# Patent

## Title
Methods and compositions for enhanced forage quality

## Abstract

The invention provides a method to select an alfalfa plant with enhanced feed value and increased flexibility in management either to increase quality of forage provided or to enhance biomass available earlier.

## Background
REFERENCE TO RELATED APPLICATIONS
This application is a 371 National Stage Entry of PCT/US2013/47911, filed Jun. 26, 2013, which claims the priority from U.S. Provisional Patent Application Ser. No. 61/664,359, filed Jun. 26, 2012, the entire disclosures of which are specifically incorporated herein by reference.


FIELD OF THE INVENTION
The invention relates to plant genetic engineering. More specifically, the invention relates to methods for improvement of the nutritional quality of a forage crop.
INCORPORATION OF SEQUENCE LISTING
The sequence listing file named MONS336US_ST25.txt,” which is 18 kilobytes (size as measured in Microsoft Windows®) which was electronically filed and which was created on Dec. 4, 2014 is incorporated herein by reference.
BACKGROUND OF THE INVENTION
The invention provides methods and compositions through genetic engineering wherein a transgenic alfalfa plant has reduced levels of acid detergent lignin (ADL), reduced levels of guaiacyl lignin (G lignin), improved levels of neutral detergent fiber digestibility (NDFD), and plant vigor comparable to the wild type, resulting in improved agronomic fitness. Forage crops, including legumes, grasses, corn silage, and brassicas, among others, are grown throughout the world to provide animal feed with digestible fiber. Alfalfa and/or alfalfa grass hay is the most important hay crop in the United States. Although predominantly fed as baled hay, it can also be fed as silage, chopped hay, cubes, or pellets. Alfalfa (Medicago sativa) is a forage legume and may comprise 23% to 34% of dairy cattle feed. Quality alfalfa hay is highly digestible and provides high protein, energy, vitamins and minerals. Quality alfalfa also contains less celluloses and hemicelluloses, less lignin(s), lower fiber, and higher relative feed value. Alfalfa feed value is often measured as NDFD. Analyzing alfalfa forage for NDFD provides an estimation of the energy a cow is able to obtain from that forage, and there is a need to the enhance fiber digestibility in alfalfa. For example, an increase in one percentage unit NDFD results in a 0.37-pound increase in forage dry matter intake per day (lb/d), and a 0.55 lb/d increase in 4% fat corrected milk (FCM) yield. Cows fed forages with greater NDFD are able to obtain more total energy and nutritive value from the forages. As a result, the energy requirements can be fulfilled with less grain provided in the diet. Lower NDFD in forage legumes is most often related to the maturity of the forage plant, which is accompanied by an increase in lignin concentrations and associated with an increase in cellulose fibers.
Factors that affect NDFD include the amount of acid detergent fiber (ADF). ADF refers to the cell wall portions of the forage, which is the most indigestible part of forage and includes lignin, cellulose, silica, and insoluble forms of nitrogen. These values are particularly important because they relate to the digestibility of the forage by livestock. Forages with higher ADF are lower in digestible energy than forages with lower ADF. Thus, as the ADF level increases, the digestible energy levels decrease.
SUMMARY OF THE INVENTION
The invention provides a method and compositions through genetic engineering wherein a transgenic alfalfa plant may be selected for enhanced feed value components, such as reduced concentrations of ADL and G lignin, improved levels of NDFD in the lower stem resulting from at least equal vigor, and agronomic fitness compared to non-transgenic control plants not comprising the DNA molecules of the invention. Alfalfa events with reduced lignin are generated by using RNAi constructs to down regulate the lignin biosynthetic enzyme Medicago sativa S-adenosyl-L-methionine: caffeoyl-CoA 3-O-methyltransferase (CCoAOMT). All constructs utilized the stabilized antisense technology described in U.S. Patent Application publication 2005/0176670, incorporated herein by reference. The method to select events for reduced lignin alfalfa is “a reduction in the lignin content to provide an 8-15% increase in whole plant digestibility when cutting prior to the 10% bloom stage of maturity. The method selects an alfalfa plant from a population of alfalfa plants, wherein the population of alfalfa plants comprises recombinant DNA molecules that are homologous or complementary to SEQ ID NO:1 and SEQ ID NO:2. The method comprises assaying the lower stem of a population of alfalfa plants and selecting plants for: (1) a reduced concentration of acid detergent lignin, where the concentration of acid detergent lignin is reduced by between 12% and 31%; (2) a reduced concentration of guaiacyl lignin, where the concentration is reduced by about 25% or greater; (3) an increased neutral fiber digestibility, where the NDFD value is increased by greater than 18%, when compared to alfalfa plants not comprising such recombinant DNA molecules.
In one aspect of the invention, the selected alfalfa plant with enhanced feed value components has vigor substantially equal to an alfalfa plant not comprising said recombinant DNA molecule.
In another aspect, the invention provides a method to assay and select transgenic alfalfa plants with enhanced feed value components that have been transformed with a suppression construct for caffeoyl CoA 3-O-methyltransferase (CCoAOMT), SEQ ID NO:7, which further comprises a vascular-enhanced promoter to regulate transcription of recombinant DNA molecules that are homologous or complementary to SEQ ID NO:1 and SEQ ID NO:2.
In yet another aspect, the invention provides an alfalfa plant or progeny of the plant selected by the method of the present invention, or hay or silage derived from the plant or progeny plant, wherein the alfalfa plant or plant product comprises the DNA molecules that are homologous or complementary to SEQ ID NO:1 and SEQ ID NO:2, and comprises enhanced feed value components that are a result of reduced concentrations of ADL and G lignin, improved level of NDFD in the lower stem.



BRIEF DESCRIPTION OF THE FIGURES
The following drawings form part of the present specification and are included to further demonstrate certain aspects of the present invention. The invention may be better understood by reference to one or more of these drawings and their corresponding descriptions below, in combination with the detailed description of specific embodiments presented herein.
FIG. 1—Illustrates and outlines in black the elite transgenic alfalfa events with suppressed caffeoyl CoA 3-O-methyltransferase (CCoAOMT) that have an ADL concentration of between 80% and 91%; an NDFD value between 110% and 125%; and a lower G lignin value, compared to non-transgenic events.
FIG. 2—Illustrates elite events and reduced lignin alfalfa events for KK179-2 that meet the required performance criteria based on the levels on percent ADL, NDFD, and vigor for enhanced forage digestibility and enhanced nutritive quality, defined as the “sweet spot.”



