, a variant α-SNAP protein that is less capable of binding to a “wild-type” NSF protein, are localized to the regions near the N-terminus of the protein. In particular embodiments, the NSF variants of the present disclosure that facilitate binding to, or functionally interacting with, a variant α-SNAP protein that is less capable of binding to a “wild-type” NSF protein comprise an NSF protein with one or more variant N-terminal residues at conserved residues corresponding to R 10  or RK 114-115  in the Chinese hamster NSF protein sequence. In some embodiments, the NSF variants of the disclosure that facilitate binding to, or functionally interacting with, a variant α-SNAP protein that is less capable of binding to a “wild-type” NSF protein comprises a soybean NSF protein with one or both of an N 21 Y mutation or a  {circumflex over ( )}   116 F mutation in the soybean NSF protein sequence. 
     In some embodiments, the NSF proteins are modified by amino acid mutations at positions 4, 21, 25, 116, and 181 by NSF numbering as set for in SEQ ID NOS:17 or 18. The mutations enhance growth and viability of the plant versus plants that express the wild type NSF sequence as provided in SEQ ID NO: 17. The amino acid mutations at positions 4 and 21 enhance growth and viability of the plant. In some embodiments the encoded modified polypeptides comprises amino acid modifications selected from the modifications: R4N/N21F; R4N/N21W; R4N/N21Y; R4C/N21F; R4C/N21W; R4C/N21Y; R4Q/N21F; R4Q/N21W; R4Q/N21Y; R4S/N21F; R4S/N21W; R4S/N21Y; R4T/N21F; R4T/N21W; and R4T/N21Y, each with number relative to positions set forth in SEQ ID NOS: 17 or 18. 
     In yet another embodiment the encoded modified NSF has one or more polynucleotides alterations that encode a modified NSF protein wherein the modified polypeptide comprises other amino acids in the same family. In one aspect, R4 can be modified to amino acids N, C, Q, S or T or any functionally equivalent amino acid. In yet another aspect the amino acid at position 21 can be modified to F, W, or any functionally equivalent amino acid. In another, aspect S25 can be optionally modified to N or a functionally equivalent amino acid. In still another embodiment the optional gap at position 116 can be optionally modified to an F or functionally equivalent amino acid. In still another aspect, the M at 181 can be optional modified to an I or functionally equivalent amino acid. The numbering herein is relative to the positions in SEQ ID NO: 17. 
     In certain embodiments, expression of α-SNAP variants disclosed herein is substantially toxic, or lethal, or otherwise intolerable, to a plant or transgenic plant, or plant cell in which it is expressed, unless a complementary NSF protein is co-expressed. In certain embodiments, an α-SNAP protein with point mutations, substitutions, deletions, or other mutagenic sequence variants that are toxic to a transgenic plant or plant cell, is co-expressed with one or more NSF variants with point mutations, substitutions, deletions, or other mutagenic sequence variants. In particular embodiments, one or more α-SNAP proteins with C-terminal point mutations, substitutions, deletions, or other mutagenic sequence is co-expressed with one or more NSF proteins with point mutations, substitutions, deletions, or other mutagenic sequence. In embodiments, α-SNAP proteins with C-terminal point mutations, substitutions, deletions, or other mutagenic sequence is co-expressed with one or more NSF proteins with mutations localized to the regions near the N-terminus of the protein. In particular embodiments, the NSF variants of the present disclosure comprise an NSF protein with one or more variant N-terminal residues at conserved residues corresponding to R 10  or RK 114-115  in the Chinese hamster NSF protein sequence. In some embodiments, the NSF of the present disclosure comprises a soybean NSF protein with one or both of an N 21 Y mutation or a  {circumflex over ( )}   116 F mutation in the soybean NSF protein sequence. In other particular embodiments, the NSF of the present disclosure comprises a soybean NSF protein as identified in SEQ ID NO: 18 or encoded by a polynucleotide as identified in SEQ ID NO: 9, or homologues or functionally conserved variants thereof. 
     In certain embodiments, an NSF protein is expressed in a plant or plant cell containing the Rhg1 tandem repeat segment. In exemplary embodiments, NSF protein variants are expressed in a plant or plant cell containing the Rhg1 tandem repeat segment. In certain embodiments, the NSF variants expressed in a plant or plant cell containing the Rhg1 tandem repeat segment comprise an NSF protein with one or more variant N-terminal residues at conserved residues corresponding to R 10  or RK 114-115  in the Chinese hamster NSF protein sequence. In some embodiments, the NSF variant expressed in a plant or plant cell containing the Rhg1 tandem repeat segment comprises a soybean NSF protein with one or both of an R 4 Q mutation, an N 21 Y mutation, or a  {circumflex over ( )}   116 F mutation in the soybean NSF protein sequence. 
     In various embodiments disclosed herein, an NSF protein is expressed in plants or plant cells that also carry Rhg1He (high copy) loci carrying four or more, and frequently nine or ten, Rhg1 repeats. In other embodiments, an NSF protein is expressed in plants or plant cells that also carry Rhg1 LC  (low-copy) loci carrying three or fewer Rhg1 repeats. (Rhg1Lc is also known as rhg1-a and Rhg1He is also known as rhg1-b.) Rhg1 HC  and Rhg1 Lc  encode similar yet distinct α-SNAP variants that are impaired in normal α-SNAP-NSF interactions (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). 
     In further embodiments, the disclosure provides methods and compositions for producing plant cells with increased resistance to nematodes comprising reducing a level of a “wild-type” α-SNAP allele relative to a variant α-SNAP allele. In some embodiments, the level of an α-SNAP encoded by the sequence identified in SEQ ID NO: 2 is reduced relative to a variant α-SNAP encoded by either of the sequences identified in SEQ ID NO: 5 and SEQ ID NO: 6. 
     In alternative embodiments, a variant NSF protein capable of functionally complementing one or more variant α-SNAP genes is expressed in a plant cell that contains the one or more variant α-SNAP genes. In embodiments, the variant NSF protein capable of functionally complementing one or more variant α-SNAP genes improves the growth of a cell expressing the variant α-SNAP genes. In further embodiments, a variant NSF protein capable of functionally complementing one or more variant α-SNAP genes confers cyst nematode resistance on a cell expressing the variant α-SNAP genes. In certain embodiments, the one or more variant α-SNAP genes disclosed herein function analogously to α-SNAP alleles encoded by Rhg1 HC  or Rhg1 LC , and/or α-SNAP alleles similar to Rhg1 HC  or Rhg1 LC  that have been generated or introduced at other loci in the soybean genome. In still further embodiments, the one or more variant α-SNAP genes disclosed herein impact α-SNAP function in a manner similar to the αSNAPs encoded by Rhg1 HC  or Rhg1 LC  α-SNAP alleles. In yet further embodiments, the variant α-SNAP genes disclosed herein alter expression patterns relative to the wild-type α-SNAP protein encoded at the single-copy Rhg1 locus of soybean accession Williams 82. 
     In a certain aspect, the methods of the disclosure provide a breeding stock of a Rhg1 plant expressing an NSF variant. Also provided are methods of breeding a Rhg1 plant expressing one or more NSF variants. In addition, methods of growing or improving the lifecycle of a Rhg1 plant expressing one or more NSF variants are provided. 
     In other embodiments, the amino acids at the NSF and α-SNAP binding interface can be manipulated to enhance nematode resistance of plant species. In one aspect NSF amino acid residues 4, 21, 25, 116, 181 or adjacent residues with numbering relative to the NSF polypeptide set forth in SEQ ID NOS: 17 or 18 are mutated. 
     In another aspect residues 208, 284, 285, 286, 287, or adjacent residues of α-SNAP are mutated to impact the NSF/α-SNAP interface. The amino acid mutations at the binding interface of NSF/α-SNAP can enhance nematode resistance versus the wild type plant. 
     In another aspect, amino acids residing at the NSF/α-SNAP protein interaction interface can be mutated to achieve enhanced nematode resistance and plant viability and growth. For instance, NSF amino acid residues 4, 21, 25, 116, 181 or adjacent residues with numbering relative to the NSF polypeptide set forth in SEQ ID NOS: 17 or 18 interact with α-SNAP as designated in the NSF/α-SNAP/SNARE protein structure PDB ID code 3j97. Residues 208, 284, 285, 286, and 287 of α-SNAP or other α-SNAP residues that are at, or adjacent to residue at the NSF/α-SNAP 1 protein interaction interface with numbering relative to the NSF polypeptide set forth in SEQ ID NO: 11 can also be mutated to confer nematode resistance and plant cell growth viability. 
     In certain embodiments, the methods of the disclosure confer resistance to cyst nematode. Resistance (or susceptibility) to cyst nematode, including but not limited to SCN, can be measured in a variety of ways, several of which are known to those of skill in the art. In some embodiments of the disclosure, soybean roots are experimentally inoculated with SCN and the ability of the nematodes to mature (molt and proceed to developmental stages beyond the J2) on the roots is evaluated as compared to a susceptible and/or resistant control plant. A SCN greenhouse test is also described in U.S. Patent Application Publ. No. 2013-0305410 A1, which is incorporated herein in its entirety, and provides an indication of the number of cysts on a plant and is reported as the female index. Increased resistance to nematodes can also be manifested as a shift in the efficacy of resistance with respect to particular nematode populations or genotypes. Additionally, but not exclusively, SCN-susceptible soybeans grown on SCN-infested fields will have significantly decreased crop yield as compared to a comparable SCN-resistant soybean. Improvement of any of these metrics has utility even if all of the above metrics are not altered. 
     In certain embodiments, expression of one or more of the polynucleotides and polypeptides described in SEQ ID NOS: 1-18 is increased in a root of the plant. Suitably, expression of these polynucleotides and polypeptides is increased in root cells of the plant. The plant is suitably a soybean plant or portions thereof. In particular embodiments, these polynucleotides can also be transferred into other non-soybean plants, or homologs of these polypeptides or polynucleotides encoding these polypeptides from other plants, or synthetic genes encoding products similar to the polypeptides encoded or identified by SEQ ID NOS: 1-18 can be overexpressed in those plants. Example of such other plants include but are not limited to sugar beets, potatoes, corn, wheat, peas, and beans. Overexpression of these genes can increase resistance of plants from these other species to nematodes and in particular cyst nematodes, such as the soybean cyst nematode  Heterodera glycines , the sugar beet cyst nematode  Heterodera schacthii , the potato cyst nematodes  Globodera paflida  and related nematodes that cause similar disease on potato such as  Globodera rostochiensis , the cereal cyst nematode  Heterodera avenae , the corn cyst nematode  Heterodera zeae , and the pea cyst nematode  Heterodera goettingiana.    
     Expression of these polynucleotides in the various embodiments disclosed herein can be increased by increasing the copy number of these polynucleotide in the plant, in cells of the plant, suitably root cells, or by identifying plants in which this has already occurred. In some embodiments, the expression of these polynucleotides in the various embodiments can be increased using recombinant DNA technology, e.g., by using strong promoters to drive increased expression of one or more polynucleotides. 
     In some embodiments, expression of polynucleotides or polypeptides of the disclosure is reduced relative to the native amount. Reduction of a polynucleotide amount can be accomplished according to methods known in the art, such as reducing the mRNA level of a polynucleotide by interfering with promoter or enhancer function or modifying a promotor or enhancer. Alternatively, a polynucleotide amount can be reduced post-transcriptionally, such as by using antisense, morpholino, or small-interfering RNA, or by modifying the gene encoding the polynucleotide to reduce the stability of the mRNA or reduce or eliminate its translation. In embodiments, the amount of a protein is reduced, such as by peptide directed protein knockdown (e.g., as described in US Patent App. Publ. No. US 2015-0266935 A1), or other protein knock-down techniques known to the art (see, e.g., Bonger, K. M., et al. (2001) Nature Chemical Biology 7, 531-537; Banaszynski, L. A., et. al. (2006), Cell 126, 995-1004; Neklesa, T. K. et al. (2011) Nature Chemical Biology 7, 538-543.) 
     Expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can be increased in a variety of ways including several apparent to those of skill in the art and can include transgenic, non-transgenic and traditional breeding methodologies. For example, expression of the polypeptide encoded by Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 cancan be increased by introducing a construct including a promoter operational in the plant operably linked to a polynucleotide encoding the polypeptide into cells of the plant. Suitably, the cells are root cells. Alternatively, the expression of the polypeptide encoded by Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 cancan be increased by introducing a transgene including a promoter operational in the plant operably linked to a polynucleotide encoding the polypeptide into cells of the plant. The promoter can be a constitutive or inducible promoter capable of inducing expression of a polynucleotide in all or part of the plant, plant roots or plant root cells. In another embodiment, expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can be increased by increasing expression of the native polypeptide in a plant or in cells of the plant, such as the plant root cells. In another embodiment, expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can be increased by increasing expression of the native polypeptide in a plant or in cells of the plant such as the nematode feeding site, the syncytium, or cells adjacent to the syncytium. In another embodiment, expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can be increased by increasing expression of the native polypeptide in a plant or in cells of the plant such as sites of nematode contact with plant cells. In another embodiment, expression can be increased by increasing the copy number of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900. Other mechanisms for increasing expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can include, but are not limited to, increasing expression of a transcriptional activator, reducing expression of a transcriptional repressor, addition of an enhancer region capable of increasing expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900, increasing mRNA stability, altering DNA methylation, histone acetylation or other epigenetic or chromatin modifications in the vicinity of the relevant genes, altering protein or polypeptide subcellular localization, or increasing protein or polypeptide stability. 
     In addition, methods of increasing resistance of a plant to cyst nematodes can be achieved by cloning sequences upstream from Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 from resistant lines into susceptible lines. For these methods, nucleotide sequences having at least 60%, 70% or 80% identity to nucleotide sequences that flank the protein-coding regions of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 (or sequences having at least 75%, 80%, 85%, or 90% identity to those protein-coding regions), said flanking regions including 5′ and 3′ untranslated regions of the mRNA for these genes, and also including any other genomic DNA sequences that extend from the protein coding region of these genes to the protein coding regions of immediately adjacent genes can be used. 
     In addition to the traditional use of transgenic technology to introduce additional copies or increase expression of the genes and mediate the increased expression of the polypeptides of the disclosure in plants, transgenic or non-transgenic technology can be used in other ways to increase expression of the polypeptides. For example, plant tissue culture and regeneration, mutations or altered expression of plant genes other than those expressly recited herein, or transgenic technologies, can be used to create instability in the Rhg1 locus or the plant genome more generally that create changes in Rhg1 locus, or Rgh1 associated gene, copy number or gene expression behavior. The new copy number or gene expression behavior can then be stabilized by removal of the variation-inducing mutations or treatments, for example by further plant propagation or a conventional cross. Examples of transgenic technologies that might be used in this way include targeted zinc fingers, ribozymes or other sequence-targeted enzymes that create double stranded DNA breaks at or close to the Rhg1 locus or Rgh1 associated gene, the cre/loxP system from bacteriophage lambda, Transcription Activator-Like Effector Nucleases (TALENs), Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) systems using CRISPR-associated proteins such as Cas9 or other nucleases, artificial DNA or RNA sequences designed to recombine with Rhg1 that can be introduced transiently, or enzymes that “shuffle” DNA such as the mammalian Rag1 enzyme or DNA transposases. Mutations or altered expression of endogenous plant genes involved in DNA recombination, DNA rearrangement and/or DNA repair pathways are additional examples. 
     Non-transgenic means of generating soybean varieties carrying traits of interest such as increased resistance to SCN are available to those of skill in the art and include traditional breeding, chemical or other means of generating chromosome abnormalities, such as chemically induced chromosome doubling and artificial rescue of polyploids followed by chromosome loss, knocking-out DNA repair mechanisms or increasing the likelihood of recombination or gene duplication by generation of chromosomal breaks. Other means of non-transgenically increasing the expression or copy number include the following: screening for mutations in plant DNA encoding miRNAs or other small RNAs, plant transcription factors, or other genetic elements that impact Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 expression; screening large field or breeding populations for spontaneous variation in copy number or sequence at Rhg1 or Glyma.07G195900 by screening of plants for nematode resistance, Rhg1 copy number or other Rhg1 or Glyma.07G195900 gene or protein expression traits as described in preceding paragraphs; crossing of lines that contain different or the same copy number at Rhg1 or Glyma.07G195900 but have distinct polymorphisms on either side, followed by selection of recombinants at Rhg1 or Glyma.07G195900 using molecular markers from two distinct genotypes flanking the Rhg1 or Glyma.07G195900 locus; chemical or radiation mutagenesis or plant tissue culture/regeneration that creates chromosome instability or gene expression changes, followed by screening of plants for nematode resistance, Rhg1 or Glyma.07G195900 copy number or other Rhg1 or Glyma.07G195900 gene or protein expression traits as described in preceding paragraphs; or introduction by conventional genetic crossing of non-transgenic loci that create or increase genome instability into Rhg1- or Glyma.07G195900-containing lines, followed by screening of plants for either nematode resistance or Rhg1 copy number. Examples of loci that could be used to create genomic instability include active transposons (natural or artificially introduced from other species), loci that activate endogenous transposons (for example mutations affecting DNA methylation or small RNA processing such as equivalent mutations to met1 in  Arabidopsis  or mop1 in maize), mutation of plant genes that impact DNA repair or suppress illegitimate recombination such as those orthologous or similar in function to the Sgs1 helicase of yeast or RecQ of  E. coli , or overexpression of genes such as RAD50 or RAD52 of yeast that mediate illegitimate recombination. Those of skill in the art can find other transgenic and non-transgenic methods of increasing expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900. 
     Polynucleotides and/or polypeptides described and used herein can encode the full-length or a functional fragment of Glyma.18G022700, Glyma.18G022500, and/or Glyma.18G022400, from the Rhg1 locus, or Glyma.07G195900, or a naturally occurring or engineered variant of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900, or a derived polynucleotide or polypeptide all or part of which is based upon nucleotide or amino acid combinations similar to all or portions of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 or their encoded products. Additional polynucleotides encoding polypeptides can also be included in the construct such as Glyma18g02600 (which encodes the polypeptide of SEQ ID NO:4). The polypeptide can be at least 75% 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the sequences provided herein. The polynucleotides encoding the polypeptides can be at least 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% identical to the sequences available in the public soybean genetic sequence database. 
     Expression of the polypeptide encoded by Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can be increased, suitably the level of polypeptide is increased at least 1.2, 1.5, 1.7, 2, 3, 4, 5, 7, 10, 15, 20 or 25-fold in comparison to the untreated, susceptible or other control plants or plant cells. Control cells or control plants are comparable plants or cells in which Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 expression has not been increased, such as a plant of the same genotype transfected with empty vector or transgenic for a distinct polynucleotide. 
     The increase in expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 in the plant can be measured at the level of expression of the mRNA or at the level of expression of the polypeptide encoded by Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900. The level of expression can be increased relative to the level of expression in a control plant as shown in the Examples. The control plant can be an SCN-susceptible plant or an SCN-resistant plant. For example, a susceptible plant such as ‘Williams 82’ can be transformed with an expression vector such that the roots of the transformed plants express increased levels of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 as compared to an untransformed plant or a plant transformed with a construct that does not change expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900, resulting in increased resistance to nematodes. Alternatively, the control can be a plant partially resistant to nematodes and increased expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can result in increased resistance to nematodes. Alternatively, the plant can be resistant to nematodes and increasing expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can result in further increased resistance to nematodes. Alternatively, the plant can be more resistant to certain nematode populations, races, Hg types or strains and less resistant to other nematode populations, races, Hg types or strains, and increasing expression of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 can result in increased resistance to certain of these nematode populations, races, Hg types or strains. 
     Increased resistance to nematodes can be measured as described above. Increased resistance in a transgenic cell of the disclosure can be measured relative to a “native” cell not having any introduced polynucleotide sequences, or exogenous polynucleotide or polypeptide control elements. Increased resistance can be measured by the plant having a lower percentage of invading nematodes that develop past the J2 stage, a lower rate of cyst formation on the roots, reduced SCN egg production within cysts, reduced overall SCN egg production per plant, and/or greater grain yield of SCN-infested soybeans on a per-plant basis or a per-growing-area basis as compared to a control plant grown in a similar growth environment. Other methods of measuring SCN resistance also will be known to those with skill in the art. In methods of increasing resistance to nematodes described herein, the resulting plant can have at least 10% increased resistance as compared to the untreated or control plant or plant cells. Suitably the increase in resistance is at least 15%, 20%, 30%, 50%, 100%, 200%, 500% as compared to a control. Suitably, the female index of the plant with increased resistance to nematodes is about 80% or less of the female index of an untreated or control plant derived from the same or a similar plant genotype, infested with a similar nematode population within the same experiment. More suitably, the female index after experimental infection is no more than 60%, 40%, or 20% of that of the control plant derived from the same or a similar plant genotype, infested with a similar nematode population within the same experiment. Suitably, when grown in fields heavily infested with SCN (for example, more than 2500 SCN eggs per 100 cubic centimeters of soil), soybean grain yields of field-grown plants are 2% greater than isogenic control plants. More suitably, the grain yield increase is at least 3%, 4%, or 5% over that of isogenic control plants grown in similar environments. 
     Also provided herein are constructs including a promoter operably linked to one or more of a Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 polynucleotide encoding a polypeptide comprising SEQ ID NO: 12, SEQ ID NO: 11, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 10, SEQ ID NO: 18, or a fragment or variant thereof. Also included are homologs or variants of these sequences from other soybean varieties. The constructs can further include other genes. The constructs can be introduced into plants to make transgenic plants or can be introduced into plants, or portions of plants, such as plant tissue, plant calli, plant roots or plant cells. Suitably the promoter is a plant promoter, suitably the promoter is operational in root cells of the plant. The promoter can be tissue specific, inducible, constitutive, or developmentally regulated. The constructs can be an expression vector. Constructs can be used to generate transgenic plants or transgenic cells. The polypeptide can be at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the sequences of SEQ ID NO: 12, SEQ ID NO: 11, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 10, or SEQ ID NO: 18. The constructs can comprise all three polynucleotides and can mediate expression of all three polypeptides. 
     Transgenic plants including a non-native or exogenous polynucleotide encoding the rhg1-b polypeptides identified and described herein are also provided. Suitably these transgenic plants are soybeans. The transgenic plants express increased levels of Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900 polypeptide as compared to a control non-transgenic plant from the same line, variety or cultivar or a transgenic control expressing a polypeptide other than Glyma.18G022700, Glyma.18G022500, Glyma.18G022400, and/or Glyma.07G195900. These transgenic plants also have increased resistance to nematodes, in particular SCN, as compared to a control plant. Portions or parts of these transgenic plants are also provided. Portions and parts of plants includes, but is not limited to, plant cells, plant tissue, plant progeny, plant asexual propagates, plant seeds. 
     Transgenic plant cells comprising a polynucleotide encoding a polypeptide capable of increasing resistance to nematodes such as SCN are also provided. Suitably the plant cells are soybean plant cells. Suitably these cells are capable of regenerating a plant. The polypeptide comprises the sequences of SEQ ID NOs:10-18, or fragments, variants or combinations thereof. The polypeptide can be 70%, 75%, 85%, 90%, 95%, 97%, 98%, 99% or 100% identical to the sequences provided. The transgenic cells can be found in a seed. A plant, such as a soybean plant, can include the transgenic cells. The plant can be grown from a seed comprising transgenic cells or can be grown by any other means available to those of skill in the art. Chimeric plants comprising transgenic cells are also provided. 
     Expression of polypeptides and polynucleotides encoding the polypeptides in the transgenic plant is altered relative to the level of expression of the native polypeptides in a control soybean plant. In particular the expression of the polypeptides in the root of the plant is increased. The transgenic plant has increased resistance to nematodes as compared to the control plant. The transgenic plant can be generated from a transgenic cell or callus using methods available to those skilled in the art. 
     EXAMPLES 
     The Examples that follow are illustrative of specific embodiments disclosed herein and various uses thereof. They are set forth for explanatory purposes only and are not to be taken as limiting. 
     Example 1: Abundance of WT and Resistance-Associated α-SNAP Proteins in Rhg1 HC  and Rhg1 LC  Soybean Varieties 
     To investigate the relative abundances of wildtype (WT) and resistance-associated α-SNAPs, immunoblots were performed using standard HG type test Rhg1 HC  and Rhg1 LC  soybean varieties and previously described anti-α-SNAP antibodies (Niblack et al., 2002, J Nematol 34, 279-288; Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). NSF abundance was also studied in these samples using an antibody raised to a conserved NSF domain. As shown in  FIG. 1A , immunoblots from root tissue indicated that WT α-SNAP abundance in all tested Rhg1 LC  lines (PI 548402/Peking, PI 90763, PI 437654, PI 89772) was dramatically reduced compared with the Rhg1 HC  lines (PI 88788, PI 209332, PI 548316). Probing of the same samples with antibodies that recognize α-SNAP Rhg1 LC or α-SNAP Rhg1 HC but not WT α-SNAP confirmed that, between the Rhg1 HC  and Rhg1 LC  soybean varieties, there was a pronounced difference in the abundance of WT α-SNAP relative to the abundance of Rhg1 α-SNAP ( FIG. 1A ). 
     WT α-SNAP expression was similarly reduced in a more recent agriculturally utilized Rhg1 LC  soybean variety, “Forrest.” Immunoblots on both total leaf or root proteins from Williams82 (Rhg1 single copy), Forrest (Rhg1 LC ) and Fayette (Rhg1 HC ), again revealed sharp decreases in total WT α-SNAP abundance in the Rhg1 LC  source Forrest ( FIG. 1C ). Altogether, a sharply reduced total abundance of WT α-SNAPs was observed to be a shared trait of Rhg1 LC  soybean varieties but not Rhg1 HC  varieties. This strikingly low abundance of WT α-SNAPs is likely due to the absence of a WT-α-SNAP-encoding allele at Rhg1 Lc , low or no product from the Glyma.11G234500 (α-SNAP Ch11 ) allele containing an intronic splice site mutation, and a relatively low contribution of protein from the other three putative α-SNAP-encoding loci (Table 1.) 
     Table 1: Normalized RNA seq reads for soybean α-SNAP transcripts from Williams82 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Normalized RNA seq reads for soybean α-SNAP transcripts from Willams82 
               
