INTERNATIONAL PATENT APPLICATION

MOLECULAR MARKERS AND PHENOTYPIC SCREENING FOR METRIBUZIN

TOLERANCE

Cross-Reference to Related Applications

[0001] This application claims the benefit of United States Provisional Application Serial No. 61/694,990 filed August 30, 2012, which is incorporated herein by reference in its entirety.

Incorporation of Sequence Listing

[0002] A sequence listing containing the file named "46_21_59410.txt" which is 21,685 bytes (measured in MS-Windows®) and created on August 26, 2013, contains 42 nucleotide sequences, is provided herewith via the USPTO's EFS system, and is incorporated herein by reference in its entirety.

Incorporation of Table 2

[0003] A listing of various soybean linkage group N (chromosome 3) markers is provided herewith in the Specification as Table 2. Table 2 is provided at the end of the specification following the Examples and is incorporated herein in its entirety.

Background

[0004] Distinct soybean varieties have been shown to exhibit different degrees of tolerance to the herbicide metribuzin (Wax et al. Agron. Journal. 68:484-486, 1976). Genetic linkage between soybean loci associated with Phytophora resistance and loci associated with metribuzin tolerance have also been reported (Klein, Journal of Heredity, 77(4):275-277, 1986).

Summary

[0005] "Metribuzin sensitivity" is an undesirable phenotype observed in certain soybean varieties. It has been discovered that after application of metribuzin, the leaves of certain soybean plant varieties can exhibit a "metribuzin sensitivity phenotype" ranging from mild leaf chlorosis and/or necrosis to severe leaf chlorosis and/or necrosis upon exposure to metribuzin. In the most extreme cases, application of metribuzin to certain sensitive soybean varieties that exhibit severe leaf chlorosis and/or necrosis can result in plant death. However, other tolerant soybean varieties that are exposed to metribuzin in parallel with the sensitive soybean varieties will exhibit little to no leaf chlorosis and/or necrosis and will complete their life cycle. The metnbuzin sensitivity phenotype can be observed within about 7 to about 21 days after herbicide application in certain soybean varieties that are sensitive to metribuzin. The metribuzin sensitivity phenotype is undesirable as it can lead to reduced yield in certain soybean plant varieties exposed to metribuzin.

[0006] Provided herein are soybean plants comprising an introgressed genomic region associated with a metribuzin tolerance phenotype. Also provided herein are markers that reside outside of a genomic region associated with a metribuzin tolerance 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 metribuzin tolerance phenotype are also provided. Methods of obtaining a soybean plant that exhibits a metribuzin tolerance phenotype and methods of obtaining a soybean plant comprising in its genome at least one metribuzin tolerance locus are also provided. Methods that provide for the introgression of a genomic region associated with a metribuzin tolerance phenotype into soybean germplasm that has a genomic region associated with a metribuzin sensitivity phenotype are also provided. Identification of molecular markers associated with loci that confer the metribuzin tolerance phenotype has significant economic value. By using markers associated with the metribuzin tolerance trait, breeders can select soybean varieties with the favorable alleles (i.e. alleles that are not associated with the metribuzin sensitivity 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 metribuzin sensitivity trait) in soybeans. In certain embodiments, commercially desirable soybean lines that carry a genomic region that is associated with a "metribuzin tolerance" phenotype and tolerate dosages of metribuzin sufficient to provide for control of undesirable weeds are thus provided.

[0007] Methods for selecting a metribuzin tolerant plant from a population of plants comprising both metribuzin sensitive and metribuzin tolerant plants are provided. In certain embodiments, the plurality of soybean plants comprises a population that is obtained by: i) crossing a parent plant comprising at least one metribuzin tolerance locus with a parent plant comprising at least one metribuzin sensitivity locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one metribuzin tolerance locus. In certain embodiments, the aforementioned methods can further comprise the step of assaying for the presence of at least one additional marker, where the additional marker is either linked or unlinked to the linkage group N 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 metribuzin sufficient to cause metribuzin sensitivity in a sensitive variety. In certain embodiments of the aforementioned methods, a plant that exhibits a metribuzin tolerance phenotype is selected.

[0008] Also provided herewith are methods for producing a soybean plant comprising in its genome at least one introgressed metribuzin tolerance locus. Also provided herewith are soybean plants comprising an introgressed metribuzin tolerance locus made by the aforementioned methods. In certain embodiments, a soybean plant comprising an introgressed metribuzin tolerance locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a metribuzin tolerant soybean variety and that are linked to the introgressed metribuzin tolerance locus, where the plant is produced by the aforementioned methods are provided.

[0009] Also provided are soybean plants comprising an introgressed metribuzin tolerance locus and one or more polymorphic loci comprising alleles or combinations of alleles that are not found in a metribuzin tolerant soybean variety and that are linked to the introgressed metribuzin tolerance locus.

[0010] Methods for obtaining a soybean plant comprising in its genome at least one metribuzin tolerance locus, compromising the steps of: genotyping a plurality of soybean plants with respect to at least one genetic locus in a linkage group N genomic region flanked by loci NGMAX006077640 (SEQ ID NO: 3) and NSO 138011 (SEQ ID NO: 9); and selecting a soybean plant comprising in its genome at least one genetic locus comprising a genotype associated with metribuzin tolerance are provided herein. In certain embodiments, the genotype associated with metribuzin tolerance comprises at least one polymorphic allele of at least one marker in a sub-region of the linkage group N region flanked by loci

NGMAX006077928 (SEQ ID NO: 4) and NGMAX006080885 (SEQ ID NO: 8). In certain embodiments of the aforementioned methods, the genotype associated with metribuzin tolerance comprises at least one polymorphic allele of at least one marker in the first linkage group N region or the sub-region, wherein the marker comprises a TT allele of

NGMAX006079502 (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 metribuzin tolerance locus with a parent plant comprising at least one metribuzin sensitivity locus; or, ii) obtaining seed or progeny from a parental plant segregating for at least one metribuzin tolerance locus. In certain embodiments, the population contains plants that contain a transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. In certain embodiments, the 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 N genomic region. In certain embodiments, the methods can comprise exposing the selected soybean plant or progeny thereof comprising the genetic locus to a dosage of metribuzin sufficient to cause a deleterious effect in a variety that is moderately sensitive or sensitive to metribuzin and isolating a metribuzin tolerant plant therefrom. In certain embodiments, the selection comprises exposing a genotyped soybean plant comprising the genetic locus to a dosage of metribuzin sufficient to cause a deleterious effect in a variety that is moderately sensitive or sensitive to metribuzin and isolating a metribuzin tolerant plant therefrom.

[0011] Methods for producing a soybean plant comprising in its genome at least one introgressed metribuzin tolerance locus comprising the steps of: crossing a first soybean plant with a metribuzin tolerance locus with a second soybean plant comprising: a metribuzin sensitivity locus in a first linkage group N genomic region flanked by loci

NGMAX006077640 (SEQ ID NO: 3) and NS0138011 (SEQ ID NO: 9) and at least one linked polymorphic locus not present in the first soybean plant to obtain a population segregating for the metribuzin tolerance loci and the linked polymorphic locus; 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 linkage group N region and wherein at least one of the polymorphic amino acids is a linked polymorphic locus not present in the first soybean plant; and selecting a soybean plant comprising a genotype associated with metribuzin tolerance and at least one linked marker found in the second soybean plant comprising a metribuzin sensitivity locus but not found in the first soybean plant, thereby obtaining a soybean plant comprising in its genome an introgressed metribuzin tolerance locus are also provided. In certain embodiments, at least one of the first or the second soybean plants comprises a transgene that confers resistance to dicamba and/or a transgene that confers resistance to glyphosate. In certain embodiments of the methods, the population, the selected soybean plant, and/or progeny of the selected soybean plant is exposed to a dosage of metribuzin sufficient to cause a deleterious effect in a metribuzin sensitive variety. In certain embodiments of the methods, the polymorphic nucleic acid detected in step (b) is detected with marker NGMAX006079502 (SEQ ID NO: 7). In certain embodiments of the methods, the polymorphic nucleic acid detected in step (b) comprises a

TT allele of NGMAX006079502 (SEQ ID NO: 7). In certain embodiments of any of the aforementioned methods, the linked polymorphic locus is detected with a genotypic marker, a phenotypic marker, or both. In certain embodiments of any of the aforementioned 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 metribuzin tolerance locus. In certain embodiments of any of the aforementioned methods, the linked polymorphic locus is detected with at least one marker selected from the group consisting of NGMAX006083631 (SEQ ID NO: 10), NS0202926 (SEQ ID NO: 11), NGMAX006084289 (SEQ ID NO: 12), and NGMAX006088354 (SEQ ID NO: 13).

[0012] Also provided herein are soybean plants made any of the aforementioned methods, wherein the soybean plant comprises an introgressed metribuzin tolerance locus.

[0013] Also provided herein are soybean plants comprising an introgressed metribuzin tolerance locus, wherein at least one linked marker found in the soybean plant is characteristic of germplasm comprising a metribuzin sensitivity locus and is not associated with germplasm comprising the metribuzin tolerance locus. In certain embodiments, the introgressed metribuzin tolerance locus comprises a TT allele of NGMAX006079502 (SEQ ID NO: 7).

[0014] Also provided herein are soybean plants comprising an introgressed metribuzin tolerance locus, wherein at least one linked marker found in the soybean plant is characteristic of parental germplasm comprising a metribuzin sensitivity locus but is not associated with germplasm comprising the metribuzin tolerance locus. In certain embodiments, the introgressed metribuzin tolerance locus comprises a TT allele of NGMAX006079502 (SEQ ID NO: 7). In certain embodiments, the linked marker is selected from the group consisting of NGMAX006083631 (SEQ ID NO: 10), NS0202926 (SEQ ID NO: 11), NGMAX006084289 (SEQ ID NO: 12), and NGMAX006088354 (SEQ ID NO: 13). In certain embodiments, the linked marker comprises at least one of: a TT or a CT allele of NGMAX006083631 (SEQ ID NO: 10), an AC allele of NS0202926 (SEQ ID NO: 11), a GG allele of NGMAX006084289 (SEQ ID NO: 12), or a GG allele of NGMAX006088354 (SEQ ID NO: 13).

[0015] Methods of identifying a soybean plant that comprises a genotype associated with metribuzin tolerance, comprising: detecting in a soybean plant an allele in at least one genetic locus associated with metribuzin tolerance, wherein the genetic locus is in a linkage group N genomic region flanked by loci NGMAX006077640 (SEQ ID NO: 3) and NS0138011 (SEQ

ID NO: 9), and denoting that the plant comprises a genotype associated with metribuzin tolerance are also provided. In certain embodiments, the methods can further comprise the step of selecting the denoted plant from a population of plants. In certain embodiments, the methods can further comprise the steps of exposing the denoted soybean plant or progeny thereof to a dosage of metribuzin sufficient to cause a deleterious effect in a variety that is moderately sensitive or sensitive to metribuzin and scoring the exposed plants for metribuzin tolerance. In certain embodiments, the selection comprises exposing the denoted soybean plant or progeny thereof comprising the genetic locus to a dosage of metribuzin sufficient to cause a deleterious effect in a variety that is moderately sensitive or sensitive to metribuzin and isolating a metribuzin tolerant plant therefrom. In certain embodiments, the genotype associated with a metribuzin tolerance comprises at least one polymorphic allele of at least one marker in a sub-region of the linkage group N region that is flanked by loci NGMAX006077928 (SEQ ID NO: 4) and NGMAX006080885 (SEQ ID NO: 8). In certain embodiments, the genotype associated with metribuzin tolerance comprises at least one polymorphic allele of at least one marker in the linkage group N region or sub-region that comprises a TT allele of NGMAX006079502 (SEQ ID NO: 7).

[0016] Methods of producing a population of soybean plants with a metribuzin tolerance phenotype are also provided. In certain embodiments, these methods of producing a population of soybean plants comprising a genotype associated with a metribuzin tolerance phenotype can comprise: providing a first population of soybean plants, detecting in the soybean plants of the first population an allele in at least one metribuzin tolerance marker locus associated with a metribuzin tolerance phenotype wherein the metribuzin tolerance marker locus is in a linkage group N genomic region flanked by or including: a) NGMAX006077640 (SEQ ID NO: 3) and NS0138011 (SEQ ID NO: 9); or b) NGMAX006077928 (SEQ ID NO: 4) and NGMAX006080885 (SEQ ID NO: 8); selecting one or more soybean plants exhibiting an allele in the at least one metribuzin tolerance locus from the first population of soybean plants; and producing offspring from the one or more selected soybean plants. In certain embodiments, the genotype associated with metribuzin tolerance comprises at least one polymorphic allele of at least one marker in the first linkage group N region or the sub-region, wherein the marker comprises a TT allele of NGMAX006079502 (SEQ ID NO:7). In certain embodiments, the genotype associated with metribuzin tolerance comprises at least one polymorphic allele of at least one marker in the linkage group N region or sub-region that comprises a TT allele of NGMAX006079502 (SEQ ID NO: 7).

[0017] 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

Definitions

[0018] 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.

[0019] 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) tag, 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.

[0020] 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.

[0021] As used herein, "linkage group N" corresponds to the soybean linkage group N described in Choi, et al, Genetics. 2007 May; 176(1): 685-696. Linkage group N, as used herein, also corresponds to soybean chromosome 3 (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.

[0022] 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.

[0023] 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. [0024] 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.

[0025] 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. Introgression 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 metribuzin sensitivity locus with a corresponding metribuzin tolerance locus or by conversion of a locus from a metribuzin sensitivity genotype to a metribuzin tolerance genotype.

[0026] As used herein, "phenotype" means the detectable characteristics of a cell or organism which can be influenced by gene expression.

[0027] 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 ¼ of the gametes will of each genotype. Segregation of gametes into a genotypes differing from ¼ are attributed to linkage.

[0028] 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.

[0029] 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.

[0030] 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.

[0031] 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.

[0032] 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.

[0033] 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.

[0034] As used herein, the phrase "metribuzin sensitivity" refers to undesirable phenotypic traits observed in certain soybean germplasms after exposure to metribuzin at a rate of about 0.25 pounds per acre of metribuzin acid to about 0.75 pounds per acre of metribuzin. Such undesirable phenotypic traits include, but are not limited to, leaf chlorosis, leaf necrosis, and plant death.

[0035] As used herein, the phrase "metribuzin tolerant" refers to either the absence or reduction of undesirable phenotypic traits observed after exposure to metribuzin in "metribuzin sensitive" soybean germplasms.

[0036] As used herein, the term "comprising" means "including but not limited to." Description

[0037] In accordance with the present invention, Applicants have discovered genomic regions, associated markers, and associated methods for identifying and associating genotypes that effect the levels of metribuzin tolerance observed in soybean plants. Metribuzin ( 4-Amino-6-(l,l-dimethylethyl)-3-(methylthio)-l,2,4-triazin-5 (4H)-one) is a useful broad spectrum herbicide for controlling weeds. For example, in one embodiment, a method of the invention comprises screening a plurality of germplasm entries displaying a heritable variation for at least one metribuzin tolerance trait wherein the heritable variation is linked to at least one genotype; and associating at least one genotype from the germplasm entries to at least one metribuzin 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 metribuzin 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 metribuzin tolerance trait.

[0038] 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 (US Patent 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 "metribuzin tolerance" or "metribuzin sensitivity" phenotype can be supplanted by genotypic assays that provide for identification of a plant or plants that contain the desired genomic region that confers metribuzin tolerance. A Genomic Region Associated with a Metribuzin Tolerance Phenotype

[0039] Provided herewith is a soybean genomic region that is shown herein to be associated with a desirable metribuzin tolerance phenotype when present in certain allelic forms.

[0040] A soybean genomic region provided that can be associated with a desirable metribuzin tolerance phenotype when present in certain allelic forms is located on the telomere proximal end of the short arm of soybean linkage group N (chromosome 3). 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 N (soybean chromosome 3), and sources for the markers.

[0041] Table 1. Markers spanning a genomic region associated with a desirable metribuzin tolerance phenotype

The relative positions of the approximate middle position of the listed markers or loci based on nucleotide positions on a physical map of soybean linkage group N (chromosome 3) of Table 2 are provided where nucleotide position 2,987,781 is telomere proximal and nucleotide position 4,075,437 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.)

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

The identified polymorphic allele of marker is located at nucleotide 201 of SEQ ID NO: 7.

[0042] Also provided herein are sub-regions of the linkage group N region that is flanked by loci NGMAX006077640 (SEQ ID NO: 3) and NS0138011 (SEQ ID NO: 9) that are associated with a metribuzin tolerance phenotype. These loci flank a region that spans telomere proximal nucleotide 3,209,230 to centromere proximal nucleotide 3,801,607 in the physical map of linkage group N provided in Table 2 of the specification. A first sub-region of the linkage group N region associated with a metribuzin tolerance phenotype is flanked by loci NGMAX006077928 (SEQ ID NO: 4) and NGMAX006080885 (SEQ ID NO: 8). These loci flank a sub-region that spans telomere proximal nucleotide 3,238,990 to centromere proximal nucleotide 3,562,215 in the physical map of linkage group N provided in Table 2 of the specification. Polymorphisms located in this first sub-region that are associated with a metribuzin tolerance phenotype can be detected with markers that include, but are not limited to, NGMAX006079502 (SEQ ID NO: 7). In certain embodiments, a polymorphism in the region or the sub-region is detected with marker NGMAX006079502 (SEQ ID NO: 7). In certain embodiments, the alleles of this marker associated with metribuzin tolerance are a TT allele of NGMAX006079502 (SEQ ID NO: 7).