BRIEF DESCRIPTION OF THE SEQUENCES
SEQ ID NO:1—The sequence of the CCoAOMT gene 1139987:1 CR-Medicago sativa CCoAOMT-1:1:1 (sense direction).
SEQ ID NO:2—The sequence of the 1150536:1 CR-Medicago truncatula CCoAOMT-1:1:2 (antisense direction).
SEQ ID NO:3—The sequence of an RNA loop between the sense and antisense arm (374-530 bp).
SEQ ID NO:4—The sequence of the 5′ end of the RNA loop (7-73 bp).
SEQ ID NO:5—The sequence of the 1141266:1 promoter (P)-Pv.Pal2-1:1:1.
SEQ ID NO:6—The sequence of the 1141267:1 leader (L)-Pv.Pal2-1:1:1.
SEQ ID NO:7—The sequence of pMON100052 CAS-Pv.Pal2//SUP-CCoAOMT//nos;CAS-CaMV.35S//npt2//nos.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides a method to select for enhanced feed value of forage crops in need of the enhancement. Aspects of the method can be applied to various forage crops, for example, including, but not limited to Alsike clover, Sainfoin, Lespedeza, Kura clover, Ladino clover, Red clover, white clover, sweet clover, Birdsfoot trefoil, Cicer milkvetch, Crown Vetch, Medicago truncatula, and alfalfa.
Methods according to the present invention may include, but are not limited to, a method to select transgenic forage crop alfalfa plants transformed with a recombinant DNA construct that reduces the expression or the activity of an S-adenosyl-L-methionine: caffeoyl-CoA 3-O methyltransferase (CCoAOMT or CCOMT) enzyme in the lignin biosynthetic pathway using the selection criteria of reduced acid detergent lignin (ADL), reduced guaiacyl lignin (G-lignin), increased neutral detergent fiber digestibility (NDFD), and at least substantially equal or improved vigor, compared to an alfalfa plant not transformed with the recombinant DNA construct. The combined selection criteria in the method of the invention allow for the selection of alfalfa plants with enhanced feed value. The invention relates to plants, plant parts, plant seeds, plant cells, agricultural products, and methods related to selecting and enhancing the nutrition of a forage crop.
The invention also provides a DNA molecule comprising a promoter molecule that functions in a vascular tissue of an alfalfa plant cell linked to a DNA segment corresponding to SEQ ID NO:1 (nucleotides 6583-6882 of SEQ ID NO:7) or a complement thereof. The invention also provides a DNA molecule comprising SEQ ID NO 1, linked to SEQ ID NO 3, linked to SEQ ID NO 2, which combination is comprised within the construct of SEQ ID NO:7). In another aspect of the invention is an alfalfa plant cell, plant part, hay, or seed comprising SEQ ID NO:1 or SEQ ID NO:2.
The present invention relates to a transgenic plant with improved economically important characteristics, more enhanced feed value. More specifically, the present invention relates to a transgenic plant comprising the nucleotide sequences of this invention, SEQ ID NO:1 or SEQ ID NO:2 of this invention and that enhanced feed value as compared to a non-transgenic control plant.
In a specific embodiment, “enhanced feed value” is described as reduced concentrations of ADL and G lignin, improved levels of NDFD in the lower stem resulting from at least equal vigor, and agronomic fitness compared to non-transgenic control plants not comprising the DNA molecules of the invention.
Plants of the present invention may pass along the recombinant DNA to a progeny. As used herein, “progeny” includes any plant, seed, plant cell, and/or a regenerated plant part comprising the recombinant DNA derived from an ancestor plant. Transgenic plants, progeny, and seeds may contain one, two, three or four copies of the transgene. In practicing the present invention, intercrossing of transgenic plants and selection for the transgene within segregating progeny may be used to increase trait purity. Back-crossing to a parental plant and out-crossing with a non-transgenic plant are also contemplated, as is vegetative propagation. Descriptions of other methods that are commonly used for different traits and crops can be found in one of several references, for example, Fehr, in Breeding Methods for Cultivar Development, Wilcox J. ed., American Society of Agronomy, Madison Wis. (1987).
The plants and seeds used in the methods disclosed herein may also contain one or more additional transgenes. Such transgene may be any nucleotide molecule encoding a protein or RNA molecule conferring a desirable trait including, but not limited to increased insect resistance, increased water use efficiency, increased yield performance, increased drought resistance, increased seed quality, improved nutritional quality, increased ruminal undegradeable proteins (RUP) and/or increased herbicide tolerance, in which the desirable trait is measured with respect to a forage plant lacking such additional transgene.
The lignin pathway starts with the conversion of phenylalanine to cinnamate by phenylalanine ammonia lyase (PAL). The second reaction is performed by cinnamate 4-hydroxylase (C4H) which converts cinnamate to 4-coumarate. These two enzymes form the core of the phenylpropanoid pathway including lignin biosynthesis. Other enzymes in the pathway include C3H or 4-coumarate 3-hydroxylase, which converts 4-coumaroyl shikimate or quinate to caffeoyl shikimate or quinate; HCT, hydroxycinnamoyl CoA: hydroxycinnamoyl transferase which acts at two places catalyzing the formation of 4-coumaroyl shikimate (or quinate), the substrate for C3H, from 4-Coumaroyl CoA, and also acting in the opposite direction on caffeoyl shikimate (or quinate), to yield caffeoyl CoA. CCoAOMT (caffeoyl-CoA 3-O-methyltransferase) converts caffeoyl CoA to feruloyl CoA and might also be involved in other reactions. COMT (caffeic acid O-methyl transferase) acts on 5-hydroxy coniferaldehyde and converts it into sinapaldehyde. Ferulate 5-hydroxylase (F5H) converts coniferaldehyde to 5-hydroxyconiferaldehyde. The DNA sequences of the lignin biosynthetic pathway enzyme genes from various plant species are disclosed in U.S. Patent Publ. No. 2007/0079398, and incorporated herein by reference. DNA sequences of the present invention include but are not limited to SEQ ID NOs:1-7.
Monolignols are incorporated into lignin in the form of the phenylpropanoids p-hydroxyphenyl (H), guaiacyl (G), and syringal (S) lignans, respectively. Dicotyledonous lignin is more often than not a mixture of G and S, and monocotyledonous lignin is a mixture of all three.
DNA constructs are made that contain various genetic elements necessary for the expression of noncoding and coding sequences in plants. Promoters, leaders, introns, transit peptide encoding polynucleic acids, and 3′ transcriptional termination regions are all genetic elements that may be operably linked by those skilled in the art of plant molecular biology to provide a desirable level of expression or functionality.
A variety of promoters active in vascular tissues or tissues that accumulate lignin can be used to express the RNA molecule of the present invention. Promoters active in xylem tissue may include, but are not limited to, promoters associated with phenylpropanoid biosynthetic pathways, such as the phenylalanine ammonia-lyase (PAL) promoters, cinnamate 4-hydroxylase (C4H) promoters, coumarate 3-hydroxylase promoters, O-methyl transferase (OMT) promoters, 4-coumarate:CoA ligase (4CL) promoters (U.S. Pat. No. 6,831,208), cinnamoyl-CoA reductase (CCR) promoters and cinnamyl alcohol dehydrogenase (CAD) promoters (U.S. Pat. No. 7,429,649). Exemplary examples of a vascular promoters are the PAL promoters. In a preferred embodiment of the invention, the PAL2 promoter from Phaseolus vulgares is used to regulate the suppression of CCoAOMT gene(s) in alfalfa.
The laboratory procedures in recombinant DNA technology used herein are those well known and commonly employed in the art. Standard techniques are used for cloning, DNA and RNA isolation, amplification and purification. Generally enzymatic reactions involving DNA ligase, DNA polymerase, restriction endonucleases and the like are performed according to the manufacturer's specifications. These techniques and various other techniques are generally performed according to Sambrook et al., Molecular Cloning—A Laboratory Manual, 2nd. ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989), herein referred to as Sambrook et al., (1989).
Polynucleic acid molecules of interest may also be synthesized, either completely or in part, especially where it is desirable to provide modifications in the polynucleotide sequences, by well-known techniques as described in the technical literature, see, for example, Carruthers et al., Cold Spring Harbor Symp. Quant. Biol. 47:411-418 (1982), and Adams et al., J. Am. Chem. Soc. 105:661 (1983). Thus, all or a portion of the polynucleic acid molecules of the present invention may be of synthetic origin and can be modified as necessary to provide the desired result in the forage crop of choice.
The DNA construct of the present invention may be introduced into the genome of a desired plant host by a variety of conventional transformation techniques that are well known to those skilled in the art. Methods of transformation of plant cells or tissues include, but are not limited to Agrobacterium mediated transformation method and the Biolistics or particle-gun mediated transformation method. Suitable plant transformation vectors for the purpose of Agrobacterium-mediated transformation include those derived from a Ti plasmid of Agrobacterium tumefaciens, as well as those disclosed, for example, by Herrera-Estrella et al., Nature 303:209 (1983); Bevan, Nucleic Acids Res. 12:8711-8721 (1984); Klee et al., Bio-Technology 3(7): 637-642 (1985). In addition to plant transformation vectors derived from the Ti or root-inducing (Ri) plasmids of Agrobacterium, alternative methods can be used to insert the DNA constructs of this invention into plant cells. As used herein, the term “transformed” refers to a cell, tissue, organ, or organism into which has been introduced a foreign polynucleotide molecule, such as a construct. Preferably, the introduced polynucleotide molecule is integrated into the genomic DNA of the recipient cell, tissue, organ, or organism such that the introduced polynucleotide molecule is inherited by subsequent progeny. A “transgenic” or “transformed” cell or organism also includes progeny of the cell or organism and progeny produced from a breeding program employing such a transgenic plant as a parent in a cross and exhibiting an altered phenotype resulting from the presence of a foreign polynucleotide molecule. A plant transformation construct containing a DNA molecule of the present invention may be introduced into plants by any plant transformation method. Methods and materials for transforming plants by introducing a plant expression construct into a plant genome in the practice of this invention can include any of the well known and demonstrated methods, including electroporation as illustrated in U.S. Pat. No. 5,384,253; microprojectile bombardment as illustrated in U.S. Pat. No. 5,015,580; U.S. Pat. No. 5,550,318; U.S. Pat. No. 5,538,880; U.S. Pat. No. 6,160,208; U.S. Pat. No. 6,399,861; and U.S. Pat. No. 6,403,865; Agrobacterium-mediated transformation as illustrated in U.S. Pat. No. 5,635,055; U.S. Pat. No. 5,824,877; U.S. Pat. No. 5,591,616; U.S. Pat. No. 5,981,840; and U.S. Pat. No. 6,384,301; and protoplast transformation as illustrated in U.S. Pat. No. 5,508,184, all of which are incorporated herein by reference.
In one embodiment of the invention, such legumes may include alfalfa (lucerne; Medicago sativa or Medicago falcata or hybrids between them); other forage legumes similar to alfalfa that can be modified for enhanced feed value for ruminant animals, include white clover (Trifolium repens), red clover (T pretense), alsike clover (T. hybridum), sweet clover (Melitotus alba and M. officinalis) and subterranean clover (T. subterranium), sainfoin (Onobrychis viciifolia), big trefoil (Lotus uliginosis), birdsfoot trefoil (L. corniculatus), cicer milkvetch (Astragalus cicer), sericea (Lespedeza cuneata), Kobe lespedeza (Kummerowia striata), Korean lespedeza (K. stipulacea), trees, shrubs, and herbaceous plants in general.
The following examples are included to demonstrate examples of certain preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples that follow represent approaches the inventors have found function well in the practice of the invention, and thus can be considered to constitute examples of preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments that are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
The following definitions and methods are provided to better define the present invention and to guide those of ordinary skill in the art of the present invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art.
As used herein, the term “forage crop” means a forage legume, and includes all plant varieties that can be bred with the forage crop, including related wild forage species.
Alfalfa (Medicago sativa) is a forage legume often used for animal feed, especially dairy cattle. As used herein, the term “alfalfa” means any Medicago species, including, but not limited to, M. sativa, M. murex, M. falcata, M. prostrata, and M. truncatula. Thus, as used herein, the term “alfalfa” means any type of alfalfa including, but is not limited to, any alfalfa commonly referred to as cultivated alfalfa, diploid alfalfa, glandular alfalfa, purple-flowered alfalfa, sickle alfalfa, variegated alfalfa, wild alfalfa, or yellow-flowered alfalfa.
The invention provides DNA molecules and their corresponding nucleotide sequences. As used herein, the term “DNA”, “DNA molecule”, “polynucleotide molecule” refers to a double-stranded DNA molecule of genomic or synthetic origin, such as, a polymer of deoxyribonucleotide bases or a polynucleotide molecule, read from the 5′ (upstream) end to the 3′ (downstream) end. As used herein, the term “DNA sequence”, “nucleotide sequence” or “polynucleotide sequence” refers to the nucleotide sequence of a DNA molecule.
“DNA construct” or “recombinant DNA molecule” refers to a combination of heterologous DNA genetic elements in operable linkage that is often used to provide new traits to a recipient organism. As used herein, the term “recombinant” refers to a form of DNA and/or protein and/or an organism that would not normally be found in nature and as such was created by human intervention. Such human intervention may produce a recombinant DNA molecule and/or a recombinant plant. As used herein, a “recombinant DNA molecule” is a DNA molecule comprising a combination of DNA molecules that would not naturally occur together and is the result of human intervention, for example, a DNA molecule that is comprised of a combination of at least two DNA molecules heterologous to each other, and/or a DNA molecule that is artificially synthesized and comprises a polynucleotide sequence that deviates from the polynucleotide sequence that would normally exist in nature. As used herein, a “recombinant plant” is a plant that would not normally exist in nature, is the result of human intervention, and contains a transgene and/or recombinant DNA molecule incorporated into its genome. A “DNA construct” as used in the present invention comprises at least one expression cassette, a promoter operable in plant cells, and the polynucleotide of the invention encoding a protein, variant of a protein, or fragment of a protein that is functionally defined to maintain activity in transgenic alfalfa, including plant cells, plant parts, explants, and plants. At least one expression cassette in a DNA construct as used herein may also comprise one or more polynucleotides that suppress the expression of at least one polypeptide encoding a trans-caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) coding sequence in a target plant.
As used herein, the term “comprising” means “including but not limited to”.
As used herein, the term “homologous or complementary” refers to polynucleotide molecules that generally demonstrate a substantial percent sequence identity with the plus sense or minus sense strands of the DNA molecules provided herein. Of particular interest are DNA molecules that share at least about 90% sequence identity, or even greater sequence identity, such as 98% or 99% sequence identity with the polynucleotide sequences described herein. Accordingly, the nucleotide sequences of the invention may be used for their ability to selectively form duplex molecules with complementary stretches of polynucleotide molecule fragments. Depending on the application envisioned, one may desire to employ varying conditions of hybridization to achieve varying degrees of selectivity towards target sequence.
Polynucleotide molecules of the present invention that are capable of regulating expression of an endogenous forage plant gene, caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) and are substantially homologous to polynucleotide molecules that provide the same function and are encompassed within the scope of this invention.
“Operably linked” or “linked” is envisioned if a first nucleic-acid molecule is “operably” linked with a second nucleic-acid molecule when the first nucleic acid molecule is placed in a functional relationship with the second nucleic-acid molecule. For example, a promoter is operably linked to a DNA molecule if the promoter effects the transcription or expression of the DNA molecule. Generally, operably linked DNA molecules are contiguous, however, additional molecules may be included in a DNA construct that separate the physical linkage without affecting the functional linkage.
The term “promoter” or “promoter region” refers to a polynucleic acid molecule that functions as a regulatory element, usually found upstream (5′) to a DNA coding sequence, that controls expression of the coding sequence by controlling the production of messenger RNA (mRNA), by providing the recognition site for RNA polymerase and/or other factors necessary for start of transcription at the correct site. As contemplated herein, a promoter or promoter region includes variations of promoters derived by means of DNA ligation to various regulatory sequences, random or controlled mutagenesis, and addition or duplication of enhancer molecules. The promoter region disclosed herein, and biologically functional equivalents thereof, are responsible for driving the transcription of coding sequences under their control when introduced into a host as part of a suitable recombinant vector, as demonstrated by its ability to produce mRNA. A DNA construct comprising a promoter can also be used to direct the transcription of noncoding RNA molecules.
The “3′ non-translated sequences” are DNA sequences located downstream of a structural nucleotide sequence and include sequences encoding polyadenylation and other regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal functions in plants to cause the addition of polyadenylate nucleotides to the 3′ end of the mRNA precursor. The polyadenylation sequence can be derived from the natural gene, from a variety of plant genes, or from T-DNA.
“Transformation” refers to a process of introducing an exogenous polynucleic acid molecule (for example, a DNA construct, a recombinant polynucleic acid molecule) into a cell or protoplast and the exogenous polynucleic acid molecule is incorporated into a host cell genome or an organelle genome (for example, chloroplast or mitochondria) or is capable of autonomous replication. “Transformed” or “transgenic” refers to a cell, tissue, organ, or organism into which a foreign polynucleic acid, such as a DNA construct or recombinant DNA molecule has been inserted. A “transgenic” or “transformed” cell or organism also includes progeny of the cell or organism and progeny produced from a breeding program employing, such a “transgenic” plant as a parent in a cross and exhibiting an altered phenotype resulting from the presence of the foreign polynucleic acid molecule. The use of Agrobacterium-mediated transformation to introduce DNA into dicotyledonous plants, including alfalfa and plant cells is well known in the art. See for example, the methods described by Fraley et al., (1985), Rogers et al., (1987) and U.S. Pat. No. 5,563,055, specifically incorporated herein by reference in its entirety. By plant transformation is meant the introduction of an external nucleic acid sequence into the plant genome. Transformation techniques include calcium phosphate transfection, DEAE-Betran transfection, electroporation, microinjection, protoplast fusion, and liposome-mediated transfection. Alternatively, a plant virus such as CaMV may be used as a vector for introducing foreign nucleic acid into plant cells or a high velocity ballistic penetration using small particles (Klein et al., 1987). A most preferred method for introducing nucleic acid segments into plant cells is to infect a plant cell or plant tissue with Agrobacterium tumefaciens which has been transformed with a selected nucleic acid segment (Horsch et al., 1984). Alfalfa was transformed following the protocol of McKersie et al., 1996. Other methods of alfalfa transformation either via, Agrobacterium or using other biological, chemical, or physical methods are feasible and thus may be used in the present invention. Methods for producing appropriate vectors, for transforming cells with those vectors and for identifying transformants are described in the scientific literature, as for example, but not limited to, Sambrook et al. (1989), Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., Gelvin and Schilperoort (1991) Plant Molecular Biology Manual, Kluwer Academic Press, and more importantly in Glick, B. R. and Thompson, J. E. 1993, Methods in Plant Molecular Biology and Biotechnology, CRC Press, Boca Raton.