               
                 Normalized RNA seq reads for soybean α-SNAP transcripts from Willams82 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                 one  
                 pod  
                 pod  
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 alpha-SNAP  
                 young_ 
                   
                 cm  
                 shell  
                 shell  
                 seed  
                 seed  
                 seed  
                 seed  
                 seed 
                 seed  
                 seed  
                   
                   
               
               
                 gene 
                 leaf 
                 flower 
                 pod 
                 10DAF 
                 14DAF 
                 10DAF 
                 14DAF 
                 21DAF 
                 25DAF 
                 28DAF 
                 35DAF 
                 42DAF 
                 root 
                 module 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
               
               
               
               
            
               
                 Glyma02g42820 
                 0 
                 0 
                 0 
                 0 
                 0 
                 0 
                 1 
                 2 
                 1 
                 0 
                 1 
                 0 
                 0 
                 0 
               
               
                 Glyma09g41590 
                 4 
                 4 
                 3 
                 2 
                 2 
                 1 
                 1 
                 2 
                 2 
                 1 
                 1 
                 1 
                 10 
                 11 
               
               
                 Glyma11g35820 
                 16 
                 17 
                 20 
                 23 
                 26 
                 13 
                 17 
                 11 
                 14 
                 6 
                 15 
                 10 
                 22 
                 12 
               
               
                 Glyma14g05920 
                 0 
                 5 
                 3 
                 2 
                 1 
                 10 
                 6 
                 2 
                 1 
                 1 
                 1 
                 2 
                 1 
                 9 
               
               
                 Glyma18g02590 
                 26 
                 28 
                 32 
                 44 
                 24 
                 21 
                 27 
                 9 
                 13 
                 7 
                 12 
                 7 
                 28 
                 10 
               
               
                   
               
            
           
         
       
     
     NSF protein abundance in the Rhg1 LC  lines was increased compared with the Rhg1 HC  lines PI 88788 and PI 209332 ( FIG. 1A ,  FIG. 7A ). In PI 548316, which carries only 7 copies of Rhg1 HC  and encodes an interrupted Chromosome 11 α-SNAP, total NSF expression was more similar to the Rhg1 LC  lines ( FIG. 1A, 7A ). These differences in NSF expression, across two independent experiments, were quantified using densitometry with ImageJ ( FIG. 1B ) 
     Whether native α-SNAP Rhg1 WT locus, if expressed, could contribute to total WT α-SNAP protein abundance in Rhg1 LC  soybean lines was also investigated. Cloning native Glyma.18G022500 α-SNAP Rhg1 WT locus from Williams 82 (Wm82), transgenic Forrest (Rhg1 Lc ) roots expressing native α-SNAP Rhg1 WT were generated and total WT α-SNAP abundance was assessed with immunoblots. Compared to empty vector controls, transgenic addition of the native Williams 82 α-SNAP Rhg1 WT locus increased wild type α-SNAP abundance in Forrest to levels similar to Williams 82 controls ( FIG. 1D ). 
     Example 2: A Unique NSF Ch07  Allele (RAN07) is Present in Rhg1-Containing NAM Parents and HG Type Test Type Varieties 
     Rhg1-resistance type α-SNAPs (α-SNAP Rhg1 LC or α-SNAP Rhg1 HC) exhibited compromised binding to wild-type NSFs and were toxic at high doses in  N. benthamiana  (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). (NSF and α-SNAP are essential housekeeping proteins in all eukaryotes and null mutations in either partner are lethal in animals, which typically encode only single copies of NSF or α-SNAP (Littleton et al., 2001, 98, 12233-12238; Sanyal and Krishnan, 2001, Neuroreport 12, 1363-1366; Horsnell et al., 2002, Biochemistry 41, 5230-5235; Chae et al., 2004, Nat Genet 36, 264-270). 
     Viability of plants harboring Rhg1-resistance type α-SNAP Rhg1 LC was investigated by examining alternative sources of α-SNAP or NSF activity. Soybean is a polyploid organism encoding multiple α-SNAP and NSF loci. Alterations in other α-SNAP (Glyma.11G234500, Glyma.14G054900, Glyma.02G260400, Glyma.09G279400) or NSF loci (Glyma.13G180100) were examined using whole genome sequence (WGS) data from multiple Rhg1-containing varieties. Briefly, reads were assembled for all α-SNAP and NSF loci, and aligned against the Williams 82 reference genome. In all α-SNAP loci from Rhg1 LC  varieties, no obvious polymorphisms were detected other than the previously reported Glyma.11G234500 (a-SNAPch 11) allele containing an intronic splice site mutation. (Cook, 2014, Plant Physiol 165, 630-647) Among all examined Rhg1Lc and Rhg1Hc lines, a novel NSFcho1 allele was present containing five N-Domain amino acid polymorphisms (R4Q, N21Y, S25 N, A 116F, M1811) ( FIG. 2A ). 
     Using cDNA from Forrest (Rhg1 LC ), this unique NSF Ch07  transcript was cloned and sequenced, and all 5 N-domain polymorphisms were confirmed. Additionally, two different PCR primer pairs were designed at the N 21 Y and S 25 N polymorphisms and this unique NSF Ch07  allele (and absence of the wild-type NSF Ch07 allele) was verified in all HG type test lines using agarose gel electrophoresis ( FIG. 7C ). 
     Whole genome sequencing (WGS) data from the SoyNAM (Nested Association Mapping) project (Song et al., 2017b, Plant Genome 10(2)) was used to determine that this unique NSF Ch07  allele was in every Rhg1-containing NAM parent, while SCN-susceptible NAM parents carried the WT NSF Ch07  allele (Table 1). The protein from this Rhg1-associated allele of Glyma.07G195900 was designated “NSF RAN07 ” for “Rhg1-associated NSF from chromosome 07.” In addition to NSF RAN07 , an allele of the chromosome 13 Glyma.13g180100 gene encoding an NSF Ch13  V 555 I protein was found in some varieties, including SCN-susceptible soybeans, but it was not present in all Rhg1 LC  or Rhg1 HC  lines (Table 2).  FIG. 8A  and  FIG. 8B  shows the complete NSF RAN07  amino acid alignment to NSF Ch07  from the Williams 82 reference genome. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 HG Type Test lines and Rhg1-containing NAM 
               
               
                 Parents Contain a Unique NSF Ch07  Allele 
               
            
           
           
               
               
               
               
            
               
                 Line 
                 Rhg1 Haplotype 
                 NSF Ch07   
                 NSF Ch13   
               
               
                   
               
               
                 Peking 
                 Rhg1 LC   
                 Rhg1 Assoc. Allele 
                 WT (Wm82-type) 
               
               
                 90763 
                 Rhg1 LC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 437654 
                 Rhg1 LC   
                 Rhg1 Assoc. Allele 
                 WT (Wm82-type) 
               
               
                 209332 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 89772 
                 Rhg1 LC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 548316 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 Prohio 
                 Susceptile 
                 WT (Wm82-type) 
                 V555I 
               
               
                 NE3001 
                 Susceptile 
                 WT (Wm82-type) 
                 Y260F 
               
               
                 4J105-34 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 V555I, L738F 
               
               
                 CL0J095-46 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 IA3023 
                 Susceptible 
                 WT (Wm82-type) 
                 V555I 
               
               
                 LD00-3309 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 WT (Wm82-type) 
               
               
                 LD02-4485 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 WT (Wm82-type) 
               
               
                 LG05-4292 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 WT (Wm82-type) 
               
               
                 LD01-5907 
                 Rhg1 LC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 LD02-9050 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                 Magellan 
                 Susceptible 
                 WT (Wm82-type) 
                 WT (Wm82-type) 
               
               
                 Maverick 
                 Rhg1 HC   
                 Rhg1 Assoc. Allele 
                 V555I 
               
               
                   
               
            
           
         
       
     
