Nematode Resistance Alleles In Soybean

Abstract

Methods for conveying soy cyst nematode (SCN) resistance into non-resistant soybean germplasm are provided. In some embodiments, the methods include introgressing SCN 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 and/or associated with SCN resistance. Also provided are single nucleotide polymorphisms (SNPs) associated with resistance to SCN. Soybean plants and seeds produced by any of the disclosed methods are provided.

Description

RELATED APPLICATION INFORMATION

[0001] This application is a Divisional of U.S. patent application Ser. No. 15/171,078, filed 2 Jun. 2016, which claims the benefit of U.S. Provisional Application No. 62/169,739, filed 2 Jun. 2015, the contents of which are incorporated by reference herein.

FIELD OF THE INVENTION

[0002] The present invention relates to compositions and methods for identifying, selecting and/or producing soybean plants having tolerance to soy cyst nematode.

STATEMENT REGARDING ELECTRONIC SUBMISSION OF A SEQUENCE LISTING

[0003] A Sequence Listing in ASCII text format, submitted under 37 C.F.R. .sctn. 1.821, entitled "80814_SeqList_ST25" generated on Jan. 21, 2021; .about.24 kb in size, and filed via EFS-Web is provided in lieu of a paper copy. This Sequence Listing is hereby incorporated by reference into the specification for its disclosures.

BACKGROUND

[0004] Soybean (Glycine max L. Merr) is a major cash crop and investment commodity in North America and elsewhere. Soybean oil is one of the most widely used edible oils, and soybeans are used worldwide both in animal feed and in human food production. The soybean cyst nematode (herein "SCN") is a small, plant-parasitic roundworm that attacks the roots of soybean plants. Responsible for causing annual losses of approximately $1.5 billion for U.S. growers, SCN has become a widespread problem across all major production areas. Nematodes not only directly rob soybeans of yield, but by feeding on the roots, they allow entry points of access for other plant pathogens. SCN damage is often misdiagnosed or confused with other crop production problems and can increase incidence of other soybean disease pests.

[0005] Historically, soybean growers used various nematicides to fight SCN. About 30 years ago, the industry began using native trait (NT) SCN resistance derived from Plant Introductions (PI) from Asia. Most of the soybean varieties feature soybean cyst nematode protection derived from PI 88788. The resistance loci from PI 88788 are found in about 95% of soybean varieties with SCN resistance. PI 88788 has no other known redeeming agronomic value to offer except for the few traits that confer SCN resistance. However, in recent years, this leading source of NT resistance against soybean cyst nematode has been weakening due to increased resistance of the pathogen. As varieties with PI88788 resistance get used continuously across soybean acres, farmers are seeing an increase in other SCN races that are immune to the PI88788 source of resistance. Different varieties of soybean vary in their sensitivity or tolerance to soy cyst nematode. Therefore a key importance in the control of SCN is to discover new sources and alleles that may be bred into commercial soy lines.

SUMMARY OF THE INVENTION

Definitions

[0006] Although the following terms are believed to be well understood by one of ordinary skill in the art, the following definitions are set forth to facilitate understanding of the presently disclosed subject matter.

[0007] As used herein, the terms "a" or "an" or "the" may refer to one or more than one. For example, "a" marker (e.g., SNP, QTL, haplotype) can mean one marker or a plurality of markers (e.g., 2, 3, 4, 5, 6, and the like).

[0008] As used herein, the term "and/or" refers to and encompasses any and all possible combinations of one or more of the associated listed items, as well as the lack of combinations when interpreted in the alternative ("or").

[0009] As used herein, the term "about," when used in reference to a measurable value such as an amount of mass, dose, time, temperature, and the like, is meant to encompass variations of 20%, 10%, 5%, 1%, 0.5%, or even 0.1% of the specified amount.

[0010] As used herein, the transitional phrase "consisting essentially of" means that the scope of a claim is to be interpreted to encompass the specified materials or steps recited in the claim and those that do not materially affect the basic and novel characteristic(s) of the claimed invention. Thus, the term "consisting essentially of" when used in a claim of this invention is not intended to be interpreted to be equivalent to "comprising."

[0011] As used herein, the term "allele" refers to one of two or more different nucleotides or nucleotide sequences that occur at a specific locus.

[0012] A "locus" is a position on a chromosome where a gene or marker or allele is located. In some embodiments, a locus may encompass one or more nucleotides.

[0013] As used herein, the terms "desired allele," "target allele" and/or "allele of interest" are used interchangeably to refer to an allele associated with a desired trait. In some embodiments, a desired allele may be associated with either an increase or a decrease (relative to a control) of or in a given trait, depending on the nature of the desired phenotype. In some embodiments of this invention, the phrase "desired allele," "target allele" or "allele of interest" refers to an allele(s) that is associated with tolerance to SCN in a soybean plant relative to a control soybean plant not having the target allele or alleles.

[0014] A marker is "associated with" a trait when said trait is linked to it and when the presence of the marker is an indicator of whether and/or to what extent the desired trait or trait form will occur in a plant/germplasm comprising the marker. Similarly, a marker is "associated with" an allele or chromosome interval when it is linked to it and when the presence of the marker is an indicator of whether the allele or chromosome interval is present in a plant/germplasm comprising the marker. For example, "a marker associated with an SCN tolerance allele" refers to a marker whose presence or absence can be used to predict whether a plant will display tolerance to SCN.

[0015] As used herein, the term "SON plant" or "SON tolerance" refers to a plant's ability to endure and/or thrive despite being exposed to growth conditions in which

[0016] SCN are low as compared to one or more control plants (e.g., a plant lacking a marker associated with SCN).

[0017] Thus, "tolerance" in a soybean plant to SCN conditions is an indication that the soybean plant is less affected by the SCN conditions with respect to yield, survivability and/or other relevant agronomic measures, compared to a less tolerant, more "susceptible" plant. Tolerance is a relative term, indicating that a "tolerant" soybean plant survives and/or produces a better yield in SCN growth conditions when compared to a different (less tolerant) soybean plant (e.g., a different soybean strain or variety) grown in similar conditions. A tolerant plant can have a greater survival rate and/or yield, as compared to a soybean plant that is susceptible or intolerant to these SCN growth conditions. SCN "tolerance" sometimes can be used interchangeably with SCN "resistance." SCN intolerant soybean varieties and cultivars are well known in the art.