As used herein, the term “transgene” refers to a polynucleotide molecule artificially incorporated into a host cell's genome. Such transgene may be heterologous to the host cell. The term “transgenic plant” refers to a plant comprising such a transgene. “Transgene” also encompasses the component parts of a native plant gene modified by insertion of a nonnative polynucleic acid molecule by directed recombination or site specific mutation. A recombinant DNA molecule inserted into the genome of a plant is a transgene. A “transgene” is defined as a segment of DNA which has been incorporated into a host genome or is capable of autonomous replication in a host cell and is capable of causing the expression of one or more coding sequences. Exemplary transgenes will provide the host cell, or plants regenerated from the host cell with an enhanced phenotype relative to the corresponding non-transformed cell or plant. Transgenes may be directly introduced into a plant by genetic transformation, or may be inherited from a transgenic progeny plant.
“Transformation vectors” of this invention used for transformation may contain one or more “expression cassettes”, each comprising a native or non-native plant promoter operably linked to a polynucleotide sequence of interest, which is operably linked to 3′ UTR termination signal, for expression in an appropriate host cell. Transformation vectors also typically comprise sequences required for proper translation of the nucleotide sequence or transgene. As used herein, the term “transgene” refers to a polynucleotide molecule artificially incorporated into a host cell's genome. Such a transgene may be heterologous to the host cell. The term “transgenic plant” refers to a plant comprising such a transgene. The coding region usually codes for a protein of interest but may also code for a functional RNA of interest, for example antisense RNA, a nontranslated RNA, in the sense or antisense direction, a microRNA, a noncoding RNA, or a synthetic RNA used in either suppression or over expression of target gene sequences. The expression cassette comprising the nucleotide sequence of interest may be chimeric, meaning that at least one of its components is heterologous with respect to at least one of its other components. As used herein the term “chimeric” refers to a DNA molecule that is created from two or more genetically diverse sources, i.e. a first molecule from one gene or organism and a second molecule from another gene or organism. A “transformation construct” is a chimeric DNA molecule which is designed for introduction into a host genome by genetic transformation. Preferred transformation constructs will comprise all of the genetic elements necessary to direct the expression of one or more exogenous genes. In particular embodiments of the instant invention, it may be desirable to introduce a transformation construct into a host cell in the form of an expression cassette.
“Regeneration” refers to the process of growing a plant from a plant cell (for example, a protoplast, callus, or explant).
The term “plant” includes whole plants, shoot vegetative organs/structures (for example, leaves, stems and tubers), roots, flowers and floral organs/structures (for example, bracts, sepals, petals, stamens, carpels, anthers, and ovules), seed (including embryo, endosperm, and seed coat) and fruit (the mature ovary), plant tissue (for example, vascular tissue, ground tissue, and the like) and cells (for example, guard cells, egg cells, and the like), and progeny of same. A plant refers to a whole plant, as well as to a plant part, such as seed, fruit, leaf, or root, plant tissue, plant cells or any other plant material, for example, a plant explant, as well as to progeny thereof, and to in vitro systems that mimic biochemical or cellular components or processes in a cell.
A “control plant” as used in the present disclosure refers to a plant cell, seed, plant component, plant tissue, plant organ, or whole plant used to compare against transgenic or genetically modified plant for the purpose of identifying an enhanced phenotype in the transgenic or genetically modified plant. A control plant may in some cases be a transgenic plant line that comprises an empty vector or marker gene, but does not contain the recombinant polynucleotide of the present invention that is expressed in the transgenic or genetically modified plant. A control plant may in other cases be a progeny of a hemizygous transgenic plant line that does not contain the recombinant DNA, known as a negative segregant or negative isoline. In general, a control plant is a plant of the same line or variety as the transgenic or genetically modified plant being tested. A suitable control plant may include a genetically unaltered or non-transgenic plant of the parental line used to generate a transgenic plant herein.
A “transgenic plant” refers to a plant that contains genetic material not found in a wild-type plant of the same species, variety, or cultivar. The genetic material may include a transgene, an insertional mutagenesis event (such as by transposon or T-DNA insertional mutagenesis), an activation tagging sequence, a mutated sequence, a homologous recombination event or a sequence modified by chimeraplasty. Typically, the foreign genetic material has been introduced into the plant by human manipulation, but any method can be used as one of skill in the art recognizes. A transgenic plant may contain an expression vector or cassette. A “transgenic plant” is a plant or progeny plant of any subsequent generation that is derived from the plant or progeny, wherein the plant or progeny contains an introduced exogenous DNA molecule not naturally present in a non-transgenic plant. The transgenic plant may additionally contain sequences which are native to the plant being transformed, but wherein the “exogenous” gene has been altered in order to alter the level or pattern of expression of the gene, for example, by use of one or more heterologous regulatory or other elements.
“Wild type” or “wild-type”, as used herein, refers to a plant cell, seed, plant component, plant part, plant tissue, plant organ, or whole plant that has not been genetically modified or treated in an experimental sense. Wild-type cells, seeds, components, parts, tissues, organs, or whole plants may be used as controls to compare levels of expression, the extent and nature of trait modification with cells, tissue or plants of the same species, variety or cultivar in which a polypeptide's expression is altered, for example, in that it has been knocked out, overexpressed, or ectopically expressed.
An R0 transgenic plant refers to a plant that has been genetically transformed or has been regenerated from a plant cell or cells that have been genetically transformed.
A “population” of plants refers to a local group of organisms of the same species that can under normal conditions interbreed and share similarity among the frequencies of alleles and genotypes within that population.
As used herein, the term “callus” refers to a clump of undifferentiated plant cells that are capable of repeated cell division and growth, and in some species, can be induced to form a whole plant.
As used herein, the term “somatic tissues” refers to tissues not including germ cells or gametes. Somatic tissues are composed of vegetative tissues and cells.
As used herein, the term “somatic embryogenesis” refers to the process of embryo initiation and development from vegetative or non-gametic cells. The embryos from a given tissue source are presumed to be genetically identical. Somatic embryogenesis is an important pathway for the regeneration of plants from cell culture systems and a method commonly used in large scale production of plants and synthetic seeds (Stuart et al. 1987). In somatic (asexual) embryogenesis, embryo-like structures develop into whole plants in a way analogous to zygotic embryos formed from somatic tissues. Somatic embryos can be produced from a cell or small group of cells without the production of an intervening callus. Somatic embryos can also be produced from an intermediary callus tissue or from a cell suspension produced from that callus. Somatic embryogenesis is one of a number of methods known in the art for the propagation of desirable species or varieties of plants. There are many advantages which favor somatic embryogenesis as a propagative method of choice. One advantage is that a plant which has a known and desirable phenotype can be chosen as the source of cells, and, in accordance with somatic embryogenesis techniques, these cells can be rapidly cultured into many genetically uniform embryos. The resulting embryos can then be cultivated into entire plants possessing roots and shoots. Thus, in accordance with this technique, plants with the same desirable phenotype as the parent can be mass produced, potentially at costs comparable to and often more quickly and with better genetic uniformity than other propagative techniques such as described in U.S. Pat. No. 5,187,092 incorporated herein by reference.
Cultured cells may be grown either on solid supports or in the form of liquid suspensions. In either instance, nutrients may be provided to the cells in the form of media, and environmental conditions controlled. There are many types of tissue culture media comprised of various amino acids, salts, sugars, growth regulators and vitamins. Various types of media suitable for culture of plant cells have been previously described. Examples of these media include, but are not limited to, the medium described by Schenk and Hildebrandt formulation (1972). Embryogenic callus cultures may be used with certain transformation techniques for the preparation of cells for transformation and for the regeneration of forage plants, for example, alfalfa. Schenk and Hildebrant medium formulation (S&H media, 1972) was used in the transformation and maintenance of embryogenic tissue cultures. The S&H medium is a mixture of various categories of ingredients (salts, amino acids, growth regulators, sugars, buffers) that are required for growth of most cell types. The S&H media, pH at 5.8, provides a mixture of macro-nutrients, micro-nutrients, vitamins, iron that is supplemented with hormones, 2,4-D at a final concentration of 0.2 μM and kinetin at a concentration 0.5 μM. Under selective conditions primary somatic embryos are visible after 12-15 weeks.
As used herein, the term “explant” refers to a piece of tissue taken from a donor plant for culturing.
A “host cell” may be defined as a cell invaded by or capable of being invaded by an infectious agent. A host cell that has been transformed with DNA (or RNA), such as a bacterial cell acting as a host cell of recombinant DNA, is capable of replicating the recombinant DNA reproduced along with the host cell. A reference to a “host cell” includes a plurality of such host cells. Suitable host cells for the introduction of recombinant DNA include but are not limited to plant cells, bacterial cells, yeast cells, insect cells, synthetic cells or a combination thereof. A synthetic host cell can encompass a chemically synthesized chromosome transplanted into a cell to produce a synthetic cell (for example, a synthetic bacterium), which is capable of self replicating. The genomes of synthetic bacterial host cells may be assembled in naturally grown host cells (for example, yeast host cells). Synthetic host cells are particularly useful for making a minimal synthetic genome containing all of the properties of a living.
The term “expression” refers to the combination of intracellular processes, including transcription and translation undergone by a coding DNA molecule such as a structural gene to produce a polypeptide.
The term “suppression” as used herein refers to a lower expression level of a gene in a plant, plant cell or plant tissue, compared to the expression in a wild-type or control plant, cell or tissue, at any developmental or temporal stage for the gene. Suppression can be applied using numerous approaches; to suppress a mutation that has resulted in decreased activity of a protein, to suppress the production of an inhibitory agent, to elevate, reduce or eliminate the level of substrate that a enzyme requires for activity, to produce a new protein; or to activate a normally silent gene, to accumulate a product that does not normally increase under natural conditions. The suppressor can be another mutation on a different gene, a suppressor mutation on the same gene but located some distance from the first mutation, or a suppressor in the cytoplasm that has generated due to a change in non-chromosomal DNA. There are multiple approaches to suppress a gene, for example, RNAi-mediated gene suppression can be used to suppress the expression of targeted genes within plants. A recombinant DNA construct comprising a promoter that is functional in a plant cell and that is operably-linked to a polynucleotide that when expressed in a plant cell is transcribed into an RNA molecule that suppresses the level of an endogenous protein in the plant cell relative to a control, wherein the RNA molecule is a dsRNA which is processed into siRNAs which targets a messenger RNA encoding the protein; a miRNA that targets a messenger RNA encoding the protein; a ta-siRNA which is processed into siRNAs and which targets a messenger RNA encoding the protein; or is transcribed into an RNA molecule resulting in the suppression of a miRNA activity relative to a control, and wherein a RNA molecule is a cleavage blocker of a miRNA or is a miRNA decoy of a miRNA (Examples of such RNAi-mediated gene suppression approaches are disclosed in U.S. Patent Publ. 2009/61288019 and incorporated herein by reference). “Suppression” refers to a plant or plant cell having a disruption in at least one gene in the plant or cell, where the disruption results in a reduced expression or activity of the polypeptide encoded by that gene compared to a control cell. The knockout can be the result of, for example, genomic disruptions, including transposons, tilling, and homologous recombination, antisense constructs, sense constructs, RNA silencing constructs, or RNA interference. A T-DNA insertion within a gene is an example of a genotypic alteration that may abolish expression of that gene.
In the selection of an “event”, a transformation construct responsible for a trait is introduced into the genome via a transformation method. Numerous independent transformants (events) are usually generated for each construct. These events are evaluated to select those with superior performance. The event evaluation process is based on several criteria including: 1) transgene expression and phenotype “efficacy” of the trait; 2) molecular characterization of the trait, such as the selection of events showing a clean single intact insert are found by conducting molecular assays for copy number, insert number, insert complexity, presence of the vector backbone, and development of event-specific assays and are used for further development; 3) segregation of the trait, segregation of the trait is tested to select transgenic events that follow a single-locus segregation pattern. A direct approach is to evaluate the segregation of the trait; 4) agronomics of the developed event; and 5) stability of the transgenic trait expression. Evaluation of large populations of independent events and more thorough evaluation result in the greater chance of success. The stability of transgenic trait expression is ascertained by testing in different generations, environments, and in different genetic backgrounds. Events that exhibit unstable phenotype efficacy are discarded. Generally, events with a single intact insert that inherited as a single dominant gene and follow Mendelian segregation ratios are used in commercial trait integration strategies such as backcrossing and forward breeding.
“G lignin” refers to guaiacyl lignin. Guaiacyl lignin is composed principally of coniferyl alcohol units, while guaiacyl-syringyl lignin contains monomeric units from coniferyl and sinapyl alcohol. In general, guaiacyl lignin is found in softwoods, while guaiacyl-syringyl lignin is present in hardwoods.
“Enhance feed value” refers to the forage quality, such as fiber content, digestibility, and available carbohydrate resources available to livestock. Enhanced feed value or alfalfa quality is determined by the Relative Feed Value (RFV) expressed as a percentage of alfalfa at 100% bloom and is used as a predictor of feed value in the field. Components that effect feed value are acid detergent lignin concentration and G lignin and neutral detergent fiber digestibility. The measurement of these feed value components is an aspect of the invention.
Plant “vigor” is a measure of agronomic fitness, such as plant growth, foliage volume, or biomass over a set period of time after planting.
“Acid detergent lignin” (ADL) is an estimate of lignin content. Lignin is an indigestible component of forage fiber (NDF) that is believed to limit the extent to which forage fiber can be digested by ruminant animals.
“Neutral Detergent Fiber Digestibility” (NDFD) content of forage is a measure of the digestibility of a forage fiber and can be measured in vitro and predicted using Near Infrared Reflectance Spectroscopy (NIRS). The higher the NDFD value the more digestible the forage.
The “lower stem” of the alfalfa plant is described as the 15-cm stem sections of the stems of the alfalfa plant that have been harvested 2.5′′ above ground level with the leaves completely removed. The lower stem is the most ligninfied part of the alfalfa plant, and the least digestible.
Alfalfa is generally harvested as alfalfa “hay” or “silage”, the differences between the two being based on percent moisture and crude protein. For alfalfa silage, digestible protein should be 60% to 70% of crude protein. For example, in alfalfa silage, digestible protein should be 60% to 70% of crude protein). Alfalfa is most often harvested as “hay” and can be stored as bales or stacks but can also be made into silage, grazed or fed as greenchop. For the purposes of this invention “whole plant” is the equivalent of “hay”. On a dry matter basis, cattle livestock eat more silage than hay. Silage or haylage is made from direct-cut alfalfa.
As used herein, “ruminal undegradable protein” or “RUP” refers to a measure of feed quality. The feed quality “nutritive value” of alfalfa may be greatly improved by an increase in its RUP concentration. Forage proteins are often not utilizable by ruminants because they are degraded during silage fermentation and thus an increase in RUP concentration in alfalfa enhances its nutritive value.
As used herein, “a” or “an” may mean one or more. As used herein in the claim(s), when used in conjunction with the word “comprising,” the words “a” or “an” may mean one or more than one.
As used herein the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.” As used herein “another” may mean at least a second or more.
EXAMPLES
The following examples provide illustrative embodiments of the invention. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in specific aspects of these embodiments without departing from the concept, spirit, and scope of the invention. Moreover, it is apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope, and concept of the invention as defined by the appended claims.
Example 1
Plant Expression Constructs for Alfalfa Transformation
This example illustrates the construction of expression constructs for transferring recombinant DNA into an alfalfa plant cell nucleus that can be regenerated into transgenic alfalfa plants. The transformation vector pMON100052 (also known as pFG118) comprising the elements as described in Table 1, was fabricated for use in preparing recombinant DNA for Agrobacterium-mediated transformation into alfalfa tissue for suppressing Caffeoyl-CoA3-O-methyltransferase (CCoAOMT) comprising the sequences identified as SEQ ID NO:1 and SEQ ID NO:2 of this invention. The alfalfa cell, plant part, or plant was transformed with the expression cassette SEQ ID NO:7 of this invention, which comprises the Pv.PAL2 promoter from Phaseolus vulgaris that allows for the controlled expression of the CCoAOMT polypeptide in sites of lignin deposition. The expression cassette can be introduced into a plant by transformation or by breeding after transformation of a parent plant and harvesting of progeny seed.







