# Patent

## Title
Molecular markers associated with yellow flash in glyphosate tolerant soybeans

## Abstract

The present invention provides methods and compositions for the identification and selection of loci modulating phenotypic expression of a herbicide tolerance trait in plant breeding. In addition, methods are provided for screening germplasm entries for the performance and expression of this trait.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a continuation of U.S. application Ser. No. 13/224,036, now U.S. Pat. No. 8,921,647, filed Sep. 1, 2011 and incorporated herein by reference in its entirety, which claims the benefit of U.S. Provisional Application Ser. No. 61/380,024, filed Sep. 3, 2010 and incorporated herein by reference in its entirety.


INCORPORATION OF SEQUENCE LISTING
A sequence listing containing the file named “46_21_54534.txt” which is 19,851 bytes (measured in MS-Windows®) and created on Nov. 6, 2014, comprises 32 nucleotide sequences, is provided herewith via the USPTO's EFS system and is herein incorporated by reference in its entirety. Also incorporated herein by reference are the 32 nucleotide sequences and pertinent identifying information in the Sequence Listing containing the file named “46_21_54534.txt” which is 18477 bytes (measured in MS-Windows®), created on Aug. 30, 2010, and filed with U.S. Provisional Application Ser. No. 61/380,024 on Sep. 3, 2010.
INCORPORATION OF TABLE 2
A listing of various soybean linkage group L (chromosome 19) markers is provided herewith in the Specification as Table 2. Also incorporated herein by reference is the listing of various soybean linkage group L (chromosome 19) markers that was provided in the document “Appendix to the Specification as Table 2” that was 4541064 bytes (as measured in MS-Windows®), filed with U.S. Provisional Application Ser. No. 61/380,024 on Sep. 3, 2010. Table 2 appears in the final pages of the specification.
BACKGROUND OF INVENTION
“Yellow Flash” is an undesirable phenotype observed in certain soybean varieties that comprise a transgene that confers tolerance to the broad-spectrum herbicide glyphosate. After application of glyphosate, or applications of glyphosate under certain environmental conditions such as high temperature, the leaves of certain soybean plant varieties comprising the transgene that confers glyphosate tolerance can exhibit a yellowish color (hence, the term “Yellow Flash”). The Yellow Flash phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate tolerance. The yellow flash phenotype is undesirable as it leads to a visually displeasing off-type yellow leaf color in soybean plants exposed to glyphosate.
SUMMARY OF INVENTION
Although the Yellow Flash phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate tolerance, distinct soybean varieties that comprise the same glyphosate tolerant transgene integrated at the same chromosomal locus (i.e. the same transgenic event) can show various degrees of yellow flash upon exposure to high doses of glyphosate. Some varieties comprising the glyphosate tolerant transgene insertion are highly resistance to high dosages of glyphosate, showing no yellow flash phenotype (i.e. a “no flash phenotype”), while other varieties comprising the same glyphosate tolerant transgene insertion are highly susceptible to high dosages of glyphosate, showing a severe yellow flash phenotype. Provided herein are soybean plants comprising an introgressed genomic region associated with a no flash phenotype. Also provided herein are markers that reside outside of a genomic region associated with a no flash phenotype and that facilitate breeding activities that include, but are not limited to, introgression of this genomic region. Markers and specific alleles thereof that are associated with a no flash phenotype are also provided. Methods of obtaining a soybean plant that exhibits a no flash phenotype and methods of obtaining a soybean plant comprising in its genome at least one no flash locus are also provided. Methods that provide for the introgression of a genomic region associated with a no flash phenotype into soybean germplasm that has a genomic region associated with a yellow flash phenotype. Identification of molecular markers associated with loci that confer the no flash phenotype has significant economic value. By using markers associated with the no flash trait, breeders can select soybean varieties with the favorable alleles (i.e. alleles that are not associated with the yellow flash trait) for use in trait integration. They can also use the markers to help them eliminate unfavorable alleles (i.e. alleles that are associated with the yellow flash trait) in soybean unfavorable allele. This invention thus provides for commercially desirable transgenic soybean lines that carry a genomic region that is associated with a “no flash” phenotype and tolerate high dosages of glyphosate.
Methods of identifying a soybean plant that comprises a genotype associated with a no flash phenotype are thus provided. In certain embodiments, methods of identifying a soybean plant that comprises a genotype associated with a no flash phenotype, comprising: detecting in the soybean plant an allele in at least one yellow flash marker locus associated with the no flash phenotype wherein the yellow flash marker locus is in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14), and denoting that the plant comprises a genotype associated with a no flash phenotype. In certain embodiments, the methods further comprise the step of selecting the denoted plant from a population of plants. In certain embodiments of any of the aforementioned methods, the denoted plant comprises a transgene that confers tolerance to glyphosate are provided. In certain embodiments where the denoted plant comprises a transgene that confers tolerance to glyphosate, the soybean plant or progeny thereof is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety. In certain embodiments of the aforementioned methods, a plant that exhibits a no flash phenotype is selected. In certain embodiments of the aforementioned methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16) and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). In certain embodiments of the aforementioned methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in the linkage group L region selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7) that is associated with a no flash phenotype.
Also provided are methods for obtaining a soybean plant comprising in its genome at least one no flash locus. In certain embodiments, a method for obtaining a soybean plant comprising in its genome at least one no flash locus, compromising the steps of: a. genotyping a plurality of soybean plants with respect to at least one yellow flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14); and, b. selecting a soybean plant comprising in its genome at least one no flash locus comprising a genotype associated with no flash phenotype are provided. In certain embodiments of these methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). In certain embodiments of the aforementioned methods, the genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in the first linkage group L region, the first sub-region, or the second sub-region, wherein the marker is selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7). In certain embodiments, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one no flash locus with a parent plant comprising at least one yellow flash locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one no flash locus. In certain embodiments, the population contains plants that comprise a transgene that confers tolerance to glyphosate. In certain embodiments, the aforementioned methods can further comprise the step of assaying for the presence of at least one additional marker, wherein the additional marker is either linked or unlinked to the linkage group L genomic region. In certain embodiments of the aforementioned methods, the plurality of soybean plants, the soybean plant, and/or progeny thereof are exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety. In certain embodiments of the aforementioned methods, a plant that exhibits a no flash phenotype is selected.
Also provided herewith are methods for producing a soybean plant comprising in its genome at least one introgressed no flash locus. In certain embodiments, a method for producing a soybean plant comprising in its genome at least one introgressed no flash locus comprising the steps of: a. crossing a first no flash soybean plant with a second soybean plant comprising: a yellow flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14), and at least one linked polymorphic locus not present in the first no flash soybean plant to obtain a population segregating for the no flash loci and the linked polymorphic locus; b. detecting at least two polymorphic nucleic acids in at least one soybean plant from the population, wherein at least one of the polymorphic nucleic acids is located in the first linkage group L region and wherein at least one of the polymorphic amino acids is a linked polymorphic locus not present in the first no flash soybean plant; and c. selecting a soybean plant comprising a genotype associated with a no flash phenotype and at least one linked marker found in the second soybean plant comprising a yellow flash locus but not in the first no flash soybean plant, thereby obtaining a soybean plant comprising in its genome at least one introgressed no flash locus are provided. In certain embodiments of the methods, at least one of the first or the second soybean plants comprises a transgene that confers tolerance to glyphosate. In certain embodiments of the methods, the population, the selected soybean plant, and/or progeny of selected soybean plant is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety. In certain embodiments, the yellow flash locus comprises at least one polymorphic allele of at least one marker in a first sub-region of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of the linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). In certain embodiments of the aforementioned methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7). In certain embodiments of the aforementioned methods, the polymorphic nucleic acid detected in step (b) is detected with at least one marker selected from the group consisting of M0101742 (SEQ ID NO:5) and M0129925 (SEQ ID NO:7). In certain embodiments of the aforementioned methods, the polymorphic nucleic acids are detected with marker M0101742 (SEQ ID NO:5) and with marker M0129925 (SEQ ID NO:7). In certain embodiments of the aforementioned methods, the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. In certain embodiments of the methods, the linked polymorphic locus is detected with a marker that is located within about 1000, 500, 100, 40, 20, 10, or 5 kilobases (Kb) of the no flash locus. In certain embodiments of the methods, the linked polymorphic locus is detected with at least one marker selected from the group consisting of M0205928 (SEQ ID NO:3), M0205537 (SEQ ID NO:8), M0202715 (SEQ ID NO:9), M0206286 (SEQ ID NO:10), M0206054 (SEQ ID NO:11) and M0205375 (SEQ ID NO:12). Also provided herewith are soybean plants comprising an introgressed no flash locus made by the aforementioned methods. In certain embodiments, a soybean plant comprising an introgressed no flash locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a no flash soybean variety and that are linked to the introgressed no flash locus, wherein the plant is produced by the aforementioned methods are provided.
Also provided are soybean plants comprising an introgressed no flash locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a no flash soybean variety and that are linked to the introgressed no flash locus.
Also provided are substantially purified nucleic acid molecules comprising a nucleic acid molecule selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7), or a fragment thereof that contains a specific allelic variant of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), or M0129925 (SEQ ID NO:7). In certain embodiments, the fragment that contains the allelic variant is at least 15, at least 18, at least 20, at least 22, at least 25, or at least 30 nucleotides in length.
In certain embodiments, methods for obtaining a soybean plant that exhibits a no flash phenotype comprising the steps of: a) crossing a soybean plant that exhibits a no flash phenotype with a soybean plant that exhibits a yellow flash phenotype, wherein at least one of the soybean plants comprises a transgene that confers tolerance to glyphosate, and b) selecting a progeny plant from the cross, wherein the progeny plant comprises the transgene that confers glyphosate tolerance and wherein the progeny plant exhibits a no flash phenotype are provided. In certain embodiments of the methods, the selection in step b can comprise: i) genotyping the progeny plant with respect to a yellow flash locus in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14); and/or ii) exposing the progeny plant to glyphosate and scoring the plant for a no flash phenotype. In certain embodiments of the methods, a soybean plant that exhibits a yellow flash phenotype comprises at least one linked or unlinked marker not present in the first no flash soybean plant. In certain embodiments, the progeny plant is further selected for the presence of the linked or unlinked marker.
Also provided are methods of breeding soybean plants comprising the steps of:
a. selecting a first soybean plant comprising a genotype in the linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) that is associated with a no flash phenotype from a population of soybean plants that is segregating for the genotype; and, b) crossing the selected soybean plant with a second soybean plant. In certain embodiments of these methods, one or both of the soybean plants comprises a transgene that confers glyphosate tolerance.
Further areas of applicability will become apparent from the description provided herein. It should be understood that the description and specific examples are intended for purposes of illustration only and are not intended to limit the scope of the present disclosure.


DETAILED DESCRIPTION OF INVENTION
I. Definition
As used herein, an “allele” refers to one of two or more alternative forms of a genomic sequence at a given locus on a chromosome. When all the alleles present at a given locus on a chromosome are the same, that plant is homozygous at that locus. If the alleles present at a given locus on a chromosome differ, that plant is heterozygous at that locus.
As used herein, the term “denoting” when used in reference to a plant genotype refers to any method whereby a plant is indicated to have a certain genotype. Such indications of a certain genotype include, but are not limited to, any method where a plant is physically marked or tagged. Physical markings or tags that can be used include, but not limited to, a barcode, a radio-frequency identification (RFID), a label or the like. Indications of a certain genotype also include, but are not limited to, any entry into any type of written or electronic database whereby the plant's genotype is provided.
A “locus” is a position on a genomic sequence that is usually found by a point of reference; e.g., a short DNA sequence that is a gene, or part of a gene or intergenic region. A locus may refer to a nucleotide position at a reference point on a chromosome, such as a position from the end of the chromosome.
As used herein, “linkage group L” corresponds to the soybean linkage group L described in Choi, et al., Genetics. 2007 May; 176(1): 685-696. Linkage group L, as used herein, also corresponds to soybean chromosome 19 (as described on the World Wide Web at soybase.org/LG2Xsome.php). As used herein, “polymorphism” means the presence of one or more variations of a nucleic acid sequence at one or more loci in a population of at least two members. The variation can comprise but is not limited to one or more nucleotide base substitutions, the insertion of one or more nucleotides, a nucleotide sequence inversion, and/or the deletion of one or more nucleotides.
As used herein, the term “single nucleotide polymorphism,” also referred to by the abbreviation “SNP,” means a polymorphism at a single site wherein the polymorphism constitutes any or all of a single base pair change, an insertion of one or more base pairs, and/or a deletion of one or more base pairs.
As used herein, “marker” means a detectable characteristic that can be used to discriminate between organisms. Examples of such characteristics include, but are not limited to, genetic markers, biochemical markers, fermentation yield, fermentation efficiency, energy yield, secondary compounds, metabolites, morphological characteristics, and agronomic characteristics.
As used herein, “marker assay” means a method for detecting a polymorphism at a particular locus using a particular method. Marker assays thus include, but are not limited to, measurement of at least one phenotype (such as seed color, flower color, or other visually detectable trait as well as any biochemical trait), restriction fragment length polymorphism (RFLP), single base extension, electrophoresis, sequence alignment, allelic specific oligonucleotide hybridization (ASO), random amplified polymorphic DNA (RAPD), microarray-based polymorphism detection technologies, and the like.
As used herein, “genotype” means the genetic component of the phenotype and it can be indirectly characterized using markers or directly characterized by nucleic acid sequencing.
As used herein, the term “introgressed”, when used in reference to a genetic locus, refers to a genetic locus that has been introduced into a new genetic background. Intro gression of a genetic locus can thus be achieved through both plant breeding methods or by molecular genetic methods. Such molecular genetic methods include, but are not limited to, various plant transformation techniques and/or methods that provide for homologous recombination, non-homologous recombination, site-specific recombination, and/or genomic modifications that provide for locus substitution or locus conversion. In certain embodiments, introgression could thus be achieved by substitution of a yellow flash locus with a corresponding no flash locus or by conversion of a locus from a yellow flash genotype to a no flash genotype.
As used herein, “phenotype” means the detectable characteristics of a cell or organism which can be influenced by gene expression.
As used herein, “linkage” refers to relative frequency at which types of gametes are produced in a cross. For example, if locus A has genes “A” or “a” and locus B has genes “B” or “b” and a cross between parent I with AABB and parent B with aabb will produce four possible gametes where the genes are segregated into AB, Ab, aB and ab. The null expectation is that there will be independent equal segregation into each of the four possible genotypes, i.e. with no linkage 1⁄4 of the gametes will of each genotype. Segregation of gametes into a genotypes differing from 1⁄4 are attributed to linkage.
As used herein, the termed “linked”, when used in the context of markers and/or genomic regions, means that the markers and/or genomic regions are located on the same linkage group or chromosome.
As used herein, a “nucleic acid molecule,” be it a naturally occurring molecule or otherwise may be “substantially purified”, if desired, referring to a molecule separated from substantially all other molecules normally associated with it in its native state. More preferably, a substantially purified molecule is the predominant species present in a preparation. A substantially purified molecule may be at least about 60% free, preferably at least about 75% free, more preferably at least about 90% free, and most preferably at least about 95% free from the other molecules (exclusive of solvent) present in the natural mixture. The term “substantially purified” is not intended to encompass molecules present in their native state.
As used herein, “quantitative trait locus (QTL)” means a locus that controls to some degree numerically representable traits that are usually continuously distributed. As used herein, the term “transgene” means nucleic acid molecules in the form of DNA, such as cDNA or genomic DNA, and RNA, such as mRNA or microRNA, which may be single or double stranded.
As used herein, the term “event”, when used in the context of describing a transgenic plant, refers to a particular transformed plant line. In a typical transgenic breeding program, 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.
As used herein, the term “soybean” means Glycine max and includes all plant varieties that can be bred with soybean, including wild soybean species. In certain embodiments, soybean plants from the species Glycine max and the subspecies Glycine max L. ssp. max or Glycine max ssp. formosana can be genotyped using the compositions and methods of the present invention. In an additional aspect, the soybean plant is from the species Glycine soja, otherwise known as wild soybean, can be genotyped using these compositions and methods. Alternatively, soybean germplasm derived from any of Glycine max, Glycine max L. ssp. max, Glycine max ssp. Formosana, and/or Glycine soja can be genotyped using compositions and methods provided herein.
As used herein, the term “bulk” refers to a method of managing a segregating population during inbreeding that involves growing the population in a bulk plot, harvesting the self pollinated seed of plants in bulk, and using a sample of the bulk to plant the next generation
As used herein, the phrase “Single Plant Selection” (or the acronym “SPS”) refers to a method that is often used instead of bulk method (see immediately above) to advance segregating germplasm in early generations. SPS is always used to advance germplasm to “Progeny Row” (Prow) and “Progeny Row Yield Trial” (PRYT) analyses.
As used herein, the phrase “Progeny Row” (Prow) refers to a plant breeding and analysis method where a row of progeny plants from SPS is grown for observation, further selection, and/or bulking
As used herein, the phrase “Progeny Row Yield Trial” (PRYT) refers to a plant breeding and analysis method where a row of plants from a SPS is grown in a small yield trial with other SPS material. In most instances, the PRYT is usually from the same population and usually consists of one rep at one location.
As used herein, the term “comprising” means “including but not limited to”.
II. Description of the Invention
Overview
In accordance with the present invention, Applicants have discovered genomic regions, associated markers, and associated methods for identifying and associating genotypes that effect a transgene-mediated glyphosate tolerance trait. For example, in one embodiment, a method of the invention comprises screening a plurality of transgenic germplasm entries displaying a heritable variation for at least one transgene mediated glyphosate tolerance trait wherein the heritable variation is linked to at least one genotype; and associating at least one genotype from the transgenic germplasm entries to at least one transgene mediated glyphosate tolerance trait. In another embodiment, a method of the invention comprises crossing at least two germplasm entries with a test germplasm entry for the evaluation of performance of at least one transgene mediated glyphosate tolerance trait in order to determine preferred crossing schemes. The methods of the present invention can be used with traditional breeding techniques as described below to more efficiently screen and identify genotypes affecting a transgene-mediated glyphosate tolerance trait.
The use of markers to infer a phenotype of interest results in the economization of a breeding program by substituting costly, time-intensive phenotyping assays with genotyping assays. Further, breeding programs can be designed to explicitly drive the frequency of specific, favorable phenotypes by targeting particular genotypes (U.S. Pat. No. 6,399,855). Fidelity of these associations may be monitored continuously to ensure maintained predictive ability and, thus, informed breeding decisions (US Patent Application 2005/0015827). In this case, costly, time-intensive phenotyping assays required for determining if a plant or plants contains a genomic region associated with a “no flash” or “yellow flash” phenotype can be supplanted by genotypic assays that provide for identification of a plant or plants that contain the desired genomic region.
III. A Genomic Region Associated with a No Flash Phenotype
Provided herewith is a soybean genomic region that is shown herein to be associated with a desirable no flash phenotype when present in certain allelic forms and when combined with certain transgenic loci that confer glyphosate tolerance.
A soybean genomic region provided that can be associated with a desirable no flash phenotype when present in certain allelic forms is located on the telomere proximal end of the short arm of soybean linkage group L (chromosome 19). A series of markers useful in practicing the methods of this invention are provided herewith in Table 1. Additional markers useful in the practice of the invention are provided herewith in Table 2 of the Specification, which is incorporated herewith by reference in its entirety. Table 2 provides the Table 1 markers, additional nucleic acid markers or loci that have been disclosed in various databases, the relative positions of the markers on a physical map of linkage group L (soybean chromosome 19), and sources for the markers.







TABLE 1







Markers spanning a genomic region associated


with a desirable no flash phentoype















Allelic form(s)



Marker or
SEQ
Map
Associated with No



Locus Name
ID NO:
Position 1
Flash Phenotype 2






M0205350
1
423935




M0114388
2
380897




M0205928
3
 92526




M01291383
4
114013
GG7 or AA8



M01017424
5
112836
TT7 or CC8



M00931165
6
805580
AA7 or TT8



M01299256
7
831128
CC7 or GG7,8



M0205537
8
890254




M0202715
9
921431




M0206286
10 
1209977 




M0206054
11 
1465354 




M0205375
12 
2009800 




BG406195
13 
107207




BU082700
14 
864145





1 The relative positions of the middle position of the listed markers or loci based on nucleotide positions on a physical map of soybean linkage group L (chromosome 19) of Table 2 are provided where nucleotide position 0 (zero) is telomere proximal and nucleotide position 2009800 is centromere proximal. Polymorphic nucleotide bases are designated in the sequence listing provided herewith according to the WIPO Standard ST.25 (1998), Table 1, as follows: r = g or a (purine); y = t/u or c (pyrimidine); m = a or c; (amino); k = g or t/u (keto); s = g or c (strong interactions 3 H-bonds); w = a or t/u (weak interactions 2H-bonds); b = g or c or t/u (not a); d = a or g or t/u (not c); h = a or c or t/u (not g); v = a or g or c (not t, not u); and n = a or g or c or t/u (unknown, or other; any.)


2 Both the maternal and paternal alleles of the single nucleotide polymorphisms that can be associated with a non flash phenotype are shown.


3The identified polymorphic allele of marker M0129138 is located at nucleotide 218 of SEQ ID NO: 4.


4The identified polymorphic allele of marker M0101742 is located at nucleotide 1206 of SEQ ID NO: 5.


5The identified polymorphic allele of marker M0093116 is located at nucleotide 183 of SEQ ID NO: 6.


6The identified polymorphic allele of marker M0129925 is located at nucleotide 328 of SEQ ID NO: 7.


7The identified polymorphic allele of marker M0129138 “GG” can be associated with a no flash phenotype when the identified polymorphic alleles of the other markers are: “TT” for M0101742, “AA” for marker M0093116, and either “GG” or “CC” for marker M0129925.


8The identified polymorphic allele of marker M0129138 “AA” can be associated with a no flash phenotype when the identified polymorphic alleles of the other markers are: “CC” for M0101742, “TT” for marker M0093116, and “GG” for marker M0129925.