     Example 3: NSF RAN07  and Rhg1 α-SNAP Polymorphisms are Both at the NSF/α-SNAP Binding Interface 
     The NSF/α-SNAP interface consists of complementary electrostatic patches at the NSF N-domain and α-SNAP C-terminus (Zhao and Brunger, 2016, J Mol Biol 428, 1912-1926). These binding patches are conserved in yeast, animals and plants, with the soybean NSF N-domain (N 21 , RR 82-83 , KK 117-118 ) and α-SNAP C-terminus (D 208 DEED 243-246 , EEDD 284-287 ) corresponding to NSF CHO  (R 10 , RK 67-68 , KK 104-105 ) and rat α-SNAP (D 217 E 249 EE 252-253 , DEED 290-293 ) respectively. Accordingly, inter-kingdom interactions between α-SNAP and NSF have been reported both in vitro and for heterologous expression systems in vivo, including between soybean WT α-SNAP and Chinese Hamster NSF (NSF CHO ) (Griff et al., 1992,  J. Biol. Chem.  267, 12106-12115; Bassham and Raikhel, 1999, Plant J 19, 599-603; Rancour et al., 2002, Plant Physiol 130, 1241-1253; Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). 
     To assess where the NSF RAN07  polymorphisms are positioned in the N-domain, NSF RAN07  was modeled to the NSF CHO  cryo-EM structure from Zhao and colleagues (Zhao, 2015, Nature 518, 61-67) ( FIG. 2B ). NSFs in many plants, including soybean, encode a variable length polyserine/glycine patch, starting at ˜residue 6. Therefore, modeling to NSF CHO  began at residue 14. The NSF RAN07  homology model to NSF CHO  placed two of the NSF RAN07  polymorphisms at two NSF CHO  regions that bind α-SNAP: N 21 Y and S 25 N at and near R 10 , and  {circumflex over ( )}   116 F at RK 114-115 , respectively ( FIG. 2B ,  FIG. 2C ,  FIG. 9A ). While R 4 Q was omitted from the model (because of the omission of the variable length polyserine/glycine patch), we examined R 4  frequency across 22 diverse eukaryotes (9 animals, 3 fungi, 10 plants) ( FIG. 2D ). In all but four model organisms, R 4  was present in the NSF of 18 of the 22 species, while  S. cerevisiae, Drosophila, C. elegans  and  Physcomitrella  carry an R and/or K at the adjacent residue #3 and/or #5. The final NSF RAN07  polymorphism, M 181 I, was not located near the α-SNAP binding patches and was not highly conserved among model organism NSFs. Examination of N-domain conservation in plant NSFs revealed that residues corresponding to N 21  and F 115  are present in a majority of plants and do not carry N 21 Y or the  {circumflex over ( )}   118 F insertion ( FIG. 9B ). These results modeling to NSF demonstrate that three of the five NSF RAN07  N-domain polymorphisms are located in or adjacent to the NSF binding patches that interact with α-SNAP. 
     Polymorphisms of both α-SNAP Rhg1 HC and α-SNAP Rhg1 LC, are located at conserved C-terminal residues that bind and stimulate NSF (Cook et al., 2014, Plant Physiol 165, 630-647; Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). Multiple α-SNAP proteins bound to a SNARE bundle recruit six NSF proteins to form a “20S supercomplex” (4× α-SNAPs, 6×NSF, 3-4×SNAREs) and stimulate SNARE complex disassembly (Zhao et al., 2015). The proximity of the NSF RAN07  N-domain polymorphisms to α-SNAP C-terminal contacts was assessed by identifying and coloring the complementary NSF and α-SNAP binding residues, and then the NSF RAN07  and Rhg1 α-SNAP polymorphisms, on the mammalian 20S cryo-EM structure ( FIG. 3A ,  FIG. 3B ,  FIG. 10A ,  FIG. 10B ). This confirmed that NSF RAN07  N 21 Y, S 25 N,  {circumflex over ( )}   116 F are predicted to locate adjacent to NSF residues that bind α-SNAP residues, including residues that contact the WT α-SNAP amino acid residues that are altered in α-SNAP Rhg1 HC and α-SNAP Rhg1 LC. R 4  on the NSF CHO  structure was closely positioned to a D 28  side chain, present in soybean as D 39  ( FIG. 10B ). Altogether, the location and structural modeling of the NSF RAN07  polymorphisms suggest that NSF RAN07  modifies the normal NSF binding interface that maintains complementary binding contacts with α-SNAP sites that are altered in Rhg1 α-SNAPs. 
     Example 4: NSF RAN07  Polymorphisms Promote Binding with Rhg1 Resistance-Type α-SNAPs 
     All Rhg1-containing HG type test and NAM lines contained NSF RAN07 , and α-SNAP Rhg1 HC and α-SNAP Rhg1 LC are polymorphic at C-terminal residues that bind and stimulate NSF. Therefore, the impact of NSF RAN07  polymorphisms on binding to both Rhg1 resistance-type α-SNAPs and α-SNAP Rhg1 WT was investigated. Recombinant NSF RAN07 , NSF Ch07  and Rhg1 α-SNAP proteins were produced for in vitro binding studies as previously described in (Barnard et al., 1997, J Cell Biol 139, 875-883; (Bayless et al. 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). NSF RAN07  and NSF Ch07  binding was quantified using ImageJ densitometry across three independent experiments ( FIG. 3D ). NSF Ch07  binding to α-SNAP Rhg1 HC and α-SNAP Rhg1 LC was reduced compared to α-SNAP Rhg1 WT ( FIG. 3C ). In contrast, NSF RAN07  binding to α-SNAP Rhg1 HC or α-SNAP Rhg1 LC was similar to α-SNAP Rhg1 WT binding, and was increased ˜30% relative to NSF Ch07 . 
     To verify that NSF RAN07 /α-SNAP binding is dependent upon NSF-binding patches at the α-SNAP C-terminus, NSF RAN07  binding to an otherwise WT α-SNAP lacking the final 10 C-terminal residues (α-SNAP Rhg1 WT 1-279 ) was determined. Binding of NSF Ch07 WT or NSF RAN07  binding with α-SNAP  Rhg1 WT 1-279  was disrupted, similar to the no α-SNAP binding controls ( FIG. 10C ). Hence NSF RAN07 /α-SNAP binding requires the conserved NSF-binding contacts located at the α-SNAP C-terminus. Combined, these binding assays suggested that NSF RAN07  not only maintains normal binding to WT α-SNAPs, but also at least partially accommodates the unusual C-terminal NSF-binding interface of Rhg1 resistance-type α-SNAPs. 
     Example 5: NSF RAN07  Polymorphisms Guard Against Cell Death Induced by Rhg1-Resistance-Type α-SNAP 
     Transient expression of either α-SNAP Rhg1 HC or α-SNAP Rhg1 LC in  N. benthamiana  leaves, via  Agrobacterium  infiltration, was cytotoxic and elicited hyperaccumulation of the endogenous NSF protein (Bayless et al., 2016 Proc. Natl. Acad. Sci. USA 113, E7375-E7382). Co-expression of WT-α-SNAP with the Rhg1 α-SNAP diminished this toxicity (Bayless et al., 2016 Proc. Natl. Acad. Sci. USA 113, E7375-E7382). The penultimate leucine/isoleucine of α-SNAP, which has been implicated in stimulation of NSF ATPase, was needed for this  N. benthamiana  cytotoxicity (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). 
     The ability of soybean NSF co-expression to alleviate the toxicity of Rhg1 resistance-type α-SNAPs in  N. benthamiana  was determined. Mixed  Agrobacterium  cultures containing 1 part WT α-SNAP to 3 parts α-SNAP Rhg1 LC were used for cytotoxicity complementation assays as previously described Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). NSF RAN07  and NSF Ch07  were more effective than WT α-SNAP at reducing Rhg1 α-SNAP cytotoxicity ( FIG. 11A ). The proportion of NSF-delivering bacteria in the mixed  Agrobacterium  cultures was then decreased down to 1 part to 9 or 14 parts α-SNAP Rhg1 LC-delivering bacteria. Co-expressing soybean NSF Ch07 , NSF Ch13  or NSF RAN07  reduced cell death caused by α-SNAP Rhg1 LC compared to empty vector controls ( FIG. 4A ), and NSF RAN07  co-expression consistently conferred greater protection than either NSF Ch07  or NSF Ch13  ( FIG. 4A ). Infiltrated leaf patches had less death and/or slower death with NSF RAN07 . Both NSF RAN07  and NSF Ch07  were more effective than NSF Ch13  at complementing cell death ( FIG. 4A ). NSF RAN07  was observed to confer at least partial protection out to a 1:19 mixture, again outperforming complementation by NSF Ch07  ( FIG. 11B ). Complementation of α-SNAP Rhg1 HC-induced cell death with NSF RAN07  vs. NSF Ch07  produced similar results ( FIG. 11C ). 
     Mixed cultures of  N. benthamiana  NSF (NSF N.benth , 81% identity to NSF Ch07 , see  FIG. 12  for alignment) and α-SNAP Rhg1 LC, were agroinfiltrated as in  FIG. 4A . EV, NSF Ch13  and NSF RAN07  were agroinfiltrated as controls. NSF Ch13  gave visible protection relative to an empty vector, while NSF RAN07  co-expression gave strong protection ( FIG. 4B ). In contrast, NSF N.benth  co-expression was similar to empty vector controls ( FIG. 4B ). Expressing soybean NSFs or NSF N.benth  with an empty vector at the same ratios used for complementation did not cause macroscopic phenotypes suggestive of stress ( FIG. 11D ). 
     Physical binding with Rhg1 resistance-type α-SNAPs using recombinant NSF N.benth  protein was determined. Whereas NSF N.benth  readily bound α-SNAP Rhg1 WT, NSF N.benth  binding to Rhg1 resistance-type α-SNAPs was much lower, only slightly over controls (α-SNAP lacking the C-terminus or no-α-SNAP) ( FIG. 4C ). This suggested a biochemical explanation for why Rhg1 resistance type α-SNAPs—but not WT α-SNAPs—provoke strong cell death responses in  N. benthamiana : the endogenous  N. benthamiana  NSF binds WT α-SNAPs but not Rhg1 resistance type α-SNAPs. 
     Complementation assays using NSF RAN07  or NSF Ch07  were performed to determine if either could prevent cell-death caused by α-SNAP Rhg1 LC 1-279 , which lacks the final 10 C-terminal residues and does not bind NSF RAN07  or NSF Ch07  in vitro. Neither NSF RAN07  nor NSF Ch07  prevented the cell death caused by α-SNAP Rhg1 LC 1-279  whereas either complemented the cell death induced by full length α-SNAP Rhg1 LC ( FIG. 11E ). 
     The impact of the penultimate α-SNAP residue implicated in NSF-ATPase stimulation was determined using complementation assays with NSF RAN07  or NSF Ch07 . Complementation of α-SNAP Rhg1 LC I 289 A was evident, but was less than that observed for α-SNAP Rhg1 LC ( FIG. 4D ). 
     Example 6: 100% of the Predicted Rhg1 +  Soybean Accessions in the USDA Soybean Collection, and 7% of the Rhg1 −  Soybean Accessions, Contain the SoySNP50K NSF RAN07  R 4 Q Amino Acid Polymorphism 
     NSF RAN07  was present in all Rhg1-containing HG type and NAM lines, but whether this Rhg1/NSF RAN07  association was universal rather than “frequent” was further investigated. First, the approximate NSF RAN07  allele frequency was determined. In 2015, Song et al. reported genotyping the USDA soybean germplasm collection of ˜20,000 accessions—collected from over 80 countries—using a 50,000 SNP DNA microarray chip (SoySNP50K iSelect BeadChip). These data were available in a searchable SNP database at Soybase (Soybase.org/snps/) (Grant et al., 2010, Nucleic Acids Res 38, D843-846; Song et al., 2013, PLoS One 8, e54985; Song et al., 2015, PLoS Genet 11, e1005200). Using the Soybase genome browser, a C/T SNP was found to be involved using the SoySNP50K (ss715597431, Gm07:36,449,014) that causes the NSF RAN07  R 4 Q polymorphism. Analyzing all 19,645 USDA soybean accessions for ss715597431, the NSF RAN07  allele frequency in the USDA collection was estimated at 11.0% (2,165+/+, 33+/−) ( FIG. 5A ). While NSF in most model eukaryotes contains R 4 , it remained unclear whether Q 4  occurs in other plant NSFs. To determine if the NSF RAN07  R 4 Q is unusual among plants, R 4  conservation across plant NSF sequences available on Phytozome (Goodstein et al., 2012, Nucleic Acids Res 40, D1178-D1186) was examined. Notably, Q 4  was not in the queried NSF predicted protein sequences for any other plant species ( FIG. 13 ). 
     Rhg1-mediated SCN resistance is uncommon among soybean accessions and less than 5% of the USDA soybean collection carries a multi-copy Rhg1 haplotype. Previously, Lee et al. identified SoySNP50K signatures for Rhg1 HC , Rhg1 LC  and single copy (SCN-susceptible) haplotypes, and estimated that 705 Rhg1 LC  and 150 Rhg1 HC  accessions were in the USDA  Glycine max  collection (Lee et al., 2015, Mol Ecol 24, 1774-1791). Using these 855 Rhg1-signature accessions, a 100% incidence of the ss715597431 NSF RAN07  signature was determined for multi-copy Rhg1-signature  Glycine max  ( FIG. 5B ). 
     If NSF RAN07  is needed for the survival of Rhg1-containing soybean plants, then, all Rhg1 accessions should carry NSF RAN07 . As such, SNPs within the locus underlying Rhg1 co-segregation should be maintained, while SNPs at neighboring loci, though tightly linked, would not be under stringent selection and hence should be less conserved. To narrow in on the Rhg1 co-segregating locus within the interval, amino acid changes within candidate loci adjacent to RAN07 from Rhg1-carrying HG and NAM lines, between markers ss715597415 and ss715597431, were examined. NSF RAN07  SNPs, especially those causing the 5 N-domain polymorphisms, were 100% maintained across all Rhg1-containing varieties. On the other hand, SNPs causing amino acid changes within candidate loci adjacent to NSF RAN07 , were not 100% conserved across all Rhg1-containing varieties, unlike NSF RAN07  (Table 3). The predicted amino acid sequence of most candidate loci matches Wm82 (SCN-susceptible) sequence, and among candidate loci with amino acid substitutions, only NSF RAN07  has the same consistent amino acid changes across all examined Rhg1-containing germplasm (Table 3). In addition to the observed biochemical and genetic complementation of Rhg1 α-SNAPs by NSF RAN07 , candidate gene allele frequency further implicates NSF RAN07  as the gene responsible for co-segregation with Rhg1. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Amino acid polymorphisms of genes within the chromosome 07 interval co-segregating with Rhg1. 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                   
                 ss715597431 
                   
                   
                   
                 ss715597413 
                   
                   
                 ss715597410 
                   
               
            
           
           
               
               
            
               
                   
                 Soybean Line 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                 Glyma 
                   
                   
                   
                   
                   
                   
                 Glyma 
               
               
                   
                   
                 07g195800 
                 Glyma 
                 Glyma 
                 Glyma 
                 Glyma 
                 Glyma 
                 Glyma 
                 07g195100 
               
               
                   
                 Glyma 
                 Rubber 
                 07g195700 
                 07g195600 
                 07g195500 
                 07g195400 
                 07g195300 
                 07g195200 
                 LRR 
               
               
                   
                 07g195900 
                 Elongation 
                 DNA Mismatch 
                 No annotated 
                 TFII H 
                 E3 Ubiquitin 
                 Asparagine 
                 Conserved 
                 Containing 
               
               
                   
                 NSF 
                 Factor 
                 Repair MutS2 
                 domains 
                 Polypeptide 4 
                 Ligase 
                 Synthase 
                 Protein 
                 Protein 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                 PI89772 
                 R 4 Q, N 21 Y, 
                 K 3 N, F 137 S 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                   
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 161 I 
                   
                 M 406 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 PI90763 
                 R 4 Q, N 21 Y, 
                 K 3 N, L 42 R, 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                 F 137 S 
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 406 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 PI209332 
                 R 4 Q, N 21 Y, 
                 K 3 N, L 42 R, 
                 T 21 A, K 23 R, V 345 I, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                 F 137 S 
                 D 364 N, M 408 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 CLOJO95-4-6 
                 R 4 Q, N 21 Y 
                 K 3 N, L 42 R, 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                 F 137 S 
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 408 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 IA3023 
                 WT 
                 L 42 R, F 437 S 
                 D 364 N, M 406 T, Y 576 F 
                 WT 
                 WT 
                 WT 
                 E 46 G 
                 D 60 A, S 64 P 
                 WT 
               
               
                 LD00-3309 
                 R 4 Q, N 21 Y 
                 K 3 N, L 42 R, 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                 F 137 S 
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 406 T, G 518 C, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 PI 437654 
                 R 4 Q, N 21 Y 
                 K 3 N, F 137 S 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                   
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 406 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 PI548402 
                 R 4 Q, N 21 Y 
                 K 3 N, F 137 S 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                   
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 406 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 Magellan 
                 WT 
                 L 42 R, F 137 S 
                 D 364 N, M 406 T 
                 WT 
                 WT 
                 WT 
                 E 46 G 
                 D 60 A, S 64 P 
                 WT 
               
               
                 Maverick 
                 R 4 Q, N 21 Y 
                 K 3 N, F 137 S 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                   
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 406 T, Q 818 K 
                   
                   
                   
                   
                   
                   
               
               
                 PI548316 
                 R 4 Q, N 21 Y 
                 K 3 N, F 137 S 
                 T 21 A, K 23 R, G 109 C, 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
                 WT 
               
               
                   
                 S 25 N, ∧ 116 F, 
                   
                 H 115 Q, V 345 I, D 364 N, 
                   
                   
                   
                   
                   
                   
               
               
                   
                 M 181 I 
                   
                 M 406 T, Q 818 K 
               
               
                   
               
            
           
         
       
     
     Example 7: All Rhg1 + F5-Derived Recombinant Inbred Lines (RILs) from NAM Population Crosses Also Carry NSF RAN07    
     The NSF RAN07  data from the USDA soybean germplasm collection are an indication of strong segregation distortion. However, Webb et al. (1995) reported that only 91 of 96 lines with a resistant parent marker type linked to Rhg1 also had a resistant parent marker type near the NSF RAN07  QTL (Webb et al., 1995, Theor Appl Genet 91, 574-581). Therefore, lines with Rhg1 were investigated for inheritance of NSF RAN07  in the progeny of more recent biparental crosses. From the Soybean Nested Associated Mapping (SoyNAM) project (Song et al., 2017,Plant Genome 10(2)), genotypic data for populations of RILs developed from crosses of the IA3023 (SCN-susceptible) hub-parent to eight different soybean accessions carrying either Rhg1 HC  (seven accessions) or Rhg1 LC  (one accession) were examined. There were 122 to 139 RILs in each population and the segregation for NSF RAN07 :NSF Ch07 WT in soybean lines lacking Rhg1 did not deviate from the null hypothesis of 1:1 segregation in six of the eight populations. Across populations, there was a significant (α=0.05) deviation from a 1:1 segregation with a significantly greater number of RILs with NSF RAN07  than NSF Ch07 WT. The segregation distortion for NSF RAN07  was obvious among RILs that carried a resistance-associated Rhg1 allele but, out of a total of 309 Rhg1 + RILs, 8 appeared to have possibly inherited Rhg1 HC  or Rhg1 LC  but not NSF RAN07  while the remainder had NSF RAN07 . This was based upon the lower-density SoySNP6K mapping data that that did not include perfect genetic markers for Rhg1 and NSF. Polymorphisms within Rhg1 and NSF RAN07  genes were genotyped using primers that detect the Rhg1 repeat junction and a WT NSF Ch07  vs. NSF RAN07  allele. All 8 re-examined RILs that inherited Rhg1 HC  or Rhg1 LC  also inherited the NSF RAN07  {circumflex over ( )}116 F and M 181 I mutations meaning that all 309 RILs that carried the resistance associated Rhg1 also carried NSF RAN07  (Table 4). 
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 NSF RAN07  co-segregates with Rhg1 in all Rhg1-containing F 2:5  offspring from Rhg1 +  × rhg1 −  crosses 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                 Diverse  
                 RR (Ch07,  
                 RS(Ch07,  
                 SR(Ch07,  
                 SS(Ch07,  
                 HR(Ch07,  
                 HS(Ch07,  
                 HH(Ch07,  
                 RH(Ch07,  
                 SH(Ch07,  
               
               
                 Parent 
                 Ch18) 
                 Ch18) 
                 Ch18) 
                 Ch18) 
                 Ch18) 
                 Ch18) 
                 Ch18) 
                 Ch18) 
                 Ch18) 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
            
               
                 4J105-3-4 
                 41 
                 41 
                 2 
                 31 
                 9 
                 3 
                 1 
                 9 
                 0 
               
               
                 CL0J095-4-6 
                 35 
                 45 
                 0 
                 37 
                 6 
                 7 
                 0 
                 7 
                 1 
               
               
                 LD00-3309 
                 38 
                 45 
                 1 
                 27 
                 8 
                 10 
                 3 
                 7 
                 0 
               
               
                 LD01-5907 
                 32 
                 32 
                 1 
                 42 
                 0 
                 6 
                 1 
                 6 
                 2 
               
               
                 LD02-4485 
                 37 
                 50 
                 1 
                 28 
                 10 
                 7 
                 1 
                 5 
                 0 
               
               
                 LD02-9050 
                 43 
                 31 
                 2 
                 34 
                 10 
                 10 
                 1 
                 4 
                 0 
               
               
                 Maverick 
                 31 
                 34 
                 0 
                 41 
                 8 
                 8 
                 3 
                 8 
                 1 
               
               
                 LG05-4292 
                 44 
                 41 
                 1 
                 30 
                 1 
                 3 
                 0 
                 7 
                 0 
               
               
                 Totals 
                 301 
                 319 
                  8* 
                 270 
                 52 
                 54 
                 10 
                 53 
                 4 
               
               
                   
               
               
                 R refers to allele from Rhg1 resistant parent. 
               
               
                 S refers to allele from SCN-susceptible parent 
               
               
                 Genotype order: first allele is chr 7 (RAN07 interval) and second is chr 18 (Rhg1 interval) 
               
               
                 *All 8 re-examined RILs that inherited Rhg1  HC  or Rhg1  LC  also inherited the NSF  RAN07    ∧ 116 F and MI mutations meaning that all 309 RILs that carried the resistance associated Rhg1 also carried NSF  RAN07   
               
            
           
         
       
     
     Example 8: NSF-RAN07 Aids in the Production of Transgenic Soybean Lines that Express an SCN-Resistance-Associated Rhg1 α-SNAP 
     In previous work, attempts to generate transgenic soybean lines with DNA constructs derived in part from the Rhg1 locus had failed to generate lines that express α-SNAP Rhg1 LC or α-SNAP Rhg1 HC protein variants. This was despite successes within the same project in generating stably transformed transgenic soybean lines that express other genes or gene silencing constructs. That work was done using soybean variety Thorne, which does not carry an NSF RAN07 -encoding allele of Glyma.07G195900. In subsequent collaborative work with the University of Wisconsin—Madison Wis. Crop Innovation Center (Middleton, Wis.), an experiment was initiated in which soybean variety Williams 82 was transformed with DNA constructs designed to express α-SNAP Rhg1 LC or α-SNAP Rhg1 WT protein, together with either NSF RAN07  or NSF Ch07 WT protein, or no added NSF protein. Williams 82 lacks NSF RAN07  and lacks resistance-associated Rhg1. The respective DNA constructs, which used a  Glycine max  ubiquitin promoter sequence to drive expression of Glyma.18G022500 protein coding sequences, or Glyma.07G195900 and Glyma.18G022500 protein coding sequences on the same plasmid, were built into plasmid pC23S, a binary plasmid conferring spectinomycin resistance. Similar numbers of Williams 82 embryos were treated with the respective  Agrobacterium tumefaciens  strain for each DNA construct (approximately 300 embryos per  Agrobacterium  strain). After co-culture of the embryos with the designated  Agrobacterium  strain, counter-selection against the  Agrobacterium  was applied, and embryos were then grown on growth media containing spectinomycin. Embryos that were able to grow successfully on spectinomycin were transferred to new spectinomycin selection media, and plantlets producing new leaves and roots were then transferred to the greenhouse and grown for seed production. If the DNA used for plant transformation was phenotypically neutral, similar numbers of Williams 82 transformants would be expected for each DNA construct if using the same plasmid vector and processing all of the transformants similarly within the same experiment. However, there was a notable lack of recovery of spectinomycin-resistant transformants for soybean lines that received a DNA construct encoding α-SNAP Rhg1 LC expression. Zero lines were recovered for expression of only α-SNAP Rhg1 LC, and only one line was recovered for expression of α-SNAP Rhg1 LC+NSF Ch07 WT (Table 5). Immunoblot testing for presence of α-SNAP Rhg1 LC protein revealed that the one transgenic line for the α-SNAP Rhg1 LC+NSF Ch07 WT DNA construct failed to express α-SNAP Rhg1 LC protein ( FIG. 14 ). In contrast, four of the five lines that received the α-SNAP Rhg1 LC+NSF RAN07 WT DNA construct did express α-SNAP Rhg1 LC protein ( FIG. 14 ). These findings provide further evidence that presence of a nematode resistance-associated Rhg1 α-SNAP protein is poorly tolerated in soybean lines that express only wild-type NSF proteins, and that NSF RAN07 WT or a similarly suitable NSF partner protein is necessary to recover viable soybean lines that express a nematode resistance-associated Rhg1 α-SNAP. 
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Recovery rate of transgenic soybean lines expressing 
               