TABLE 1







Elements of transformation vector pMON100052 (also known as pFG118)













Coordinates





of SEQ ID


Function
Name
Annotation
NO: 36444





Agrobacterium
B-AGRtu.left
Agro left border sequence, essential
1516-1957


T-DNA transfer
border
for transfer of T-DNA.



Plant selectable
L-CaMV.35S
5′UTR of 35S RNA from CaMV
1142-1172


marker expression

gene



cassette
P-CaMV.35S
Promoter for 35S RNA from CaMV
1173-1465




containing a duplication of the −90 





to −350 region.




CR-Ec.nptII-Tn5
Coding region for neomycin
 314-1108




phosphotransferase gene from





transposon Tn5 which confers





resistance to neomycin and





kanamycin.




T-AGRtu.nos
A 3′ non-translated region of the
 30-282




nopaline synthase gene of





Agrobacterium tumefaciens Ti





plasmid which functions to direct





polyadenylation of the mRNA.



Gene of interest
L-Pv.Pal2
5′UTR of Phaseolus vulgaris PAL2
7426-7479


expression

gene



cassette
P-Pv.Pal2
Promoter from the Phaseolus
7480-8502




vulgaris PAL2 gene




GOI
A polynucleotide or polypeptide-
6322-6882




coding SEQ ID NO: 1 Medicago





sativa CCoAOMT gene or SEQ ID





NO: 2 Medicago truncatula





CCoAOMT gene




T-AGRtu.nos
A 3′ non-translated region of the
6322-6574




nopaline synthase gene of





Agrobacterium tumefaciens Ti





plasmid which functions to direct





polyadenylation of the mRNA.



Agrobacterium
B-AGRtu.right
Agro right border sequence,
10196-10552


T-DNA transfer
border
essential for transfer of T-DNA.









Alfalfa clone R2336, selected from elite germplasm, was transformed with the DNA construct, pFG118 (SEQ ID NO:8; pMON100052) comprising a DNA segment complimentary to the coding sequence of caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) using Agrobacterium strain ABI. All RNAi constructs to generate reduced lignin transgenic events by down regulating the lignin biosynthetic enzyme CCoAOMT from Medicago sativa utilized the stabilized antisense technology described in U.S. Patent Publication No. US2005/0176670, incorporated herein by reference. Two different coding sequences were used in the transformation construct pMON100052, one encoding the RNAi arm and loop for the CCoAOMT gene (SEQ ID NO:1) containing a 5′ end of the RNA loop, and the other sequence (SEQ ID NO:2) containing an antisense arm, loop (374-530 bp) and sense arm (531-836 bp) to suppress or down-regulate the expression of the CCoAOMT enzyme. In the pMON100052 construct, the expression of the genes used to suppress the CCoAOMT gene was regulated under the control of a single PAL2 promoter from Phaseolus vulgarus. Transformation of leaflets or leaf-derived explants from alfalfa clone R2336 was carried out using a standard Agrobacterium method (Walker and Sato, Plant Cell Tissue Organ Cult, 1:109-121, 1981). The neomycin phosphotransferase gene, which confers resistance to neomycin and kanamycin, was used as a selectable marker to select transformed material, which was then transferred to shoot induction medium supplemented with ticarcillin (250 μg/mL) or Timentin (150 μg/mL). Transformed plants were transferred to soil in approximately 20-24 weeks. When shoots had formed, they were rooted and initially placed in Magenta boxes and subsequently in pots containing a sterilized vermiculite:perlite mix at a ratio of 5:1 combined with an equal amount of potting Pro-mix PGX containing biofungicide (Hummert, Cat. No. 10-2093) and maintained under moderate light at 25-26° C. The plants were maintained under sealed conditions either under Magenta box covers or sealed with thin plastic bags for a period of 7-10 days, after which time the humidity was gradually reduced as the plants acclimated. Plants were fertilized with a general purpose fertilizer. Once plants were established, they were transferred to a conventional soil mix and transferred to the greenhouse.
Example 2
Identification of Sequences for Suppression of Caffeoyl-CoA3-O-Methyltransferase (CCoAOMT)
This example illustrates phenolic acid analysis of transgenic alfalfa expressing a DNA construct for the suppression of expression of an enzyme in the lignin biosynthetic pathway. Alfalfa cells were transformed with a DNA construct comprising a DNA segment (SEQ ID NO:7) complimentary to a caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) coding sequence in order to down regulate the expression of the enzyme. The resultant transgenic alfalfa plant cell, plant part, or plant comprised a recombinant DNA molecule of this invention, wherein a portion of the DNA molecule is homologous or complementary to SEQ ID NO:1 or SEQ ID NO:2.
Example 3
Selection Method for Alfalfa Plants with Reduced Acid Detergent Lignin
Acid detergent fiber (ADF) was measured by modifications to standard protocols of Goering and Van Soest (Forage Fiber Analysis, USDA Agricultural Handbook No. 379, 1970). Powdered samples (0.35 g) were placed in an F57 ANKOM filter bag (ANKOM Technology Corporation, Fairport, N.Y.), and heated at 100° C. with agitation for 1 h in the respective solutions in an ANKOM Fiber Analyzer. After washing in near boiling water, samples were dried at 105° C. for 6 h, and then weighed to determine fiber loss. ADL determinations were performed on the residue from ADF determination by incubation in 72% (v/v) sulfuric acid for 3 h, washing thoroughly, and drying for 6 h at 105° C. prior to weighing (Guo et al., Transgenic Res, 10(5):457-464, 2001).
Samples (30 mg) were dried overnight at 50° C. before weighing into glass culture vial (16×150 mm) fitted with Teflon lined screw caps. Samples were heated for 4 h at 50° C. after adding 3 mL of freshly prepared 25% (v/v) acetyl bromide in glacial acetic acid. After cooling down the samples, 3 mL of acetic acid were added into the tubes and centrifuged at 3000 rpm for 5 min. An aliquot (5 mL) of the upper layer was quantitatively transferred to a 50-mL volumetric flask that contained 10 mL of 2 M NaOH and 12 mL of acetic acid. Hydroxylamine (1 mL of 0.5 M) was added to each flask and samples were diluted to 50 mL with acetic acid. Absorption spectra (250 to 350 nM) were determined for each sample and used to determine the absorption maxima at 280 nm. The following regression equation was used: Acetyl bromide lignin (mg/ml)=absorbance reading/F, where F=17.20 for young tissue and F=17.12 for mature tissue.
Thioacidolysis and Lignin Composition
Three milliliters of thioacidolysis reagent [2.5% boron trifluoride etherate and 10% ethanethiol, in dioxane (v/v)] was added to 30 mg dried ground sample in a 15-mL glass vial. The sealed vial was then placed into an oil bath (>80° C.) for 4 h with periodic (every 30 min) manual agitation. The reaction was stopped by placing the vial on ice. Internal standard (200 μL), water (3 mL), and saturated sodium bicarbonate (until pH  ̃3 to 4) were added. The mix was vortexed and allowed to settle. The lower layer (methane chloride containing the lignin breakdown products) was transferred to another glass vial. The aqueous layer was extracted two more times with 3 mL methane chloride. The methane chloride layers were combined and dried over anhydrous sodium sulfate. An aliquot (3 mL) was dried under nitrogen. The dried extracted lignin monomers were derivatized with 25 microliter (μL) pyridine and 80 μL N-Methyl-N-(trimethylsilyl)trifluoroacetamide (MSTFA). After incubation for 30 min at 37° C., 0.5 μL of this reaction product was analyzed by GC/MS. The GC/MS was performed on a Hewlett Packard 5890 series II gas chromatograph with a 5971 series mass selective detector (column: HP-1, 60 m×0.25 mm×0.25 μm film thickness), and the mass spectra were record in electron impact mode (70 eV) with a 60 to 650 m/z scanning range.
Example 4
Alfalfa Plants with Enhanced Feed Value Components
Alfalfa (Medicago sativa L.) is one of the most important forages in the United States. Increasing alfalfa fiber digestibility would improve forage quality, ration formulation flexibility, and enhance feed value. Currently, growers and breeders relay on near infrared spectroscopy (NIRS) to predict forage quality traits for alfalfa. With the introduction of lignin down regulated alfalfa plants, the NIRS methods of analysis and equations are accurate for predicting forage quality traits for novel low-lignin alfalfa samples. NIR analysis has been used for the prediction of lignin content and composition, for example to determine Klason lignin and in the ration of syringl (S-lignin) to guaiacyl (G-lignin) sub-units (Bailléres et al., 2002). This example reports in vitro neutral detergent fiber digestibility (NDFD) and lignin analysis (ADL, Klason, total thioacidolysis yield, S-lignin, and G-lignin of caffeic acid 3-O-methyltransferase (COMT) and caffeoyl CoA 3-O-methyltransferase (CCoAOMT) down-regulated alfalfa.
Amounts of ADL as a percentage of dry matter (DM), and NDFD as a percentage of neutral detergent fiber were calculated using the NIRS equation developed separately for lower stem and whole plant samples using tissues of transgenic alfalfa (40 COMT and 40 CCoAOMT down-regulated plants) and 20 non-transgenic control null-type alfalfa plants. Chemical analyses generated total amounts of lignins in the lower stem of alfalfa plants, which comprised measurements for ADL, Klason lignin, total thioacidolysis lignin, S-lignin, G-lignin, and H-lignin represented on a percentage of DM basis.
Lower stem samples of 40 COMT, 40 CCoAOMT, and 20 null-type alfalfa plants were collected over three locations from a total of 10 harvested by location combinations, which equals a total of 2900 field samples. The results of NIRS analysis indicated lower lignin and higher digestibility for COMT and CCoAOMT transgenic alfalfa stems. The results also revealed that the relative values among down regulated alfalfa differed for thioacidolysis measured lignin compared to ADL and Klason lignin. Total thioacidolysis yield appeared to be the best predictor of NDFD. In particular, S-lignin levels were highly correlated with NDFD in the alfalfa stem tissues.
Table 2 provides a summary of the ADL and NDFD values represented as a percent of the non-transgenic alfalfa control plants for the reduced lignin alfalfa transgenic event, KK179-2, compared to the Round-up Ready (RR) event in the whole plant, which is equivalent to hay (A) and the lower stem (B). Column 1 identifies alfalfa transgenic event KK179-2 and the Round-up Ready (RR) event. Column 2 provides average amounts of ADL represented as a percent of the non-transgenic alfalfa control plant. Column 3 provides average amounts of NDFD as a percent of the non-transgenic alfalfa control plant.







TABLE 2





Comparison of ADL and NDFD analysis between transgenic 


alfalfa event KK179-2 with pMON100052 and Round-up 


(Ready RR) alfalfa event J-101 (ATCC Accession No.


PTA-4814, as described in U.S. Pat. application No. 7,566,817).







A. Whole









Entry
ADL % control
NDFD % control





RKK179
90.82
121.69


RR only
100
100


RKK179
82.05
125.3


RR only
100
100


RKK179
85.88
111.37


RR only
100
100










B. Lower











ADL %
G Lignin
NDFD


Entry
control
% control
% control





RKK179
83.84
778.41
135.2


RR only
100
100
100


RKK179
80.79
78.63
138.46


RR only
100
100
100


RR/RL 2
75.94
73.63
136.19


RR/-2
100
100
100









Table 3 shows raw data values used to create “Sweet Spot” selection for reduced lignin alfalfa events represented in FIG. 2, as defined by performance criteria based on percent ADL, percent G lignin, a measure of NDFD, and a vigor rating score. Column 1 provides the graph identification number associated with the individual alfalfa plants (shown in FIG. 2). Column 2 provides the event designation. Column 3 contains vigor rating scores of ranked from 1-10, with a score of 10 resulting in the best vigor. Column 4 provides mean ADL measurements. Column 5 provides a percent ADL measurement based on the comparison to the non-transgenic null control plants. Column 7 provides a measurement for mean NDFD. Column 8 provides a measure of percent NDFD based on the comparison to the non-transgenic null control plants. Column 9 provides a measurement of mean G lignin. Column 10 provides a percent G lignin measurement based on the comparison to the non-transgenic null control plants. Alfalfa events that met the performance criteria were classified as follows: ADL concentration in the lower stem reduced by between approximately 15 to 30%, and an ADL concentration of between 80 to 91%, a reduction in G lignin by at least 25%, and an NDFD value between 110 and 125%, relative to events with an ADL and NDFD value of alfalfa hay below the performance criteria.