[0043] 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(l):685-96, 2007; Yoon et al., Theor Appl Genet. 2007 Mar;l 14(5):885-99; and Hyten et al. Crop Sci. 2010 50: 960-968. Given the provision herein of a genomic region on linkage group N (chromosome 3) delimited or flanked by the telomere proximal locus NGMAX006077640 (SEQ ID NO: 3) of Table 2 and the centromere proximal locus and NS0138011 (SEQ ID NO: 9) of Table 2 as well as an assortment of soybean germplasms exhibiting either a "metribuzin sensitivity" or "metribuzin tolerant" 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 N (chromosome 3) delimited or flanked by the telomere proximal locus NGMAX006077640 (SEQ ID NO: 3) of Table 2 and the centromere proximal locus NS0138011 (SEQ ID NO: 9) 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. In this regard, publicly available markers SATJ86, SATT152, SATT641, SATT009, and SATT149 can be used to place the linkage group N (chromosome 3) delimited or flanked by the telomere proximal locus NGMAX006077640 (SEQ ID NO: 3) of Table 2 and the centromere proximal locus NS0138011 (SEQ ID NO: 9) on publically available soybean genetic maps.

Identification of Plants Exhibiting the "Metribuzin sensitivity" or "Metribuzin Tolerance" Phenotype

[0044] To observe the presence or absence of the "metribuzin sensitivity" or metribuzin tolerance phenotypes, soybean plants are typically exposed in early to mid- vegetative growth stages to one or more doses of metribuzin. Typical doses of metribuzin that can elicit a metribuzin sensitivity phenotype can range from about a 1-fold label application rate of a commercially available metribuzin formulation (i.e. about 0.25 pounds per acre) to about a 3- fold label application rate (i.e. about 0.75 pounds per acre) of a commercially available metribuzin formulation. Commercially available formulations containing metribuzin that can be used include, but are not limited to, Authority®MTZ (FMC Corporation, Philadelphia, PA, USA); Boundary ® (Syngenta, Wilmington, Delaware, USA); Canopy® or Lexone® (Dupont, Wilmington, DE, USA); Sencor® (Bayer Crop Science, Research Triangle Park, NC, USA); or TriCor® DF (United Phosphorus, Inc., King of Prussia, PA, USA. In certain embodiments, the commercially available metribuzin formulation used is TriCor® 75DF. In certain embodiments, doses of metribuzin that can elicit a metribuzin sensitivity phenotype can range from about a 1 fold application rate of about 0.25 pounds per acre to about a three fold application rate of 0.75 pounds per acre. [0045] The metribuzin sensitivity phenotype can be observed approximately one week to three weeks after herbicide application in certain soybean varieties that are sensitive to metribuzin. Metribuzin is typically applied during pre and post-emergent vegetative growth stages. In certain embodiments of these methods, metribuzin can be applied to the soil about 2 days prior to soybean seed planting and activated by irrigation of the planted seed to score for the presence of the metribuzin sensitivity phenotype. Genotypes provided herein are especially useful for providing metribuzin tolerance to plants exposed to metribuzin by a pre- emergence soil drench. As discussed herein, the vegetative stages of soybean are as follows: VE (emergence), VC (cotyledon stage), VI (first trifoliate leaf), V2 (second trifoliate leaf), V3 (third trifoliate leaf), V(n) (nth trifoliate leaf), and V6 (flowering will soon start). As discussed herein, the reproductive stages of soybean are as follows: Rl (beginning bloom), R2 (full bloom), R3 (beginning pod), R4 (full pod), R5 (beginning seed), R6 (full seed), R7 (beginning maturity) and R8 (full maturity). A description of the soybean vegetative and reproductive stages can be found on the World Wide Web (internet) at ag.ndsu.edu/pubs/plantsci/rowcrops/al l74/al l74w.htm (North Dakota State University publication A-l 174, June 1999, Reviewed and Reprinted August 2004).

[0046] A rating scale that evaluates the degree of metribuzin sensitivity can also be employed to identify "metribuzin sensitive" and "metribuzin tolerant" plants. An exemplary and non- limiting scale for evaluating the Metribuzin sensitivity phenotype is as follows, where a low number corresponds to a "metribuzin tolerance" phenotype and the a high number correlates to a "metribuzin sensitivity" phenotype:

A rating of 1: Little to no leaf chlorosis/necrosis

A rating of 3: Mild leaf chlorosis/necrosis; plants survive and make full recovery A rating of 4: Moderate leaf chlorosis/necrosis; plants survive and make full recovery A rating of 6: Moderate leaf chlorosis/necrosis; plants survive and typically recover A rating of 7: Severe leaf chlorosis/necrosis; plants survive and typically recover;

A rating of 9: Severe chlorosis/necrosis; plants survive leading to plant death

Introgression of a Genomic Region Associated with a Metribuzin Tolerance Phenotype

[0047] Also provided herewith is unique soybean germplasm comprising an introgressed genomic region that is associated with a metribuzin tolerance 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 metribuzin tolerance germplasm) and both linked and unlinked markers characteristic of the desired genetic background of a second germplasm (i.e. a metribuzin sensitivity germplasm). In addition to the markers provided herewith that identify alleles of genomic region that is associated with a metribuzin tolerance phenotype, flanking markers that fall on both the telomere proximal end of the genomic region on linkage group

N (chromosome 3) and the centromere proximal end of the linkage group N (chromosome 3) genomic region are also provided in Tables 1 and 2. Table 2 is provided at the end of the specification immediately before the claims. 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 metribuzin tolerance 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 "Metribuzin sensitivity" phenotype. Telomere proximal flanking markers that can be used in these methods include, but are not limited to,

NS0206337 (SEQ ID NO: 1), NS0262835 (SEQ ID NO: 21), NGMAX006076547 (SEQ ID

NO: 18), NGMAX006076962 (SEQ ID NO: 22), NGMAX006077074 (SEQ ID NO: 2),

NGMAX006077513 (SEQ ID NO: 23), SAT_186, and NGMAX006077555 (SEQ ID NO:

24), and/or polymorphisms in any of the loci listed in Table 2 of the Specification located between starting base 2,994,256 (the telomere proximal base) of locus NS0206337 (SEQ ID

NO: 1) and starting base 3389647 of centromere proximal locus NGMAX006079484 (SEQ

ID NO: 6). Centromere proximal flanking markers that can be used in these methods include, but are not limited to, NGMAX006082782 (SEQ ID NO: 25), NGMAX006083256 (SEQ ID

NO: 26), NGMAX006083447 (SEQ ID NO: 27), NGMAX006083554 (SEQ ID NO: 28),

NGMAX006083631 (SEQ ID NO: 10), NS0202926 (SEQ ID NO: 11), NGMAX006084289

(SEQ ID NO: 12), and NGMAX006088354 (SEQ ID NO: 13) and/or polymorphisms in any of the other loci listed in Table 2 that are centromere proximal to NS0138011 (SEQ ID NO:

9). Soybean plants wherein the sub regions that is flanked by loci NGMAX006077928 (SEQ

ID NO: 4) and NGMAX006080885 (SEQ ID NO: 8) is introgressed can be obtained by using the NGMAX006077878 (SEQ ID NO: 19), NGMAX006078122 (SEQ ID NO: 29),

NGMAX006078495 (SEQ ID NO: 30), NS0262836 (SEQ ID NO: 31), NGMAX006078838

(SEQ ID NO: 5), NGMAX006079484 (SEQ ID NO: 6), SATT152, SATT641,

NGMAX006081942 (SEQ ID NO: 32), NGMAX006081999 (SEQ ID NO: 33),

NGMAX006082115 (SEQ ID NO: 34), NGMAX006082688 (SEQ ID NO: 35),

NGMAX006082778 (SEQ ID NO: 36), NS0118425 (SEQ ID NO: 37), NGMAX006080509 (SEQ ID NO: 38), or NGMAX006079911 (SEQ ID NO: 20) markers, or by using any of the markers located between this subregions and the telomere and/or centromere proximal portions of the genome that are provided in Table 2. Any of the aforementioned polymorphisms can be identified by sequencing loci from metribuzin sensitivity and metribuzin tolerance germplasms. Additional markers located on linkage group N (chromosome 3) and other chromosomes are disclosed in US Patent Application Publication 2009/0208964. Publicly available marker databases from which additional useful markers located on linkage group N (chromosome 3) 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 metribuzin tolerance 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 Metribuzin sensitivity phenotype are thus provided.

[0048] In certain embodiments, metribuzin tolerant soybean plant are provided that comprise an introgressed linkage group N region comprising a metribuzin tolerance locus where adjacent or linked genomic regions comprise markers that are not typically linked or associated with the metribuzin tolerance locus in metribuzin tolerant strains. Non-limiting examples of alleles of linked markers that can be used to detect such introgressed metribuzin tolerance regions can include, but are not limited to, a "TT" or a "CT" allele of NGMAX006083631 (SEQ ID NO: 10), an "AC" allele of NS0202926 (SEQ ID NO: 11), a "GG" allele of NGMAX006084289 (SEQ ID NO: 12), and/or a "GG" allele of NGMAX006088354 (SEQ ID NO: 13).

Soybean plants comprising genomic region associated with the metribuzin sensitivity and metribuzin tolerance phenotypes

[0049] A non-limiting and exemplary list of soybean plants that comprise genomic regions associated with either a metribuzin sensitivity or a metribuzin tolerance phenotype are provided herewith in Table 3. [0050] Table 3. Soybean varieties comprising a genomic region associated with a metribuzin tolerance or metribuzin sensitivity phenotype.

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.

³ Metribuzin phenotype is the phenotype observed in the indicated germplasm containing a metribuzin sensitivity or metribuzin tolerance locus when exposed to metribuzin.

[0051] Also provided herewith are additional soybean plants that comprising a genomic region associated with a metribuzin sensitivity or metribuzin tolerance 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 metribuzin tolerance locus, obtaining a soybean plant that exhibits a metribuzin tolerance phenotype, or obtaining a soybean plant comprising in its genome a genetic region associated with a metribuzin tolerance phenotype.

[0052] In certain embodiments, the soybean plants provided herein or used in the methods provided herein can comprise a transgene that confers resistance to dicamba. In certain embodiments, the dicamba tolerant soybean plants can comprise a transgene encoding a dicamba-degrading dicamba monoxygenase (DMO) enzyme that catalyzes the conversion of herbicidal dicamba (3,6-dichloro-o-anisic acid) to a non-toxic 3,6-dichlorosalicylic acid. In certain embodiments, the dicamba-degrading dicamba monoxygenase (DMOw) comprise a DMO enzyme disclosed in US Patent Nos. 7,022,896, 7,105,724, and 7,812,224, each incorporated herein by reference in their entireties. In certain embodiments, the metribuzin tolerant soybean plants can comprise a dicamba monoxygenase variant which exhibits improved catalytic parameters such as increased turnover number and/or a lower km for the substrate, improved catalysis at lower pH values, and/or improved catalysis at higher temperatures relative to an unaltered dicamba monooxygenase. In certain embodiments, the dicamba monoxygenase variant comprises a DMOc variant enzyme disclosed in US Patent No. 7,884,262, incorporated herein by reference in its entirety. In certain embodiments, a dicamba monooxygenase is operably linked to a chloroplast transit peptide (CTP). Operable linkage of certain CTPs to DMO is disclosed in US Patent No. 8,084,666, which is incorporated herein by reference in its entirety. In certain embodiments, it is contemplated that the soybean plants used herein can comprise one or more specific genomic insertion(s) of a dicamba tolerant transgene including, but not limited to, as those found in MON87708 soybean (deposited under ATCC accession number PTA-9670 and described in US Patent Application Publication Number 20110067134).

[0053] 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 US

Patent Nos. 6,803,501, RE39,247, 6,225,114, 5,188,642, and 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 US patent 5,776,760 and US Reissue patent

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 US Patent 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 insertions) 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 2010/0099859), 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 2009/0036308), or any combination of i (MON89788 soybean), ii (GTS 40-3-2 soybean), and iii (event 3560.4.3.5 soybean).

[0054] In certain embodiments, metribuzin tolerant soybean provided herein can further comprise transgenes that confer resistance to both dicamba and glyphosate.

[0055] In certain embodiments, it is contemplated that genotypic assays that provide for nondestructive identification of the plant or plants can be performed either in seed, the emergence stage, the "VC" stage (i.e. cotyledons unfolded), the VI 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 US Patents 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 2010/0086963, 2009/0215060, and 2009/0025288, which are incorporated herein by reference in their entireties. Published US 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 each 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. Molecular Assisted Breeding Techniques

[0056] 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.

[0057] As a set, polymorphic markers serve as a useful tool for fingerprinting plants to inform the degree of identity of lines or varieties (US Patent 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.

[0058] 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.

[0059] 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 metribuzin tolerance loci, regions flanking metribuzin tolerance loci, regions linked to metribuzin tolerance loci, and/or regions that are unlinked to metribuzin tolerance loci can be used in certain embodiments of the instant invention.

[0060] 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 metribuzin tolerance loci, regions flanking metribuzin tolerance loci, regions linked to metribuzin tolerance loci, and/or regions that are unlinked to metribuzin tolerance loci can be used in certain embodiments of the instant invention.

[0061] Nucleic acid analysis methods provided herein 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.

[0062] 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; US Patent 4,683,202; US Patent 4,582,788; and US Patent 4,683,194), using primer pairs that are capable of hybridizing to the proximal sequences that define a polymorphism in its double-stranded form.

[0063] Methods for typing DNA based on mass spectrometry can also be used. Such methods are disclosed in US Patents 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 US Patent 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.

[0064] For instance, polymorphisms in DNA sequences can be detected by hybridization to allele-specific oligonucleotide (ASO) probes as disclosed in US Patent No. 5,468,613 and 5,217,863. US Patent 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 US Patent 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.

[0065] 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 US Patent Nos. 6,799,122; 6,913,879; and 6,996,476.

[0066] Target nucleic acid sequence can also be detected by probe linking methods as disclosed in US Patent 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. [0067] 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 US Patent 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.

[0068] In another method for detecting polymorphisms, SNPs and Indels can be detected by methods disclosed in US Patent 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.

[0069] 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, CT), Agencourt

Bioscience (Beverly, MA), Applied Biosystems (Foster City, CA), LI-COR Biosciences (Lincoln, NE), NimbleGen Systems (Madison, WI), Illumina (San Diego, CA), and VisiGen Biotechnologies (Houston, TX). 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.

[0070] 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

[0071] 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: Metribuzin Phenotyping: Field Screening and Greenhouse Screening.

[0072] Field screening for metribuzin tolerance in soybeans was performed at the Monsanto Company Soybean Research Station near Mount Olive, NC in 2010 and 2011. Metribuzin application rate was 0.5 lbs/acre metribuzin (Sencor®, Bayer Crop Science, Research Triangle Park, NC, USA) one day prior to planting. Rows were planted as single 6' row plots with 9 seed per foot. Multiple repetitions were grown per row. Within 24 hours after planting, the trial was irrigated with 0.5" of water to help incorporate and activate the herbicide. Injury ratings were taken fourteen to twenty one (14-21) days after planting using a 1-9 scale (for example, 1 = no damage, 9 = completely killed).

[0073] Greenhouse screening for metribuzin tolerance in soybeans was performed using 10 seeds per entry planted in a pot filled with a sandy soil. Pots were then sprayed with 0.25 lbs / acre metribuzin then lightly soaked with water to incorporate herbicide. Metribuzin ratings were then taken seven (7), fourteen (14), and twenty one (21) days after spraying using a 1-9 scale as in the field.

Example 2: Mapping Populations to Screen for Metribuzin Tolerance

[0074] A mapping population from a cross between a metribuzin sensitive and a metribuzin tolerant plant (AG6730 x AG4531) generated 232 F2:3 rows. Tissue was sampled and genotyped with 127 SNP markers. Then, F2:4 seed from all 232 plant rows were phenotyped in the greenhouse using the method described in Example 1. A major locus was mapped using R/qtl software (http://www.rqtl.org/).

Example 3. Marker-Trait Association for Metribuzin Tolerance

[0075] After identifying the target region through the mapping population described in Example 2, a molecular marker was identified. An association study was done using a soybean molecular marker database. Over 200 commercial and breeding lines were characterized for metribuzin tolerance in field and greenhouse screening, as described in Example 1. The marker NGMAX006079502 was found to be tightly linked to the metribuzin tolerance trait and could be useful for marker assisted selection (MAS) to select for metribuzin tolerance and sensitivity in pre-commercial lines. Field studies demonstrate that a line containing the TT allele of NGMAX006079502 (SEQ ID NO:7) has a "metribuzin sensitivity" rating ranging from about 1.0 to about 3.7, indicating tolerance or moderate tolerance to metribuzin 10 days after spray herbicide application, whereas a line containing the CC allele of NGMAX006079502 (SEQ ID NO:7) has a "metribuzin sensitivity" rating ranging from about 7.0 to about 8.0, indicating sensitivity to metribuzin 10 days after spray herbicide application. Lines containing a heterozygous (CT) allele of NGMAX006079502 (SEQ ID NO:7) display a mixed phenotype of both tolerance and sensitivity in the field.

