SOY GENE CLUSTER REGIONS AND METHODS OF USE

TECHNICAL FIELD

The presently disclosed subject matter relates to markers associated with pathogen resistance and methods of use therefor. More particularly, the presently disclosed subject matter relates to markers that are associated with a particular region of Glycine sp. chromosome 13 that is associated with resistance to several different classes of pathogens, and for producing soybean lines with improved resistance to pathogens, the methods involving the use of markers developed from this region in a precision plant breeding program.

BACKGROUND

Plant pathogens are known to cause considerable damage to important crops, resulting in significant agricultural losses with widespread consequences for both the food supply and other industries that rely on plant materials. As such, there is a long felt need to reduce the incidence and/or impact of agricultural pests on crop production.

Several pathogens have been associated with damage to soybeans, which individually and collectively have the potential to cause significant yield losses in the United States and throughout the world. Exemplary such pathogens include, but are not limited to fungi {e.g., genus Phytophthora), nematodes {e.g., genus Meloidogyne, particularly, Meloidogyne javanica), and insects {e.g., aphids). Given the significant threat to food supplies that these pathogens present and the time and expense associated with treating soybean crops to prevent loss, new methods for producing pathogen resistant soybean cultivars are needed.

SUMMARY This summary lists several embodiments of the presently disclosed subject matter, and in many cases lists variations and permutations of these embodiments.

Thus, it is an object of the presently disclosed subject matter to provide methods for conveying pathogen resistance into non-resistant soybean germplasm, which object is achieved in whole or in part by the presently disclosed subject matter.

BRIEF DESCRIPTION OF THE SEQUENCE LISTING SEQ ID NOs: 1 -35 are nucleotide sequences of the soybean genome comprising single nucleotide polymorphisms (SNPs) identified as being associated with pathogen resistance as set forth in Table 1 .

Table 1

16 NC_016100.1 28842751 -28843251

17 NC_016100.1 28869448-28869948

18 NC_016100.1 28977905-28978405

19 NC_016100.1 28977987-28978487

20 NC_016100.1 29065592-29066092

21 NC_016100.1 29098149-29098649

22 NC_016100.1 29100447-29100947

23 NC_016100.1 29156962-29156777

24 NC_016100.1 29156546-29157046

25 NC_016100.1 29191313-29191513

26 NC_016100.1 29191307-29191807

27 NC_016100.1 29529477-29529674

28 NC_016100.1 29208269-29208769

29 NC_016100.1 29224127-29223975

30 NC_016100.1 29224141 -29223980

31 NC_016100.1 29224141 -29223976

32 NC_016100.1 29273135-29272831

33 NC_016100.1 31395098-31395273

34 NC_016100.1 19330494-19330596

35 NC_016100.1 19943947-19944447

SEQ ID NOs 1 -35 can be referenced to Soy Chronnosonne 13 and share high similarity to genome shotgun clone as represented in GENBANK® reference number NC_016100.1 .

Nucleotide sequences of oligonucleotide primers that can be employed to amplify and/or otherwise assay {e.g., by one-step and/or two-step PCR- based allelic discrimination assays) subsequences of soybean chromosome 13 that are associated with pathogen resistance loci as set forth in Table 2.

TAQMAN® Assay Primers

Table 2

Exemplary Assay Primers and Probes for Genotypinq and/or Amplifying Subsequences of SEQ ID NOs: 1-35

34 151 152 247 / 248

35 153 154 249 / 250

The numbers in these columns correspond to the SEQ ID NOs. of the representative oligonucleotide primers. It is understood that the oligonucleotide primers disclosed in Table 2 are exemplary only, and additional oligonucleotide primers can be designed to assay the SNPs at these loci.

With respect to Table 2, for each Glycine sp. genomic sequence to be assayed, a TAQMAN® assay (e.g. generally a two-step allelic discrimination assay or similar), a KASP™ assay (generally a one-step allelic discrimination assay defined below or similar), or both can be employed to assay the SNPs as disclosed herein. In an exemplary two-step assay, a forward primer, a reverse primer, and two assay probes (or hybridization oligos) are employed. The forward and reverse primers are employed to amplify subsequences of soybean chromosome 13 that comprise SNPs that are associated with pathogen resistance loci. The particular nucleotides that are present at the SNP positions are then assayed using the assay primers (which in some embodiments are differentially labeled with, for example, fluorophores to permit distinguishing between the two assay probes in a single reaction), which in each pair differ from each other with respect to the nucleotides that are present at the SNP position (although it is noted that in any given pair, the probes can differ in their 5' or 3' ends without impacting their abilities to differentiate between nucleotides present at the corresponding SNP positions). In some embodiments, the assay primers and the reaction conditions are designed such that an assay primer will only hybridize to the reverse complement of a 100% perfectly matched sequence, thereby permitting identification of which allele(s) is/are present based upon detection of hybridizations.

It is noted that the phrase "two-step" does not imply that two separate reaction steps would necessarily have to be performed sequentially in the assay. In some embodiments, the amplification and hybridization steps are performed as a part of the same reaction. Alternatively or in addition, which nucleotide is present at an SNP position associated with a pathogen resistance locus can be determined using a one-step allelic discrimination assay such as, but not limited to the KASP™ SNP Genotyping System (KBioscience, Beverly, Massachusetts, United States of America). In an exemplary embodiment of this system, allele- specific primers are employed with non-specific upstream or downstream oligonucleotide primers to amplify subsequences of soybean chromosome 13. For any particular SNP, the allele-specific primers differ in their 3'-terminal nucleotides such that each different allele-specific primer can only amplify a subsequence of soybean chromosome 13 if a particular nucleotide is present at the SNP position. For example, the SNP that is present at nucleotide 249 of SEQ ID NO: 1 can be determined using oligonucleotide primers that comprise the sequences set forth as SEQ ID NOs as depicted in Table 2. More particularly, SEQ ID NO: 1 has an SNP at nucleotide position 249. The nucleotide present at this position in the genome of Glycine sp. is in some embodiments a C or a T. Oligonucleotide primers that comprise the nucleotide sequences of SEQ ID NOs depicted in Table 2 relative to SEQ ID NO: 1 .

In one embodiment of the invention, a minimum identifier can be used in the identification, selection, and confirmation of a plant that will confer a favorable phenotype (e.g. resistance to aphids, RKN and/or phytophthora). "Minimum identifiers" comprise a sequence of 15-20 nucleotide base pairs that enable one to select and/or identify a plant through use of the markers as disclosed herein. It is contemplated that the amplicon could be the minimum identifier (e.g. the 6 nucleotide sequence) or that a minimum identifier for a phenotype of interest could be comprised in a larger sequence (e.g. for instance a amplicon of 25 nucleotide base pairs may in some instaces comprise a 6 base pair minimum identifier). In one embodiment of the invention, these minimum identifiers are useful in selection and/or identification of markers disclosed herein located on soy chromosome 13. One aspect of the invention are minimum identifiers that may be used to identify and/or select plants conferring a favorable phenotype. Table 3 is a listing of minimum identifiers that may be diagnostic for a soy plant in allowing one to identify and/or select for a plant having a favorable phenotype (e.g. resistance to aphids, RKN and/or phytophthora). It is further contemplated and a further embodiment of the invention that reverse compliments of the minimum identifiers in Table 3 may be used as a diagnostic tool in selecting and identifying plants having a favorable phenotype.

Table 3

Exemplary Minimum Identifiers for Identvfinq and/or Selecting for Plants

Conferring a Favorable Phenotype

171 9 Phytophthora(+)

172 9 Phytophthora(-)

173 10 Phytophthora(+)

174 10 Phytophthora(-)

175 1 1 Phytophthora(+)

176 1 1 Phytophthora(-)

177 12 Aphid (+)

178 12 Aphid (-)

179 13 Phytophthora(+)

180 13 Phytophthora(-)

181 14 Aphid (+)

182 14 Aphid (-)

183 15 Phytophthora(+)

184 15 Phytophthora(-)

185 16 Phytophthora(+)

186 16 Phytophthora(-)

187 17 Phytophthora(+)

188 17 Phytophthora(-)

189 18 Phytophthora(+)

190 18 Phytophthora(-)

191 19 Aphid (+)

192 19 Aphid (-)

193 20 Phytophthora(+)

194 20 Phytophthora(-)

195 21 Phytophthora(+)

196 21 Phytophthora(-)

197 22 Phytophthora(+)

198 22 Phytophthora(-)

199 23 Aphid (+)

200 23 Aphid (-)

201 24 Aphid (+)

202 24 Aphid (-) 203 25 Aphid (+)

204 25 Aphid (-)

205 26 Aphid (+)

206 26 Aphid (-)

207 27 Phytophthora(+)

208 27 Phytophthora(-)

209 28 Aphid (+)

210 28 Aphid (-)

21 1 29 Aphid (+)

212 29 Aphid (-)

213 30 Aphid (+)

214 30 Aphid (-)

215 31 Aphid (+)

216 31 Aphid (-)

217 32 Aphid (+)

218 32 Aphid (-)

219 33 Aphid (+)

220 33 Aphid (-)

221 34 RKN (+)

222 34 RKN (-)

223 35 RKN (+)

224 35 RKN (-)

DETAILED DESCRIPTION

The presently disclosed subject matter relates at least in part to the identification of several SNPs associated with pathogen resistance in Glycine sp. These SNPs are located within an approximately 4.4 megabase (MB) region of Glycine sp. chromosome 13 (Linkage Group F). Provided herein in some embodiments are methods of conveying pathogen resistance into non- resistant soybean germplasm, which employ one or more of the identified SNPs in various approaches.