               
                 SCN-resistance-associated Rhg1 α-SNAP 
               
            
           
           
               
               
               
            
               
                   
                 DNA construct used to 
                 Number of  
               
               
                   
                 transform soybean 
                 Williams 82 
               
               
                   
                 variety Williams 82 
                 transformants recovered 
               
               
                   
                   
               
            
           
           
               
               
               
            
               
                   
                 pC23S (empty vector) 
                 11 
               
               
                   
                 α-SNAP-WT (no added NSF) 
                 5 
               
               
                   
                 α-SNAP-Rhg1-LC (no added 
                 0 
               
               
                   
                 NSF) 
                   
               
               
                   
                 NSF-WT + α-SNAP-WT 
                 3 
               
               
                   
                 NSF-RAN07 + α-SNAP-WT 
                 2 
               
               
                   
                 NSF-WT + α-SNAP-Rhg1-LC 
                 1 
               
               
                   
                 NSF-RAN07 + α-SNAP-Rhg1-LC 
                 5 
               
               
                   
                   
               
            
           
         
       
     
     Example 9: Modified NSF BLASTp Alignment in Plant Species 
     The WT NSF sequence for wild type  Glycine max  (accession number AWH66430.1 was entered into BLASTp and modified at R4Q, N21Y, S25N, (del)116F, and M1811. The modified sequence was then entered into BLASTp to determine the occurrence, in the NSF proteins of 100 other plant species, of amino acids at the protein residue positions of the above key NSF RAN07  amino acids. The amino acid expressed at positions 4, 21, 25, 116 and 181 in the BLASTp results were compared against the  Glycine max  NSF RAN07  and the data entered into Table 6. In sequences for which BLASTp protein alignment started after the designated amino acid position, that position is marked N/A. Naturally occurring proteins encoding the R4Q or N21Y residues found in  Glycine max  NSF RAN07  were not present in the sequences for any of the other plant species compared via BLASTp. 
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Modified NSF BLASTp Alignment in Plant Species 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
                 % 
               
               
                   
                   
                 NSF Accession 
                 % 
                   
                   
                   
                   
                 — 
                 M181I 
                 Query 
               
               
                 Genus Species 
                 Plant 
                 Number 
                 Identity 
                 Identities 
                 R4Q 
                 N21Y 
                 S25N 
                 116F 
                 (Subst) 
                 Cover 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 
                   Glycine Max 
                 
                 Soybean 
                 XP_003529321.1 
                 99.33 
                 742/747 
                 R 
                 N 
                 S 
                 — 
                 M 
                 99.73 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 XP_003541535.1 
                 97.57 
                 724/742 
                 N/A 
                 N 
                 S 
                 — 
                 M 
                 98.65 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Soja 
                 
                 Wild Soybean 
                 KHN10009.1 
                 95.98 
                 717/747 
                 N/A 
                 N 
                 S 
                 — 
                 M 
                 97.19 
               
               
                 
                   Phaseolus 
                 
                 Common/ 
                 XP_007159324.1 
                 92.50 
                 691/747 
                 L 
                 N 
                 T 
                 — 
                 L 
                 96.79 
               
               
                 
                   Vulgaris 
                 
                 Green Bean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Hypo  Glycine   
                 KRH50034.1 
                 99.00 
                 696/703 
                 R 
                 N 
                 S 
                 — 
                 M 
                 99.57 
               
               
                   
                 
                   Max 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   Vigna Radiata  var. 
                 Mung Bean 
                 XP_014510227.1 
                 92.60 
                 688/743 
                 N/A 
                 N 
                 S 
                 — 
                 M 
                 96.77 
               
               
                 
                   radiata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vigna angularis 
                 
                 Adzuki Bean 
                 XP_017411260.1 
                 92.60 
                 688/743 
                 N/A 
                 N 
                 S 
                 — 
                 M 
                 96.64 
               
               
                 
                   Arachis ipaensis 
                 
                 Peanut 
                 XP_016190089.1 
                 89.83 
                 671/747 
                 L 
                 N 
                 Q 
                 — 
                 M 
                 94.78 
               
               
                 
                   Arachis 
                 
                 Wild Peanut 
                 XP_015956468.1 
                 89.83 
                 671/747 
                 L 
                 N 
                 Q 
                 — 
                 M 
                 94.91 
               
               
                 
                   duranensis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lupinus 
                 
                 Lupin 
                 XP_019445668.1 
                 88.89 
                 664/747 
                 W 
                 N 
                 Q 
                 — 
                 M 
                 94.78 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lupinus 
                 
                 Narrow leaf 
                 XP_019421896.1 
                 90.29 
                 660/731 
                 N/A 
                 N 
                 Q 
                 — 
                 M 
                 95.21 
               
               
                 
                   angustifolius 
                 
                 Lupiin (Herb) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cajanus cajan 
                 
                 Pigeon Pea 
                 XP_020225776.1 
                 90.85 
                 665/732 
                 N/A 
                 N 
                 Q 
                 — 
                 M 
                 95.36 
               
               
                   
                 (Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cajanus cajan 
                 
                 Pigeon Pea 
                 KYP76270.1 
                 90.45 
                 663/733 
                 N/A 
                 N 
                 Q 
                 — 
                 M 
                 95.23 
               
               
                   
                 (Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vigna angularis 
                 
                 Adzuki Bean 
                 KOM31050.1 
                 88.69 
                 659/743 
                 N/A 
                 N 
                 S 
                 — 
                 M 
                 92.6 
               
               
                 
                   Medicago 
                 
                 BarrelClover 
                 XP_024637282.1 
                 85.41 
                 638/747 
                 R 
                 N 
                 Q 
                 I 
                 M 
                 93.04 
               
               
                 
                   truncatula 
                 
                 (small 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Mediterranean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   cephalotus 
                 
                 Australian 
                 GAV67671.1 
                 84.74 
                 633/747 
                 R 
                 N 
                 A 
                 — 
                 I 
                 92.37 
               
               
                 
                   follicularis 
                 
                 Pitcher Plant 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Quercus suber 
                 
                 Cork Oak 
                 XP_023924241.1 
                 86.44 
                 631/730 
                 N/A 
                 N 
                 A 
                 — 
                 M 
                 95.07 
               
               
                 
                   Citrus clementina 
                 
                 Clementine 
                 XP_006428558.1 
                 84.739 
                 633/747 
                 R 
                 N 
                 A 
                 — 
                 I 
                 93.57 
               
               
                 
                   Medicago 
                 
                 BarrelClover 
                 KEH31080.1 
                 84.707 
                 637/752 
                 R 
                 N 
                 Q 
                 I 
                 M 
                 92.29 
               
               
                   truncatula ] 
                 (small 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Mediterrian 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cicer arietinum 
                 
                 ChickPea 
                 XP_004505051.1 
                 88.615 
                 646/729 
                 N/A 
                 N 
                 T 
                 I 
                 M 
                 95.2 
               
               
                 
                   Citrus sinensis 
                 
                 Sweet 
                 KDO54905.1 
                 84.626 
                 633/748 
                 R 
                 N 
                 A 
                 — 
                 I 
                 93.45 
               
               
                   
                 Oranges 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 (blood, navel) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Populus 
                 
                 Black 
                 XP_002305796.2 
                 84.605 
                 632/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 91.97 
               
               
                 
                   trichocarpa 
                 
                 cottonwood 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Herrania 
                 
                 Colombian 
                 XP_021294427.1 
                 84.584 
                 631/746 
                 R 
                 S 
                 T 
                 — 
                 M 
                 92.63 
               
               
                 
                   umbratica 
                 
                 Cocoa 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Populus 
                 
                 Desert Poplar 
                 XP_011027829.1 
                 84.605 
                 632/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 91.83 
               
               
                 euphratica 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Jatropha curcas 
                 
                 Jatropha 
                 XP_012091606.1 
                 85.346 
                 629/737 
                 N/A 
                 N 
                 P 
                 — 
                 M 
                 93.22 
               
               
                   
                 curcas 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Ziziphus jujuba 
                 
                 Jujube red 
                 XP_015890094.1 
                 85.121 
                 635/746 
                 R 
                 N 
                 P 
                 — 
                 M 
                 92.63 
               
               
                   
                 date 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Durio zibethinus 
                 
                 
                   Durio 
                 
                 XP_022720468.1 
                 84.471 
                 631/747 
                 R 
                 G 
                 T 
                 — 
                 M 
                 92.5 
               
               
                   
                 
                   zibethinus 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Manihot esculenta 
                 
                 Yuca 
                 XP_021597323.1 
                 84.987 
                 634/746 
                 R 
                 N 
                 A 
                 — 
                 M 
                 91.69 
               
               
                   Pyrus  × 
                 Chinese white 
                 XP_009339728.1 
                 85.007 
                 635/747 
                 R 
                 N 
                 P 
                 — 
                 M 
                 93.17 
               
               
                 
                   bretschneideri 
                 
                 pear 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Morus notabilis 
                 
                 Black 
                 XP_024029108.1 
                 84.718 
                 632/746 
                 R 
                 S 
                 T 
                 — 
                 M 
                 93.16 
               
               
                   
                 Mulberry 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Plant 
                 XP_012450449.1 
                 84.07 
                 628/747 
                 L 
                 S 
                 T 
                 — 
                 M 
                 92.37 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Citrus unshiu 
                 
                 Mandarin 
                 GAY44590.1 
                 84.337 
                 630/747 
                 R 
                 N 
                 A 
                 — 
                 I 
                 92.9 
               
               
                   
                 Orange 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Quercus suber 
                 
                 Cork Oak 
                 XP_023927780.1 
                 85.753 
                 626/730 
                 T 
                 N 
                 A 
                 — 
                 M 
                 94.38 
               
               
                 
                   Malus domestica 
                 
                 Apple Tree 
                 XP_008364158.1 
                 84.873 
                 634/747 
                 R 
                 N 
                 P 
                 — 
                 M 
                 93.04 
               
               
                 
                   Gossypium 
                 
                 Cotton Tree 
                 XP_017642474.1 
                 84.853 
                  633/7465 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.82 
               
               
                 
                   arboreum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Tree 
                 XP_017646058.1 
                 83.668 
                 625/747 
                 L 
                 S 
                 T 
                 — 
                 M 
                 92.1 
               
               
                 
                   arboreum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Mexican 
                 XP_016676150.1 
                 83.534 
                 624/747 
                 L 
                 S 
                 T 
                 — 
                 M 
                 92.1 
               
               
                 
                   hirsutum 
                 
                 Cotton Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Hevea brasiliensis 
                 
                 Rubberwood 
                 XP_021641739.1 
                 84.584 
                 631/746 
                 R 
                 N 
                 S 
                 — 
                 M 
                 91.42 
               
               
                 
                   Durio zibethinus 
                 
                 Durian Tree 
                 XP_022724072.1 
                 84.048 
                 686/746 
                 R 
                 S 
                 T 
                 — 
                 M 
                 91.96 
               
               
                 
                   Lupinus 
                 
                 Lupin 
                 OIV94352.1 
                 91.215 
                 623/683 
                 N/A 
                 N/A 
                 N/A 
                 — 
                 M 
                 96.34 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Mexican 
                 XP_016683459.1 
                 83.802 
                 626/747 
                 L 
                 S 
                 T 
                 — 
                 M 
                 91.97 
               
               
                 
                   hirsutum 
                 
                 Cotton Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton 
                 XP_012450761.1 
                 84.048 
                 627/746 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.96 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton 
                 KJB68632.1 
                 83.936 
                 627/747 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.83 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Prunus avium 
                 
                 Sweet/wild 
                 XP_021825850.1 
                 83.78 
                 625/746 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.76 
               
               
                   
                 Cherry tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Hevea brasiliensis 
                 
                 Rubberwood 
                 XP_021640046.1 
                 83.512 
                 623/746 
                 R 
                 N 
                 L 
                 — 
                 M 
                 91.69 
               
               
                 
                   Lupinus 
                 
                 Blue Lupine 
                 OIW10410.1 
                 85.007 
                 635/747 
                 W 
                 N 
                 Q 
                 — 
                 M 
                 90.36 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Plant 
                 XP_012450763.1 
                 84.048 
                 686/746 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.96 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Theobroma cacao 
                 
                 Cacao Tree 
                 XP_007025619.2 
                 83.78 
                 625/746 
                 R 
                 S 
                 A 
                 — 
                 M 
                 92.23 
               
               
                 
                   Populus 
                 
                 Black 
                 XP_006377363.1 
                 83.936 
                 627/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 91.43 
               
               
                 
                   trichocarpa 
                 
                 cottonwood 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypim 
                 
                 Cotton Plant 
                 XP_012450762.1 
                 84.048 
                 627/746 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.96 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Hevea brasiliensis 
                 
                 Rubber Tree 
                 XP_021657769.1 
                 84.316 
                 629/746 
                 R 
                 N 
                 D 
                 — 
                 M 
                 91.15 
               
               
                 
                   Eucalyptus grandis 
                 
                 Eucalyptus or 
                 XP_010057417.1 
                 83.914 
                 626/746 
                 R 
                 N 
                 A 
                 — 
                 K 
                 92.36 
               
               
                   
                 Rose Gum 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Populus 
                 
                 Black 
                 PNT11917.1 
                 83.936 
                 627/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 91.43 
               
               
                 
                   trichocarpa 
                 
                 Cottonwood 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Prunus persica 
                 
                 Peach 
                 XP_007214647.1 
                 83.78 
                 691/746 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.63 
               
               
                 
                   Prunus mume 
                 
                 Japanese 
                 XP_008225100.1 
                 83.646 
                 624/746 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.76 
               
               
                   
                 Apricot 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   Pyrus  × 
                 Chinese white 
                 XP_009352914.1 
                 83.802 
                 626/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.77 
               
               
                 
                   bretschneideri 
                 
                 pear 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Hevea brasiliensis 
                 
                 Rubber Tree 
                 XP_021640045.1 
                 83.378 
                 622/746 
                 R 
                 N 
                 L 
                 — 
                 M 
                 91.55 
               
               
                 
                   Gossypium 
                 
                 Mexican 
                 XP_016751989.1 
                 83.668 
                 625/747 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.7 
               
               
                 
                   hirsutum 
                 
                 Cotton 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Extra long 
                 PPS13789.1 
                 83.202 
                 634/762 
                 W 
                 S 
                 P 
                 — 
                 M 
                 89.76 
               
               
                 
                   barbadense 
                 
                 staple cotton 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 (Sea Island 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Cotton) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Upland Cotton 
                 XP_016751992.1 
                 83.78 
                 625/746 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.82 
               
               
                 
                   hirsutum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Theobroma cacao 
                 
                 Cacao tree 
                 XP_017978707.1 
                 83.556 
                 625/746 
                 R 
                 S 
                 A 
                 — 
                 M 
                 91.98 
               
               
                 
                   Gossypium 
                 
                 Upland Cotton 
                 XP_016751991.1 
                 83.78 
                 625/746 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.82 
               
               
                 
                   hirsutum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Upland Cotton 
                 XP_016751990.1 
                 83.78 
                 625/746 
                 W 
                 S 
                 P 
                 — 
                 M 
                 91.82 
               
               
                 
                   hirsutum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Tarenaya 
                 
                 Spider Flower 
                 XP_010529424.1 
                 83.133 
                 621/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.1 
               
               
                 
                   hassleriana 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Juglans regia 
                 
                 Walnut Tree 
                 XP_018860049.1 
                 84.146 
                 621/738 
                 N/A 
                 S 
                 P 
                 — 
                 M 
                 92.95 
               
               
                 
                   Populus 
                 
                 Desert Poplar 
                 XP_011043386.1 
                 83.534 
                 624/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 90.9 
               
               
                 
                   euphratica 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Prunus yedoensis 
                 
                 King Cherry 
                 PQM34143.1 
                 83.512 
                 623/746 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.09 
               
               
                 var.  nudiflora   
                 (Korean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Cherry) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Carica papaya 
                 
                 Papaya 
                 XP_021902227.1 
                 84.182 
                 628/746 
                 R 
                 N 
                 S 
                 — 
                 M 
                 92.36 
               
               
                 
                   Cucumis melo 
                 
                 Muskmelon 
                 XP_008463616.1 
                 82.038 
                 612/746 
                 R 
                 N 
                 Q 
                 — 
                 M 
                 92.23 
               
               
                 
                   Manihot esculenta 
                 
                 Yuca 
                 XP_021598339.1 
                 83.244 
                 680/746 
                 W 
                 N 
                 A 
                 — 
                 M 
                 91.15 
               
               
                 
                   Populus 
                 
                 Black 
                 PNT11918.1 
                 82.827 
                 627/757 
                 R 
                 N 
                 A 
                 — 
                 M 
                 90.22 
               
               
                 
                   trichocarpa 
                 
                 cottonwood 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Extra long 
                 PPD95675.1 
                 82.26 
                 626/761 
                 W 
                 S 
                 P 
                 — 
                 M 
                 90.01 
               
               
                 
                   barbadense 
                 
                 staple cotton 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 (Sea Island 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Cotton) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita pepo 
                 
                 Winter Squash 
                 XP_023519438.1 
                 81.66 
                 610/747 
                 L 
                 S 
                 A 
                 — 
                 M 
                 91.7 
               
               
                 subsp.  Pepo   
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Tarenaya 
                 
                 Spider Flower 
                 XP_010538665.1 
                 82.597 
                 617/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 91.43 
               
               
                 
                   hassleriana 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Pumpkin 
                 XP_022927355.1 
                 81.769 
                 610/746 
                 L 
                 S 
                 A 
                 — 
                 M 
                 91.69 
               
               
                 
                   moschata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucumis sativus 
                 
                 Cucumber 
                 XP_004139535.1 
                 81.769 
                 610/746 
                 R 
                 N 
                 Q 
                 — 
                 M 
                 92.09 
               
               
                 
                   Cucurbita maxima 
                 
                 Squash 
                 XP_023001327.1 
                 81.769 
                 610/746 
                 L 
                 S 
                 A 
                 — 
                 M 
                 91.69 
               
               
                 
                   Trifolium 
                 
                 Clover 
                 GAU38492.1 
                 82.097 
                 642/782 
                 R 
                 N 
                 Q 
                 I 
                 M 
                 88.75 
               
               
                 
                   subterraneum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Nicotiana tabacum 
                 
                 Cultivated 
                 BAA13101.1 
                 81.233 
                 606/746 
                 R 
                 Y 
                 K 
                 — 
                 M 
                 91.96 
               
               
                 
                   Tobacco 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vitis vinifera 
                 
                 Grape Vine 
                 XP_002284987.1 
                 82.568 
                 611/740 
                 R 
                 N 
                 R 
                 — 
                 I 
                 92.03 
               
               
                 
                   Nicotiana 
                 
                 Tobacco Plant 
                 XP_009626763.1 
                 81.233 
                 606/746 
                 R 
                 N 
                 K 
                 — 
                 M 
                 91.96 
               
               
                 
                   tomentosiformis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Theobroma cacao 
                 
                 Cacao Tree 
                 EOY28241.1 
                 85.278 
                 614/720 
                 N/A 
                 N/A 
                 N/A 
                 — 
                 M 
                 93.06 
               
               
                 
                   Sesamum indicum 
                 
                 Seasame 
                 XP_011098317.1 
                 82.763 
                 605/731 
                 N/A 
                 N 
                 K 
                 — 
                 I 
                 91.93 
               
               
                 
                   Malus domestica 
                 
                 Apple 
                 XP_008383736.1 
                 83.802 
                 626/747 
                 R 
                 N 
                 A 
                 — 
                 M 
                 92.64 
               
               
                 
                   Nicotiana 
                 
                 Coyote 
                 XP_019251692.1 
                 80.965 
                 604/746 
                 R 
                 N 
                 K 
                 — 
                 M 
                 91.69 
               