TABLE 3







Raw data values used to create “Sweet Spot” selection for reduced 


lignin alfalfa events represented in FIG. 2.



















% 

% 

% 


Graph

Mean
Mean
Null
Mean
Null
Mean
Null


Id
Event
vigor
ADL
ADL
NDFD
NDFD
G
G


















1
JJ255-3
7.0
10.3
104% 
23.7
 81%
3.6
110%


2
KK010-3
10.0
10.4
105% 
24.2
 83%
3.6
110%


3
KK038-1
8.0
9.9
100% 
24.5
 84%
3.2
 97%


4
JJ195-2
8.0
10.2
103% 
24.5
 84%
3.7
112%


5
JJ234-2
8.0
10.9
110% 
24.6
 84%
3.8
115%


6
KK189-3
9.0
11.3
114% 
24.7
 84%
3.9
119%


7
KK004-2
8.0
9.9
100% 
24.9
 85%
3.2
 96%


8
KK189-3
9.0
10.3
104% 
25.0
 86%
3.7
112%


9
KK155-3
5.0
10.4
105% 
25.2
 86%
3.6
108%


10
KK038-1
8.0
9.4
95%
25.2
 86%
3.0
 90%


11
KK010-3
7.0
9.8
98%
25.3
 87%
3.4
103%


12
JJ195-2
7.0
10.2
103% 
25.4
 87%
3.5
106%


13
KK296-1
9.0
10.0
101% 
25.4
 87%
3.4
103%


14
KK038-1
8.0
9.8
99%
25.5
 87%
3.3
101%


15
KK019-2
8.0
9.7
98%
25.6
 88%
3.0
 90%


16
KK010-2
9.0
10.3
104% 
25.7
 88%
3.6
108%


17
KK306-2
7.0
10.4
106% 
25.8
 88%
3.7
111%


18
KK189-3
9.0
10.6
108% 
25.9
 89%
3.9
118%


19
KK038-1
8.0
10.0
101% 
26.0
 89%
2.9
 89%


20
JJ054-3
7.0
10.3
104% 
26.0
 89%
3.5
105%


21
KK010-2
8.0
10.0
101% 
26.2
 90%
2.8
 84%


22
KK010-3
7.0
10.1
102% 
26.2
 90%
3.1
 93%


23
KK019-3
9.0
10.7
108% 
26.3
 90%
3.6
109%


24
JJ134-2
7.0
9.5
96%
26.4
 90%
2.7
 82%


25
KK416-2
8.0
10.5
106% 
26.4
 90%
3.5
107%


26
KK155-3
8.0
9.7
98%
26.5
 91%
3.0
 90%


27
JJ173-1
6.0
10.4
105% 
26.6
 91%
3.0
 92%


28
JJ173-1
8.0
10.2
103% 
26.6
 91%
3.5
106%


29
KK417-3
8.0
11.4
116% 
26.6
 91%
3.5
107%


30
KK417-3
8.0
10.4
105% 
26.7
 91%
3.3
100%


31
KK416-2
7.0
9.7
98%
26.8
 92%
2.8
 84%


32
KK010-1
6.0
9.9
99%
26.8
 92%
2.8
 85%


33
JJ198-2
8.0
10.1
102% 
26.8
 92%
3.0
 90%


34
JJ325-4
8.0
9.2
93%
26.9
 92%
2.9
 88%


35
KK216-1
8.0
9.5
96%
26.9
 92%
3.0
 91%


36
JJ189-3
9.0
10.3
104% 
27.0
 92%
3.2
 97%


37
KK417-3
8.0
10.1
102% 
27.3
 93%
3.4
102%


38
KK019-3
8.0
10.0
101% 
27.3
 93%
3.4
104%


39
JJ173-2
10.0 
10.2
103% 
27.4
 94%
3.4
103%


40
KK038-3
7.0
10.7
108% 
27.4
 94%
3.5
107%


41
JJ173-1
7.0
10.3
104% 
27.4
 94%
3.3
100%


42
KK019-3
8.0
10.5
106% 
27.4
 94%
3.7
111%


43
JJ173-1
8.0
10.3
104% 
27.5
 94%
3.5
105%


44
KK004-3
8.0
9.9
100% 
27.5
 94%
3.4
103%


45
KK189-3
7.0
9.6
97%
27.6
 94%
3.0
 92%


46
KK155-3
8.0
10.0
101% 
27.6
 94%
3.2
 96%


47
KK155-3
7.0
10.2
103% 
27.6
 94%
3.4
103%


48
JJ255-3
8.0
9.9
100% 
27.6
 95%
3.2
 97%


49
JJ259-3
7.0
9.9
100% 
27.6
 95%
3.2
 98%


50
JJ255-3
7.0
9.9
100% 
27.7
 95%
3.2
 97%


51
JJ109-2
7.0
10.3
104% 
27.7
 95%
3.5
106%


52
JJ259-3
6.0
10.4
105% 
27.8
 95%
3.3
 99%


53
KK308-3
10.0
10.6
107% 
27.8
 95%
3.7
111%


54
JJ198-2
9.0
10.0
101% 
27.9
 95%
3.2
 98%


55
JJ055-2
8.0
9.9
100% 
27.9
 95%
3.3
101%


56
JJ173-2
8.0
10.8
109% 
27.9
 95%
3.5
105%


57
KK189-3
8.0
10.7
108% 
27.9
 95%
3.8
116%


58
KK019-3
7.0
8.4
85%
27.9
 96%
2.6
 79%


59
KK010-2
9.0
10.0
101% 
27.9
 96%
3.2
 98%


60
KK155-3
6.0
10.0
101% 
28.0
 96%
3.0
 92%


61
JJ109-2
7.0
9.6
97%
28.0
 96%
3.3
 98%


62
JJ109-2
10.0
8.9
89%
28.0
 96%
2.7
 83%


63
KK189-3
6.0
10.5
106% 
28.0
 96%
3.7
111%


64
KK417-3
8.0
10.8
109% 
28.0
 96%
3.9
117%


65
KK416-2
8.0
10.3
104% 
28.1
 96%
3.3
100%


66
JJ055-3
8.0
10.1
102% 
28.1
 96%
3.5
107%


67
JJ109-1
8.0
10.4
105% 
28.1
 96%
3.6
109%


68
KK010-1
8.0
10.6
107% 
28.3
 97%
3.7
113%


69
KK038-3
8.0
8.9
90%
28.3
 97%
2.3
 69%


70
JJ325-4
7.0
9.7
98%
28.3
 97%
3.1
 93%


71
JJ173-1
7.0
9.6
97%
28.4
 97%
3.0
 91%


72
JJ173-2
8.0
9.8
99%
28.4
 97%
3.2
 98%


73
KK155-3
6.0
9.8
99%
28.4
 97%
3.3
 99%


74
JJ054-2
5.0
9.8
98%
28.5
 97%
2.8
 85%


75
KK155-3
8.0
9.7
98%
28.5
 97%
3.0
 90%


76
KK019-3
7.0
9.9
100% 
28.5
 97%
3.3
 99%


77
JJ041-1
8.0
8.9
90%
28.5
 98%
2.7
 82%


78
KK416-2
8.0
10.2
103% 
28.5
 98%
3.3
100%


79
JJ255-3
8.0
10.6
107% 
28.5
 98%
3.5
105%


80
JJ255-3
7.0
10.5
106% 
28.5
 98%
3.6
110%


81
KK155-3
9.0
9.4
95%
28.6
 98%
3.2
 97%


82
KK010-3
7.0
10.2
103% 
28.6
 98%
3.6
109%


83
JJ255-3
8.0
9.8
99%
28.6
 98%
3.3
100%


84
KK189-3
7.0
10.2
103% 
28.6
 98%
3.5
105%


85
JJ173-1
8.0
10.8
109% 
28.6
 98%
3.7
111%


86
JJ109-2
8.0
7.5
76%
28.7
 98%
2.2
 67%


87
JJ041-1
8.0
8.7
88%
28.7
 98%
2.6
 79%


88
JJ325-5
7.0
10.2
103% 
28.7
 98%
3.2
 98%


89
KK189-3
8.0
10.1
102% 
28.7
 98%
3.5
106%


90
KK019-2
7.0
9.9
100% 
28.8
 98%
3.0
 91%


91
KK189-3
8.0
10.2
103% 
28.8
 98%
3.5
107%


92
JJ109-1
8.0
9.9
100% 
28.9
 99%
3.2
 97%


93
KK417-3
7.0
10.0
101% 
28.9
 99%
3.5
105%


94
KK216-1
7.0
9.4
95%
28.9
 99%
2.9
 89%


95
KK038-1
7.0
9.2
93%
28.9
 99%
2.9
 89%


96
JJ325-4
7.0
9.2
93%
29.0
 99%
3.0
 91%


97
JJ173-2
8.0
10.3
104% 
29.0
 99%
3.6
109%


98
JJ195-2
7.0
9.8
99%
29.1
100%
3.0
 91%


99
KK038-1
8.0
8.4
85%
29.2
100%
2.6
 80%


100
KK019-2
8.0
9.7
98%
29.2
100%
3.0
 91%


101
KK416-2
8.0
10.4
105% 
29.2
100%
3.6
110%


102
KK019-2
8.0
9.6
97%
29.2
100%
3.1
 93%


103
JJ126-3
8.0
8.0
81%
29.3
100%
2.0
 60%


104
JJ325-4
7.0
10.3
104% 
29.3
100%
3.6
110%


105
JJ325-4
9.0
9.0
91%
29.4
101%
3.0
 92%


106
JJ255-3
7.0
10.0
101% 
29.4
101%
3.3
 99%


107
JJ259-2
5.0
9.7
98%
29.4
101%
3.2
 98%


108
KK010-2
10.0
9.9
100% 
29.5
101%
3.3
100%


109
JJ173-2
7.0
10.6
107% 
29.5
101%
3.6
109%


110
KK306-2
7.0
8.6
87%
29.6
101%
2.6
 78%


111
JJ259-2
7.0
9.9
100% 
29.6
101%
3.1
 93%


112
JJ195-2
8.0
9.8
99%
29.6
101%
3.3
 99%


113
JJ325-5
7.0
9.4
95%
29.6
101%
2.9
 88%


114
KK416-2
8.0
10.6
107% 
29.6
101%
3.5
106%


115
JJ109-3
7.0
9.7
98%
29.7
102%
3.1
 94%


116
JJ255-3
7.0
9.7
98%
29.7
102%
3.3
100%


117
KK416-2
8.0
9.9
100% 
29.7
102%
3.5
105%


118
JJ325-4
9.0
9.1
92%
29.7
102%
2.9
 88%


119
JJ325-5
7.0
8.2
83%
29.8
102%
2.5
 75%


120
KK010-3
8.0
9.6
97%
29.8
102%
3.0
 90%


121
JJ287-2
8.0
9.0
91%
29.8
102%
3.0
 92%


122
JJ109-1
8.0
10.1
102% 
29.9
102%
3.2
 98%


123
KK038-3
8.0
10.0
101% 
29.9
102%
3.5
107%


124
JJ325-5
7.0
8.8
89%
29.9
102%
2.2
 67%


125
JJ198-2
7.0
9.8
99%
29.9
102%
3.2
 97%


126
KK038-3
8.0
9.7
98%
29.9
102%
3.3
100%


127
KK010-2
5.0
9.9
100% 
30.0
103%
3.1
 93%


128
JJ109-3
9.0
9.7
98%
30.0
103%
3.3
 99%


129
KK010-3
6.0
10.3
104% 
30.0
103%
3.7
112%


130
JJ198-2
6.0
9.2
93%
30.0
103%
2.7
 83%


131
JJ255-3
8.0
10.0
101% 
30.0
103%
3.6
108%


132
JJ325-4
7.0
9.9
100% 
30.1
103%
3.2
 97%


133
KK019-3
8.0
10.1
102% 
30.1
103%
3.2
 98%


134
JJ109-3
8.0
9.9
100% 
30.1
103%
3.2
 97%


135
KK014-3
8.0
8.1
82%
30.2
103%
2.2
 66%


136
KK216-1
7.0
9.6
97%
30.2
103%
3.0
 92%


137
JJ198-2
7.0
10.4
105% 
30.2
103%
3.3
100%


138
JJ234-2
4.0
8.8
89%
30.3
104%
2.2
 68%


139
JJ109-1
7.0
10.5
106% 
30.3
104%
3.6
108%


140
KK019-2
6.0
8.8
89%
30.3
104%
2.4
 73%


141
JJ325-5
8.0
9.5
96%
30.3
104%
3.3
 99%


142
KK038-1
9.0
10.3
104% 
30.3
104%
3.5
107%


143
KK155-3
7.0
10.4
105% 
30.3
104%
3.6
110%


144
JJ109-1
7.0
10.4
105% 
30.4
104%
3.7
111%


145
JJ109-2
7.0
9.6
97%
30.4
104%
2.9
 89%


146
KK137-2
8.0
7.9
80%
30.5
104%
2.3
 71%


147
KK416-2
6.0
9.6
97%
30.5
104%
2.5
 77%


148
JJ004-2
8.0
8.6
87%
30.5
104%
2.8
 85%


149
JJ325-4
8.0
9.5
95%
30.5
104%
2.8
 86%


150
JJ271-2
7.0
8.2
83%
30.6
105%
2.4
 72%


151
KK216-1
7.0
9.5
96%
30.7
105%
3.0
 90%


152
JJ234-2
8.0
9.8
99%
30.7
105%
3.2
 98%


153
KK019-3
8.0
9.9
100% 
30.8
105%
3.0
 92%


154
JJ195-2
7.0
9.8
99%
30.8
105%
3.3
 99%


155
KK010-2
6.0
10.1 
102% 
30.8
105%
3.3
100%


156
JJ173-2
7.0
10.5
106% 
30.8
105%
3.8
116%


157
KK010-1
9.0
9.1
92%
30.8
105%
2.9
 88%


158
KK019-2
7.0
9.8
99%
30.8
105%
2.9
 89%


159
JJ109-3
9.0
8.2
83%
30.9
106%
2.5
 76%


160
KK038-1
7.0
9.1
91%
30.9
106%
2.7
 82%


161
JJ173-1
8.0
9.9
100% 
31.0
106%
3.2
 96%


162
JJ031-2
10.0
8.6
87%
31.1
106%
2.9
 87%


163
KK038-3
6.0
9.6
97%
31.1
106%
3.1
 93%


164
JJ325-5
7.0
9.5
96%
31.2
107%
3.1
 95%


165
JJ325-4
7.0
9.3
94%
31.2
107%
2.9
 87%


166
KK416-2
6.0
9.6
97%
31.2
107%
3.1
 93%


167
KK010-2
9.0
9.7
97%
31.2
107%
3.2
 96%


168
JJ325-5
7.0
9.1
92%
31.3
107%
2.8
 85%


169
JJ325-5
9.0
9.5
96%
31.3
107%
3.0
 92%


170
JJ255-3
7.0
9.3
94%
31.3
107%
3.0
 92%


171
KK010-3
7.0
9.8
98%
31.4
107%
3.3
100%


172
KK179-2
9.0
7.8
79%
31.4
108%
2.1
 62%


173
KK019-3
7.0
10.2
103% 
31.4
108%
3.2
 98%


174
JJ031-2
7.0
8.6
87%
31.5
108%
2.6
 77%


175
KK019-2
8.0
9.4
95%
31.5
108%
3.0
 92%


176
KK010-1
7.0
9.9
100% 
31.6
108%
3.1
 95%


177
KK038-3
8.0
8.6
87%
31.6
108%
2.8
 84%


178
JJ195-2
8.0
9.5
96%
31.6
108%
3.0
 90%


179
KK010-1
7.0
9.9
100% 
31.6
108%
3.0
 91%


180
JJ041-1
8.0
8.6
87%
31.7
108%
2.3
 69%


181
JJ331-5
8.0
7.9
79%
31.7
109%
2.1
 62%


182
JJ325-4
8.0
9.4
95%
31.7
109%
2.7
 83%


183
JJ325-5
8.0
10.0
101% 
31.7
109%
3.3
100%


184
JJ234-2
6.0
9.2
93%
31.8
109%
3.1
 93%


185
KK004-2
6.0
9.7
98%
31.8
109%
3.2
 96%


186
JJ109-3
9.0
8.1
81%
31.8
109%
2.3
 69%


187
JJ109-1
8.0
8.4
85%
31.8
109%
2.6
 80%


188
KK179-2
8.0
8.0
81%
31.9
109%
2.0
 62%


189
JJ173-2
6.0
9.2
93%
31.9
109%
2.3
 70%


190
JJ122-3
8.0
8.0
81%
31.9
109%
2.4
 73%


191
JJ189-3
8.0
9.1
92%
31.9
109%
3.1
 95%


192
KK038-1
7.0
9.8
98%
32.0
109%
3.0
 92%


193
KK019-2
8.0
9.5
95%
32.0
109%
3.2
 96%


194
JJ109-3
8.0
9.8
99%
32.0
109%
3.5
106%


195
KK004-2
7.0
8.6
87%
32.0
110%
2.6
 79%


196
JJ331-5
7.0
8.6
87%
32.1
110%
2.3
 69%


197
KK010-1
8.0
9.6
97%
32.1
110%
2.8
 85%


198
KK417-3
7.0
10.2
103% 
32.1
110%
3.3
101%


199
JJ325-4
6.0
9.6
97%
32.2
110%
3.1
 95%


200
JJ109-3
8.0
7.8
78%
32.2
110%
1.9
 58%


201
KK014-2
9.0
8.3
84%
32.2
110%
2.5
 77%


202
JJ325-4
7.0
9.3
94%
32.2
110%
2.8
 86%


203
JJ109-3
7.0
9.5
96%
32.3
110%
2.9
 87%


204
KK179-3
7.0
7.5
76%
32.4
111%
2.0
 60%


205
JJ134-3
8.0
8.1
82%
32.4
111%
1.9
 59%


206
JJ134-3
8.0
7.2
73%
32.5
111%
1.9
 59%


207
KK014-3
8.0
7.5
76%
32.5
111%
2.1
 64%


208
JJ134-3
9.0
8.2
83%
32.6
111%
2.3
 69%


209
JJ031-3
8.0
7.8
79%
32.6
111%
2.3
 70%


210
KK038-3
8.0
8.5
86%
32.6
111%
2.6
 78%


211
JJ109-1
8.0
7.9
80%
32.6
112%
2.2
 68%


212
KK410-2
8.0
8.3
84%
32.7
112%
2.6
 78%


213
KK155-3
5.0
9.3
93%
32.7
112%
2.8
 85%


214
KK216-1
7.0
9.5
96%
32.8
112%
3.2
 96%


215
JJ331-5
7.0
8.0
80%
32.8
112%
2.2
 68%


216
KK038-3
9.0
8.3
84%
32.8
112%
2.3
 69%


217
KK306-2
7.0
8.8
89%
32.8
112%
2.8
 85%


218
KK004-3
7.0
7.8
79%
32.9
113%
2.3
 68%


219
KK004-2
8.0
7.8
79%
33.0
113%
2.1
 65%


220
KK004-3
7.0
7.9
79%
33.0
113%
2.0
 61%


221
JJ004-2
7.0
8.0
81%
33.0
113%
2.4
 74%


222
KK014-2
7.0
7.6
77%
33.1
113%
2.1
 62%


223
JJ126-3
8.0
8.2
83%
33.1
113%
2.1
 62%


224
JJ259-3
7.0
7.8
78%
33.1
113%
2.2
 65%


225
KK186-2
8.0
7.8
79%
33.1
113%
2.2
 66%


226
KK014-2
9.0
8.3
83%
33.1
113%
2.7
 81%


227
JJ325-4
7.0
9.4
95%
33.1
113%
2.8
 85%


228
KK136-3
10.0
7.3
74%
33.2
114%
1.9
 57%


229
JJ234-2
8.0
7.6
76%
33.2
114%
2.1
 63%


230
JJ109-2
9.0
7.8
79%
33.2
114%
2.1
 64%


231
JJ173-2
6.0
9.5
96%
33.2
114%
3.0
 91%


232
JJ287-3
8.0
8.3
84%
33.3
114%
2.5
 76%


233
JJ031-1
8.0
8.5
86%
33.3
114%
2.3
 70%


234
JJ031-3
8.0
7.3
73%
33.4
114%
1.6
 49%


235
KK533-3
6.0
7.5
76%
33.4
114%
2.0
 62%


236
KK010-2
6.0
9.4
95%
33.4
114%
3.0
 90%


237
JJ004-1
7.0
8.0
81%
33.5
115%
2.3
 71%


238
KK179-3
7.0
7.4
75%
33.5
115%
2.0
 59%


239
JJ031-3
9.0
7.6
76%
33.5
115%
2.2
 67%


240
JJ331-5
7.0
7.8
79%
33.5
115%
2.3
 69%


241
JJ195-2
7.0
9.4
95%
33.6
115%
2.7
 81%


242
JJ031-3
7.0
7.2
72%
33.7
115%
1.8
 53%


243
JJ109-3
7.0
7.6
77%
33.7
115%
1.9
 59%


244
JJ109-2
8.0
7.1
72%
33.7
115%
2.0
 61%


245
JJ271-2
7.0
8.2
83%
33.7
115%
2.5
 77%


246
KK186-1
8.0
7.4
75%
33.7
115%
1.8
 56%


247
KK306-2
8.0
7.8
79%
33.7
115%
2.1
 63%


248
JJ004-2
7.0
7.8
79%
33.7
115%
2.2
 68%


249
JJ126-3
9.0
7.4
75%
33.7
115%
2.2
 68%


250
JJ126-3
8.0
8.1
82%
33.7
115%
2.5
 75%


251
KK038-1
7.0
8.4
85%
33.7
115%
2.6
 79%


252
JJ259-3
7.0
8.4
85%
33.8
116%
2.4
 72%


253
KK038-1
5.0
8.0
80%
33.8
116%
2.1
 63%


254
JJ004-2
7.0
7.4
75%
33.8
116%
2.2
 68%


255
KK136-3
6.0
7.4
75%
33.9
116%
1.9
 57%


256
JJ031-1
6.0
8.0
81%
33.9
116%
2.3
 69%


257
JJ181-3
8.0
8.1
82%
33.9
116%
2.4
 73%


258
KK186-2
8.0
8.0
80%
34.0
116%
2.0
 62%


259
JJ031-2
7.0
7.8
78%
34.0
116%
2.1
 64%


260
KK004-2
7.0
9.0
91%
34.0
116%
2.6
 80%


261
JJ109-1
7.0
7.7
78%
34.0
116%
2.0
 62%


262
KK038-1
6.0
8.3
84%
34.0
116%
2.3
 70%


263
JJ122-2
8.0
7.1
72%
34.1
117%
2.1
 63%


264
JJ271-2
10.0 
7.3
73%
34.1
117%
2.1
 64%


265
JJ122-2
6.0
7.4
75%
34.1
117%
1.5
 45%


266
JJ271-2
7.0
8.7
87%
34.1
117%
2.2
 67%


267
JJ122-2
10.0 
8.0
81%
34.1
117%
2.5
 76%


268
JJ134-2
8.0
7.8
78%
34.2
117%
2.0
 60%


269
KK480-3
7.0
7.1
72%
34.2
117%
2.1
 65%


270
JJ004-2
8.0
7.9
79%
34.2
117%
2.2
 66%


271
JJ259-2
8.0
8.2
83%
34.2
117%
2.4
 72%


272
KK533-1
7.0
8.4
85%
34.3
117%
2.3
 70%


273
KK038-3
6.0
8.6
87%
34.3
117%
2.0
 62%


274
JJ134-3
8.0
7.7
78%
34.3
117%
2.1
 64%


275
KK179-2
7.0
7.9
80%
34.3
117%
2.5
 76%


276
JJ259-3
7.0
7.1
71%
34.4
118%
1.6
 49%


277
JJ004-1
7.0
7.6
76%
34.4
118%
1.9
 58%


278
KK533-2
7.0
8.1
82%
34.4
118%
2.2
 65%


279
JJ234-2
7.0
7.1
72%
34.4
118%
1.8
 55%


280
JJ258-3
7.0
7.8
79%
34.4
118%
2.2
 66%


281
JJ331-5
7.0
8.1
81%
34.4
118%
2.3
 71%


282
JJ122-3
7.0
7.4
75%
34.5
118%
2.0
 60%


283
JJ331-5
9.0
7.6
77%
34.5
118%
2.3
 69%


284
KK014-2
7.0
7.6
77%
34.5
118%
2.0
 62%


285
KK136-2
7.0
7.2
73%
34.6
118%
2.0
 59%


286
JJ031-3
7.0
7.5
76%
34.6
118%
2.1
 63%


287
JJ109-2
8.0
8.1
81%
34.6
118%
2.1
 64%


288
JJ331-5
7.0
8.8
89%
34.6
118%
2.5
 75%


289
JJ109-3
7.0
7.6
77%
34.6
118%
1.8
 53%


290
JJ271-1
8.0
7.4
75%
34.6
118%
2.1
 63%


291
JJ031-2
7.0
8.0
81%
34.6
118%
2.2
 66%


292
KK038-1
6.0
8.3
84%
34.6
118%
2.4
 72%


293
JJ031-1
9.0
7.1
71%
34.7
119%
1.6
 49%


294
JJ234-2
6.0
7.8
79%
34.7
119%
2.0
 59%


295
KK306-2
7.0
7.8
78%
34.7
119%
2.2
 67%


296
KK199-2
7.0
7.8
79%
34.7
119%
2.3
 71%


297
JJ031-3
8.0
7.6
77%
34.8
119%
2.1
 65%


298
KK106-1
9.0
7.9
80%
34.8
119%
2.2
 68%


299
KK014-2
9.0
8.2
83%
34.8
119%
2.4
 73%


300
JJ109-2
8.0
8.3
83%
34.8
119%
2.6
 78%


301
JJ004-1
7.0
7.6
76%
34.9
119%
1.9
 58%


302
JJ109-1
10.0 
7.8
79%
35.0
120%
2.1
 63%


303
KK106-1
7.0
7.2
73%
35.0
120%
1.8
 55%


304
KK179-3
7.0
6.9
70%
35.0
120%
1.8
 56%


305
JJ259-3
8.0
7.4
75%
35.0
120%
1.8
 56%


306
JJ109-2
10.0 
7.8
79%
35.0
120%
2.2
 67%


307
JJ031-2
6.0
7.9
80%
35.0
120%
2.2
 67%


308
KK038-1
8.0
8.6
86%
35.0
120%
2.3
 71%


309
JJ271-1
8.0
7.2
73%
35.1
120%
1.7
 52%


310
JJ234-2
7.0
7.4
74%
35.1
120%
1.9
 57%


311
JJ004-1
8.0
8.0
81%
35.1
120%
1.8
 54%


312
JJ122-2
8.0
6.9
70%
35.1
120%
1.9
 58%


313
JJ331-5
7.0
8.4
85%
35.1
120%
2.3
 70%


314
JJ109-3
8.0
7.7
78%
35.1
120%
2.4
 71%


315
JJ041-1
7.0
8.3
84%
35.1
120%
2.4
 72%


316
KK004-3
7.0
8.1
82%
35.1
120%
2.5
 74%


317
JJ259-2
5.0
7.2
73%
35.2
120%
1.5
 45%


318
JJ031-1
6.0
7.4
74%
35.2
120%
1.8
 55%


319
JJ234-2
6.0
7.8
79%
35.2
120%
2.1
 62%


320
JJ266-3
7.0
7.9
80%
35.2
120%
2.3
 70%


321
JJ331-5
7.0
8.1
82%
35.3
121%
2.1
 65%


322
KK014-2
8.0
8.0
80%
35.3
121%
2.5
 76%


323
JJ122-3
8.0
7.3
74%
35.3
121%
1.7
 51%


324
JJ134-2
9.0
7.8
78%
35.3
121%
2.0
 60%


325
JJ234-2
7.0
7.4
75%
35.3
121%
2.1
 63%


326
KK014-2
7.0
7.1
72%
35.4
121%
2.0
 60%


327
JJ126-3
6.0
7.8
79%
35.4
121%
2.3
 68%


328
JJ242-1
7.0
7.4
75%
35.4
121%
1.8
 56%


329
KK014-2
6.0
7.5
76%
35.4
121%
2.1
 65%


330
KK106-3
9.0
7.9
79%
35.4
121%
2.3
 70%


331
KK533-3
8.0
7.0
71%
35.5
121%
1.6
 47%


332
KK004-3
5.0
7.8
79%
35.5
121%
2.1
 63%


333
JJ109-3
8.0
7.7
78%
35.5
122%
1.9
 58%


334
KK533-3
7.0
7.7
78%
35.5
122%
2.0
 59%


335
KK136-3
5.0
7.6
76%
35.5
122%
2.0
 60%


336
JJ109-1
8.0
7.8
78%
35.5
122%
2.3
 70%


337
JJ173-2
7.0
9.4
94%
35.5
122%
3.4
103%


338
JJ122-2
6.0
7.4
74%
35.6
122%
1.7
 51%


339
JJ298-3