All references listed below, as well as all references cited in the instant disclosure, including but not limited to all patents, patent applications and publications thereof, scientific journal articles, and database entries {e.g., GENBANK® database entries and all annotations available therein) are incorporated herein by reference in their entireties to the extent that they supplement, explain, provide a background for, or teach methodology, techniques, and/or compositions employed herein.

L General Considerations

A 6 Mb region on chromosome 13 in the soybean genome has been investigated with respect to multiple pathogen resistance genes. Five soybean defense related genes (P27, MMP2, PR1a, RPG1-b, LTCOR11; see Li et al. (2008) New Phytologist 179:185-195), two soybean homologous melon defense related genes (Cucumis melo NBS-2 (GENBANK® Accession No. AF354505) and Cucumis melo NBS-46-7 (GENBANK® Accession No. AF354516) genes), and three soy disease resistance genes (soybean mosaic virus (SMV) resistance genes 3gG2, 5gG3, and 6gG9, corresponding to GENBANK® Accession Nos. AY518517, AY518518, and AY518519, respectively) were selected for Sanger sequencing to identify polymorphisms that are associated with resistance genes and/or resistance gene clusters to aphids, Root Knot Nematode (RKN), Phytophthora. Solexa sequence data was also analyzed for similarly associated polymorphisms. 539 polymorphsms were initially identified. 447 polymorphisms identified from the Solexa sequencing data showed an association with aphid resistance. 92 polymorphisms identified from the Sanger sequencing data showed association with aphid, RKN, and Phytophthora resistance. A selected set of 127 polymorphisms are being further evaluated for their efficacy.

In another aspect of the invention, a gene cluster region has been identified comprising a large number of markers that may be associated with disease and insect resistance (e.g. Aphid resistance, RKN and or phytoptera resistance in soy) located at physical base positions 19,000,000 - 32,000,000 bp of the soy chromosome 13 map or equivantly map positions 36 - 64 cM. Or between SSR markers Satt325 - Satt362 as can be deferred from publically available databases as is well known in the art. It is contemplated that genes associated with disease and/or aphid resistance may be present within this gene cluster region. Herein "gene cluster region" refers to a region on soy chromosome 13 having a physical base positions 19,000,000 - 32,000,000 bp or within the mathematical range of SEQ ID NOs 1 -35 as in respect to reference sequence GENBANK® accession number NC_016100.1 .

Disclosed herein is the identification and design of markers for SNPs that can be used to identify alleles associated with resistance to several pests and diseases in soybean. Linkage disequilibrium can result in a single SNP or set of SNPs associating with several resistance traits. Marker assisted breeding exploiting these SNPs can enhance conventional breeding in various ways: (i) early selection of traits in the lab before phenotypic expression of traits are observed in the field, subsequently saving time, space and cost, (ii) independence from environmental conditions allows for screening of pest resistant traits any time anywhere, and (iii) stacking genes by incorporating additional pest resistances within a plant. Because of rapid co-evolution of plant pests and plant resistance, tracking these genes with molecular markers can aid in breeding efforts to incorporate these genes. L Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood to one of ordinary skill in the art to which the presently disclosed subject matter belongs.

Following long-standing patent law convention, the articles "a", "an", and "the" refer to "one or more" when used in this application, including in the claims. For example, the phrase "a marker" refers to one or more markers. Similarly, the phrase "at least one", when employed herein to refer to an entity, refers to, for example, 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, or more of that entity, including but not limited to whole number values between 1 and 100 and greater than 100. Unless otherwise indicated, all numbers expressing quantities of ingredients, reaction conditions, and so forth used in the specification and claims are to be understood as being modified in all instances by the term "about". Accordingly, unless indicated to the contrary, the numerical parameters set forth in this specification and attached claims are approximations that can vary depending upon the desired properties sought to be obtained by the presently disclosed subject matter.

As used herein, the term "about," when referring to a value or to an amount of mass, weight, time, volume, concentration or percentage is meant to encompass variations of in some embodiments ±20%, in some embodiments ±10%, in some embodiments ±5%, in some embodiments ±1 %, in some embodiments ±0.5%, and in some embodiments ±0.1 % from the specified amount, as such variations are appropriate to perform the disclosed method.

As used herein, the term "allele" refers to any of one or more alternative forms of a gene, all of which relate to at least one trait or characteristic. In a diploid cell, two alleles of a given gene occupy corresponding loci on a pair of homologous chromosomes, although one of ordinary skill in the art understands that the alleles in any particular individual do not necessarily represent all of the alleles that are present in the species. Since the presently disclosed subject matter relates in some embodiments to SNPs, it is in some instances more accurate to refer to a "haplotype" (i.e., an allele of a chromosomal segment) instead of "allele". However, in such instances, the term "allele" should be understood to comprise the term "haplotype".

As used herein, the term "and/or" when used in the context of a list of entities, refers to the entities being present singly or in combination. Thus, for example, the phrase "A, B, C, and/or D" includes A, B, C, and D individually, but also includes any and all combinations and subcombinations of A, B, C, and D.

As used herein, the phrase "associated with" refers to a recognizable and/or assayable relationship between two entities. For example, a trait, locus, QTL, SNP, gene, marker, phenotype, etc. is "associated with pathogen resistance" if the presence or absence of the trait, locus, QTL, SNP, gene, marker, phenotype, etc., influences an extent or degree of pathogen resistance (e.g., resistance to fungi, nematodes, and/or insects).

In some embodiments, an allele associated with pathogen resistance comprises an allele having a favorable allele associated with a pathogen resistance phenotype as set forth in Table 4.

Table 4

Favorable Alleles Associated with Pathogen Resistance Phenotypes

21 251 Phytophthora T C

22 251 Phytophthora A G

23 88 Aphid G C

24 251 Aphid T A

25 101 Aphid A G

26 251 Aphid C G

27 101 Phytophthora G C

28 251 Aphid A T

29 53 Aphid A T

30 62 Aphid A G

31 66 Aphid A T

32 228 Aphid A T

33 51 Aphid G T

34 61 RKN A G

35 251 RKN A C

^* The polymorphism at nucleotides 731 -732 of SEQ ID NO: 4 is an Indel, in which the unfavorable allele has a CA dinucleotide at these positions and the favorable allele has a deletion of the CA dinucleotide. Hence, "Del" indicates that the accession had the deletion at the SNP position and

"Ins" indicates that the accession had the CA dinucleotide insertion at the SNP position.

RKN: Root Knot Nematode (i.e., a member of the genus Meloiddogyne).

As used herein, the term "backcross", and grammatical variants thereof, refers to a process in which a breeder crosses a progeny individual back to one of its parents, for example, a first generation individual with one of the parental genotypes of the first generation individual. In some embodiments, a backcross is performed repeatedly, with a progeny individual of one backcross being itself backcrossed to the same parental genotype.

The term "chromosome" is used herein in its art-recognized meaning of the self-replicating genetic structure in the cellular nucleus containing the cellular DNA and bearing in its nucleotide sequence the linear array of genes. The term "comprising", which is synonymous with "including" "containing", or "characterized by", is inclusive or open-ended and does not exclude additional, unrecited elements and/or method steps. "Comprising" is a term of art that means that the named elements and/or steps are present, but that other elements and/or steps can be added and still fall within the scope of the relevant subject matter.

As used herein, the phrase "consisting of excludes any element, step, or ingredient not specifically recited. For example, when the phrase "consists of appears in a clause of the body of a claim, rather than immediately following the preamble, it limits only the element set forth in that clause; other elements are not excluded from the claim as a whole.

As used herein, the phrase "consisting essentially of limits the scope of the related disclosure or claim to the specified materials and/or steps, plus those that do not materially affect the basic and novel characteristic(s) of the disclosed and/or claimed subject matter.

With respect to the terms "comprising", "consisting essentially of, and "consisting of, where one of these three terms is used herein, the presently disclosed and claimed subject matter can include the use of either of the other two terms. For example, the presently disclosed subject matter relates in some embodiments to oligonucleotides that comprise specific sequences {e.g., any of SEQ ID NOs: 105-302) that can be employed for assaying the genomes of plants {e.g., soybeans) for the presence of SNPs. It is understood that the presently disclosed subject matter thus also encompasses oligonucleotides that in some embodiments consist essentially of specific sequences that can be employed for assaying the genomes of plants for the presence of SNPs, as well as oligonucleotides that in some embodiments consist of specific sequences {e.g., any of SEQ ID NOs: 36- 280) that can be employed for assaying the genomes of plants for the presence of SNPs. Similarly, it is also understood that in some embodiments the methods of the presently disclosed subject matter comprise the steps that are disclosed herein, in some embodiments the methods of the presently disclosed subject matter consist essentially of the steps that are disclosed herein, and in some embodiments the methods of the presently disclosed subject matter consist of the steps that are disclosed herein.