Also provided herein are sub-regions of the linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID: 14) that are associated with a no flash phenotype. A first sub-region of the linkage group L region associated with a no flash phenotype is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16). These loci flank a first sub-region that spans telomere proximal nucleotide 107039 to centromere proximal nucleotide 115956 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this first sub-region that are associated with a no flash phenotype can be detected with markers that include, but are not limited to, M0129138 (SEQ ID NO: 4) and M0101742 (SEQ ID NO: 5). A second sub-region of the linkage group L region associated with a no flash phenotype is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14). These loci flank the second sub-region that spans telomere proximal nucleotide 800932 to centromere proximal nucleotide 864449 in the physical map of linkage group L provided in Table 2 of the specification. Polymorphisms located in this second sub-region that are associated with a no flash phenotype can be detected with markers that include, but are not limited to, M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7). In certain embodiments of invention, a polymorphism associated with a no-flash phenotype is detected in only one of these sub-regions. In other embodiments of the invention, at least one polymorphism associated with a no-flash phenotype is detected in both of these sub-regions. Thus, one or more markers selected from the group consisting of M0129138 (SEQ ID NO: 4), M0101742 (SEQ ID NO: 5), and markers located between loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16) can be used either independently of, or in combination with, one or more markers selected from the group consisting of M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7), and markers located between loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14) to detect polymorphisms associated with a no flash phenotype. Conversely, one or more markers selected from the group consisting of M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7), and markers located between loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14) can also be used independently of, or in combination with, any markers located in the first sub-region to detect polymorphisms associated with a no flash phenotype. In certain embodiments, a polymorphism in the first sub-region is detected with marker M0101742 (SEQ ID NO: 5) and a polymorphism in the second sub-region is detected with marker M0129925 (SEQ ID NO: 7).
Additional genetic markers can be used either in conjunction with the markers provided in Table 1 and/or Table 2 or independently of the markers provided in Table 1 and/or Table 2 to practice the methods of the instant invention. Publicly available marker databases from which useful markers can be obtained include, but are not limited to, the soybase.org website on the internet (World Wide Web) that is administered by the United States Agricultural Research Service, the United States Department of Agriculture, and Iowa State University. Additional soybean markers that can be used and that have been described in the literature include, but are not limited to, Hyten et al., BMC Genomics. 11:38, 2010; Choi et al., Genetics. 176(1):685-96, 2007; Yoon et al., Theor Appl Genet. 2007 March; 114(5):885-99; and Hyten et al. Crop Sci. 2010 50: 960-968. Given the provision herein of a genomic region on linkage group L (chromosome 19) delimited or flanked by the telomere proximal locus BG406195 (SEQ ID NO: 13) of Table 2 and the centromere proximal locus BU082700 (SEQ ID NO: 14) of Table 2 as well as an assortment of soybean germplasms exhibiting either a “yellow-flash” or “no flash” phenotype, additional markers located either within or near this genomic region that are associated with these phenotypes can be obtained by merely typing the new markers in the various germplasms provided herewith. The genomic region on linkage group L (chromosome 19) delimited or flanked by the telomere proximal locus BG406195 (SEQ ID NO: 13) of Table 2 and the centromere proximal locus BU082700 (SEQ ID NO: 14) of Table 2 can also be mapped relative to markers provided in any publicly available or other soybean physical or genetic map to place this genetic locus on that map.
IV. Identification of Plants Exhibiting the “Flash” or “No-Flash” Phenotype
To observe the presence or absence of the “Yellow Flash” or no flash phenotypes, transgenic soybean plants comprising a transgene that confers glyphosate tolerance are typically exposed in early to mid-vegetative growth stages to one or more high doses of glyphosate. Typical doses of glyphosate that can elicit a yellow flash phenotype can range from about a 2-fold label application rate of a commercially available glyphosate formulation to about a 3-fold label application rate of a commercially available glyphosate formulation. In terms of acid equivalents of glyphosate acid applied, typical doses of glyphosate that can elicit a yellow flash phenotype can range from an application rate of about 1.5 pounds of acid equivalent per acre (about 1.68 kilograms per hectare) of glyphosate acid to about 2.25 pounds of acid equivalent per acre (i.e. about 2.52 kilograms per hectare) of glyphosate acid when the indicated amounts of glyphosate acid are provided in either a commercially available glyphosate formulation or when the indicated amounts of glyphosate acid is provided in a similar formulation suitable for application to glyphosate-tolerant crops. Commercially available glyphosate formulations that can be used include, but are not limited to, Roundup Original MAX®, Roundup PowerMAX®, Roundup UltraMax®, or RoundUp WeatherMAX® (Monsanto Co., St. Louis, Mo., USA); Touchdown IQ® or Touchdown Total® (Syngenta, Wilmington, Del., USA); Glyphomax®, Glyphomax Plus®, or Glyphomax XRT® (Dow Agrosciences LLC, Indianapolis, Ind., USA). In certain embodiments, the commercially available glyphosate formulation used is RoundUp WeatherMAX®. In certain embodiments, doses of glyphosate that can elicit a yellow flash phenotype can range from about a 2 fold application rate of about 42.6 ounces per acre RoundUp WeatherMax® (1.68 kilograms per hectare) to about a three fold application rate of about 63.9 ounces per acre RoundUp WeatherMax® (i.e. about 2.52 kilograms per hectare).
The Yellow Flash phenotype can be observed approximately a week after herbicide application in certain soybean varieties comprising the transgene that confers glyphosate tolerance. Glyphosate is typically applied during vegetative growth stages. In certain embodiments of these methods, glyphosate can be applied in weekly intervals (i.e. once a week) for any of 2, 3, 4 or more successive weeks to score for the presence of the yellow flash phenotype. In certain embodiments, soybean plants at about the V3-V4 vegetative development stage are exposed to an initial glyphosate spray followed by three subsequent sprays at weekly intervals. The first spray can be based on stage of growth and remaining sprays were scheduled at 7 day intervals following initial spray. As discussed herein, the vegetative stages of soybean are as follows: VE (emergence), VC (cotyledon stage), V1 (first trifoliolate leaf), V2 (second trifoliolate leaf), V3 (third trifoliolate leaf), V(n) (nth trifoliolate leaf), and V6 (flowering will soon start). A description of the soybean vegetative stages can be found on the world wide web (internet) at ag.ndsu.edu/pubs/plantsci/rowcrops/a1174/a1174w.htm (North Dakota State University publication A-1174, June 1999, Reviewed and Reprinted August 2004). Expression of the yellow flash trait can also be influenced by temperature, where the trait in varieties that display the yellow flash phenotype is more pronounced following treatment at temperatures of about 32 degrees Celsius or more.
A rating scale that evaluates the degree of yellow flash can also be employed to identify “flash” and “no flash” plants. An exemplary and non limiting scale for evaluating the yellow flash phenotype is as follows, where the low numbers correspond to a “no flash” phenotype and the high numbers correlate to a “flash” phenotype:
1: Green—No Yellowing
2: Mostly green, very slight yellowing <5% (1-2 plants with some yellowing)
3: 5-10% plants with yellowing
4: 11-20% plants with yellowing
5: 21-35% plants with yellowing
6: 36-50% plants with yellowing
7: 51-65% plants with yellowing
8: 66-80% plants with yellowing, some necrosis
9: 81-100% plants with yellowing and or necrosis
V. Introgression of a Genomic Region Associated with a No Flash Phenotype
Also provided herewith are unique soybean germplasm comprising an introgressed genomic region that is associated with a no flash phenotype and methods of obtaining the same. Marker-assisted introgression involves the transfer of a chromosomal region, defined by one or more markers, from one germplasm to a second germplasm. Offspring of a cross that contain the introgressed genomic region can be identified by the combination of markers characteristic of the desired introgressed genomic region from a first germplasm (i.e. such as a no flash germplasm) and both linked and unlinked markers characteristic of the desired genetic background of a second germplasm (i.e. a yellow flash germplasm). In addition to the markers provided herewith that identify alleles of genomic region that is associated with a no flash phenotype, flanking markers that fall on both the telomere proximal end of the genomic region on linkage group L (chromosome 19) and the centromere proximal end of the linkage group L (chromosome 19) genomic region are also provided in Tables 1 and 2. Such flanking markers are useful in a variety of breeding efforts that include, but are not limited to, introgression of the genomic region associated with a no flash phenotype into a genetic background comprising markers associated with germplasm that ordinarily contains the allelic forms of the genomic region that is associated with a “yellow flash” phenotype. Telomere proximal flanking markers that can be used in these methods include, but are not limited to, M0205928 (SEQ ID NO: 3) and/or polymorphisms in any of the loci listed in Table 2 of the Specification located between starting base 16426 (the telomere proximal base) of locus asmbl_11856 and starting base 107039 of locus BG406195. Such polymorphisms can be identified by sequencing loci from flash and no flash germplasms. Centromere proximal flanking markers that can be used in these methods include, but are not limited to, M0202715 (SEQ ID NO: 9), M0206286 (SEQ ID NO: 10), M0206054 (SEQ ID NO: 11), and M0205375 (SEQ ID NO: 12). Additional markers located on linkage group L (chromosome 19) and other chromosomes are disclosed in US Patent Application Publication 20090208964. Publicly available marker databases from which additional useful markers located on linkage group L (chromosome 19) and other chromosomes can be obtained include, but are not limited to, the soybase.org website on the internet that is administered by the United States Agricultural Research Service, the United States Department of Agriculture, and Iowa State University. Soybean plants or germplasm comprising an introgressed genomic region that is associated with a no flash phenotype wherein at least 10%, 25%, 50%, 75%, 90%, or 99% of the remain genomic sequences carry markers characteristic of soybean plants or germplasm that are otherwise or ordinarily comprise a genomic region associated with the yellow flash phenotype are thus provided.
VI. Soybean Plants Comprising Genomic Region Associated with the Flash and No Flash Phenotypes and Transgenes that Confer Tolerance to Glyphosate
A non-limiting and exemplary list of soybean plants that comprise genomic regions associated with either a flash or a no flash phenotype are provided herewith in Table 3.







TABLE 3







Soybean varieties comprising a genomic region


associated with a no flash or flash phenotype.















ATCC






Depository


Branded

U.S.
Variety Name
Accession


Name 1
Phenotype
Pat. No.
in Patent
Number 2





AG4201
Flash
7,071,388
SE71112
PTA-5728


AG4601
Flash
5,659,116
927113675
  97556.


AG4603
Flash
7,067,723
SE73753
PTA-5730


AG4702
Flash
5,750,857
9390369478967
209547


AG4902
Flash
6,143,953
931474956907
PTA-2214


DKB31-51
Flash
6,346,658
950045734453
PTA-3871


DKB37-51
Flash
7,294,764
SD82997
PTA-5737


DKB38-52
Flash
6,660,912
SD92955
PTA-5382


DKB40-51
Flash
6,683,233
SD93038
PTA-5329


DKB46-51
Flash
6,933,423
SE73090
PTA-5733


AG0801
Non-Flash
6,005,170
9422009600716
PTA-269


AG0803
Non-Flash
7,498,489
4498438
PTA-9064


AG0901
Non-Flash
6,080,917
942193611352
203207


AG2403
Non-Flash
6,900,372
SN71173
PTA-5727


AG2603
Non-Flash
7,388,131
4599695
PTA-9070


AG2703
Non-Flash
6,184,442
9323265446452
PTA-2577


AG3006
Non-Flash
7,482,516
0387907
PTA-9029


AG3302
Non-Flash
5,973,235
943470629664
203939


AG3505
Non-Flash
7,569,750
4559809
PTA-9023


AG3703
Non-Flash
6,881,879
SW90702
PTA-5738


AG3903
Non-Flash
6,632,982
SW84112
PTA-5299


AG4403
Non-Flash
6,348,644
9472569612611
PTA-3870


AG4503
Non-Flash
7,378,578
0358232
PTA-9003


AG4703
Non-Flash
7,554,014
437973
PTA-9066


DKB06-51
Non-Flash
6,143,953
931474956907
PTA-2214


DKB08-51
Non-Flash
7,504,565
4878185
PTA-9702


DKB22-52
Non-Flash
6,858,783
0491727
PTA-6187


DKB29-51
Non-Flash
6,884,927
0509249
PTA 6272


DKB42-51
Non-Flash
7,479,582
4671685
PTA-9027





1 Branded names of Asgrow ® (designated “AG”) and DEKALB ® soybean varieties from Monsanto Co. 800 N. Lindbergh Blvd., St. Louis, MO, USA.


2 Deposit numbers of seed available through the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, Va., USA, 20110-2209.






Also provided herewith are additional soybean plants that comprising a genomic region associated with a flash or no flash phenotype that are identified by use of the markers provided in Table 1 and/or Table 2 and/or methods provided herein. Any of the soybean plants identified in Table 3 or other soybean plants that are otherwise identified using the markers or methods provided herein can be used in methods that include, but are not limited to, methods of obtaining soybean plants with an introgressed no flash locus, obtaining a soybean plant that exhibits a no flash phenotype, or obtaining a soybean plant comprising in its genome a genetic region associated with a no flash phenotype.
In certain embodiments, the soybean plants provided herein or used in the methods provided herein can comprise a transgene that confers tolerance to glyphosate. Transgenes that can confer tolerance to glyphosate include, but are not limited to, transgenes that encode glyphosate tolerant Class I EPSPS (5-enolpyruvylshikimate-3-phosphate synthases) enzymes or glyphosate tolerant Class II EPSPS (5-enolpyruvylshikimate-3-phosphate synthases) enzymes. Useful glyphosate tolerant EPSPS enzymes provided herein are disclosed in U.S. Pat. No. 6,803,501, RE39,247, U.S. Pat. No. 6,225,114, U.S. Pat. No. 5,188,642, and U.S. Pat. No. 4,971,908. In certain embodiments, the glyphosate tolerant soybean plants can comprise a transgene encoding a glyphosate oxidoreductase or other enzyme which degrades glyphosate. Glyphosate oxidoreductase enzymes had been described in U.S. Pat. No. 5,776,760 and U.S. Reissue Pat. RE38,825. In certain embodiments the soybean plant can comprise a transgene encoding a glyphosate N-acetyltransferase gene that confers tolerance to glyphosate. In certain embodiments, the soybean plant can comprise a glyphosate n-acetyltransferase encoding transgene such as those described in U.S. Pat. No. 7,666,644. In still other embodiments, soybean plants comprising combinations of transgenes that confer glyphosate tolerance are provided. Soybean plants comprising both a glyphosate resistant EPSPS and a glyphosate N-acetyltransferase are also provided herewith. In certain embodiments, it is contemplated that the soybean plants used herein can comprise one or more specific genomic insertion(s) of a glyphosate tolerant transgene including, but not limited to, as those found in: i) MON89788 soybean (deposited under ATCC accession number PTA-6708 and described in US Patent Application Publication Number 20100099859), ii) GTS 40-3-2 soybean (Padgette et al., Crop Sci. 35: 1451-1461, 1995), iii) event 3560.4.3.5 soybean (seed deposited under ATCC accession number PTA-8287 and described in US Patent Publication 20090036308), or any combination of i (MON89788 soybean), ii (GTS 40-3-2 soybean), and iii (event 3560.4.3.5 soybean).
In certain embodiments, it is contemplated that genotypic assays that provide for non-destructive identification of the plant or plants can be performed either in seed, the emergence stage, the “VC” stage (i.e. cotyledons unfolded), the V1 stage (appearance of first node and unifoliate leaves), the V2 stage (appearance of the first trifoliate leaf), and thereafter. In certain embodiments, non-destructive genotypic assays are performed in seed using apparati and associated methods as described in U.S. Pat. Nos. 6,959,617; 7,134,351; 7,454,989; 7,502,113; 7,591,101; 7,611,842; and 7,685,768, which are incorporated herein by reference in their entireties. In certain embodiments, non-destructive genotypic assays are performed in seed using apparati and associated methods as described in US Patent Application Publications 20100086963, 20090215060, and 20090025288, which are incorporated herein by reference in their entireties. Published U.S. Patent Applications US 2006/0042527, US 2006/0046244, US 2006/0046264, US 2006/0048247, US 2006/0048248, US 2007/0204366, and US 2007/0207485, which are incorporated herein by reference in their entirety, also disclose apparatus and systems for the automated sampling of seeds as well as methods of sampling, testing and bulking seeds. Thus, in a certain embodiments, any of the methods provided herein can comprise screening for markers in individual seeds of a population wherein only seed with at least one genotype of interest is advanced.
VII. Molecular Assisted Breeding Techniques
Genetic markers that can be used in the practice of the instant invention include, but are not limited to, are Restriction Fragment Length Polymorphisms (RFLP), Amplified Fragment Length Polymorphisms (AFLP), Simple Sequence Repeats (SSR), Single Nucleotide Polymorphisms (SNP), Insertion/Deletion Polymorphisms (Indels), Variable Number Tandem Repeats (VNTR), and Random Amplified Polymorphic DNA (RAPD), and others known to those skilled in the art. Marker discovery and development in crops provides the initial framework for applications to marker-assisted breeding activities (US Patent Applications 2005/0204780, 2005/0216545, 2005/0218305, and 2006/00504538). The resulting “genetic map” is the representation of the relative position of characterized loci (DNA markers or any other locus for which alleles can be identified) along the chromosomes. The measure of distance on this map is relative to the frequency of crossover events between sister chromatids at meiosis.
As a set, polymorphic markers serve as a useful tool for fingerprinting plants to inform the degree of identity of lines or varieties (U.S. Pat. No. 6,207,367). These markers form the basis for determining associations with phenotype and can be used to drive genetic gain. The implementation of marker-assisted selection is dependent on the ability to detect underlying genetic differences between individuals.
Certain genetic markers for use in the present invention include “dominant” or “codominant” markers. “Codominant markers” reveal the presence of two or more alleles (two per diploid individual). “Dominant markers” reveal the presence of only a single allele. The presence of the dominant marker phenotype (e.g., a band of DNA) is an indication that one allele is present in either the homozygous or heterozygous condition. The absence of the dominant marker phenotype (e.g., absence of a DNA band) is merely evidence that “some other” undefined allele is present. In the case of populations where individuals are predominantly homozygous and loci are predominantly dimorphic, dominant and codominant markers can be equally valuable. As populations become more heterozygous and multiallelic, codominant markers often become more informative of the genotype than dominant markers.
In another embodiment, markers that include. but are not limited, to single sequence repeat markers (SSR), AFLP markers, RFLP markers, RAPD markers, phenotypic markers, isozyme markers, single nucleotide polymorphisms (SNPs), insertions or deletions (Indels), single feature polymorphisms (SFPs, for example, as described in Borevitz et al. 2003 Gen. Res. 13:513-523), microarray transcription profiles, DNA-derived sequences, and RNA-derived sequences that are genetically linked to or correlated with no flash loci, regions flanking no flash loci, regions linked to no flash loci, and/or regions that are unlinked to no flash loci can be used in certain embodiments of the instant invention.
In one embodiment, nucleic acid-based analyses for determining the presence or absence of the genetic polymorphism (i.e. for genotyping) can be used for the selection of seeds in a breeding population. A wide variety of genetic markers for the analysis of genetic polymorphisms are available and known to those of skill in the art. The analysis may be used to select for genes, portions of genes, QTL, alleles, or genomic regions (Genotypes) that comprise or are linked to a genetic marker that is linked to or correlated with no flash loci, regions flanking no flash loci, regions linked to no flash loci, and/or regions that are unlinked to no flash loci can be used in certain embodiments of the instant invention.
Herein, nucleic acid analysis methods include, but are not limited to, PCR-based detection methods (for example, TaqMan assays), microarray methods, mass spectrometry-based methods and/or nucleic acid sequencing methods. In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means.
A method of achieving such amplification employs the polymerase chain reaction (PCR) (Mullis et al. 1986 Cold Spring Harbor Symp. Quant. Biol. 51:263-273; European Patent 50,424; European Patent 84,796; European Patent 258,017; European Patent 237,362; European Patent 201,184; U.S. Pat. No. 4,683,202; U.S. Pat. No. 4,582,788; and U.S. Pat. No. 4,683,194), using primer pairs that are capable of hybridizing to the proximal sequences that define a polymorphism in its double-stranded form.
Methods for typing DNA based on mass spectrometry can also be used. Such methods are disclosed in U.S. Pat. Nos. 6,613,509 and 6,503,710, and references found therein.
Polymorphisms in DNA sequences can be detected or typed by a variety of effective methods well known in the art including, but not limited to, those disclosed in U.S. Pat. Nos. 5,468,613, 5,217,863; 5,210,015; 5,876,930; 6,030,787; 6,004,744; 6,013,431; 5,595,890; 5,762,876; 5,945,283; 5,468,613; 6,090,558; 5,800,944; 5,616,464; 7,312,039; 7,238,476; 7,297,485; 7,282,355; 7,270,981 and 7,250,252 all of which are incorporated herein by reference in their entireties. However, the compositions and methods of the present invention can be used in conjunction with any polymorphism typing method to type polymorphisms in genomic DNA samples. These genomic DNA samples used include but are not limited to genomic DNA isolated directly from a plant, cloned genomic DNA, or amplified genomic DNA.
For instance, polymorphisms in DNA sequences can be detected by hybridization to allele-specific oligonucleotide (ASO) probes as disclosed in U.S. Pat. Nos. 5,468,613 and 5,217,863. U.S. Pat. No. 5,468,613 discloses allele specific oligonucleotide hybridizations where single or multiple nucleotide variations in nucleic acid sequence can be detected in nucleic acids by a process in which the sequence containing the nucleotide variation is amplified, spotted on a membrane and treated with a labeled sequence-specific oligonucleotide probe.
Target nucleic acid sequence can also be detected by probe ligation methods as disclosed in U.S. Pat. No. 5,800,944 where sequence of interest is amplified and hybridized to probes followed by ligation to detect a labeled part of the probe.
Microarrays can also be used for polymorphism detection, wherein oligonucleotide probe sets are assembled in an overlapping fashion to represent a single sequence such that a difference in the target sequence at one point would result in partial probe hybridization (Borevitz et al., Genome Res. 13:513-523 (2003); Cui et al., Bioinformatics 21:3852-3858 (2005). On any one microarray, it is expected there will be a plurality of target sequences, which may represent genes and/or noncoding regions wherein each target sequence is represented by a series of overlapping oligonucleotides, rather than by a single probe. This platform provides for high throughput screening a plurality of polymorphisms. A single-feature polymorphism (SFP) is a polymorphism detected by a single probe in an oligonucleotide array, wherein a feature is a probe in the array. Typing of target sequences by microarray-based methods is disclosed in U.S. Pat. Nos. 6,799,122; 6,913,879; and 6,996,476.
Target nucleic acid sequence can also be detected by probe linking methods as disclosed in U.S. Pat. No. 5,616,464, employing at least one pair of probes having sequences homologous to adjacent portions of the target nucleic acid sequence and having side chains which non-covalently bind to form a stem upon base pairing of the probes to the target nucleic acid sequence. At least one of the side chains has a photoactivatable group which can form a covalent cross-link with the other side chain member of the stem.
Other methods for detecting SNPs and Indels include single base extension (SBE) methods. Examples of SBE methods include, but are not limited, to those disclosed in U.S. Pat. Nos. 6,004,744; 6,013,431; 5,595,890; 5,762,876; and 5,945,283. SBE methods are based on extension of a nucleotide primer that is adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. In certain embodiments, the SBE method uses three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to sequence of the locus of genomic DNA which flanks a region containing the polymorphism to be assayed. Following amplification of the region of the genome containing the polymorphism, the PCR product is mixed with the third oligonucleotide (called an extension primer) which is designed to hybridize to the amplified DNA adjacent to the polymorphism in the presence of DNA polymerase and two differentially labeled dideoxynucleosidetriphosphates. If the polymorphism is present on the template, one of the labeled dideoxynucleosidetriphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected.
In another method for detecting polymorphisms, SNPs and Indels can be detected by methods disclosed in U.S. Pat. Nos. 5,210,015; 5,876,930; and 6,030,787 in which an oligonucleotide probe having a 5′ fluorescent reporter dye and a 3′ quencher dye covalently linked to the 5′ and 3′ ends of the probe. When the probe is intact, the proximity of the reporter dye to the quencher dye results in the suppression of the reporter dye fluorescence, e.g. by Forster-type energy transfer. During PCR forward and reverse primers hybridize to a specific sequence of the target DNA flanking a polymorphism while the hybridization probe hybridizes to polymorphism-containing sequence within the amplified PCR product. In the subsequent PCR cycle DNA polymerase with 5′→3′ exonuclease activity cleaves the probe and separates the reporter dye from the quencher dye resulting in increased fluorescence of the reporter.
In another embodiment, the locus or loci of interest can be directly sequenced using nucleic acid sequencing technologies. Methods for nucleic acid sequencing are known in the art and include technologies provided by 454 Life Sciences (Branford, Conn.), Agencourt Bioscience (Beverly, Mass.), Applied Biosystems (Foster City, Calif.), LI-COR Biosciences (Lincoln, Nebr.), NimbleGen Systems (Madison, Wis.), Illumina (San Diego, Calif.), and VisiGen Biotechnologies (Houston, Tex.). Such nucleic acid sequencing technologies comprise formats such as parallel bead arrays, sequencing by ligation, capillary electrophoresis, electronic microchips, “biochips,” microarrays, parallel microchips, and single-molecule arrays, as reviewed by R. F. Service Science 2006 311:1544-1546.
The markers to be used in the methods of the present invention should preferably be diagnostic of origin in order for inferences to be made about subsequent populations. Experience to date suggests that SNP markers may be ideal for mapping because the likelihood that a particular SNP allele is derived from independent origins in the extant populations of a particular species is very low. As such, SNP markers appear to be useful for tracking and assisting introgression of QTLs, particularly in the case of Genotypes.
EXAMPLES
The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventor to function well in the practice of the invention, and thus can be considered to constitute 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 which are disclosed and still obtain a like or similar result without departing from the spirit and scope of the invention.
Example 1
Identification of a Locus Associated with Yellow Flash
In yield trials being conducted at Thomasboro, Ill. in August, 2003, it was observed that some F3:5 soybean lines of the pedigree A3525/DKB31-51 (that contained a transgene that confers glyphosate tolerance and exhibited yellow flash when sprayed with glyphosate (i.e. RoundUp WeatherMax®) while other lines of the same pedigree showed glyphosate tolerance and no yellow flash symptoms. Repeat experiments conducted in 2004 produced similar results in 130 F3:6 lines in yield trials conducted at Hopedale, Ill. A3525 is a commercially available Asgrow® soybean variety and is also known under the variety name SN70025. DKB31-51 is described in U.S. Pat. No. 6,346,658 and samples of this seed have been deposited previously under ATCC accession number PTA-3871.
Fifty-three lines were categorized as either “Flash” or “No-Flash” with the remainder of the material falling between the extremes.
The fifty-three lines categorized in 2004 were planted at Covell, Ill. in 2005 and were sprayed with Roundup WeatherMax® at a rates of about 42 oz/acre on a weekly basis beginning at about the V3 to V4 stage for up to four weeks, thus in certain instances attaining a total rate of glyphosate exposure of a 4 week span of about 168 oz/acre. Tissue samples were collected from one individual plant from each of fifteen lines that demonstrated the most severe yellow flash and fifteen that showed no symptoms. Table 4 shows the breeding and testing history of the materials used in this study.