9.0
7.4
75%
35.6
122%
1.8
 54%


340
JJ031-3
8.0
7.6
77%
35.6
122%
1.9
 57%


341
KK179-3
9.0
8.0
81%
35.6
122%
2.4
 73%


342
JJ134-2
6.0
7.2
73%
35.6
122%
1.6
 49%


343
JJ271-1
6.0
7.1
71%
35.6
122%
1.7
 51%


344
KK410-3
9.0
7.3
73%
35.6
122%
1.9
 58%


345
JJ242-1
6.0
7.4
75%
35.7
122%
1.8
 55%


346
JJ181-3
8.0
7.3
73%
35.7
122%
2.0
 60%


347
JJ031-2
7.0
7.9
79%
35.7
122%
2.1
 65%


348
JJ259-2
7.0
7.6
77%
35.7
122%
2.3
 69%


349
KK136-3
7.0
7.9
80%
35.7
122%
2.3
 70%


350
JJ004-1
6.0
7.1
72%
35.7
122%
1.6
 49%


351
KK306-2
7.0
7.3
74%
35.7
122%
2.0
 62%


352
JJ126-3
6.0
7.1
72%
35.8
123%
1.7
 51%


353
JJ234-2
7.0
7.8
79%
35.8
123%
2.0
 60%


354
JJ109-1
8.0
8.0
80%
35.8
123%
2.5
 77%


355
JJ173-1
7.0
9.5
96%
35.8
123%
3.1
 93%


356
JJ181-3
7.0
7.7
77%
35.9
123%
2.1
 63%


357
KK106-3
7.0
8.1
82%
35.9
123%
2.2
 65%


358
JJ122-2
8.0
7.1
72%
36.0
123%
2.0
 59%


359
KK306-2
7.0
7.5
75%
36.0
123%
1.9
 56%


360
JJ259-3
6.0
7.4
75%
36.0
123%
1.9
 59%


361
JJ271-1
7.0
7.3
74%
36.1
123%
2.1
 63%


362
JJ266-3
7.0
7.7
78%
36.1
123%
2.2
 68%


363
JJ122-1
8.0
8.4
85%
36.1
124%
2.3
 69%


364
JJ126-3
8.0
7.5
75%
36.1
124%
2.3
 71%


365
JJ126-3
8.0
7.6
77%
36.2
124%
1.8
 55%


366
JJ031-3
7.0
7.2
73%
36.2
124%
2.1
 64%


367
JJ122-2
10.0
7.7
78%
36.3
124%
2.2
 66%


368
KK199-2
7.0
8.1
82%
36.3
124%
2.4
 72%


369
JJ004-1
6.0
7.9
80%
36.3
124%
1.7
 51%


370
JJ271-2
7.0
7.6
77%
36.3
124%
2.0
 60%


371
JJ242-1
7.0
7.2
73%
36.4
124%
1.7
 51%


372
KK306-2
7.0
7.3
74%
36.4
124%
1.8
 54%


373
KK533-3
8.0
7.2
73%
36.4
125%
2.1
 64%


374
KK179-3
8.0
8.2
83%
36.4
125%
2.4
 73%


375
JJ031-2
9.0
8.3
84%
36.5
125%
2.9
 87%


376
KK179-2
9.0
7.7
78%
36.6
125%
2.1
 64%


377
KK014-2
8.0
7.7
78%
36.6
125%
2.3
 69%


378
KK106-3
8.0
8.3
84%
36.6
125%
2.5
 76%


379
JJ298-1
7.0
7.2
72%
36.6
125%
1.7
 51%


380
JJ122-1
8.0
7.2
73%
36.6
125%
1.9
 59%


381
JJ271-2
7.0
7.7
78%
36.6
125%
2.0
 59%


382
JJ126-3
8.0
8.0
80%
36.6
125%
2.1
 65%


383
KK533-2
7.0
6.9
69%
36.7
126%
1.7
 51%


384
KK480-3
6.0
7.3
73%
36.7
126%
1.9
 58%


385
KK306-2
8.0
7.0
70%
36.7
126%
2.1
 63%


386
JJ271-2
7.0
8.1
82%
36.7
126%
2.5
 77%


387
JJ031-3
7.0
8.0
81%
36.7
126%
2.1
 63%


388
JJ234-2
3.0
8.0
81%
36.7
126%
2.8
 86%


389
JJ134-3
8.0
7.6
76%
36.8
126%
1.9
 57%


390
KK480-3
8.0
7.4
75%
36.8
126%
1.9
 58%


391
JJ109-1
8.0
7.4
75%
36.8
126%
2.2
 66%


392
JJ122-2
8.0
8.4
85%
36.8
126%
2.4
 71%


393
KK306-2
6.0
7.1
71%
36.9
126%
1.6
 47%


394
JJ004-2
7.0
7.6
76%
36.9
126%
1.7
 51%


395
KK038-3
7.0
8.1
81%
36.9
126%
2.2
 66%


396
KK480-3
5.0
7.1
71%
36.9
126%
1.3
 41%


397
JJ122-2
6.0
8.1
81%
36.9
126%
2.1
 63%


398
KK533-2
9.0
7.3
74%
36.9
126%
2.2
 66%


399
KK136-2
7.0
7.0
70%
37.0
127%
1.5
 46%


400
KK136-2
7.0
7.1
72%
37.0
127%
1.9
 58%


401
JJ298-1
5.0
7.3
74%
37.0
127%
1.9
 58%


402
JJ004-1
8.0
7.3
73%
37.0
127%
2.1
 64%


403
KK004-2
8.0
8.0
81%
37.0
127%
2.6
 78%


404
KK410-3
7.0
7.0
71%
37.0
127%
1.8
 55%


405
JJ126-3
10.0 
7.2
73%
37.0
127%
2.0
 60%


406
JJ259-3
6.0
7.8
79%
37.1
127%
1.9
 59%


407
JJ259-2
7.0
7.4
75%
37.1
127%
2.0
 59%


408
JJ004-2
8.0
7.8
79%
37.1
127%
2.2
 67%


409
KK179-3
5.0
6.6
66%
37.1
127%
1.8
 55%


410
KK136-2
6.0
7.4
75%
37.1
127%
1.9
 58%


411
JJ181-3
8.0
8.0
81%
37.2
127%
2.3
 68%


412
KK106-1
7.0
7.0
71%
37.2
127%
1.8
 54%


413
JJ031-1
8.0
8.0
80%
37.2
127%
2.3
 70%


414
KK136-2
6.0
7.4
75%
37.3
128%
1.7
 53%


415
KK253-1
7.0
7.5
76%
37.3
128%
1.6
 49%


416
JJ266-3
7.0
7.8
79%
37.3
128%
1.6
 49%


417
KK014-2
5.0
6.8
69%
37.4
128%
1.5
 44%


418
KK014-2
7.0
7.1
72%
37.4
128%
1.3
 40%


419
JJ242-1
9.0
7.6
76%
37.4
128%
2.1
 64%


420
KK186-2
7.0
7.1
72%
37.5
128%
1.9
 58%


421
JJ031-2
6.0
7.3
74%
37.5
128%
1.7
 50%


422
JJ266-3
10.0 
6.9
69%
37.5
128%
1.7
 53%


423
JJ266-3
7.0
7.0
71%
37.5
128%
1.8
 54%


424
JJ031-3
6.0
6.9
70%
37.5
128%
1.8
 55%


425
JJ109-1
8.0
7.6
77%
37.5
128%
2.1
 63%


426
JJ004-2
8.0
7.5
75%
37.5
128%
2.2
 66%


427
JJ122-1
6.0
7.8
78%
37.5
128%
2.2
 67%


428
JJ181-3
6.0
7.6
77%
37.6
129%
1.9
 57%


429
JJ031-2
7.0
7.5
76%
37.6
129%
2.1
 62%


430
KK136-2
7.0
7.2
73%
37.7
129%
1.6
 48%


431
KK136-2
9.0
6.8
68%
37.7
129%
1.8
 56%


432
KK306-2
8.0
7.1
72%
37.7
129%
2.1
 63%


433
JJ271-1
5.0
6.4
65%
37.8
129%
1.3
 41%


434
JJ259-2
6.0
8.0
81%
37.8
129%
2.5
 75%


435
KK136-2
6.0
7.4
75%
37.8
129%
1.6
 48%


436
JJ031-1
5.0
7.6
76%
37.8
129%
1.8
 54%


437
JJ122-2
9.0
7.2
73%
37.8
129%
2.0
 60%


438
JJ259-2
7.0
6.9
69%
37.9
130%
0.9
 26%


439
KK136-3
5.0
7.4
75%
38.0
130%
1.7
 52%


440
KK179-2
8.0
7.8
78%
38.0
130%
2.3
 70%


441
JJ271-1
8.0
7.4
74%
38.1
130%
1.6
 50%


442
JJ298-1
9.0
6.5
65%
38.1
130%
1.7
 51%


443
JJ198-1
7.0
7.6
77%
38.1
130%
1.6
 48%


444
KK106-3
7.0
7.0
70%
38.1
130%
1.6
 49%


445
KK014-2
7.0
7.9
80%
38.2
131%
2.2
 67%


446
KK480-3
6.0
7.3
74%
38.3
131%
1.6
 48%


447
KK106-1
8.0
7.7
78%
38.3
131%
2.3
 69%


448
JJ122-3
6.0
6.6
67%
38.3
131%
1.5
 44%


449
JJ004-2
7.0
7.6
77%
38.3
131%
2.0
 60%


450
JJ271-1
5.0
7.3
74%
38.4
131%
1.4
 43%


451
KK136-2
6.0
7.1
72%
38.4
131%
2.0
 62%


452
KK306-2
7.0
6.6
66%
38.4
132%
1.6
 47%


453
JJ122-3
7.0
7.0
71%
38.5
132%
1.5
 47%


454
KK186-1
5.0
7.0
71%
38.5
132%
1.7
 52%


455
KK179-3
8.0
7.7
78%
38.5
132%
2.5
 75%


456
JJ266-3
7.0
7.7
78%
38.6
132%
2.4
 74%


457
JJ031-1
6.0
7.3
74%
38.7
132%
1.4
 44%


458
JJ266-3
6.0
6.9
69%
38.7
132%
1.7
 52%


459
JJ004-2
5.0
6.0
61%
38.7
133%
1.0
 31%


460
KK480-3
7.0
6.6
67%
38.7
133%
1.6
 50%


461
JJ031-2
7.0
7.5
75%
38.7
133%
1.7
 53%


462
JJ126-3
7.0
6.8
68%
38.8
133%
1.8
 53%


463
KK179-2
6.0
7.4
74%
38.8
133%
1.8
 54%


464
KK136-3
7.0
7.7
77%
38.9
133%
1.9
 57%


465
KK136-2
6.0
6.2
63%
39.0
133%
1.3
 41%


466
JJ259-2
6.0
7.4
75%
39.0
133%
1.7
 50%


467
KK106-3
6.0
7.0
71%
39.0
133%
1.8
 55%


468
KK253-1
7.0
7.2
72%
39.0
133%
1.8
 55%


469
KK306-2
7.0
7.6
76%
39.1
134%
2.1
 62%


470
KK004-3
7.0
7.6
77%
39.1
134%
2.1
 63%


471
KK480-3
7.0
7.1
71%
39.2
134%
1.6
 50%


472
JJ126-3
8.0
7.5
76%
39.2
134%
1.9
 58%


473
KK306-2
6.0
6.6
67%
39.2
134%
1.5
 45%


474
KK480-3
8.0
7.5
76%
39.2
134%
2.0
 60%


475
JJ242-1
7.0
6.9
69%
39.4
135%
1.4
 41%


476
JJ122-2
8.0
7.2
73%
39.4
135%
2.1
 63%


477
KK533-2
7.0
6.6
67%
39.5
135%
1.6
 50%


478
JJ122-2
7.0
7.3
74%
39.5
135%
1.8
 54%


479
JJ122-2
7.0
6.7
68%
39.5
135%
1.8
 55%


480
KK136-2
5.0
7.3
74%
39.6
135%
1.5
 45%


481
KK136-3
7.0
7.0
71%
39.7
136%
1.8
 56%


482
KK533-2
7.0
7.8
79%
39.7
136%
1.9
 58%


483
KK106-3
8.0
7.2
72%
39.7
136%
2.0
 60%


484
KK533-2
7.0
7.2
73%
39.9
136%
2.0
 61%


485
KK533-2
6.0
7.1
72%
40.0
137%
1.5
 44%


486
KK306-2
7.0
7.1
72%
40.0
137%
2.0
 60%


487
JJ259-3
6.0
6.9
70%
40.2
138%
1.5
 45%


488
JJ242-1
8.0
7.2
73%
40.2
138%
1.6
 49%


489
JJ109-2
8.0
7.8
79%
40.3
138%
2.3
 70%


490
JJ271-1
8.0
7.6
77%
40.3
138%
2.1
 65%


491
JJ331-5
5.0
6.9
70%
40.4
138%
1.7
 52%


492
KK004-2
7.0
7.0
71%
40.5
139%
1.6
 49%


493
KK179-2
6.0
7.1
72%
40.5
139%
1.8
 54%


494
JJ122-3
7.0
7.1
72%
40.7
139%
1.7
 53%


495
KK136-3
6.0
7.4
75%
40.9
140%
1.9
 57%


496
KK306-2
8.0
6.6
67%
41.0
140%
1.7
 51%


497
KK306-2
8.0
6.9
70%
41.1
141%
1.2
 38%


498
JJ259-2
6.0
7.3
74%
41.3
141%
1.7
 53%


499
KK306-2
7.0
7.0
70%
42.0
144%
1.8
 56%


500
KK186-1
5.0
7.2
72%
42.6
146%
1.8
 54%


525
Nulls
7.3
9.9
100% 
29.2
100%
3.3
100%









Example 5
Data Quality for ADL, NDFD, and Yield Results
Data quality checks were performed prior to analysis using linear models, and outlying plots with large deleted-Studentized residuals were identified. Two passes of this method were used, in order to detect subtler outliers in the second pass that might be hidden by larger outliers removed in the first pass. Outliers identified by this method were removed from the analysis of quality traits. For the analysis of yield, plots with CV of 25% or greater were removed from the analysis. The analysis of response variables was completed using standard analysis of variance models with a mixture of fixed and random effects. The actual statistical calculations were performed using SAS/STAT software Version 9.1.3. Analysis of Variance calculations were performed using PROC MIXED. The model treated constructs and events within constructs as fixed effects, while locations, reps within locations, and location by construct interactions were treated as random effects. Other attributes of the events being tested involved fall dormant or non dormant germplasm (FD, ND). These were all treated as fixed effects. In the cross-year analysis, year was treated as a random effect. Varying numbers of harvest cuts were made at different locations in different years. The yield was analyzed for each cut at each location. In the cross-location, cross-generation, and cross-year analyses, the yield was summed over cuts to obtain a total yield for each plot. The experimental design included matched negative segregants for some events, as well as a pooled null segregant. This allowed two analyses to be performed: in the first analysis, all events were compared to the pooled null segregant, while in the second analysis, events were compared to their matched negative segregants.
Example 6
ADL Measurements in the Lower Stem of Reduced Lignin Alfalfa Events







TABLE 4







Lower stem ADL measurements for the 6 reduced lignin alfalfa events in two fall


dormant (FD) germplasms from 3 locations in 2008. Event positive plants showed a


significant (p ≦ 0.05) decrease in lower stem ADL, which ranged from 18-31% when


compared to the pooled negative control. KK179 alfalfa event has the reduced lignin


phenotype identified by the “sweet spot” selection method.


















Delta
Delta





Dormancy
Event

LCI @
UCI @
%



Event
germplasm
Mean
Delta
90%
90%
Diff.
P-value





JJ041
FD
7.91
−1.75
−1.97
−1.52
−18.09
<.001


JJ266
FD
7.48
−2.18
−2.39
−1.98
−22.60
<.001


KK136
FD
7.01
−2.64
−2.90
−2.39
−27.40
<.001


KK179
FD
7.65
−2.01
−2.24
−1.79
−20.83
<.001


KK376
FD
7.37
−2.29
−2.55
−2.04
−23.75
<.001


KK465
FD
7.30
−2.36
−2.59
−2.13
−24.44
<.001


JJ041
FD
7.71
−1.77
−2.01
−1.53
−18.70
<.001


JJ266
FD
6.98
−2.50
−2.74
−2.26
−26.38
<.001


KK136
FD
7.38
−2.10
−2.34
−1.86
−22.14
<.001


KK179
FD
7.56
−1.92
−2.16
−1.68
−20.24
<.001


KK376
FD
6.51
−2.97
−3.21
−2.73
−31.33
<.001


KK465
FD
7.33
−2.15
−2.39
−1.91
−22.68
<.001





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 5







Lower stem ADL measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasm 1 grown in 4 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value





JJ041
9.46
10.79
−1.32
−1.55
−1.09
−12.26
<.001


JJ266
8.53
10.79
−2.26
−2.47
−2.05
−20.95
<.001


KK136
8.52
10.79
−2.27
−2.53
−2.02
−21.06
<.001


KK179
8.52
10.79
−1.96
−2.53
−1.74
−18.20
<.001


KK376
8.49
10.79
−2.29
−2.54
−2.04
−21.26
<.001


KK465
8.55
10.79
−2.24
−2.47
−2.00
−20.73
<.001





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 6







Lower stem ADL measurements for the 6 reduced lignin alfalfa lead 


events in non-dormant (ND) germplasm 1 grown at 2 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value





JJ041
9.42
11.73
−2.31
−2.61
−2.02
−19.72
<.001


JJ266
8.84
11.73
−2.89
−3.18
−2.59
−24.61
<.001


KK136
9.27
11.73
−2.46
−2.79
−2.12
−20.94
<.001


KK179
9.45
11.73
−1.28
−2.57
−1.98
−19.41
<.001


KK376
8.73
11.73
−3.00
−3.30
−2.70
−25.57
<.001


KK465
9.17
11.73
−2.56
−2.85
−2.27
−21.84
<.001





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD= Least Significant Difference;


FD= Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 7







Lower stem ADL measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasm 2 grown at 4 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value





JJ041
9.31
10.89
−1.58
−1.81
−1.35
−14.50
<.001


JJ266
8.11
10.89
−2.79
−3.01
−2.56
−25.58
<.001


KK136
8.55
10.89
−2.34
−2.57
−2.11
−21.50
<.001


KK179
8.87
10.89
−2.03
−2.26
−1.80
−18.61
<.001


KK376
8.26
10.89
−2.63
−2.86
−2.40
−24.14
<.001


KK465
9.09
10.89
−1.81
−2.03
−1.58
−16.58
<.001





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 8







Lower stem ADL measurements for 6 reduced lignin alfalfa lead events 


in non dormant (ND) germplasm 2 grown at 2 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value





JJ041
8.91
11.16
−2.26
−2.64
−1.87
−20.21
<.001


JJ266
8.53
11.16
−2.63
−3.02
−2.25
−23.61
<.001


KK136
8.85
11.16
−2.31
−2.69
−1.92
−20.67
<.001


KK179
8.75
11.16
−2.41
−2.80
−2.02
−21.58
<.001


KK376
8.35
11.16
−2.81
−3.20
−2.42
−25.16
<.001


KK465
9.14
11.16
−2.03
−2.41
−1.64 
−18.15
<.001





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Tables 4-8 show 2009 data for lower stem ADL in a fall dormant (FD) and non dormant (ND) germplasms at 4 and 2 locations, respectively. The 6 event positive lines showed a significant (p≦0.05) reduction in ADL ranging from 12-26% when compared to the pooled negative control, with the lead event KK179 showing a reduction in ADL of 18-22%.
Example 7
NDFD Measurements in the Lower Stem of Reduced Lignin Alfalfa Events







TABLE 9







Lower stem NDFD measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasms grown at 3 locations in 2008.




















Delta
Delta









LCI 
UCI 





Dormancy
Event
Control

@
@
%
P-


Event
germplasm
Mean
Mean
Delta
90%
90%
Diff.
value


















JJ041
FD
32.68
27.70
4.98
4.23
5.73
17.98
<.001


JJ266
FD
33.58
27.70
5.88
5.20
6.56
21.23
<.001


KK136
FD
35.46
27.70
7.76
6.91
8.61
28.01
<.001


KK179
FD
33.52
27.70
5.82
5.08
6.57
21.02
<.001


KK376
FD
34.12
27.70
6.43
5.57
7.28
23.20
<.001


KK465
FD
35.33
27.70
7.63
6.88
8.38
27.55
<.001


JJ041
FD
33.27
27.70
5.56
4.69
6.44
20.08
<.001


JJ266
FD
34.98
27.70
7.27
6.40
8.15
26.25
<.001


KK136
FD
34.29
27.70
6.59
5.71
7.46
23.77
<.001


KK179
FD
33.13
27.70
5.42
4.54
6.30
19.57
<.001


KK376
FD
37.44
27.70
9.74
8.86
10.61
35.14
<.001


KK465
FD
35.34
27.70
7.64
6.76
8.52
27.57
<.001





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Lower stem NDFD for the 6 reduce lignin events in fall dormant (FD) germplasms at 3 locations. Event positive plants showed a significant (p≦0.05) increase in lower stem NDFD which ranged from 18-35% when compared to the pooled negative control.







TABLE 10







Lower stem NDFD measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasm 1 grown at 4 locations in 2009.




















Delta
Delta









LCI
UCI





Dormancy
Event
Control

@
@
%



Event
germplasm
Mean
Mean
Delta
90%
90%
Diff.
P-value





JJ041
FD
28.09
22.31
5.79
4.89
6.69
25.95
<.001


JJ266
FD
28.58
22.31
6.27
5.46
7.08
28.11
<.001


KK136
FD
28.88
22.31
6.57
5.58
7.56
29.46
<.001


KK179
FD
27.20
22.31
4.90
4.01
5.78
21.95
<.001


KK376
FD
28.65
22.31
6.34
5.38
7.31
28.43
<.001


KK465
FD
28.21
22.31
5.91
4.99
6.83
26.49
<.001





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 11







Lower stem NDFD measurements for the 6 reduced lignin alfalfa lead 


events in non dormant (ND) germplasm 1 grown at 2 locations in 2009.




















Delta
Delta









LCI 
UCI 





Dormancy
Event
Control

@
@
%



Event
germplasm
Mean
Mean
Delta
90%
90%
Diff. 
P-value





JJ041
ND
26.84
20.88
5.96
4.62
7.30
28.52
<.001


JJ266
ND
27.79
20.88
6.90
5.63
8.18
33.06
<.001


KK136
ND
27.47
20.88
6.59
5.14
8.05
31.56
<.001


KK179
ND
26.73
20.88
5.85
4.51
7.18
27.99
<.001


KK376
ND
27.19
20.88
6.31
4.97
7.65
30.21
<.001


KK465
ND
27.02
20.88
6.14
4.86
7.42
29.41
<.001





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 12







Lower stem NDFD measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasm 2 grown at 4 locations in 2009.




