As used herein, the terms "cultivar" and "variety" refer to a group of similar plants that by structural or genetic features and/or performance can be distinguished from other varieties within the same species.

Disclosed herein are exemplary polymorphisms that are associated with increases and decreases in plant resistance to various pathogens {e.g., aphids, RKN, and/or Phytophthora). With respect to the instant disclosure, the phrase "favorable allele" refers in some embodiments to an allele that when present results in a quantitatively higher resistance to one or more pathogens versus the case when the "unfavorable allele" is present. It is noted, however, then in the case where a lower pathogen resistance is desirable, the alleles listed in the instant disclosure {e.g., in Tables 4 and 6-9) as "unfavorable" would in fact be the favorable alleles. As such, the terms "favorable" and "unfavorable" are employed in Tables 4 and 6-9 in the context of increased pathogen resistance, and would be reversed in the context of decreased pathogen resistance.

As used herein, the term "gene" refers to a hereditary unit including a sequence of DNA that occupies a specific location on a chromosome and that contains the genetic instruction for a particular characteristics or trait in an organism.

As used herein, the term "hybrid" in the context of plant breeding refers to a plant that is the offspring of genetically dissimilar parents produced by crossing plants of different lines or breeds or species, including but not limited to the cross between two inbred lines.

As used herein, the term "inbred" refers to a substantially homozygous individual or line.

As used herein, the phrase "informative fragment" refers to a nucleic acid molecule and/or its nucleotide sequence that allows for the proper identification of which allele of an allele set {e.g., an SNP) the nucleic acid molecule and/or the nucleotide sequence corresponds to. For example, whereas the locus that corresponds to SEQ ID NO: 1 comprises to a T or a C SNP at position 249 of SEQ ID NO: 1 , an "informative fragment" of SEQ ID NO: 1 would be any sequence that comprises position 249 of SEQ ID NO: 1 . Similarly, an informative fragment of the same locus that is isolated from a soybean genome that might differ to a degree from SEQ ID NO: 1 could include the nucleotide that corresponds to position 249 of SEQ ID NO: 1 , thereby allowing the nucleotide that is present in that position of the differing soybean genome to be determined.

As used herein, the terms "introgression", "introgressed", and "introgressing" refer to both a natural and artificial process whereby genomic regions of one species, variety, or cultivar are moved into the genome of another species, variety, or cultivar, by crossing those species, varieties, or cultivars. The process can optionally be completed by backcrossing to the recurrent parent.

As used herein, the term "linkage" refers to a phenomenon wherein alleles on the same chromosome tend to be transmitted together more often than expected by chance if their transmission was independent. Thus, in some embodiments two alleles on the same chromosome are said to be "linked" when they segregate from each other in the next generation less than 50% of the time, less than 25% of the time, less than 20% of the time, less than 15% of the time, less than 10% of the time, less than 5% of the time, less than 4% of the time, less than 3% of the time, less than 2% of the time, or less than 1 % of the time. Thus, two loci are linked if they are within 50, 25, 20, 15, 10, 5, 4, 3, 2, 1 , 0.5, or 0.1 centiMorgans (cM) of each other. For example, in some embodiments an SNP is linked to a marker if it is within 50, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 cM of the marker.

As used herein, the phrase "linkage group" refers to all of the genes or genetic traits that are located on the same chromosome. Within the linkage group, those loci that are close enough together can exhibit linkage in genetic crosses. Since the probability of crossover increases with the physical distance between loci on a chromosome, loci for which the locations are far removed from each other within a linkage group might not exhibit any detectable linkage in direct genetic tests. The term "linkage group" is mostly used to refer to genetic loci that exhibit linked behavior in genetic systems where chromosomal assignments have not yet been made. Thus, the term "linkage group" is synonymous with the physical entity of a chromosome, although one of ordinary skill in the art will understand that a linkage group can also be defined as corresponding to a region of (i.e., less than the entirety) of a given chromosome.

As used herein, the term "locus" refers to a position that a given gene or a regulatory sequence occupies on a chromosome of a given species.

As used herein, the term "marker" refers to an identifiable position on a chromosome the inheritance of which can be monitored. In some embodiments, a marker comprises a known or detectable nucleic acid sequence.

In some embodiments, a marker corresponds to an amplification product generated by amplifying a Glycine sp. nucleic acid with two oligonucleotide primers, for example, by the polymerase chain reaction (PCR). As used herein, the phrase "corresponds to an amplification product" in the context of a marker refers to a marker that has a nucleotide sequence that is the same (allowing for mutations introduced by the amplification reaction itself) as an amplification product that is generated by amplifying Glycine sp. genomic DNA with a particular set of primers. In some embodiments, the amplifying is by PCR, and the primers are PCR primers that are designed to hybridize to opposite strands of the Glycine sp. genomic DNA in order to amplify a Glycine sp. genomic DNA sequence present between the sequences to which the PCR primers hybridize in the Glycine sp. genomic DNA. In some embodiments, a marker that "corresponds to" an amplified fragment is a marker that has the same sequence of one of the strands of the amplified fragment.

As used herein, the term "soybean" refers to a plant, or a part thereof, of the genus Glycine including, but not limited to Glycine max.

As used herein, the phrase "soybean-specific DNA sequence" refers to a polynucleotide sequence having a nucleotide sequence homology of in some embodiments more than 50%, in some embodiments more than 60%, in some embodiments more than 70%, in some embodiments more than 80%, in some embodiments more than 85%, in some embodiments more than 90%, in some embodiments more than 92%, in some embodiments more than 95%, in some embodiments more than 96%, in some embodiments more than 97%, in some embodiments more than 98%, and in some embodiments more than 99% with a sequence of the genome of the species Glycine that shows the greatest similarity to it. In the case of markers for any of the pathogen resistance loci disclosed herein, a "soybean-specific DNA sequence" can comprise a part of the DNA sequence of a soybean genome that flanks and/or is a part of any of the pathogen resistance loci disclosed herein.

As used herein, the phrase "molecular marker" refers to an indicator that is used in methods for visualizing differences in characteristics of nucleic acid sequences. Examples of such indicators are restriction fragment length polymorphism (RFLP) markers, amplified fragment length polymorphism (AFLP) markers, single nucleotide polymorphisms (SNPs), insertion and deletion mutations (INDEL), microsatellite markers (SSRs), sequence- characterized amplified regions (SCARs), cleaved amplified polymorphic sequence (CAPS) markers or isozyme markers or combinations of the markers described herein which defines a specific genetic and chromosomal location. A molecular marker "linked to" or "associated with" a pathogen resistance gene or locus as defined herein can thus refer to SNPs, insertion mutations, as well as more usual AFLP markers or any other type of marker used in the field.

As used herein, the phrase "nucleotide sequence homology" refers to the presence of homology between two polynucleotides. Polynucleotides have "homologous" sequences if the sequence of nucleotides in the two sequences is the same when aligned for maximum correspondence. The "percentage of sequence homology" for polynucleotides, such as 50, 60, 70, 80, 90, 95, 98, 99 or 100 percent sequence homology, can be determined by comparing two optimally aligned sequences over a comparison window {e.g., about 20-200 contiguous nucleotides), wherein the portion of the polynucleotide sequence in the comparison window can include additions or deletions (i.e., gaps) as compared to a reference sequence for optimal alignment of the two sequences. Optimal alignment of sequences for comparison can be conducted by computerized implementations of known algorithms, or by visual inspection. Readily available sequence comparison and multiple sequence alignment algorithms are, respectively, the Basic Local Alignment Search Tool (BLAST; Altschul et al. (1990) J Mol Biol 215:403-10; Altschul et al. (1997) Nucleic Acids Res 25:3389-3402) and ClustalX (Chenna et al. (2003) Nucleic Acids Res 31 :3497-3500) programs, both available on the Internet. Other suitable programs include, but are not limited to, GAP, BestFit, PlotSimilarity, and FASTA, which are part of the Accelrys GCG Package available from Accelrys Software, Inc. of San Diego, California, United States of America.

As used herein, the term "offspring" plant refers to any plant resulting as progeny from a vegetative or sexual reproduction from one or more parent plants or descendants thereof. For instance, an offspring plant can be obtained by cloning or selfing of a parent plant or by crossing two parent plants and include selfings as well as the F1 or F2 or still further generations. An F1 is a first-generation offspring produced from parents at least one of which is used for the first time as donor of a trait, while offspring of second generation (F2) or subsequent generations (F3, F4, and the like) are specimens produced from selfings or crossings of F1 s, F2s and the like. An F1 can thus be (and in some embodiments is) a hybrid resulting from a cross between two true breeding parents (the phrase "true-breeding" refers to an individual that is homozygous for one or more traits), while an F2 can be (and in some embodiments is) an offspring resulting from self-pollination of the F1 hybrids.