TABLE 4







Breeding and testing history of the materials











Gen.
Season
Year
Location
Bulk/SPS/Prow/PRYT





Cross
Summer
01
Ames, IA
Cross


F1
Winter
01
Isabella, Puerto Rico
Bulk


F2
Winter
01
Isabella, Puerto Rico
Pod Pick


F3
Summer
02
Bloomington, IL
SPS


F4
Winter
02
Rancagua, Chile
Progeny Row


F5
Summer
03
Bloomington, IL
Yield Trial


F6
Summer
04
Bloomington, IL
Yield Trial


F7
Summer
05
Bloomington, IL
Spray Trial





SPS: Single Plant Selection.


Prow: Progeny Row.


PRYT: Progeny Row Yield Trial.






Example 2
Identification of Molecular Markers that are Associated with a “Yellow Flash” Phenotype
To identify marker associated with yellow flash symptom, we used a “Genome Scan” approach. Fifteen samples from lines showing no flash and 15 samples from lines with severe flash were collected from a segregating population (F3:6). DNA were extracted from these 30 samples and used as templates to screen a set of 2746 SNP markers that provide a high-density coverage of the entire soybean genome with approximate two markers per CentiMorgan Unit (cM). Allelic scores at each marker were collected and compared across 30 lines. Of the 2746 markers tested, 776 were segregating and 226 were heterozygous. Two markers, M0102027 and M0101742, clearly showed one allele in no flash and another allele in flash samples (Table 5), indicating a linkage between these two markers and the phenotypes. Having 15 plants showing the same allele and the same phenotype by chance is very low (1/215). Therefore, this could not be explained by a random event. A third marker, M0129138, show one allele on the flash lines and another allele on 14 out of 15 no flash lines, indicating a linkage of this marker to the flash phenotypes. M0101742 and M0129138 turned out to be mapped on the same chromosomal location with no recombination on the mapping population. Other data supporting the linkage is that all seven commercial varieties with known flash phenotypes matched perfectly with the allelic data on the two markers.







TABLE 5







Genotypes for Yellow Flash Phenotype










Map













Linkage
Position
Flash Varieties
No Flash Varieties

















Locus
Group
(cM)
DKB26-52
DKB31-51
DKB38-52
CI3478
AG3602
AG3305
037014-11-18
A3525





M0101742
L
2.4
CC
CC
CC
TT
TT
TT
TT
TT


M0129138
L
2.4
AA
AA
AA
GG
GG
GG
GG
GG


M0093116
L
4.0
AA
AA
AA
AA
AA
AA
AA
AA


M0129925
L
4.0
CC
CC
CC
CC
CC
CC
CC
CC


Phenotype


FL
FL
FL
?
NF
NF
NF
NF





FL: exhibit yellow flash phenotype


NF: exhibit a no flash phenotype






Example 3
Analysis of the Genotype of Soybean Varieties and Yellow Flash Phenotype
Approximately 1,700 soybean varieties (lines) were assayed or typed for the presence or absence of allelic variants of the markers M0101742 (SEQ ID NO: 5), M0129138 (SEQ ID NO: 4), M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7). Of these lines, complete scores for all four markers were obtained in 844 lines. A summary of the genotypes observed in these 844 lines is provided in Table 6.









TABLE 6





#Samples 




(lines)
Genotype1
Phenotype

















706
TTGGAACC
No Flash


 


193
CCAAAACC
Yellow Flash


 


113
CCAATTGG



 


46
TTAAAACC



 


43
TTGGAAGG



 


16
TTGGTTGG



 


11
TTAATTGG



 


9
CCAATTCC
All Plant Introductions (PIs)


 


8
CCAAAAGG



 


5
TTGGTTCC



 


4
TTAATTCC
All Plant Introductions (PIs)


 


3
TTAAAAGG
All Plant Introductions (PIs)


 


1
CCGGTTGG
All Plant Introductions (PIs)





1The genotype of a line is shown as N1N2N3N4N5N6N7N8, where N can be A, T, G, or C depending on the position and the line and where N1 is nucleotide 1, N2 is nucleotide 2, N3 is nucleotide 3, N4 is nucleotide 4, N5 is nucleotide 5, N6 is nucleotide 6, N7 is nucleotide 7, and N8 is nucleotide 8. The genotype represents the both the paternal and maternal allelic forms of the markers M0101742 (SEQ ID NO: 5; position 1206; nucleotides 1 and 2 in genotype shown), M0129138 (SEQ ID NO: 4; position 218; nucleotides 3 and 4 in genotype shown), M0093116 (SEQ ID NO: 6; position 183; nucleotides 5 and 6 in genotype shown), and M0129925 (SEQ ID NO: 7; position 328; nucleotides 3 and 4 in genotype shown). Thus the genotype “TTGGAACC” means that the line is “TT” for both the paternal and maternal contributions to the M0101742 polymorphism, “GG” for both the paternal and maternal contributions to the M0129138 polymorphism, “AA” for both the paternal and maternal contributions to the M0129116 polymorphism, and “CC” for both the paternal and maternal contributions to the M0129925 polymorphism.






Sixty 63 soybean varieties were subsequently selected from various genotype groups and tested for yellow flash essentially as described in Example 1 (i.e. were sprayed with Roundup WeatherMax® at a rates of about 42 oz/acre on a weekly basis beginning at about the V3 to V4 stage for up to four weeks, thus in certain instances attaining a total rate of glyphosate exposure of a 4 week span of about 168 oz/acre). The results of those analyses are provided in Table 7.







TABLE 7







Genotypes and Phenotypes of Selected Varieties













M0101742
M0129138
M0093116
M0129925
Overall




(SEQ ID
(SEQ ID
(SEQ ID
(SEQ ID
Flash

Number of


NO: 5) 1
NO: 4) 1
NO: 6) 1
NO: 7) 1
Score 2
Phenotype
lines tested
















CC
AA
TT
GG
1.8
No flash
14


CC
AA
AA
CC
4.4
Flash
15


TT
GG
TT
GG
2.4
Partial resistance
1


TT
GG
AA
GG
2.6
Partial resistance
3


TT
GG
AA
CC
1.7
No Flash
30





The genotype represents the both the paternal and maternal allelic forms of the markers M0101742 (SEQ ID NO: 5 position 1206), M0129138 (SEQ ID NO: 4, position 218), M0093116 (SEQ ID NO: 6; position 183), and M0129925 (SEQ ID NO: 7, position 328).


Flash Rating Scale:


1: Green - No Yellowing


2: Mostly green, very slight yellowing <5% (1-2 plants with some yellowing)


3: 5-10% plants with yellowing


4: 11-20% plants with yellowing


5: 21-35% plants with yellowing


6: 36-50% plants with yellowing


7: 51-65% plants with yellowing


8: 66-80% plants with yellowing, some necrosis


9: 81-100% plants with yellowing and or necrosis






For optimal prediction of yellow flash phenotype, all four markers (M0101742, M0129138, M0093116, and M0129925) can be used. However, one can achieve high predictability with only two markers, M0101742 and M0129925. Based on fingerprint information, these two markers would identify two genotypes: CCAAAACC and CCAATTCC. CCAAAACC is the predicted genotype for plants which exhibit yellow flash (193/844 varieties screened based on fingerprint analysis). CCAATTCC is an additional genotype which only represented 9/844 varieties based on fingerprint data. All 9 varieties comprising the CCAATTCC genotype were Plant Introductions (PIs). As used herein in reference to soybean, Plant Introductions (PIs) refer to mostly typical germplasms that have not been subjects of breeding improvements. For example, PIs are include lines that have not been obtained by intercrossing followed by selection. PIs can also include lines obtained from seeds or vegetative propagules of plants that have been introduced from another country. Therefore, the two markers M0101742 and M0129925 could distinguish between the three most common genotypes observed: CCAAAACC (associated with a yellow flash phenotype), TTGGAACC (associated with a non-flash phenotype) and CCAATTGG (associated with a non-flash phenotype). More specifically, where M0101742 is CC and M0129925 is CC, one would predict that most soybean lines thus identified, and that were obtained from, or related to, the varieties analyzed in this Example, would have a Yellow Flash phenotype.
Example 4
Genotypes and Phenotypes of Various Commercial Varietie
In field tests conducted in 2006, a number of commercial varieties were genotyped with the markers M0101742 (SEQ ID NO: 5), M0129138 (SEQ ID NO: 4), M0093116 (SEQ ID NO: 6), and M0129925 (SEQ ID NO: 7) and exposed to glyphosate to test for the presence or absence of the yellow flash phenotype essentially as described in Example 1 (i.e. were sprayed with Roundup WeatherMax® at a rates of about 42 oz/acre on a weekly basis beginning at about the V3 to V4 stage for up to four weeks, thus in certain instances attaining a total rate of glyphosate exposure of a 4 week span of about 168 oz/acre). The results of this analysis is provided in Table 8.















TABLE 8






M0101742
M0129138
M0093116
M0129925






Branded
(SEQ ID
(SEQ ID
(SEQ ID
(SEQ ID

U.S.
Variety
ATCC Depository


Name 1
NO: 5) 1
NO: 4) 1
NO: 6) 1
NO: 7) 1
Phenotype
Pat. No.
Name in Patent
Accession Number 2







AG4201
CC
AA
AA
CC
Flash
7,071,388
SE71112
PTA-5728


AG4601
CC
AA
AA
CC
Flash
5,659,116
927113675
 97556


AG4603
CC
AA
AA
CC
Flash
7,067,723
SE73753
PTA-5730


AG4702
CC
AA
AA
CC
Flash
5,750,857
9390369478967
209547


AG4902
CC
AA
AA
CC
Flash
6,143,953
931474956907
PTA-2214


DKB31-51
CC
AA
AA
CC
Flash
6,346,658
950045734453
PTA-3871


DKB37-51
CC
AA
AA
CC
Flash
7,294,764
SD82997
PTA-5737


DKB38-52
CC
AA
AA
CC
Flash
6,660,912
SD92955
PTA-5382


DKB40-51
CC
AA
AA
CC
Flash
6,683,233
SD93038
PTA-5329


DKB46-51
CC
AA
AA
CC
Flash
6,933,423
SE73090
PTA-5733


AG0801
TT
GG
AA
CC
Non-Flash
6,005,170
9422009600716
PTA-269


AG0803
TT
GG
AA
C
Non-Flash
7,498,489
4498438
PTA-9064


AG0901
C
A
T
G
Non-Flash
6,080,917
942193611352
203207


AG2403
T
G
A
G
Non-Flash
6,900,372
SN71173
PTA-5727


AG2603
T
G
A
C
Non-Flash
7,388,131
4599695
PTA-9070


AG2703
T
G
A
C
Non-Flash
6,184,442
9323265446452
PTA-2577


AG3006
T
G
A
C
Non-Flash
7,482,516
0387907
PTA-9029


AG3302
T
G
A
C
Non-Flash
5,973,235
943470629664
203939


AG3505
T
G
A
C
Non-Flash
7,569,750
4559809
PTA-9023


AG3703
T
G
A
C
Non-Flash
6,881,879
SW90702
PTA-5738


AG3903
T
G
AA
CC
Non-Flash
6,632,982
SW84112
PTA-5299


AG4403
T
G
A
C
Non-Flash
6,348,644
9472569612611
PTA-3870


AG4503
T
G
A
C
Non-Flash
7,378,578
0358232
PTA-9003


AG4703
T
G
A
C
Non-Flash
7,554,014
437973
PTA-9066


DKB06-51
C
A
T
G
Non-Flash
6,143,953
931474956907
PTA-2214


DKB08-51
T
G
A
C
Non-Flash
7,504,565
4878185
PTA-9702


DKB22-52
T
G
A
C
Non-Flash
6,858,783
0491727
PTA-6187


DKB29-51
C
A
T
G
Non-Flash
6,884,927
0509249
PTA-6272


DKB42-51
T
G
A
C
Non-Flash
7,479,582
4671685
PTA-9027





1 The genotype represents the both the paternal and maternal allelic forms of the markers M0101742 (SEQ ID NO: 5 position 1206), M0129138 (SEQ ID NO: 4; position 218), M0093116 (SEQ ID NO: 6; position 183), and M0129925 (SEQ ID NO: 7; position 328)


2 Deposit numbers of seed available through the American Type Culture Collection (ATCC), 10801 University Blvd., Manassas, Va., USA, 20110-2209.






Example 5
Exemplary Marker Assays for Detecting Polymorphisms
In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means. Exemplary primers and probes for amplifying and detecting genomic regions associated with a no flash phenotype are given in Table 9.







TABLE 9







Exemplary Assays for Detecting Polymorphisms
















SEQ ID
SEQ ID




Marker or
Marker
SNP
Forward
Reverse
SEQ ID
SEQ ID


Locus Name
SEQ ID
Position
Primer
Primer
Probe 1
Probe 2
















M0129138
4
218
17
18
19
20


M0101742
5
1206
21
22
23
24


M0093116
6
183
25
26
27
28


M0129925
7
328
29
30
31
32









Example 6
Oligonucleotide Probes Useful for Detecting Polymorphisms by Single Base Extension Methods
Oligonucleotides can also be used to detect or type the polymorphisms disclosed herein by single base extension (SBE)-based SNP detection methods. Exemplary oligonucleotides for use in SBE-based SNP detection are provided in Table 10. SBE methods are based on extension of a nucleotide primer that is hybridized to sequences adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. It is also anticipated that the SBE method can use three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to the sequence of the locus which flanks a region containing the polymorphism to be assayed. Exemplary PCR primers that can be used to type polymorphisms disclosed in this invention are provided in Table 4 in the columns labeled “Forward Primer SEQ ID” and “Reverse Primer SEQ ID”. Following amplification of the region containing the polymorphism, the PCR product is hybridized with an extension primer which anneals to the amplified DNA adjacent to the polymorphism. DNA polymerase and two differentially labeled dideoxynucleoside triphosphates are then provided. If the polymorphism is present on the template, one of the labeled dideoxynucleoside triphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected. Exemplary forward and reverse SBE probes are provided in Table 10.







TABLE 10







Exemplary SBE Probes for Detecting Polymorphisms











Marker or
Marker


Probe


Locus
SEQ ID
SNP

(SEQ


Name
NO:
Position
Probe (SBE)
ID NO.)














M0129138
4
218
TGTGTCCTATATGATCTT
19


 


M0129138
4
218
TGTCCTGTATGATCTTA
20


 


M0101742
5
1206
TGACTAGCATGTATCTAT
23


 


M0101742
5
1206
ATGACTAACATGTATCTAT
24


 


M0093116
6
183
CCAACACCAAACTA
27


 


M0093116
6
183
CAACACCAAACAAA
28


 


M0129925
7
328
AGTAGTAGCTAGTGAAATA
31


 


M0129925
7
328
AGCTAGTCAAATATTT
32









Example 7
Summary Table of Nucleic Acid Sequences







TABLE 11







Nucleotide Sequences









Marker 
SEQ



or Locus
ID



Name
NO:
Sequence





M0205350
1
gggcttctccgctcgaacttatgcaagggctatgtgatggtgatgatgattgaatttgaagctgctactgca




ttactctctttggtaatgaatttgaagaagcagaaagaaaggaaatgatggtctttacaccgtcaattttaa




tatwtgtaagtgtaaactctgtagtagcacagtgatgtagtgtagattaggcatttggcagcgtggtaaata




ttcttagattgaattgtgttatcaacagtattaaacgttttaggctgaatgaatgatattgatgaatttata




aggtggggaggctaagatggaatcatgtagtta


 


M0114388
2
aattacacacatcatgatcttgtaatcatcatctcccaaatcagggatagccttggccttcttaccccaggg




attccataccactgcactctcattatcaccaaaccaataagtgacatcaattgtagattaaattaacaaact




tatgtaaatctgaatgctggatctggcccttataaagtgaaaaacacgttgtagagactaaagtaagtaatc




cccttgtttttgatgaggaaatgaacagttgatattatgtgcacttgtataacaaaacatggatattttaaa




atatcagtcgttgattttctcatcaataaattaggattgttttactctctaaagtgacttgttcagattaga




agagccaaatagatacaatgccatgcaaaatttttattactgactaataactaataacaacctgcatctggc




attcctttcttctggagtacaaaagttctttttttctcatggtctatgatggcaattttagttgggctrtgc




aagtacactctgtccatctacaaggtaaccacaaatgtccttagagaacacttgaaaaaaaagttgatttgg




tatctattatatatattcatacactcgaaaatcaatcagaatatatataggttatgtgcacttatgtgctta




tgatgtcaattttcttagcctgtgagacacctccaaccaattgaatgaaaggaccagaaaatcaaattatac




ctctccatcaaaagtgagtgcatctgcctgctctgtgaaccttgatctgttcaacagattgtcaaagtaatc




cagtgtctccaatccctcaatacgcacttc


 


M0205928
3
attcctatttcctacacaacactacactgtctggtggaagaatctcttcactctccatgcaacaacgttggc




tatgtctccttattctctctctttgttagcctctgtctcccccaaaatgcacacccttctttctttctcctc




atcacactctccacatcttccaaaccacaacataaccaaatccaataataaactctctcattccatcaatgg




actttcatcmtgcccttcttctcctttgctccccagtgccacaaaatcttctccctttctcatttccacttc




aaaaattgcatctttcagggtccttgctgcttcctctatacctgatgctagaagtgatgaaccagccaaaac




tagtgatttcttaaaaactcttcag


 


M0129138
4
cgccagcttgcatgcctgcagttccaagaattatttcaaaccgctgcttccattttagaatccttgttatgt




ccttttctgcacagtagattagtatgtcacaagttgcatgttgggccggttgattttatgaaattaataaga




gttaaatatgtttttagtccttgcaaataggaaaaagttctccttttggtcctcaattatgaaaatgtgtcc




trtatgatcttatttacataaatgaggaaatgaaagcagatgatacttttatgaaggacaaagattacattt




gacacattttcataaatgagtgactaaaaagaagcattttattttttagtgattaaattaattggaaacatt




acaagattacttttggtcatgggttcaagaatccggaaacagtttctttgcatatgcaagggtaatgctgct




tacaatatccctcccccataccttggcatagtgaggagcctccgggcaatggaatacactagtttttatagt




acaatatttttcatttagagttactgtgggacaaaaggaacttaccaaaaatgaattgatctaagctcttgt




taggtaggtactcatacacaatgaggctctcagggccttcaatgctgcaacccaatagtttgacaaggttct




tgtgttgcattccactaatcaaattcacttcattgaagaaatcatccacccattgcctattattgaagacca




atctcttaacagcaacatcattcccatttggcagagtccctttgtatacagaaccagatcctccttgaccta




tctttcttgaagagctgaaataatccgtcgccttctctagagtttcatatttgtaattcaagctagaattct




tcaaggaaggaggaacctcaataaaattgttttctgagtgattcaggagaaaatgaaatacagcatcagcaa




aattaacaaacaatcattccaaatatatattattggtatgaacaagagtgttctccagaacattacttcttc




tctttttggtgaaggccacataagagactgcaagagtgagaactacaac


 


M0101742
5
acacagaaatcacaaacaagtggtgactacttacccatattcaccaaagaaatggaaaaacttctagaactt




gtgacaaaacaaaactgggggactcactctgagggcatgtcatcaacaacaaccactcctatctatggcttg




gcacaatgcttccaagacctttccagcattgattgccttcaatgctttgcagccagccgcaccaagctccct




cgctgcctcccttcggtttcggctcgaatttaccttgatggctgcttccttcgctatgacaattacagtttc




tacactgaaaactatgaccctttgagggacacagtgaattgcacctcagagtatggttctgtggttggtgat




ggtgagaagttggtgtttgctgagagtgttggcaaagtggttgagagtgtggtgagggtggctgtgaataat




aatgagggaagaggcttttttgcagttggagaaggtgggggagtttatgcattggcacagtgctggaaaact




gttggggtaaaagggtgtagtgattgcttgaggaaagctgaaaatgaggtcaaaggatgtttgcctaagagg




gaagggagggccttgaatactgggtgctatttgagatactcaactgttaagttctacaatcaaggaggtcaa




gatggtcaaggagatggtaagagctgttgctctagtttgaagtttttatattcttcattagtttcttggttc




cttttggataaacttctcaaccactagttataggagaaaaaaatgaattaaacatctcttgtaagttaaaat




caatttgtgcacttcgataagttttataaaaactctctcgtttaacttttccaaaagctgagatgtataagt




taattttaacttacagaagaagtttgattcatttttgctttttatgttcttctcctttaagtatttattgag




aagcttatcggttggaatttggaaactgaagctcaactgggaatttcaattgcatattgttaccatgcagtt




tcaaattccttgtgttgcttataggttaaatgacaaatggagaaggaaagaagtaaagatgaatgttactgt




atcattgtgaatgaaatgctgcttttcaactttaactttgctataactcttaggttagttttggtgtctaaa




agtttgtcctgaatgaatcctaggtttcagttcatagatggcatagatacatgytagtcatttattttgtat




acatgttgatgcaattgtccatgttttaatttttcagattcttccagaaaacgagtcattatagcagcaggg




tcagtctt


 


M0093116
6
attatatgagggctcttgggtttttcaaggacactgatgcacccttacctgtaagaatatgattttgttatt




attattattatatttattgtgagtctatatatataagaagaattttccattttgtttcatctaattaatata




gttttaataatttttaaattttgctttgtttaatgcttwgtttggtgttggaaattaagattgttccagggt




ttgatgctgctggtgtggtggtgagagtgggaagtaaagtgagcaaattcaaggttggagatgaagtttatg




gtgatatcattgagtatgcttggaataatccaaagaccattgggactttggcagaatatactgctactgagg




agaaagtgttggctcacaaaccctccaatttaagctttattgaagcagctagcctt


 


M0129925
7
aggcaccaaaccaagggatttaaaatttattaaattataaacatgaaatgattaaataaagagttgaattcc




cataattttatacgttttattaaatttcactcagcaaaaaatgtattaaaaaatatattattcccatttgtc




tgtctttatttatgtcatctattttaatttttctgatgtatttaactggggccaaactgaaacatgttgatc




atgcaaaggcctactcaccatttcacatgtacgtgtcatcacccagcaaccccatttttctacataacacac




actccctctctaacactcacactccaataacaaatatttsactagctactactcttcttagtttctctgttg




tatcatttttattgctatatcctaatcaaacttcactctcaaaatgagtgatcccacactagcacaacagca




tctagtcaaagtccacacaacaacacacgaaacagttgttaccacacacaatcataaccaaacaccctcaat




aaatgtgtgttactgaattatttaattatttgtacacctaactatgattaatatttaattatcaaaactttg




tttatgcatgataaccgtgattaatttttatttttttcccctatgattgagaacaggcctcaggtgaaaaga




agaagattgtgggggtgttctacaaagggaatgaatatgctaaattgaatccaaattttgttggatgtgttg




aaggtgcattgggaatacgtgagtggctggaatcacagggtcatcagtacattgtcactgatgacaaagaag




gacctgattctggttagtacttagtatcttgccaacttaattcaagtttgagtaaactattattttgatgat




ttgatctataaaagtgtacaacattgtgaaattagtctctaacattgtcacattagtctctgaaattaagat




aatttcatatgacaaatgacatgttattaactctttttcgtactgtaaattgaaaaatgtggctacgtgtta




tatgaaaattggttgggacctggtctcggatcatgtaataatttctatcaaacaaggtatcagagtaatcaa




cactataatatcatggaatgcaaatgtgtttgtcccttcaagattttaattgcttgaactcaatggaatttg




atgttct


 