Example 4: Exemplary Marker Assays for Detecting Polymorphisms

[0076] 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 metribuzin tolerance phenotype are given in Table 4.

[0077] Table 4: Exemplary Assays for Detecting Polymorphisms

Example 5: Oligonucleotide Probes Useful for Detecting Polymorphisms by Single Base Extension Methods

[0078] 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 5. 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 5. [0079] Table 5: Exemplary SBE Probes for Detecting Polymorphisms

[0080] 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.

[0081] 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.

[0082] Table 2 of the Specification.

SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

similar to

UniRefl00_Q30CZ8 3- phosphoshikimate 1- carboxyvinyltransferase -

GMGI.04221 Fagus sylvatica

TC396920 0 2990455 2990911 (Beechnut), partial (12%)

BARCSOYSSR 0 Wm82_poten

3 0169 rial SSR 2992305 2992342 NA

Transketolase 7

Glycine_max [Craterostigma

BG726324 release 2 2993161 2993597 plantagineum]

cajanus_caja

Contig5194 n 2993322 2993456 NA

420200 3495 335 cajanus_caja

6 n 2993449 2993647 NA

321475 2492 211 cajanus_caja

4 n 2993543 2993598 NA

Transketolase= C-

Glycine_max terminal-like [Medicago

TA47385 3847 release 2 2993258 2993936 truncatula (Barrel medic)]

283539 1537 351 cajanus_caja

7 n 2993575 2993647 NA

BARC-028645- Wm82xPI46

05979 8916 2993383 2993935 NA

Phaseolus co

ccineus_relea Transketolase, chloroplast

CA901097 se 2 2993660 2993887 [Zea mays (Maize)]

419871 3332 083 cajanus_caja

8 n 2993675 2993950 NA

076083 1270 313 cajanus caja

0 n 2993778 2993858 NA

UniRefl00_Q7SIC9 Transketolase, chloroplastic n=l

Tax=Zea mays

Phaseolus v RepID=TKTC MAIZE

CB543460 ulgaris 2993758 2994188 8.00E-72

NS0206337 1 2994256 2993925

NS0262835 21 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl 00 A7QGQ5 Chromosome chrl6 scaffold_94, whole genome shotgun sequence

GMGL04221 - Vitis vinifera (Grape),

TC350652 0 2993763 2994578 partial (36%)

cajanus_caja

Contig47295 n 2994121 2994425 NA homologue to

UniRefl 00_A7QGQ5 Chromosome chrl6 scaffold_94, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC415391 0 2993161 2995388 partial (75%)

Transketolase= C-

Glycine_max terminal-like [Medicago

TA47387 3847 release 2 2993421 2995388 truncatula (Barrel medic)]

086553 2836 098 cajanus_caja

1 n 2994220 2994625 NA

Phaseolus co Putative transketolase ccineus_relea [Oryza sativa (japonica

TA3218 3886 se 2 2993945 2994914 cultivar-group)]

Vigna_ungui

asmbl 1387 culata 2993464 2995403 NA

Hypothetical protein

Lupinus alb [Arabidopsis thaliana

TA389 3870 us release 2 2994040 2994941 (Mouse-ear cress)]

Lotusjaponi

cus release Transketolase

TA4041 34305 1 2993956 2995456 [Polygonum tinctorium] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl00_A7QGQ5 Cluster: Chromosome chrl6 scaffold_94, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl6 scaffold_94, whole genome shotgun sequence - Vitis vinifera (Grape),

TC32586 LJGI.070108 2993956 2995456 partial (52%)

Cluster: Transketolase, C- terminal-like, n=l,

Medicago truncatula|Rep:

Arachis hyp Transketolase, C-terminal- ogaea releas like - Medicago truncatula

EG030594 e 5 2994096 2995502 (Barrel medic)

327358 3627 181 cajanus_caja

1 n 2994925 2995342 NA

Average Cons

Position=LG06 29.4 cM: Q7SIC9 Transketolase, chloroplast 0 ; Q43848

Gm W82 CR03.G Gm W82 C Transketolase, chloroplast 17750 R03 2993068 2997229 precursor 0

SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:2.2.1.1

(EC)=Transketolase. ;

ID:CALVIN-PWY

(SoyCyc)=Activity=transk etolase; Pathway=Calvin-

Benson-Bassham cycle;

ID:GO:0003824

(GO)=catalytic activity;

ID:GO:0008152

(GO)=metabolism;

ID:K00615

(KO)=E2.2.1.1, tktA, tktB; transketolase

[EC:2.2.1.1 ]

[COG:COG0021 ]

[GO:0004802 ];

ID:KOG0523

(KOG)=Transketolase;

ID:P21-PWY

(SoyCyc)=Activity=transk etolase; Pathway=pentose phosphate pathway partial; ID:PF02780

(PFAM)=Transketolase,

C-terminal domain;

ID:PTHR11624

(Panther)=DEHYDROGE

NASE RELATED;

ID:PWY-5723

(SoyCyc)=Activity=transk etolase; Pathway=Rubisco

Glyma03g03200 Glymal 2993113 2997229 shunt

UniRefl00_A9P7Z7 Putative uncharacterized protein n=l Tax=Populus trichocarpa

Phaseolus_v RepID=A9P7Z7 POPTR

CB540475 ulgaris 2994918 2995549 7.00E-66

Phaseolus v

ulgarisjrelea Transketolase

CB540475 se 2 2994932 2995549 [Polygonum tinctorium] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl 00_A7QGQ5 Cluster: Chromosome chrl6 scaffold_94, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl6 scaffold_94, whole genome shotgun sequence

MTGL07170 - Vitis vinifera (Grape),

TC127321 8 2994911 2995908 partial (30%)

162536 1790 169 cajanus caja

2 n 2995327 2995533 NA

Chafal_lcle

Cfl4551d an 2995413 2995523 NA

similar to

UniRefl 00_Q7SIC9 Transketolase, chloroplast

GMGI.04221 - Zea mays (Maize),

BE660224 0 2995327 2997132 partial (28%)

Putative transketolase

Glycine_max [Oryza sativa (japonica

TA74539 3847 release 2 2995336 2997165 cultivar-group)]

homologue to

UniRefl 00_Q7SIC9 Transketolase, chloroplast

GMGI.04221 - Zea mays (Maize),

TC356209 0 2995467 2997215 partial (25%)

Chafaljcle

Cfl8959d an 2996710 2996972 NA

017718 3891 134 cajanus_caja

1 n 3001808 3001894 NA

Vigna_ungui

asmbl 1388 culata 3001905 3002039 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: similar to

UniRefl00_Q2HS72 RecA bacterial DNA recombination protein - Medicago truncatula

GMGI.04221 (Barrel medic), partial

TC363195 0 3001739 3003321 (73%)

RecA bacterial DNA recombination protein; Rad51= N-terminal

Glycine_max [Medicago truncatula

TA72645 3847 release 2 3001802 3003321 (Barrel medic)] homologue to

UniRefl00_Q2HS72 Cluster: RecA bacterial DNA recombination protein, n=l, Medicago truncatula|Rep: RecA bacterial DNA

recombination protein -

MTGI.07170 Medicago truncatula

TCI 18321 8 3001993 3003907 (Barrel medic), complete

ID:KOG1434

(KOG)=Meiotic recombination protein Dmcl; ID:PF08423 (PFAM)=Rad51;

ID:PTHR22942

(Panther)=RECA/RAD51/ RADA DNA STRAND- PAIRING FAMILY

Glyma03g03210 Glymal 3001993 3005606 MEMBER

Average Cons

Position=LG06 29.5 cM: Q2HS72 RecA bacterial

Gm W82 CR03.G Gm W82 C DNA recombination 17760 R03 3001993 3005606 protein 1E-115 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl00_Q2HS72 RecA bacterial DNA recombination protein - Medicago truncatula

GMGI.04221 (Barrel medic), partial

TC376154 0 3002839 3005687 (55%)

RecA bacterial DNA recombination protein; Rad51 = N-terminal

Glycine_max [Medicago truncatula

AW203630 release 2 3003133 3005645 (Barrel medic)]

Vigna ungui

asmbl 1389 culata 3003153 3005658 NA similar to

UniRefl00_A7PYE0 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC397626 0 3003192 3005712 partial (41%)

GMGI.04221

GD956184 0 3008221 3008344 NA

Glycine_max

AI988137 release 2 3008222 3008482 NA similar to

UniReflOO_Q2HS71 SAM (And some other nucleotide) binding motif, Methyltransferase small, Tetratricopeptide-like helical - Medicago

GMGI.04221 truncatula (Barrel medic),

TC372542 0 3008222 3008967 partial (19%)

Chafal_lcle

Cf3692d an 3008508 3009020 NA

Chafal lcle

Cfl8146d an 3011112 3011259 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:KOG3191

(KOG)=Predicted N6- DNA-methyltransferase; ID:PF08242

(PFAM)=Methyltransfera se domain;

ID:PTHR18895

(Panther)=METHYLTRA

Glyma03g03230 Glymal 3008222 3014755 NSFERASE

Average Cons

Position=LG06 29.5 cM: Q2HS71 SAM (And some other nucleotide) binding motif; Methyltransferase

Gm W82 CR03.G Gm W82 C small; Tetratricopeptide- 17770 R03 3008221 3014755 like helical IE- 120

ID:PTHR10483

(Panther)=PENTATRICO PEPTIDE REPEAT- CONTAINING

Glyma03g03240 Glymal 3011139 3012212 PROTEIN

Average Cons

Position=LG06 29.5 cM: Q2HS71 SAM (And some other nucleotide) binding motif; Methyltransferase

Gm W82 CR03.G Gm W82 C small; Tetratricopeptide- 17780 R03 3011139 3012212 like helical IE- 162

Methyltransferase small

Phaseolus co domain, putative ccineus_relea [Medicago truncatula

TA4527 3886 se 2 3008884 3014665 (Barrel medic)] SEQ

Locus / Display

ID Start End Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: similar to

UniRefl00_Q2HS71 SAM (And some other nucleotide) binding motif, Methyltransferase small, Tetratricopeptide-like helical - Medicago

GMGI.04221 truncatula (Barrel medic),

TC354042 0 3008857 3014753 partial (11%)

BARC-056039- marker map

14002 4 3017669 3018289 NA

BARC-056115- marker map

14110 4 3017705 3018289 NA

Vigna ungui

asmbl 1390 culata 3021474 3022546 NA

Glycoprotease family=

Glycine_max putative [Medicago

BI970682 release 2 3021390 3024499 truncatula (Barrel medic)]

Phaseolus v Glycoprotease family= ulgaris_relea putative [Medicago

CB542218 se 2 3021591 3024498 truncatula (Barrel medic)]

Glycoprotease family=

Glycine max putative [Medicago

TA63194 3847 release 2 3021411 3024685 truncatula (Barrel medic)]

NGMAX0060765

47 18 3023578 3023879 homologue to

UniRefl00_Q2HS64 Peptidase M22, glycoprotease - Medicago

GMGI.04221 truncatula (Barrel medic),

TC405131 0 3021335 3030119 partial (67%)

Glycoprotease family=

Glycine max putative [Medicago

TA63193 3847 release 2 3021718 3030109 truncatula (Barrel medic)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

UniRefl00_Q2HS64 Cluster: Peptidase M22, glycoprotease, n=l, Medicago truncatula|Rep: Peptidase M22, glycoprotease - Medicago

MTGI.07170 truncatula (Barrel medic),

TC125199 8 3021786 3032333 complete

ID:GO:0004222

(GO)=metalloendopeptida se activity;

ID:GO:0006508

(GO)=proteolysis and peptidolysis;

ID:KOG2707

(KOG)=Predicted metalloprotease with chaperone activity

(RNAse H/HSP70 fold);

ID:PF00814

(PFAM)=Glycoprotease family; ID:PTHR11735

(Panther)=0-

SIALOGLYCOPROTEIN

Glyma03g03250 Glymal 3021324 3034049 ENDOPEPTIDASE

Average Cons

Position=LG06 29.6 cM: 022145 Putative O-

Gm W82 CR03.G Gm W82 C sialoglycoprotein

17790 R03 3021323 3034105 endopeptidase 0

Chafal lcle

Cfl3676d an 3024476 3031407 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: similar to

UniRefl00_A7PYD9 Cluster: Chromosome chrl 5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

MTGI.07170 - Vitis vinifera (Grape),

TC137301 8 3029622 3033990 partial (54%)

Glycoprotease family protein= expressed [Oryza

Glycinejtnax sativa (japonica cultivar-

TA63618 3847 release_2 3029959 3034049 group)] similar to

UniRefl00_A7PYD9 Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC382576 0 3029959 3034049 partial (37%)

Putative O- sialoglycoprotein endopeptidase

Glycine_max [Arabidopsis thaliana

BG363097 release 2 3031745 3033870 (Mouse-ear cress)]

Chafaljcle

Cf633d an 3042871 3043868 NA

cajanus_caja

Contig37404 n 3043758 3044495 NA

Glycine_max Arginase [Glycine max

AW780582 release 2 3043770 3045739 (Soybean)]

Glycine_soja Arginase [Glycine max

BM524551 release 2 3043778 3047793 (Soybean)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:ARG-PRO-PWY (SoyCyc)=Activity=argin ase; Pathway=arginine degradation VI arginase 2 pathway;

ID:ARGASEDEG-PWY (SoyCyc)=Activity=argin ase; Pathway=arginine degradation I arginase pathway; ID:GO:0016813 (GO)=hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines;

ID:GO:0046872

(GO)=metal ion binding; ID:KOG2964

(KOG)= Arginase family protein; ID:PF00491 (PFAM)=Arginase family; ID:PTHR11358

(Panther)==ARGINASE/A GMATINASE- RELATED; ID:PWY-31 (SoyCyc)=Activity=argin ase; Pathway=canavanine degradation; ID:PWY- 4984

(SoyCyc)=Activity =argin

Glyma03g03270 Glymal 3042599 3050225 ase; Pathway=urea cycle

Glycinejtnax Arginase [Glycine max

TA47821 3847 release 2 3042608 3050217 (Soybean)]

homologue to

UniRefl00_O49046

GMGI.04221 Arginase - Glycine max

TC349067 0 3042608 3050222 (Soybean), complete

Average Cons

Position=LG06 29.7 cM: 049046 Arginase 0 ;

Gm W82 CR03.G Gm W82 C Q9ZPF5 Probable 17800 R03 3042608 3050226 arginase IE- 149

AF035671.1 GenBank 3042649 3050212 arginase (pAGl) mRNA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Glycine soja Arginase [Glycine max

TA2587 3848 release 2 3042694 3050217 (Soybean)]

Glycine_max Arginase [Glycine max

AW201630 release 2 3044392 3050203 (Soybean)]

Glycine_max Arginase [Glycine max

TA47820 3847 release 2 3044443 3050217 (Soybean)]

Glycine max Arginase [Glycine max

BE555381 release 2 3044476 3050215 (Soybean)]

Glycine max Arginase [Glycine max

AW760224 release 2 3045393 3050217 (Soybean)]

BARCSOYSSR 0 Wm82_poten

3 0170 tial SSR 3049488 3049513 NA

087411 2830 103 cajanus caja

3 n 3057794 3057947 NA

BARCSOYSSR 0 Wm82_poten

3 0171 tial SSR 3060741 3060796 NA similar to

UniRefl00_A7PYD6 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence - Vitis vinifera (Grape),

CB829372 LJGI.070108 3064721 3066034 partial (25%)

Lotusjaponi Protein Atlg02020 cus release [Arabidopsis thaliana

CB829372 1 3064721 3066048 (Mouse-ear cress)]

Chafal_lcle

Cf9076d an 3065839 3066273 NA

Glyma03g03280 Glymal 3064341 3068565 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Gm W82 CR03.G Gm W82 C Position=LG06 29.7 cM: 18410 R03 3064341 3068565 023673 T7I23.2 protein 0

Chafal_lcle

Cf 022d an 3067253 3068192 NA similar to

UniRefl00_A7PYD6 Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC359066 0 3067284 3068559 partial (12%) homologue to

UniRefl00_A7PYD6 Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC372531 0 3068073 3068531 partial (6%)

Hypothetical protein OSJNBa0040E17.29

Glycine_max [Oryza sativa (japonica

TA75426 3847 release 2 3068073 3068565 cultivar-group)]

087411 2830 103 cajanus_caja

3 n 3068301 3068451 NA

GMGI.04221

TC415540 0 3070549 3071117 NA

Glycine_max

TA70620 3847 release 2 3070549 3071597 NA

NGMAX0060769

62 22 3071027 3071328 weakly similar to

UniRefl00_A7PYD5 Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

BI786980 0 3071177 3071597 partial (22%) SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:PF04483

(PFAM)=Protein of unknown function

Glyma03g03290 Glymal 3070549 3072650 (DUF565)

Average Cons

Position=LG06 29.8 cM:

Gm W82 CR03.G Gm W82 C Q0DLP9 Os03g0852600 18420 R03 3070422 3073399 protein 1E-34

GMGI.04221

TC418355 0 3075339 3075497 NA

cajanus_caja

Contigl8691 n 3075406 3075624 NA

Hypothetical protein P0450A04.130 [Oryza

Glycine_max sativa (japonica cultivar-

TA55073 3847 release 2 3075408 3076254 group)]

UniRefl00_A5ASW2 Putative uncharacterized protein (Chromosome chrl4 scaffold_54, whole genome shotgun sequence) n=l Tax=Vitis vinifera

Phaseolus v RepID=A5ASW2 VITVI

CV543227 ulgaris 3075585 3076188 3.00E-53

238610 1965 051 cajanus_caja

1 n 3076032 3076243 NA

Vigna ungui

asmbl 1391 culata 3075856 3076521 NA

Chafal_lcle

Cf9860d an 3075867 3077453 NA

Phaseolus_co T12H1.6 protein ccineus relea [Arabidopsis thaliana

TA4520 3886 se 2 3076094 3077495 (Mouse-ear cress)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0008152

(GO)=metabolism;

ID:GO:0008168

(GO)=methyltransferase activity; ID:PF08241

(PFAM)=Methyltransfera

Glyma03g03300 Glymal 3075339 3078303 se domain

Average Cons

Position=LG06 29.8 cM:

Gm W82 CR03.G Gm W82 C Q9MAA9 T12H1.6 18430 R03 3075339 3078304 protein IE- 122

T12H1.6 protein

Glycine max [Arabidopsis thaliana

TA55075 3847 release 2 3076131 3077516 (Mouse-ear cress)]

GMGI.04221

TC354860 0 3075416 3078301 NA

T12H1.6 protein

Glycine_max [Arabidopsis thaliana

CA853858 release 2 3076316 3077605 (Mouse-ear cress)]

185290 3395 287 cajanus_caja

5 n 3079604 3079688 NA

444994 2753 364 cajanus_caja

4 n 3079467 3079945 NA

Contig2609_prime cajanus_caja

rs n 3079569 3079914 NA

444994_2753_364 cajanus_caja

4_primers n 3079569 3079932 NA

291757 0504 115 cajanus caja

7 n 3079486 3080310 NA

cajanus_caja

Contig37450 n 3079464 3081239 NA

Contig37450_prim cajanus caja

ers n 3079563 3081184 NA

cajanus_caja

Contig2609 n 3079433 3081345 NA

Contig 15720_prim cajanus caja

ers n 3079543 3081269 NA

cajanus caja

Contigl5720 n 3079444 3081466 NA

cajanus_caja

Contigl5959 n 3079586 3081351 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

cajanus_caja

Contig 10545 n 3079604 3081484 NA

297476_1912_225 cajanus_caja

2_primers n 3079917 3081197 NA

134435 3488 171 cajanus_caja

4 n 3079885 3081264 NA

297476 1912 225 cajanus_caja

2 n 3079885 3081282 NA

354427 2886 207 cajanus_caja

4 n 3079885 3081283 NA

400685 3217 246 cajanus caja

4 n 3079885 3081302 NA

213795_0367_400 cajanus caja

2_primers n 3079929 3081272 NA

Contig 10545_prim cajanus caja

ers n 3079921 3081281 NA

213795 0367 400 cajanus_caja

2 n 3079850 3081361 NA

Hypothetical protein At2g45260 [Arabidopsis

Glycine_max thaliana (Mouse-ear

TA50789 3847 release 2 3079539 3081720 cress)]

cajanus caja

Contig40445 n 3079885 3081386 NA

Vigna_ungui

asmbl 1393 culata 3079530 3081795 NA

Hypothetical protein

Phaseolus_co At2g45260 [Arabidopsis ccineus_relea thaliana (Mouse-ear

CA912097 se 2 3079548 3081861 cress)] homologue to

UniRefl00_A7PYD3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC352567 0 3079521 3081925 partial (52%) SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

UniRefl00_A7PYD3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax=Vitis vinifera

Phaseolus v RepID=A7PYD3 VITVI

CV537759 ulgaris 3079566 3081984 1.00E-119

Vigna_ungui

asmbl 1392 culata 3079530 3082028 NA

UniRefl00_A7PYD3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax=Vitis vinifera

Phaseolus_v RepID=A7PYD3 VITVI

FE898754 ulgaris 3079885 3081807 3.00E-71

314959 2658 054 cajanus_caja

3 n 3081064 3081283 NA

ID:PF04859

(PFAM)=Plant protein of unknown function

Glyma03g03310 Glymal 3079477 3082885 (DUF641) similar to

UniRefl00_A7PYD3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC388566 0 3079495 3082869 complete

286143 2148 117 cajanus_caja

1 n 3081239 3081430 NA

443764 2874 402 cajanus_caja

0 n 3081315 3081484 NA

358725 3113 372 cajanus_caja

3 n 3081352 3081476 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: similar to

UniRefl00_A7PYD3 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence - Vitis vinifera (Grape),

BW631067 LJGI.070108 3081192 3081649 partial (31%)

Chafal lcle

Cf2278d an 3081259 3081599 NA

020962 2290 063 cajanus_caja

1 n 3081485 3081697 NA similar to

UniRefl00_A7PYD3 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence

MTGI.07170 - Vitis vinifera (Grape),

TCI 15824 8 3081192 3082028 partial (58%)

Chafal_lcle

Cf20941d an 3081615 3082518 NA

cajanus caja

Contig45852 n 3082034 3082358 NA

Expressed protein [Oryza

Glycine_max sativa (japonica cultivar-

BI425936 release 2 3081947 3082470 group)]

Expressed protein [Oryza

Glycine_soja sativa (japonica cultivar-

BG156189 release 2 3082080 3082515 group)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Hypothetical protein At2g45260 [Arabidopsis

Glycine_max thaliana (Mouse-ear

BE824427 release 2 3082147 3082623 cress)]

UniRefl00_A7PYD3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax=Vitis vinifera

Phaseolus v RepID=A7PYD3 VITVI

Pvcon6930 ulgaris 3082096 3082715 3.00E-66

Vigna_ungui

asmbl 1394 culata 3082089 3082756 NA

032057 1031 092 cajanus caja

7 n 3082397 3082465 NA

113211 0242 110 cajanus_caja

8 n 3082410 3082520 NA

004558 3078 099 cajanus caja

0 n 3082438 3082655 NA

cajanus_caja

Contig21707 n 3082447 3082655 NA

ID:GO:0004857

(GO)-enzyme inhibitor activity; ID:GO:0030599 (GO)=pectinesterase activity; ID:PF04043 (PFAM)=Plant invertase/pectin

Glyma03g03320 Glymal 3085834 3086493 methylesterase inhibitor

Average Cons

Position=LG06 29.8 cM:

Gm W82 CR03.G Gm W82 C 081309 F6 15.9 protein 18450 R03 3085834 3086493 2E-36

NGMAX0060770

74 2 3087650 3087951

similar to

UniRefl00_Q89EJ0 C4- dicarboxylate transport

GMGI.04221 protein - Bradyrhizobium

TC352616 0 3091655 3092472 japonicum, partial (5%) SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0004857

(GO)=enzyme inhibitor activity; ID:GO:0030599 (GO)=pectinesterase activity; ID:PF04043 (PFAM)=Plant

invertase/pectin

Glyma03g03330 Glymal 3091658 3092522 methylesterase inhibitor

Average Cons

Position=LG06 29.8 cM:

Gm W82 CR03.G Gm W82 C 081309 F6N15.9 protein 18460 R03 3091658 3092522 6E-39

Glycine max

BM139947 release 2 3092245 3092450 NA

BARCSOYSSR 0 Wm82_poten

3 0172 tial SSR 3099116 3099163 NA

ID:GO:0016747

(GO)=transferase activity, transferring groups other than amino-acyl groups; ID:PF02458

(PFAM)=Transferase

Glyma03g03340 Glymal 3100904 3102449 family

BARCSOYSSR 0 Wm82_poten

3 0173 tial SSR 3103341 3103396 NA

Contig9906_prime cajanus_caja

rs n 3104938 3105569 NA

homologue to

UniRefl00_Q0ZPT8

Methionine

aminopeptidase - Ananas

GMGI.04221 comosus (Pineapple),

TC413526 0 3104626 3106429 partial (31%)

Methionine

Glycine_max aminopeptidase 1 [Ananas

TA60719 3847 release 2 3104635 3106432 comosus (Pineapple)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

homologue to

UniRefl00_Q0ZPT8

Methionine

aminopeptidase - Ananas

GMGI.04221 comosus (Pineapple),

TC374413 0 3104626 3106880 partial (33%)

cajanus_caja

Contig9906 n 3104585 3106940 NA

Phaseolus v Methionine

ulgaris_relea aminopeptidase 1 [Ananas

CB539349 se 2 3104890 3107370 comosus (Pineapple)]

034894 1456 008 cajanus_caja

0 n 3106877 3107085 NA

ID:GO:0009987

(GO)=cellular process;

ID:KOG2738

(KOG)=Putative methionine

aminopeptidase;

ID:PF00557

(PFAM)=metallopeptidas e family M24;

ID:PTHR10804

(Panther)=PROTEASE FAMILY M24

(METHIONYL

AMINOPEPTIDASE,

Glyma03g03350 Glymal 3104902 3109883 AMINOPEPTIDASE P)

Chafal_lcle

CD363d an 3104911 3109882 NA

UniRefl00_A7PYC9 Methionine

aminopeptidase n=l Tax=Vitis vinifera

Phaseolus v RepID=A7PYC9 VITVI

Pvcon6396 ulgaris 3104890 3111389 E-0

Methionine

Phaseolus_co aminopeptidase 1A ccineus relea [Arabidopsis thaliana

CA906284 se 2 3106886 3109505 (Mouse-ear cress)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 29.9 cM: Q9SLN5 Methionine aminopeptidase 1A 0 ;

Gm W82 CR03.G Gm W82 C A7PYC9 Methionine 18480 R03 3104558 3111952 aminopeptidase 0

297876 2793 195 cajanus_caja

7 n 3108527 3109322 NA

316713 3644 151 cajanus_caja

6 n 3109394 3109635 NA

BARCSOYSSR 0 Wm82_poten

3 0174 tial SSR 3120776 3120805 NA

ID:GO:0005618

(GO)=cell wall;

ID:GO:0030599

(GO)=pectinesterase activity; ID:GO:0042545

(GO)=cell wall modification; ID:PF01095

(PFAM)=Pectinesterase;

ID:PWY-1081

(SoyCyc)=Activity=pectin esterase;

Pathway=homogalacturon

Glyma03g03360 Glymal 3120992 3124949 an degradation

Average Cons

Position=LG06 30 cM:

Gm W82 CR03.G Gm W82 C Q84R10 Putative

18490 R03 3120992 3124987 pectinesterase IE- 149

BARCSOYSSR 0 Wm82_poten

3 0175 tial SSR 3125342 3125373 NA

BARCSOYSSR 0 Wm82_poten

3 0176 tial SSR 3125603 3125626 NA

Glyma03g03370 Glymal 3128348 3128906 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:PTHR11615:SF7 (Panther)=gb def: putative formate dehydrogenase alpha subunit

Glyma03g03380 Glymal 3129953 3130354 [thermococcus litoralis]

Average Cons

Position=LG06 30 cM: Q8L924 UPF0497

Gm W82 CR03.G Gm W82 C membrane protein 18510 R03 3129953 3130354 At2g35760 3E-20

418082 2891 037 cajanus_caja

3 n 3137176 3137447 NA

375319 2742 193 cajanus_caja

8 n 3137533 3137620 NA

ID:3.1.1.11

(EC)=Pectinesterase. ; ID:GO:0005618

(GO)=cell wall;

ID:GO:0030599

(GO)=pectinesterase activity; ID:GO:0042545 (GO)=cell wall modification; ID:K01051 (KO)=E3.1.1.11;

pectinesterase

[EC:3.1.1.11 ]

[GO:0030599 ];

ID:PF01095

(PFAM)=Pectinesterase; ID:PWY-1081

(SoyCyc)=Activity=pectin esterase;

Pathway=homogalacturon

Glyma03g03390 Glymal 3136859 3138892 an degradation

cajanus_caja

Contig23415 n 3138247 3138699 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl00_A7PYC6 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC388963 0 3138211 3138811 partial (38%)

418082 2891 037 cajanus_caja

3 n 3150943 3151220 NA

375319 2742 193 cajanus_caja

8 n 3151307 3151394 NA

BARCSOYSSR 0 Wm82_poten

3 0177 tial SSR 3151786 3151827 NA

ID:3.1.1.11

(EC)=Pectinesterase. ; ID:GO:0005 18

(GO)=cell wall;

ID:GO:0030599

(GO)=pectinesterase activity; ID:GO:0042545 (GO)=cell wall modification; ID:K01051 (KO)=E3.1.1.11;

pectinesterase

[EC:3.1.1.11 ]

[GO:0030599 ];

ID-.PF01095

(PFAM)=Pectinesterase; ID:PWY-1081

(SoyCyc)=Activity=pectin esterase;

Pathway=homogalacturon

Glyma03g03400 Glymal 3150626 3154197 an degradation

cajanus_caja

Contig23415 n 3153333 3153797 NA

Pectinesterase-2 precursor

Glycine_max [Citrus sinensis (Sweet

TA72681 3847 release 2 3158234 3158915 orange)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl00_A7PYC6 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC388963 0 3158315 3158915 partial (38%)

cajanus_caja

Contig23415 n 3158426 3158880 NA

UniRefl00_Q6PQ93 Cluster: Pectin

methylesterase 9, n=l, Medicago truncatula|Rep: Pectin methylesterase 9 -

MTGI.07170 Medicago truncatula

TC135041 8 3158575 3158878 (Barrel medic), complete

Chafaljcle

Cfl6829d an 3158264 3159610 NA

ID:3.1.1.11

(EC)=Pectinesterase. ; ID:GO:0005618

(GO)=cell wall;

ID:GO:0030599

(GO)=pectinesterase activity; ID:GO:0042545 (GO)=cell wall modification; ID:K01051 (KO)=E3.1.1.11;

pectinesterase

[EC:3.1.1.11 ]

[GO:0030599 ];

ID:PF01095

(PF AM)=Pectinesterase ; ID:PWY-1081

(SoyCyc)=Activity=pectin esterase;

Pathway=homogalacturon

Glyma03g03410 Glymal 3158102 3160282 an degradation

375319 2742 193 cajanus_caja

8 n 3159522 3159607 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

418082 2891 037 cajanus_caja

3 n 3159695 3159964 NA

BARCSOYSSR 0 Wm82_poten

3 0178 tial SSR 3163958 3164025 NA

Glyma03g03420 Glymal 3166793 3167020 NA

Average Cons

Position=LG06 30.2 cM: Q8L924 UPF0497

Gm W82 CR03.G Gm W82 C membrane protein 18550 R03 3166793 3167020 At2g35760 2E-13

BARCSOYSSR 0 Wm82_poten

3 0179 tial SSR 3167750 3167781 NA

SATT159 3169968 3170252

marker map

Sattl59 4 3169968 3170252 NA

BARCSOYSSR 0 Wm82_poten

3 0180 tial SSR 3170121 3170162 NA

305096 0951 107 cajanus_caja

0 n 3170506 3170717 NA

Glyma03g03430 Glymal 3170171 3171595 NA

Average Cons

Position=LG06 30.2 cM: Q6PQ93 Pectin methylesterase 9 1E-26 ; 004887 Pectinesterase-2 precursor 4E-24 ;

Q6PQ97 Pectin methylesterase 5 2E-22 ; Q43143 Pectinesterase Ul precursor 2E-16 ;

Q9FY03 Putative pectin

Gm W82 CR03.G Gm W82 C methylesterase precursor 18560 R03 3170171 3171595 4E-14

cajanus_caja

Contig23415 n 3170968 3171431 NA

NGMAX0060775

13 23 3172140 3172441 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

NGMAX0060775

55 24 3181380 3181681

Glyma03g03440 Glymal 3192517 3192801 NA

Average Cons

Position=LG06 30.3 cM: Q9SM60

Phosphoglucomutase, cytoplasmic 4E-25 ;

P93262

Gm W82 CR03.G Gm W82 C Phosphoglucomutase, 18570 R03 3192517 3192801 cytoplasmic 3E-24

BARCSOYSSR 0 Wm82_poten

3 0181 tial SSR 3194639 3194700 NA

ID:PTHR13856

(Panther)=VHS DOMAIN CONTAINING

Glyma03g03450 Glymal 3193959 3198116 PROTEIN FAMILY

Average Cons

Position=LG06 30.4 cM:

Gm W82 CR03.G Gm W82 C Q2V732 VHS and GAT 18580 R03 3193959 3198116 domain protein 3E-12

Glycine_max

TA67921 3847 release 2 3197245 3197763 NA

similar to

UniRefl00_Q2HSP6 General substrate transporter - Medicago

GMGI.04221 truncatula (Barrel medic),

TC407739 0 3197272 3197763 partial (4%)