As used herein, the phrases "pathogen resistance locus" and "pathogen resistance gene" refer to loci and/or genes that have been associated with pathogen resistance as defined by the markers disclosed herein. For the purposes of the instant disclosure, these loci are said to be present on Glycine linkage group F of Glycine sp. Chromosome 13, and linked to the markers represented by SEQ ID NOs: 1 -35 or within the gene cluster region. Similarly, the phrase "pathogen resistance phenotype" refers to a phenotype the expression of which is influenced by a pathogen resistance locus and/or a pathogen resistance gene.

As used herein, the term "phenotype" refers to a detectable characteristic of a cell or organism, which characteristics are at least partially a manifestation of gene expression. An exemplary phenotype is a pathogen resistance phenotype. Pathogen resistance phenotypes include, but are not limited to aphid resistance, Root Knot Nematode (RKN) resistance, and Phytophthora resistance. Phenotyping of soybean accessions with respect to Phytophthora resistance and/or aphid resistance was performed as set forth in EXAMPLES 6 and 7 below. Phenotyping of soybean accessions with respect to RKN resistance can be performed using the greenhouse screening procedure described in Tamulonis et al. (1997) Crop Sci 37:783-788. For example, seedlings can be inoculated with Meloidogyne javanica eggs 7 days after planting. Thirty days later, soil can be gently washed from the roots so that galls can be counted.

As used herein, the phrase "plant part" refers to a part of a plant, including single cells and cell tissues such as plant cells that are intact in plants, cell clumps, and tissue cultures from which plants can be regenerated. Examples of plant parts include, but are not limited to, single cells and tissues from pollen, ovules, leaves, embryos, roots, root tips, anthers, flowers, fruits, stems, shoots, and seeds; as well as scions, rootstocks, protoplasts, calli, and the like.

As used herein, the term "population" refers to a genetically heterogeneous collection of plants that in some embodiments share a common genetic derivation.

As used herein, the term "primer" refers to an oligonucleotide which is capable of annealing to a nucleic acid target and serving as a point of initiation of DNA synthesis when placed under conditions in which synthesis of a primer extension product is induced {e.g., in the presence of nucleotides and an agent for polymerization such as DNA polymerase and at a suitable temperature and pH). A primer (in some embodiments an extension primer and in some embodiments an amplification primer) is in some embodiments single stranded for maximum efficiency in extension and/or amplification. In some embodiments, the primer is an oligodeoxyribonucleotide. A primer is typically sufficiently long to prime the synthesis of extension and/or amplification products in the presence of the agent for polymerization. The minimum lengths of the primers can depend on many factors, including, but not limited to temperature and composition (A T vs. G/C content) of the primer.

In the context of amplification primers, these are typically provided as a pair of bi-directional primers consisting of one forward and one reverse primer or provided as a pair of forward primers as commonly used in the art of DNA amplification such as in PCR amplification.

As such, it will be understood that the term "primer", as used herein, can refer to more than one primer, particularly in the case where there is some ambiguity in the information regarding the terminal sequence(s) of the target region to be amplified. Hence, a "primer" can include a collection of primer oligonucleotides containing sequences representing the possible variations in the sequence or includes nucleotides which allow a typical base pairing.

Primers can be prepared by any suitable method. Methods for preparing oligonucleotides of specific sequence are known in the art, and include, for example, cloning and restriction of appropriate sequences and direct chemical synthesis. Chemical synthesis methods can include, for example, the phospho di- or tri-ester method, the diethylphosphoramidate method and the solid support method disclosed in U.S. Patent No. 4,458,066.

Primers can be labeled, if desired, by incorporating detectable moieties by for instance spectroscopic, fluorescence, photochemical, biochemical, immunochemical, or chemical moieties.

The PCR method is well described in handbooks and known to the skilled person. After amplification by PCR, target polynucleotides can be detected by hybridization with a probe polynucleotide which forms a stable hybrid with that of the target sequence under stringent to moderately stringent hybridization and wash conditions. If it is expected that the probes are essentially completely complementary (i.e., about 99% or greater) to the target sequence, stringent conditions can be used. If some mismatching is expected, for example if variant strains are expected with the result that the probe will not be completely complementary, the stringency of hybridization can be reduced. In some embodiments, conditions are chosen to rule out nonspecific/adventitious binding. Conditions that affect hybridization, and that select against non-specific binding are known in the art, and are described in, for example, Sambrook & Russell (2001 ). Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, United States of America. Generally, lower salt concentration and higher temperature hybridization and/or washes increase the stringency of hybridization conditions.

Continuing, the term "probe" refers to a single-stranded oligonucleotide sequence that will form a hydrogen-bonded duplex with a complementary sequence in a target nucleic acid sequence analyte or its cDNA derivative.

As used herein, the term "quantitative trait locus" (QTL; plural quantitative trait loci; QTLs) refers to a genetic locus (or loci) that controls to some degree a numerically representable trait that, in some embodiments, is continuously distributed. As such, the term QTL is used herein in its art- recognized meaning to refer to a chromosomal region containing alleles {e.g., in the form of genes or regulatory sequences) associated with the expression of a quantitative phenotypic trait. Thus, a QTL "associated with" pathogen resistance refers to one or more regions located in some embodiments on Glycine sp. chromosome 13 and/or in linkage group F that includes at least one gene the expression of which influences a level of resistance to one or more pathogens and/or at least one regulatory region that controls the expression of one or more genes involved in pathogen resistance. QTLs can be defined by indicating their genetic location in the genome of a specific Glycine sp. accession using one or more molecular genomic markers. One or more markers, in turn, indicate a specific locus. Distances between loci are usually measured by the frequency of crossovers between the loci on the same chromosome {e.g., chromosome 13). The farther apart two loci are, the more likely that a crossover will occur between them. Conversely, if two loci are close together, a crossover is less likely to occur between them. Typically, one centiMorgan (cM) is equal to 1 % recombination between loci. When a QTL can be indicated by multiple markers, the genetic distance between the end-point markers is indicative of the size of the QTL. As used herein, the term "regenerate", and grammatical variants thereof, refers in some embodiments to the production of a plant from tissue culture and use to the production of a plant by growing in soil.

As used herein, the term "resistant" and "resistance" encompass both partial and full resistance to infection with and/or damage by a pathogen {e.g., infection with and/or damage by a pathogenic mold, nematode, or insect). A susceptible plant can either be non-resistant or have lower levels of resistance relative to a resistant plant. The term is used to include such separately identifiable forms of resistance as "full resistance", "immunity", "hypersensitivity", "intermediate resistance", "partial resistance", "tolerance" and "susceptibility".

As used herein, the phrase "stringent hybridization conditions" refers to conditions under which a polynucleotide hybridizes to its target subsequence, typically in a complex mixture of nucleic acids, but to essentially no other sequences. Stringent conditions are sequence-dependent and can be different under different circumstances. Exemplary guidelines for the hybridization of nucleic acids can be found in Tijssen (1993) ]n Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier, New York, New York, United States of America; Ausubel et al. (1999) Short Protocols in Molecular Biology Wiley. New York, New York, United States of America; and Sambrook & Russell, 2001 (supra). Generally, stringent conditions are selected to be about 5-10°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength pH. The Tm is the temperature (under defined ionic strength, pH, and nucleic acid concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at Tm, 50% of the probes are occupied at equilibrium). In some embodiments, hybridization conditions are employed (in some embodiments in conjunction with considerations of the nucleotide sequences of the polynucleotides that are intended to hybridize) such that oligonucleotides (such as, but not limited to the forward, reverse, and assay primers listed in Table 2) only hybridize to sequences with which they can form 100% matched duplexes (i.e., the oligonucleotide is 100% identical to the reverse-complement of the sequence to which it hybridizes or includes a 3' sequence that is 100% identical to the reverse-complement of the sequence to which it hybridizes allowing the oligonucleotide to function in an amplification reaction.)

As used herein, the term "susceptible" refers to a plant having no resistance to infection with and/or damage by a pathogen resulting in the plant being affected by the pathogen, in some embodiments resulting in disease symptoms. The term "susceptible" is therefore equivalent to "non-resistant". Alternatively, the term "susceptible" can be employed in a relative context, in which one plant is considered "susceptible" because it is less resistant to infection with and/or damage by a pathogen than is a second plant (which in the context of these terms in a relative usage, would be referred to as the "resistant" plant"). i!L. Conveying Pathogen Resistance into Non-resistant Germplasm

In some embodiments, the presently disclosed subject matter provides methods for conveying pathogen resistance into non-resistant germplasm [e.g., soybean germplasm). In some embodiments, the presently disclosed methods comprise introgressing pathogen resistance into a non-resistant soybean using one or more nucleic acid markers for marker-assisted breeding among soybean lines to be used in a soybean breeding program, wherein the markers are linked to a pathogen resistance locus present in Linkage Group F of Glycine max associated with any of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224. In some embodiments, the pathogen resistance is resistance to a pathogen selected from among aphids, RKN, and Phytophthora. In some embodiments, the one or more nucleic acid markers are at least 80%, 85%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%, identical to any of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224 over their respective full length.