               
                 
                   attenuata 
                 
                 Tobacco 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Actinidia chinensis 
                 
                 Kiwifruit 
                 PSR95688.1 
                 81.511 
                 604/741 
                 N/A 
                 N 
                 K 
                 — 
                 I 
                 91.36 
               
               
                 var.  chinensis   
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Punica granatum 
                 
                 Pomegranate 
                 PKI69442.1 
                 83.469 
                 616/738 
                 N/A 
                 N 
                 A 
                 — 
                 M 
                 92.14 
               
               
                 
                   Capsicum annuum 
                 
                 Chili Peppers 
                 XP_016574871.1 
                 80.697 
                 602/746 
                 R 
                 N 
                 K 
                 — 
                 M 
                 91.82 
               
               
                 
                   Ipomoea nil 
                 
                 Morning Glory 
                 XP_019187191.1 
                 81.905 
                 602/735 
                 N/A 
                 N 
                 K 
                 — 
                 L 
                 91.97 
               
               
                 
                   Handroanthus 
                 
                 Pink Trumpet 
                 PIN22741.1 
                 82.538 
                 605/733 
                 N/A 
                 N 
                 K 
                 — 
                 M 
                 92.22 
               
               
                 
                   impetiginosus 
                 
                 Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vitis vinifera 
                 
                 Grape Vine 
                 CBI20305.3 
                 82.027 
                 607/740 
                 N/A 
                 N 
                 R 
                 — 
                 I 
                 91.62 
               
               
                 
                   Daucus carota 
                 
                 Carrot 
                 XP_017252931.1 
                 83.083 
                 609/733 
                 N/A 
                 S 
                 K 
                 — 
                 M 
                 91.68 
               
               
                 
                   subsp. Sativus 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Solanum Pennellii 
                 
                 Tomato 
                 XP_015062393.1 
                 83.083 
                 599/746 
                 R 
                 N 
                 K 
                 — 
                 M 
                 91.82 
               
               
                 
                   Solanum 
                 
                 Potato 
                 XP_006351809.1 
                 80.295 
                 599/746 
                 R 
                 N 
                 K 
                 — 
                 M 
                 91.69 
               
               
                 
                   tuberosum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Solanum 
                 
                 Tomato 
                 XP_004230528.1 
                 80.295 
                 598/746 
                 R 
                 N 
                 K 
                 — 
                 M 
                 91.96 
               
               
                 
                   lycopersicum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Helianthus annuus 
                 
                 Sunflower 
                 XP_022013369.1 
                 81.351 
                 607/740 
                 N/A 
                 N 
                 K 
                 — 
                 M 
                 91.35 
               
               
                 
                   Gossypium 
                 
                 Cotton Plant 
                 KJB66715.1 
                 81.928 
                 612/747 
                 L 
                 S 
                 T 
                 — 
                 M 
                 89.69 
               
               
                   raimondii  (Hypo) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Macleaya cordata 
                 
                 Plume Poppy 
                 OVA14922.1 
                 81.325 
                 614/755 
                   
                 N 
                 S 
                 — 
                 M 
                 89.4 
               
               
                   
               
            
           
         
       
     
     Example 10: Modified α-SNAP BLASTp Alignment in Plant Species 
     The Rhg1 LC haplotype Glyma.18G022500 encoded protein sequence was entered into BLASTp and the results for 100 plant species were further examined. The BLASTp results at the α-SNAP C-terminus amino acid residues of interest (amino acid positions 208, 284, 285, 286, and 287, in the soybean Glyma.18G022500 product) were compared against the Rhg1 LC haplotype and entered into Table 7. The majority of plant species alignments terminated prior to the sequences of interest and are represented in the table as N/A. 
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Modified α-SNAP BLASTp Alignment in Plant Species 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                   
                   
                 α-SNAP 
                   
                   
                   
                   
                   
                   
                   
                 % 
               
               
                 Genus 
                   
                 Accession 
                 % 
                   
                   
                   
                   
                   
                   
                 Query 
               
               
                 Species 
                 Plant 
                 Number 
                 Identity 
                 Identities 
                 D208E 
                 E284 
                 E285 
                 D286 
                 D287 
                 Cover 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 
                   Glycine Max 
                 
                 Soybean 
                 NP_001242059.2 
                 100 
                 289/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 100 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 ACU19524.1 
                 99.308 
                 287/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 99.65 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 ARD05064.1 
                 99.649 
                 284/285 
                 E 
                 E 
                 E 
                 N/A 
                 N/A 
                 100 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 ACU18668.1 
                 99.298 
                 283/285 
                 D 
                 E 
                 Q 
                 N/A 
                 N/A 
                 100 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 NP_001344346.1 
                 97.578 
                 282/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 98.96 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cajanus 
                 
                 Pigeon Pea 
                 XP_020237258.1 
                 95.848 
                 277/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 97.92 
               
               
                 
                   cajan 
                 
                 (Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Trifolium 
                 
                 Clover 
                 GAU29434.1 
                 91.003 
                 263/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.89 
               
               
                 
                   subterraneum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Medicago 
                 
                 Barrel Clover 
                 XP_003601014.1 
                 89.619 
                 259/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.19 
               
               
                 
                   truncatula 
                 
                 (small 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Mediterranean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Quercus 
                 
                 Cork Oak 
                 XP_023896842.1 
                 89.273 
                 258/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.89 
               
               
                 
                   suber 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Durio 
                 
                 
                   Durio 
                 
                 XP_022774310.1 
                 88.581 
                 256/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.16 
               
               
                 
                   zibethinus 
                 
                 
                   zibethinus 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lupinus 
                 
                 Lupin 
                 XP_019456553.1 
                 88.235 
                 255/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.54 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Phaseolus 
                 
                 Common/ 
                 XP_007163598.1 
                 94.464 
                 273/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 97.58 
               
               
                 
                   vulgaris 
                 
                 Green Bean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 KRH14886.1 
                 87.889 
                 254/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.89 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vigna 
                 
                 Adzuki 
                 XP_017407790.1 
                 93.772 
                 271/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 97.23 
               
               
                 
                   angularis 
                 
                 Bean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cajanus 
                 
                 Pigeon Pea 
                 XP_020237651.1 
                 87.543 
                 253/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.54 
               
               
                 
                   cajan 
                 
                 (Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Juglans 
                 
                 Walnut Tree 
                 XP_018821859.1 
                 88.235 
                 255/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   regia 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vigna 
                 
                 Mung Bean 
                 XP_014490390.1 
                 94.118 
                 272/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.89 
               
               
                   radiata  var. 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   radiata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Medicago 
                 
                 BarrelClover  
                 XP_003616738.1 
                 86.505 
                 250/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.19 
               
               
                 
                   truncatula 
                 
                 (small 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Mediterranean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Theobroma 
                 
                 Cacao Tree 
                 EOY02634.1 
                 88.235 
                 255/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.5 
               
               
                 
                   cacao 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Herrania 
                 
                 Colombian 
                 XP_021299224.1 
                 87.889 
                 254/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.5 
               
               
                 
                   umbratica 
                 
                 Cocoa 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Theobroma 
                 
                 Cacao Tree 
                 XP_007031708.2 
                 87.889 
                 254/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.5 
               
               
                 
                   cacao 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cicer 
                 
                 ChickPea 
                 XP_004500538.1 
                 92.042 
                 266/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.89 
               
               
                 
                   arietinum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Phaseolus 
                 
                 Common/ 
                 XP _007141718.1 
                 86.159 
                 249/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.19 
               
               
                 
                   vulgaris 
                 
                 Green 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Bean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Phaseolus 
                 
                 Common/ 
                 AHA84269.1 
                 93.38 
                 268/287 
                 D 
                 E 
                 E 
                 D 
                 E 
                 96.86 
               
               
                 
                   vulgaris 
                 
                 Green Bean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vigna 
                 
                 Adzuki 
                 XP_017429402.1 
                 84.775 
                 277/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   angularis 
                 
                 Bean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lotus 
                 
                 Trefoil/Wild 
                 AFK46359.1 
                 91.696 
                 265/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 97.23 
               
               
                 
                   japonicus 
                 
                 Legume 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Juglans 
                 
                 Walnut Tree 
                 XP_018838975.1 
                 90.311 
                 261/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 97.58 
               
               
                 
                   regia 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Vigna 
                 
                 Mung Bean 
                 XP_014504530.1 
                 84.775 
                 245/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                   radiata  var. 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   radiata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Plant 
                 XP_012453802.1 
                 85.467 
                 247/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Mexican 
                 NP_001314193.1 
                 86.851 
                 251/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.16 
               
               
                 
                   hirsutum 
                 
                 Cotton Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 XP_003519412.1 
                 85.813 
                 248/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.81 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Arachis 
                 
                 Peanut 
                 XP_016180830.1 
                 91.003 
                 263/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   ipaensis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Plant 
                 XP_012445339.1 
                 86.505 
                 250/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.81 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine Max 
                 
                 Soybean 
                 NP_001242555.1 
                 85.813 
                 248/289 
                 G 
                 E 
                 G 
                 D 
                 D 
                 94.81 
               
               
                 Predicted 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lupinus 
                 
                 Lupin 
                 XP_019437582.1 
                 90.311 
                 261/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lupinus 
                 
                 Lupin 
                 XP_019415244.1 
                 90.657 
                 262/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.16 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Mexican 
                 XP_016677490.1 
                 84.775 
                 245/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.5 
               
               
                 
                   hirsutum 
                 
                 Cotton Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Manihot 
                 
                 Yuca 
                 XP_021617295.1 
                 85.121 
                 246/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.5 
               
               
                 
                   esculenta 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Malus 
                 
                 Apple Tree 
                 XP_008369314.1 
                 83.737 
                 242/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.81 
               
               
                 
                   domestica 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cicer 
                 
                 ChickPea 
                 XP_004491041.1 
                 83.737 
                 242/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   arietinum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucumis 
                 
                 Muskmelon 
                 XP_008456753.1 
                 85.813 
                 248/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.43 
               
               
                 
                   melo 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   Pyrus  × 
                 Chinese 
                 XP_009369241.1 
                 83.045 
                 240/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.81 
               
               
                 
                   bretschneideri 
                 
                 white pear 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Corchorus 
                 
                 White Jute 
                 OMO73552.1 
                 84.88 
                 247/291 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.44 
               
               
                 
                   capsularis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Plant 
                 XP_012489506.1 
                 84.775 
                 245/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.08 
               
               
                 
                   raimondii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Prunus 
                 
                 Sweet/wild  
                 XP_021824795.1 
                 83.391 
                 241/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.12 
               
               
                 
                   avium 
                 
                 Cherry tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Lupinus 
                 
                 Lupin 
                 OIW15090.1 
                 88.176 
                 261/296 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.58 
               
               
                 
                   angustifolius 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Extra long 
                 PPR99271.1 
                 79.677 
                 247/310 
                 D 
                 E 
                 E 
                 D 
                 D 
                 89.35 
               
               
                 
                   barbadense 
                 
                 staple cotton  
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 (Sea Island 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Cotton) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Glycine soja 
                 
                 Wild Soybean 
                 KHN38559.1 
                 86.17 
                 243/282 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.39 
               
               
                 
                   Rosa 
                 
                 China 
                 XP_024170812.1 
                 83.737 
                 242/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.43 
               
               
                 
                   chinensis 
                 
                 rose/Chinese 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 rose 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Extra long 
                 PPS02529.1 
                 84.083 
                 243/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.08 
               
               
                 
                   barbadense 
                 
                 staple cotton  
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 (Sea Island 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Cotton) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Parasponia 
                 
                 
                   Parasponia 
                 
                 PON79077.1 
                 87.889 
                 254/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.89 
               
               
                 
                   andersonii 
                 
                 
                   andersonii 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Morus 
                 
                 Black 
                 XP_024018217.1 
                 87.889 
                 254/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.19 
               
               
                 
                   notabilis 
                 
                 Mulberry 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Jatropha 
                 
                 Jatropha 
                 XP_012091205.1 
                 84.083 
                 243/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.12 
               
               
                 
                   curcas 
                 
                 curcas 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Citrus 
                 
                 Clementine 
                 XP_006435852.1 
                 86.851 
                 251/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   clementina 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cephalotus 
                 
                 Australian 
                 GAV62462.1 
                 87.197 
                 252/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.85 
               
               
                 
                   follicularis 
                 
                 Pitcher Plant 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Durio 
                 
                 
                   Durio 
                 
                 XP_022741218.1 
                 87.543 
                 253/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.16 
               
               
                 
                   zibethinus 
                 
                 
                   zibethinus 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Populus 
                 
                 Desert Poplar 
                 XP_011005868.1 
                 84.321 
                 242/287 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.73 
               
               
                 
                   euphratica 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 Populus 
                 Black 
                 XP_002312193.1 
                 83.972 
                 241/287 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.73 
               
               
                 
                   trichocarpa 
                 
                 cottonwood 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Populus 
                 
                 Black 
                 XP_006378643.2 
                 83.624 
                 240/287 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.43 
               
               
                 
                   trichocarpa 
                 
                 cottonwood 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Cotton Tree 
                 XP_017628059.1 
                 83.391 
                 241/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   arboreum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Trema 
                 
                 Charcoal- 
                 PON83245.1 
                 87.543 
                 253/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.54 
               
               
                 
                   orientalis 
                 
                 tree/Indian 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 charcoal- 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 tree/pigeon 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 wood/Oriental 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 trema 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucumis 
                 
                 Cucumber 
                 XP_004138403.1 
                 84.429 
                 244/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   sativus 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Gossypium 
                 
                 Mexican 
                 XP_016708559.1 
                 83.391 
                 241/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   hirsutum 
                 
                 Cotton Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Winter 
                 XP_023515361.1 
                 84.775 
                 245/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.08 
               
               
                   pepo  subsp. 
                 Squash 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Pepo 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Manihot 
                 
                 Yuca 
                 XP_021626521.1 
                 86.851 
                 251/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 96.19 
               
               
                 
                   esculenta 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Durio 
                 
                 
                   Durio 
                 
                 XP_022750516.1 
                 87.591 
                 240/274 
                 D 
                 N/A 
                 N/A 
                 N/A 
                 N/A 
                 94.16 
               
               
                 
                   zibethinus 
                 
                 
                   zibethinus 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Arachis 
                 
                 Wild 
                 XP_015973743.1 
                 82.007 
                 237/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.46 
               
               
                 
                   duranensis 
                 
                 Peanut 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Carica 
                 
                 Papaya 
                 XP_021904215.1 
                 87.889 
                 254/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.46 
               
               
                 
                   papaya 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Arachis 
                 
                 Peanut 
                 XP_016165661.1 
                 81.661 
                 236/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.12 
               
               
                 
                   ipaensis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Squash 
                 XP_022991069.1 
                 84.083 
                 243/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   maxima 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Corchorus 
                 
                 Jute 
                 OMO69109.1 
                 83.162 
                 242/291 
                 D 
                 E 
                 E 
                 D 
                 D 
                 91.41 
               
               
                 
                   olitorius 
                 
                 Mallow 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Hevea 
                 
                 Rubberwood 
                 XP_021668979.1 
                 87.197 
                 252/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.81 
               
               
                 
                   brasiliensis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Populus 
                 
                 Desert Poplar 
                 XP_011015133.1 
                 82.578 
                 237/287 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.08 
               
               
                 
                   euphratica 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Pumpkin 
                 XP_022964687.1 
                 84.429 
                 244/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   moschata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Hevea 
                 
                 Rubberwood 
                 XP_021688775.1 
                 86.159 
                 249/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.16 
               
               
                 
                   brasiliensis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Erythranthe 
                 
                 Seep 
                 XP_012840021.1 
                 80.969 
                 234/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.77 
               
               
                 
                   guttata 
                 
                 monkeyflower/ 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 yellow 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 monkeyflower 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Sesamum 
                 
                 Sesame 
                 XP_011084853.1 
                 84.083 
                 243/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.46 
               
               
                 
                   indicum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Medicago 
                 
                 BarrelClover 
                 XP_024639705.1 
                 87.97 
                 234/266 
                 D 
                 N/A 
                 N/A 
                 N/A 
                 N/A 
                 97.37 
               
               
                 
                   truncatula 
                 
                 (small 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Mediterranean 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Legume) 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Ricinus 
                 
                 Castor bean  
                 XP_002520820.1 
                 85.813 
                 248/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 95.5 
               
               
                 
                   communis 
                 
                 or castor oil 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Ziziphus 
                 
                 Jujube red 
                 XP_015877477.1 
                 80.969 
                 234/289 
                 D 
                 E 
                 D 
                 D 
                 D 
                 93.77 
               
               
                 
                   jujuba 
                 
                 date 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Eucalyptus 
                 
                 Eucalyptus or  
                 XP_010067574.1 
                 81.661 
                 236/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.43 
               
               
                 
                   grandis 
                 
                 Rose Gum 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Pumpkin 
                 XP_022956354.1 
                 80.969 
                 234/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.77 
               
               
                 
                   moschata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Squash 
                 XP_022991930.1 
                 80.969 
                 234/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.77 
               
               
                 
                   maxima 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Momordica 
                 
                 Bitter Melon 
                 XP_022146873.1 
                 80.969 
                 234/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.43 
               
               
                 
                   charantia 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Morus 
                 
                 Black 
                 EXB25858.1 
                 81.613 
                 253/310 
                 D 
                 E 
                 E 
                 D 
                 D 
                 89.68 
               
               
                 
                   notabilis 
                 
                 Mulberry 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Malus 
                 
                 Apple Tree 
                 XP_008374460.1 
                 84.083 
                 243/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.81 
               
               
                 
                   domestica 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Prunus 
                 
                 Peach 
                 XP_007218769.1 
                 83.391 
                 241/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.77 
               
               
                 
                   persica 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Prunus 
                 
                 Japanese 
                 XP_008233838.1 
                 83.045 
                 240/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 93.77 
               
               
                 
                   mume 
                 
                 Apricot 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Sesamum 
                 
                 Sesame 
                 XP_011076626.1 
                 82.699 
                 239/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.04 
               
               
                 
                   indicum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Squash 
                 XP_022992586.1 
                 85.467 
                 247/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.46 
               
               
                 
                   maxima 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Momordica 
                 
                 Bitter Melon 
                 XP_022134286.1 
                 85.813 
                 248/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.12 
               
               
                 
                   charantia 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Olea 
                 
                 Wild-olive 
                 XP _022880461.1 
                 81.661 
                 236/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   europaea 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 var. 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   sylvestris 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Cucurbita 
                 
                 Pumpkin 
                 XP_022939232.1 
                 85.121 
                 246/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 94.46 
               
               
                 
                   moschata 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Handroanthus 
                 
                 Pink Trumpet 
                 PIN13349.1 
                 82.007 
                 237/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 91.7 
               
               
                 
                   impetiginosus 
                 
                 Tree 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Nicotiana 
                 
                 Coyote 
                 XP_019225807.1 
                 79.585 
                 230/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.39 
               
               
                 
                   attenuata 
                 
                 Tobacco 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Punica 
                 
                 Pomegranate 
                 PKI40618.1 
                 78.547 
                 227/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 91.35 
               
               
                 
                   granatum 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Nicotiana 
                 
                 Woodland 
                 XP_009798526.1 
                 79.585 
                 230/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   sylvestris 
                 
                 tobacco/ 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 Flowering 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 tobacco 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Nicotiana 
                 
                 Tobacco Plant 
                 XP_009614295.1 
                 79.585 
                 230/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.73 
               
               
                 
                   tomentosiformis 
                 
                   
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Erythranthe 
                 
                 Seep 
                 XP_012858890.1 
                 79.239 
                 229/289 
                 D 
                 E 
                 D 
                 D 
                 D 
                 92.39 
               
               
                 
                   guttata 
                 
                 monkeyflower/ 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 yellow 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                   
                 monkeyflower 
                   
                   
                   
                   
                   
                   
                   
                   
                   
               
               
                 
                   Solanum 
                 
                 Tomato 
                 XP_004240900.1 
                 79.585 
                 230/289 
                 D 
                 E 
                 E 
                 D 
                 D 
                 92.04 
               