[0018] As used herein, the terms "backcross" and "backcrossing" refer to the process whereby a progeny plant is crossed back to one of its parents one or more times (e.g., 1, 2, 3, 4, 5, 6, 7, 8, etc.). In a backcrossing scheme, the "donor" parent refers to the parental plant with the desired gene or locus to be introgressed. The "recipient" parent (used one or more times) or "recurrent" parent (used two or more times) refers to the parental plant into which the gene or locus is being introgressed. For example, see Ragot, M. et al. Marker-assisted Backcrossing: A Practical Example, in TECHNIQUES ET UTILISATIONS DES MARQUEURS MOLECULAIRES LES COLLOQUES, Vol. 72, pp. 45-56 (1995); and Openshaw et al., Marker-assisted Selection in Backcross Breeding, in PROCEEDINGS OF THE SYMPOSIUM "ANALYSIS OF MOLECULAR MARKER DATA," pp. 41-43 (1994). The initial cross gives rise to the F1 generation. The term "BC1" refers to the second use of the recurrent parent, "BC2" refers to the third use of the recurrent parent, and so on.

[0019] As used herein, the terms "cross" or "crossed" refer to the fusion of gametes via pollination to produce progeny (e.g., cells, seeds or plants). The term encompasses both sexual crosses (the pollination of one plant by another) and selfing (self-pollination, e.g., when the pollen and ovule are from the same plant).

[0020] The term "crossing" refers to the act of fusing gametes via pollination to produce progeny.

[0021] 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.

[0022] As used herein, the terms "elite" and/or "elite line" refer to any line that is substantially homozygous and has resulted from breeding and selection for desirable agronomic performance.

[0023] As used herein, the terms "exotic," "exotic line" and "exotic germplasm" refer to any plant, line or germplasm that is not elite. In general, exotic plants/germplasms are not derived from any known elite plant or germplasm, but rather are selected to introduce one or more desired genetic elements into a breeding program (e.g., to introduce novel alleles into a breeding program).

[0024] A "genetic map" is a description of genetic linkage relationships among loci on one or more chromosomes within a given species, generally depicted in a diagrammatic or tabular form. For each genetic map, distances between loci are measured by the recombination frequencies between them. Recombination between loci can be detected using a variety of markers. A genetic map is a product of the mapping population, types of markers used, and the polymorphic potential of each marker between different populations. The order and genetic distances between loci can differ from one genetic map to another.

[0025] As used herein, the term "genotype" refers to the genetic constitution of an individual (or group of individuals) at one or more genetic loci, as contrasted with the observable and/or detectable and/or manifested trait (the phenotype). Genotype is defined by the allele(s) of one or more known loci that the individual has inherited from its parents. The term genotype can be used to refer to an individual's genetic constitution at a single locus, at multiple loci, or more generally, the term genotype can be used to refer to an individual's genetic make-up for all the genes in its genome. Genotypes can be indirectly characterized, e.g., using markers and/or directly characterized by nucleic acid sequencing.

[0026] As used herein, the term "germplasm" refers to genetic material of or from an individual (e.g., a plant), a group of individuals (e.g., a plant line, variety or family), or a clone derived from a line, variety, species, or culture. The germplasm can be part of an organism or cell, or can be separate from the organism or cell. In general, germplasm provides genetic material with a specific genetic makeup that provides a foundation for some or all of the hereditary qualities of an organism or cell culture. As used herein, germplasm includes cells, seed or tissues from which new plants may be grown, as well as plant parts that can be cultured into a whole plant (e.g., leaves, stems, buds, roots, pollen, cells, etc.).

[0027] A "haplotype" is the genotype of an individual at a plurality of genetic loci, i.e., a combination of alleles. Typically, the genetic loci that define a haplotype are physically and genetically linked, i.e., on the same chromosome segment. The term "haplotype" can refer to polymorphisms at a particular locus, such as a single marker locus, or polymorphisms at multiple loci along a chromosomal segment.

[0028] As used herein, the term "heterozygous" refers to a genetic status wherein different alleles reside at corresponding loci on homologous chromosomes.

[0029] As used herein, the term "homozygous" refers to a genetic status wherein identical alleles reside at corresponding loci on homologous chromosomes.

[0030] 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.

[0031] As used herein, the term "inbred" refers to a substantially homozygous plant or variety. The term may refer to a plant or plant variety that is substantially homozygous throughout the entire genome or that is substantially homozygous with respect to a portion of the genome that is of particular interest.

[0032] As used herein, the term "indel" refers to an insertion or deletion in a pair of nucleotide sequences, wherein a first sequence may be referred to as having an insertion relative to a second sequence or the second sequence may be referred to as having a deletion relative to the first sequence.

[0033] As used herein, the terms "introgression," "introgressing" and "introgressed" refer to both the natural and artificial transmission of a desired allele or combination of desired alleles of a genetic locus or genetic loci from one genetic background to another. For example, a desired allele at a specified locus can be transmitted to at least one progeny via a sexual cross between two parents of the same species, where at least one of the parents has the desired allele in its genome. Alternatively, for example, transmission of an allele can occur by recombination between two donor genomes, e.g., in a fused protoplast, where at least one of the donor protoplasts has the desired allele in its genome. The desired allele may be a selected allele of a marker, a QTL, a transgene, or the like. Offspring comprising the desired allele can be backcrossed one or more times (e.g., 1, 2, 3, 4, or more times) to a line having a desired genetic background, selecting for the desired allele, with the result being that the desired allele becomes fixed in the desired genetic background. For example, a marker associated with SCN tolerance may be introgressed from a donor into a recurrent parent that is SCN intolerant. The resulting offspring could then be backcrossed one or more times and selected until the progeny possess the genetic marker(s) associated with SCN tolerance in the recurrent parent background.