BARCSOYSSR 0 Wm82_poten

3 0182 tial SSR 3199583 3199604 NA

BARCSOYSSR 0 Wm82_poten

3 0183 tial SSR 3199966 3200010 NA

cajanus_caja

Contig32455 n 3200657 3200918 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

cajanus caja

Contigl9141 n 3200851 3201091 NA

C afal_lcle

Cfl0417d an 3200836 3201120 NA similar to

UniRefl00_A7PYC6 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC377879 0 3200720 3201287 partial (27%)

418082 2891 037 cajanus_caja

3 n 3201086 3201309 NA

375319 2742 193 cajanus_caja

8 n 3201519 3201601 NA similar to

UniRefl00_O04887 Pectinesterase-2 precursor

GMGI.04221 - Citrus sinensis (Sweet

BQ576469 0 3201494 3201914 orange), partial (10%)

Pectinesterase-2 precursor

Glycine_max [Citrus sinensis (Sweet

BQ576469 release 2 3201494 3202078 orange)]

ID:GO:0005618

(GO)=cell wall;

ID:GO:0030599

(GO)=pectinesterase activity; ID:GO:0042545 (GO)=cell wall modification; ID:PF01095

Glyma03g03460 Glymal 3200770 3204918 (PFAM)=Pectinesterase

214452 2123 125 cajanus_caja

9 n 3201638 3204052 NA

UniRefl00_A7PYC6 Pectinesterase n=l Tax=Vitis vinifera

Phaseolus_v RepID=A7PYC6 VITVI

Pvcon9735 ulgaris 3201498 3204566 1.00E-120 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Phaseolus v Pectinesterase-2 precursor ulgaris_relea [Citrus sinensis (Sweet

TA5573 3885 se 2 3201498 3204566 orange)]

Pectinesterase-2 precursor

Glycine_max [Citrus sinensis (Sweet

TA41878 3847 release 2 3201659 3204609 orange)] similar to

UniRefl00_A7PYC6 Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

AW706153 0 3203771 3204190 partial (14%)

Pectinesterase-2 precursor

Glycine_max [Citrus sinensis (Sweet

AW706153 release 2 3203769 3204345 orange)]

cajanus_caja

Contig23415 n 3204034 3204496 NA

Vigna_ungui

asmbl 1395 culata 3204001 3204659 NA

Pectinesterase-2 precursor

Glycine max [Citrus sinensis (Sweet

AI941403 release 2 3204411 3204540 orange)]

Pectinesterase-2 precursor

Glycine_max [Citrus sinensis (Sweet

TA41886 3847 release 2 3204278 3204684 orange)]

Pectinesterase-2 precursor

Glycine_max [Citrus sinensis (Sweet

BQ453360 release 2 3204384 3204908 orange)]

NGMAX0060776

40 3 3209230 3209531

188924 1171 403 cajanus caja

6 n 3211646 3211879 NA

ID:PF01657

(PFAM)=Domain of

Glyma03g03470 Glymal 3211521 3212299 unknown function DUF26 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 30.4 cM: Q6NKQ9 Cysteine-rich

Gm W82 CR03.G Gm W82 C repeat secretory protein 15 18800 R03 3211521 3212299 precursor 3E-47

Chafal_lcle

Cf5097d an 3225804 3226039 NA

ID:PF02519

(PFAM)=Auxin

Glyma03g03480 Glymal 3225520 3226992 responsive protein similar to

UniRefl00_A7PYC4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC362898 0 3225774 3226757 partial (51%)

BARCSOYSSR 0 Wm82jpoten

3 0184 tial SSR 3226514 3226540 NA

Glycine max

TA61385 3847 release 2 3226092 3226992 NA

GMGI.04221

TC399758 0 3226663 3226990 NA

NGMAX0060778

78 19 3232914 3233215

NGMAX0060779

28 4 3238990 3239291

NGMAX0060781

22 29 3253689 3253990

Lotusjaponi Golgi SNARE 12 protein cus release [Arabidopsis thaliana

TAD 126 34305 1 3254515 3259837 (Mouse-ear cress)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: homologue to

UniRefl00_A7PYC3 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence - Vitis vinifera (Grape),

TC24266 LJGI.070108 3254515 3259837 partial (57%) similar to

UniRefl00_A7PYC3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC365000 0 3254378 3260002 partial (72%)

Golgi SNARE 12 protein

Glycine_max [Arabidopsis thaliana

BM094071 release 2 3254443 3259972 (Mouse-ear cress)]

Chafal_lcle

Cfl646d an 3254532 3261153 NA similar to

UniRefl00_A7PYC3 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence

MTGI.07170 - Vitis vinifera (Grape),

TC120084 8 3254540 3261190 partial (98%) SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

UniRefl00_A7PYC3 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax-Vitis vinifera

Phaseolus v RepID=A7PYC3 VITVI

Pvcon4074 ulgaris 3254499 3261367 1.00E-112

ID:GO:0006886

(GO)=intracellular protein transport; ID:GO:0016020 (GO)=membrane;

ID:K08495 (KO)=;

ID:KOG3208

(KOG)=SNARE protein GS28; ID:PF05008 (PFAM)=Vesicle transport v-SNARE protein; ID:PTHR21094 (Panther)=FAMILY NOT

Glyma03g03490 Glymal 3254361 3261723 NAMED

Average Cons

Position=LG06 30.7 cM:

Gm W82 CR03.G Gm W82 C 022151 Golgi SNARE 12 19220 R03 3254361 3261723 protein lE-101

Lotusjaponi Golgi SNARE 12 protein cus release [Arabidopsis thaliana

BP048935 1 3259926 3261261 (Mouse-ear cress)] similar to

UniRefl00_A7PYC3 Chromosome chrl 5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

DB979241 0 3260857 3261372 partial (29%)

Golgi SNARE 12 protein

Glycine_max [Arabidopsis thaliana

CD399194 release 2 3260921 3261324 (Mouse-ear cress)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

BARCSOYSSR 0 Wm82_poten

3 0185 tial SSR 3267129 3267172 NA

BARCSOYSSR 0 Wm82_poten

3 0186 tial SSR 3269087 3269130 NA

BARCSOYSSR 0 Wm82_poten

3 0187 tial SSR 3270199 3270218 NA

cajanus caja

Contig23197 n 3272203 3272416 NA

415445 2756 238 cajanus_caja

8 n 3272279 3272416 NA

183101_0466_096 cajanus caj

6_primers n 3273791 3273999 NA

183101 0466 096 cajanus caja

6 n 3273730 3274095 NA

206423 3853 389 cajanus_caja

1 n 3273959 3274097 NA similar to

UniRefl00_Q6SSOO YABBY-like transcription factor GRAMINIFOLIA - Antirrhinum majus

GMGI.04221 (Garden snapdragon),

TC361285 0 3273414 3276514 partial (86%)

ID:PF04690

Glyma03g03500 Glymal 3273412 3276522 (PFAM)=YABBY protein

Average Cons

Position=LG06 30.7 cM: Q6SS00 YABBY-like

Gm W82 CR03.G Gm W82 C transcription factor 19230 R03 3273412 3276522 GRAMINIFOLIA 5E-96

YABBY-like transcription factor GRAMINIFOLIA

Glycine_max [Antirrhinum majus

TA52412 3847 release 2 3273416 3276522 (Garden snapdragon)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Chafal_lcle

Cfl l77d an 3273757 3276225 NA

YABBY-like transcription factor GRAMINIFOLIA

Glycine_soja [Antirrhinum majus

TA3613 3848 release 2 3273754 3276461 (Garden snapdragon)]

BARCSOYSSR 0 Wm82_poten

3 0188 tial SSR 3275263 3275282 NA

Chafaljcle

Cf21553d an 3274365 3276226 NA

homologue to

UniReflOO Q6SS00 Cluster: YABBY-like transcription factor GRAMINIFOLIA, n=l, Antirrhinum majus|Rep: YABBY-like transcription factor GRAMINIFOLIA - Antirrhinum majus (Garden snapdragon),

BP041062 LJGI.070108 3274309 3276373 partial (46%)

YABBY-like transcription factor GRAMINIFOLIA

Glycine max [Antirrhinum majus

CD416578 release 2 3274359 3276514 (Garden snapdragon)]

YABBY-like transcription factor GRAMINIFOLIA

Glycine_max [Antirrhinum majus

CD414741 release 2 3274379 3276514 (Garden snapdragon)]

YABBY-like transcription factor GRAMINIFOLIA

Glycine_max [Antirrhinum majus

AW311204 release 2 3275751 3276514 (Garden snapdragon)] SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5)

NO: Information (6)

Glycinejnax

CD390542 release 2 3276017 3276470 NA

BARCSOYSSR 0 Wm82jpoten

3 0189 tial SSR 3276885 3276948 NA

ID:PTHR23258

(Panther)=SERINE- THREONINE PROTEIN

Glyma03g03510 Glymal 3282203 3283893 KINASE, PLANT-TYPE

Glycinejnax

BM094865 release 2 3298597 3298959 NA

Cytochrome P450 monooxygenase

Glycinejnax CYP83E8 [Glycine max

BI698917 release 2 3298949 3299117 (Soybean)]

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

CYP83E8 n=l

Tax=Glycine max

Phaseolus v RepID=Q2LAL4 SOYB

Pvcon9484 ulgaris 3298902 3299318 N 2.00E-56

BARC-031833- marker map

07221 4 3298950 3299349 NA

BARC-028619- Wm82xPI46

05977 8916 3298952 3299501 NA

Cytochrome P450

Glycine soja monooxygenase CYP83A

BM526084 release 2 3299204 3299786 [Glycine max (Soybean)]

UniRefl 00_Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC373025 0 3299110 3299920 (Soybean), partial (29%) SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

homologue to

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC371473 0 3298933 3300311 (Soybean), partial (47%)

Cytochrome P450 monooxygenase

Glycine max CYP83E8 [Glycine max

BE658696 release 2 3298946 3300315 (Soybean)]

Cytochrome P450 monooxygenase

Glycine max CYP83E8 [Glycine max

BU080942 release 2 3299348 3299922 (Soybean)]

UniRefl 00_Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

CA820617 0 3299236 3300308 (Soybean), partial (30%)

ID:GO:0004497

(GC ^monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:K00517 (KO)=E1.14.- .-; [EC: 1.14.-.- ]

[COG:COG2124 ];

ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03520 Glymal 3298597 3301147 E P450

Glyma03g03530 Glymal 3298597 3301147 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Cytochrome P450 monooxygenase

Glycine_max CYP83E8 [Glycine max

TA41485 3847 release 2 3298610 3301147 (Soybean)]

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC349887 0 3298612 3301147 (Soybean), complete

Cytochrome P450 monooxygenase

Glycine_max CYP83E8 [Glycine max

BE610066 release 2 3299270 3300511 (Soybean)]

cytochrome P450 monooxygenase

CYP83E8 (CYP83E8)

DQ340234.1 GenBank 3298639 3301147 mRNA

Average Cons

Position=LG06 30.7 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-104 ; Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 19650 R03 3298597 3301192 CYP83E8 1E-74

Average Cons

Position=LG06 30.7 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 0 ; Q2MJ14 Cytochrome P450

Gm W82 CR03.G Gm W82 C monooxygenase

19660 R03 3298597 3301192 CYP83E8 1E-162

Cytochrome P450

Glycine_soja monooxygenase CYP83A

TA2512 3848 release 2 3298823 3301065 [Glycine max (Soybean)]

Cytochrome P450 monooxygenase

Glycine_max CYP83E8 [Glycine max

BQ785233 release 2 3299398 3301060 (Soybean)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Cytochrome P450 monooxygenase

Glycinejmax CYP83E8 [Glycine max

TA41499 3847 release 2 3299888 3300578 (Soybean)]

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

BM177920 0 3300031 3300450 (Soybean), partial (19%)

Cytochrome P450 monooxygenase

Glycinejmax CYP83E8 [Glycine max

BI892902 release 2 3300324 3300877 (Soybean)]

Cytochrome P450 monooxygenase

Glycine max CYP83E8 [Glycine max

BE806353 release 2 3300458 3300769 (Soybean)]

Cytochrome P450 monooxygenase

Glycine_max CYP83E8 [Glycine max

BF009836 release 2 3300695 3301046 (Soybean)]

NGMAX0060784

95 30 3302666 3302967

NS0262836 31

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03540 Glymal 3319774 3321759 E P450 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 30.8 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-141 ; Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 19670 R03 3319774 3321759 CYP83E8 1E-109

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

CYP83E8 n=l

Tax=Glycine max

Phaseolus_v RepID=Q2LAL4 SOYB

CV535331 ulgaris 3321369 3321648 N 1.00E-34

117509 1962 039 cajanus_caja

7 n 3321863 3321957 NA

cajanus caja

Contig30301 n 3321862 3321958 NA

cajanus_caja

Contig5456 n 3321879 3321947 NA

cajanus_caja

Contig2767 n 3321862 3321990 NA

BARCSOYSSR 0 Wm82_poten

3 0190 tial SSR 3325908 3325927 NA

Chafal_lcle

Cfl 7433d an 3328712 3328856 NA

SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03550 Glymal 3328724 3335906 E P450

Average Cons

Position=LG06 30.8 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-180 ;

Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 19680 R03 3328724 3335906 CYP83E8 1E-162

UniRefl 00_Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC418102 0 3298810 3366106 (Soybean), partial (32%)

Wm82xPI46

ssl81360642 8916 3333672 3333793 NA

NGMAX0060788

38 5 3335895 3336196

BARCSOYSSR 0 Wm82_poten

3 0191 tial SSR 3337556 3337597 NA

S ATT 152 3338479 3338729

marker map

Sattl52 4 3338479 3338729 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

BARCSOYSSR 0 Wm82_poten

3 0192 tial SSR 3338620 3338682 NA

BARCSOYSSR 0 Wm82_poten

3 0193 tial SSR 3338831 3338878 NA

BARCSOYSSR 0 Wm82_poten

3 0194 tial SSR 3343344 3343393 NA

BARCSOYSSR 0 Wm82_poten

3 0195 tial SSR 3343831 3343884 NA

Average Cons

Position=LG06 30.9 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 0 ; Q2MJ14 Cytochrome P450

Gm W82 CR03.G Gm W82 C monooxygenase

19690 R03 3344402 3346608 CYP83E8 1E-166

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

( OG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03560 Glymal 3344405 3346608 E P450

Cytochrome P450

Glycine_soja monooxygenase CYP83A

DT083744 release 2 3346117 3346593 [Glycine max (Soybean)]

Glyma03g03570 Glymal 3365144 3365263 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 31 cM: Q9T0K5 Extensin-like

Gm W82 CR03.G Gm W82 C protein 2E-8 ; Q9SN46 19700 R03 3365144 3365263 Extensin-like protein 9E-8

BARCSOYSSR 0 Wm82jpoten

3 0196 tial SSR 3366060 3366097 NA

373244 3126 334 cajanus_caja

3 n 3372997 3373302 NA

BARCSOYSSR 0 Wm82_poten

3 0197 tial SSR 3374862 3374925 NA

RuBisCO-associated

Glycine_max protein [Glycine max

BE021801 release 2 3375080 3375675 (Soybean)]

Glyma03g03580 Glymal 3375014 3376090 NA

Average Cons

Position=LG06 31 cM: P39657 RuBisCO- associated protein 7E-52 ;

Gm W82 CR03.G Gm W82 C Q2HU30 2-S globulin 2E- 19710 R03 3375014 3376090 35

weakly similar to

UniRefl00_P39657 RuBisCO-associated

GMGI.04221 protein - Glycine max

TC379722 0 3375263 3375949 (Soybean), partial (31%)

RuBisCO-associated

Glycine max protein [Glycine max

TA65108 3847 release 2 3375299 3375949 (Soybean)]

NGMAX0060794

84 6 3389647 3389948

Wm82xPI46

ssl81360636 8916 3390391 3390512 NA

NGMAX0060795

02 7 3390962 3391263

BARCSOYSSR 0 Wm82_poten

3 0198 tial SSR 3392252 3392297 NA SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

BARCSOYSSR 0 Wm82_poten

3 0199 tial SSR 3397544 3397571 NA

similar to

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC376705 0 3399170 3399602 (Soybean), partial (26%)

Cytochrome P450 monooxygenase

Glycine_max CYP83H2 [Medicago

TA68858 3847 release 2 3399170 3399761 truncatula (Barrel medic)] weakly similar to

UniRefl 00_Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

BQ742710 0 3399724 3400146 (Soybean), partial (24%)

Cytochrome P450 monooxygenase

Glycine_max CYP83H2 [Medicago

BQ742710 release 2 3399724 3400170 truncatula (Barrel medic)]

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03590 Glymal 3399194 3401129 E P450 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

similar to

UniRefl 00 Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC379046 0 3400601 3401037 (Soybean), partial (29%)

Cytochrome P450 monooxygenase

Glycine_max CYP83E8 [Glycine max

TA64119 3847 release 2 3400601 3401129 (Soybean)]

WmFPC Contigl2

49 Wm82 3269223 3539380 NA

BARCSOYSSR 0 Wm82_poten

3 0200 tial SSR 3411398 3411447 NA

Average Cons

Position=LG06 31.2 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-178 ;

Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 19720 R03 3399152 3432251 CYP83E8 1E-161

BARCSOYSSR 0 Wm82_poten

3 0201 tial SSR 3416401 3416428 NA

ID:PTHR23354

(Panther)=NUCLEOLAR

PROTEIN 7/ESTROGEN

RECEPTOR

COACTIVATOR-

Glyma03g03610 Glymal 3417813 3418036 RELATED

ID:PTHR11353:SF19 (Panther)=CHAPERONI N CONTAINING T- COMPLEX PROTEIN 1, THETA SUBUNIT,

Glyma03g03620 Glymal 3420542 3421382 TCPQ SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 31.2 cM: Q75HJ3 Putative TCP-

Gm W82 CR03.G Gm W82 C l/cpn60 chaperonin 19940 R03 3420542 3421382 family protein 2E-14

BARCSOYSSR 0 Wm82_poten

3 0202 tial SSR 3428245 3428290 NA

Vigna_ungui

asmbl 1396 culata 3430242 3431029 NA

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03630 Glymal 3430214 3432112 E P450

Chafal_lcle

Cf884d an 3399773 3462808 NA

similar to

UniRefl 00_Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC383713 0 3430945 3431920 (Soybean), partial (41%)

Cytochrome P450 monooxygenase

Glycine max CYP83E8 [Glycine max

TA64120 3847 release 2 3430945 3432088 (Soybean)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 31.2 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 0 ; Q2MJ14 Cytochrome P450

Gm W82 CR03.G Gm W82 C monooxygenase

19950 R03 3434392 3437069 CYP83E8 1E-168

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:K00517 (KO)=E1.14.- .-; [EC: 1.14.-.- ]

[COG:COG2124 ];

ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03640 Glymal 3434532 3437069 E P450

BARCSOYSSR 0 Wm82_poten

3 0203 tial SSR 3441948 3441974 NA

cajanus_caja

Contig41065 n 3444039 3444288 NA

Chafal_lcle

Cfl9649d an 3444522 3444589 NA

ID:PTHR10641

(Panther)=MYB-

Glyma03g03660 Glymal 3453314 3454353 RELATED SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 31.3 cM: 004498 F21M12.15

Gm W82 CR03.G Gm W82 C protein 1E-13 ; Q8W149 19960 R03 3453314 3454353 CDC5 protein 1E-13

UniRefl00_A7QMU6 Cluster: Chromosome chrl4 scaffold_128, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl4 scaffold_128, whole genome shotgun sequence

MTGI.07170 - Vitis vinifera (Grape),

CX529111 8 3454177 3454324 partial (5%)

NGMAX0060799

11 20 3454832 3455133

Cytochrome P450 monooxygenase

Glycine max CYP83H2 [Medicago

TA76562 3847 release 2 3460426 3460986 truncatula (Barrel medic)] similar to

UniRefl 00_Q2LAL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC353924 0 3460363 3462296 (Soybean), partial (55%)

SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

(KOG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03670 Glymal 3460363 3463031 E P450

Vigna_ungui

asmbl 1397 culata 3461063 3462810 NA

Cytochrome P450

Glycine_soja monooxygenase CYP83A

BM526518 release 2 3461266 3462638 [Glycine max (Soybean)]

Cytochrome P450 monooxygenase

Glycine max CYP83H2 [Medicago

TA74906 3847 release 2 3461106 3462803 truncatula (Barrel medic)] similar to

UniRefl00_Q2MJ14 Cytochrome P450 monooxygenase

CYP83E8 - Medicago

GMGI.04221 truncatula (Barrel medic),

TC350978 0 3461205 3463031 partial (45%)

cajanus caja

Contigl6050 n 3463437 3463904 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0003735

(GO)=structural constituent of ribosome;

ID:GO:0005622

(GO)=intracellular;

ID:GO:0005840

(GO)=ribosome;

ID:GO:0006412

(GO)=protein

biosynthesis; ID:PF00318

(PFAM)=Ribosomal protein S2;

ID:PTHR12534

(Panther)=30S

RIBOSOMAL PROTEIN

S2 (PROKARYOTIC

Glyma03g03680 Glymal 3463500 3463884 AND ORGANELLAR)

Average Cons

Position=LG06 31.3 cM: Q2PMT2 Chloroplast 30S ribosomal protein S2 5E-

Gm W82 CR03.G Gm W82 C 66 ; A4GGA8 Ribosomal 19980 R03 3463500 3463884 protein S2 3E-60

282842 2235 030 cajanus_caja

0 n 3463717 3463904 NA

SAT 186 3465323 3465611

marker map

Sat 186 4 3465323 3465611 NA

BARCSOYSSR 0 Wm82_poten

3 0204 tial SSR 3465436 3465507 NA

ID:PTHR19383

(Panther)=CYTOCHROM

Glyma03g03690 Glymal 3466673 3467512 E P450 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 31.3 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 2E-59 ;

Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 19990 R03 3466673 3467512 CYP83E8 6E-53

Average Cons

Position=LG06 31.4 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-174 ;

Q2MJ14 Cytochrome P450 monooxygenase CYP83E8 1E-174 ;

Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-174 ;

Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 19970 R03 3460310 3482068 CYP83E8 1E-174

BARCSOYSSR 0 Wm82_poten

3 0205 tial SSR 3480208 3480258 NA

ID:PTHR19383

(Panther)=CYTOCHROM

Glyma03g03700 Glymal 3479524 3482068 E P450

Cytochrome P450 monooxygenase

Glycine_max CYP83H2 [Medicago

TA71903 3847 release 2 3481704 3482068 truncatula (Barrel medic)] cajanus_caja

Contig35199 n 3494004 3494295 NA

cajanus_caja

Contig3959 n 3494076 3494316 NA

048713 3862 040 cajanus_caja

4 n 3494085 3494309 NA

cajanus_caja

Contigl3534 n 3494085 3494316 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

cajanus_caja

Contig26881 n 3494172 3494315 NA

ID:PTHR19383

(Panther)=CYTOCHROM

Glyma03g03710 Glymal 3496238 3496656 E P450

Average Cons

Position=LG06 31.5 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-28 ;

Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 20000 R03 3496238 3496656 CYP83E8 3E-24

similar to

UniRefl00_O23451 Retrotransposon like protein - Arabidopsis

GMGI.04221 thaliana (Mouse-ear

AI855899 0 3498286 3498702 cress), partial (18%)

ID:GO:0004497

(GO)=monooxygenase activity; ID:GO:0005506 (GO)=iron ion binding; ID:GO:0009055

(GO)=electron carrier activity; ID:GO:0020037 (GO)=heme binding; ID:KOG0156

( OG)=Cytochrome P450 CYP2 subfamily;

ID:PF00067

(PFAM)=Cytochrome P450; ID:PTHR19383 (Panther)=CYTOCHROM

Glyma03g03720 Glymal 3496909 3507131 E P450 SEQ

Locus / Display Start End

ID Source (3) Additional Locus Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 31.5 cM: Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 0 ; Q2MJ14 Cytochrome P450 monooxygenase

CYP83E8 1E-176 ;

Q2LAL4 Cytochrome P450 monooxygenase CYP83E8 1E-173 ;

Q2MJ14 Cytochrome

Gm W82 CR03.G Gm W82 C P450 monooxygenase 20010 R03 3496909 3507191 CYP83E8 1E-167

Cytochrome P450 monooxygenase

Glycine_max CYP83H2 [Medicago

DY577297 release 2 3502642 3506305 truncatula (Barrel medic)] similar to

UniRefl 00 Q2L AL4 Cytochrome P450 monooxygenase

GMGI.04221 CYP83E8 - Glycine max

TC390056 0 3506393 3507131 (Soybean), partial (43%)

Cytochrome P450 monooxygenase

Glycine_max CYP83H2 [Medicago

BU090520 release 2 3506586 3507131 truncatula (Barrel medic)]

BARCSOYSSR 0 Wm82_poten

3 0206 tial SSR 3509060 3509091 NA

ID:PF07160

(PFAM)=Protein of unknown function

Glyma03g03730 Glymal 3519958 3523194 (DUF1395)

Chafal_lcle

Cf6842d an 3519956 3523224 NA

NGMAX0060805

09 38 3523345 3523646 SEQ

Locus / Display Start End

ID Source (3) Additional Locus Name (1) Base (4) Base (5)

NO: Information (6)

BARCSOYSSR 0 Wm82_poten

3 0207 tial SSR 3532126 3532179 NA

Glycine max

TA57125 3847 release 2 3533027 3533555 NA

Glyma03g03740 Glymal 3533027 3534997 NA

homologue to

UniRefl00_A4TTL5 Membrane protein - Magnetospirillum

GMGI.04221 gryphiswaldense, partial

TC382189 0 3533027 3534997 (7%)

Glycine_max

TA57124 3847 release 2 3533481 3534997 NA

186545 1436 241 cajanus_caja

3 n 3539771 3539988 NA

351424 2925 335 cajanus_caja

1 n 3539773 3539988 NA

cajanus_caja

Contig20883 n 3539773 3539988 NA

cajanus_caja

Contigl4745 n 3539774 3539988 NA

cajanus_caja

Contig38065 n 3539781 3539989 NA

cajanus_caja

Contig6509 n 3539784 3539988 NA

219748 2942 075 cajanus_caja

3 n 3539790 3539988 NA

293431 2369 288 cajanus_caja

4 n 3539793 3539988 NA

cajanus_caja

Contig27022 n 3539767 3540015 NA

cajanus_caja

Contig42885 n 3539793 3539992 NA

cajanus_caja

Contig4926 n 3539802 3540002 NA SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

similar to

UniRefl00_A5KCL8 Variable surface protein Vir24-related -

GMGI.04221 Plasmodium vivax, partial

TC412519 0 3547628 3547947 (5%)

303716 2876 127 cajanus_caja

1 n 3548384 3548512 NA

Chafal_lcle

Cfl7931d an 3548408 3548488 NA

Hypothetical protein

Glycine soja P0018A03.7 [Oryza sativa

BG046534 release 2 3547861 3549153 (japonica cultivar-group)]

Chafal_lcle

Cfl9308d an 3548421 3549288 NA

131874 4007 080 cajanus_caja

7 n 3549054 3549310 NA

F20B17.3 [Arabidopsis

Glycine_max thaliana (Mouse-ear

BQ785172 release 2 3548932 3549589 cress)]

ID:K08869 (KO)=;

ID:KOG1235

( OG)=Predicted unusual protein kinase;

ID:PF03109

(PFAM)=ABC1 family; ID:PTHR10566

(Panther)=CHAPERONE- ACTIVITY OF BC1 COMPLEX (CABC1)-

Glyma03g03750 Glymal 3547452 3551110 RELATED

Chafal_lcle

Cfl7860d an 3549758 3550319 NA

Chafal_lcle

Cfl4536d an 3550122 3550244 NA

Chafaljcle

Cf5190d an 3550872 3551786 NA SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4)

NO: Base (5) Information (6)

similar to

UrriRefl00_Q9MA15 Cluster: Uncharacterized aarF domain-containing protein kinase Atlg79600, chloroplast precursor, n=2, Arabidopsis thaliana|Rep:

Uncharacterized aarF domain-containing protein kinase Atlg79600, chloroplast precursor - Arabidopsis thaliana

MTGI.07170 (Mouse-ear cress), partial

AW736224 8 3550986 3551846 (9%) similar to

UniRefl00_Q9MA15 Uncharacterized aarF domain-containing protein kinase Atlg79600, chloroplast precursor - Arabidopsis thaliana

GMGI.04221 (Mouse-ear cress), partial

AW459587 0 3551428 3551782 (6%)

Glycinejnax

TA71197 3847 release 2 3551413 3552423 NA

similar to

UniRefl00_A7SRHl Predicted protein - Nematostella vectensis

GMGI.04221 (Starlet sea anemone),

BI321376 0 3552012 3552423 partial (3%)

NGMAX0060808

85 8 3561914 3562215

BARCSOYSSR 0 Wm82_poten

3 0208 tial SSR 3578993 3579090 NA

225723 2718 286 cajanus_caja

3 n 3581358 3581429 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

cajanus_caja

Contig36250 n 3581439 3581816 NA

Vigna_ungui

asmbl 1398 culata 3581431 3582042 NA

GRAS transcription factor

Glycinejnax [Medicago truncatula

TA49427 3847 release 2 3581425 3582129 (Barrel medic)]

Chafaljcle

Cfl5586d an 3581734 3581838 NA

GRAS transcription factor

Glycine_max [Medicago truncatula

BE820512 release 2 3581448 3582150 (Barrel medic)]

Lotusjaponi GRAS transcription factor cus release [Medicago truncatula

TA7292 34305 1 3581441 3582214 (Barrel medic)] weakly similar to

UniRefl00_A7PYF4 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence - Vitis vinifera (Grape),

TC27537 LJGI.070108 3581441 3582214 partial (21%) weakly similar to

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC365523 0 3581299 3582452 partial (23%) weakly similar to

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC369657 0 3581425 3582630 partial (30%) SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Chafal_lcle

Cfl3385d an 3581734 3582618 NA

GRAS transcription factor

Glycine max [Medicago truncatula

TA49425 3847 release 2 3581746 3582728 (Barrel medic)]

Scarecrow-like 6

Glycine soja [Arabidopsis thaliana

TA4094 3848 release 2 3581788 3582699 (Mouse-ear cress)] similar to

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC354455 0 3581939 3582741 partial (22%)

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax= Vitis vinifera

Phaseolus v RepID=A7PYF4 VITVI

Pvcon6489 ulgaris 3581822 3582979 1.00E-117

Phaseolus v GRAS transcription factor ulgaris_relea [Medicago truncatula

TA5736 3885 se 2 3581822 3582979 (Barrel medic)]

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax= Vitis vinifera

Phaseolus v RepID=A7PYF4 VITVI

EX304728 ulgaris 3582172 3582953 9.00E-62

Chafal_lcle

Cfl4326d an 3582263 3582870 NA

Lotusjaponi GRAS transcription factor cus release [Medicago truncatula

AV419737 1 3582457 3582866 (Barrel medic)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: similar to

UniRefl00_A7PYF4 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence - Vitis vinifera (Grape),

AV419737 LJGI.070108 3582470 3582866 partial (15%)

Average Cons

Position=LG06 31.8 cM:

Gm W82 CR03.G Gm W82 C Q8LL10 Hairy meristem 20850 R03 3581403 3584467 1E-105

ID:PF03514

(PFAM)=GRAS family

Glyma03g03760 Glymal 3581425 3584467 transcription factor

GRAS transcription factor

Glycine_max [Medicago truncatula

TA49424 3847 release 2 3582576 3583493 (Barrel medic)]

Vigna_ungui

asmbl 1399 culata 3582925 3583548 NA similar to

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC384787 0 3582755 3583811 partial (8%)

cajanus_caja

Contig33774 n 3583334 3583523 NA

GRAS transcription factor

Glycine_max [Medicago truncatula

BM107962 release 2 3583135 3583811 (Barrel medic)]

Glycine soja

BM526478 release 2 3583674 3584202 NA SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO: similar to

UniRefl00_A7PYF4 Chromosome chrl5 scaffold_37, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC399328 0 3583626 3584467 partial (4%)

BARCSOYSSR 0 Wm82_poten

3 0209 tial SSR 3585574 3585641 NA

BARCSOYSSR 0 Wm82jpoten

3 0210 tial SSR 3597635 3597672 NA

Glyma03g03770 Glymal 3600654 3600771 NA

BARCSOYSSR 0 Wm82_poten

3 0211 tial SSR 3602587 3602608 NA

BARCSOYSSR 0 Wm82_poten

3 0212 tial SSR 3608155 3608176 NA

BARCSOYSSR 0 Wm82jpoten

3 0213 tial SSR 3608387 3608446 NA

FACT complex subunit

Glycine_max SSRPl [Vicia faba (Broad

AW598654 release 2 3613044 3613631 bean)]

183966 2432 163 cajanus_caja

7 n 3613341 3613924 NA

328630 4036 377 cajanus_caja

9 n 3614035 3614253 NA

cajanus_caja

Contig39949 n 3614034 3614741 NA

cajanus_caja

Contigl2168 n 3614710 3614977 NA

Average Cons

Position=LG06 31.9 cM:

Gm W82 CR03.G Gm W82 C 004235 FACT complex 21470 R03 3612970 3619158 subunit SSRPl 0 SEQ

Locus / Display Start

ID End

Source (3) Additional Locus Name (1) Base (4)

NO: Base (5) Information (6)

ID:GO:0003677

(GO)=DNA binding; ID:GO:0005634

(GO)=nucleus;

ID:K09272 (KO)=;

ID:KOG0526

(KOG)=Nucleosome- binding factor SPN, POB3 subunit; ID:PF00505 (PFAM)=HMG (high mobility group) box; ID:PTHR13711

(Panther)=SWI/SNF- RELATED

CHROMATIN BINDING

Glyma03g03780 Glymal 3613002 3619158 PROTEIN

Chafaljcle

Cfl771d an 3613313 3618874 NA

Contig22956_prim cajanus_caja

ers n 3616077 3616304 NA

cajanus caja

Contig22956 n 3615797 3616789 NA

FACT complex subunit

Glycine_max SSRPl [Vicia faba (Broad

BG508541 release 2 3616283 3617889 bean)]

homologue to

UniRefl00_O04235 FACT complex subunit SSRPl - Vicia faba

GMGI.04221 (Broad bean), partial

TC394940 0 3615339 3619158 (52%)