Delta
Delta









LCI 
UCI 





Dormancy
Event
Control

@
@
%



Event
germplasm
Mean
Mean
Delta
90%
90%
Diff. 
P-value





JJ041
FD
27.96
22.11
5.85
5.01
6.69
26.46
<.001


JJ266
FD
29.97
22.11
7.86
7.01
8.70
35.54
<.001


KK136
FD
28.84
22.11
6.73
5.89
7.58
30.45
<.001


KK179
FD
27.32
22.11
5.21
4.37
6.06
23.58
<.001


KK376
FD
29.81
22.11
7.70
6.85
8.54
34.82
<.001


KK465
FD
27.37
22.11
5.26
4.41
6.10
23.78
<.001





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


FD = Fall Dormant;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 13







Lower stem NDFD measurements for the 6 reduced lignin alfalfa lead 


events in non dormant (ND) germplasm 2 grown at 2 locations in 2009.




















Delta
Delta









LCI
UCI





Dormancy
Event
Control

@
@
%
P-


Event
germplasm
Mean
Mean
Delta
90%
90%
Diff.
value


















JJ041
ND
28.10
22.39
5.71
4.15
7.26
25.48
<.001


JJ266
ND
28.73
22.39
6.34
4.78
7.89
28.29
<.001


KK136
ND
28.66
22.39
6.27
4.71
7.82
28.00
<.001


KK179
ND
27.76
22.39
5.37
3.81
6.92
23.98
<.001


KK376
ND
29.87
22.39
7.48
5.93
9.04
33.40
<.001


KK465
ND
28.95
22.39
56.56
5.00
8.11
29.29
<.001





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Tables 10-13 show 2009 data for lower stem NDFD in fall dormant (FD) and non dormant (ND) germplasm at 4 and 2 locations, respectively. The 6 event positive reduced lignin alfalfa events showed a significant (p≦0.05) increase in NDFD ranging from 22-36% when compared to the pooled negative control, with the lead event KK179 showing an increase in NDFD of 22-28%.
Example 8
Vigor Rating for Reduced Lignin Alfalfa Events







TABLE 14







Vigor ratings for the 2 reduced lignin alfalfa events, JJ266 and KK179 compared


to commercial checks and the null controls in 3 locations. The reduced lignin event KK179


resulted in no off-types for vigor rating scale. Plant vigor (scored 1-10, 10 being best) was


taken 21 days after previous harvest, and in the second week of May for the spring score.











Event
Location 1 
Location 2
Location 3
Mean





JJ266
8.0
7.4
7.8
7.7


JJ266, null
7.8
7.4
8.0
7.7


KK179
8.0
7.6
7.6
7.7


KK179, null
7.4
7.7
8.1
7.7


Commercial Check 1
6.9
6.7
7.1
6.9


Commercial Check 2
7.1
7.0
6.7
6.9


Commercial Check 3
7.8
8.1
8.1
8.0


Commercial Check 4
7.3
7.6
7.9
7.6









Example 9
ADL Measurements in the Whole Plant for Reduced Lignin Alfalfa Events







TABLE 15







Whole plant hay ADL measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasm 1 grown in 4 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
4.96
5.66
−0.69
−1.55
−0.44
−12.27
<.001


JJ266
4.85
5.66
−1.04
−2.47
−0.59
−14.37
<.001


KK136
4.81
5.66
−1.12
−2.53
−0.59
−15.09
<.001


KK179
5.11
5.66
−0.80
−2.19
−0.31
−9.79
<.001


KK376
4.73
5.66
−1.19
−2.54
−0.66
−16.39
<.001


KK465
5.18
5.66
−0.74
−2.47
−0.22
−8.49
0.002





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 16







Whole plant hay ADL measurements for the 6 reduced lignin alfalfa lead 


events in non dormant (ND) germplasm 1 grown in 2 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
5.40
6.16
−0.77
−1.22
−0.31
−12.43
0.006


JJ266
5.27
6.16
−0.89
−1.30
−0.48
−14.47
0.000


KK136
5.56
6.16
−0.61
−1.07
−0.15
−9.87
0.030


KK179
5.41
6.16
−0.76
−1.19
−0.32
−12.25
0.004


KK376
5.20
6.16
−0.97
−1.42
−0.51
−15.66
0.001


KK465
5.57
6.16
−0.60
−1.00
−0.19
−9.69
0.016





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 17







Whole plant hay ADL measurements for the 6 reduced lignin alfalfa lead 


events in fall dormant (FD) germplasm 2 grown in 4 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
4.93
5.77
−0.85
−1.07
−0.62
−14.64
<0.001


JJ266
4.66
5.77
−1.11
−1.33
−0.89
−19.25
<0.001


KK136
5.12
5.77
−0.65
−0.88
−0.43
−11.34
<0.001


KK179
5.23
5.77
−0.54
−0.77
−0.32
−9.41
<0.001


KK376
4.61
5.77
−1.16
−1.39
−0.93
−20.09
<0.001


KK465
5.28
5.77
−0.49
−0.71
−0.26
−8.43
<0.001





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Whole plant ADL data from 2009 across 4 locations is shown in Tables 15 and 17. The 6 reduced lignin positive events showed a significant (p≦0.05) decrease in ADL ranging from 8-19% when compared to the pooled negative control for both fall dormant germplasms. Event KK179 had a 9.8% and a 9.4% reduction in ADL in the fall dormant germplasms 1 and 2, respectively.







TABLE 18







Whole plant hay ADL measurements for the 6 reduced lignin alfalfa lead 


events in non dormant (ND) germplasm 2 grown in 2 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
5.25
5.94
−0.69
−1.10
−0.28
−11.59
0.006


JJ266
4.86
5.94
−1.08
−1.48
−0.69
−18.21
<0.001


KK136
5.57
5.94
−0.37
−0.76
−0.02
−6.22
0.123


KK179
5.29
5.94
−0.65
−1.04
−0.25
−10.91
0.007


KK376
5.02
5.94
−0.92
−1.33
−0.51
−15.47
<0.001


KK465
5.37
5.94
−0.57
−0.96
−0.18
−9.61
0.018





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


LSD = Least Significant Difference;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Whole plant ADL data from 2009 across 2 locations is shown in Tables 16 and 18. The 6 reduced lignin positive events in the non dormant germplasms showed a significant (p≦0.05) decrease in ADL ranging from 10-16% when compared to the pooled negative control. Five of the 6 events showed a significant decrease in ADL ranging from 10-18% when compared to the pooled negative control. Event KK179 had a 12.3% and 10.9% reduction in ADL in the non dormant germplasms 1 and 2, respectively.







TABLE 19







Whole plant hay ADL measurements for the reduced lignin alfalfa event KK179


in two fall dormant (FD) germplasms grown in 4 locations in 2009 compared to 


commercial checks.




















Delta
Delta




Commercial
Dormancy

Check 

LCI @
UCI @
%



Check
Germplasm
KK179
Mean
Delta
90%
90%
Diff.
P-value


















1
FD germplasm 1
5.22
6.12
−0.90
−1.19
−0.62
−14.77
<.001


2
FD germplasm 1
5.22
5.69
−0.47
−0.76
−0.18
−8.31
0.008


3
FD germplasm 1
5.22
5.38
−0.17
−0.46
0.13
−3.08
0.350


4
FD germplasm 1
5.22
5.59
−0.38
−0.67
−0.09
−6.75
0.034


1
FD germplasm 2
5.10
6.12
−1.02
−1.31
−0.73
−16.67
<.001


2
FD germplasm 2
5.10
5.69
−0.59
−0.89
−0.29
−10.35
0.001


3
FD germplasm 2
5.10
5.38
−0.28
−0.58
0.02
−5.24
0.119


4
FD germplasm 2
5.10
5.59
−0.49
−0.79
−0.20
−8.83
0.006





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 20







Whole plant hay ADL measurements for the reduced lignin alfalfa event KK179


in two non dormant (ND) germplasm grown in 2 locations in 2009 compared to 


commercial checks.




















Delta
Delta




Commercial


Check

LCI @
UCI @
%



Check
Germplasm
KK179
Mean
Delta
90%
90%
Diff.
P-value


















1
ND germplasm 1
5.29
5.73
−0.44
−0.96
0.09
−7.62
0.173


2
ND germplasm 1
5.29
5.81
−0.52
−1.04
0.01
−8.92
0.106


3
ND germplasm 1
5.29
5.77
−0.48
−1.01
0.05
−8.34
0.133


4
ND germplasm 1
5.29
5.92
−0.63
−1.15
−0.10
−10.61
0.050


1
ND germplasm 2
5.39
5.73
−0.33
−0.88
0.21
−5.77
0.318


2
ND germplasm 2
5.39
5.81
−0.41
−0.96
0.13
−7.11
0.213


3
ND germplasm 2
5.39
5.77
−0.38
−0.92
0.17
−6.51
0.257


4
ND germplasm 2
5.39
5.92
−0.52
−1.07
0.02
−8.82
0.115





Abbreviations:


ADL = Acid Detergent Lignin, % of dry matter;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Tables 19 and 20 contain whole plant ADL data for the reduced lignin alfalfa event KK179 compared to commercial checks. The KK179 event showed a significant (p≦0.1) decrease in ADL when compared to 3 of the 4 fall dormant commercial checks, which ranged from 6.8-16.7% (Table 19, data from 4 locations). KK179 event in non dormant background germplasm (ND germplasm 1) showed a decrease (p≦0.2) in ADL compared to all 4 non dormant commercial checks ranging from 7.6-10.6% (Table 20, data from 2 locations). The KK179 event in non dormant background germplasm 2 showed an overall decrease (p≦0.2) in ADL compared to all 4 non dormant commercial checks with a significant (p≦0.1) decrease of 8.8% compared to commercial check 4 (data from 2 locations).
Example 10
NDFD Measurements in the Whole Plant for Reduced Lignin Alfalfa Events







TABLE 21







Whole plant hay NDFD measurements for the 6 


reduced lignin alfalfa lead events in fall dormant


(FD) germplasm 1 grown in 4 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
45.38
39.47
5.90
4.32
7.49
14.96
<0.001


JJ266
44.00
39.47
4.53
3.15
5.92
11.48
<0.001


KK136
43.92
39.47
4.45
2.80
6.10
11.27
<0.001


KK179
42.44
39.47
2.97
1.47
4.47
7.53
0.001


KK376
44.82
39.47
5.35
3.71
6.99
13.55 
<0.001


KK465
42.13
39.47
2.66
1.07
4.25
6.74
0.006





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 22







Whole plant hay NDFD measurements for the 6 reduced lignin alfalfa lead 


events in non dormant (ND) germplasm 1 grown in 2 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
40.63
35.41
5.23
1.84
8.61
14.76
0.011


JJ266
40.81
35.41
5.41
2.35
8.46
15.27
0.004


KK136
38.66
35.41
3.25
−0.19
6.70
9.19
0.120


KK179
40.37
35.41
4.96
1.73
8.19
14.01
0.012


KK376
39.75
35.41
4.35
0.96
7.73
12.28
0.035


KK465
38.72
35.41
3.32
0.26
6.37
9.37
0.074





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 23







Whole plant hay NDFD measurements for the 6 


reduced lignin alfalfa lead events in fall dormant


(FD) germplasm 2 grown in 4 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
44.42
38.96
5.46
3.92
7.00
14.02
<.001


JJ266
45.19
38.96
6.22
4.72
7.73
15.98
<.001


KK136
43.63
38.96
4.66
3.16
6.17
11.97
<.001


KK179
42.56
38.96
3.60
2.10
5.10
9.24
<.001


KK376
45.41
38.96
6.45
4.90
7.99
16.54
<.001


KK465
41.52
38.96
2.55
1.05
4.06
6.55
0.005





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF; (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Whole plant NDFD data from 2009 across 4 locations is shown in Tables 21 and 23. The 6 reduced lignin positive events in fall dormant germplasms showed a significant (p≦0.05) increase in NDFD ranging from 7-16% when compared to the pooled negative control. Event KK179 had a 7.5% and 9.2% increase in NDFD in the fall dormant germplasms 1 and 2 respectively.







TABLE 24







Whole plant hay NDFD measurements for the 6 reduced lignin alfalfa lead 


events in non dormant (ND) germplasm 2 grown in 2 locations in 2009.


















Delta
Delta





Event
Control

LCI @
UCI @




Event
Mean
Mean
Delta
90%
90%
% Diff.
P-value

















JJ041
40.95
37.21
3.74
0.68
6.81
10.06
0.045


JJ266
42.06
37.21
4.85
1.92
7.79
13.05
0.007


KK136
40.24
37.21
3.03
0.10
5.97
8.15
0.089


KK179
41.48
37.21
4.27
1.34
7.21
11.49
0.017


KK376
42.22
37.21
5.01
1.95
8.08
13.47
0.007


KK465
40.35
37.21
3.15
0.21
6.08
8.46
0.078





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Whole plant NDFD data from 2009 across 2 locations is shown in Tables 22 and 24. The 6 reduced lignin positive events in non dormant germplasms showed a significant (p≦0.1) increase in NDFD ranging from 8-15% when compared to the pooled negative control. Event KK179 had a 14.0% and 11.5% increase in NDFD in the non dormant germplasms 1 and 2 respectively.







TABLE 25







Whole plant hay NDFD measurements for the reduced lignin alfalfa 


event KK179 in two fall dormant (FD) germplasms grown in 4 locations 


in 2009 compared to commercial checks.




















Delta
Delta




Commercial


Check

LCI @
UCI @
%



Check
Germplasm
KK179
Mean
Delta
90%
90%
Diff.
P-value


















1
FD germplasm
42.17
36.10
6.07
4.27
7.86
16.80
<.001



1









2
FD germplasm
42.17
40.34
1.83
0.00
3.66
4.53
0.101



1









3
FD germplasm
42.17
41.27
0.89
−0.94
2.72
2.16
0.423



1









4
FD germplasm
42.17
38.87
3.29
1.46
5.12
8.47
0.003



1









1
FD germplasm
42.03
36.10
5.93
4.11
7.76
16.44
<.001



2









2
FD germplasm
42.03
40.34
1.70
−0.17
3.56
4.21
0.134



2









3
FD germplasm
42.03
41.27
0.76
−1.10
2.63
1.84
0.502



2









4
FD germplasm
42.03
38.87
3.16
1.30
5.03
8.13
0.005



2





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


FD = Fall Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).













TABLE 26







Whole plant hay NDFD measurements for the reduced lignin alfalfa event KK179


in two non dormant (ND) germplasms grown in 2 locations in 2009 compared to 


commercial checks.




















Delta
Delta




Commercial


Check

LCI @
UCI @
%



Check
Germplasm
KK179
Mean
Delta
90%
90%
Diff.
P-value


















1
ND germplasm 1
41.46
37.77
3.68
−0.27
7.64
9.75
0.126


2
ND germplasm 1
41.46
37.12
4.34
0.39
8.30
11.70
0.071


3
ND germplasm 1
41.46
34.71
6.74
2.79
10.70
19.43
0.005


4
ND germplasm 1
41.46
35.70
5.75
1.80
9.71
16.12
0.017


1
ND germplasm 2
40.38
37.77
2.60
−1.49
6.70
6.89
0.296


2
ND germplasm 2
40.38
37.12
3.26
−0.84
7.36
8.79
0.190


3
ND germplasm 2
40.38
34.71
5.66
1.57
9.76
16.31
0.023


4
ND germplasm 2
40.38
35.70
4.67
0.58
8.77
13.09
0.061





Abbreviations:


NDFD = Neutral Detergent Fiber Digestibility, % of NDF (NDF = neutral detergent fiber. Represents the indigestible and slowly digestible components in plant cell wall (cellulose, hemicellulose, lignin (units = % of dry matter));


ND= Non Dormant; Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Tables 25 and 26 contain whole plant NDFD data for the reduced lignin alfalfa event KK179 compared to commercial checks. The KK179 event showed an increase (p≦0.2) in NDFD when compared to 3 of the 4 fall dormant commercial checks which ranged from 4.2-16.8% (Table 25, data from 4 locations). KK179 event showed an increase (p≦0.2) in NDFD compared to all 4 non dormant commercial checks (ND germplasm 1) ranging from 9.8-19.4% (Table 26, data from 2 locations). The KK179 event showed an increase (p≦0.2) in NDFD compared to all 4 non dormant commercial checks (ND germplasm 2), which ranged from 8.8-16.3% (Table 26, data from 2 locations).
Example 11
Yield Across Location Analysis for Reduced Lignin Alfalfa Events







TABLE 27







Yield (fresh weight) across location analysis for 6 reduced lignin events for in fall


dormant (FD) and non-dormant (ND) backgrounds compared to pooled negative 


controls. There were no significant decreases in yield detected for lead event KK179 


when compared to the pooled negative control.






