[0034] As used herein, the term "linkage" refers to the degree with which one marker locus is associated with another marker locus or some other. The linkage relationship between a genetic marker and a phenotype may be given as a "probability" or "adjusted probability." Linkage can be expressed as a desired limit or range. For example, in some embodiments, any marker is linked (genetically and physically) to any other marker when the markers are separated by less than about 50, 40, 30, 25, 20, or 15 map units (or cM).

[0035] A centimorgan ("cM") or a genetic map unit (m.u.) is a unit of measure of recombination frequency and is defined as the distance between genes for which one product of meiosis in 100 is recombinant. One cM is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation. Thus, a recombinant frequency (RF) of 1% is equivalent to 1 m.u.

[0036] 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.

[0037] As used herein, the term "linkage disequilibrium" refers to a non-random segregation of genetic loci or traits (or both). In either case, linkage disequilibrium implies that the relevant loci are within sufficient physical proximity along a length of a chromosome so that they segregate together with greater than random (i.e., non-random) frequency (in the case of co-segregating traits, the loci that underlie the traits are in sufficient proximity to each other). Markers that show linkage disequilibrium are considered linked. Linked loci co-segregate more than 50% of the time, e.g., from about 51% to about 100% of the time. In other words, two markers that co-segregate have a recombination frequency of less than 50% (and, by definition, are separated by less than 50 cM on the same chromosome). As used herein, linkage can be between two markers, or alternatively between a marker and a phenotype. A marker locus can be "associated with" (linked to) a trait, e.g., SCN.

[0038] The degree of linkage of a genetic marker to a phenotypic trait is measured, e.g., as a statistical probability of co-segregation of that marker with the phenotype.

[0039] Linkage disequilibrium is most commonly assessed using the measure r.sup.2, which is calculated using the formula described by Hill and Robertson, Theor. Appl. Genet. 38:226 (1968). When r.sup.2=1, complete linkage disequilibrium exists between the two marker loci, meaning that the markers have not been separated by recombination and have the same allele frequency. Values for r.sup.2 above 1/3 indicate sufficiently strong linkage disequilibrium to be useful for mapping. Ardlie et al., Nature Reviews Genetics 3:299 (2002). Hence, alleles are in linkage disequilibrium when r.sup.2 values between pairwise marker loci are greater than or equal to about 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, or 1.0.

[0040] As used herein, the term "linkage equilibrium" describes a situation where two markers independently segregate, i.e., sort among progeny randomly. Markers that show linkage equilibrium are considered unlinked (whether or not they lie on the same chromosome).

[0041] As used herein, the terms "marker" and "genetic marker" are used interchangeably to refer to a nucleotide and/or a nucleotide sequence that has been associated with a phenotype and/or trait. A marker may be, but is not limited to, an allele, a gene, a haplotype, a chromosome interval, a restriction fragment length polymorphism (RFLP), a simple sequence repeat (SSR), a random amplified polymorphic DNA (RAPD), a cleaved amplified polymorphic sequence (CAPS) (Rafalski and Tingey, Trends in Genetics 9:275 (1993)), an amplified fragment length polymorphism (AFLP) (Vos et al., Nucleic Acids Res. 23:4407 (1995)), a single nucleotide polymorphism (SNP) (Brookes, Gene 234:177 (1993)), a sequence-characterized amplified region (SCAR) (Paran and Michelmore, Theor. Appl. Genet. 85:985 (1993)), a sequence-tagged site (STS) (Onozaki et al., Euphytica 138:255 (2004)), a single-stranded conformation polymorphism (SSCP) (Orita et al., Proc. Natl. Acad. Sci. USA 86:2766 (1989)), an inter-simple sequence repeat (ISSR) (Blair et al., Theor. Appl. Genet. 98:780 (1999)), an inter-retrotransposon amplified polymorphism (IRAP), a retrotransposon-microsatellite amplified polymorphism (REMAP) (Kalendar et al., Theor. Appl. Genet. 98:704 (1999)), an isozyme marker, an RNA cleavage product (such as a Lynx tag) or any combination of the markers described herein. A marker may be present in genomic or expressed nucleic acids (e.g., ESTs). A large number of soybean genetic markers are known in the art, and are published or available from various sources, such as the SoyBase internet resource (www.soybase.org). In some embodiments, a genetic marker of this invention is an SNP allele, a SNP allele located in a chromosome interval and/or a haplotype (combination of SNP alleles) each of which is associated with SCN tolerance.

[0042] Markers corresponding to genetic polymorphisms between members of a population can be detected by methods well-established in the art. These include, but are not limited to, nucleic acid sequencing, hybridization methods, amplification methods (e.g., PCR-based sequence specific amplification methods), detection of restriction fragment length polymorphisms (RFLP), detection of isozyme markers, detection of polynucleotide polymorphisms by allele specific hybridization (ASH), detection of amplified variable sequences of the plant genome, detection of self-sustained sequence replication, detection of simple sequence repeats (SSRs), detection of randomly amplified polymorphic DNA (RAPD), detection of single nucleotide polymorphisms (SNPs), and/or detection of amplified fragment length polymorphisms (AFLPs). Thus, in some embodiments of this invention, such well known methods can be used to detect the SNP alleles as defined herein (See, e.g., Table 1).

[0043] Accordingly, in some embodiments of this invention, a marker is detected by amplifying a Glycine sp. nucleic acid with two oligonucleotide primers by, for example, the polymerase chain reaction (PCR).

[0044] A "marker allele," also described as an "allele of a marker locus," can refer to one of a plurality of polymorphic nucleotide sequences found at a marker locus in a population that is polymorphic for the marker locus.

[0045] "Marker-assisted selection" (MAS) is a process by which phenotypes are selected based on marker genotypes. Marker assisted selection includes the use of marker genotypes for identifying plants for inclusion in and/or removal from a breeding program or planting.