               
                 
                   lycopersicum 
                 
               
               
                   
               
            
           
         
       
     
     Materials &amp; Methods 
     Recombinant Protein Production 
     Vectors encoding recombinant α-SNAP Rhg1 HC, α-SNAP Rhg1 LC, α-SNAP Rhg1 WT, α-SNAP Rhg1 WT 1-285  and the WT alleles of NSF Glyma.07G195900 (NSF Ch07 ) and Glyma.13G180100 (NSF Chl3 ) were generated in Bayless et al., 2016. The open reading frames (ORFs) encoding the soybean NSF RAN07  allele of Glyma.07G195900 or  N. benthamiana  NSF were cloned into the expression vector pRham N-His-SUMO Kan according to manufacturer instructions (Lucigen). Recombinant α-SNAP and NSF proteins were also produced and purified as in Bayless et al. 2016. All expression constructs were chemically transformed into the expression strain “E. cloni 10G” (Lucigen), grown to OD 600 ˜0.60-0.70, and induced with 0.2% L-Rhamnose (Sigma) for either 8 hr at 37° C. or overnight at 28° C. Soluble, native recombinant His-SUMO-α-SNAPs or His-SUMO-NSF proteins were purified with PerfectPro Ni-NTA resin (5 PRIME), and eluted with imidazole, though no subsequent gel filtration steps were performed. Following the elution of the His-SUMO-fusion proteins, overnight dialysis was performed at 4° C. in 20 mM Tris (pH 8.0), 150 mM NaCl, 10% (vol/vol) glycerol, and 1.5 mM Tris (2-carboxyethyl)-phosphine. The His-SUMO affinity/solubility tags were cleaved from α-SNAP or NSF using 1 or 2 units of SUMO Express protease (Lucigen) and separated by rebinding of the tag with Ni-NTA resin and collecting the recombinant protein from the flowthrough. Recombinant protein purity was assessed by Coomassie blue staining and quantified via a spectrophotometer. 
     In Vitro NSF-α-SNAP Binding Assays 
     In vitro NSF binding assays were performed essentially as described in Barnard et. al. (1997) J Cell Biol 139(4): 875-883; and Bayless et al. (2016), Proc Natl Acad Sci USA 113(47): E7375-E7382; Briefly, 20 μg of each respective recombinant α-SNAP protein was added to the bottom of a 1.5-mL polypropylene tube and incubated at 25° C. for 20 min. Unbound α-SNAP proteins were then washed by adding α-SNAP wash buffer [25 mM Tris, pH 7.4, 50 mM KCl, 1 mM DTT, 0.4 mg/mL bovine serum albumin (BSA)]. After removal of wash buffer, 20 μg of recombinant NSF (1 μg/μL in NSF binding buffer), was then immediately added and incubated on ice for 10 min. The solution was then removed, and samples were immediately washed 2× with NBB to remove any unbound NSF. Samples were then boiled in 1×SDS loading buffer and separated on a 10% Bis-Tris SDS-PAGE, and silver-stained using the ProteoSilver Kit (Sigma-Aldrich), according to the manufacturer directions. The percentage of NSF bound by α-SNAP was then calculated using densitometric analysis with ImageJ. 
     Antibody Production and Validation 
     Affinity-purified polyclonal rabbit antibodies raised against α-SNAP Rhg1 HC, α-SNAP Rhg1 LC and wild-type α-SNAPs were previously generated and validated using recombinant proteins in Bayless 2016. The epitopes for these custom antibodies are the final six or seven C-terminal α-SNAP residues: “EEDDLT” (SEQ ID NO: 127), “EQHEAIT” (SEQ ID NO: 128), or “EEYEVIT” (SEQ ID NO: 129) for wild-type, high-, or low-copy α-SNAPs, respectively. For NSF, a synthetic peptide, “ETEKNVRDLFADAEQDQRTRGDESD” (SEQ ID NO: 130), corresponding to residues 300 to 324 of Glyma.07G195900 was used. This NSF antibody was previously shown to be cross-reactive with the  N. benthamiana -encoded NSF. 
     Immunoblotting 
     Tissue preparation and immunoblots were performed essentially as in (Song et al., 2015a; Bayless et al., 2016). Soybean roots or  N. benthamiana  leaf tissues were flash-frozen in N 2 (L), massed, and homogenized in a PowerLyzer 24 (MO BIO) for three cycles of 15 seconds, with flash-freezing in-between each cycle. Protein extraction buffer [50 mM Tris.HCl (pH 7.5), 150 mM NaCl, 5 mM EDTA, 0.2% Triton X-100, 10% (vol/vol) glycerol, 1/100 Sigma protease inhibitor cocktail] was then added at a 3:1 volume to mass ratio and samples were centrifuged and stored on ice. In noted experiments, Bradford assays were performed on each sample, and equal OD amounts of total protein were loaded in each sample lane for SDS/PAGE. Immunoblots for either Rhg1 α-SNAP were incubated overnight at 4° C. in 5% (wt/vol) nonfat dry milk TBS-T (50 mM Tris, 150 mM NaCl, 0.05% Tween 20) at 1:1,000. NSF immunoblots were performed similarly, except incubations were for 1 h at room temperature. Secondary horseradish peroxidase-conjugated goat anti-rabbit IgG was added at 1:10,000 and incubated for 1 h at room temperature on a platform shaker, followed by four washes with TBS-T. Chemiluminescence detection was performed with SuperSignal West Pico or Dura chemiluminescent substrate (Thermo Scientific) and developed using a ChemiDoc MP chemiluminescent imager (Bio-Rad). 
     Transgenic Soybean Root Generation 
     Binary expression constructs were transformed into  Agrobacterium rhizogenes  strain, “Arqua1”. Transgenic soybean roots were produced as described in (Cook et al., 2012, Science 338, 1206-1209). 
     Transient  Agrobacterium  Expression in  Nicotiana benthamiana. Agrobacterium tumefaciens  strain GV3101 was used for transient protein expression of all constructs via syringe-infiltration at OD 600  0.60 for NSF constructs or OD 600  0.80 for α-SNAP constructs into young leaves of ˜4-wk-old  N. benthamiana  plants. GV3101 cultures were grown overnight at 28° C. in 25 μg/mL kanamycin and rifampicin and induced for ˜3.5 h in 10 mM Mes (pH 5.60), 10 mM MgCl2, and 100 μM acetosyringone prior to leaf infiltration.  N. benthamiana  plants were grown in a Percival set at 25° C. with a photoperiod of 16 h light at 100 μE·m-2·s-1 and 8 h dark. For α-SNAP complementation assays, GV3101 cultures were well-mixed with one volume of an empty vector control, or of the respective NSF construct immediately before co-infiltration. NSF RAN07  or the  N. benthamiana  NSF were PCR amplified from a root cDNA library of Rhg1 LC  variety, “Forrest” or a  N. benthamiana  leaf cDNA library using KAPA HiFi polymerase, respectively. Expression cassettes for NSF N.benthamiana , NSF Ch13 , NSF Ch07  and NSF RAN07  ORFs were directly assembled into a pBluescript vector containing the soybean ubiquitin (GmUbi) promoter and NOS terminator using Gibson assembly. The NSF expression cassettes were then digested with the restriction enzymes NotI-SalI and ligated with T4 DNA ligase into the previously described binary vector, pSM101-linker, which was cut with PspOMI-SalI restriction sites. The ORF encoding the α-SNAP Ch11  Intron-Retention (IR) allele was amplified with Kapa HiFi from a root cDNA library of Rhg1 LC  variety “Forrest” while the ORF encoding WT α-SNAP Ch11  was previously generated in (Bayless et al., 2016, Proc. Natl. Acad. Sci. USA 113, E7375-E7382). Both α-SNAP Ch11  and α-SNAP Ch11  IR were Gibson assembled into a pBluescript vector containing a GmUbi-N-HA tag and NOS terminator, cut with PstI-XbaI and ligated into the binary vector, pSM101, cut with the same restriction pair. An 11.14 kb native genomic region encoding α-SNAP Rhg1 WT was amplified with Kapa HiFi from a previously described fosmid subclone (Fosmid 19) with AvrII-SbfI restriction ends, and then digested and ligated into the binary vector, pSM101, cut with XbaI-PstI. A 6.85 kb native locus encoding α-SNAP Chi I  was amplified from gDNA of Williams82 into two fragments (3.25 kb and 3.60 kb fragments) and Gibson assembled into pSM101 vector cut with BamHI-PstI. 
     Protein Structure Modeling and Sequence Logo 
     NSFRAN07, α-SNAPCh11 and α-SNAPCh11IR structural homology models were generated using SWISS-MODEL and output PDB files viewed and labeled using PyMol. NSFRAN07 was modeled to NSFCHO (Chinese hamster ovary) (PDB 3j97.1) cryo-EM structure from Zhao et al (Brunger group). 20S supercomplex modeling also generated using PDB 3j97, with α-SNAPs and SNAREs of  Rattus norvegicus  origin (Zhao et al., 2015, Nature 518: 61-67). α-SNAPCh11 and α-SNAPCh11IR were modeled to sec17 (yeast α-SNAP) crystal structure 1QQE donated courtesy of Rice et al (Rice and Brunger, 1999, Mol Cell 4: 85-95). 
     The R4Q NSF amino acid consensus logo was generated using WebLogo. (Crooks G E, et al. (2004), Genome Res 14: 1188-1190). 
     Whole-Genome Sequencing Data Analysis 
     Whole-genome sequencing data of 12 soybean varieties was obtained from previously published studies (Song et al., 2017, The Plant Genome 10); Cook et al., 2014 Plant Physiol 165, 630-647)). Illumina sequencing reads were aligned to the Williams 82 reference genome (Wm82.a2.v1; www.phytozome.org/) using BWA (version 0.7.12) (Li and Durbin, 2009, Bioinformatics, 25:1754-60). Reads were initially mapped using the default settings of the aln command with the subsequent pairings performed with the sampe command. Alignments were next processed using the program Picard (version 2.9.0) to add read group information (AddOrReplaceReadGroups), mark PCR duplicates (MarkDuplicates, and merge alignments from separate sequencing runs (MergeSamFiles). The processed .bam files were then converted to vcf format using a combination of samtools (version 0.1.19) and bcftools (version 0.1.19). Finally, consensus sequences were generated from these .vcf files using the FastaAlternateReferenceMaker tool within GATK (version 3.7.0; DePristo et al., 2011, Nat Genet 43: 491-498). 
     Having described the invention in detail and by reference to specific embodiments thereof, it will be apparent that modifications and variations are possible without departing from the scope of the invention defined in the appended claims. More specifically, although some aspects of the present invention are identified herein as particularly advantageous, it is contemplated that the present invention is not necessarily limited to these particular aspects of the invention. 
     
       
         
           
               
               
               
             
               
                   
               
               
                 SEQ 
                 Gene 
                   
               
               
                 ID NO 
                 Designator 
                 Nucleotide Sequence 
               
               
                   
               
             
            
               
                  1 
                 Glyma.18G022 
                 ATGTCTCCGGCCGCCGGAGTCAGCGTCCCCCTCCTGGGG 
               
               
                   
                 400 
                 GATTCCAAAGGAACGCCGCCGCCGGCTTCCGTCCCCGGC 
               
               
                   
                   
                 GCGGTGTTCAACGTGGCCACCAGCATAGTCGGCGCCGGA 
               
               
                   
                   
                 ATCATGTCGATTCCGGCGATCATGAAGGTTCTCGGCGTAG 
               
               
                   
                   
                 TTCCCGCTTTCGCGATGATTCTCGTGGTGGCCGTGCTGGC 
               
               
                   
                   
                 GGAACTGTCCGTGGACTTCCTGATGCGGTTCACGCACTCC 
               
               
                   
                   
                 GGCGAAACGACGACGTACGCTGGCGTCATGAGGGAGGC 
               
               
                   
                   
                 GTTCGGATCGGGTGGAGCATTgGCCGCGCAAGTTTGCGT 
               
               
                   
                   
                 CATCATCACCAACGTTGGGGGTTTAATTCTCTACCTTATCA 
               
               
                   
                   
                 TCATCGGAGATGTGCTATCTGGAAAGCAAAATGGAGGGGA 
               
               
                   
                   
                 AGTGCATTTGGGCATTTTGCAACAGTGGTTTGGAATTCACT 
               
               
                   
                   
                 GGTGGAATTCCCGGGAATTTGCTTTGCTTTTCACCTTGGT 
               
               
                   
                   
                 CTTTGTTATGCTTCCATTGGTATTGTACAAACGTGTAGAGT 
               
               
                   
                   
                 CCTTGAAGTACAGCTCTGCAGTGTCAACTCTTCTTGCAGT 
               
               
                   
                   
                 GGCATTTGTTGGCATATGTTGTGGGTTGGCTATCACAGCT 
               
               
                   
                   
                 CTGGTGCAAGGAAAAACACAAACTCCTAGATTGTTTCCTC 
               
               
                   
                   
                 GGCTAGACTACCAAACCTCATTCTTTGATCTGTTCACTGCA 
               
               
                   
                   
                 GTTCCTGTTGTTGTCACAGCCTTCACATTTCACTTTAATGT 
               
               
                   
                   
                 GCACCCCATTGGGTTTGAGCTTGCCAAGGCATCCCAAATG 
               
               
                   
                   
                 ACAACAGCAGTTCGATTAGCATTATTGCTTTGTGCTGTGAT 
               
               
                   
                   
                 CTACCTTGCAATAGGCTTATTTGGGTACATGTTATTTGGGG 
               
               
                   
                   
                 ATTCAACCCAGTCAGACATTCTCATCAATTTTGACCAGAAT 
               
               
                   
                   
                 GCTGGTTCAGCAGTTGGTTCCTTGCTCAATAGTTTGGTCC 
               
               
                   
                   
                 GTGTAAGCTATGCCCTCCACATCATGCTGGTGTTTCCTCT 
               
               
                   
                   
                 CTTGAACTTCTCTTTGAGAACCAACATAGATGAAGTTCTCT 
               
               
                   
                   
                 TCCCTAAGAAGCCTATGCTAGCCACAGACAACAAAAGATT 
               
               
                   
                   
                 TATGATCCTCACTCTGGTGCTGCTTGTATTCTCCTACCTTG 
               
               
                   
                   
                 CAGCTATAGCAATCCCAGATATTTGGTACTTCTTTCAGTTC 
               
               
                   
                   
                 CTGGGATCCTCATCCGCAGTGTGCCTTGCCTTCATTTTCC 
               
               
                   
                   
                 CCGGCTCTATTGTTTTAAGGGATGTTAAAGGTATATCAACG 
               
               
                   
                   
                 AGAAGAGACAAAATTATTGCACTGATAATGATTATACTAGC 
               
               
                   
                   
                 TGTGGTTACAAGTGTGCTTGCCATTTCCACCAACATATATA 
               
               
                   
                   
                 ATGCTTTTAGTAGCAAGTCATAA 
               
               
                   
               
               
                  2 
                 Glyma.18G022 
                 ATGGCCGATCAGTTATCGAAGGGAGAGGAATTCGAGAAAA 
               
               
                   
                 500 
                 AGGCTGAGAAGAAGCTCAGCGGTTGGGGCTTGTTTGGCT 
               
               
                   
                   
                 CCAAGTATGAAGATGCCGCCGATCTCTTCGATAAAGCCGC 
               
               
                   
                   
                 CAATTGCTTCAAGCTCGCCAAATCATGGGACAAGGCTGGA 
               
               
                   
                   
                 GCGACATACCTGAAGTTGGCAAGTTGTCATTTGAAGTTGG 
               
               
                   
                   
                 AAAGCAAGCATGAAGCTGCACAGGCCCATGTCGATGCTG 
               
               
                   
                   
                 CACATTGCTACAAAAAGACTAATATAAACGAGTCTGTATCT 
               
               
                   
                   
                 TGCTTAGACCGAGCTGTAAATCTTTTCTGTGACATTGGAAG 
               
               
                   
                   
                 ACTCTCTATGGCTGCTAGATATTTAAAGGAAATTGCTGAAT 
               
               
                   
                   
                 TGTACGAGGGTGAACAGAATATTGAGCAGGCTCTTGTTTA 
               
               
                   
                   
                 CTATGAAAAATCAGCTGATTTTTTTCAAAATGAAGAAGTGA 
               
               
                   
                   
                 CAACTTCTGCGAACCAATGCAAACAAAAAGTTGCCCAGTT 
               
               
                   
                   
                 TGCTGCTCAGCTAGAACAATATCAGAAGTCGATTGACATTT 
               
               
                   
                   
                 ATGAAGAGATAGCTCGCCAATCCCTCAACAATAATTTGCT 
               
               
                   
                   
                 GAAGTATGGAGTTAAAGGACACCTTCTTAATGCTGGCATC 
               
               
                   
                   
                 TGCCAACTCTGTAAAGAGGACGTTGTTGCTATAACCAATG 
               
               
                   
                   
                 CATTAGAACGATATCAGGAACTGGATCCAACATTTTCAGG 
               
               
                   
                   
                 AACACGTGAATATAGATTGTTGGCGGACATTGCTGCTGCA 
               
               
                   
                   
                 ATTGATGAAGAAGATGTTGCAAAGTTTACTGATGTTGTCAA 
               
               
                   
                   
                 GGAATTTGATAGTATGACCCCTCTGGATTCTTGGAAGACC 
               
               
                   
                   
                 ACACTTCTCTTAAGGGTGAAGGAAAAGCTGAAAGCCAAAG 
               
               
                   
                   
                 AACTTGAGGAGGATGATCTTACTTGA 
               
               
                   
               
               
                  3 
                 Glyma.18G022 
                 ATGCGCATGCTCACCGGCGACTCCGCCGCCGACAACTCC 
               
               
                   
                 700 
                 TTCCGATTCGTTCCGCAGTCCATCGCCGCCTTCGGCTCCA 
               
               
                   
                   
                 CCGTCATCGTCGAGGGCTGCGACTCCGCCCGCAACATTG 
               
               
                   
                   
                 CCTGGGTCCACGCCTGGACCGTCACTGATGGGATGATCA 
               
               
                   
                   
                 CTCAAATCAGAGAGTACTTCAACACCGCCCTCACCGTCAC 
               
               
                   
                   
                 TCGCATCCACGATTCCGGCGAGATTGTTCCGGCCAGATCC 
               
               
                   
                   
                 GGCGCCGGCCGTTTGCCCTGCGTCTGGGAGAGCAGCGT 
               
               
                   
                   
                 CTCCGGTCGGGTCGGGAAATCCGTCCCCGGTTTGGTTCT 
               
               
                   
                   
                 CGCAATATAA 
               
               
                   
               
               
                  4 
                 Glyma.18G022 
                 ATGGTTTCGGTTGATGATGGGATTGTGAATCCCAATGATG 
               
               
                   
                 600 
                 AAATTGAGAAATCTAACGGGAGTAAAGTGAATGAGTTTGC 
               
               
                   
                   
                 ATCTATGGATATTTCAGCAACTCAAAAATCATATCTGAACA 
               
               
                   
                   
                 GTGAAGATCCTCAGAGAAGGCTTCAGGGAACCTTAATAAG 
               
               
                   
                   
                 TTCTTCTGTTACTAATAGGATAAACTTTCTTAAATTTGGTTC 
               
               
                   
                   
                 TGCATCTGCCAAATTCAAAAGGCTTGCTACTGAGAGAGAC 
               
               
                   
                   
                 CAGGTTTCTATATCTGTGCCTTCTCCTCGTTCAAAGAGCCT 
               
               
                   
                   
                 AAGATCACGTTTCAGTGGCATGTTTGCTCAGAAACTTGACT 
               
               
                   
                   
                 GGGCTTCAGTCAAGAAAATGTGCATGGAATGGATTAGAAA 
               
               
                   