In some embodiments, the presently disclosed methods further comprise screening an introgressed soybean plant, or a cell or tissue thereof, for pathogen resistance. The presently disclosed subject matter also provides methods for reliably and predictably introgressing pathogen resistance into non-resistant germp!asm (e.g., soybean germplasm) comprising using one or more nucleic acid markers for marker-assisted breeding among soybean lines to be used in a soybean breeding program, wherein the nucleic acid markers are selected from the group consisting of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224, and informative fragments thereof, and introgressing the resistance into the non-resistant soybean germplasm.

The presently disclosed subject matter also provides methods for producing an inbred soybean plant adapted for conferring pathogen resistance in hybrid combination with a suitable second inbred. In some embodiments, the methods comprise (a) selecting a first donor parental line possessing a desired pathogen resistance and having at least one of the resistant locus selected from a locus mapping to Glycine max Linkage Group F between markers mapped by one or more of the markers SEQ ID NOs: 1-35 and/or utilizing minimum identifiers as represented by SEQ ID NOs: 155-224; (b) crossing the first donor parent line with a second parental line in hybrid combination to produce a segregating plant population; (c) screening the segregating plant population for identified chromosomal loci of one or more genes associated with the resistance to one or more pathogens; and (d) selecting plants from the population having the identified chromosomal loci for further screening until a line is obtained which is homozygous for resistance to pathogen at sufficient loci to give resistance to pathogen in hybrid combination. In some embodiments, the pathogen resistance is resistance to a pathogen selected from among aphids, RKN, and Phytophthora.

IV. Production of Pathogen-resistant Soybean Plants

As such, in some embodiments the presently disclosed subject matter provides methods for marker-assisted breeding (MAB). The presently disclosed subject matter therefore relates to methods of plant breeding and to methods to select plants, in particular soybean plants, particularly cultivated soybean plants as breeder plants for use in breeding programs or cultivated soybean plants for having desired genotypic or potential phenotypic properties, in particular related to producing valuable soybeans, also referred to herein as commercially valuable plants. Herein, a cultivated plant is defined as a plant being purposely selected or having been derived from a plant having been purposely selected in agricultural or horticultural practice for having desired genotypic or potential phenotypic properties, for example a plant obtained by inbreeding.

The presently disclosed subject matter thus also provides methods for selecting a plant of the genus Glycine exhibiting resistance towards one or more pathogens comprising detecting in the plant the presence of one or more pathogen resistance alleles as defined herein. In an exemplary embodiment of the presently disclosed methods for selecting such a plant, the method comprises providing a sample of genomic DNA from a soybean plant; and (b) detecting in the sample of genomic DNA at least one molecular marker associated with pathogen resistance. In some embodiments, the detecting can comprise detecting one or more SNPs that are associated with pathogen resistance.

The providing of a sample of genomic DNA from a soybean plant can be performed by standard DNA isolation methods well known in the art.

The detecting of a molecular marker can in some embodiments comprise the use of one or more sets of primer pairs that can be used to produce one or more amplification products that are suitable markers for one of the SNPs. Such a set of primers can comprise, in some embodiments, nucleotide sequences as set forth in SEQ ID NOs: 36-154.

In some embodiments, the detecting of a molecular marker can comprise the use of a nucleic acid probe having a base sequence that is substantially complementary to the nucleic acid sequence defining the molecular marker and which nucleic acid probe specifically hybridizes under stringent conditions with a nucleic acid sequence defining the molecular marker. A suitable nucleic acid probe can for instance be a single strand of the amplification product corresponding to the marker. In some embodiments, the detecting of a molecular marker is designed to discriminate whether a particular allele of an SNP is present or absent in a particular plant.

The presently disclosed methods can also include detecting an amplified DNA fragment associated with the presence of a particular allele of an SNP. In some embodiments, the amplified fragment associated with a particular allele of an SNP has a predicted length or nucleic acid sequence, and detecting an amplified DNA fragment having the predicted length or the predicted nucleic acid sequence is performed such that the amplified DNA fragment has a length that corresponds (plus or minus a few bases; e.g., a length of one, two or three bases more or less) to the expected length as based on a similar reaction with the same primers with the DNA from the plant in which the marker was first detected or the nucleic acid sequence that corresponds (i.e., has a homology of in some embodiments more than 80%, in some embodiments more than 90%, in some embodiments more than 95%, in some embodiments more than 97%, and in some embodiments more than 99%) to the expected sequence as based on the sequence of the marker associated with that SNP in the plant in which the marker was first detected. Upon a review of the instant disclosure, one of ordinary skill in the art would appreciate that markers {e.g., SNP alleles) that are absent in resistant plants, while they were present in the susceptible parent(s) (so-called trans-markers), can also be useful in assays for detecting resistance among offspring plants.

The detecting of an amplified DNA fragment having the predicted length or the predicted nucleic acid sequence can be performed by any of a number or techniques, including but not limited to standard gel- electrophoresis techniques or by using automated DNA sequencers. The methods are not described here in detail as they are well known to those of ordinary skill in the art, although exemplary approaches are set forth in the EXAMPLES.

The presently disclosed subject matter thus also relates to methods for producing pathogen-resistant soybean plants comprising detecting the presence of an allele associated with pathogen resistance in a donor soybean plant according to the presently disclosed subject matter as described herein and transferring a nucleic acid sequence comprising at least one allele thus detected, or a pathogen resistance-conferring part thereof, from the donor plant to a pathogen-susceptible recipient soybean plant. The transfer of the nucleic acid sequence can be performed by any of the methods described herein. An exemplary embodiment of such a method comprises the transfer by introgression of the nucleic acid sequence from a pathogen-resistant donor soybean plant into a pathogen-susceptible recipient soybean plant by crossing the plants. This transfer can thus suitably be accomplished by using traditional breeding techniques. Pathogen-resistance loci are introgressed in some embodiments into commercial soybean varieties using marker-assisted selection (MAS) or marker-assisted breeding (MAB). MAS and MAB involves the use of one or more of the molecular markers for the identification and selection of those offspring plants that contain one or more of the genes that encode for the desired trait. In the context of the presently disclosed subject matter, such identification and selection is based on selection of SNP alleles of the presently disclosed subject matter or markers associated therewith. MAB can also be used to develop near-isogenic lines (NIL) harboring one or more pathogen resistant alleles of interest, allowing a more detailed study of an effect of such allele(s), and is also an effective method for development of backcross inbred line (BIL) populations. Soybean plants developed according to these embodiments can in some embodiments derive a majority of their traits from the recipient plant, and derive pathogen resistance from the donor plant.

As discussed herein, traditional breeding techniques can be used to introgress a nucleic acid sequence associated with pathogen resistance into a pathogen-susceptible recipient soybean plant. For example, inbred pathogen- resistant soybean plant lines can be developed using the techniques of recurrent selection and backcrossing, selfing, and/or dihaploids, or any other technique used to make parental lines. In a method of recurrent selection and backcrossing, pathogen resistance can be introgressed into a target recipient plant (the recurrent parent) by crossing the recurrent parent with a first donor plant, which differs from the recurrent parent and is referred to herein as the "non-recurrent parent". The recurrent parent is a plant that is non-resistant or has a low level of resistance to pathogens and , in some embodiments, possesses commercially desirable characteristics, such as, but not limited to (additional) disease and/or insect resistance, valuable nutritional characteristics, valuable abiotic stress tolerance (including, but not limited to drought tolerance), and the like. In some embodiments, the non-recurrent parent exhibits pathogen resistance and comprises a nucleic acid sequence that is associated with pathogen resistance. The non-recurrent parent can be any plant variety or inbred line that is cross-fertile with the recurrent parent.

In some embodiments, the progeny resulting from a cross between the recurrent parent and non-recurrent parent are backcrossed to the recurrent parent. The resulting plant population is then screened for the desired characteristics, wh ich screen ing can occur in a number of d ifferent ways . For instance, the population can be screened using phenotypic pathology screens or quantitative bioassays as known in the art. Alternatively, instead of using bioassays, MAB can be performed using one or more of the hereinbefore described molecular markers, hybridization probes, or polynucleotides to identify those progeny that comprise a nucleic acid sequence encoding pathogen resistance. Also, MAB can be used to confirm the results obtained from the quantitative bioassays. In some embodiments, the markers defined herein are suitable to select proper offspring plants by genotypic screening.

Following screening, the F1 hybrid plants that exhibit a pathogen- resistant phenotype or, in some embodiments genotype, and thus comprise the requisite nucleic acid sequence associated with pathogen resistance, are then selected and backcrossed to the recurrent parent for a number of generations in order to allow for the soybean plant to become increasingly inbred. This process can be performed for two, three, four, five, six, seven, eight, or more generations. In principle, the progeny resulting from the process of crossing the recurrent parent with the pathogen-resistant nonrecurrent parent are heterozygous for one or more genes that encode pathogen resistance.