[0046] As used herein, the terms "marker locus" and "marker loci" refer to a specific chromosome location or locations in the genome of an organism where a specific marker or markers can be found. A marker locus can be used to track the presence of a second linked locus, e.g., a linked locus that encodes or contributes to expression of a phenotypic trait. For example, a marker locus can be used to monitor segregation of alleles at a locus, such as a QTL or single gene, that are genetically or physically linked to the marker locus.

[0047] As used herein, the terms "marker probe" and "probe" refer to a nucleotide sequence or nucleic acid molecule that can be used to detect the presence of one or more particular alleles within a marker locus (e.g., a nucleic acid probe that is complementary to all of or a portion of the marker or marker locus, through nucleic acid hybridization). Marker probes comprising about 8, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more contiguous nucleotides may be used for nucleic acid hybridization. Alternatively, in some aspects, a marker probe refers to a probe of any type that is able to distinguish (i.e., genotype) the particular allele that is present at a marker locus.

[0048] As used herein, the term "molecular marker" may be used to refer to a genetic marker, as defined above, or an encoded product thereof (e.g., a protein) used as a point of reference when identifying a linked locus. A molecular marker can be derived from genomic nucleotide sequences or from expressed nucleotide sequences (e.g., from a spliced RNA, a cDNA, etc.). The term also refers to nucleotide sequences complementary to or flanking the marker sequences, such as nucleotide sequences used as probes and/or primers capable of amplifying the marker sequence. Nucleotide sequences are "complementary" when they specifically hybridize in solution, e.g., according to Watson-Crick base pairing rules. Some of the markers described herein can also be referred to as hybridization markers when located on an indel region. This is because the insertion region is, by definition, a polymorphism vis-a-vis a plant without the insertion. Thus, the marker need only indicate whether the indel region is present or absent. Any suitable marker detection technology may be used to identify such a hybridization marker, e.g., SNP technology.

[0049] 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 (NT 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.

[0050] 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. Pat. No. 4,458,066.

[0051] Primers can be labeled, if desired, by incorporating detectable moieties by for instance spectroscopic, fluorescence, photochemical, biochemical, immunochemical, or chemical moieties.

[0052] 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 non-specific/adventitious binding.

[0053] 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, N.Y., United States of America. Generally, lower salt concentration and higher temperature hybridization and/or washes increase the stringency of hybridization conditions.

[0054] As used herein, 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.

[0055] Different nucleotide sequences or polypeptide sequences having homology are referred to herein as "homologues." The term homologue includes homologous sequences from the same and other species and orthologous sequences from the same and other species. "Homology" refers to the level of similarity between two or more nucleotide sequences and/or amino acid sequences in terms of percent of positional identity (i.e., sequence similarity or identity). Homology also refers to the concept of similar functional properties among different nucleic acids, amino acids, and/or proteins.

[0056] 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, 55, 60, 65, 70, 75, 80, 85, 90, 95, 96, 97, 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, Calif., United States of America.

[0057] As used herein "sequence identity" refers to the extent to which two optimally aligned polynucleotide or polypeptide sequences are invariant throughout a window of alignment of components, e.g., nucleotides or amino acids. "Identity" can be readily calculated by known methods including, but not limited to, those described in: Computational Molecular Biology (Lesk, A. M., ed.) Oxford University Press, New York (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, New York (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, New Jersey (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, New York (1991).

[0058] As used herein, the term "substantially identical" or "corresponding to" means that two nucleotide sequences have at least 50%, 60%, 70%, 75%, 80%, 85%, 90% or 95% sequence identity. In some embodiments, the two nucleotide sequences can have at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity.

[0059] An "identity fraction" for aligned segments of a test sequence and a reference sequence is the number of identical components which are shared by the two aligned sequences divided by the total number of components in the reference sequence segment, i.e., the entire reference sequence or a smaller defined part of the reference sequence. Percent sequence identity is represented as the identity fraction multiplied by 100. As used herein, the term "percent sequence identity" or "percent identity" refers to the percentage of identical nucleotides in a linear polynucleotide sequence of a reference ("query") polynucleotide molecule (or its complementary strand) as compared to a test ("subject") polynucleotide molecule (or its complementary strand) when the two sequences are optimally aligned (with appropriate nucleotide insertions, deletions, or gaps totaling less than 20 percent of the reference sequence over the window of comparison). In some embodiments, "percent identity" can refer to the percentage of identical amino acids in an amino acid sequence.

[0060] Optimal alignment of sequences for aligning a comparison window is well known to those skilled in the art and may be conducted by tools such as the local homology algorithm of Smith and Waterman, the homology alignment algorithm of Needleman and Wunsch, the search for similarity method of Pearson and Lipman, and optionally by computerized implementations of these algorithms such as GAP, BESTFIT, FASTA, and TFASTA available as part of the GCG.RTM. Wisconsin Package.RTM. (Accelrys Inc., Burlington, Mass.). The comparison of one or more polynucleotide sequences may be to a full-length polynucleotide sequence or a portion thereof, or to a longer polynucleotide sequence. For purposes of this invention "percent identity" may also be determined using BLASTX version 2.0 for translated nucleotide sequences and BLASTN version 2.0 for polynucleotide sequences.

[0061] The percent of sequence identity can be determined using the "Best Fit" or "Gap" program of the Sequence Analysis Software Package.TM. (Version 10; Genetics Computer Group, Inc., Madison, Wis.). "Gap" utilizes the algorithm of Needleman and Wunsch (Needleman and Wunsch, J Mol. Biol. 48:443-453, 1970) to find the alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. "BestFit" performs an optimal alignment of the best segment of similarity between two sequences and inserts gaps to maximize the number of matches using the local homology algorithm of Smith and Waterman (Smith and Waterman, Adv. Appl. Math., 2:482-489, 1981, Smith et al., Nucleic Acids Res. 11:2205-2220, 1983).