                   
                 TCCAGTGAACATGGCCCTTTTTGTGTGGATCATTTGTGTC 
               
               
                   
                   
                 GCGGTTTCGGGTGCTATTCTGTTCCTTGTCATGACAGGCA 
               
               
                   
                   
                 TGTTGAATGGTGTGCTACCAAGAAAGTCTAAGAGAAATGC 
               
               
                   
                   
                 ATGGTTTGAAGTAAACAACCAAATACTCAATGCAGTGTTTA 
               
               
                   
                   
                 CACTCATGTGTTTGTACCAACACCCTAAGAGATTCTACCAC 
               
               
                   
                   
                 CTTGTTCTTCTGACCAGATGAAGACCAAATGACATCTCTAG 
               
               
                   
                   
                 CCTTAGGAAGGTATATTGCAAGAATGTCACTTACAAGCCC 
               
               
                   
                   
                 CATGAGTGGACACATATGATGGTAGTTGTCATTCTCCTTCA 
               
               
                   
                   
                 TGTTAACTGTTTTGCTCAATATGCACTTTGTGGTCTAAACT 
               
               
                   
                   
                 TAGGGTATAAAAGGTCCGAGAGACCTGCCATTGGAGTTGG 
               
               
                   
                   
                 AATATGCATATCTTTTGCAATTGCTGGTTTGTACACCATTC 
               
               
                   
                   
                 TTAGCCCACTTGGGAAGGACTATGATTGTGAGATGGATGA 
               
               
                   
                   
                 AGAAGCACAGGTTCAAATTACAGCTTCTCAAGGGAAAGAG 
               
               
                   
                   
                 CAGCTGAGAGAGAAACCAACTGAGAAGAAATATTCATTTG 
               
               
                   
                   
                 CATCCAAAGATCAACAAAGGGTTGTTGAAAATAGACCAAA 
               
               
                   
                   
                 GTGGAGTGGAGGAATACTTGACATTTGGAACGATATTTCC 
               
               
                   
                   
                 TTAGCATATCTCTCACTTTTCTGCACCTTTTGTGTGCTTGG 
               
               
                   
                   
                 GTGGAATATGAAGAGGCTTGGCTTTGGAAACATGTATGTT 
               
               
                   
                   
                 CACATTGCCATTTTTATGCTGTTCTGTATGGCTCCTTTCTG 
               
               
                   
                   
                 GATTTTTCTTTTGGCTTCCGTTAACATAGATGATGACAATG 
               
               
                   
                   
                 TTAGGCAGGCTCTAGCAGCTGTTGGAATCATTCTTTGTTTT 
               
               
                   
                   
                 CTTGGTTTATTGTATGGTGGATTTTGGAGGATCCAAATGAG 
               
               
                   
                   
                 AAAGAGGTTCAATTTACCAGCCTATGACTTCTGTTTTGGCA 
               
               
                   
                   
                 AACCTTCAGCTTCTGATTGCACACTTTGGCTACCCTGTTGC 
               
               
                   
                   
                 TGGTGCTCTCTCGCTCAAGAAGCGCGTACCAGGAATAACT 
               
               
                   
                   
                 ATGATCTTGTAGAAGATAAATTCTCAAGGAAAGAAACTGAT 
               
               
                   
                   
                 ACTAGTGATCAACCATCAATTTCACCTTTGGCTCGTGAAGA 
               
               
                   
                   
                 TGTAGTGTCAACCAGATCTGGCACAAGTTCTCCTATGGGT 
               
               
                   
                   
                 AGCACTAGCAACTCTTCCCCTTATATGATGAAAACATCTAG 
               
               
                   
                   
                 TTCTCCAAATTCAAGCAATGTCTTAAAGGGATATTACAGTC 
               
               
                   
                   
                 CAGATAAGATGCTATCAACTTTGAATGAAGACAATTGTGAA 
               
               
                   
                   
                 AGAGGTCAAGATGGAACAATGAACCCCTTATATGCACAAA 
               
               
                   
                   
                 AATAA 
               
               
                   
               
               
                  5 
                 Glyma.18G022 
                 ATGGCCGATCAGTTATCGAAGGGAGAGGAATTCGAGAAAA 
               
               
                   
                 500. Fayette 
                 AGGCTGAGAAGAAGCTCAGCGGTTGGGGCTTGTTTGGCT 
               
               
                   
                   
                 CCAAGTATGAAGATGCCGCCGATCTCTTCGATAAAGCCGC 
               
               
                   
                   
                 CAATTGCTTCAAGCTCGCCAAATCATGGGACAAGGCTGGA 
               
               
                   
                   
                 GCGACATACCTGAAGTTGGCAAGTTGTCATTTGAAGTTGG 
               
               
                   
                   
                 AAAGCAAGCATGAAGCTGCACAGGCCCATGTCGATGCTG 
               
               
                   
                   
                 CACATTGCTACAAAAAGACTAATATAAACGAGTCTGTATCT 
               
               
                   
                   
                 TGCTTAGACCGAGCTGTAAATCTTTTCTGTGACATTGGAAG 
               
               
                   
                   
                 ACTCTCTATGGCTGCTAGATATTTAAAGGAAATTGCTGAAT 
               
               
                   
                   
                 TGTACGAGGGTGAACAGAATATTGAGCAGGCTCTTGTTTA 
               
               
                   
                   
                 CTATGAAAAATCAGCTGATTTTTTTCAAAATGAAGAAGTGA 
               
               
                   
                   
                 CAACTTCTGCGAACCAATGCAAACAAAAAGTTGCCCAGTT 
               
               
                   
                   
                 TGCTGCTCAGCTAGAACAATATCAGAAGTCGATTGACATTT 
               
               
                   
                   
                 ATGAAGAGATAGCTCGCCAATCCCTCAACAATAATTTGCT 
               
               
                   
                   
                 GAAGTATGGAGTTAAAGGACACCTTCTTAATGCTGGCATC 
               
               
                   
                   
                 TGCAAACTCTGTAAAGAGGACGTTGTTGCTATAACCAATG 
               
               
                   
                   
                 CATTAGAACGATATCAGGAACTGGATCCAACATTTTCAGG 
               
               
                   
                   
                 AACACGTGAATATAGATTGTTGGCGGACATTGCTGCTGCA 
               
               
                   
                   
                 ATTGATGAAGAAGATGTTGCAAAGTTTACTGATGTTGTCAA 
               
               
                   
                   
                 GGAATTTGATAGTATGACCCCTCTGGATTCTTGGAAGACC 
               
               
                   
                   
                 ACACTTCTCTTAAGGGTGAAGGAAAAGCTGAAAGCCAAAG 
               
               
                   
                   
                 AACTTGAGCAGCATGAGGCTATTACTTGA 
               
               
                   
               
               
                  6 
                 Glyma.18G022 
                 ATGGCCGATCAGTTATCGAAGGGAGAGGAATTCGAGAAAA 
               
               
                   
                 500 
                 AGGCTGAGAAGAAGCTCAGCGGTTGGGGCTTGTTTGGCT 
               
               
                   
                 Peking 
                 CCAAGTATGAAGATGCCGCCGATCTCTTCGATAAAGCCGC 
               
               
                   
                   
                 CAATTGCTTCAAGCTCGCCAAATCATGGGACAAGGCTGGA 
               
               
                   
                   
                 GCGACATACCTGAAGTTGGCAAGTTGTCATTTGAAGTTGG 
               
               
                   
                   
                 AAAGCAAGCATGAAGCTGCACAGGCCCATGTCGATGCTG 
               
               
                   
                   
                 CACATTGCTACAAAAAGACTAATATAAACGAGTCTGTATCT 
               
               
                   
                   
                 TGCTTAGACCGAGCTGTAAATCTTTTCTGTGACATTGGAAG 
               
               
                   
                   
                 ACTCTCTATGGCTGCTAGATATTTAAAGGAAATTGCTGAAT 
               
               
                   
                   
                 TGTACGAGGGTGAACAGAATATTGAGCAGGCTCTTGTTTA 
               
               
                   
                   
                 CTATGAAAAATCAGCTGATTTTTTTCAAAATGAAGAAGTGA 
               
               
                   
                   
                 CAACTTCTGCGAACCAATGCAAACAAAAAGTTGCCCAGTT 
               
               
                   
                   
                 TGCTGCTCAGCTAGAACAATATCAGAAGTCGATTGACATTT 
               
               
                   
                   
                 ATGAAGAGATAGCTCGCCAATCCCTCAACAATAATTTGCT 
               
               
                   
                   
                 GAAGTATGGAGTTAAAGGACACCTTCTTAATGCTGGCATC 
               
               
                   
                   
                 TGCCAACTCTGTAAAGAGGAGGTTGTTGCTATAACCAATG 
               
               
                   
                   
                 CATTAGAACGATATCAGGAACTGGATCCAACATTTTCAGG 
               
               
                   
                   
                 AACACGTGAATATAGATTGTTGGCGGACATTGCTGCTGCA 
               
               
                   
                   
                 ATTGATGAAGAAGATGTTGCAAAGTTTACTGATGTTGTCAA 
               
               
                   
                   
                 GGAATTTGATAGTATGACCCCTCTGGATTCTTGGAAGACC 
               
               
                   
                   
                 ACACTTCTCTTAAGGGTGAAGGAAAAGCTGAAAGCCAAAG 
               
               
                   
                   
                 AACTTGAGGAGTATGAGGTTATTACTTGA 
               
               
                   
               
               
                  7 
                 Glyma.18G022 
                 ATGGCCGATCAGTTATCGAAGGGAGAGGAATTCGAGAAAA 
               
               
                   
                 500 
                 AGGCTGAGAAGAAGCTCAGCGGTTGGGGCTTGTTTGGCT 
               
               
                   
                 Peking Iso 
                 CCAAGTATGAAGATGCCGCCGATCTCTTCGATAAAGCCGC 
               
               
                   
                   
                 CAATTGCTTCAAGCTCGCCAAATCATGGGACAAGGCTGGA 
               
               
                   
                   
                 GCGACATACCTGAAGTTGGCAAGTTGTCATTTGAAGTTGG 
               
               
                   
                   
                 AAAGCAAGCATGAAGCTGCACAGGCCCATGTCGATGCTG 
               
               
                   
                   
                 CACATTGCTACAAAAAGACTAATATAAACGAGTCTGTATCT 
               
               
                   
                   
                 TGCTTAGACCGAGCTGTAAATCTTTTCTGTGACATTGGAAG 
               
               
                   
                   
                 ACTCTCTATGGCTGCTAGATATTTAAAGGAAATTGCTGAAT 
               
               
                   
                   
                 TGTACGAGGGTGAACAGAATATTGAGCAGGCTCTTGTTTA 
               
               
                   
                   
                 CTATGAAAAATCAGCTGATTTTTTTCAAAATGAAGAAGTGA 
               
               
                   
                   
                 CAACTTCTGCGAACCAATGCAAACAAAAAGTTGCCCAGTT 
               
               
                   
                   
                 TGCTGCTCAGCTAGAACAATATCAGAAGTCGATTGACATTT 
               
               
                   
                   
                 ATGAAGAGATAGCTCGCCAATCCCTCAACAATAATTTGCT 
               
               
                   
                   
                 GAAGTATGGAGTTAAAGGACACCTTCTTAATGCTGGCATC 
               
               
                   
                   
                 TGCCAACTCTGTAAAGAGGAGGAACTGGATCCAACATTTT 
               
               
                   
                   
                 CAGGAACACGTGAATATAGATTGTTGGCGGACATTGCTGC 
               
               
                   
                   
                 TGCAATTGATGAAGAAGATGTTGCAAAGTTTACTGATGTTG 
               
               
                   
                   
                 TCAAGGAATTTGATAGTATGACCCCTCTGGATTCTTGGAA 
               
               
                   
                   
                 GACCACACTTCTCTTAAGGGTGAAGGAAAAGCTGAAAGCC 
               
               
                   
                   
                 AAAGAACTTGAGGAGTATGAGGTTATTACTTGA 
               
               
                   
               
               
                  8 
                 Glyma.07G195 
                 ATGGCGAGTCGGTTCGGGTTATCGTCTTCGTCTTCCTCTGCGTC 
               
               
                   
                 900 WT 
                 CAGCATGAGAGTTACCAACACGCCCGCGAGCGACCTCGCCCTC 
               
               
                   
                   
                 ACCAACCTCGCCTTCTGTTCCCCCTCCGATCTCCGCAATTTCGC 
               
               
                   
                   
                 CGTCCCTGGCCACAATAACCTCTACCTCGCCGCCGTCGCCGATT 
               
               
                   
                   
                 CCTTCGTCTTATCTCTCTCTGCTCATGACACCATAGGCAGCGGT 
               
               
                   
                   
                 CAGATTGCGTTGAATGCCGTTCAACGCCGGTGTGCCAAAGTTTC 
               
               
                   
                   
                 TTCCGGTGATTCCGTACAAGTGAGCCGATTTGTGCCGCCTGAAG 
               
               
                   
                   
                 ATTTCAACCTCGCACTGCTAACTCTTGAATTGGAATTTGTTAAAA 
               
               
                   
                   
                 AGGGGAGTAAGAGTGAGCAGATTGATGCTGTTCTACTGGCTAAG 
               
               
                   
                   
                 CAACTTCGTAAGAGATTTATGAACCAGGTTATGACTGTGGGGCA 
               
               
                   
                   
                 GAAAGTATTATTTGAGTATCACGGAAATAATTATAGCTTTACTGT 
               
               
                   
                   
                 CAGTAATGCTGCTGTTGAGGGCCAAGAAAAGTCTAATTCTCTTG 
               
               
                   
                   
                 AAAGAGGGATGATTTCAGATGACACATACATTGTTTTTGAAACAT 
               
               
                   
                   
                 CACGTGATAGTGGAATTAAGATTGTCAATCAACGAGAGGGTGCC 
               
               
                   
                   
                 ACTAGCAACATTTTCAAGCAGAAAGAATTTAACCTTCAGTCACTG 
               
               
                   
                   
                 GGTATTGGTGGCCTGAGTGCAGAATTTGCAGATATATTTCGAAG 
               
               
                   
                   
                 AGCTTTTGCCTCTCGTGTTTTCCCACCCCATGTGACATCTAAATT 
               
               
                   
                   
                 AGGAATCAAGCATGTGAAGGGCATGCTTCTTTATGGGCCTCCTG 
               
               
                   
                   
                 GAACTGGAAAGACACTTATGGCACGCCAAATTGGAAAAATTTTG 
               
               
                   
                   
                 AATGGGAAGGAACCCAAGATTGTAAATGGCCCTGAAGTTTTGAG 
               
               
                   
                   
                 CAAATTTGTTGGTGAAACTGAAAAGAATGTGAGAGACCTTTTTGC 
               
               
                   
                   
                 TGATGCTGAACAGGATCAGAGGACCCGAGGGGATGAAAGTGAT 
               
               
                   
                   
                 TTGCATGTTATAATCTTTGATGAAATTGATGCTATTTGCAAGTCAA 
               
               
                   
                   
                 GAGGTTCAACTCGAGATGGTACTGGAGTTCATGATAGTATTGTA 
               
               
                   
                   
                 AATCAGCTTCTTACTAAGATAGATGGTGTGGAGTCACTAAATAAT 
               
               
                   
                   
                 GTTTTACTTATTGGAATGACTAACAGAAAGGACATGCTTGATGAA 
               
               
                   
                   
                 GCTCTCTTAAGACCAGGGAGGTTGGAAGTCCAGGTTGAGATAAG 
               
               
                   
                   
                 CCTTCCTGATGAAAATGGTCGATTGCAAATTCTTCAAATCCATAC 
               
               
                   
                   
                 TAACAAAATGAAAGAGAATTCTTTTCTAGCTGCTGATGTGAACCT 
               
               
                   
                   
                 TCAAGAGCTTGCTGCTCGAACGAAAAACTACAGTGGTGCAGAAC 
               
               
                   
                   
                 TTGAAGGTGTTGTGAAAAGTGCTGTCTCATATGCTTTAAATAGAC 
               
               
                   
                   
                 AATTGAGTCTAGAGGATCTCACTAAGCCAGTGGAGGAAGAGAAC 
               
               
                   
                   
                 ATTAAGGTTACAATGGATGACTTTTTGAATGCACTCCACGAAGTT 
               
               
                   
                   
                 ACTTCCGCATTTGGAGCTTCAACTGATGATCTTGAAAGATGCAG 
               
               
                   
                   
                 ACTCCATGGCATGGTTGAGTGTGGTGATCGACATAAGCACATTT 
               
               
                   
                   
                 ATCAAAGAGCAATGCTACTTGTGGAGCAAGTTAAAGTGAGTAAA 
               
               
                   
                   
                 GGAAGCCCACTTGTCACTTGTCTCCTGGAAGGTTCCCGTGGCA 
               
               
                   
                   
                 GTGGTAAAACTGCACTTTCAGCTACTGTTGGTATCGACAGCGAC 
               
               
                   
                   
                 TTCCCATACGTCAAGATAGTTTCAGCTGAATCAATGATTGGTCTA 
               
               
                   
                   
                 CATGAGAGCACCAAATGTGCACAGATTATTAAGGTTTTTGAGGAT 
               
               
                   
                   
                 GCATACAAGTCACCATTGAGTGTCATCATTCTTGATGACATTGAG 
               
               
                   
                   
                 AGATTATTGGAGTATGTGCCCATTGGTCCTCGATTTTCAAACTTG 
               
               
                   
                   
                 ATTTCTCAGACACTGCTGGTTCTGCTCAAACGGCTTCCTCCAAA 
               
               
                   
                   
                 GGGGAAAAAACTAATGGTTATTGGCACAACAAGTGAACTAGATT 
               
               
                   
                   
                 TCTTGGAATCAATTGGATTTTGTGATACCTTCTCTGTTACTTACCA 
               
               
                   
                   
                 TATTCCTACCTTGAACACAACGGATGCAAAGAAGGTCCTAGAAC 
               
               
                   
                   
                 AGTTGAATGTGTTTACTGATGAAGATATTGATTCTGCTGCAGAGG 
               
               
                   
                   
                 CGTTGAATGATATGCCTATCAGGAAACTATACATGTTGATCGAGA 
               
               
                   
                   
                 TGGCAGCGCAAGGGGAGCATGGTGGATCTGCAGAAGCCATCTT 
               
               
                   
                   
                 TTCTGGCAAAGAGAAGATTAGTATCGCTCATTTCTATGATTGCCT 
               
               
                   
                   
                 CCAGGATGTTGTTAGGTTATAA 
               
               
                   
               
               
                  9 
                 Glyma.07G195 
                 ATGGCGAGTCAGTTCGGGTTATCGTCTTCGTCTTCCTCTGCGTC 
               
               
                   
                 900 RAN07 
                 CAGCATGAGAGTTACCTACACGCCCGCGAACGACCTCGCCCTC 
               
               
                   
                   
                 ACCAACCTCGCCTTCTGTTCCCCCTCCGATCTCCGCAATTTCGC 
               
               
                   
                   
                 CGTCCCTGGCCACAATAACCTCTACCTCGCCGCCGTCGCCGATT 
               
               
                   
                   
                 CCTTCGTCTTATCTCTCTCTGCTCATGACACCATAGGCAGCGGT 
               
               
                   
                   
                 CAGATTGCGTTGAATGCCGTTCAACGCCGGTGTGCCAAAGTTTC 
               
               
                   
                   
                 TTCCGGTGATTCCGTACAAGTGAGCCGATTTGTGCCGCCTGAAG 
               
               
                   
                   
                 ATTTCAACCTCGCACTGCTAACTCTTGAATTGGAATTTTTTGTTAA 
               
               
                   
                   
                 AAAGGGGAGTAAGAGTGAGCAGATTGATGCTGTTCTACTGGCTA 
               
               
                   
                   
                 AGCAACTTCGTAAGAGATTTATGAACCAGGTTATGACTGTGGGG 
               
               
                   