Delta
Delta





Dormancy

Event
Control

LCI @
UCI @
%



Event
germplasm
Year
Mean
Mean
Delta
90%
90%
Diff.
P-value



















JJ041
FD
2008
337.56
349.32
−11.76
−42.86
19.35
−3.37
0.532


JJ266
FD
2008
364.72
349.32
15.40
−12.94
43.74
4.41
0.370


KK136
FD
2008
306.67
349.32
−42.65
−78.12
−7.19
−12.21
0.048


KK179
FD
2008
368.51
349.32
19.19
−11.91
50.30
5.49
0.309


KK376
FD
2008
354.92
349.32
5.60
−29.85
41.05
1.60
0.794


KK465
FD
2008
358.74
349.32
9.42
−21.68
40.53
2.70
0.617


JJ041
FD
2009
1148.41
1591.58
−143.17
−278.80
−7.55
−9.00
0.083


JJ266
FD
2009
156.50
1591.58
−26.08
−147.97
95.82
−1.64
0.724


KK136
FD
2009
1468.30
1591.58
−123.28
−269.17
22.61
−7.75
0.164


KK179
FD
2009
1577.84
1591.58
−13.74
−145.29
117.81
−0.86
0.863


KK376
FD
2009
1371.19
1591.58
−220.39
−361.43
−79.35
−13.85
0.011


KK465
FD
2009
1459.44
1591.58
−132.14
−272.37
8.09
−8.30
0.121


JJ041
ND
2009
591.17
764.86
−173.70
−292.96
−54.43
−22.71
0.018


JJ266
ND
2009
758.32
764.86
−6.54
−119.09
106.01
−0.86
0.923


KK136
ND
2009
771.81
764.86
6.95
−121.20
135.10
0.91
0.928


KK179
ND
2009
754.11
764.86
−10.75
−130.04
108.54
−1.41
0.881


KK376
ND
2009
584.31
764.86
−180.55
−299.84
−61.25
−23.61
0.014


KK465
ND
2009
637.67
764.86
−127.20
−239.75
−14.65
−16.63
0.064





Abbreviations:


Yield= Yield calculated on a per plant basis in grams;


FD= Fall Dormant;


ND= Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






The data in Table 27 shows the across location yield analysis for the 6 reduced lignin events in the fall dormant (FD) and non dormant (ND) germplasms compared to the pooled negative control. No significant decrease in yield is detected for KK179 when compared to the pooled negative controls.







TABLE 28







Yield (fresh weight) across location analysis for Event KK179 compared to commercial checks. 


Yield data for reduced lignin alfalfa lead event in fall dormant (FD) and non-dormant (ND) 


germplasms resulted in no significant yield decrease when compared to 8 commercial checks.
















Commercial
Dormancy 

Event
Control

LCI @ 
Delta UCI 
% 



Check
germplasm
Year
Mean
Mean
Delta
90%
@ 90%
Diff.
P-value



















1
FD
2008
368.51
239.29
129.22
92.13
166.31
54.00
<.001


2
FD
2008
368.51
308.06
60.45
23.35
97.54
19.62
0.008


3
FD
2008
368.51
349.47
19.05
−18.05
56.14
5.45
0.397


4
FD
2008
368.51
301.09
67.42
30.33
104.51
22.39
0.003


1
FD
2009
1361.60
1106.96
254.64
112.59
396.69
23.00
0.003


2
FD
2009
1361.60
1289.66
71.94
−72.74
216.62
5.58
0.412


3
FD
2009
1361.60
1396.58
−34.99
−179.66
109.69
−2.51
0.690


4
FD
2009
1361.60
1225.01
136.59
−8.09
281.27
11.15
0.120


5
ND
2009
752.63
735.61
17.03
−95.75
129.80
2.31
0.802


6
ND
2009
752.63
803.99
−51.36
−164.13
61.42
−6.39
0.451


7
ND
2009
752.63
698.51
54.12
−58.66
166.89
7.75
0.427


8
ND
2009
752.63
618.75
133.89
21.11
246.66
21.64
0.052





Abbreviations:


Yield = Yield calculated on a per plant basis in grams;


FD = Fall Dormant;


ND = Non Dormant;


Delta = difference between Event and Control means (Event − Control);


% Diff = Percent difference between Event and Control (Delta/Control * 100);


Delta LCI @90% = Lower Confidence Interval of Delta value using an alpha level of 0.10;


Delta UCI @90% = Upper Confidence Interval of Delta value using an alpha level of 0.10;


P-value = probability of a greater absolute difference under the null hypothesis (2-tailed test for significance).






Improving fiber digestibility of alfalfa offers growers the ability to manage risk and increase the likelihood of harvesting high quality alfalfa hay/haylage. Sixty-one events were initially studied in 2007 with multi-year, multi-location plots established in 2008 with six elite events. Results demonstrate a significant increase in forage digestibility as measured by neutral detergent fraction (NDFD) at the 10% bloom stage.
Multi-location trials were planted in 2008 in two dormancy backgrounds; data was collected over two seasons in 2008 and 2009. Significant increases (6.7-16%) in whole plant digestibility for positive selections versus null controls were observed for all six events by dormancy combinations. The field performance along with the molecular analysis has identified a lead event KK179, which demonstrated significant digestibility increase across two dormancies, fall dormant (FD) and non-dormant germplasm groupings. KK179 shows a 7.5-14% increase in digestibility (NDFD) when compared to the pooled null control, 2-19% increase in digestibility when compared to commercial checks and 20-28% increase in lower stem across multiple years (as compared to the pooled null control). Whole plant KK179 lignin levels (ADL) are reduced by approximately 10-12% when compared to the pooled null control, and 18-22% reduction in lower stem across multiple years (as compared to the pooled null control). No significant decrease in yield was detected for KK179 as compared to the pooled null control.
Example 12
Alfalfa Management Practices
Planting (Alfalfa Management Guide, 2011): The Spring season is the preferred season over late summer seeding to plant alfalfa in the northern states and provides for increased opportunities for successful stand establishment. Spring seeding of alfalfa can begin as soon as the potential for damage from spring frosts has passed. For late summer seedings, alfalfa is grown for at least 6 weeks after germination in order to promote survival during the winter. This allows for the crown of the plant to store root reserves for winter survival and spring re-growth.
Factors That Effect Quality (Orloff and Marble, 1997): Alfalfa management includes cutting and harvesting practices, which are the primary methods by which growers can influence the nutritional quality of alfalfa hay, and it has profound effects on forage yield and stand life, High nutritive forage quality of alfalfa from a nutrition perspective depends on the livestock source class as it relates to the feeding value of the hay. Forage quality is a direct function of both forage intake and digestibility. As forage quality increases, feed intake and digestibility increase. Alfalfa management practices influence alfalfa hay quality. Stage of maturity at the time of cutting is one of the most important factors in alfalfa management. Yield increases with advancing maturity. In contrast to yield, forage quality declines with advancing maturity of the alfalfa plant, so harvest management is a compromise between maximizing yields and maximizing quality. Forage quality is also influenced by alfalfa variety selection, hay-making practices, and environmental inputs, such as seasonal variations in light, moisture, temperature, and photoperiod or day length.
Harvest Management (Orloff and Marble, 1997): The decision of when to cut and how to cut alfalfa are major factors in yield, quality, and stand persistence. As a perennial plant, alfalfa stores some of the carbohydrates in its crown and roots, After cutting, this process takes about 2 to 3 weeks, or until the alfalfa plant attains a height of 6 to 8 inches. From this point, the plant begins replenishing root reserves. The carbohydrate reserves in roots and crowns increase with plant maturity until the time of full flowering. The grower can obtain maximum yield when alfalfa reaches full bloom, however the highest yields are sometimes obtained at around 50% bloom. The interval between first and second cuttings, or second and third cuttings, is generally between 30 to 50 days. The time depends on the weather conditions and the alfalfa variety. Too-frequent cutting results in reduced vigor and, often, weed infestation, Another method of scheduling alfalfa harvests uses the growth stage of alfalfa to indicate the appropriate time to cut and the number of cuttings per season. Alfalfa harvests can also occur at a specific growth stage (such as bud, late-bud, 10% bloom, etc.). This method takes into account the effects of environmental and varietal differences and results in more consistent, predictable forage yield and quality.
Cutting (Alfalfa Management Guide, 2011): Maximum yields can be obtained at the 3-inch cutting height with a time of two to three weeks recommended as a re-growth period or until the alfalfa attains a height of 6 to 8 inches. From this point, the plant begins replenishing the carbohydrate reserve stores in its crown and roots. Current recommendations regarding cutting height of alfalfa are designed to maximize yield while maintaining high quality forages and stand longevity. Forage growers frequently cut forages at a height of 3-inches or more. However, alfalfa forages harvested three or four times per season produced more total forage when cut at a 1-inch height versus cutting at 3 inches or more (Kust and Smith, 1961, Smith and Nelson, 1967). These practices result in a forage yield benefit to cutting at shorter heights when alfalfa plants are not under stress or low in root carbohydrate levels (Sheaffer et al., 1988).
First Cutting
The first cutting from fall-planted or previously established stands of the alfalfa plants is normally timed to coincide with most plants having flower buds formed or when new crown shoots have grown no more than 1 to 2 inches. Since flowering is controlled by day length, the first growth is often ready to harvest before flower formation, which usually occurs in late April or early May. The first growth has a tendency to be fast and have increased height and is prone to increased lodging, and thus it is recommended to harvest before lodging occurs. Alfalfa growth in the spring is primarily from crown buds and depends on temperature and available root energy reserves. Shoot growth after the first harvest originates from both crown and axillary buds. When alfalfa is cut very short (1-inch or less), most of the axillary buds are removed and new shoots must come from the crown buds (Wiederholt and Schneider, 2007). Seedling stands planted in spring should not be harvested until at least 50% of stems show flower formation, or lodging appears evident. Delaying harvest will allow seedling roots to develop further.
Second and Subsequent Cuttings
The second and subsequent cuttings are made when 10% to 25% of stems have flowers present. It takes approximately 5 to 10 days for alfalfa to advance from the bud stage of growth to the 25% flower stage. In general the re-growth period for alfalfa will reach favorable cutting stage every 28 to 35 days. During hot, dry weather, plants may flower profusely prior to 30 days of a re-growth period and before the plants reach a height of 10 inches. In such cases, it is best to graze or cut the short growth when it has been 35 to 40 days since last harvest cutting. Once the plants have flowered extensively, those specific stems will not produce any more growth and their continued presence tends to retard new growth, even when favorable conditions occur.
Fall Cutting Management
For Fall cutting management, four to six weeks of re-growth is needed for plants to build carbohydrates prior to the first killing frost (24° F.); 10 to 14 inches of growth is recommended. After several frosts but before the leaves begin to wilt and drop, this growth should be harvested to maintain the quality of the feed and reduce residue, which assists with pest control.
Agronomic Practices and Sample Collection: Optimal agronomic practices used for this plot included fertility management, weed control, insect control, and moisture. The first growth on the transplants in the field was clipped with no data collection, in order to avoid variable data on the young transplants. The target maturity for remaining data collection was 10% bloom. This level of maturity allows for lignification of the stem to help in sorting events. Plant tissue is collected using hand shears to avoid losing any of the samples and to keep cutting height uniform. The uniform cutting height for all harvests was 2.5′′ above ground level. This is the typical height for commercial forage harvesting. All locations were managed for optimum growth and winter survival. Insect and weed control were done as needed to eliminate variability within the plot. Plant spacing within a row was 15′′ with 30′′ between rows.
REFERENCES


    Kust, C. A., and D. Smith. 1961. Influence of harvest management on levels of carbohydrate reserves, longevity of stands and yield so hay and protein from Vernal alfalfa. Crop Sci. 1:267-269.
    Orloff, S. B. and Marble, V. L Intermountain Alfalfa Management Steve B. Orloff, Editor Cooperative Extension Siskiyou County, CA, University of California copy right date=1997
    Sheaffer, C. C., G. D. Lacefield, and V. L. Marble. 1988. Cutting schedules and stands. P. 411-437. In A. A. Hanson et al. (ed.) Alfalfa and alfalfa improvement. Agron. Monogr. 29. ASA, CSSA, SSSA, Madison, Wis.
    Smith, D. and C. J. Nelson. 1967. Growth of birdsfoot trefoil and alfalfa. I. Responses to height and frequency of cutting. Crop Sci. 7:130-133.
    University of Wisconsin Forage and Research Extension—Alfalfa Management Guide
    University of Wisconsin Cooperative Extension, Minnesota Extension Center, University of Minnesota, Iowa State University, Alfalfa Management Guide, American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, copy right 2011.
    Wiederholdt, R. and Schneider N. 2007. The long and short of Alfalfa cutting height, Marshfield Agriculture Research Station (MARS) Agriculture Research Station (MARS)

## Claims

1. A method to select an alfalfa plant with enhanced food value components from a population of alfalfa plants, wherein said population of alfalfa plants comprises a recombinant DNA molecule and wherein a portion of said recombinant DNA molecule is homologous or complementary to SEQ ID NO:1 or SEQ ID NO:2, comprising:
(a) measuring the concentration of acid detergent lignin (ADL) in a lower stem tissue from each of said alfalfa plants in said population of alfalfa plants, wherein said concentration of ADL is reduced between 12% and about 31% compared to a lower stem tissue of an alfalfa plant not comprising said DNA molecule;
(b) measuring the concentration of guaiacyl lignin (G lignin) in said lower stem tissue, wherein said G lignin is reduced by about 25% or greater in said lower stem tissue compared to a lower stem tissue of an alfalfa plant not comprising said DNA molecule;
(c) measuring the neutral detergent fiber digestibility (NDFD) components in said lower stem tissue, wherein said NDFD value is increased by greater than 18% in said lower stem tissue compared to a lower stem tissue of an alfalfa plant not comprising said DNA molecule;
(d) selecting an alfalfa plant that comprises the enhanced feed value components of steps (a)-(c); and
(e) growing said alfalfa plant selected in step (d).

2. The method of claim 1, wherein said recombinant DNA molecule comprises a promoter molecule capable of transcription of an operably linked DNA molecule in a plant vascular tissue, and wherein a portion of said operably linked DNA molecule is homologous or complementary to SEQ ID NO:1 or SEQ ID NO:2.

3. The method of claim 1, further comprising the step of measuring the vigor of said growing alfalfa plant, wherein said vigor is 90% or greater compared to an alfalfa plant not comprising said recombinant DNA molecule.

4. The method of claim 1, wherein a hay or haylage is produced by growing said alfalfa plant.

5. The method of claim 4, wherein said hay or haylage is measured for said enhanced feed value components comprising:
(a) measuring the ADL concentration of a sample of said hay or haylage, wherein said ADL concentration is between 80% and 92% compared to alfalfa hay not comprising said recombinant DNA molecule; and
(b) measuring the neutral detergent fiber digestibility (NDFD) component in said sample of said hay or haylage, wherein said NDFD value is between 107% and 125% compared to alfalfa hay not comprising said recombinant DNA molecule.

6. The method of claim 1, further comprising growing said alfalfa plant to maturity and collecting progeny alfalfa seed from said plant.

7. An alfalfa seed produced by the method of claim 6, wherein said seed comprises a recombinant DNA molecule and wherein a portion of said recombinant DNA molecule is homologous or complementary to SEQ ID NO:1 or SEQ ID NO:2 and wherein the plant grown from said seed comprises
(a) a concentration of ADL in the lower stem that is reduced between 12% and about 31% compared to a lower stem tissue of an alfalfa plant not comprising said DNA molecule; and,
(b) a guaiacyl lignin in lower stem tissue that is reduced by about 25% or greater compared to a lower stem tissue of an alfalfa plant not comprising said DNA molecule; and,
(c) a neutral detergent fiber digestibility value that is increased by greater than 18% in lower stem tissue compared to the lower stem tissue of an alfalfa plant not comprising said DNA molecule.

8. An alfalfa plant grown from the seed of claim 7, wherein said plant comprises an ADL concentration in a lower stem tissue that is reduced by between 12% and 31% and an ADL concentration in a hay produced from said plant that is reduced to between 80% and 92%, compared to a lower stem tissue and hay of an alfalfa plant not comprising said recombinant DNA molecule.

9. An alfalfa plant grown from the seed of claim 7, wherein said plant comprises a G lignin concentration in a lower stem tissue that is reduced by about 25% or greater compared to a lower stem tissue or hay of an alfalfa plant not comprising said recombinant DNA molecule.

10. An alfalfa plant grown from the seed of claim 7, wherein said plant comprises an NDFD value in a lower stem tissue of 122% or greater compared to a lower stem tissue of an alfalfa plant not comprising said recombinant DNA molecule.

11. An alfalfa plant grown from the seed of claim 7, wherein said plant comprises an NDFD value in a hay produced from said plant of between about 107% and about 125% or greater compared to a hay of an alfalfa plant not comprising said recombinant DNA molecule.

12. An alfalfa hay with enhanced feed value components, the hay comprising a recombinant DNA molecule, wherein a portion of said recombinant DNA molecule is homologous or complementary to SEQ ID NO:1 or SEQ ID NO:2, and wherein said alfalfa hay further comprises:
(a) an ADL concentration of between about 80% and about 92% of an ADL concentration of an alfalfa hay not comprising said recombinant DNA molecule,
(b) a G lignin concentration that is reduced by about 25% or greater compared to an alfalfa hay not comprising said recombinant DNA molecule; and
(c) an NDFD value of between 107% and 125% compared to an alfalfa hay not comprising said recombinant DNA molecule.

13. A processed alfalfa product comprising enhanced feed value components, the product comprising a recombinant DNA molecule, wherein a portion of said DNA molecule is homologous or complementary to SEQ ID NO:1 or SEQ ID NO:2, and wherein said processed alfalfa produce further comprises:
(a) an ADL concentration of between about 80% and about 92% of an ADL concentration of an alfalfa product not comprising said recombinant DNA molecule;
(b) a G lignin concentration that is reduced by about 25% greater compared to an alfalfa product not comprising said recombinant DNA molecule; and
(c) an NDFD value of between 107% and 125% compared to an alfalfa product not comprising said recombinant DNA molecule.

14. The method of claim 4, wherein said haylage is measured for said enhanced feed value components comprising measuring the ADL concentration of a sample of said hay, wherein said ADL concentration in the lower stem is decreased by between 15% and 30% compared to commodity alfalfa and by between 8% and 15% in the plant.

15. The method of claim 1, wherein one or more transgenic events are selected to produce enhanced forage quality and good agronomic performance.