[0062] Useful methods for determining sequence identity are also disclosed in Guide to Huge Computers (Martin J. Bishop, ed., Academic Press, San Diego (1994)), and Carillo et al. (Applied Math 48:1073 (1988)). More particularly, preferred computer programs for determining sequence identity include but are not limited to the Basic Local Alignment Search Tool (BLAST) programs which are publicly available from National Center Biotechnology Information (NCBI) at the National Library of Medicine, National Institute of Health, Bethesda, Md. 20894; see BLAST Manual, Altschul et al., NCBI, NLM, NIH; (Altschul et al., J. Mol. Biol. 215:403-410 (1990)); version 2.0 or higher of BLAST programs allows the introduction of gaps (deletions and insertions) into alignments; for peptide sequence BLASTX can be used to determine sequence identity; and for polynucleotide sequence BLASTN can be used to determine sequence identity.

[0063] As used herein, the terms "phenotype," "phenotypic trait" or "trait" refer to one or more traits of an organism. The phenotype can be observable to the naked eye, or by any other means of evaluation known in the art, e.g., microscopy, biochemical analysis, or an electromechanical assay. In some cases, a phenotype is directly controlled by a single gene or genetic locus, i.e., a "single gene trait." In other cases, a phenotype is the result of several genes.

[0064] As used herein, the term "polymorphism" refers to a variation in the nucleotide sequence at a locus, where said variation is too common to be due merely to a spontaneous mutation. A polymorphism must have a frequency of at least about 1% in a population. A polymorphism can be a single nucleotide polymorphism (SNP), or an insertion/deletion polymorphism, also referred to herein as an "indel." Additionally, the variation can be in a transcriptional profile or a methylation pattern. The polymorphic site or sites of a nucleotide sequence can be determined by comparing the nucleotide sequences at one or more loci in two or more germplasm entries.

[0065] As used herein, the term "plant" can refer to a whole plant, any part thereof, or a cell or tissue culture derived from a plant. Thus, the term "plant" can refer to a whole plant, a plant component or a plant organ (e.g., leaves, stems, roots, etc.), a plant tissue, a seed and/or a plant cell. A plant cell is a cell of a plant, taken from a plant, or derived through culture from a cell taken from a plant.

[0066] As used herein, the term "soybean" refers to a plant, and any part thereof, of the genus Glycine including, but not limited to Glycine max.

[0067] As used herein, the term "plant part" includes but is not limited to embryos, pollen, seeds, leaves, flowers (including but not limited to anthers, ovules and the like), fruit, stems or branches, roots, root tips, cells including cells that are intact in plants and/or parts of plants, protoplasts, plant cell tissue cultures, plant calli, plant clumps, and the like. Thus, a plant part includes soybean tissue culture from which soybean plants can be regenerated. Further, as used herein, "plant cell" refers to a structural and physiological unit of the plant, which comprises a cell wall and also may refer to a protoplast. A plant cell of the present invention can be in the form of an isolated single cell or can be a cultured cell or can be a part of a higher-organized unit such as, for example, a plant tissue or a plant organ.

[0068] As used herein, the term "population" refers to a genetically heterogeneous collection of plants sharing a common genetic derivation.

[0069] As used herein, the terms "progeny", "progeny plant," and/or "offspring" refer to a plant generated from a vegetative or sexual reproduction from one or more parent plants. A progeny plant may be obtained by cloning or selfing a single parent plant, or by crossing two parental plants and includes 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 F1s, 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.

[0070] As used herein, the term "reference sequence" refers to a defined nucleotide sequence used as a basis for nucleotide sequence comparison. The reference sequence for a marker, for example, can be obtained by genotyping a number of lines at the locus or loci of interest, aligning the nucleotide sequences in a sequence alignment program, and then obtaining the consensus sequence of the alignment. Hence, a reference sequence identifies the polymorphisms in alleles at a locus. A reference sequence may not be a copy of an actual nucleic acid sequence from any particular organism; however, it is useful for designing primers and probes for actual polymorphisms in the locus or loci.

Genetic Mapping

[0071] Genetic loci correlating with particular phenotypes, such as SCN tolerance can be mapped in an organism's genome. By identifying a marker or cluster of markers that co-segregate with a trait of interest, the breeder is able to rapidly select a desired phenotype by selecting for the proper marker (a process called marker-assisted selection, or MAS). Such markers may also be used by breeders to design genotypes in silico and to practice whole genome selection.

[0072] The present invention provides markers associated with SCN tolerance in soybean. Detection of these markers and/or other linked markers can be used to identify, select and/or produce soybean plants having SCN tolerance and/or to eliminate soybean plants from breeding programs or from planting that do not have SCN tolerance.

Markers Associated with SCN Tolerance

[0073] 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., SNP, 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, Fla., United States of America; Zietkiewicz et al. (1994) Genomics 20:176-183.

[0074] In one embodiment of the invention involves a method of identifying or selecting soybean lines having increased resistance to SCN wherein a molecular marker as indicated in Table 1 is detected in a soybean genomic DNA sample and used to identify and/or select a SCN line having resistance to SCN.

[0075] In another embodiment, the invention provides methods of producing soybean lines having increased resistance to SCN wherein a soybean plant comprising any marker listed in Table 1 is crossed with a soybean plant not comprising said respective marker thus creating a progeny plant comprising said respective marker. In a preferred embodiment the marker is derived from any one of soybean lines PI494182, PI507354, PI467312, PI548317, PI89772, PI5675160, PI507422, CE1210290 or a progeny thereof.

[0076] In addition to the markers detailed in Table 1, it is contemplated that the following SNP markers would be useful in selecting, identifying or producing soybean lines resistant to SCN (positions correspond to 8.times. public build of the Williams82 soybean genome at the SoyBase internet resource (www.soybase.org/SequenceIntro.php) or USDA at (bfgl.anri.barc.usda.gov/cgi-bin/soybean/Linkage.pl): Chromosome 11 at position 37073829 having a A; Chromosome 11 at position 37112108 having a G; Chromosome 11 at position 37335482 having a A; Chromosome 11 at position 37496850 having a G; Chromosome 11 at position 37863691 having a G; Chromosome 11 at position 38221754 having a G; Chromosome 8 at position 8219013 having a C; Chromosome 8 at position 8251158 having a C; or Chromosome 8 at position 8281297 having a T. It is contemplated that any one of these markers & loci associated with these markers may be derived from any one of soybean lines PI494182, PI507354, PI467312, PI548317, PI89772, PI567516C, PI507422, CE1210290 or a progeny thereof.