                   
                 CAGAAAGTATTATTTGAGTATCACGGAAATAATTATAGCTTTACT 
               
               
                   
                   
                 GTCAGTAATGCTGCTGTTGAGGGCCAAGAAAAGTCTAATTCTCT 
               
               
                   
                   
                 TGAAAGAGGGATTATTTCAGATGACACATACATTGTTTTTGAAAC 
               
               
                   
                   
                 ATCACGTGATAGTGGAATTAAGATTGTCAATCAACGAGAGGGTG 
               
               
                   
                   
                 CCACTAGCAACATTTTCAAGCAGAAAGAATTTAACCTTCAGTCAC 
               
               
                   
                   
                 TGGGTATTGGTGGCCTGAGTGCAGAATTTGCAGATATATTTCGA 
               
               
                   
                   
                 AGAGCTTTTGCCTCTCGTGTTTTCCCACCCCATGTGACATCTAAA 
               
               
                   
                   
                 TTAGGGATCAAGCATGTGAAGGGCATGCTTCTTTATGGGCCTCC 
               
               
                   
                   
                 TGGAACTGGAAAGACACTTATGGCACGCCAAATTGGAAAAATTT 
               
               
                   
                   
                 TGAATGGGAAGGAACCCAAGATTGTAAATGGCCCTGAAGTTTTG 
               
               
                   
                   
                 AGCAAATTTGTTGGTGAAACTGAAAAGAATGTGAGAGACCTTTTT 
               
               
                   
                   
                 GCTGATGCTGAACAGGATCAGAGGACCCGAGGGGATGAAAGTG 
               
               
                   
                   
                 ATTTGCATGTTATAATCTTTGATGAAATTGATGCTATTTGCAAGTC 
               
               
                   
                   
                 AAGAGGTTCAACTCGAGATGGTACTGGAGTTCATGATAGTATTG 
               
               
                   
                   
                 TAAATCAGCTTCTTACTAAGATAGATGGTGTGGAGTCACTAAATA 
               
               
                   
                   
                 ATGTTTTACTTATTGGAATGACTAACAGAAAGGACATGCTTGATG 
               
               
                   
                   
                 AAGCTCTCTTAAGACCAGGGAGGTTGGAAGTCCAGGTTGAGATA 
               
               
                   
                   
                 AGCCTTCCTGATGAAAATGGTCGATTGCAAATTCTTCAAATTCAT 
               
               
                   
                   
                 ACTAACAAAATGAAAGAGAATTCTTTTCTAGCTGCTGATGTGAAC 
               
               
                   
                   
                 CTTCAAGAGCTTGCTGCTCGAACGAAAAACTACAGTGGTGCAGA 
               
               
                   
                   
                 ACTTGAAGGTGTTGTGAAAAGTGCTGTCTCATATGCTTTAAATAG 
               
               
                   
                   
                 ACAATTGAGTCTAGAGGATCTCACTAAGCCAGTGGAGGAAGAGA 
               
               
                   
                   
                 ACATTAAGGTTACAATGGATGACTTTTTGAATGCACTCCACGAAG 
               
               
                   
                   
                 TTACTTCCGCATTTGGAGCTTCAACTGATGATCTTGAAAGATGCA 
               
               
                   
                   
                 GACTCCATGGCATGGTTGAGTGTGGTGATCGACATAAGCACATT 
               
               
                   
                   
                 TATCAAAGAGCAATGCTACTTGTGGAGCAAGTTAAAGTGAGTAA 
               
               
                   
                   
                 AGGAAGCCCACTTGTCACTTGTCTCCTGGAAGGTTCCCGTGGCA 
               
               
                   
                   
                 GTGGTAAAACTGCACTTTCAGCTACTGTTGGTATCGACAGCGAC 
               
               
                   
                   
                 TTCCCATACGTCAAGATAGTTTCAGCTGAATCAATGATTGGTCTA 
               
               
                   
                   
                 CATGAGAGCACCAAATGTGCACAGATTATTAAGGTTTTTGAGGAT 
               
               
                   
                   
                 GCATACAAGTCACCATTGAGTGTCATCATTCTTGATGACATTGAG 
               
               
                   
                   
                 AGATTATTGGAGTATGTGCCCATTGGTCCTCGATTTTCAAACTTG 
               
               
                   
                   
                 ATTTCTCAGACACTGCTGGTTCTGCTCAAACGCTTCCTCCAAAG 
               
               
                   
                   
                 GGGAAAAAACTCATGGTTATTGGCACAACAAGTGAACTAGATTT 
               
               
                   
                   
                 CTTGGAATCAATTGGATTTTGTGATACCTTCTCTGTTACTTACCAT 
               
               
                   
                   
                 ATTCCTACCTTGAACACAACGGATGCAAAGAAGGTCCTAGAACA 
               
               
                   
                   
                 GTTGAATGTGTTTACTGATGAAGATATTGATTCTGCTGCAGAGGC 
               
               
                   
                   
                 GTTGAATGATATGCCTATCAGGAAACTATACATGTTGATCGAGAT 
               
               
                   
                   
                 GGCAGCGCAAGGGGAGCATGGTGGATCTGCAGAAGCCATCTTT 
               
               
                   
                   
                 TCTGGCAAAGAGAAGATTAGTATCGCTCACTTCTATGATTGCCTC 
               
               
                   
                   
                 CAGGATGTTGTTAGGTTATGA 
               
               
                   
               
               
                 10 
                 Glyma.18G022400 
                 MSPAAGVSVPLLGDSKGTPPPASVPGAVFNVATSIVGAG 
               
               
                   
                   
                 IMSIPAIMKVLGVVPAFAMILVVAVLAELSVDFLMRFTHSG 
               
               
                   
                   
                 ETTTYAGVMREAFGSGGALAAQVCVIITNVGGLILYLIIIGD 
               
               
                   
                   
                 VLSGKQNGGEVHLGILQQWFGIHWWNSREFALLFTLVFV 
               
               
                   
                   
                 MLPLVLYKRVESLKYSSAVSTLLAVAFVGICCGLAITALVQ 
               
               
                   
                   
                 GKTQTPRLFPRLDYQTSFFDLFTAVPVVVTAFTFHFNVHP 
               
               
                   
                   
                 IGFELAKASQMTTAVRLALLLCAVIYLAIGLFGYMLFGDST 
               
               
                   
                   
                 QSDILINFDQNAGSAVGSLLNSLVRVSYALHIMLVFPLLNF 
               
               
                   
                   
                 SLRTNIDEVLFPKKPMLATDNKRFMILTLVLLVFSYLAAIAI 
               
               
                   
                   
                 PDIWYFFQFLGSSSAVCLAFIFPGSIVLRDVKGISTRRDKII 
               
               
                   
                   
                 ALIMIILAVVTSVLAISTNIYNAFSSKS 
               
               
                   
               
               
                 11 
                 Glyma.18G022500 
                 MADQLSKGEEFEKKAEKKLSGWGLFGSKYEDAADLFDK 
               
               
                   
                   
                 AANCFKLAKSWDKAGATYLKLASCHLKLESKHEAAQAHV 
               
               
                   
                   
                 DAAHCYKKTNINESVSCLDRAVNLFCDIGRLSMAARYLKE 
               
               
                   
                   
                 IAELYEGEQNIEQALVYYEKSADFFQNEEVTTSANQCKQK 
               
               
                   
                   
                 VAQFAAQLEQYQKSIDIYEEIARQSLNNNLLKYGVKGHLL 
               
               
                   
                   
                 NAGICQLCKEDVVAITNALERYQELDPTFSGTREYRLLADI 
               
               
                   
                   
                 AAAIDEEDVAKFTDVVKEFDSMTPLDSWKTTLLLRVKEKL 
               
               
                   
                   
                 KAKELEEDDLT 
               
               
                   
               
               
                 12 
                 Glyma.18G022700 
                 MRMLTGDSAADNSFRFVPQSIAAFGSTVIVEGCDSARNIA 
               
               
                   
                   
                 WVHAWTVTDGMITQIREYFNTALTVTRIHDSGEIVPARSG 
               
               
                   
               
               
                 13 
                 Glyma.18G022600 
                 MVSVDDGIVNPNDEIEKSNGSKVNEFASMDISATQKSYL 
               
               
                   
                   
                 NSEDPQRRLQGTLISSSVTNRINFLKFGSASAKFKRLATE 
               
               
                   
                   
                 RDQVSISVPSPRSKSLRSRFSGMFAQKLDWASVKKMCM 
               
               
                   
                   
                 EWIRNPVNMALFVWIICVAVSGAILFLVMTGMLNGVLPRK 
               
               
                   
                   
                 SKRNAWFEVNNQILNAVFTLIPNDISSLRKVYCKNVTYKP 
               
               
                   
                   
                 HEWTHMMVVVILLHVNCFAQYALCGLNLGYKRSERPAIG 
               
               
                   
                   
                 VGICISFAIAGLYTILSPLGKDYDCEMDEEAQVQITASQGK 
               
               
                   
                   
                 EQLREKPTEKKYSFASKDQQRVVENRPKVVSGGILDIWN 
               
               
                   
                   
                 DISLAYLSLFCTFCVLGWNMKRLGFGNMYVHIAIFMLFCM 
               
               
                   
                   
                 APFWIFLLASVNIDDDNVRQALAAVGIILCFLGLLYGGFWR 
               
               
                   
                   
                 IQMRKRFNLPAYDFCFGKPSASDCTLWLPCCWCSLAQE 
               
               
                   
                   
                 ARTRNNYDLVEDKFSRKETDTSDQPSISPLAREDVVSTR 
               
               
                   
                   
                 SGTSSPMGSTSNSSPYMMKTSSSPNSSNVLKGYYSPDK 
               
               
                   
                   
                 MLSTLNEDNCERGQDGTMNPLYAQK 
               
               
                   
               
               
                 14 
                 Glyma.18G022500. 
                 MADQLSKGEEFEKKAEKKLSGWGLFGSKYEDAADLFDK 
               
               
                   
                 Fayette 
                 AANCFKLAKSWDKAGATYLKLASCHLKLESKHEAAQAHV 
               
               
                   
                   
                 DAAHCYKKTNINESVSCLDRAVNLFCDIGRLSMAARYLKE 
               
               
                   
                   
                 IAELYEGEQNIEQALVYYEKSADFFQNEEVTTSANQCKQK 
               
               
                   
                   
                 VAQFAAQLEQYQKSIDIYEEIARQSLNNNLLKYGVKGHLL 
               
               
                   
                   
                 NAGICKLCKEDVVAITNALERYQELDPTFSGTREYRLLADI 
               
               
                   
                   
                 AAAIDEEDVAKFTDVVKEFDSMTPLDSWKTTLLLRVKEKL 
               
               
                   
                   
                 KAKELEQHEAIT 
               
               
                   
               
               
                 15 
                 Glyma.18G022500 
                 MADQLSKGEEFEKKAEKKLSGWGLFGSKYEDAADLFDK 
               
               
                   
                 Peking 
                 AANCFKLAKSWDKAGATYLKLASCHLKLESKHEAAQAHV 
               
               
                   
                   
                 DAAHCYKKTNINESVSCLDRAVNLFCDIGRLSMAARYLKE 
               
               
                   
                   
                 IAELYEGEQNIEQALVYYEKSADFFQNEEVTTSANQCKQK 
               
               
                   
                   
                 VAQFAAQLEQYQKSIDIYEEIARQSLNNNLLKYGVKGHLL 
               
               
                   
                   
                 NAGICQLCKEEVVAITNALERYQELDPTFSGTREYRLLADI 
               
               
                   
                   
                 AAAIDEEDVAKFTDVVKEFDSMTPLDSWKTTLLLRVKEKL 
               
               
                   
                   
                 KAKELEEYEVIT 
               
               
                   
               
               
                 16 
                 Glyma.18G022500 
                 MADQLSKGEEFEKKAEKKLSGWGLFGSKYEDAADLFDK 
               
               
                   
                 Peking Iso 
                 AANCFKLAKSWDKAGATYLKLASCHLKLESKHEAAQAHV 
               
               
                   
                   
                 DAAHCYKKTNINESVSCLDRAVNLFCDIGRLSMAARYLKE 
               
               
                   
                   
                 IAELYEGEQNIEQALVYYEKSADFFQNEEVTTSANQCKQK 
               
               
                   
                   
                 VAQFAAQLEQYQKSIDIYEEIARQSLNNNLLKYGVKGHLL 
               
               
                   
                   
                 NAGICQLCKEEELDPTFSGTREYRLLADIAAAIDEEDVAKF 
               
               
                   
                   
                 TDVVKEFDSMTPLDSWKTTLLLRVKEKLKAKELEEYEVIT 
               
               
                   
               
               
                 17 
                 Glyma.07G195900 
                 MASRFGLSSSSSSASSMRVTNTPASDLALTNLAFCSPSD 
               
               
                   
                 WT 
                 LRNFAVPGHNNLYLAAVADSFVLSLSAHDTIGSGQIALNA 
               
               
                   
                   
                 VQRRCAKVSSGDSVQVSRFVPPEDFNLALLTLELEFVKK 
               
               
                   
                   
                 GSKSEQIDAVLLAKQLRKRFMNQVMTVGQKVLFEYHGN 
               
               
                   
                   
                 NYSFTVSNAAVEGQEKSNSLERGMISDDTYIVFETSRDS 
               
               
                   
                   
                 GIKIVNQREGATSNIFKQKEFNLQSLGIGGLSAEFADIFRR 
               
               
                   
                   
                 AFASRVFPPHVTSKLGIKHVKGMLLYGPPGTGKTLMARQI 
               
               
                   
                   
                 GKILNGKEPKIVNGPEVLSKFVGETEKNVRDLFADAEQD 
               
               
                   
                   
                 QRTRGDESDLHVIIFDEIDAICKSRGSTRDGTGVHDSIVN 
               
               
                   
                   
                 QLLTKIDGVESLNNVLLIGMTNRKDMLDEALLRPGRLEVQ 
               
               
                   
                   
                 VEISLPDENGRLQILQIHTNKMKENSFLAADVNLQELAAR 
               
               
                   
                   
                 TKNYSGAELEGVVKSAVSYALNRQLSLEDLTKPVEEENIK 
               
               
                   
                   
                 VTMDDFLNALHEVTSAFGASTDDLERCRLHGMVECGDR 
               
               
                   
                   
                 HKHIYQRAMLLVEQVKVSKGSPLVTCLLEGSRGSGKTAL 
               
               
                   
                   
                 SATVGIDSDFPYVKIVSAESMIGLHESTKCAQIIKVFEDAY 
               
               
                   
                   
                 KSPLSVIILDDIERLLEYVPIGPRFSNLISQTLLVLLKRLPPK 
               
               
                   
                   
                 GKKLMVIGTTSELDFLESIGFCDTFSVTYHIPTLNTTDAKK 
               
               
                   
                   
                 VLEQLNVFTDEDIDSAAEALNDMPIRKLYMLIEMAAQGEH 
               
               
                   
                   
                 GGSAEAIFSGKEKISIAHFYDCLQDVVRL 
               
               
                   
               
               
                 18 
                 Glyma.07G195900 
                 MASQFGLSSSSSSASSMRVTYTPANDLALTNLAFCSPSD 
               
               
                   
                 RAN07 
                 LRNFAVPGHNNLYLAAVADSFVLSLSAHDTIGSGQIALNA 
               
               
                   
                   
                 VQRRCAKVSSGDSVQVSRFVPPEDFNLALLTLELEFFVK 
               
               
                   
                   
                 KGSKSEQIDAVLLAKQLRKRFMNQVMTVGQKVLFEYHG 
               
               
                   
                   
                 NNYSFTVSNAAVEGQEKSNSLERGIISDDTYIVFETSRDS 
               
               
                   
                   
                 GIKIVNQREGATSNIFKQKEFNLQSLGIGGLSAEFADIFRR 
               
               
                   
                   
                 AFASRVFPPHVTSKLGIKHVKGMLLYGPPGTGKTLMARQI 
               
               
                   
                   
                 GKILNGKEPKIVNGPEVLSKFVGETEKNVRDLFADAEQD 
               
               
                   
                   
                 QRTRGDESDLHVIIFDEIDAICKSRGSTRDGTGVHDSIVN 
               
               
                   
                   
                 QLLTKIDGVESLNNVLLIGMTNRKDMLDEALLRPGRLEVQ 
               
               
                   
                   
                 VEISLPDENGRLQILQIHTNKMKENSFLAADVNLQELAAR 
               
               
                   
                   
                 TKNYSGAELEGVVKSAVSYALNRQLSLEDLTKPVEEENIK 
               
               
                   
                   
                 VTMDDFLNALHEVTSAFGASTDDLERCRLHGMVECGDR 
               
               
                   
                   
                 HKHIYQRAMLLVEQVKVSKGSPLVTCLLEGSRGSGKTAL 
               
               
                   
                   
                 SATVGIDSDFPYVKIVSAESMIGLHESTKCAQIIKVFEDAY 
               
               
                   
                   
                 KSPLSVIILDDIERLLEYVPIGPRFSNLISQTLLVLLKRLPPK 
               
               
                   
                   
                 GKKLMVIGTTSELDFLESIGFCDTFSVTYHIPTLNTTDAKK 
               
               
                   
                   
                 VLEQLNVFTDEDIDSAAEALNDMPIRKLYMLIEMAAQGEH 
               
               
                   
                   
                 GGSAEAIFSGKEKISIAHFYDCLQDVVRL 
               
               
                   
               
               
                 19 
                 NSF from Chinese 
                 MAGRSMQAARCPTDELSLSNCAVVSEKDYQSGQHVIVR 
               
               
                   
                 Hamster Ovary 
                 TSPNHKYIFTLRTHPSVVPGSVAFSLPQRKWAGLSIGQEI 
               
               
                   
                 Cells ( Cricetulus   
                 EVALYSFDKAKQCIGTMTIEIDFLQKKNIDSNPYDTDKMAA 
               
               
                   
                   griseus ) 
                 EFIQQFNNQAFSVGQQLVFSFNDKLFGLLVKDIEAMDPSI 
               
               
                   
                   
                 LKGEPASGKRQKIEVGLVVGNSQVAFEKAENSSLNLIGKA 
               
               
                   
                   
                 KTKENRQSIINPDWNFEKMGIGGLDKEFSDIFRRAFASRV 
               
               
                   
                   
                 FPPEIVEQMGCKHVKGILLYGPPGCGKTLLARQIGKMLNA 
               
               
                   
                   
                 REPKVVNGPEILNKYVGESEANIRKLFADAEEEQRRLGA 
               
               
                   
                   
                 NSGLHIIIFDEIDAICKQRGSMAGSTGVHDTVVNQLLSKID 
               
               
                   
                   
                 GVEQLNNILVIGMTNRPDLIDEALLRPGRLEVKMEIGLPDE 
               
               
                   
                   
                 KGRLQILHIHTARMRGHQLLSADVDIKELAVETKNFSGAE 
               
               
                   
                   
                 LEGLVRAAQSTAMNRHIKASTKVEVDMEKAESLQVTRGD 
               
               
                   
                   
                 FLASLENDIKPAFGTNQEDYASYIMNGIIKWGDPVTRVLD 
               
               
                   
                   
                 DGELLVQQTKNSDRTPLVSVLLEGPPHSGKTALAAKIAEE 
               
               
                   
                   
                 SNFPFIKICSPDKMIGFSETAKCQAMKKIFDDAYKSQLSC 
               
               
                   
                   
                 VVVDDIERLLDYVPIGPRFSNLVLQALLVLLKKAPPQGRKL 
               
               
                   
                   
                 LIIGTTSRKDVLQEMEMLNAFSTTIHVPNIATGEQLLEALEL 
               
               
                   
                   
                 LGNFKDKERTTIAQQVKGKKVWIGIKKLLMLIEMSLQMDP 
               
               
                   
                   
                 EYRVRKFLALLREEGASPLDFD