In general, a method of introducing a desired trait into a hybrid soybean variety can comprise:

(a) crossing an inbred soybean parent with another soybean plant that comprises one or more desired traits, to produce F1 progeny plants, wherein the desired trait is pathogen resistance; (b) selecting the F1 progeny plants that have the desired trait to produce selected Fl progeny plants, in some embodiments using molecular markers as defined herein;

(c) backcrossing the selected progeny plants with the inbred soybean parent plant to produce backcross progeny plants;

(d) selecting for backcross progeny plants that have the desired trait and morphological and physiological characteristics of the inbred soybean parent plant, wherein the selection comprises the isolation of genomic DNA and testing the DNA for the presence of at least one molecular marker for pathogen resistance, in some embodiments as described herein;

(e) repeating steps (c) and (d) two or more times in succession to produce selected third or higher backcross progeny plants;

(f) optionally selfing selected backcross progeny in order to identify homozygous plants; and

(g) crossing at least one of the backcross progeny or selfed plants with another soybean parent plant to generate a hybrid soybean variety with the desired trait and all of the morphological and physiological characteristics of hybrid soybean variety when grown in the same environmental conditions.

As indicated, the last backcross generation can be selfed in order to provide for homozygous pure breeding (inbred) progeny for pathogen resistance. Thus, a result of recurrent selection, backcrossing, and/or selfing can be the production of lines that are genetically homogenous for the alleles associated with pathogen resistance, and in some embodiments as well as for other loci associated with traits of commercial interest.

V. Molecular Markers and SNPs

Molecular markers are used for the visualization of differences in nucleic acid sequences. This visualization can be due to DNA-DNA hybridization techniques after digestion with a restriction enzyme {e.g., an RFLP) and/or due to techniques using the polymerase chain reaction {e.g., STS, SSR/microsatellites, AFLP, and the like). In some embodiments, all differences between two parental genotypes segregate in a mapping population based on the cross of these parental genotypes. The segregation of the different markers can be compared and recombination frequencies can be calculated. Methods for mapping markers in plants are disclosed in, for example, Glick & Thompson (1993) Methods in Plant Molecular Biology and Biotechnology, CRC Press, Boca Raton, Florida, United States of America; Zietkiewicz et al. (1994) Genomics 20:176-183.

The recombination frequencies of molecular markers on different chromosomes and/or in different linkage groups are generally 50%. Between molecular markers located on the same chromosome or in the same linkage group, the recombination frequency generally depends on the physical distance between the markers on a chromosome. A low recombination frequency typically corresponds to a low genetic distance between markers on a chromosome. Comparing all recombination frequencies among a set of molecular markers results in the most logical order of the molecular markers on the chromosomes or in the linkage groups. This most logical order can be depicted in a lin kage map. A group of adjacent or contiguous markers on the linkage map that is associated with an increased level of resistance to a disease; e.g., to a reduced incidence of acquiring the disease upon infectious contact with the disease agent and/or a reduced lesion growth rate upon establishment of infection, can provide the position of a locus associated with resistance to that disease.

The markers disclosed herein can be used in various aspects of the presently disclosed subject matter as set forth herein. Aspects of the presently disclosed subject matter are not to be limited to the use of the markers identified herein, however. It is stressed that the aspects can also make use of markers not explicitly disclosed herein or even yet to be identified.

The markers provided by the presently disclosed subject matter can be used for detecting the presence of one or more pathogen resistance alleles of the presently disclosed subject matter in a suspected pathogen-resistant soybean plant, and can therefore be used in methods involving marker- assisted breeding and selection of pathogen -resistant soybean plants. In some embodiments, detecting the presence of a particular allele of an SNP of the presently disclosed subject matter is performed with at least one of the markers for the resistance loci defined herein. The presently disclosed subject matter therefore relates in another aspect to a method for detecting the presence of a particu lar allele associated with pathogen resistance, comprising detecting the presence of a nucleic acid sequence of the SNP in a suspected pathogen-resistant soybean plant, which presence can be detected by the use of the disclosed markers and oligonucleotides.

The nucleotide sequence of an SNP of the presently disclosed subject matter can for instance be resolved by determining the nucleotide sequence of one or more markers associated with the SNP and designing internal primers for the marker sequences that can be used to determine which allele of the SNP is present in the plant.

In embodiments of such methods for detecting the presence of an SNP in a suspected pathogen-resistant soybean plant, the method can also comprise providing a oligonucleotide or polynucleotide capable of hybridizing under stringent hybridization conditions to a particular nucleic acid sequence of an SNP, in some embodiments selected from the SNPs disclosed herein, contacting the oligonucleotide or polynucleotide with genomic nucleic acid (or a fragment thereof, including, but not limited to a restriction fragment thereof) of a suspected pathogen-resistant soybean plant, and determining the presence of specific hybridization of the oligonucleotide or polynucleotide to the genomic nucleic acid (or the fragment thereof).

In some embodiments, the method is performed on a nucleic acid sample obtained from the suspected pathogen-resistant soybean plant, although in situ hybridization methods can also be employed. Alternatively, one of ordinary skill in the art can design specific hybridization probes or oligonucleotides capable of hybridizing under stringent hybridization conditions to the nucleic acid sequence of the allele associated with pathogen resistance and can use such hybridization probes in methods for detecting the presence of an SNP allele disclosed herein in a suspected pathogen-resistant soybean plant. VI. Pathogen-resistant Soybean Plants, and Seeds and Parts therefrom

The development of a hybrid soybean variety in a soybean plant breeding program can, in some embodiments, involve three steps: (1 ) the selection of plants from various germplasm pools for initial breeding crosses; (2) the selfing of the selected plants from the breeding crosses for several generations to produce a series of inbred lines, which, individually breed true and are highly uniform; and (3) crossing a selected variety with an different variety to produce the hybrid progeny (F1 ). After a sufficient amount of inbreeding successive filial generations will merely serve to increase seed of the developed inbred. In some embodiments, an inbred line comprises homozygous alleles at about 95% or more of its loci.

As such , pathogen-resistant soybean plants or parts thereof, obtainable by the methods of the presently disclosed subject matter, are aspects of the presently disclosed subject matter.

The pathogen-resistant soybean plants of the presently disclosed subject matter, or part thereof, can be heterozygous or homozygous for the resistance traits (in some embodiments, homozygous). Although the pathogen resistance loci of the presently disclosed subject matter, as well as resistance- conferring subsequences thereof, can be transferred to any plant in order to provide for a pathogen-resistant plant, the methods and plants of the presently disclosed subject matter are in some embodiments related to plants of the genus Glycine.

Another aspect of the presently disclosed subject matter relates to a method of producing seeds that can be grown into pathogen-resistant soybean plants. In some embodiments, the method comprises providing a pathogen-resistant soybean plant of the presently disclosed subject matter, crossing the pathogen-resistant plant with another soybean plant, and collecting seeds resulting from the cross, which when planted, produce pathogen-resistant soybean plants.

As such, the methods of the presently disclosed subject matter can in some embodiments comprise providing a pathogen-resistant soybean plant of the presently disclosed subject matter, crossing the pathogen-resistant plant with a soybean plant, collecting seeds resulting from the cross, regenerating the seeds into plants, selecting pathogen-resistant plants by any of the methods described herein, self-pollinating the selected plants for a sufficient number of generations to obtain plants that are fixed for an allele associated with pathogen-resistance in the plants, backcrossing the plants thus produced with soybean plants having desirable phenotypic traits for a sufficient number of generations to obtain soybean plants that are pathogen-resistant and have desirable phenotypic traits, and collecting the seeds produced from the plants resulting from the last backcross, which when planted, produce soybean plants which are pathogen-resistant.

Thus, in some embodiments the presently disclosed subject matter provides methods for selecting pathogen-resistant soybean plants. In some embodiments, the methods comprise (a) genotyping one or more soybean plants with respect to one or more single nucleotide polymorphisms (SNPs), wherein the one or more SNPs are present within one or more molecular markers selected from the group consisting of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224, and informative fragments thereof; and (b) selecting a soybean plant that includes at least one resistance allele associated with the SNPs, thereby selecting a pathogen resistant soybean plant. In some embodiments, the at least one resistance allele is associated with an allele having:

(i) an A at nucleotide 249 of SEQ ID NO: 1; an A at nucleotide 631 of SEQ ID NO: 2; a C at nucleotide 710 of SEQ ID NO: 3; a deletion of nucleotides 731 and 732 of SEQ ID NO: 4; a C at nucleotide 251 of SEQ ID NO: 12; a C at nucleotide 251 of SEQ ID NO: 14; a G at nucleotide 251 of SEQ ID NO: 19; a G at nucleotide 88 of SEQ ID NO: 23; a T at nucleotide 251 of SEQ ID NO: 24; an A at nucleotide 101 of SEQ ID NO: 25; a C at nucleotide 251 of SEQ ID NO: 26; an A at nucleotide 251 of SEQ ID NO: 28; an A at nucleotide 53 of SEQ ID NO: 29; an A at nucleotide 62 of SEQ ID NO: 30; an A at nucleotide 66 of SEQ ID NO: 31; an A at nucleotide 228 of SEQ ID NO: 32; and/or a G at nucleotide 51 of SEQ ID NO: 33, and that is associated with aphid resistance;

(ii) a A at nucleotide 61 of SEQ ID NO: 34; and/or a A at nucleotide 251 of SEQ ID NO: 35; a G at nucleotide of 251 SEQ ID NO: 7, and that is associated with RKN resistance; and/or

(iii) a T at nucleotide 251 of SEQ ID NO: 6; a C at nucleotide 251 of SEQ ID NO: 7; a G at nucleotide 251 of SEQ ID NO: 9; an A at nucleotide 251 of SEQ ID NO: 10; a G at nucleotide 251 of SEQ ID NO: 1 ; a G at nucleotide 251 of SEQ ID NO: 13; an A at nucleotide 251 of SEQ ID NO: 15; an A at nucleotide 251 of SEQ ID NO: 16; an A at nucleotide 251 of SEQ ID NO: 17; a G at nucleotide 251 of SEQ ID NO: 18; a T at nucleotide 251 of SEQ ID NO: 20; a T at nucleotide 251 of SEQ ID NO: 21 ; an A at nucleotide 251 of SEQ ID NO: 22; a C at nucleotide 101 of SEQ ID NO: 27, and that is associated with Phytophthora resistance.