Vigna_ungui

asmbl 1400 culata 3616459 3618878 NA

Contig45189_prim cajanus_caja

ers n 3617561 3617828 NA

cajanus_caja

Contig45189 n 3617516 3617932 NA

Chafal_lcle

Cf4868d an 3629189 3629480 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:PF00036 (PFAM)=EF hand; ID:PTHR10891 (Panther)=CALMODULI

Glyma03g03790 Glymal 3629021 3632958 N

Average Cons

Position=LG06 32 cM: Q01IH6

OSIGBaOl 59110.9 protein 2E-24 ; Q9FDZ8

Atlg73440 1E-22 ;

Q01IH6

OSIGBa0159I10.9 protein

Gm W82 CR03.G Gm W82 C 1E-22 ; Q9FDZ8

21680 R03 3629021 3632958 Atlg73440 3E-22

Chafal_lcle

Cfl9325d an 3630769 3632619 NA

Calcium-binding EF- hand; Ubiquitin

Phaseolus v interacting motif ulgaris_relea [Medicago truncatula

DQ117561 se 2 3630860 3632639 (Barrel medic)]

Atlg73440 [Arabidopsis

Glycine_max thaliana (Mouse-ear

BI699366 release 2 3632020 3632958 cress)]

BARCSOYSSR 0 Wm82_poten

3 0214 tial SSR 3632687 3632736 NA

312855 0711 327 cajanus_caja

1 n 3633856 3634022 NA

265958_3391_185 cajanus_caja

7 primers n 3634131 3635827 NA

Chafal_lcle

Cf7889d an 3634101 3635886 NA

265958 3391 185 cajanus caja

7 n 3634130 3635954 NA

cajanus caja

Contigl5510 n 3633837 3636562 NA

Vigna_ungui

asmbl 1401 culata 3633846 3636561 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Putative VAMP- associated protein

Glycine_max [Arabidopsis thaliana

BE658586 release 2 3633896 3637470 (Mouse-ear cress)]

similar to

UniRefl00_A8W459 Vesicle-associated protein - Medicago truncatula

GMGI.04221 (Barrel medic), partial

TC372625 0 3633896 3637470 (72%)

ID:GO:0005198

(GO)=structural molecule activity; ID:KOG0439 (KOG)=VAMP- associated protein involved in inositol metabolism; ID:PF00635 (PFAM)=MSP (Major sperm protein) domain; ID:PTHR10809

(Panther)=VESICLE- ASSOCIATED MEMBRANE PROTEIN

Glyma03g03800 Glymal 3633770 3638147 (VAMP)

Average Cons

Position=LG06 32 cM: A8W459 Vesicle- associated protein 5E-98 ; Q7XM58

Gm W82 CR03.G Gm W82 C OS JNBb0020011.15 21690 R03 3633770 3638151 protein 3E-11

similar to

UniRefl00_A8W459 Vesicle-associated protein - Medicago truncatula

GMGI.04221 (Barrel medic), partial

TC356639 0 3633778 3638147 (98%)

F11M15.13 protein

Glycine_max [Arabidopsis thaliana

TA48856 3847 release 2 3633830 3638098 (Mouse-ear cress)] SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

UniRefl00_A8W459 Vesicle-associated protein n=l Tax=Medicago truncatula

Phaseolus v RepID=A8W459 MEDT

Pvcon2313 ulgaris 3633861 3638070 R l.OOE-110

Putative VAMP- associated protein (At2g45140) (Putative VAMP (Vesicle- associated membrane protein)-associated protein) [Arabidopsis

Glycine max thaliana (Mouse-ear

CA801352 release 2 3636253 3636956 cress)]

homologue to

UniRefl00_A8W459 Vesicle-associated protein - Medicago truncatula

GMGI.04221 (Barrel medic), partial

CA801352 0 3636557 3636956 (28%)

135152 1291 248 cajanus_caja

2 n 3636646 3636929 NA

F11M15.13 protein

Lupinus_alb [Arabidopsis thaliana

CA411541 us release 2 3636648 3638013 (Mouse-ear cress)]

Putative VAMP- associated protein

Glycine_max [Arabidopsis thaliana

AW598332 release 2 3636682 3638032 (Mouse-ear cress)]

F11M15.13 protein

Glycine_max [Arabidopsis thaliana

CK606662 release 2 3636684 3638114 (Mouse-ear cress)]

Putative VAMP-

Phaseolus co associated protein ccineus_relea [Arabidopsis thaliana

TA4535 3886 se 2 3636737 3638091 (Mouse-ear cress)]

cajanus_caja

Contig23898 n 3637449 3638104 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Contig23898_prim cajanus_caja

ers n 3637768 3637969 NA

cajanus_caja

Contig21922 n 3644450 3644630 NA

Chafal_lcle

Cfl 6623d an 3644762 3644875 NA similar to

UniRefl00_A7PYF8 Cluster: Chromosome chrl5 scaffold_37, whole genome shotgun sequence, n=l, Vitis vinifera|Rep:

Chromosome chrl5 scaffold_37, whole genome shotgun sequence - Vitis vinifera (Grape),

TC33304 LJGI.070108 3644744 3645015 partial (28%)

Hypothetical protein

Lotusjaponi T8B10_250 [Arabidopsis cus release thaliana (Mouse-ear

TA13096 34305 1 3644744 3645016 cress)]

Glyma03g03810 Glymal 3644726 3645652 NA

Vigna_ungui

asmbl 1402 culata 3645125 3645437 NA

UniRefl00_A7PYF8 Chromosome chrl5 scaffold_37, whole genome shotgun sequence n=l Tax= Vitis vinifera

Phaseolus v RepID=A7PYF8 VITVI

Pvcon2861 ulgaris 3645118 3645700 1.00E-131

BARCSOYSSR 0 Wm82_poten

3 0215 tial SSR 3648008 3648059 NA

BARCSOYSSR 0 Wm82_poten

3 0216 tial SSR 3648947 3648980 NA

079763 0879 056 cajanus_caja

8 n 3659098 3659198 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Chafal_lcle

Cfl9857d an 3674397 3674718 NA

NGMAX0060819

42 32 3675970 3676271

Average Cons

Position=LG06 32.1 cM: Q7XJM6 At2g45130 protein 2E-62 ;

UPI000023DC34

Gm W82 CR03.G Gm W82 C hypothetical protein 22310 R03 3674151 3678330 FG01544.1 9E-11

ID:PTHR10783

(Panther)=XENOTROPIC AND POLYTROPIC MURINE LEUKEMIA

Glyma03g03820 Glymal 3674153 3678330 VIRUS RECEPTOR

Chafaljcle

Cf21636d an 3678001 3678119 NA

NGMAX0060819

99 33 3688804 3689105

214701 1085 281 cajanus_caja

9 n 3696674 3696867 NA weakly similar to UniRefl00_Q40287 Anthocyanidin 3-0- glucosyltransferase - Manihot esculenta

GMGI.04221 (Cassava) (Manioc),

TC354431 0 3696212 3698076 partial (25%)

Putative flavonol 3-0- glucosyltransferase

Glycine_max [Arabidopsis thaliana

TA65213 3847 release 2 3696212 3698092 (Mouse-ear cress)]

ID:KOG1192

(KOG)=UDP- glucuronosyl and UDP- glucosyl transferase; ID:PTHR11926

(Panther)=GLUCOSYL/G LUCURONOSYL

Glyma03g03830 Glymal 3696212 3698853 TRANSFERASES SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 32.2 cM: Q40287 Anthocyanidin 3-

Gm W82 CR03.G Gm W82 C O-glucosyltransferase 1E-

22320 R03 3696212 3698880 100

BARCSOYSSR 0 Wm82_poten

3 0217 tial SSR 3697753 3697776 NA

223169 0358 179 cajanus caja

0 n 3698268 3698529 NA

Glycine_max

BI973614 release 2 3698266 3698839 NA

222017 1187 236 cajanus_caja

3 n 3698533 3698709 NA

214701 1085 281 cajanus_caja

9 n 3718709 3718902 NA

ID:PTHR11926

(Panther)=GLUCOSYL/G LUCURONOSYL

Glyma03g03840 Glymal 3718497 3720038 TRANSFERASES

Average Cons

Position=LG06 32.3 cM: Q9ZU72 Putative flavonol 3-O-glucosyltransferase 1E-52 ; Q9ZU71 Putative

Gm W82 CR03.G Gm W82 C flavonol 3-O- 22330 R03 3718497 3720038 glucosyltransferase 7E-50

Glycine_max

CA936681 release 2 3720697 3720966 NA

AT3g50740/T3A5_120

Glycine soja [Arabidopsis thaliana

BG045196 release 2 3720668 3721159 (Mouse-ear cress)]

214701 1085 281 cajanus_caja

9 n 3720896 3721089 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:KOG1192

(KOG)=UDP- glucuronosyl and UDP- glucosyl transferase; ID:PTHR11926

(Panther)=GLUCOSYL/G LUCURONOSYL

Glyma03g03850 Glymal 3720509 3723198 TRANSFERASES

Average Cons

Position=LG06 32.3 cM: Q40287 Anthocyanidin 3-

Gm W82 CR03.G Gm W82 C O-glucosyltransf erase 1E- 22340 R03 3720509 3723198 102

BARCSOYSSR 0 Wm82_poten

3 0218 tial SSR 3721975 3721994 NA

Glycine max

BG362737 release 2 3722227 3722623 NA

223169 0358 179 cajanus_caja

0 n 3722497 3722758 NA similar to

UniRefl00_A7QXH2 Chromosome

undetermined

scaffold_224, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC377946 0 3722365 3723183 partial (8%)

222017 1187 236 cajanus_caja

3 n 3722772 3722938 NA

NGMAX0060821

15 34 3723411 3723712

ID:PTHR11926

(Panther)=GLUCOSYL/G LUCURONOSYL

Glyma03g03860 Glymal 3739483 3743064 TRANSFERASES SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 32.4 cM: Q9ZU72 Putative flavonol 3-O-glucosyltransferase 3E-30 ; Q9ZU71 Putative

Gm W82 CR03.G Gm W82 C flavonol 3-O- 22350 R03 3739483 3743064 glucosyltransferase 4E-28

214701 1085 281 cajanus_caja

9 n 3742136 3742309 NA

BARCSOYSSR 0 Wm82_poten

3 0219 tial SSR 3743233 3743280 NA

WmFPC Contig25

77 Wm82 3597056 3899983 NA

214701 1085 281 cajanus_caja

9 n 3767176 3767369 NA

ID:KOG1192

(KOG)=UDP- glucuronosyl and UDP- glucosyl transferase; ID:PTHR11926

(Panther)=GLUCOSYL/G LUCURONOSYL

Glyma03g03870 Glymal 3766840 3769211 TRANSFERASES

BARCSOYSSR 0 Wm82_poten

3 0220 tial SSR 3768104 3768125 NA

Average Cons

Position=LG06 32.5 cM: Q40287 Anthocyanidin 3-

Gm W82 CR03.G Gm W82 C O-glucosyltransferase 1E- 22360 R03 3766840 3769398 100

223169 0358 179 cajanus caja

0 n 3768626 3768887 NA

222017 1187 236 cajanus_caja

3 n 3768901 3769067 NA

BARCSOYSSR 0 Wm82_poten

3 0221 tial SSR 3780830 3780877 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:PTHR10110:SF2 (Panther)=SODIUM/HYD ROGEN EXCHANGER

(NA+/H+ ANTIPORTER

Glyma03g03880 Glymal 3780953 3782165 NHX)

Average Cons

Position=LG06 32.5 cM: Q5XWR7

Sodium/hydrogen exchanger 6E-41 ;

Q4VT46

Gm W82 CR03.G Gm W82 C Sodium/hydrogen

22370 R03 3780953 3782165 exchanger 4E-40

NGMAX0060826

88 35 3783513 3783814

120013 0199 072 cajanus_caja

6 n 3795534 3795754 NA

cajanus_caja

Contigl0071 n 3795582 3795791 NA similar to

UniRefl00_A7P J2 Chromosome chrl5 scaffold_19, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC404918 0 3796084 3796372 partial (6%)

NS0118425 37 3797329 3796787

ID:PF03828

(PFAM)=Poly(A) polymerase;

ID:PTHR23092

(Panther)=FAMILY NOT

Glyma03g03890 Glymal 3795505 3806070 NAMED

Average Cons

Position=LG06 32.6 cM:

Gm W82 CR03.G Gm W82 C Q8RX81

22380 R03 3795505 3806070 AT4g00060/F6N15 10 0

NS0138011 9 3800866 3801607 SEQ

Locus / Display Start

ID End Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

AT4g00060/F6N15_10

Glycine max [Arabidopsis thaliana

BM309798 release 2 3800952 3802710 (Mouse-ear cress)] similar to

UniRefl00_A7PKJ2 Chromosome chrl5 scaffold_19, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC415453 0 3800952 3802834 partial (3%) similar to

UniRefl00_A7P J2 Chromosome chrl5 scaffold l 9, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC415366 0 3800607 3805890 partial (8%)

AT4g00060/F6N15_10

Glycine_max [Arabidopsis thaliana

TA59649 3847 release 2 3800607 3805959 (Mouse-ear cress)]

GMGI.04221

TC398829 0 3803354 3804019 NA

Glycine_max

BI469325 release 2 3803354 3804126 NA

376070 3692 283 cajanus_caja

5 n 3803828 3804020 NA

Glycine max

TA59648 3847 release 2 3804176 3806049 NA

UniRefl00_O28156 Uncharacterized protein

GMGI.04221 AF_2124 - Archaeoglobus

TC370427 0 3804176 3806049 fulgidus, partial (7%)

GMGI.04221

GD950777 0 3804468 3805861 NA

Glycine_max

TA59650 3847 release 2 3805151 3806065 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

GMGI.04221

TC349966 0 3805151 3806073 NA

NGMAX0060827

78 36 3806350 3806651

NGMAX0060827

82 25 3808878 3809179

BARCSOYSSR 0 Wm82_poten

3 0222 tial SSR 3817624 3817665 NA

ID:GO:0004659

(GO)=prenyltransferase activity; ID:GO:0016021 (GO)=integral to membrane; ID:PF01040 (PFAM)=UbiA prenyltransferase family; ID:PTHR11048

(Panther)=PRENYLTRA

Glyma03g03910 Glymal 3814802 3820907 NSFERASES

Average Cons

Position=LG06 32.8 cM: Q647J9 Homogentisate phytylprenyltransferase 1E-123 ; Q58FG4 Homogentisate

Gm W82 CR03.G Gm W82 C phytylprenyltransferase 22790 R03 3814802 3820907 1E-120

086263 3714 217 cajanus_caja

8 n 3820244 3820452 NA

Glycine max

TA67363 3847 release 2 3825407 3826540 NA similar to

UniRefl00_A7PKJl Chromosome chrl5 scaffold_19, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC382671 0 3825409 3826540 partial (23%)

059050 2801 063 cajanus caja

9 n 3826082 3826873 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Chafal lcle

Cf8743d an 3826817 3827351 NA

GMGI.04221

GD676001 0 3827061 3827202 NA

BARC-064351- marker map

18627 4 3826875 3827418 NA

ID:3.1.-.- (EC)=Acting on ester bonds.;

ID:GO:0005737

(GO)=cytoplasm;

ID:GO:0006281

(GO)=DNA repair;

ID:GO:0006310

(GO)=DNA

recombination;

ID:GO:0006974

(GO)=response to DNA damage stimulus;

ID:GO:0016788

(GO)=hydrolase activity, acting on ester bonds; ID:K07447 (KO)=;

ID:PF03652

(PFAM)=Uncharacterised

Glyma03g03920 Glymal 3826814 3829735 protein family (UPF0081)

Chafal_lcle

Cfl9457d an 3829491 3829653 NA

Glycine_max

TA60403 3847 release 2 3831923 3832830 NA

GMGI.04221

TC406296 0 3832100 3833014 NA

046766 3073 132 cajanus_caja

6 n 3832854 3833064 NA

Glycine_max

BI973221 release 2 3832711 3833221 NA SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5)

NO: Information (6) similar to

UniRefl00_A7U5Z3

GMGI.04221 Glucan synthase catalytic,

BI973221 0 3832796 3833221 partial (0%)

ID:PTHR23067

(Panther)=DOUBLE- STRANDED RNA- BINDING ZINC FINGER

Glyma03g03930 Glymal 3831954 3839129 PROTEIN

Glycine_max

BU544624 release 2 3837285 3837804 NA similar to

UniRefl00_A6Q8J9 NADH-quinone oxidoreductase, chain K -

GMGI.04221 Sulfurovum sp. (strain

TC395926 0 3837285 3837973 NBC37-1), partial (17%)