[0077] In another embodiment of the invention is provided an elite soybean plant produced by crossing soybean line CE121029 with a second soybean plant wherein said cross results in a SCN resistant plant. In a preferred embodiment the second soybean plant has introgressed into its genome a SCN resistant loci that associates with any one of the molecular markers as demonstrated in Table 1 or any one SNP marker corresponding with Chromosome 11 at position 37073829 having a A; Chromosome 11 at position 37112108 having a G; Chromosome 11 at position 37335482 having a A; Chromosome 11 at position 37496850 having a G; Chromosome 11 at position 37863691 having a G; Chromosome 11 at position 38221754 having a G; Chromosome 8 at position 8219013 having a C; Chromosome 8 at position 8251158 having a C; or Chromosome 8 at position 8281297 having a T.

[0078] Table 1 provides information about the SCN tolerance/resistant associated markers presented including the physical location of the marker on the respective CE1210290 soybean chromosome, and the target allele that is associated with soy cyst nematode tolerance/resistance. Markers of the present invention are described herein with respect to the positions of marker loci in the 8.times. public build of the Williams82 soybean genome at the SoyBase internet resource (www.soybase.org/SequenceIntro.php) or USDA at (bfgl.anri.barc.usda.gov/cgi-bin/soybean/Linkage.pl).

TABLE-US-00001 TABLE 1 The respective soybean chromosome AND physical positions comprising the favorable allele associated with increased resistance to each respective SCN race. Marker Physical I.D. Position (SEQ Soy of Favorable Unfavorable SCN Race ID NO:) Chromosome Marker Allele Allele Resistance 1 (12) 18 1638718 G A 1, 3 & 5 2 18 1690438 G A 1, 3 & 5 3 (7) 18 1712035 C A 1, 3 & 5 4 (8) 18 1712922 G A 1, 3 & 5 5 18 1735950 C G 1, 3 & 5 6 18 1736100 A C 1, 3 & 5 7 (2) 18 1736136 G A 1, 3 & 5 8 19 37734309 A G 2 9 19 37877119 G A 2

[0079] The above examples clearly illustrate the advantages of the invention. Although the present invention has been described with reference to specific details of certain embodiments thereof, it is not intended that such details should be regarded as limitations upon the scope of the invention except as and to the extent that they are included in the accompanying claims.

[0080] Throughout this application, various patents, patent publications and non-patent publications are referenced. The disclosures of these patents, patent publications and non-patent publications in their entireties are incorporated by reference herein into this application in order to more fully describe the state of the art to which this invention pertains.