M0205537
8
aggaaatactagattttgatatactattatttaataattttcctactcgactaaaatgaaaaaaaaaacact




aaaataatgatatcactaatattattagctgaattttttttgtttgttgaatctttagttgactgaatttag




tatttgactaaaamaagaatcatatcacaaactaatttgcctgtaactcattgctttaatttgcttttaata




attgtcagcaagtctagatttttaatgattagatagatagctaacaaaaataccacactggatacatatgaa




atcaatattaagtttaaagagatgcaatacgcaatcgatttgattaatgaatttcaaatgttctgcgttaat




ttattcaattaccttttaaattgaatgttttcattcctgggctctg


 


M0202715
9
atgatgggatcttgcatatgcccgttggagactccggcgaggttgctttggaccacaagcttcttccgtcat




aagcttatgatcttctaataattaataattcacgcacacaaacaaacaaacaaacaaacaaaaaacacttca




taacaacaacaacaacccttctgaaattctcaacacaagtttcaaaaaacagagtaaaagaaacagagcaaa




aacacacacacaaaaacacaaacacagacaccttttaagtattaaggtgtctctttctctcsccggaaagtt




tctccgtcggcggtggtgattgaccggagtgccatggagtctggacggattttctttggtgcctctgcttca




agcggcaacaacatgctctttctcggcacaactgaact


 


M0206286
10
tagtaaagccaccaactccaacaccaacttccccagtggtgtaccctcctcctnnntttccatctccaccag




ctcctgtagtgaaatcaaacaagggtaagtgtgtaccacatctatstctttagtaactcctttccgatctct




aatgtaattaaatgaaatgattctgtcacatttttctgctaatttaacttttacgttatttagaaaaaaaat




ataaaagaaatttgtatcactttttctttaaaaataggaaaaatatgtgtgataaaatagataatgttttac




aatttcattacagaaatactttatattttataatgttaatattttttatttttcacaatttttttcttcttt




cttattagtttttggacttaaattaaataatatttttaatcctgtcatgtgggttttagtattcttaatatt




attttcttgatttgattactgtaaaatgttttagtaaggcttaactaaaacagacaaagaaaaatatttcaa




gaagattaaaatggaaaaaaagaatcttataatacatggattaaaaaattagtgaagccttacttttgtttt




tcttttctctttgttacacgtcttcaccttgttgtctttgttatcctttttcacatctaatgatggatgtga




gagaagaaccatgcatggtcttaattgtttatgtgattaatggctttaaagtatagaacttttaagtaagat




cagttgagttaattaatgaaacatggtcttttgttttccaaatttttttgtgggcagattgcattccactaa




gggattataggtgctcattacactcaaggaagaaattgt


 


M0206054
11
atcttggttttccaatcgcgcagcccgagcggccatcwgaacaacagtatctacgtcaactcctttagcaaa




aatctacagaaaacattgaaaacacttgtgtgagcatacgacaaggcaaataagaaaacaacacagtacaaa




actgactacttctaacctcaataagattcttgtcaactgtcagtttattcaaagtcaaagttccagttttgt




cgctacataatacatccattcctgccatctcttctattgctgtcattcttttagtaatagcaccctgcaatg




attatataaagcataaactataaagactaacatctaattgattaaaacttgagacaactgcnttcaagaagc




actaatgtctacctgctgagctaagcgatgggatccaattgccattgtcactgacaaaacagtaggcatggc




aataggaattcctccgataagaagcacgagcagattgtcaatcccaggacgatattcccggtgttgaattgg




gtacatgacaatgat


 


M0205375
12
ctttgattcttgccagtctttttcattctttttcattcttaaatccatcaaatgaacctattgatatgactg




aaacctttggattagccaagactaaagctactccacttgagattttaattaagccacgattatcttctagtt




gttatytataaaagcatgtgaatcttgtcttagcggtttgtggaaagtctgttgttaaactatgtgatcttc




ttttagataaatcaggtttgcctgataaattatattttcgtcaaaagggcatttttggaattcacaaaattg




tcatcatgtggtgttgaaataaggtgtgttgtaataaggtttaaggctt


 


BG406195
13
tattgtcttttgtgaatgatcaataacttcctaatggtaattcctttcattagagagcccatggatttatat




tcccatggtttggaaaaaagttcttcaagcagtgtaagtaacaccaatggttttactgaaaatctggtattc




ggtgacgcttattaacatcaatttgaccaatggttttactatggacgcttattaacatcagttaacggtatg




aagcttgggaaagctgttggaaaatggggtctttgagatgcttgatgcaagtttgccatcatgacttccatt




tcacacttagacattgagtggtgaacgtccatagtatttgatataaatg


 


BU082700
14
gcaccagtccacacaaagaagattgtccacagagatgttaaaacagaaaatatgcttctggacaagacacga




accttgaaaatagctgattttggagtagctcgtattgaggcctccaatcctcatgacatgacaggtgaaact




ggaacccttggttacatggctcctgaggtacatgcttcaattcctttgaaaatttctctctcctgtgcattg




ttcttttggggtttgtttcaaacacccttaatgtctagtccttacctcagaaaattttgaaaatgctggctt




aggacttgttacttgcgaccggctctgttgtctaactaattgtgaaagaactgggttgaatatttttggact




taaaatataaggaaaaattactaaacaggaattcttgattaaaatattaaccatgttggaaagataaggaca




ttgaattgttccatcactgtccttactttcatcaggaattccttttgttttatagttcacccaacaattatg




tatatatccatgttggttttggtacataattacaggaagaaatctttacctcagtcccatttacaattactg




agatctagaactgcagcatgtcactactcactaatcttga


 


TA14086
15
atggcaagcatttctagcattccatcacacataaaaacttgggtttattctgaatatgggaacacagaagag


34305
 
attctaaaatttgatcccaacgtacctataccagacatcaaggaagaccaggtgctcatcaaggttgtggct




acagctcttaatcctgtggattataagagggctcttggctatttcaagaacactgactctcccttacctgta




agatcatgattttaaatttatatttgcgtggattattaattagtatagtttccattttgtataccaccttat




ataattcttttttgtttaaatatatttttagtttttataatttatatttttttgttttttgttattgtaaaa




ttatttttttgtttttgtttttataaattatgtttgttttatttttctttcctaaattattttagataatgt




tttgaatagtaaaaaaatattataacaataaaaaataaaataaacataatttgtaagaatcaaaaataaaaa




ataatttgtaagtaaaaaaataaaaaataaataaattataaggattaaaattgtatttaagccatttttttt




tatcattgcattgtttaatttgtgtttggtttttgaaattaagagtgttccggggtacgatgttgctggtgt




ggtggtaagagtgggaagtaaagtgaggaaattcaaggttggggatgaggtttatggtgatatcaatgagta




tgctgtgaataatccaaagaccattgggactttggcagagtacactgctactgaagagaaattgttggctca




caaaccctccaatttgagctttattgaagctgctagccttcctttagctatcatcactgcttatcaaggact




tgaaagagttgatttttctgctggaaaatctatacttgttctaggaggtgctggtggagttggatcccttgt




tattcaggtttgatatcttccatctccattggttaatttgacaataagtttcaattaaacagtgtcttactg




aaatattgagccattaatttcactttttcagtattttagttatttattttattcttcttctctaatcatatg




atttaggagcaatgatatttagatatctctctaaatttcagacacctcatatcatatcatttatcatttatt




tatattttctctttcctctctatctctcttagcataattatataattaataatgaattgttgggtatttgat




tgatatgatgtagctcgccaagcacgtttttggcgcatccaaggttgcagctactgctagttccgcaaaact




ggatttattaaggaacttgggagcagactttcctattgattacacaaaggagaattttgaagagcttgcaga




gaagtttgatgtagtgtacgatacaataggtcagatgttgaaattgaacttaaattatttgtttcacatgaa




gtcagtttggtcatgactaatacaatattaacatatgagatgtggtatgagtacaacaattggtacagaact




attagtttttatacctatcttacttatttatgacatgtaataaataatgtacaccagagatattaacacaaa




agaatgttgttatacaattaatttaaagtgcattaacatgtaacatacaacttattacttttgttatcttat




tattgattaccatgtgtaataagattgttgataataataaattactttaagaattgttatctatttttttta




ttagtggatagtataaaagtattttcatgtgtatcaatattattattgaaaatgaagacatggttgattcca




aaaacagggcagagtgacaaggcattgaaggctatcaaagaaggggggaaagttgtgacaatagcaccacca




gcaactccacctgctatcccattctttctcacttcagatggtgctgtgttggagaagttacaacctcactta




gaaagtgggaaggtgaagccagtattggatcctaagagtccctttccattttctcagattgtggaagcatat




tcatacttgaagacaaatagagccattgggaaagtagtcatacatcccatcccttgaacatatataactatg




caaatatactatcaagtcctgctgtgcattctgaccttaatttgtgttaataaggttaatatttatatgatt




gataaggagagagc


 


BU551345
16
tttagtcattagaattttacttgtttactcggttcgaaagttccatctcgctggtctcaattactattaaaa




aatctcatattgcttacctcaattagtgggatgaggtttaagtacgtgatgaacaacttcacttnntgctaa




ttagtttgaagttataatgtaacatgctctatccttctttttggttggttgcttggggggagctcccnnnna




catggaattattgggaatcaagcttccataattgtttcttcacttcttgatggcctaattaagctgcatgtg




ctagagaactcagaggggctgtaggacacaccaatcttcttaaatgtgtttgatgaggagctgtctatgcta




aaacctaatggagatgtttgatct









Polymorphic nucleotide bases are designated in Table 11 and in the sequence listing provided herewith according to the WIPO Standard ST.25 (1998), Table 1, as follows: r=g or a (purine); y=t/u or c (pyrimidine); m=a or c; (amino); k=g or t/u (keto); s=g or c (strong interactions 3 H-bonds); w=a or t/u (weak interactions 2H-bonds); b=g or c or t/u (not a); d=a or g or t/u (not c); h=a or c or t/u (not g); v=a or g or c (not t, not u); and n=a or g or c or t/u (unknown, or other; any.)
Having illustrated and described the principles of the present invention, it should be apparent to persons skilled in the art that the invention can be modified in arrangement and detail without departing from such principles.
Although the materials and methods of this invention have been described in terms of various embodiments and illustrative examples, it will be apparent to those of skill in the art that variations can be applied to the materials and methods described herein without departing from the concept, spirit and scope of the invention. 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.










Table 2 of the Specification











Locus/Display

Start
End
ADDITTIONAL LOCUS


Name (1)
Source (2)
Base (3)
Base (4)
INFORMATION (5)














asmbl_11856
Vigna_unguiculata
16426
16586
NA


TA2790_3886
Phaseolus_coccineus_release_2
16423
17393
ADP-ribosylation factor [Vigna






unguiculata (Cowpea)]


TA43459_3847
Glycine_max_release_2
16434
18055
ADP-ribosylation factor 1






[Oryza sativa (Rice)]


TC276541
GMGI.071508
16434
18076
UniRef100_P36397 Cluster:






ADP-ribosylation factor 1; n = 1;






Arabidopsis thaliana|Rep: ADP-






ribosylation factor 1 -






Arabidopsis thaliana (Mouse-






ear cress) = partial (38%)


CD392203
Glycine_max_release_2
16216
18687
ADP-ribosylation factor






[Glycine max (Soybean)]


BQ610865
Glycine_max_release_2
16327
18667
ADP-ribosylation factor 1






[Oryza sativa (Rice)]


EH046324
Arachis_stenosperma_release_5
16405
18745
Cluster: ADP-ribosylation






factor 1, n = 1, Arabidopsis






thaliana|Rep: ADP-ribosylation






factor 1 - Arabidopsis thaliana






(Mouse-ear cress)


AW202311
Glycine_max_release_2
16378
19070
ADP-ribosylation factor






[Glycine max (Soybean)]


TC242702
GMGI.071508
16234
20195
UniRef100_Q38JU3 Cluster:






ADP ribosylation factor 002;






n = 2; core eudicotyledons|Rep:






ADP ribosylation factor 002 -






Daucus carota (Carrot) =






complete


BI321678
Glycine_max_release_2
17384
19066
ADP-ribosylation factor [Zea






mays (Maize)]


AW348317
Glycine_max_release_2
16355
20097
ADP-ribosylation factor






[Glycine max (Soybean)]


EH042959
Arachis_stenosperma_release_5
16401
20182
Cluster: ADP-ribosylation






factor 1, n = 2, Medicago|Rep:






ADP-ribosylation factor 1 -






Medicago truncatula (Barrel






medic)


TC20337
LJGI.070108
16420
20191
UniRef100_Q5QQ33 Cluster:






ADP-ribosylation factor 1, n = 2,






Medicago|Rep: ADP-






ribosylation factor 1 -






Medicago truncatula (Barrel






medic), complete


EH047563
Arachis_stenosperma_release_5
16430
20182
Cluster: ADP-ribosylation






factor 1, n = 2, Medicago|Rep:






ADP-ribosylation factor 1 -






Medicago truncatula (Barrel






medic)


TA2789_3886
Phaseolus_coccineus_release_2
16436
20196
ADP-ribosylation factor 1-like






protein [Solanum tuberosum






(Potato)]


TA43462_3847
Glycine_max_release_2
16229
20438
ADP-ribosylation factor






[Medicago sativa (Alfalfa)]


TA1120_34305
Lotus_japonicus_release_1
16522
20191
ADP-ribosylation factor






[Medicago sativa (Alfalfa)]


TA2306_3848
Glycine_soja_release_2
16442
20440
ADP-ribosylation factor






[Medicago sativa (Alfalfa)]


TC273941
GMGI.071508
16426
20464
homologue to






UniRef100_Q38JU3 Cluster:






ADP ribosylation factor 002;






n = 2; core eudicotyledons|Rep:






ADP ribosylation factor 002 -






Daucus carota (Carrot) =






complete


TC238119
GMGI.071508
16455
20449
UniRef100_Q38JU3 Cluster:






ADP ribosylation factor 002;






n = 2; core eudicotyledons|Rep:






ADP ribosylation factor 002 -






Daucus carota (Carrot) =






complete


EG373880
Arachis_hypogaea_release_5
17101
20182
Cluster: ADP-ribosylation






factor 1, n = 2, Medicago|Rep:






ADP-ribosylation factor 1 -






Medicago truncatula (Barrel






medic)


BF066818
Glycine_max_release_2
17081
20378
ADP-ribosylation factor 1






[Populus tomentosa]


BF596154
Glycine_max_release_2
17083
20397
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


AW760997
Glycine_max_release_2
17116
20397
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


BF424079
Glycine_max_release_2
17112
20417
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


AW596022
Glycine_max_release_2
17121
20415
ADP-ribosylation factor 1






[Populus tomentosa]


TA43446_3847
Glycine_max_release_2
17106
20436
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


TA43455_3847
Glycine_max_release_2
17125
20452
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


BW595867
Lotus_japonicus_release_1
17418
20191
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


AW507598
Glycine_max_release_2
17343
20437
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


TA43447_3847
Glycine_max_release_2
17343
20445
ADP-ribosylation factor






[Hyacinthus orientalis






(Common hyacinth)]


TA43448_3847
Glycine_max_release_2
17355
20438
ADP-ribosylation factor 1






[Populus tomentosa]


AW596189
Glycine_max_release_2
17358
20442
ADP-ribosylation factor 1






[Populus tomentosa]


BI469983
Glycine_max_release_2
17410
20438
ADP-ribosylation factor 1






[Populus tomentosa]


AW472058
Glycine_max_release_2
18655
20160
ADP-ribosylation factor 1






[Daucus carota (Carrot)]


CB063805
Glycine_max_release_2
18623
20432
ADP-ribosylation factor 1






[Populus tomentosa]


BM891090
GMGI.071508
18995
20429
homologue to






UniRef100_A7PRL9 Cluster:






Chromosome chr14






scaffold_27 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_27 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(42%)


BM731935
Glycine_max_release_2
19949
20444
ADP-ribosylation factor 1






[Populus tomentosa]


AW695591
MTGI.071708
30054
31388
similar to UniRef100_Q40542






Cluster: NPK2, n = 1, Nicotiana






tabacum|Rep: NPK2 -






Nicotiana tabacum (Common






tobacco), partial (35%)


TC130040
MTGI.071708
30054
31482
similar to UniRef100_A7PM42






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(30%)


TC122822
MTGI.071708
30054
34162
Protein kinase, Nuclear






transport factor 2


Pvcon9203
Phaseolus_vulgaris
31194
34247
UniRef100_A7PM42






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM42_VITVI E−0


TA66103_3847
Glycine_max_release_2
31879
34559
Protein kinase; Nuclear






transport factor 2 [Medicago






truncatula (Barrel medic)]


CA801261
GMGI.071508
33896
34304
similar to UniRef100_Q40542






Cluster: NPK2; n = 1; Nicotiana






tabacum|Rep: NPK2 -






Nicotiana tabacum (Common






tobacco) = partial (16%)


TC120073
MTGI.071708
35367
38178
Glycoside hydrolase, family 28


NP004759
GMGI.071508
34976
39622
GB|AF128266.1|AAD46483.1






polygalacturonase PG1


AF128266
Glycine_max_release_2
34980
39622
Polygalacturonase PG1






[Glycine max (Soybean)]


TA69799_3847
Glycine_max_release_2
58988
65870
Ubiquitin-associated [Medicago






truncatula (Barrel medic)]


TA7619_47247
Lotus_corniculatus_release_1
63855
65940
Putative DNA cytosine






methyltransferase Zmet3






related cluster


TA8711_34305
Lotus_japonicus_release_1
63855
65940
UBA-like [Medicago truncatula






(Barrel medic)]


TC34762
LJGI.070108
65619
65940
NA


Pvcon5587
Phaseolus_vulgaris
65216
67090
UniRef100_A7PM76






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM76_VITVI E−0


TA5046_3885
Phaseolus_vulgaris_release_2
65808
67002
UBA-like [Medicago truncatula






(Barrel medic)]


asmbl_11857
Vigna_unguiculata
65951
67042
NA


TA58707_3847
Glycine_max_release_2
66006
67253
UBA-like [Medicago truncatula






(Barrel medic)]


TC241193
GMGI.071508
66006
67253
similar to UniRef100_A7PM76






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(38%)


BI967232
Glycine_max_release_2
66170
67203
UBA-like [Medicago truncatula






(Barrel medic)]


AV417590
LJGI.070108
66745
67090
similar to UniRef100_A7PM76






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(19%)


AV768315
Lotus_japonicus_release_1
66699
67155
UBA-like [Medicago truncatula






(Barrel medic)]


TC32114
LJGI.070108
66699
67275
similar to UniRef100_Q76KU6






Cluster: DNA






methyltransferase, n = 1,






Nicotiana tabacum|Rep: DNA






methyltransferase - Nicotiana






tabacum (Common tobacco),






partial (20%)


TA1535_34305
Lotus_japonicus_release_1
66745
67277
UBA-like [Medicago truncatula






(Barrel medic)]


TA2793_47247
Lotus_corniculatus_release_1
66745
67277
DNA methyltransferase related






cluster


AV768911
Lotus_japonicus_release_1
66943
67155
Ubiquitin-associated [Medicago






truncatula (Barrel medic)]


CB540531
Phaseolus_vulgaris
73267
73561
UniRef100_A7PM74






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM74_VITVI






5.00E−27


BE347690
GMGI.071508
73509
73770
similar to






UniRef100_Q5VQL1-2






Cluster: Isoform 2 of Q5VQL1;






n = 1; Oryza sativa Japonica






Group|Rep: Isoform 2 of






Q5VQL1 - Oryza sativa subsp.






japonica (Rice) = partial (5%)


BE347690
Glycine_max_release_2
73509
73822
WW/Rsp5/WWP; Helicase = C-






terminal [Medicago truncatula






(Barrel medic)]


BE608496
GMGI.071508
73444
73947
similar to UniRef100_A7PM74






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(16%)


AI416763
GMGI.071508
74073
74520
similar to UniRef100_Q9SP26






Cluster: P72 DEAD box






protein; n = 1; Pisum






sativum|Rep: P72 DEAD box






protein - Pisum sativum






(Garden pea) = partial (16%)


AI416763
Glycine_max_release_2
74073
74743
ATP-dependent RNA helicase-






like protein DB10 [Nicotiana






sylvestris (Wood tobacco)]


BW615083
LJGI.070108
74256
74855
similar to UniRef100_A7PM74






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(24%)


TA8332_34305
Lotus_japonicus_release_1
74256
75446
WW/Rsp5/WWP, Helicase, C-






terminal [Medicago truncatula






(Barrel medic)]


TC27807
LJGI.070108
74343
75446
similar to UniRef100_Q9SP26






Cluster: P72 DEAD box






protein, n = 1, Pisum






sativum|Rep: P72 DEAD box






protein - Pisum sativum






(Garden pea), partial (34%)


asmbl_11858
Vigna_unguiculata
75228
75500
NA


TA60825_3847
Glycine_max_release_2
74963
75981
P72 DEAD box protein [Pisum






sativum (Garden pea)]


TC249436
GMGI.071508
74985
75966
similar to UniRef100_Q9SP26






Cluster: P72 DEAD box






protein; n = 1; Pisum






sativum|Rep: P72 DEAD box






protein - Pisum sativum






(Garden pea) = partial (12%)


TC269249
GMGI.071508
86882
87576
similar to UniRef100_A7PM72






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(42%)


TA64136_3847
Glycine_max_release_2
86882
89066
Putative






phosphate/phosphoenolpyruvate






translocator [Arabidopsis






thaliana (Mouse-ear cress)]


CO982132
Glycine_max_release_2
87225
91497
Phosphate/phosphoenolpyruvate






translocator [Nicotiana






tabacum (Common tobacco)]


TC274531
GMGI.071508
87225
91497
similar to UniRef100_A4UTS3






Cluster: Chloroplast






phosphoenolpyruvate/phosphate






translocator; n = 1; Pisum






sativum|Rep: Chloroplast






phosphoenolpyruvate/phosphate






translocator - Pisum sativum






(Garden pea) = partial (53%)


Pvcon2802
Phaseolus_vulgaris
87119
92616
UniRef100_A9PD12 Putative






uncharacterized protein n = 1






Tax = Populus trichocarpa






RepID = A9PD12_POPTR






1.00E−121


TA4406_3885
Phaseolus_vulgaris_release_2
89055
92616
Phosphate/phosphoenolpyruvate






translocator [Nicotiana






tabacum (Common tobacco)]


TA74766_3847
Glycine_max_release_2
91397
92725
Phosphoenolpyruvate/phosphate






translocator






[Mesembryanthemum






crystallinum (Common ice






plant)]


TC265023
GMGI.071508
91686
92725
similar to UniRef100_A7PM71






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(15%)


M0205928
SEQ. LISTING
92718
92334
SEQ ID NO: 3


BG406195
GMGI.071508
107039
107366
(SEQ ID NO: 13)


BG406195
Glycine_max_release_2
107039
107375
NA


M0101742
SEQ. LISTING
112189
113483
SEQ ID NO: 5


BG550728
GMGI.071508
112663
113757
weakly similar to






UniRef100_A7PM60 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(13%)


BG550728
Glycine_max_release_2
112663
113867
Receptor-like serine/threonine






kinase [Arabidopsis thaliana






(Mouse-ear cress)]


CV535605
Phaseolus_vulgaris
112548
113982
UniRef100_A7PM60






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM60_VITVI






9.00E−79


M0129138
SEQ. LISTING
114532
113494
SEQ ID NO: 4


BU551345
Glycine_max_release_2
115956
116339
(SEQ ID NO: 16)