The presently disclosed subject matter also provides methods for selecting pathogen resistant soybean plants comprising (a) isolating one or more nucleic acids from a plurality of soybean plants; (b) detecting in said isolated nucleic acids the presence of one or more marker molecules associated with pathogen resistance, wherein each of said one or more marker molecules comprises a nucleotide sequence that is at least 85% identical to one of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224, informative fragments thereof, and any marker molecule mapped within 1 , 2, 3, 4, 5, 6, 7, 8, 9, or 10 centiMorgans or less from said marker molecules; and (c) selecting a soybean plant comprising said one or more marker molecules, thereby selecting a pathogen resistant soybean plant. In some embodiments, the pathogen resistance is resistance to a pathogen selected from among aphids, RKN, and Phytophthora. In some embodiments, each of said one or more marker molecules comprises a nucleotide sequence comprising:

(i) an A at nucleotide 249 of SEQ ID NO: 1 ; an A at nucleotide 631 of SEQ ID NO: 2; a C at nucleotide 710 of SEQ ID NO: 3; a deletion of nucleotides 731 and 732 of SEQ ID NO: 4; a C at nucleotide 251 of SEQ ID NO: 12; a C at nucleotide 251 of SEQ ID NO: 14; a G at nucleotide 251 of SEQ ID NO: 19; a G at nucleotide 88 of SEQ ID NO: 23; a T at nucleotide 251 of SEQ ID NO: 24; an A at nucleotide 101 of SEQ ID NO: 25; a C at nucleotide 251 of SEQ ID NO: 26; an A at nucleotide 251 of SEQ ID NO: 28; an A at nucleotide 53 of SEQ ID NO: 29; an A at nucleotide 62 of SEQ ID NO: 30; an A at nucleotide 66 of SEQ ID NO: 31 ; an A at nucleotide 228 of SEQ ID NO: 32; and/or a G at nucleotide 51 of SEQ ID NO: 33, and that is associated with aphid resistance;

(ii) a A at nucleotide 61 of SEQ ID NO: 34; and/or a A at nucleotide 251 of SEQ ID NO: 35; a G at nucleotide of 251 SEQ ID NO: 7, and that is associated with RKN resistance; and/or (iii) a T at nucleotide 251 of SEQ ID NO: 6; a C at nucleotide 251 of

SEQ ID NO: 7; a G at nucleotide 251 of SEQ ID NO: 9; an A at nucleotide 251 of SEQ ID NO: 10; a G at nucleotide 251 of SEQ ID NO: 1 1 ; a G at nucleotide 251 of SEQ ID NO: 13; an A at nucleotide 251 of SEQ ID NO: 15; an A at nucleotide 251 of SEQ ID NO: 16; an A at nucleotide 251 of SEQ ID NO: 17; a G at nucleotide 251 of SEQ ID NO: 18; a T at nucleotide 251 of SEQ ID NO: 20; a T at nucleotide 251 of SEQ ID NO: 21 ; an A at nucleotide 251 of SEQ ID NO: 22; a C at nucleotide 101 of SEQ ID NO: 27, and that is associated with Phytophthora resistance.

The presently disclosed subject matter also provides pathogen resistant soybean plants selected using the presently disclosed methods, or a cell, tissue culture, seed thereof. In some embodiments, the presently disclosed subject matter provides methods for producing seeds that generate soybean plants resistant to a pathogen. In some embodiments, the methods comprise (a) providing a Glycine max plant which contains one or more alleles that confer resistance to one or more pathogens, which alleles are associated with a pathogen resistance locus present in Linkage Group F of Glycine max associated with any of SEQ ID NOs: SEQ ID NOs: 1 -35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224, wherein: (i) the pathogen resistance locus is an aphid resistance locus that is defined by one or more of the following aphid resistance markers: an aphid resistance marker of about 504 bp as set forth in SEQ ID NO: 1 ; an aphid resistance marker of about 848 bp as set forth in SEQ ID NO: 2; an aphid resistance marker of about 848 bp as set forth in SEQ ID NO: 3; an aphid resistance marker of about 848 bp as set forth in SEQ ID NO: 4; an aphid resistance marker of about 501 bp as set forth in SEQ ID NO: 12; an aphid resistance marker of about 501 bp as set forth in SEQ ID NO: 14; an aphid resistance marker of about 501 bp as set forth in SEQ ID NO: 19; an aphid resistance marker of about 187 bp as set forth in SEQ ID NO: 23; an aphid resistance marker of about 501 bp as set forth in SEQ ID NO: 24; an aphid resistance marker of about 201 bp as set forth in SEQ ID NO: 25; an aphid resistance marker of about 501 bp as set forth in SEQ ID NO: 26; an aphid resistance marker of about 501 bp as set forth in SEQ ID NO: 28; an aphid resistance marker of about 153 bp as set forth in SEQ ID NO: 29; an aphid resistance marker of about 161 bp as set forth in SEQ ID NO: 30; an aphid resistance marker of about 165 bp as set forth in SEQ ID NO: 31 ; an aphid resistance marker of about 251 bp as set forth in SEQ ID NO: 32; and/or an aphid resistance marker of about 79 bp as set forth in SEQ ID NO: 33; or any part of a DNA sequence linked within 1 , 2, 5, or 10 c to at least one of these markers conferring resistance to aphids; (ii) the pathogen resistance locus is an RKN resistance locus that is defined by one or more of the following RKN resistance markers: an RKN resistance marker of about 501 bp as set forth in SEQ ID NO: 5; an RKN resistance marker of about 501 bp as set forth in SEQ ID NO: 34; an RKN resistance marker of about 501 bp as set forth in SEQ ID NO:35;, or any part of a DNA sequence linked within 1 , 2, 5, or 10 cM to at least one of these markers conferring resistance to RKN; and/or (iii)the pathogen resistance locus is a Phytophthora resistance locus that is defined by one or more of the following Phytophthora resistance markers: a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 6; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 7; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 9; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 10; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 1 1 ; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 13; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 15; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 16; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 17; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 18; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 20; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 21 ; a Phytophthora resistance marker of about 501 bp as set forth in SEQ ID NO: 22; a Phytophthora resistance marker of about 201 bp as set forth in SEQ ID NO: 27, or any part of a DNA sequence linked within 1 , 2, 5, or 10 cM to at least one of these markers conferring resistance to Phytophthora; (b) crossing the Glycine max plant provided in step (a) with Glycine max culture breeding material; and (c) collecting seeds resulting from the cross in step (b) that result in soybean plants which are resistant to pathogen.

In some embodiments, the presently disclosed methods further comprise detecting at least one allelic form of a single nucleotide polymorphism (SNP) associated with at least one of the one or more alleles that confer resistance to pathogen. For example, the detecting can comprise amplifying the marker locus or a portion of the marker locus and detecting the resulting amplified marker amplicon. In some embodiments, the amplifying comprises (a) admixing an amplification primer or amplification primer pair with a nucleic acid isolated from the first Glycine max plant or germplasm, wherein the primer or primer pair is complementary or partially complementary to at least a portion of the marker locus, and is capable of initiating DNA polymerization by a DNA polymerase using the soybean nucleic acid as a template; and (b) extending the primer or primer pair in a DNA polymerization reaction comprising a DNA polymerase and a template nucleic acid to generate at least one amplicon. The nucleic acid that is amplified can be selected from DNA and RNA. In some embodiments, the amplifying comprises employing a polymerase chain reaction (PCR) or ligase chain reaction (LCR) using a nucleic acid isolated from the first soybean plant or germplasm as a template in the PCR or LCR.

In one aspect of the invention one may select or identify a soybean plant having increased pathogen resistance utilizing the minimum identifiers depicted in Table 3. In another aspect a soybean plant comprising at least one to two of the minimum identifiers as depicted in Table 3 is contemplated. In another aspect a soybean plant that may be identifie having 2 or more of the minimum identifiers described in Table 3, wherein the plant confers increased resistance to plant pathogens can be useful in various aspects of the invention. In one aspect a plant identified using 2 or more minimum identifiers as depicted in Table 3 may be useful in various aspects of the invention

The presently disclosed subject matter also provides improved soybean plants, seeds, and/or tissue cultures produced by the presently disclosed methods.