Sequence CWU 1

1

6011353DNAArtificialMolecular markermisc_feature(292)..(292)n = a or cmisc_feature(512)..(512)n is a, c, g, or tmisc_feature(658)..(658)n is a, c, g, or t 1agagatataa agctccaaat ctcagaccct cgaatgcaca tgctaaacgc aaaaacaaca 60gtgatggcca caagcccaca acaactagta gaaaattttc ttaatctcaa cacccaagca 120cttggttttt atggtattaa tattagtaat acacacaaaa ccacgaacac aatgagggac 180caaattaggt caccgaagca tatagtccac aacacagcga aagccacttc atcaatttct 240acgaatttcc ttaaaaaaat tcaaaactac attatcaggg gtttgactcg tnacactttg 300tgactataaa tggcatctac aataacgata aatgaatagt tacagtgtat agagcatatc 360gcagatcacg aaatagaaga aatcgaaaga ataaggacct gatcagaaaa tggagaactg 420gcaatgtgcg gttgccggcg ggaagaacca acggcgttta gggtttgggc tatgaaggga 480atggaaagga aaggcagagt gaagcaaact gntgaatcga acgcaagctt cactcatcat 540tctgctacca gaatttagtt taaacaaatt aagataaaca ataataataa taataataat 600aataataata ataataataa taataataat ttatatatta aattaaagaa aaaaatanct 660gatgtgttaa aattgagagg aaaaaaagaa tctaaactat gatccattac ttcaaatctt 720caatatgggt tttaaacaaa aatattttta tttattaaaa tagtttagta tatatttatg 780ataaaaatat taagtttaat tgtcatgtat ttatcaatgt aaactttcag ttctgttaga 840aattgttccc agtatgacta caagatggtt acttatgaaa ataaaaaaaa atattatata 900tgaaaattta aaatccatag taaagaaatg tttttaaact ataagttata ttttttaatt 960tataataaat aattcacatt gtgaacctta ttttttctaa tatcaataat tgttttaaaa 1020aaatgttgaa attcaattta aaaattaaga tgaaaaatat aagaaattaa gaaaaccaag 1080tgaacaatta caaataaaga taaatcataa taatttgaga tgatggaaaa ataaattttt 1140ggggataata gttaaatcaa attaaaaaat atatatttaa aagtaataaa aaataaaatg 1200taaactaaaa gcttaatata acaaattagg acaaggcatg taactcaatg tgaatgataa 1260taattcttaa aattgcttcc atgtaagaaa aactactaaa aacattataa ttgctagtga 1320aaatattcgt ctaaattata catgggtggg ctg 13532716DNAArtificialMolecular markermisc_feature(104)..(104)n is a, c, g, or tmisc_feature(113)..(113)n is a, c, g, or tmisc_feature(274)..(274)n = a or gmisc_feature(310)..(310)n is a, c, g, or tmisc_feature(460)..(460)n is a, c, g, or tmisc_feature(670)..(670)n is a, c, g, or tmisc_feature(701)..(701)n is a, c, g, or t 2gaaactaaaa aaaccttaaa taaaacccga aactaattag ttttctcatt tttcttccta 60aacttttatt attattatta ttattattat tattattatt attntgactt aantactggg 120aaccaaaacg agaaaaaaga cgccaatttg aaggactcga attaaatcat aaaaaaatca 180aaatttattt gactcttcca taactttggg gattaaaata acactgaaat ataaactcaa 240gcactaattc atttaaaaaa acattgaaaa tgcnttgtat gtacaataca tcaaatcaaa 300tctaatttan gttattatta cgttttgtag atgttggatg aggatacatt cagtcaattg 360gtgttctgtg tggtacttat aaccgcgatt gtaacaccct tggttaacat attgtacaag 420catcgccctc gagtacacgc agaaagctta ttcgaagggn aactgagaac gatccaaagc 480actccaagaa acagagagtt tcacattgtt tgttgtgtac ataatgaagc aaacgtgcgt 540ggcatcactg ccttattaga agagtgcaac ccagtgcaag agagccccat atgcgtctac 600gcagtccacc ttatcgagct cgtggggaaa agtgcaccca ttctccttcc cataaaacat 660agacacggtn gcagaaaatt cttgtctgtg aattacccca ncccaaaaac tcgaaa 7163337DNAArtificialMolecular markermisc_feature(206)..(206)n = c or g 3ctgatattca gttttccagg ctaagctgag atatatttta tatccctctt aaaaacaatt 60ccaagatgag aggatatctg ctttgaccct tcaattgcag gattatccgc caggttgaat 120gacttctttt tcaacatgaa ccgcaaacgt aaccgttggt ggctgcaagc tctgcacaaa 180caagttgaaa taaaacagtt caaatngagg aaccaattat gggtattaca tataacataa 240tcatggttca tgcacatacc gttattctgc aatgaatatt aagatcatcg tgcatctgac 300taagacggtt ctttgcaagt tcttcagctg cacatgc 3374466DNAArtificialMolecular markermisc_feature(128)..(128)n is a, c, g, or tmisc_feature(157)..(157)n is a, c, g, or tmisc_feature(415)..(415)n = a or g 4caaacactat ttgactttga gggaatttgg atttttctta ctacgtgtag aattgtatta 60agattctaaa ccaagtgatg ttgacatgaa ggtcttggtc ctaatcagtt ctcgtctaaa 120tctactgnaa aaaaatatgg cagattggat acaatgntaa tgcatgattc atgaatgtgc 180tacaataaga caacacctgt caacacttgc aaaaggtaca aggaagtggg aaagtgcaaa 240tccatttcct tcggcatatc actttcaacc aattgacaat aatagagcaa acatcacaag 300aaaatggcaa gtttcactag ttttttatta tgagacatat ttgaaatgat catggaagga 360agggatggag attcagatgg gtgttctttg tcatcaggtt cttggatcta aaagngtggc 420ttagtccatc tttgactttc aaaataagag aaacctctga ttagtt 4665501DNAArtificialMolecular markermisc_feature(251)..(251)n = a or gmisc_feature(257)..(257)n is a, c, g, or tmisc_feature(501)..(501)n is a, c, g, or t 5agaatatttg attatccagt gaagagctga gctcgtgaga tgtcacgtga ctagagagta 60gcaaccacac gcgagtacta cgcagctatg gatcagaatt acaactacta ataatcaaga 120tttgcagatt tgtgaactca cacacaccaa agactgaaac taaacaaaca aacaaacatc 180gtcgtcttca tcgtcataat catctaattc ttcttctttg ttcagcttcc gtaaccgtaa 240cgttaacgtc ntcgtcntcg tcatcgtcgt ttatcccaaa acgatggact tcaccacttt 300cgcaaattcc atatcctatt ctcatgcaat tcctccaata cacccttatc gccttcaacc 360ctctcctttt ccccttcacc tcccattttc ggtacgtaat tctctctctc tctctctctc 420tctctctctc tctatatata tatatatata tattattttt gttatttcat ttactgtgaa 480ttttttgttg ttgtaatttt n 5016501DNAArtificialMolecular markermisc_feature(251)..(251)n = c or g 6agcaaatgtc atcattgctt cagctttcat aatatgatca aactccctcg tatacaacag 60ttgagtttga ttggttggac acaaagacat ggagttattc aagttatctt gacttttgtt 120aagacattcc tctatggatg ttgaaggagg ggggttaaag ctctcaaagg aaggaaaccc 180aacaggcaaa agtatttgac ctggaacatc tatcacacca cctggactgc tgttgacatc 240tccacaatcc ngggcagaaa gcataagtgc ctgagattct gcagttcctg ggggctttgt 300cagaaaatga ccacacaata agaaaccaat atacaagaga ccaagaagca gagagaaaaa 360aacaatatta gaataataaa gaggaagagc ttataaattt gaagtattca tgagttaaac 420aaaaagattc tgagtaaatt tatagaaatt atacaatcta tacagtcaac catatcttat 480atccaaattt taatttgaag a 5017601DNAArtificialMolecular markermisc_feature(218)..