Glycine_max

AW201693 release 2 3837556 3837973 NA

GMGI.04221

CA785507 0 3838481 3838623 NA

Glyma03g03940 Glymal 3845294 3846057 NA

NGMAX0060832

56 26 3861274 3861575

186230 3992 393 cajanus_caja

0 n 3865200 3865357 NA

Average Cons

Position=LG06 33.2 cM: Q4U316 Cys2/His2 zinc- finger transcription factor

Gm W82 CR03.G Gm W82 C 3E-43 ; 022090 ZPT3-3 23030 R03 3865550 3866901 6E-43 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0005622

(GO)=intracellular;

ID:GO:0008270

(GO)=zinc ion binding; ID:PF00096

(PFAM)=Zinc finger, C2H2 type;

ID:PTHR11389

(Panther)=ZINC FINGER

Glyma03g03950 Glymal 3865609 3866901 PROTEIN similar to

UniRefl00_A7PKI9 Chromosome chrl5 scaffold_19, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC392384 0 3866249 3866901 partial (26%)

Glycine_soja

TA2788 3848 release 2 3868578 3869195 NA

Glycine soja

DT084159 release 2 3868668 3869195 NA

ID:PTHR23258

(Panther)=SERINE- THREONINE PROTEIN

Glyma03g03960 Glymal 3876581 3877716 KINASE, PLANT-TYPE

NGMAX0060834

47 27 3877288 3877589

Glyma03g03970 Glymal 3882286 3882732 NA

Average Cons

Position=LG06 33.3 cM: Q4U314 Cys2/His2 zinc-

Gm W82 CR03.G Gm W82 C finger transcription factor 23450 R03 3882286 3882732 4E-41

BARCSOYSSR 0 Wm82_poten

3 0223 tial SSR 3888578 3888641 NA

Wm82xPI46

ssl81361770 8916 3889537 3889658 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

261825 3183 083 cajanus_caja

0 n 3889663 3889920 NA

061251 3291 142 cajanus_caja

7 n 3889901 3890022 NA

NGMAX0060835

54 28 3891696 3891997

NGMAX0060836

31 10 3901266 3901567

BARCSOYSSR 0 Wm82_poten

3 0224 tial SSR 3906951 3907016 NA

ID:PF01357

Glyma03g03980 Glymal 3905784 3908385 (PFAM)=Pollen allergen

Average Cons

Position=LG06 33.5 cM:

Gm W82 CR03.G Gm W82 C A1X8W4 Beta expansin 1 23660 R03 3905784 3908385 precursor 2E-79

Phaseolus_co Putative beta-expansin ccineus_relea [Eucalyptus globulus

CA908583 se 2 3905871 3908326 (Blue gum)l

BARCSOYSSR 0 Wm82_poten

3 0225 tial SSR 3908619 3908672 NA

SATT009 3910203 3910364

BARCSOYSSR 0 Wm82_poten

3 0226 tial SSR 3910260 3910307 NA

marker map

Satt009 4 3910203 3910364 NA

BARCSOYSSR 0 Wm82_poten

3 0227 tial SSR 3910269 3910307 NA

cajanus_caja

Contig43957 n 3911076 3911325 NA

cajanus caja

Contig33449 n 3911127 3911325 NA

000154 3576 027 cajanus_caja

8 n 3911285 3911325 NA

003004 1235 127 cajanus_caja

5 n 3911285 3911325 NA SEQ

Locus / Display Start

ID End

Source (3) Additional Locus Name (1) Base (4)

NO: Base (5) Information (6)

006900 1493 192 cajanus_caja

9 n 3911285 3911325 NA

007460 3338 129 cajanus_caja

1 n 3911285 3911325 NA

014289 3939 044 cajanus_caja

0 n 3911285 3911325 NA

025966 0192 222 cajanus caja

3 n 3911285 3911325 NA

026227 0909 100 cajanus_caja

5 n 3911285 3911325 NA

026294 1598 254 cajanus_caja

4 n 3911285 3911325 NA

028308 3640 043 cajanus_caja

9 n 3911285 3911325 NA

037852 0303 109 cajanus_caja

7 n 3911285 3911325 NA

040619 1093 194 cajanus_caja

2 n 3911285 3911325 NA

043547 3658 341 cajanus_caja

9 n 3911285 3911325 NA

053059 3470 195 cajanus_caja

8 n 3911285 3911325 NA

056612 0743 344 cajanus_caja

1 n 3911285 3911325 NA

059660 2583 188 cajanus_caja

8 n 3911285 3911325 NA

062864 3768 319 cajanus caja

3 n 3911285 3911325 NA

063186 3037 255 cajanus caja

0 n 3911285 3911325 NA

066572 1541 318 cajanus_caja

4 n 3911285 3911325 NA

070863 3199 368 cajanus caja

2 n 3911285 3911325 NA

081478 2276 270 cajanus_caja

3 n 3911285 3911325 NA

095517 3300 260 cajanus_caja

0 n 3911285 3911325 NA

096113 2367 017 cajanus_caja

6 n 3911285 3911325 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

102296 1998 203 cajanus caja

3 n 3911285 3911325 NA

102601 2987 344 cajanus_caja

3 n 3911285 3911325 NA

102878 3507 114 cajanus_caja

6 n 3911285 3911325 NA

104948 3016 009 cajanus caja

5 n 3911285 3911325 NA

110539 3656 201 cajanus caja

3 n 3911285 3911325 NA

112098 1843 059 cajanus_caja

2 n 3911285 3911325 NA

112753 1668 382 cajanus_caja

5 n 3911285 3911325 NA

125992 3730 189 cajanus_caja

0 n 3911285 3911325 NA

132002 0047 018 cajanus_caja

2 n 3911285 3911325 NA

153038 2371 269 cajanus_caja

5 n 3911285 3911325 NA

153557 3248 266 cajanus_caja

0 n 3911285 3911325 NA

175695 2245 173 cajanus_caja

9 n 3911285 3911325 NA

178644 1078 244 cajanus_caja

4 n 3911285 3911325 NA

208712 2112 321 cajanus caja

5 n 3911285 3911325 NA

215158 3041 269 cajanus caja

0 n 3911285 3911325 NA

228589 1830 391 cajanus caja

0 n 3911285 3911325 NA

248892 2596 329 cajanus_caja

9 n 3911285 3911325 NA

261459 3344 235 cajanus_caja

8 n 3911285 3911325 NA

264549 3459 334 cajanus_caja

6 n 3911285 3911325 NA

288926 0121 392 cajanus_caja

8 n 3911285 3911325 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

291320 3644 189 cajanus caja

5 n 3911285 3911325 NA

303787 1960 352 cajamis_caja

5 n 3911285 3911325 NA

cajanus_caja

Contigl8363 n 3911285 3911325 NA

cajanus caja

Contig254 n 3911285 3911325 NA

cajanus caja

Contig29855 n 3911285 3911325 NA

cajanus_caja

Contig38972 n 3911285 3911325 NA

cajanus_caja

Contig4328 n 3911285 3911325 NA

cajanus_caja

Contig6579 n 3911285 3911325 NA

cajanus_caja

Contig6979 n 3911285 3911325 NA

cajanus_caja

Contig911 n 3911285 3911325 NA

cajanus_caja

Contig9432 n 3911285 3911325 NA

036604 1796 344 cajanus_caja

6 n 3911285 3911331 NA

082281 3494 161 cajanus_caja

2 n 3911285 3911331 NA

222096 3093 387 cajanus_caja

6 n 3911285 3911331 NA

BARCSOYSSR 0 Wm82_poten

3 0228 tial SSR 3915417 3915468 NA

397302 2219 254 cajanus_caja

8 n 3931040 3931321 NA

230041 2755 277 cajanus_caja

8 n 3931097 3931329 NA

Chafal_lcle

Cf7593d an 3931207 3931427 NA

039239 1483 025 cajanus_caja

8 n 3931282 3931499 NA

320914 3315 246 cajanus caja

8 n 3931330 3931491 NA SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

039239_1483_025 cajanus caja

8_primers n 3931429 3932086 NA

ID:KOG1674

(KOG)=Cyclin;

ID:PF00134

(PFAM)=Cyclin, N- terminal domain;

ID:PTHR15615

(Panther)=FAMILY NOT

Glyma03g03990 Glymal 3930986 3932577 NAMED

Average Cons

Position-LG06 33.7 cM:

Gm W82 CR03.G Gm W82 C Q9SHD3 Cyclin-U2-1 1E- 23670 R03 3930986 3932577 79

Wm82xPI46

ssl81361769 8916 3934845 3934966 NA

BARCSOYSSR 0 Wm82_poten

3 0229 tial SSR 3935235 3935256 NA

BARCSOYSSR 0 Wm82_poten

3 0230 tial SSR 3938921 3938980 NA

Wm82xPI46

ssl81361768 8916 3944184 3944305 NA

Glycine_max

TA56046 3847 release 2 3950098 3952011 NA similar to

UniRefl00_A7PKI5 Chromosome chrl5 scaffold_19, whole genome shotgun sequence

GMGI.04221 - Vitis vinifera (Grape),

TC352554 0 3950098 3952011 partial (30%)

Average Cons

Position=LG06 33.8 cM: Q8GZ38 Putative bHLH

Gm W82 CR03.G Gm W82 C transcription factor 23680 R03 3950090 3953935 bHLH016 1E-38 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0030528

(GO)=transcription regulator activity;

ID:GO:0045449

(GO)=regulation of transcription; ID:PF00010

(PFAM)=Helix-loop-helix

DNA-binding domain;

ID:PTHR23042

(Panther)=CIRCADIAN

PROTEIN

CLOCK/ARNT/BMAL/P

Glyma03g04000 Glymal 3950104 3953935 AS

Glycine max

TA56045 3847 release 2 3950331 3953930 NA

similar to

UniRefl00_O81306 F6N15.11 protein - Arabidopsis thaliana

GMGI.04221 (Mouse-ear cress), partial

TC375851 0 3950914 3953930 (25%)

Putative bHLH

transcription factor

Glycine_soja [Arabidopsis thaliana

BF715766 release 2 3951913 3953143 (Mouse-ear cress)]

Glycine soja

BG043888 release 2 3953326 3953902 NA

Contig34254_prim cajanus_caja

ers n 3963399 3964485 NA

cajanus_caja

Contig34254 n 3963346 3964851 NA

Glycine_max Sec61beta [Medicago

CD404584 release 2 3963347 3964851 truncatula (Barrel medic)]

GMGI.04221

TC374606 0 3963320 3965078 NA SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:KOG3457

(KOG)=Sec61 protein translocation complex, beta subunit; ID:PF03911 (PFAM)=Sec61beta family; ID:PTHR13509 (Panther)=FAMILY NOT

Glyma03g04010 Glymal 3963336 3965289 NAMED

Average Cons

Position=LG06 33.9 cM:

Gm W82 C 03.G Gm W82 C Q9M206 Transport 23690 R03 3963336 3965289 protein subunit-like 9E-15

Glycine max Sec61beta [Medicago

BM085010 release 2 3964232 3964709 truncatula (Barrel medic)]

GMGI.04221

TC400303 0 3964232 3964775 NA

Chafal_lcle

Cfl4447d an 3964462 3964710 NA

Chafaljcle

Cf2942d an 3964462 3964710 NA

NS0202926 11 3964906 3964512

cajanus_caja

Contig38009 n 3964588 3964869 NA

SEQ

Locus / Display Start End

ID Additional Locus

Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

ID:GO:0004713

(GO)=protein-tyrosine kinase activity;

ID:GO:0005524

(GO)=ATP binding; ID:GO:0006468

(GO)=protein amino acid phosphorylation;

ID:KOG1187

(KOG)=Serine/threonine protein kinase;

ID:PF07714

(PFAM^Protein tyrosine kinase; ID:PTHR23258 (Panther)=SERINE- THREONINE PROTEIN

Glyma03g04020 Glymal 3968405 3971501 KINASE, PLANT-TYPE

296480 1060 005 cajanus_caja

4 n 3970036 3970281 NA

cajanus_caja

Contig33933 n 3971440 3971708 NA

BARCSOYSSR 0 Wm82_poten

3 0231 tial SSR 3972030 3972069 NA

127767 0193 052 cajanus_caja

9 n 3972578 3972652 NA

086083 3139 073 cajanus_caja

3 n 3972567 3972678 NA

107263 3116 188 cajanus_caja

9 n 3972567 3972745 NA

cajanus_caja

Contig3427 n 3972567 3972745 NA

cajanus_caja

Contig8717 n 3972566 3972746 NA

339396 1511 086 cajanus_caja

3 n 3972612 3972746 NA

NGMAX0060842

89 12 3979463 3979764 SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

BARCSOYSSR 0 Wm82_poten

3 0232 tial SSR 3982356 3982407 NA

Average Cons

Position=LG06 34.2 cM: Q2YE87 NBS-LRR type disease resistance protein Rpsl-k-2 0 ; Q2YE88 NBS-LRR type disease

Gm W82 CR03.G Gm W82 C resistance protein Rpsl-k- 24110 R03 3992073 3996230 1 0

ID:GO:0005515

(GO)=protein binding; ID:KOG4658

(KOG)=Apoptotic ATPase; ID:PF00560 (PFAM)=Leucine Rich Repeat; ID:PTHR23155 (Panther)=LEUCINE- RICH REPEAT- CONTAINING

Glyma03g04030 Glymal 3992594 3996230 PROTEIN

BARCSOYSSR 0 Wm82_poten

3 0233 tial SSR 4001862 4001917 NA

Glyma03g04040 Glymal 4017654 4019180 NA

Average Cons

Position=LG06 34.3 cM: Q2YE87 NBS-LRR type disease resistance protein Rpsl-k-2 0 ; Q2YE88 NBS-LRR type disease

Gm W82 CR03.G Gm W82 C resistance protein Rpsl-k- 24720 R03 4017654 4019180 1 0

ID:PTHR23346

(Panther)=TRANSLATIO NAL ACTIVATOR

Glyma03g04050 Glymal 4027661 4027913 GCN1 -RELATED SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 34.4 cM:

Gm W82 CR03.G Gm W82 C Q53K35 HEAT repeat, 24730 R03 4027661 4027913 putative 2E-14

ID:PTHR11875:SF9

Glyma03g04060 Glymal 4029392 4031456 (Panther)=SET

Average Cons

Position=LG06 34.4 cM: Q9M9V0 F6A14.10 protein 2E- 11 ; A9RDJ7

Gm W82 CR03.G Gm W82 C Nucleosome assembly 24740 R03 4029392 4031456 protein family 8E-11

ID-.PTHR11043

(Panther)=ZETA-COAT

Glyma03g04070 Glymal 4032514 4033581 PROTEIN

Average Cons

Position=LG06 34.5 cM: Q9MAZ9 Nonclathrin coat protein zetal-COP

Gm W82 CR03.G Gm W82 C IE- 13 ; A2Q5T5 Longin- 24750 R03 4032514 4033581 like 7E-12

147515 0361 052 cajanus caja

4 n 4037444 4037666 NA

NBS-LRR type disease resistance protein Rpsl-k-

Glycine_max 1 [Glycine max

AI443099 release 2 4037901 4038186 (Soybean)]

ID:GO:0005515

(GO)=protein binding; ID:KOG4658

(KOG)=Apoptotic ATPase; ID:PF00560 (PFAM)=Leucine Rich Repeat; ID:PTHR23155 (Panther)=LEUCINE- RICH REPEAT- CONTAINING

Glyma03g04080 Glymal 4037251 4041010 PROTEIN SEQ

Locus / Display Start End Additional Locus

ID Source (3)

Name (1) Base (4) Base (5) Information (6)

NO:

Average Cons

Position=LG06 34.5 cM: Q2YE87 NBS-LRR type disease resistance protein Rpsl-k-2 0 ; Q2YE88 NBS-LRR type disease

Gm W82 CR03.G Gm W82 C resistance protein Rpsl-k- 24760 R03 4037251 4041010 1 0

BARCSOYSSR 0 Wm82jpoten

3 0234 tial SSR 4050233 4050272 NA

146317 0436 022 cajanus_caja

0 n 4052175 4052344 NA

069073 0816 007 cajanus_caja

4 n 4052178 4052368 NA

ID:PTHR11550

(Panther)=CTP

Glyma03g04090 Glymal 4065369 4065479 SYNTHASE

Average Cons

Position=LG06 34.5 cM:

Gm W82 CR03.G Gm W82 C Q8L6Z9 CTP synthase- 24770 R03 4065369 4065479 Hke protein 3E-9

Glycine_soja

DT082886 release 2 4075130 4075437 NA

[0083] Sequences for the genes provided above can be obtained jfrom the World Wide Web

(or Internet) using the identifiers provided in Column 1 (Locus/Display Name) or Column 5

(ADDITTIONAL LOCUS INFORMATION ) from the following internet locations:

"soybase.org" (described in Grant et al., Nucleic Acids Research, 2010, Vol. 38, Database issue D843-D846) or soybase.org/gbrowse/cgi-bin/gbrowse/gmaxl.01/ (see Hyten DL, Choi I-Y, Song Q, Specht JE, Carter TE 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 DL, Cannon SB, Song Q, Weeks N, Fickus EW 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);

"phytozome.net" or "phytozome.net/cgi-bin/gbrowse/soybean/?name=Gm09"; "www.plantgdb.org" or "plantgdb.org/GmGDB/ (Assembly version Glyrnal.170 (Apr 2009)" ; and,

"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".