TA58315_3847
Glycine_max_release_2
118318
120087
NA


TC236438
GMGI.071508
118318
120087
NA


BE611751
Glycine_max_release_2
119165
119645
NA


BE611751
GMGI.071508
119229
119645
NA


TA70371_3847
Glycine_max_release_2
137417
137864
Hypothetical protein [Medicago






truncatula (Barrel medic)]


TC267549
GMGI.071508
137417
137864
similar to UniRef100_Q9FI64






Cluster: Genomic DNA =






chromosome 5 = TAC






clone: K21I16; n = 1;






Arabidopsis thaliana|Rep:






Genomic DNA = chromosome






5 = TAC clone: K21I16 -






Arabidopsis thaliana (Mouse-






ear cress) = partial (43%)


BG156330
GMGI.071508
155872
156903
similar to UniRef100_A7PM41






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 2; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(23%)


BG156330
Glycine_max_release_2
155872
157058
WD40-like [Medicago






truncatula (Barrel medic)]


Pvcon10326
Phaseolus_vulgaris
155691
157835
UniRef100_A7PM41






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM41_VITVI






3.00E−93


CD397113
Glycine_max_release_2
157474
157813
NA


TA12653_34305
Lotus_japonicus_release_1
159489
161341
NADP-specific isocitrate






dehydrogenase [Lupinus albus






(White lupin)]


TC27381
LJGI.070108
159489
161341
similar to UniRef100_Q7Y0W7






Cluster: NADP-specific






isocitrate dehydrogenase, n = 1,






Lupinus albus|Rep: NADP-






specific isocitrate






dehydrogenase - Lupinus albus






(White lupin), partial (25%)


DT084057
Glycine_soja_release_2
161638
162192
NADP-specific isocitrate






dehydrogenase [Lupinus albus






(White lupin)]


BE661051
Glycine_max_release_2
170271
172034
Cyclin-like F-box [Medicago






truncatula (Barrel medic)]


TA11305_34305
Lotus_japonicus_release_1
170700
172307
Cyclin-like F-box [Medicago






truncatula (Barrel medic)]


TC34049
LJGI.070108
170700
172307
similar to UniRef100_A7PF14






Cluster: Chromosome chr11






scaffold_13, whole genome






shotgun sequence, n = 1,Vitis






vinifera|Rep: Chromosome






chr11 scaffold_13, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(32%)


NP7256876
MTGI.071708
171929
173188
GB|AC157983.16|ABE86510.1






Cyclin-like F-box


TA68495_3847
Glycine_max_release_2
194920
195696
Oleosin [Sesamum indicum






(Oriental sesame) (Gingelly)]


TC265354
GMGI.071508
194920
195696
weakly similar to






UniRef100_P29530 Cluster:






P24 oleosin isoform A; n = 1;






Glycine max|Rep: P24 oleosin






isoform A - Glycine max






(Soybean) = partial (40%)


BE658264
Glycine_max_release_2
195176
195925
Oleosin [Sesamum indicum






(Oriental sesame) (Gingelly)]


CV539661
Phaseolus_vulgaris
217885
218101
No significant hit (e−20)


CA912681
Phaseolus_coccineus_release_2
220374
220748
Arabidopsis thaliana genomic






DNA, chromosome 3, P1 clone:






MGF10 [Arabidopsis thaliana






(Mouse-ear cress)]


CA785107
Glycine_soja_release_2
221393
221885
NA


TC276537
GMGI.071508
221407
222104
weakly similar to






UniRef100_Q4RYK7 Cluster:






Chromosome 3 SCAF14975 =






whole genome shotgun






sequence; n = 1; Tetraodon






nigroviridis|Rep: Chromosome






3 SCAF14975 = whole genome






shotgun sequence - Tetraodon






nigroviridis (Green puffer) =






partial (21%)


TA71044_3847
Glycine_max_release_2
221407
222133
NA


CD406643
Glycine_max_release_2
222113
222297
NA


AV416316
LJGI.070108
223773
223869
similar to UniRef100_A7PM35






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(9%)


EC911350
Phaseolus_vulgaris
224587
225958
UniRef100_A5C233 Putative






uncharacterized protein n = 1






Tax = Vitis vinifera






RepID = A5C233_VITVI 3.00E−77


BU760697
GMGI.071508
224857
225965
similar to UniRef100_A7PM35






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(22%)


BU760697
Glycine_max_release_2
224857
226145
Protein At5g19130






[Arabidopsis thaliana (Mouse-






ear cress)]


TC119982
MTGI.071708
224248
226812
Gaa1-like, GPI transamidase






component


CV541515
Phaseolus_vulgaris
225934
226374
UniRef100_A7PM35






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM35_VITVI






2.00E−34


TA76349_3847
Glycine_max_release_2
226118
226768
Protein At5g19130






[Arabidopsis thaliana (Mouse-






ear cress)]


TA12045_47247
Lotus_corniculatus_release_1
226354
226789
GPAA1-like protein related






cluster


TA13675_34305
Lotus_japonicus_release_1
226354
226789
Protein At5g19130






[Arabidopsis thaliana (Mouse-






ear cress)]


TC29330
LJGI.070108
226354
226789
similar to UniRef100_A7PM35






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(13%)


NP7254537
MTGI.071708
233411
237212
GB|AC152349.11|ABP03404.1






Protein of unknown function






DUF266, plant


EH256962
GMGI.071508
235306
237649
similar to UniRef100_A7PM54






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(33%)


CX708677
Glycine_max_release_2
247269
248145
NA


BW599077
LJGI.070108
255475
261945
similar to UniRef100_A7QD90






Cluster: Peptidyl-prolyl cis-






trans isomerase, n = 1, Vitis






vinifera|Rep: Peptidyl-prolyl






cis-trans isomerase - Vitis






vinifera (Grape), partial (18%)


BW625918
LJGI.070108
257810
262980
similar to UniRef100_Q93YQ8






Cluster: Peptidyl-prolyl cis-






trans isomerase, n = 1,






Arabidopsis thaliana|Rep:






Peptidyl-prolyl cis-trans






isomerase - Arabidopsis






thaliana (Mouse-ear cress),






partial (32%)


DT083826
Glycine_soja_release_2
260886
261121
NA


CB063628
GMGI.071508
271592
271900
similar to UniRef100_A7PM52






Cluster: Chromosome chr14






scaffold_21 whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: = partial (2%)


CB063628
Glycine_max_release_2
271592
271928
NA


TA5835_34305
Lotus_japonicus_release_1
273868
275906
Vegetative cell wall protein






gp1-like [Oryza sativa (japonica






cultivar-group)]


TC32024
LJGI.070108
275152
275906
similar to UniRef100_A7PM52






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(9%)


TC252667
GMGI.071508
275739
276506
similar to UniRef100_A7PM52






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(12%)


AW311416
Glycine_max_release_2
276269
276455
NA


WmFPC_Contig850

99810
475910
NA


CV534998
Phaseolus_vulgaris
288050
288585
UniRef100_A7PM50






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM50_VITVI






6.00E−39


TA75806_3847
Glycine_max_release_2
288290
290376
Arabidopsis thaliana genomic






DNA = chromosome 3 = P1






clone: MGF10 [Arabidopsis






thaliana (Mouse-ear cress)]


TC276120
GMGI.071508
288290
290376
similar to UniRef100_A7PM50






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(62%)


BI786388
GMGI.071508
291666
292088
similar to UniRef100_A7PM49






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(7%)


BI786388
Glycine_max_release_2
291666
292099
NA


TA63308_3847
Glycine_max_release_2
291633
294397
NA


TC243765
GMGI.071508
293681
294426
weakly similar to






UniRef100_Q0JDM0 Cluster:






Os04g0394300 protein; n = 1;






Oryza sativa Japonica






Group|Rep: Os04g0394300






protein - Oryza sativa subsp.






japonica (Rice) = partial (3%)


TA6412_34305
Lotus_japonicus_release_1
293803
294412
NA


TC24112
LJGI.070108
293803
294412
NA


CA899930
Phaseolus_coccineus_release_2
294054
294263
NA


TA3887_3886
Phaseolus_coccineus_release_2
302301
303033
Hypothetical protein MJH23.3






[Arabidopsis thaliana (Mouse-






ear cress)]


AW705271
Glycine_max_release_2
302299
303855
Hypothetical protein MJH23.3






[Arabidopsis thaliana (Mouse-






ear cress)]


TC237313
GMGI.071508
303227
306007
similar to UniRef100_A7PM30






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(54%)


TA61594_3847
Glycine_max_release_2
303227
306056
Similarity to RNA binding






protein [Arabidopsis thaliana






(Mouse-ear cress)]


asmbl_11859
Vigna_unguiculata
303952
305921
NA


toGm05
DAGchainer
30059
580791
Ks0.2335


BU544029
Glycine_max_release_2
305220
305762
NA


TC23280
LJGI.070108
305373
305839
similar to UniRef100_A7PM30






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(17%)


AI461058
Glycine_max_release_2
305614
305834
NA


BE555571
Glycine_max_release_2
305656
306011
NA


asmbl_11860
Vigna_unguiculata
319622
320527
NA


EV270366
GMGI.071508
319893
320575
similar to UniRef100_P15792






Cluster: Protein kinase PVPK-






1; n = 1; Phaseolus vulgaris|Rep:






Protein kinase PVPK-1 -






Phaseolus vulgaris (Kidney






bean) (French bean) = partial






(34%)


J04555
Phaseolus_vulgaris_release_2
318937
322709
Protein kinase PVPK-1






[Phaseolus vulgaris (Kidney






bean) (French bean)]


TA11578_34305
Lotus_japonicus_release_1
320355
322024
Protein kinase PVPK-1






[Phaseolus vulgaris (Kidney






bean) (French bean)]


TC35252
LJGI.070108
320355
322381
homologue to






UniRef100_P15792 Cluster:






Protein kinase PVPK-1, n = 1,






Phaseolus vulgaris|Rep: Protein






kinase PVPK-1 - Phaseolus






vulgaris (Kidney bean) (French






bean), partial (48%)


Pvcon4227
Phaseolus_vulgaris
320098
322709
UniRef100_P15792 Protein






kinase PVPK-1 n = 1






Tax = Phaseolus vulgaris






RepID = KPK1_PHAVU E−0


CA900819
Phaseolus_coccineus_release_2
325129
325547
Sucrase-like protein






[Arabidopsis thaliana (Mouse-






ear cress)]


CA900820
Phaseolus_coccineus_release_2
325119
328122
AT3g27570/MMJ24_12






[Arabidopsis thaliana (Mouse-






ear cress)]


TC269193
GMGI.071508
325136
329359
weakly similar to






UniRef100_A7PM27 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(47%)


TA4354_3885
Phaseolus_vulgaris_release_2
325476
329154
AT5g40510/MNF13_30






[Arabidopsis thaliana (Mouse-






ear cress)]


asmbl_11861
Vigna_unguiculata
326881
329154
NA


CF920945
Glycine_max_release_2
326967
329359
AT3g27570/MMJ24_12






[Arabidopsis thaliana (Mouse-






ear cress)]


SATT723

337605
337828



Satt723
ePCR
337605
337828
Map3.0 SSR L/Gm19 cM: 1.5


TC244213
GMGI.071508
354373
354996
similar to UniRef100_A7PL06






Cluster: Chromosome chr7






scaffold_20 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr7






scaffold_20 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (17%)


BU090380
Glycine_max_release_2
354683
354871
NA


BP058294
Lotus_japonicus_release_1
355950
356319
Protein ycf2 [Lotus japonicus]


Pvcon2444
Phaseolus_vulgaris
354593
360732
UniRef100_A7PL07






Chromosome chr7 scaffold_20,






whole genome shotgun






sequence n = 1 Tax = Vitis






vinifera






RepID = A7PL07_VITVI 1.00E−144


asmbl_11862
Vigna_unguiculata
359273
359896
NA


CA800649
Glycine_max_release_2
377994
379933
AT3g01590/F4P13_13






[Arabidopsis thaliana (Mouse-






ear cress)]


TC245493
GMGI.071508
377994
381638
similar to UniRef100_A7PM21






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(96%)


CO984617
Glycine_max_release_2
379899
381537
At5g14500 [Arabidopsis






thaliana (Mouse-ear cress)]


M0114388
SEQ. LISTING
381308
380486
SEQ ID NO: 2


AW704585
Glycine_max_release_2
381210
381673
At5g14500 [Arabidopsis






thaliana (Mouse-ear cress)]


TC248588
GMGI.071508
383419
383857
NA


asmbl_11863
Vigna_unguiculata
383428
384088
NA


TC126554
MTGI.071708
383593
384668
weakly similar to






UniRef100_Q940C3 Cluster:






AT3g27530/MMJ24_7, n = 2,






Arabidopsis thaliana|Rep:






AT3g27530/MMJ24_7 -






Arabidopsis thaliana (Mouse-






ear cress), partial (38%)


AJ002216
Pisum_sativum_release_2
384088
384751
Emb|CAA07228.1 [Arabidopsis






thaliana (Mouse-ear cress)]


BI702257
GMGI.071508
384067
384789
similar to UniRef100_Q940C3






Cluster:






AT3g27530/MMJ24_7; n = 2;






Arabidopsis thaliana|Rep:






AT3g27530/MMJ24_7 -






Arabidopsis thaliana (Mouse-






ear cress) = partial (14%)


BG451913
MTGI.071708
386353
388007
similar to UniRef100_Q9LT59






Cluster: Emb|CAA07228.1,






n = 1, Arabidopsis thaliana|Rep:






Emb|CAA07228.1 -






Arabidopsis thaliana (Mouse-






ear cress), partial (19%)


CV533025
Phaseolus_vulgaris
388647
389345
UniRef100_UPI000016357E






GC6 (GOLGIN CANDIDATE






6) binding/protein transporter






Tax = n = 1






RepID = UPI000016357E 6.00E−27


AV777312
LJGI.070108
389152
391279
similar to UniRef100_Q9LT59






Cluster: Emb|CAA07228.1,






n = 1, Arabidopsis thaliana|Rep:






Emb|CAA07228.1 -






Arabidopsis thaliana (Mouse-






ear cress), partial (19%)


BM187543
GMGI.071508
394984
395407
similar to UniRef100_A7PM13






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(36%)


BM187543
Glycine_max_release_2
394984
395559
Gb|AAF01546.1 [Arabidopsis






thaliana (Mouse-ear cress)]


DN652256
LJGI.070108
395487
395708
similar to UniRef100_A7P4B1






Cluster: Chromosome chr1






scaffold_5, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome chr1






scaffold_5, whole genome






shotgun sequence - Vitis






vinifera (Grape), partial (19%)


DT044393
Arachis_hypogaea_release_5
395462
395746
Cluster: Hypothetical protein






T23K23.27, n = 1, Arabidopsis






thaliana|Rep: Hypothetical






protein T23K23.27 -






Arabidopsis thaliana (Mouse-






ear cress)


FD789910
Phaseolus_vulgaris
395555
395927
UniRef100_A7P4B1






Chromosome chr1 scaffold_5,






whole genome shotgun






sequence n = 1 Tax = Vitis






vinifera






RepID = A7P4B1_VITVI 2.00E−59


EH259382
GMGI.071508
395577
396156
similar to UniRef100_A7PM13






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(34%)


TA69305_3847
Glycine_max_release_2
403237
404175
NA


TC243910
GMGI.071508
403237
404175
similar to UniRef100_A7PM14






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(5%)


CA785084
Glycine_soja_release_2
403526
404055
NA


CV541170
Phaseolus_vulgaris
404688
406556
UniRef100_Q9LT57






Emb|CAB45506.1 n = 1






Tax = Arabidopsis thaliana






RepID = Q9LT57_ARATH






1.00E−113


BF071095
GMGI.071508
406510
407127
similar to UniRef100_Q9LT57






Cluster: Emb|CAB45506.1;






n = 1; Arabidopsis thaliana|Rep:






Emb|CAB45506.1 -






Arabidopsis thaliana (Mouse-






ear cress) = partial (8%)


BF071095
Glycine_max_release_2
406527
407127
NA


BM270669
Glycine_max_release_2
409910
410532
NA


BM270669
GMGI.071508
410045
410532
similar to UniRef100_A7PM16






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(9%)


BG550673
GMGI.071508
421541
422250
similar to UniRef100_A7PM12






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(26%)


BG550673
Glycine_max_release_2
421541
422354
Hypothetical protein






F18O22_260 [Arabidopsis






thaliana (Mouse-ear cress)]


BU551363
Glycine_max_release_2
422150
422745
NA


CD407423
Glycine_max_release_2
423719
423842
NA


M0205350
SEQ Listing
424095
423776
SEQ ID NO: 1


EV270239
GMGI.071508
425649
426181
similar to






UniRef100_Q0WVR7 Cluster:






TRNA synthase-like protein;






n = 1; Arabidopsis thaliana|Rep:






TRNA synthase-like protein -






Arabidopsis thaliana (Mouse-






ear cress) = partial (5%)


BI424448
GMGI.071508
451332
451679
similar to UniRef100_P82353






Cluster: Non-specific lipid-






transfer protein 2; n = 1; Prunus






armeniaca|Rep: Non-specific






lipid-transfer protein 2 - Prunus






armeniaca (Apricot) = partial






(68%)


TA49179_3847
Glycine_max_release_2
451332
451827
Nonspecific lipid-transfer






protein 2 [Prunus armeniaca






(Apricot)]


TC252453
GMGI.071508
451397
451828
weakly similar to






UniRef100_Q43681 Cluster:






Probable non-specific lipid-






transfer protein AKCS9






precursor; n = 1; Vigna






unguiculata|Rep: Probable non-






specific lipid-transfer protein






AKCS9 precursor - Vigna






unguiculata (Cowpea) = partial






(86%)


BE609938
Glycine_max_release_2
451607
451756
Probable lipid transfer protein






family protein [Tamarix






androssowii]


BQ612382
Glycine_max_release_2
451777
452217
NA


NS0102027

466228
466889



Pvcon7917
Phaseolus_vulgaris
466120
467338
UniRef100_A5C9E2 Putative






uncharacterized protein n = 1






Tax = Vitis vinifera






RepID = A5C9E2_VITVI 6.00E−44


asmbl_11864
Vigna_unguiculata
467520
468191
NA


TA49596_3847
Glycine_max_release_2
470086
472059
Methionine aminopeptidase 2B






[Arabidopsis thaliana (Mouse-






ear cress)]


TC255857
GMGI.071508
470086
476828
homologue to






UniRef100_A7PXX3 Cluster:






Methionine aminopeptidase;






n = 1; Vitis vinifera|Rep:






Methionine aminopeptidase -






Vitis vinifera (Grape) = partial






(91%)


FD792539
Phaseolus_vulgaris
472774
475674
UniRef100_A7PXX3






Methionine aminopeptidase






n = 1 Tax = Vitis vinifera






RepID = A7PXX3_VITVI






5.00E−56


TA3829_3848
Glycine_soja_release_2
471918
476623
Methionine aminopeptidase 2B






[Arabidopsis thaliana (Mouse-






ear cress)]


BU765955
Glycine_max_release_2
472787
475846
Methionine aminopeptidase 2B






[Arabidopsis thaliana (Mouse-






ear cress)]


EG530516
Arachis_hypogaea_release_5
472835
476690
Cluster: Methionine






aminopeptidase 2B, n = 1,






Arabidopsis thaliana|Rep:






Methionine aminopeptidase 2B -






Arabidopsis thaliana (Mouse-






ear cress)


AV425234
LJGI.070108
475562
475924
homologue to






UniRef100_A7PXX3 Cluster:






Methionine aminopeptidase,






n = 1, Vitis vinifera|Rep:






Methionine aminopeptidase -






Vitis vinifera (Grape), partial






(22%)


TA49598_3847
Glycine_max_release_2
474794
476709
Methionine aminopeptidase 2B






[Arabidopsis thaliana (Mouse-






ear cress)]


FD797260
Phaseolus_vulgaris
475768
476654
UniRef100_A7PXX3






Methionine aminopeptidase






n = 1 Tax = Vitis vinifera






RepID = A7PXX3_VITVI






6.00E−55


BE823844
Glycine_max_release_2
475751
476828
Methionine aminopeptidase 2B






[Arabidopsis thaliana (Mouse-






ear cress)]


BG726070
Glycine_max_release_2
476668
476807
NA


BQ080926
GMGI.071508
480002
480636
similar to UniRef100_A7PY54






Cluster: Chromosome chr15






scaffold_37 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr15 scaffold_37 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(39%)


TA69442_3847
Glycine_max_release_2
480002
481069
Hypothetical protein F22I13.40






[Arabidopsis thaliana (Mouse-






ear cress)]


TC262427
GMGI.071508
480002
481069
similar to UniRef100_A7P8Q6






Cluster: Chromosome chr3






scaffold_8 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr3






scaffold_8 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (20%)


BU548976
Glycine_max_release_2
481474
481970
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


CX547082
Glycine_max_release_2
481345
482173
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


TC236122
GMGI.071508
481300
482612
NA


TA57759_3847
Glycine_max_release_2
481300
482627
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


AV420909
LJGI.070108
481846
482201
weakly similar to






UniRef100_A7QTE8 Cluster:






Chromosome undetermined






scaffold_167, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






undetermined scaffold_167,






whole genome shotgun






sequence - Vitis vinifera






(Grape), partial (24%)


AW597322
Glycine_max_release_2
481965
482825
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


BM270610
Glycine_max_release_2
482034
483008
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


BI972603
GMGI.071508
482632
483190
weakly similar to






UniRef100_A7P3G6 Cluster:






Chromosome chr1 scaffold_5 =






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (20%)


BI972603
Glycine_max_release_2
482632
484113
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


TA66198_3847
Glycine_max_release_2
482595
484230
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


TC253566
GMGI.071508
482648
484405
weakly similar to






UniRef100_A7QTE8 Cluster:






Chromosome undetermined






scaffold_167 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_167 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (44%)


asmbl_11865
Vigna_unguiculata
482937
484289
NA


BG881371
Glycine_max_release_2
483075
484230
Multi antimicrobial extrusion






protein MatE [Medicago






truncatula (Barrel medic)]


WmFPC_Contig7443

384071
598745
NA


AW695419
MTGI.071708
491367
494466
similar to UniRef100_A7PU69






Cluster: Chromosome chr7






scaffold_31, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome chr7






scaffold_31, whole genome






shotgun sequence - Vitis






vinifera (Grape), partial (11%)


BF645755
MTGI.071708
494870
497474
similar to UniRef100_A7PU69






Cluster: Chromosome chr7






scaffold_31, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome chr7






scaffold_31, whole genome






shotgun sequence - Vitis






vinifera (Grape), partial (14%)


BE475242
GMGI.071508
497000
497327
similar to






UniRef100_A7NWE7 Cluster:






Chromosome chr5 scaffold_2






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: = partial (1%)


BE475242
Glycine_max_release_2
497000
497549
Hypothetical protein






At3g23590/MDB19_8






[Arabidopsis thaliana (Mouse-






ear cress)]


BW611072
LJGI.070108
497387
497795
similar to UniRef100_A7PU69






Cluster: Chromosome chr7






scaffold_31, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome chr7






scaffold_31, whole genome






shotgun sequence - Vitis






vinifera (Grape), partial (10%)


BQ613050
Glycine_max_release_2
497409
498014
ORF protein [Arabidopsis






thaliana (Mouse-ear cress)]


CV541244
Phaseolus_vulgaris
500143
500464
UniRef100_A9PGX2 Putative






uncharacterized protein n = 1






Tax = Populus trichocarpa






RepID = A9PGX2_POPTR






3.00E−28


CX856527
Glycine_max_release_2
501517
501735
NA


BG839076
Glycine_max_release_2
503126
505209
F2P3.12 protein [Arabidopsis






thaliana (Mouse-ear cress)]


FD790090
Phaseolus_vulgaris
503370
505191
No significant hit (e−20)


TC236383
GMGI.071508
503107
505675
similar to UniRef100_O82505






Cluster: Elongation factor Ts;






n = 1; Arabidopsis thaliana|Rep:






Elongation factor Ts -






Arabidopsis thaliana (Mouse-






ear cress) = partial (32%)


TA56246_3847
Glycine_max_release_2
503107
505848
Ethylene-responsive elongation






factor EF-Ts precursor






[Lycopersicon esculentum






(Tomato)]