The presently disclosed subject matter also provides introgressed Glycine max plants and/or germplasm produced by the presently disclosed methods.

VI. Compositions

In some embodiments, the presently disclosed subject matter provides methods for analyzing the genomes of plants to identify those that include favorable markers associated with pathogen resistance. In some embodiments, the analysis methods comprise amplifying subsequences of the genomes of the plants and determining the nucleotides present in one, some, or all positions of the amplified subsequences.

Thus, in some embodiments the presently disclosed subject matter provides compositions comprising one or more amplification primer pairs capable of initiating DNA polymerization by a DNA polymerase on a Glycine max nucleic acid template to generate a Glycine max marker amplicon. In some embodiments, the Glycine max marker amplicon corresponds to Glycine max marker comprising a nucleotide sequence of any of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224. In view of the disclosure of SEQ ID NOs: 1-35 and/or to minimum identifiers as represented by SEQ ID NOs: 155-224 as being linked to pathogen resistance loci, one of ordinary skill in the art would be aware of various techniques that could be employed to analyze the sequences of the corresponding soybean nucleic acids. Representative amplification primer pairs can comprise the nucleotide sequences of a forward primer and corresponding reverse primer as set forth hereinabove in Table 2.

EXAMPLES

The following Examples provide illustrative embodiments. In light of the present disclosure and the general level of skill in the art, those of skill will appreciate that the following Examples are intended to be exemplary only and that numerous changes, modifications, and alterations can be employed without departing from the scope of the presently claimed subject matter.

Introduction to the EXAMPLES

Nucleotide sequences from five (5) soybean defense-related genes (P21, MMP2, PR1a, RPG1-b, and LTCOR11), two (2) melon defense-related genes (GENBANK® Accession Nos. AF354505 and AF354516), and three (3) soybean mosaic virus (SMV) resistance genes (GENBANK® Accession Nos. AY518517, AY518518, and AY518519) were BLASTed against the 8X Soybean Genome Database (i.e., the "Phytozome" Database administered by the Joint Genome Institute and the Center for Integrative Genomics available through the World Wide Web; see also Schmutz et al. (2010) Nature 463:178-183). Sequence homologies of short spans of sequence (<100 bp) were found throughout the genome. Interestingly, homologies were found to the full length sequences of certain of these genes, and of those, several showed homology to sequences within a span of approx 6 Mb on Linkage Group F (Chromosome 13). The EXAMPLES set forth herein below describe the further analysis of these genes. EXAMPLE 1

Sanger Sequencing

A set of 28 soybean lines representing sensitivity and resistance to several soybean biotic stresses were selected as lines to be used in the sequencing panel. These lines were either resistant or sensitive to aphids, RKN, and/or Phytophthora. Table 5 summarizes the soybean varieties employed and their respective stress resistances.

Table 5

SNP Screening Panel

Soybean Lines 1 -9 lack Rps8 and are designated as susceptible Germplasm Resources Information Network, Agricultural Research Service, United States Department of Agriculture, Beltsville, Maryland, United States of America.

EXAMPLE 2

TAQMAN® Validation

To validate TAQMAN® allelic discrimination assays for association with pathogen resistance or tolerance, plants were selected based on their known phenotypic status and compared to the genotype at the specific SNP location. DNA isolated from leaf tissue of seedlings 7-10 days after planting was diluted in TE buffer and stored at 4°C until used in PCR reactions as described below.

PCR was set up in 800 nl final volumes using the NEXAR® ARRAY TAPE™ Instrumentation (Douglas Scientific, Alexandria, Minnesota, United States of America). Approximately 5 ng leaf tissue DNA was added to each well and dried. Each well then received 1 X Master Mix (JUMPSTART™ Taq READYMIX™ Sigma Catalogue No. 2893; Sigma Chemical Co., St. Louis, Missouri, United States of America), supplemented with 1 .5 mM MgCI ₂ and 0.3 μΜ Sulforhodamine 101 (ROX) reference dye solution (Sigma Catalogue No. S-7635; Sigma Chemical Co., St. Louis, Missouri, United States of America), and 0.5 X TaqMan primers and probes (primers: 1 1 .25 nM, probes: 2.5 nM).

The wells of the array tape were sealed and placed in a Duncan DT-24 water bath thermal cycler (KBioscience, Inc.). The cycling program was as follows: 95°C for 10 minutes for initial denaturation, followed by 40 cycles of 95°C for 15 seconds, 60°C for 1 minute. Fluorescence generated during thermal cycling was measured on an ARAYA® scanning unit (Douglas Scientific). Allele calls were made using software that plots FAM vs. TET fluorescence. Samples that amplified one probe (i.e., generated only FAM fluorescence or TET fluorescence) were adjudged to be homozygous for the corresponding allele. Samples which amplified both FAM and TET probes were scored as heterozygous. EXAMPLE 3

Genotyping Soybean Accessions with Respect to Aphid Resistance

Phenotyping of soybean accessions with respect to aphid resistance was performed using the following protocol: ten seeds of each soybean line were planted (two reps of five seeds each in an "X" pattern (one seed at each "end" of the "X" and one in the center)). The pots were arranged to minimize any neighbor-entry effect. One pot of aphid-susceptible/negative and one of aphid-resistant/positive checks was placed after about every 50 entries. These were planted in the same 5-seed "X" arrangement. The seedlings were infested 6-10 days after planting (DAP) at growth stage VC (large, open unifoliates) with about 5-15 aphids each. Greenhouses were maintained at about 80°F (light hours) or 70°F (dark hours), with 16 hours of light and 8 hours of dark per 24 hours. Ratings were at 15-30 days after infestation (DAI), depending on the progress of aphid development on the negative/susceptible checks. Entries that rated 1 -3.5 were categorized as "resistant" and those that rate 3.6-6 were characterized as susceptible using the ratings scale in Table 5 below.

Table 6

Ratings Scale for Scoring Aphid Susceptibility/Resistance

Rating Scale Description Estimated Aphid

Populations

1 No aphids or very few wanderers 0-5

2 very few established/wanderers 6-9

3 "moderate" number on stems or 10-49

leaves; might be colonized

4 well established on stems or leaves 50-99

5 well established on stems and leaves 100-249

6 very heavy infestation on stems and > 250

leaves ng no germination

The alleles present at SNP positions for various of soybean accessions scored as resistant or susceptible with respect to aphids are presented in Tables 6 and 7.

Table 7

Detailed SNP Genotyping Data Related to Aphid Resistance

As Determined by TAQMAN® Assays

Each column shows the nucleotide present at the SNP position for the indicated SEQ ID NO.

^* American type Culture Collection (ATCC) Accession No. PTA-873; see also U.S. Patent No. 7,335,820.

* ^* ATCC Accession No. PTA-8915; see also U.S. Patent No. 7,371 ,937. Het - accession was heterozygous at the SNP position; Del - accession had the deletion at the SNP position; Ins - accession had the CA dinucleotide insertion at the SNP position.

Table 8

Detailed SNP Genotyping Data Related to Aphid Resistance

As Determined by KASP™ Assays

Each column shows the nucleotide present at the SNP position for the indicated SEQ ID NO.

* ^* ATCC Accession No. PTA-8746; see also U.S. Patent No. 7,339,094. n.d. not determined; Het: heterozygous.

EXAMPLE 4 Genotvpinq Soybean Accessions with Respect to Phytophthora Resistance

Phenotype of soybean accessions with respect Phytophthora resistance to was determined by the method described in Sandhu et al. (2005) J Heredity 96:536-541 and Burnham et al. (2003) Crop Sci 43:101 - 105. Briefly, a slurry of P. sojae race 25 was injected into the stems of 7-day old seedlings. Resistance or susceptibility was evaluated 7 days later. Resistant lines were still alive, while susceptible seedlings were dead with brown hypocotyls.

The alleles present at the specified SNP positions for various soybean accessions scored as resistant or susceptible to Phytophthora are presented in Table 8.

Table 9

Detailed SNP Genotvpinq Data Related to Phytophthora Resistance ²

As Determined by KASP™ Assays

Each column shows the nucleotide present at the SNP position for the indicated SEQ ID NO.

Het: heterozygous.

² Rsp8 resistance germplasm available for license from ACCESS Plant Technology, Inc., Plymouth, Indiana, United States of America.

EXAMPLE 5

Genotyping Soybean Accessions with Respect to RKN Resistance

Resistant soybean accessions with respect RKN species Meloidogyne javanica were selected from the literature. Penotyping can be determined by the method described in Tamulonis, et al., Crop Sci. 37:783-788 (1997). Seedlings are inoculated with Meloidogyne javanica eggs 7 days after planting. Thirty days later, soil is gently washed from the roots and galls are counted.

The alleles present at the specified SNP positions for various soybean accessions identified as resistant or susceptible to RKN are presented in Table 10.

Table 10

Detailed SNP Genotyping Data Related to Meloidopyne javanica RKN

Resistance ² As Determined by TaqMan® Assays

It will be understood that various details of the presently disclosed subject matter may be changed without departing from the scope of the presently disclosed subject matter. Furthermore, the foregoing description is for the purpose of illustration only, and not for the purpose of limitation.