TC239475
GMGI.071508
503126
506560
similar to






UniRef100_Q9SWW0 Cluster:






Ethylene-responsive elongation






factor EF-Ts precursor; n = 1;






Solanum lycopersicum|Rep:






Ethylene-responsive elongation






factor EF-Ts precursor -






Solanum lycopersicum






(Tomato) (Lycopersicon






esculentum) = partial (74%)


TA56245_3847
Glycine_max_release_2
505512
506546
Ethylene-responsive elongation






factor EF-Ts precursor






[Lycopersicon esculentum






(Tomato)]


BG839060
Glycine_max_release_2
505661
506530
At4g11120 [Arabidopsis






thaliana (Mouse-ear cress)]


CV543527
Phaseolus_vulgaris_release_2
508539
508771
Eukaryotic translation initiation






factor 5 [Phaseolus vulgaris






(Kidney bean) (French bean)]


CD393454
Glycine_max_release_2
510651
511000
Ribosomal protein L22






[Glycine max (Soybean)]


TC245517
GMGI.071508
510651
511270
homologue to






UniRef100_O48879 Cluster:






Ribosomal protein L22; n = 1;






Glycine max|Rep: Ribosomal






protein L22 - Glycine max






(Soybean) = partial (80%)


asmbl_11866
Vigna_unguiculata
510868
511269
NA


TA51206_3847
Glycine_max_release_2
510702
512712
Ribosomal protein L22






[Glycine max (Soybean)]


TC249077
GMGI.071508
510771
512771
homologue to






UniRef100_O48879 Cluster:






Ribosomal protein L22; n = 1;






Glycine max|Rep: Ribosomal






protein L22 - Glycine max






(Soybean) = partial (98%)


BG316244
Glycine_max_release_2
511015
512722
Ribosomal protein L22






[Glycine max (Soybean)]


BQ155270
MTGI.071708
513084
514936
similar to UniRef100_A7PR59






Cluster: Chromosome chr14






scaffold_26, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_26, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(52%)


TC30151
LJGI.070108
514647
516395
similar to UniRef100_A7PR59






Cluster: Chromosome chr14






scaffold_26, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_26, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(29%)


BP044357
Lotus_japonicus_release_1
514647
516409
S-locus protein 8 [Brassica






campestris (Field mustard)]


CB540591
Phaseolus_vulgaris
514839
516355
No significant hit (e−20)


TA65114_3847
Glycine_max_release_2
523413
524053
At1g22990/F19G10_22






[Arabidopsis thaliana (Mouse-






ear cress)]


TC259745
GMGI.071508
523413
524067
similar to UniRef100_A7P3I8






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 2; Vitis






vinifera|Rep: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (56%)


TA4332_47247
Lotus_corniculatus_release_1
529321
530051
Actin-11 related cluster


TA6031_34305
Lotus_japonicus_release_1
529321
530051
Actin [Striga asiatica]


TC32457
LJGI.070108
529321
530051
homologue to






UniRef100_P30167 Cluster:






Actin-58, n = 1, Solanum






tuberosum|Rep: Actin-58 -






Solanum tuberosum (Potato),






partial (39%)


AW351005
Glycine_max_release_2
529380
530095
Actin [Striga asiatica]


TA43521_3847
Glycine_max_release_2
529306
530175
Actin-11 [Arabidopsis thaliana






(Mouse-ear cress)]


asmbl_11867
Vigna_unguiculata
529342
530189
NA


AU240079
LJGI.070108
529747
530013
homologue to






UniRef100_P93372 Cluster:






Actin-66, n = 1, Nicotiana






tabacum|Rep: Actin-66-






Nicotiana tabacum (Common






tobacco), partial (25%)


AU240079
Lotus_japonicus_release_1
529747
530039
Actin-11 [Arabidopsis thaliana






(Mouse-ear cress)]


EE127018
Arachis_hypogaea_release_5
529933
530285
Cluster: Hypothetical protein,






n = 1, Oryza sativa (indica






cultivar-group)|Rep:






Hypothetical protein - Oryza






sativa subsp. indica (Rice)


TC240040
GMGI.071508
529306
531078
homologue to






UniRef100_P02581 Cluster:






Actin-1; n = 1; Glycine max|Rep:






Actin-1 - Glycine max






(Soybean) = complete


AW666288
Glycine_max_release_2
529980
530789
Actin [Phaseolus acutifolius






(Tepary bean)]


TA43509_3847
Glycine_max_release_2
529888
530911
Actin [Glycine max (Soybean)]


TA6074_34305
Lotus_japonicus_release_1
530031
531095
Actin-1 [Sorghum bicolor






(Sorghum) (Sorghum vulgare)]


TC26188
LJGI.070108
530031
531095
homologue to






UniRef100_A1Y2A0 Cluster:






Actin, n = 1, Aegiceras






corniculatum|Rep: Actin -






Aegiceras corniculatum, partial






(81%)


BM142797
Glycine_max_release_2
530212
531095
Actin [Trifolium pratense (Red






clover)]


BP036880
Lotus_japonicus_release_1
530235
531095
Actin/actin-like [Medicago






truncatula (Barrel medic)]


AW349632
Glycine_max_release_2
533113
533701
NA


AI900119
Glycine_max_release_2
533044
534995
NA


TA51800_3847
Glycine_max_release_2
533054
535063
NA


TC241826
GMGI.071508
533055
535063
similar to UniRef100_Q2Z1Y5






Cluster: Pm52 protein; n = 1;






Prunus mume|Rep: Pm52






protein - Prunus mume






(Japanese flowering apricot) =






partial (73%)


BU494245
LJGI.070108
533191
534994
weakly similar to






UniRef100_Q2Z1Y5 Cluster:






Pm52 protein, n = 1, Prunus






mume|Rep: Pm52 protein -






Prunus mume (Japanese






flowering apricot), partial






(59%)


AI440735
Glycine_max_release_2
534517
535020
NA


AI440735
GMGI.071508
534522
535020
similar to UniRef100_Q2Z1Y5






Cluster: Pm52 protein; n = 1;






Prunus mume|Rep: Pm52






protein - Prunus mume






(Japanese flowering apricot) =






partial (41%)


TC250013
GMGI.071508
536842
537680
UniRef100_Q8L7J4 Cluster:






Pyruvate kinase; n = 1; Glycine






max|Rep: Pyruvate kinase -






Glycine max (Soybean) = partial






(29%)


TA10574_34305
Lotus_japonicus_release_1
537149
537628
Pyruvate kinase [Glycine max






(Soybean)]


TC26632
LJGI.070108
537149
537628
homologue to






UniRef100_Q42806 Cluster:






Pyruvate kinase, cytosolic






isozyme, n = 1, Glycine






max|Rep: Pyruvate kinase,






cytosolic isozyme - Glycine






max (Soybean), partial (26%)


CV536725
Phaseolus_vulgaris_release_2
537147
537846
Pyruvate kinase = cytosolic






isozyme [Glycine max






(Soybean)]


asmbl_11868
Vigna_unguiculata
537127
538325
NA


TC25282
LJGI.070108
537149
538489
homologue to






UniRef100_Q8L7J4 Cluster:






Pyruvate kinase, n = 1, Glycine






max|Rep: Pyruvate kinase -






Glycine max (Soybean), partial






(29%)


TA47094_3847
Glycine_max_release_2
536842
539314
Pyruvate kinase [Glycine max






(Soybean)]


Pvcon4373
Phaseolus_vulgaris
537147
539113
UniRef100_Q42806 Pyruvate






kinase, cytosolic isozyme n = 1






Tax = Glycine max






RepID = KPYC_SOYBN E−0


TC124922
MTGI.071708
537491
538783
homologue to






UniRef100_Q42806 Cluster:






Pyruvate kinase, cytosolic






isozyme, n = 1, Glycine






max|Rep: Pyruvate kinase,






cytosolic isozyme - Glycine






max (Soybean), partial (64%)


BF598352
Glycine_soja_release_2
538308
538971
Pyruvate kinase [Citrus sinensis






(Sweet orange)]


BG044770
Glycine_soja_release_2
538624
539149
Pyruvate kinase [Citrus sinensis






(Sweet orange)]


TC249941
GMGI.071508
538549
539314
UniRef100_Q8L7J4 Cluster:






Pyruvate kinase; n = 1; Glycine






max|Rep: Pyruvate kinase -






Glycine max (Soybean) = partial






(37%)


BE608312
Glycine_max_release_2
542536
544875
Hypothetical protein






[Arabidopsis thaliana (Mouse-






ear cress)]


TC253996
GMGI.071508
542045
546856
similar to UniRef100_A7QNQ5






Cluster: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (80%)


TC258772
GMGI.071508
548268
548805
NA


CV533614
Phaseolus_vulgaris
548540
548638
No significant hit


TA57756_3847
Glycine_max_release_2
548268
551375
Putative microtubule-severing






protein subunit [Oryza sativa






(japonicacultivar-group)]


TC239891
GMGI.071508
548323
551375
similar to UniRef100_A7QNQ6






Cluster: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (12%)


EH221990
GMGI.071508
550796
551633
weakly similar to






UniRef100_A7QNQ6 Cluster:






Chromosome undetermined






scaffold_133 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (7%)


EV263369
GMGI.071508
552842
553615
similar to UniRef100_A8D2Q2






Cluster: ATP synthase protein






8; n = 1; Caranx ignobilis|Rep:






ATP synthase protein 8 -






Caranx ignobilis = partial (37%)


BU964969
Glycine_max_release_2
556336
556943
NA


BU964969
GMGI.071508
556494
556943
similar to






UniRef100_Q9MYM4 Cluster:






Lysosomal alpha-glucosidase






precursor; n = 1; Bos taurus|Rep:






Lysosomal alpha-glucosidase =






partial (1%)


EH221989
GMGI.071508
562783
563692
homologue to






UniRef100_A7QNQ6 Cluster:






Chromosome undetermined






scaffold_133 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (3%)


AW831441
GMGI.071508
573069
573567
NA


AW831441
Glycine_max_release_2
573069
573639
NA


TA6761_34305
Lotus_japonicus_release_1
573706
580487
Sphingosine kinase [Lotus






japonicus]


TC20288
LJGI.070108
573706
580487
UniRef100_Q5KR50 Cluster:






Sphingosine kinase, n = 1, Lotus






japonicus|Rep: Sphingosine






kinase - Lotus japonicus,






complete


TC122322
MTGI.071708
574490
580620
homologue to






UniRef100_Q5KR50 Cluster:






Sphingosine kinase, n = 1, Lotus






japonicus|Rep: Sphingosine






kinase - Lotus japonicus, partial






(66%)


BI701010
Glycine_max_release_2
577145
579375
Sphingosine kinase [Lotus






japonicus]


Pvcon3123
Phaseolus_vulgaris
577107
580468
UniRef100_Q5KR50






Sphingosine kinase n = 1






Tax = Lotus japonicus






RepID = Q5KR50_LOTJA E−0


TA49258_3847
Glycine_max_release_2
579511
580791
Sphingosine kinase [Lotus






japonicus]


TC235674
GMGI.071508
579511
580791
homologue to






UniRef100_Q5KR50 Cluster:






Sphingosine kinase; n = 1; Lotus






japonicus|Rep: Sphingosine






kinase - Lotus japonicus =






partial (26%)


BI969866
Glycine_max_release_2
579600
580756
Sphingosine kinase [Lotus






japonicus]


EH043869
Arachis_stenosperma_release_5
579729
580660
Cluster: Sphingosine kinase,






n = 1, Lotus japonicus|Rep:






Sphingosine kinase - Lotus






japonicus


BQ786742
Glycine_max_release_2
580594
580719
NA


BM108235
Glycine_max_release_2
581688
582006
NA


AW508189
Glycine_max_release_2
581725
582244
Hypothetical protein






[Arabidopsis thaliana (Mouse-






ear cress)]


TC238711
GMGI.071508
581688
582562
similar to UniRef100_A7QNQ7






Cluster: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (50%)


TA46155_3847
Glycine_max_release_2
581745
582556
Hypothetical protein






[Arabidopsis thaliana (Mouse-






ear cress)]


AW278369
GMGI.071508
581988
582389
similar to UniRef100_A7QNQ7






Cluster: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: Chromosome






undetermined scaffold_133 =






whole genome shotgun






sequence - Vitis vinifera






(Grape) = partial (44%)


AW278369
Glycine_max_release_2
581988
582418
Hypothetical protein






[Arabidopsis thaliana (Mouse-






ear cress)]


CD394810
Glycine_max_release_2
582134
582328
NA


BG047332
Glycine_max_release_2
591288
592013
OSJNBb0065L13.3 protein






[Oryza sativa (japonica






cultivar-group)]


TC272805
GMGI.071508
591358
592013
similar to






UniRef100_A7NXM8 Cluster:






Chromosome chr5 scaffold_2 =






whole genome shotgun






sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr5






scaffold_2 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (15%)


BW599171
LJGI.070108
593399
593875
weakly similar to






UniRef100_A7PT63 Cluster:






Chromosome chr8 scaffold_29,






whole genome shotgun






sequence, n = 1, Vitis






vinifera|Rep: Chromosome chr8






scaffold_29, whole genome






shotgun sequence - Vitis






vinifera (Grape), partial (24%)


BE057829
Glycine_max_release_2
606858
607008
NA


TC275159
GMGI.071508
606858
607456
NA


BE612118
GMGI.071508
615853
616253
weakly similar to






UniRef100_A7GPV4 Cluster:






Citrate transporter; n = 1;






Bacillus cereus subsp.cytotoxis






NVH 391-98|Rep: Citrate






transporter - Bacillus cereus






subsp.cytotoxis (strain NVH






391-98) = partial (5%)


BE612118
Glycine_max_release_2
615869
616269
NA


CA910895
Phaseolus_coccineus_release_2
622174
622531
Arabidopsis thalianagenomic






DNA, chromosome 5, P1






clone: MPO12 [Arabidopsis






thaliana (Mouse-ear cress)]


BU763992
Glycine_max_release_2
625192
625591
NA


TA51978_3847
Glycine_max_release_2
625330
626304
Putative ethylene-responsive






protein [Oryza sativa (japonica






cultivar-group)]


TC236117
GMGI.071508
625330
626304
similar to UniRef100_A7PM86






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(43%)


TC263881
GMGI.071508
625192
627651
similar to UniRef100_A7PM86






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(76%)


TA51979_3847
Glycine_max_release_2
625252
627642
Putative ethylene response






protein [Capsicum chinense






(Scotch bonnet) (Bonnet






pepper)]


TC236300
GMGI.071508
625318
627642
similar to UniRef100_A7PM86






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(98%)


CA910548
Phaseolus_coccineus_release_2
625559
627607
Putative ethylene response






protein [Capsicum chinense






(Scotch bonnet) (Bonnet






pepper)]


Pvcon5808
Phaseolus_vulgaris
625567
627610
UniRef100_A7PM86






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PM86_VITVI






2.00E−77


EV269595
GMGI.071508
627204
627569
similar to UniRef100_A7PM86






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(29%)


BI273677
Glycine_max_release_2
637550
637816
NA


BP049107
Lotus_corniculatus_release_1
647584
649419
Cinnamoyl CoA reductase-like






protein related cluster


TC258382
GMGI.071508
646415
652371
weakly similar to






UniRef100_A7PM88 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(72%)


TA50222_3847
Glycine_max_release_2
646722
652222
Cinnamoyl CoA reductase-like






protein [Arabidopsis thaliana






(Mouse-ear cress)]


SATT495

650288
650531



Satt495
ePCR
650288
650531
Map3.0 SSR L/Gm19 cM: 2.7


AW099618
GMGI.071508
649276
652222
weakly similar to






UniRef100_A7PM88 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(23%)


TA50296_3847
Glycine_max_release_2
674409
676421
NA


BQ629031
Glycine_max_release_2
674669
676494
NA


BM520842
Glycine_soja_release_2
674685
676538
NA


TC264557
GMGI.071508
674741
676494
NA


BU765059
Glycine_max_release_2
674828
676698
NA


BU765059
GMGI.071508
674925
676698
weakly similar to






UniRef100_A7L4B0 Cluster:






Protein kinase; n = 1; Carica






papaya|Rep: Protein kinase -






Carica papaya (Papaya) = partial






(6%)


TC264815
GMGI.071508
674409
678111
weakly similar to






UniRef100_A7L4B0 Cluster:






Protein kinase; n = 1; Carica






papaya|Rep: Protein kinase -






Carica papaya (Papaya) = partial






(14%)


asmbl_11869
Vigna_unguiculata
676473
676672
NA


TA50295_3847
Glycine_max_release_2
674775
678957
NA


Pvcon1987
Phaseolus_vulgaris
674506
679702
UniRef100_A7L4B0 Protein






kinase n = 1 Tax = Carica papaya






RepID = A7L4B0_CARPA






1.00E−127


BM528477
Glycine_max_release_2
676507
678111
NA


TA11531_47247
Lotus_corniculatus_release_1
676692
678714
Protein kinase-like protein






related cluster


TA13031_34305
Lotus_japonicus_release_1
676692
678714
Hypothetical protein






At5g14720 [Arabidopsis






thaliana (Mouse-ear cress)]


TC31122
LJGI.070108
676701
678714
similar to UniRef100_A7L4B0






Cluster: Protein kinase, n = 1,






Carica papaya|Rep: Protein






kinase - Carica papaya






(Papaya), partial (14%)


TC255388
GMGI.071508
679127
681361
homologue to






UniRef100_A7PM90 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(44%)


TC124284
MTGI.071708
679117
681419
homologue to






UniRef100_A7PM90 Cluster:






Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(48%)


DV565290
Phaseolus_vulgaris
681368
681460
No significant hit (e−20)


toGm05
DAGchainer
603011
803108
Ks0.2166


NP7265365
MTGI.071708
703588
713159
GB|AC124951.19|ABE84834.1






ATPase, E1-E2 type, Peptidase






M, neutral zinc






metallopeptidases, zinc-binding






site


BF325038
Glycine_max_release_2
711165
712911
ATPase = E1-E2 type; Peptidase






M = neutral zinc






metallopeptidases = zinc-






binding site [Medicago






truncatula (Barrel medic)]


FE897117
Phaseolus_vulgaris
715539
715874
UniRef100_Q93VL6 NBS-






LRR resistance-like protein J78






n = 1 Tax = Phaseolus vulgaris






RepID = Q93VL6_PHAVU






2.00E−47


TC264844
GMGI.071508
731939
732440
weakly similar to






UniRef100_A7PD05 Cluster:






Chromosome chr17






scaffold_12 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(13%)


TA67235_3847
Glycine_max_release_2
731939
733078
NA


CD404253
GMGI.071508
732439
733078
homologue to






UniRef100_A7PM92 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(8%)


BU091162
GMGI.071508
737876
738292
NA


BU091162
Glycine_max_release_2
737876
738363
NA


asmbl_11870
Vigna_unguiculata
740144
741401
NA


BI470779
GMGI.071508
740189
741746
similar to UniRef100_Q9XQB0






Cluster: Carbonic anhydrase;






n = 1; Vigna radiata var.






radiata|Rep: Carbonic






anhydrase - Phaseolus aureus






(Mung bean) (Vigna radiata) =






partial (30%)


TA43150_3847
Glycine_max_release_2
740126
742524
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


BG509786
GMGI.071508
740265
742434
homologue to






UniRef100_Q9XQB0 Cluster:






Carbonic anhydrase; n = 1;






Vigna radiata var. radiata|Rep:






Carbonic anhydrase - Phaseolus






aureus (Mung bean) (Vigna






radiata) = partial (34%)


BG509786
Glycine_max_release_2
740265
742656
Carbonic anhydrase [Zea mays






(Maize)]


DT083317
Glycine_soja_release_2
740299
742670
Carbonic anhydrase [Zea mays






(Maize)]


AW781596
Glycine_max_release_2
740182
742860
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


BU089680
Glycine_max_release_2
741070
742671
Carbonic anhydrase [Zea mays






(Maize)]


BM887226
Glycine_max_release_2
741037
742852
Carbonic anhydrase [Zea mays






(Maize)]


BU089600
Glycine_max_release_2
741070
742891
Carbonic anhydrase [Zea mays






(Maize)]


TC23104
LJGI.070108
740127
744319
similar to UniRef100_Q9XQB0






Cluster: Carbonic anhydrase,






n = 1, Vigna radiata var.






radiata|Rep: Carbonic






anhydrase - Phaseolus aureus






(Mung bean) (Vigna radiata),






partial (98%)


TA2934_3885
Phaseolus_vulgaris_release_2
739932
744687
Carbonic anhydrase [Zea mays






(Maize)]


TC238511
GMGI.071508
740118
744639
homologue to






UniRef100_Q9XQB0 Cluster:






Carbonic anhydrase; n = 1;






Vigna radiata var. radiata|Rep:






Carbonic anhydrase - Phaseolus






aureus (Mung bean) (Vigna






radiata) = complete


TA377_34305
Lotus_japonicus_release_1
740127
744704
Carbonic anhydrase [Zea mays






(Maize)]


Pvcon229
Phaseolus_vulgaris
740125
744728
UniRef100_Q9XQB0 Carbonic






anhydrase n = 1 Tax = Vigna






radiata var. radiata






RepID = Q9XQB0_PHAAU






1.00E−176


TA2935_3885
Phaseolus_vulgaris_release_2
740178
744687
Carbonic anhydrase [Zea mays






(Maize)]


TA2376_3848
Glycine_soja_release_2
740118
744805
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


TA43157_3847
Glycine_max_release_2
740117
744844
Carbonic anhydrase [Zea mays






(Maize)]


TA43160_3847
Glycine_max_release_2
741051
744186
Carbonic anhydrase =






chloroplast precursor (EC






4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase = 27 kDa






isoform; Carbonic anhydrase =






25 kDa isoform] [Pisum






sativum (Garden pea)]


TC135779
MTGI.071708
741364
744530
homologue to






UniRef100_P17067 Cluster:






Carbonic anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27 kDa






isoform, Carbonic anhydrase,






25 kDa isoform], n = 1, Pisum






sativum|Rep: Carbonic






anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27 kDa






isoform, Carbonic anhydrase,






25 kDa isoform] - Pisum






sativum (Garden pea), partial






(79%)


TA4174_3848
Glycine_soja_release_2
742624
743398
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


Pvcon228
Phaseolus_vulgaris
741374
744687
UniRef100_Q9XQB0 Carbonic






anhydrase n = 1 Tax = Vigna






radiata var. radiata






RepID = Q9XQB0_PHAAU






1.00E−137


TA43163_3847
Glycine_max_release_2
741381
744770
Carbonic anhydrase [Zea mays






(Maize)]


TC247359
GMGI.071508
741381
744770
homologue to






UniRef100_Q9XQB0 Cluster:






Carbonic anhydrase; n = 1;






Vigna radiata var. radiata|Rep:






Carbonic anhydrase - Phaseolus






aureus (Mung bean) (Vigna






radiata) = partial (62%)


BG045644
Glycine_soja_release_2
742643
743622
Carbonic anhydrase =






chloroplast precursor (EC






4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase = 27 kDa






isoform; Carbonic anhydrase =






25 kDa isoform] [Pisum






sativum (Garden pea)]


Pvcon227
Phaseolus_vulgaris
741681
744687
UniRef100_Q9XQB0 Carbonic






anhydrase n = 1 Tax = Vigna






radiata var. radiata






RepID = Q9XQB0_PHAAU






1.00E−133


TC124201
MTGI.071708
741922
744665
homologue to






UniRef100_P17067 Cluster:






Carbonic anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27 kDa






isoform, Carbonic anhydrase,






25 kDa isoform], n = 1, Pisum






sativum|Rep: Carbonic






anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27 kDa






isoform, Carbonic anhydrase,






25 kDa isoform] - Pisum






sativum (Garden pea), partial






(57%)


CB543710
Phaseolus_vulgaris_release_2
742464
744532
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


CB539509
Phaseolus_vulgaris_release_2
742480
744557
Carbonic anhydrase [Zea mays






(Maize)]


TC126947
MTGI.071708
742434
744665
homologue to






UniRef100_P17067 Cluster:






Carbonic anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27 kDa






isoform, Carbonic anhydrase,






25 kDa isoform], n = 1, Pisum






sativum|Rep: Carbonic






anhydrase, chloroplast






precursor (Carbonate






dehydratase) [Contains:






Carbonic anhydrase, 27 kDa






isoform, Carbonic anhydrase,






25 kDa isoform] - Pisum






sativum (Garden pea), partial






(51%)


asmbl_11871
Vigna_unguiculata
742823
744369
NA


asmbl_11872
Vigna_unguiculata
742628
744687
NA


asmbl_11874
Vigna_unguiculata
742641
744687
NA


TA43165_3847
Glycine_max_release_2
742658
744772
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


TC241035
GMGI.071508
742658
744772
homologue to






UniRef100_Q9XQB0 Cluster:






Carbonic anhydrase; n = 1;






Vigna radiata var. radiata|Rep:






Carbonic anhydrase - Phaseolus






aureus (Mung bean) (Vigna






radiata) = partial (38%)


TA480_3888
Pisum_sativum_release_2
742823
744641
Carbonic anhydrase, chloroplast






precursor (EC 4.2.1.1)






(Carbonate dehydratase)






[Contains: Carbonic anhydrase,






27 kDa isoform, Carbonic






anhydrase, 25 kDa isoform]






[Pisum sativum (Garden pea)]


TC240357
GMGI.071508
742650
744828
homologue to






UniRef100_Q9XQB0 Cluster:






Carbonic anhydrase; n = 1;






Vigna radiata var. radiata|Rep:






Carbonic anhydrase - Phaseolus






aureus (Mung bean) (Vigna






radiata) = partial (38%)


BE346766
Glycine_max_release_2
743636
744227
Carbonic anhydrase =






chloroplast precursor (EC






4.2.1.1) (Carbonate






dehydratase) [Contains:






Carbonic anhydrase = 27 kDa






isoform; Carbonic anhydrase =






25 kDa isoform] [Pisum






sativum (Garden pea)]


AW596246
Glycine_max_release_2
743636
744243
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


BE807206
Glycine_max_release_2
743636
744244
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


CB280659
Phaseolus_vulgaris_release_2
743613
744419
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


asmbl_11875
Vigna_unguiculata
743587
744642
NA


DT083076
Glycine_soja_release_2
743565
744678
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


TC29040
LJGI.070108
743565
744702
similar to UniRef100_Q9XQB0






Cluster: Carbonic anhydrase,






n = 1, Vigna radiata var.






radiata|Rep: Carbonic






anhydrase - Phaseolus aureus






(Mung bean) (Vigna radiata),






partial (31%)


TA134_47247
Lotus_corniculatus_release_1
743568
744704
Carbonic anhydrase related






cluster


TA378_34305
Lotus_japonicus_release_1
743568
744704
Carbonic anhydrase,






prokaryotic and plant






[Medicago truncatula (Barrel






medic)]


TC24201
LJGI.070108
743584
744704
similar to UniRef100_Q9XQB0






Cluster: Carbonic anhydrase,






n = 1, Vigna radiata var.






radiata|Rep: Carbonic






anhydrase - Phaseolus aureus






(Mung bean) (Vigna radiata),






partial (25%)


CB539196
Phaseolus_vulgaris_release_2
743626
744687
Carbonic anhydrase [Phaseolus






aureus (Mung bean) (Vigna






radiata)]


AV413187
LJGI.070108
744089
744647
similar to UniRef100_P27140






Cluster: Carbonic anhydrase,






chloroplast precursor, n = 4,






Arabidopsis thaliana|Rep:






Carbonic anhydrase, chloroplast






precursor - Arabidopsis thaliana






(Mouse-ear cress), partial






(17%)


AV413187
Lotus_japonicus_release_1
744089
744672
Carbonic anhydrase, chloroplast






precursor [Arabidopsis thaliana






(Mouse-ear cress)]


CD860850
Pisum_sativum_release_2
744145
744641
Carbonic anhydrase, chloroplast






precursor [Arabidopsis thaliana






(Mouse-ear cress)]


CD403834
Glycine_max_release_2
744076
744732
Carbonic anhydrase =






chloroplast precursor






[Arabidopsis thaliana (Mouse-






ear cress)]


CD415400
Glycine_max_release_2
744251
744691
NA


asmbl_11873
Vigna_unguiculata
744448
744649
NA


CB541850
Phaseolus_vulgaris
747218
747570
No significant hit (e−20)


BM953717
Glycine_max_release_2
747199
748912
Peptidase S1 and S6 =






chymotrypsin/Hap [Medicago






truncatula (Barrel medic)]


EH256926
GMGI.071508
747192
749279
homologue to






UniRef100_A7Q7E6 Cluster:






Chromosome chr18






scaffold_59 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(21%)


TA51716_3847
Glycine_max_release_2
747191
749327
Putative DegP protease [Oryza






sativa (japonica cultivar-






group)]


TC243148
GMGI.071508
747199
749327
homologue to






UniRef100_A7Q7E6 Cluster:






Chromosome chr18






scaffold_59 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(25%)


AV768772
LJGI.070108
747281
749288
homologue to






UniRef100_O22609 Cluster:






Protease Do-like 1, chloroplast






precursor, n = 1, Arabidopsis






thaliana|Rep: Protease Do-like






1, chloroplast precursor -






Arabidopsis thaliana (Mouse-






ear cress), partial (23%)


BE807421
Glycine_max_release_2
748776
749688
Peptidase S1 and S6 =






chymotrypsin/Hap [Medicago






truncatula (Barrel medic)]


TA51715_3847
Glycine_max_release_2
747251
752927
Peptidase S1 and S6 =






chymotrypsin/Hap [Medicago






truncatula (Barrel medic)]


TC260884
GMGI.071508
747251
752942
homologue to






UniRef100_A7Q7E6 Cluster:






Chromosome chr18






scaffold_59 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(80%)


BE474482
Glycine_max_release_2
751068
752387
Peptidase S1 and S6 =






chymotrypsin/Hap [Medicago






truncatula (Barrel medic)]


BE474482
GMGI.071508
751070
752387
homologue to






UniRef100_A7Q7E6 Cluster:






Chromosome chr18






scaffold_59 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr18 scaffold_59 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(19%)


TC261290
GMGI.071508
755656
757218
similar to UniRef100_A7PM96






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(33%)


BG646067
MTGI.071708
756996
759297
similar to UniRef100_A7PM96






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(33%)


BE555567
Glycine_max_release_2
757210
762134
Hypothetical protein [Medicago






truncatula (Barrel medic)]


BE555567
GMGI.071508
757746
762134
similar to UniRef100_A7PM96






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(31%)


BE058948
Glycine_max_release_2
762117
763784
Hypothetical protein [Medicago






truncatula (Barrel medic)]


BE058948
GMGI.071508
762818
763784
similar to UniRef100_A7PM96






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(25%)


TC138874
MTGI.071708
768876
770881
similar to UniRef100_Q40318






Cluster: Coil protein, n = 1,






Medicago sativa|Rep: Coil






protein - Medicago sativa






(Alfalfa), partial (60%)


TC124470
MTGI.071708
768770
771318
similar to UniRef100_Q1RU40






Cluster: Lipolytic enzyme, G-






D-S-L, n = 1, Medicago






truncatula|Rep: Lipolytic






enzyme, G-D-S-L - Medicago






truncatula (Barrel medic),






partial (77%)


TC268582
GMGI.071508
768733
771727
weakly similar to






UniRef100_A7PMA0 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(89%)


BE059369
Glycine_max_release_2
770328
771326
Lipolytic enzyme = G-D-S-L






[Medicago truncatula (Barrel






medic)]


BE329784
GMGI.071508
770783
771236
similar to UniRef100_Q1RU40






Cluster: Lipolytic enzyme = G-






D-S-L; n = 1; Medicago






truncatula|Rep: Lipolytic






enzyme = G-D-S-L - Medicago






truncatula (Barrel medic) =






partial (27%)


BE329784
Glycine_max_release_2
770783
771288
Lipolytic enzyme = G-D-S-L






[Medicago truncatula (Barrel






medic)]


TA68573_3847
Glycine_max_release_2
773983
774836
Putative kinesin light chain






[Oryza sativa (japonica






cultivar-group)]


TC259227
GMGI.071508
773983
774836
similar to UniRef100_A7PD12






Cluster: Chromosome chr17






scaffold_12 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(13%)


AI759741
Glycine_max_release_2
774118
774822
Putative kinesin light chain






[Oryza sativa (japonica






cultivar-group)]


asmbl_11876
Vigna_unguiculata
774030
774978
NA


TC139308
MTGI.071708
774935
775598
similar to UniRef100_A7PMA1






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(34%)


AW186182
Glycine_max_release_2
775276
775796
Similarity to kinesin light chain






[Arabidopsis thaliana (Mouse-






ear cress)]


AW186182
GMGI.071508
775464
775796
similar to UniRef100_A7PD12






Cluster: Chromosome chr17






scaffold_12 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(16%)


BF010272
GMGI.071508
783671
784035
UniRef100_Q00K67 Cluster:






Major surface antigen; n = 1;






Hepatitis B virus|Rep: Major






surface antigen - Hepatitis B






virus (HBV) = partial (5%)


TA54422_3847
Glycine_max_release_2
783644
784982
Alcohol dehydrogenase






superfamily = zinc-containing






[Medicago truncatula (Barrel






medic)]


BI971258
Glycine_max_release_2
783921
784926
Auxin-induced protein [Vigna






radiata]


CV542673
Phaseolus_vulgaris_release_2
784213
785346
Quinone oxidoreductase-like






protein [Helianthus annuus






(Common sunflower)]


TC239445
GMGI.071508
783904
786356
similar to UniRef100_O23939






Cluster: Ripening-induced






protein; n = 1; Fragaria






vesca|Rep: Ripening-induced






protein - Fragaria vesca






(Woodland strawberry) = partial






(84%)


TA3037_3848
Glycine_soja_release_2
784204
786191
Quinone oxidoreductase-like






protein [Helianthus annuus






(Common sunflower)]


BG045149
Glycine_soja_release_2
784943
785469
Quinone oxidoreductase






[Fragaria ananassa






(Strawberry)]


TA54423_3847
Glycine_max_release_2
784420
786354
Quinone oxidoreductase-like






protein [Helianthus annuus






(Common sunflower)]


BG046280
Glycine_soja_release_2
786163
786344
NA


CA901808
Phaseolus_coccineus_release_2
800890
801759
Alcohol dehydrogenase






superfamily, zinc-containing






[Medicago truncatula (Barrel






medic)]


TA14086_34305
Lotus_japonicus_release_1
800932
801745
Alcohol dehydrogenase






superfamily, zinc-containing






[Medicago truncatula (Barrel






medic)] (SEQ ID NO: 15)


TC23841
LJGI.070108
800932
801745
similar to UniRef100_Q43677






Cluster: Auxin-induced protein,






n = 1, Vigna radiata|Rep: Auxin-






induced protein - Vigna radiata,






partial (40%)


M0093116
SEQ. Listing
805373
805788
SEQ ID NO: 6


TC252650
GMGI.071508
805357
806601
similar to UniRef100_Q43677






Cluster: Auxin-induced protein;






n = 1; Vigna radiata|Rep: Auxin-






induced protein - Vigna






radiata = partial (54%)


BARC-039375-07304
ePCR&blat
805660
806532
Map3.0 SNP L/Gm19 cM: 3.4


TA65006_3847
Glycine_max_release_2
805357
807089
Quinone oxidoreductase-like






protein [Helianthus annuus






(Common sunflower)]


TA65005_3847
Glycine_max_release_2
806611
807310
Alcohol dehydrogenase






superfamily = zinc-containing






[Medicago truncatula (Barrel






medic)]


TC274718
GMGI.071508
806611
807310
similar to UniRef100_Q43677






Cluster: Auxin-induced protein;






n = 1; Vigna radiata|Rep: Auxin-






induced protein - Vigna






radiata = partial (30%)


AW397551
Glycine_max_release_2
811245
811796
Auxin-induced protein [Vigna






radiata]


Pvcon4580
Phaseolus_vulgaris
811330
813524
UniRef100_Q43677 Auxin-






induced protein n = 1 Tax = Vigna






radiata






RepID = Q43677_9FABA






1.00E−133


asmbl_11877
Vigna_unguiculata
812523
812779
NA


BE608172
Glycine_max_release_2
821487
822389
Protein farnesyltransferase






subunit beta [Pisum sativum






(Garden pea)]


BQ273477
Glycine_max_release_2
821559
822383
NA


TC246895
GMGI.071508
821516
822443
similar to UniRef100_Q04903






Cluster: Protein






farnesyltransferase subunit






beta; n = 1; Pisum sativum|Rep:






Protein farnesyltransferase






subunit beta - Pisum sativum






(Garden pea) = partial (15%)


TC241767
GMGI.071508
824186
828116
similar to UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1; Quercus






robur|Rep: Formate






dehydrogenase - Quercus robur






(English oak) = partial (97%)


TA40711_3847
Glycine_max_release_2
824209
828372
Formate dehydrogenase






[Quercus robur (English oak)]


AI522957
Glycine_max_release_2
826883
827087
Formate dehydrogenase






[Quercus robur (English oak)]


BG044450
Glycine_soja_release_2
826544
827461
Formate dehydrogenase =






mitochondrial precursor






[Solanum tuberosum (Potato)]


asmbl_11878
Vigna_unguiculata
826586
827463
NA


CA800817
Glycine_soja_release_2
826705
827869
Formate dehydrogenase






[Quercus robur (English oak)]


TC240429
GMGI.071508
826957
828379
similar to UniRef100_Q9ZRI8






Cluster: Formate






dehydrogenase = mitochondrial






precursor; n = 1; Hordeum






vulgare|Rep: Formate






dehydrogenase = mitochondrial






precursor - Hordeum vulgare






(Barley) = partial (40%)


AW350528
Glycine_max_release_2
826986
828379
Formate dehydrogenase 1 =






mitochondrial precursor [Oryza






sativa (Rice)]


BG882062
Glycine_max_release_2
827372
828284
Formate dehydrogenase 1 =






mitochondrial precursor [Oryza






sativa (Rice)]


BE347639
Glycine_max_release_2
827443
828262
Formate dehydrogenase 1 =






mitochondrial precursor [Oryza






sativa (Rice)]


CA782711
Glycine_soja_release_2
827371
828357
Formate dehydrogenase 1 =






mitochondrial precursor [Oryza






sativa (Rice)]


TA40821_3847
Glycine_max_release_2
829640
832253
Formate dehydrogenase






[Quercus robur (English oak)]


BE330555
Glycine_max_release_2
829875
832057
Formate dehydrogenase =






mitochondrial precursor






[Solanum tuberosum (Potato)]


BU090495
Glycine_max_release_2
829863
832082
Formate dehydrogenase






[Quercus robur (English oak)]


BG044406
Glycine_soja_release_2
829915
832082
Formate dehydrogenase






[Quercus robur (English oak)]


AW508186
GMGI.071508
830914
831336
similar to UniRef100_A7PMA5






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(15%)


M0129925
SEQ LISTING
830552
831704
SEQ ID NO: 7


AW508186
Glycine_max_release_2
830914
831970
Formate dehydrogenase =






mitochondrial precursor






[Solanum tuberosum (Potato)]


AW508145
Glycine_max_release_2
830909
832061
Formate dehydrogenase






[Quercus robur (English oak)]


TA40373_3847
Glycine_max_release_2
830863
832118
Formate dehydrogenase






[Quercus robur (English oak)]


AW397259
Glycine_max_release_2
831219
832141
Formate dehydrogenase






[Quercus robur (English oak)]


TC261330
GMGI.071508
829795
833576
similar to UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1; Quercus






robur|Rep: Formate






dehydrogenase - Quercus robur






(English oak) = partial (96%)


TC249502
GMGI.071508
830866
832529
similar to UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1; Quercus






robur|Rep: Formate






dehydrogenase - Quercus robur






(English oak) = partial (72%)


TA40376_3847
Glycine_max_release_2
830879
833356
Formate dehydrogenase






[Quercus robur (English oak)]


asmbl_11879
Vigna_unguiculata
831735
833050
NA


AW569072
GMGI.071508
832471
832890
similar to UniRef100_Q7XHJ0






Cluster: Formate






dehydrogenase; n = 1; Quercus






robur|Rep: Formate






dehydrogenase - Quercus robur






(English oak) = partial (9%)


AW569072
Glycine_max_release_2
832471
832929
Formate dehydrogenase






[Quercus robur (English oak)]


TA40339_3847
Glycine_max_release_2
832130
833531
Formate dehydrogenase 1 =






mitochondrial precursor [Oryza






sativa (Rice)]


TA5191_3885
Phaseolus_vulgaris_release_2
832192
833517
Formate dehydrogenase






[Quercus robur (English oak)]


FD790937
Phaseolus_vulgaris
833039
833412
UniRef100_A6N0B2






Mitochondrial formate






dehydrogenase 1 (Fragment)






n = 1 Tax = Oryza sativa Indica






Group






RepID = A6N0B2_ORYSI






3.00E−30


CA913454
Phaseolus_coccineus_release_2
841331
841722
NA


TA70199_3847
Glycine_max_release_2
841305
841824
NA


asmbl_11880
Vigna_unguiculata
841326
841889
NA


TA3611_3848
Glycine_soja_release_2
841347
842640
Hypothetical protein






OJ1593_C11.11 [Oryza sativa






(japonicacultivar-group)]


TA5381_34305
Lotus_japonicus_release_1
841455
842700
Calcium homeostasis regulator






CHoR1 [Solanum tuberosum






(Potato)]


TC20706
LJGI.070108
841455
842700
weakly similar to






UniRef100_Q5QTN8 Cluster:






Calcium homeostasis regulator






CHoR1, n = 1, Solanum






tuberosum|Rep: Calcium






homeostasis regulator CHoR1 -






Solanum tuberosum (Potato),






partial (52%)


Pvcon2378
Phaseolus_vulgaris
841347
843522
UniRef100_A7PMA9






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMA9_VITVI






4.00E−94


TC252755
GMGI.071508
841305
843655
similar to UniRef100_A7PMA9






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(74%)


EX305183
Phaseolus_vulgaris
841682
843613
UniRef100_A7PMA9






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMA9_VITVI






1.00E−67


BI498351
GMGI.071508
844582
845168
NA


TA66563_3847
Glycine_max_release_2
844582
847078
Hypothetical protein [Ipomoea






trifida (Morning glory)]


TC247953
GMGI.071508
844582
847220
similar to UniRef100_A7Q5T8






Cluster: Chromosome chr14






scaffold_54 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_54 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(58%)


TA3593_3848
Glycine_soja_release_2
844668
847194
Hypothetical protein [Ipomoea






trifida (Morning glory)]


TA56324_3847
Glycine_max_release_2
854425
856413
Similarity to intracellular






protein [Arabidopsis thaliana






(Mouse-ear cress)]


TC235843
GMGI.071508
854425
856413
similar to UniRef100_A7PMB1






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(40%)


CD406351
Glycine_max_release_2
855627
856402
Similarity to intracellular






protein [Arabidopsis thaliana






(Mouse-ear cress)]


TC276442
GMGI.071508
855627
856402
similar to UniRef100_A7PMB1






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(14%)


TC273993
GMGI.071508
863632
864262
homologue to






UniRef100_A7PMB2 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(26%)


BU082700
Glycine_max_release_2
863841
864449
Hypothetical protein






OJ1126_B10.9 [Oryza sativa






(japonicacultivar-group)]






(SEQ ID NO: 14)


AW459960
Glycine_max_release_2
863632
865288
Hypothetical protein F4P13.4






[Arabidopsis thaliana (Mouse-






ear cress)]


AL385435
MTGI.071708
863952
865397
homologue to






UniRef100_A7PD25 Cluster:






Chromosome chr17






scaffold_12, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr17 scaffold_12, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(37%)


AI856244
GMGI.071508
864500
864958
UniRef100_A7PMB2 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(6%)


asmbl_11881
Vigna_unguiculata
863829
865710
NA


TC238318
GMGI.071508
863970
865869
homologue to






UniRef100_A7PMB2 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(34%)


TA63907_3847
Glycine_max_release_2
864500
865869
Hypothetical protein F4P13.4






[Arabidopsis thaliana (Mouse-






ear cress)]


BW598574
LJGI.070108
865265
865656
similar to UniRef100_Q8LES3






Cluster: Protein kinase, n = 1,






Arabidopsis thaliana|Rep:






Protein kinase - Arabidopsis






thaliana (Mouse-ear cress),






partial (9%)


BW598574
Lotus_japonicus_release_1
865265
865674
Protein kinase [Arabidopsis






thaliana (Mouse-ear cress)]


CD400016
Glycine_max_release_2
870972
871184
NA


CD399245
Glycine_max_release_2
870876
871427
Putative Peptidyl-prolyl cis-






trans isomerase = chloroplast






[Oryza sativa (japonica






cultivar-group)]


TC242592
GMGI.071508
870943
872827
similar to UniRef100_A6MZC4






Cluster: Peptidyl-prolyl cis-






trans isomerase; n = 2; Oryza






sativa|Rep: Peptidyl-prolyl cis-






trans isomerase - Oryza sativa






subsp. indica (Rice) = partial






(60%)


CB543642
Phaseolus_vulgaris_release_2
871229
872777
Peptidyl-prolyl cis trans






isomerase = chloroplast






precursor [Spinacia oleracea






(Spinach)]


TA52959_3847
Glycine_max_release_2
870943
873450
Poly(A) polymerase [Pisum






sativum (Garden pea)]


CB539263
Phaseolus_vulgaris_release_2
871195
873325
Poly(A) polymerase [Pisum






sativum (Garden pea)]


Pvcon1578
Phaseolus_vulgaris
870946
876143
UniRef100_O22636 Poly(A)






polymerase n = 1 Tax = Pisum






sativum RepID = O22636_PEA






E−0


TA10487_34305
Lotus_japonicus_release_1
873266
875963
Poly(A) polymerase [Pisum






sativum (Garden pea)]


TA6667_47247
Lotus_corniculatus_release_1
873266
875963
Poly(A) polymerase related






cluster


TC34747
LJGI.070108
873266
875963
similar to UniRef100_O22636






Cluster: Poly(A) polymerase,






n = 1, Pisum sativum|Rep:






Poly(A) polymerase - Pisum






sativum (Garden pea), partial






(57%)


BG363373
Glycine_max_release_2
874357
874944
Poly(A) polymerase [Pisum






sativum (Garden pea)]


TC251420
GMGI.071508
874369
876078
similar to UniRef100_O22636






Cluster: Poly(A) polymerase;






n = 1; Pisum sativum|Rep:






Poly(A) polymerase - Pisum






sativum (Garden pea) = partial






(37%)


CA901088
Phaseolus_coccineus_release_2
874490
876191
Poly(A) polymerase [Pisum






sativum (Garden pea)]


asmbl_11882
Vigna_unguiculata
886629
890018
NA


TA68870_3847
Glycine_max_release_2
886534
893419
Senescence-associated protein-






like [Oryza sativa (japonica






cultivar-group)]


TC270337
GMGI.071508
886672
893419
weakly similar to






UniRef100_A7PD28 Cluster:






Chromosome chr17






scaffold_12 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr17 scaffold_12 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(86%)


M0205537
SEQ. Listing
890458
890051
SEQ ID NO: 8


BM732054
Glycine_max_release_2
899859
901015
NA


BM732054
GMGI.071508
900006
901015
similar to UniRef100_Q04TD2






Cluster: MviN-related protein;






n = 1; Leptospira borgpetersenii






serovar Hardjo-bovis






JB197|Rep: = partial (2%)


toGm13
DAGchainer
816170
1014875
Ks0.1202


M0202715
SEQ. Listing
921233
921630
SEQ ID NO: 9


TA46168_3847
Glycine_max_release_2
921047
924660
Homeodomain leucine zipper






protein HDZ3 [Phaseolus






vulgaris (Kidney bean) (French






bean)]


TC260016
GMGI.071508
921056
924739
homologue to






UniRef100_Q93XA3 Cluster:






Homeodomain leucine zipper






protein HDZ3; n = 1; Phaseolus






vulgaris|Rep: Homeodomain






leucine zipper protein HDZ3 -






Phaseolus vulgaris (Kidney






bean) (French bean) = complete


Pvcon1101
Phaseolus_vulgaris
921086
924758
UniRef100_Q93XA3






Homeodomain leucine zipper






protein HDZ3 (Fragment) n = 1






Tax = Phaseolus vulgaris






RepID = Q93XA3_PHAVU






1.00E−124


TA3604_3885
Phaseolus_vulgaris_release_2
921111
924754
Homeodomain leucine zipper






protein HDZ3 [Phaseolus






vulgaris (Kidney bean) (French






bean)]


asmbl_11883
Vigna_unguiculata
921538
924758
NA


BG041631
Glycine_soja_release_2
923015
923340
Homeobox-leucine zipper






protein HAT5 [Arabidopsis






thaliana (Mouse-ear cress)]


AV421688
LJGI.070108
923118
924180
similar to UniRef100_Q93XA3






Cluster: Homeodomain leucine






zipper protein HDZ3, n = 1,






Phaseolus vulgaris|Rep:






Homeodomain leucine zipper






protein HDZ3 - Phaseolus






vulgaris (Kidney bean) (French






bean), partial (25%)


TC235979
GMGI.071508
923000
924768
similar to UniRef100_Q93XA3






Cluster: Homeodomain leucine






zipper protein HDZ3; n = 1;






Phaseolus vulgaris|Rep:






Homeodomain leucine zipper






protein HDZ3 - Phaseolus






vulgaris (Kidney bean) (French






bean) = partial (86%)


TA46165_3847
Glycine_max_release_2
923000
924779
Homeodomain leucine zipper






protein HDZ3 [Phaseolus






vulgaris (Kidney bean) (French






bean)]


AW351287
Glycine_max_release_2
923128
924720
Homeodomain leucine zipper






protein HDZ3 [Phaseolus






vulgaris (Kidney bean) (French






bean)]


CA785782
Glycine_soja_release_2
925713
925880
NA


Pvcon8364
Phaseolus_vulgaris
925735
926609
UniRef100_A7PMB7






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMB7_VITVI






1.00E−27


BE248998
MTGI.071708
926978
927524
similar to UniRef100_Q7F8S7






Cluster: PHD finger-like






protein, n = 1, Oryza sativa






Japonica Group|Rep: PHD






finger-like protein - Oryza






sativa subsp. japonica (Rice),






partial (4%)


TC35470
LJGI.070108
928423
929804
similar to UniRef100_A7PMB8






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(9%)


TA11035_34305
Lotus_japonicus_release_1
928423
929825
PHD finger-like protein [Oryza






sativa (japonica cultivar-






group)]


CA911004
Phaseolus_coccineus_release_2
934882
939256
T13O15.10 protein






[Arabidopsis thaliana (Mouse-






ear cress)]


AI856399
GMGI.071508
937577
938041
NA


AI856399
Glycine_max_release_2
937577
938106
NA


AW348703
Glycine_max_release_2
963043
963750
NA


TC276191
GMGI.071508
963049
964044
weakly similar to






UniRef100_A7PZY3 Cluster:






Chromosome chr8






scaffold_41 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr8






scaffold_41 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (21%)


BQ628183
Glycine_max_release_2
963625
964044
NA


BQ080193
Glycine_max_release_2
963695
967475
NA


TA52645_3847
Glycine_max_release_2
963720
967461
NA


TC256882
GMGI.071508
963774
967475
weakly similar to






UniRef100_A7PZY3 Cluster:






Chromosome chr8






scaffold_41 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr8






scaffold_41 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (45%)


BG156825
Glycine_max_release_2
971121
971284
NA


BG156825
GMGI.071508
971125
971284
NA


BU545761
Glycine_max_release_2
971300
971901
NA


BU550718
Glycine_max_release_2
971255
973578
NA


TA72701_3847
Glycine_max_release_2
972120
972806
NA


TC271942
GMGI.071508
972201
972806
NA


TC269989
GMGI.071508
971255
973827
similar to UniRef100_A7P2M9






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (63%)


BI317782
Glycine_max_release_2
971510
973827
NA


BI893512
Glycine_max_release_2
971537
973848
NA


BI893512
GMGI.071508
971671
973848
similar to UniRef100_A7P2M9






Cluster: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr1






scaffold_5 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (54%)


CO985587
Glycine_max_release_2
974859
976255
Putative GTP-binding






membrane protein LepA [Oryza






sativa (japonica cultivar-






group)]


AW596868
Glycine_max_release_2
976346
976856
NA


AW596868
GMGI.071508
976412
976856
similar to UniRef100_A2Q5T1






Cluster: Tetratricopeptide-like






helical; n = 1; Medicago






truncatula|Rep:






Tetratricopeptide-like helical -






Medicago truncatula (Barrel






medic) = partial (5%)


CA901672
Phaseolus_coccineus_release_2
983905
984264
Aldehyde dehydrogenase 1






precursor [Lotus corniculatus






(Bird's-foot trefoil)]


WmFPC_Contig4169

899736
1068750
NA


FE898889
Phaseolus_vulgaris
983908
984989
UniRef100_A7PD33






Chromosome chr17






scaffold_12, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PD33_VITVI 2.00E−79


TC273361
GMGI.071508
984396
986122
similar to UniRef100_P93344






Cluster: Aldehyde






dehydrogenase; n = 1; Nicotiana






tabacum|Rep: Aldehyde






dehydrogenase - Nicotiana






tabacum (Common tobacco) =






partial (37%)


BE473475
Glycine_max_release_2
984960
986122
Aldehyde dehydrogenase






[Nicotiana tabacum (Common






tobacco)]


CV539672
Phaseolus_vulgaris
985959
987101
UniRef100_P93344 Aldehyde






dehydrogenase (NAD+) n = 1






Tax = Nicotiana tabacum






RepID = P93344_TOBAC






7.00E−50


AV410805
LJGI.070108
987592
987888
similar to UniRef100_A7PMC7






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(6%)


TC265505
GMGI.071508
1011306
1012664
similar to UniRef100_A7PMD1






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(28%)


TA51641_3847
Glycine_max_release_2
1011306
1013783
Putative high-affinity potassium






transporter protein 1 [Nicotiana






tabacum (Common tobacco)]


CB540416
Phaseolus_vulgaris
1012333
1013531
UniRef100_A7PMD1






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD1_VITVI






5.00E−97


BM891067
GMGI.071508
1012675
1013617
similar to UniRef100_A7PMD1






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(22%)


TC131883
MTGI.071708
1012665
1014070
similar to UniRef100_A7PMD1






Cluster: Chromosome chr14






scaffold_21, whole genome






shotgun sequence, n = 1, Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21, whole






genome shotgun sequence -






Vitis vinifera (Grape), partial






(34%)


asmbl_11884
Vigna_unguiculata
1012674
1014123
NA


BE330787
Glycine_max_release_2
1013888
1014305
Putative high-affinity potassium






transporter protein [Phytolacca






esculenta (Food pokeberry)]


FD792954
Phaseolus_vulgaris
1013779
1014573
UniRef100_A7PMD1






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD1_VITVI






3.00E−57


TC244134
GMGI.071508
1014004
1014793
similar to UniRef100_A7PMD1






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(15%)


TA51642_3847
Glycine_max_release_2
1013926
1014875
Putative high-affinity potassium






transporter 1 [Nicotiana rustica






(Aztec tobacco)]


TC242106
GMGI.071508
1013926
1014875
similar to UniRef100_A7PMD1






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(15%)


BI970123
Glycine_max_release_2
1014128
1014721
Putative potassium transporter






HAK1p [Mesembryanthemum






crystallinum (Common ice






plant)]


BQ080303
Glycine_max_release_2
1018604
1019142
NA


TC270109
GMGI.071508
1018604
1019142
weakly similar to






UniRef100_UPI0000196D39






Cluster: NHL repeat-containing






protein; n = 1; Arabidopsis






thaliana|Rep: NHL repeat-






containing protein -






Arabidopsis thaliana = partial






(4%)


BQ080219
Glycine_max_release_2
1018604
1019579
NA


TA62145_3847
Glycine_max_release_2
1021347
1023221
NA


TC245123
GMGI.071508
1021347
1023221
similar to UniRef100_A7PMD2






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(31%)


asmbl_11885
Vigna_unguiculata
1022417
1022510
NA


CA784724
Glycine_max_release_2
1046117
1047384
NA


CA784724
GMGI.071508
1046400
1047384
similar to UniRef100_A7Q2E7






Cluster: Chromosome chr1






scaffold_46 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome chr1






scaffold_46 = whole genome






shotgun sequence - Vitis






vinifera (Grape) = partial (17%)


Pvcon4015
Phaseolus_vulgaris
1047011
1048610
UniRef100_A5ATC1 Putative






uncharacterized protein n = 1






Tax = Vitis vinifera






RepID = A5ATC1_VITVI






1.00E−146


BQ742289
Glycine_max_release_2
1048650
1048767
NA


BF068315
GMGI.071508
1057203
1057316
similar to UniRef100_Q8MIG1






Cluster: Skinkine; n = 1; Sus






scrofa|Rep: Skinkine - Sus






scrofa (Pig) = partial (12%)


BF068315
Glycine_max_release_2
1057203
1057506
NA


BU083500
GMGI.071508
1058026
1058431
UniRef100_Q2R023 Cluster:






Expressed protein; n = 1; Oryza






sativa Japonica Group|Rep:






Expressed protein - Oryza






sativa = partial (2%)


TA74227_3847
Glycine_max_release_2
1058026
1059408
NA


BI423963
GMGI.071508
1058432
1059275
similar to UniRef100_Q2QDD6






Cluster: Nodulin-like protein;






n = 1; Gossypium hirsutum|Rep:






Nodulin-like protein -






Gossypium hirsutum (Upland






cotton) (Gossypium






mexicanum) = partial (22%)


TC237120
GMGI.071508
1063015
1063972
UniRef100_Q39819 Cluster:






Hsp22.3; n = 1; Glycine






max|Rep: Hsp22.3 - Glycine






max (Soybean) = complete


CA802234
Glycine_soja_release_2
1061477
1067499
Similarity to nodulin






[Arabidopsis thaliana (Mouse-






ear cress)]


BI425574
GMGI.071508
1065519
1066854
weakly similar to






UniRef100_A7PMD8 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(21%)


BI425574
Glycine_max_release_2
1065519
1066940
Hypothetical protein [Medicago






truncatula (Barrel medic)]


AU251786
LJGI.070108
1066790
1067424
weakly similar to






UniRef100_A7Q2G7 Cluster:






Chromosome chr1 scaffold_46,






whole genome shotgun






sequence, n = 1, Vitis






vinifera|Rep: Chromosome chr1






scaffold_46, whole genome






shotgun sequence - Vitis






vinifera (Grape), partial (7%)


Pvcon8451
Phaseolus_vulgaris
1065511
1068752
UniRef100_A7PMD8






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD8_VITVI






7.00E−91


TC260900
GMGI.071508
1065796
1069134
weakly similar to






UniRef100_A7PMD8 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(41%)


TA63020_3847
Glycine_max_release_2
1067436
1069134
NA


CA783703
Glycine_soja_release_2
1068257
1068879
NA


TA58065_3847
Glycine_max_release_2
1074998
1076541
AT3g28050/MMG15_6






[Arabidopsis thaliana (Mouse-






ear cress)]


TC251785
GMGI.071508
1074998
1076541
similar to UniRef100_Q8L9I2






Cluster: Nodulin MtN21-like






protein; n = 1; Arabidopsis






thaliana|Rep: Nodulin MtN21-






like protein - Arabidopsis






thaliana (Mouse-ear cress) =






partial (16%)


CB280623
Phaseolus_vulgaris_release_2
1075036
1076540
AT3g28050/MMG15_6






[Arabidopsis thaliana (Mouse-






ear cress)]


EH043320
Arachis_stenosperma_release_5
1075056
1077422
Cluster: Hypothetical protein,






n = 1, Medicago truncatula|Rep:






Hypothetical protein -






Medicago truncatula (Barrel






medic)


asmbl_11886
Vigna_unguiculata
1075036
1077585
NA


BQ094260
Glycine_max_release_2
1075548
1077551
Nodulin-like protein






[Arabidopsis thaliana (Mouse-






ear cress)]


BF598290
Glycine_soja_release_2
1075557
1077593
Nodulin-like protein






[Arabidopsis thaliana (Mouse-






ear cress)]


Pvcon6314
Phaseolus_vulgaris
1075036
1078733
UniRef100_A7PMD8






Chromosome chr14






scaffold_21, whole genome






shotgun sequence n = 1






Tax = Vitis vinifera






RepID = A7PMD8_VITVI






1.00E−105


TA58064_3847
Glycine_max_release_2
1075337
1079189
AT3g28050/MMG15_6






[Arabidopsis thaliana (Mouse-






ear cress)]


TC255833
GMGI.071508
1075337
1079189
weakly similar to






UniRef100_A7PMD8 Cluster:






Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(64%)


BG042956
Glycine_soja_release_2
1078885
1079014
NA


TC263589
GMGI.071508
1086875
1091139
similar to UniRef100_A7PME0






Cluster: Chromosome chr14






scaffold_21 = whole genome






shotgun sequence; n = 1; Vitis






vinifera|Rep: Chromosome






chr14 scaffold_21 = whole






genome shotgun sequence -






Vitis vinifera (Grape) = partial






(35%)


TA50577_3847
Glycine_max_release_2
1086875
1094082
Alpha-dioxygenase [Pisum






sativum (Garden pea)]


asmbl_11887
Vigna_unguiculata
1089135
1092345
NA


CA410123
Lupinus_albus_release_2
1092182
1092694
Alpha-dioxygenase [Pisum






sativum (Garden pea)]


Pvcon4974
Phaseolus_vulgaris
1091225
1093836
UniRef100_Q5GQ66 Alpha-






dioxygenase n = 1 Tax = Pisum






sativum RepID = Q5GQ66_PEA






E−0


TC243973
GMGI.071508
1091177
1094141
similar to UniRef100_Q5GQ66






Cluster: Alpha-dioxygenase;






n = 1; Pisum sativum|Rep:






Alpha-dioxygenase - Pisum






sativum (Garden pea) = partial






(61%)


asmbl_11888
Vigna_unguiculata
1092518
1093829
NA


M0206054
SEQ. Listing
1465522
1465187
SEQ ID NO: 11


M0205375
SEQ. Listing
2010060
2009541
SEQ ID NO: 12


toGm13
DAGchainer
1046081
4647877
Ks0.2059


NA
Glyma1
1
50600000
NA









Sequences for the genes provided above can be obtained from the World Wide Web (or Internet) using the identifiers provided in Column 1 (Locus/Display Name) or Column 5 (ADDITIONAL LOCUS INFORMATION) from the following internet locations:

a) “soybase.org” (described in Grant et al., Nucleic Acids Research, 2010, Vol. 38, Database issue D843-D846) or soybase.org/gbrowse/cgi-bin/gbrowse/gmax1.01/(see Hyten D L, Choi I-Y, Song Q, Specht J E, Carter T E et al. (2010) A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Science 50:960-968. (Crop Science); and Hyten D L, Cannon S B, Song Q, Weeks N, Fickus E W et al. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11(1): 38);
b) “phytozome.net” or “phytozome.net/cgi-bin/gbrowse/soybean/?name=Gm09”;
c) “www.plantgdb.org” or “plantgdb.org/GmGDB/(Assembly version Glyrnal.170 (April 2009)”; and,
d) “ncbi.nlm.nih.gov/sites/entrez” and subsites “ncbi.nlm.nih.gov/nucest”, “ncbi.nlm.nih.gov/dbEST”, “ncbi.nlm.nih.gov/genbank/”, “.ncbi.nlm.nih.gov/sites/genome”, “ncbi.nlm.nih.gov/unigene”, and “ncbi.nlm.nih.gov/UniGene/UGOrg.cgi?TAXID=3847”.

## Claims

1. A method of breeding a soybean plant having a no flash locus, the method comprising:
(a) obtaining a population of soybean seed that is segregating for the no flash locus from:

(i) a cross of a first parental soybean plant comprising at least one no flash locus with a second parental soybean plant comprising at least one yellow flash locus; or
(ii) selfs of a plant or a population of plants segregating for the no flash locus,
(b) detecting at least one DNA polymorphism associated with a no flash phenotype in a soybean seed from the soybean seed population of step (a) with a nucleic acid analysis technique, wherein the DNA polymorphism is in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14),
(c) selecting said seed from the population of seed of step (b), wherein the selected seed comprises a genotype associated with the no flash phenotype,
(d) growing a progeny soybean plant from the selected seed of step (c); and,
(e) crossing or selfing the progeny soybean plant of step (d), thereby breeding the soybean plant having the no flash locus.

2. The method of claim 1, wherein said selected seed or progeny soybean plant grown therefrom comprises a transgene that confers tolerance to glyphosate.

3. The method of claim 2, wherein said progeny soybean plant of step (d) is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.

4. The method of claim 1, further comprising collecting seed having the no flash locus from the cross or self of step (e).

5. The method of claim 1, wherein said genotype associated with a no flash phenotype is detected by identifying at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16) and/or at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14) with a nucleic acid analysis technique.

6. The method of claim 1, wherein said genotype associated with a no flash phenotype is detected by identifying at least one polymorphic allele of at least one marker in said linkage group L region selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7) that is associated with a no flash phenotype with a nucleic acid analysis technique.

7. The method of claim 1, wherein the detecting is performed with a non-destructive genotypic assay.

8. A method of breeding soybean plants comprising the steps of:
(a) crossing a first parental soybean plant comprising at least one no flash locus with a second parental soybean plant comprising at least one yellow flash locus, or selfing a plant or population of plants segregating for a no flash locus, to obtain a population of soybean plants that is segregating for the no flash genotype;
(b) detecting at least one DNA polymorphism associated with the no flash phenotype in a soybean plant from the soybean plant population of step (a) with a nucleic acid analysis technique, wherein the DNA polymorphism is in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14);
(c) selecting a first soybean plant comprising a genotype in the linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) that is associated with a no flash phenotype from the population of soybean plants that is segregating for the no flash genotype; and,
(d) obtaining progeny soybean plants comprising the no flash genotype by crossing the selected first soybean plant of step (c) with a second soybean plant, or by selfing the first selected soybean plant of step (c), thereby breeding soybean plants.

9. The method of claim 8, wherein one or both of the first or the second soybean plant(s) comprises a transgene that confers glyphosate tolerance.

10. The method of claim 8, wherein the first soybean plant is selected by detecting with a nucleic acid analysis technique at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16), at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14), or at least one polymorphic allele of at least one marker in both the first and second sub-regions, wherein said polymorphic allele is associated with a no flash phenotype.

11. The method of claim 10, wherein first soybean plant is selected by detecting at least one polymorphic allele of at least one marker in said linkage group L region selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7) that is associated with a no flash phenotype with the nucleic acid analysis technique.

12. A method for obtaining a soybean plant comprising in its genome at least one no flash locus, the method comprising the steps of:
(a) crossing a parent plant comprising at least one no flash locus with a parent plant comprising at least one yellow flash locus;
(b) genotyping progeny soybean plants obtained from the cross of step (a) with respect to at least one no flash locus in a first linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14); and
(c) selecting a progeny soybean plant comprising in its genome at least one no flash locus comprising a genotype associated with no flash phenotype, wherein the selected plant exhibits a no flash phenotype, thereby obtaining a soybean plant comprising in its genome at least one no flash locus.

13. The method of claim 12, wherein said genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14).

14. The method of claim 12, wherein said genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in said first linkage group L region, wherein said marker is selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7).

15. The method of claim 14, wherein said genotype associated with a no flash phenotype comprises polymorphic alleles of the markers M0101742 and M0129925.

16. The method of claim 12, wherein said parent plant with a no flash locus comprises no flash germplasm deposited with the American Type Culture Collection (ATCC), and wherein said germplasm is selected from the group consisting of ATCC PTA-269, ATCC PTA-9064, ATCC 203207, ATCC PTA-5727, ATCC PTA-9070, ATCC PTA-2577, ATCC PTA-9029, ATCC 203939, ATCC PTA-9023, ATCC PTA-5738, ATCC PTA-5299, ATCC PTA-3870, ATCC PTA-9003, ATCC PTA-9066, ATCC PTA-2214, ATCC PTA-9702, ATCC PTA-6187, ATCC PTA 6272, and ATCC PTA-9027.

17. The method of claim 12, wherein said selected progeny plant of step (c) comprises a transgene that confers tolerance to glyphosate.

18. The method of claim 12, further comprising the step of assaying for the presence of at least one additional marker, wherein said additional marker is either linked or unlinked to said linkage group L genomic region.

19. The method of claim 12, wherein said selected soybean plant is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.

20. A method for obtaining a soybean plant that exhibits a no flash phenotype comprising the steps of:
(a) crossing a soybean plant that exhibits a no flash phenotype with a soybean plant that exhibits a yellow flash phenotype, wherein at least one of the soybean plants comprises a transgene that confers tolerance to glyphosate; and
(b) selecting a progeny plant from the cross for a no flash genotype by genotyping the progeny plant for presence of a no flash locus in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO: 14) with a nucleic acid analysis technique, wherein the selected progeny plant comprises the transgene that confers glyphosate tolerance, thereby obtaining a soybean plant that exhibits a no flash phenotype.

21. The method of claim 20, wherein said genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in a first sub-region of said linkage group L region that is flanked by loci BG406195 (SEQ ID NO: 13) and BU551345 (SEQ ID NO: 16); and/or at least one polymorphic allele of at least one marker in a second sub-region of said linkage group L region that is flanked by loci TA14086_34305 (SEQ ID NO: 15) and BU082700 (SEQ ID NO: 14).

22. The method of claim 20, wherein said genotype associated with a no flash phenotype comprises at least one polymorphic allele of at least one marker in said first linkage group L region, wherein said marker is selected from the group consisting of M0129138 (SEQ ID NO:4), M0101742 (SEQ ID NO:5), M0093116 (SEQ ID NO:6), and M0129925 (SEQ ID NO:7).

23. The method of claim 20, wherein said genotype associated with a no flash phenotype comprises polymorphic alleles of the markers M0101742 and M0129925.

24. The method of claim 20, wherein said parent plant that exhibits a no flash phenotype comprises no flash germplasm deposited with the American Type Culture Collection (ATCC), wherein said germplasm is selected from the group consisting of ATCC PTA-269, ATCC PTA-9064, ATCC 203207, ATCC PTA-5727, ATCC PTA-9070, ATCC PTA-2577, ATCC PTA-9029, ATCC 203939, ATCC PTA-9023, ATCC PTA-5738, ATCC PTA-5299, ATCC PTA-3870, ATCC PTA-9003, ATCC PTA-9066, ATCC PTA-2214, ATCC PTA-9702, ATCC PTA-6187, ATCC PTA 6272, and ATCC PTA-9027.

25. A method of breeding a soybean plant having a DNA polymorphism associated with a no flash phenotype, the method comprising:
(a) obtaining a population of soybean seed that is segregating for the no flash locus from:
(i) a cross of a first parental soybean plant comprising at least one no flash locus with a second parental soybean plant comprising at least one yellow flash locus; or,
(ii) selfs of a plant or a population of plants segregating for the no flash locus,
(b) detecting with a marker assay at least one DNA polymorphism associated with the no flash phenotype in a soybean seed from the seed population of (a), wherein the DNA polymorphism is in a linkage group L genomic region flanked by loci BG406195 (SEQ ID NO: 13) and BU082700 (SEQ ID NO:14),
(c) denoting the seed from step (b) with the polymorphism associated with the no flash phenotype,
(d) growing a progeny soybean plant from the denoted seed of step (c); and,
(e) crossing or selfing the progeny soybean plant from step (d), thereby breeding the soybean plant having the DNA polymorphism associated with a no flash phenotype.

26. The method of claim 25, wherein said progeny soybean plant comprises a transgene that confers tolerance to glyphosate and is exposed to a dosage of glyphosate sufficient to cause yellow flash in a susceptible variety.