(218)n is a, c, g, or tmisc_feature(301)..(301)n = a or cmisc_feature(369)..(369)n is a, c, g, or t 7caatgcttca accgtgtttc tgacaagaag aaagaaagat gcaagacaca catgaacaac 60gttaacccat gttgtttttt gtttctctta tgtgtgtgga gccttgttgt gctcccctca 120tgcgtgaggc cagttttgtg tgaagatgaa ggttgggatg gagtggttgt gacagcatca 180aacctcttag cacttgaagc tttcaagcaa gagttggntg atccagaagg gttcttgcgg 240agctggaatg acagtggcta tggagcttgt tccggaggtt gggttggaat caagtgtgct 300nagggacagg ttattgtgat ccagcttcct tggaagggtt tgaggggtcg aatcaccgac 360aaaattggnc aacttcaagg cctcaggaag cttagtcttc atgataacca aattggtggt 420tcaatccctt caactttggg acttcttccc aaccttagag gggttcagtt attcaacaat 480aggcttacag gttccatacc tctttcttta ggtttctgcc ctttgcttca gtctcttgac 540ctcagcaaca acttgctcac aggagcaatc ccttatagtc ttgctaattc cactaagctt 600t 6018601DNAArtificialMolecular markermisc_feature(90)..(90)n is a, c, g, or tmisc_feature(301)..(301)n = g or amisc_feature(455)..(455)n is a, c, g, or t 8cttctggttt ttgattacat gtctaaagga agtcttgctt ctttcctaca tggtaagttt 60cgtgtgctgt tctttcatta agtgttgtgn gtgctgttct ttaattataa tttggagttt 120taccttagta atctgtataa ttctaatcgg agaacagtac aaacaaaaac acctaaggaa 180cactatagca cctaaggaac aacaccttag ctttaatata ccatatcaat aagtgaatta 240ttttcttgtt catcttgatg caggtggtgg aactgaaaca ttcattgatt ggccaacaag 300natgaaaata gcacaagact tggcccgtgg cttgttctgc cttcattccc aggagaacat 360catacatggg aacctcacat ccagcaatgt gttgcttgat gagaatacaa atgctaaaat 420tgcagatttt ggtctttctc ggttgatgtc aactnctgct aattccaacg tgatagctac 480agctggagca ttgggatacc gggcacctga gctctcaaag ctcaagaaag caaacactaa 540aactgatatc tacagtcttg gtgttatctt gttagaactc ctaacgagga aatcacctgg 600g 6019601DNAArtificialMolecular markermisc_feature(301)..(301)n = a or c 9tggtgcttgt tcaggaggtt gggttggaat caagtgtgct cagggacagg ttatcgtgat 60ccagcttcct tggaagggtt tgaagggtcg aatcactgac aaaattggcc aacttcaagg 120ccttaggaag cttagtcttc atgataacca aattggtggt tcaatccctt caactttggg 180acttcttccc aaccttagag gggttcagtt attcaacaat aggttaactg gttccatccc 240ttcttcttta ggtttctgtc ctttgcttca gtctcttgac ctcagcaaca acttgctcac 300nggagcaatc ccttatagcc ttgccaattc caccaagctt tattggctta acttgagttt 360caactccttc tctggtactt taccaactag cctaactcac tcattttctc tcactttcct 420ttctcttcaa aataataatc tttctggcaa ccttcctaac tcttggggtg ggagtcccaa 480gagtggcttc tttaggctcc aaaatttgat cctagatcat aattttttca ctggtaatgt 540tcctgcttct ttgggtagct taagagagct cagtgagatt tcccttagtc ataataagtt 600t 60110601DNAArtificialMolecular markermisc_feature(235)..(235)n is a, c, g, or tmisc_feature(253)..(253)n is a, c, g, or tmisc_feature(283)..(283)n is a, c, g, or tmisc_feature(301)..(301)n = a or tmisc_feature(310)..(310)n is a, c, g, or tmisc_feature(321)..(321)n is a, c, g, or tmisc_feature(343)..(343)n is a, c, g, or tmisc_feature(379)..(379)n is a, c, g, or tmisc_feature(385)..(385)n is a, c, g, or tmisc_feature(394)..(394)n is a, c, g, or tmisc_feature(421)..(421)n is a, c, g, or tmisc_feature(439)..(439)n is a, c, g, or tmisc_feature(467)..(467)n is a, c, g, or tmisc_feature(490)..(490)n is a, c, g, or tmisc_feature(502)..(502)n is a, c, g, or tmisc_feature(543)..(543)n is a, c, g, or tmisc_feature(556)..(556)n is a, c, g, or tmisc_feature(562)..(562)n is a, c, g, or tmisc_feature(568)..(568)n is a, c, g, or tmisc_feature(580)..(580)n is a, c, g, or tmisc_feature(583)..(583)n is a, c, g, or tmisc_feature(592)..(592)n is a, c, g, or t 10ctggtccttc cccaccgacc tcacttcctc ctctaaccta atcgacctcg acctcgccac 60cgtatccctc accggtccct tgccggacat tttcgacaaa ttcccttccc ttcaacacct 120tcgcctctct tacaacaacc tcaccggcaa tttaccctcc tctttctccg ccgccaacaa 180tctcgaaacg ctctggctca acaaccaggc cgccggcttg tccggtaccc tcctngtcct 240ctccaacatg tcngcattaa accagtcctg gctcaataag aancagttca ccggttccat 300nccggatttn tcgcaatgca nggctttgtc tgacttgcag ctnagggata accagttaac 360tggtgtggtt cccgcttcnt tgacnagtct tccnagtttg aagaaagttt ctctggataa 420naatgagctt caggggccng tgcccgtgtt tgggaaaggt gtgaatntta ctctcgatgg 480gattaatagn ttttgtcttg anactcctgg gaattgtgat cccagggtga tggttttgct 540gcngattgcc gaggcnttcg gntatccnat tcggttggcn gantcgtgga angggaatga 600t 60111601DNAArtificialMolecular markermisc_feature(301)..(301)n = a or c 11aaaggataat tgagagtcag actctggtaa actgtctaaa aatggctcga catatctttt 60gaggcatcaa ccaccaagaa ctatgcagca aaacccccac ccaactcaac aaaacacgtg 120aaaagagcaa aatataacat tgcaaagaaa tagccacaaa gaattttgaa gtagccatgt 180atctaggaat tgagtatcaa ttattttccc ttcaactctt tctacttttt ttttgtatgt 240gagcgattac tctggtgaac tacttaaatt tgctgaacac cgaagcatga tattgaagta 300ntaaccaaca gctataacca ccaaatacga gcatataaaa tatgaacttc aaaattaagg 360cacaattgta caaaactaaa atcaaaggct ttctgtacct gcatactcag gtgcaagata 420tccaaatgtt ccagccaacc gtgtctcaac agaatacttc ccatctggtg catttttaac 480caacccaaaa tcagcaacct ttgctctcat gtcatcgcct agtagtatgt ttgagggttt 540taagtctcta tgaatgaagc tttgctgagc taaactgtgc aagtattcca ccccccgcgc 600t 60112501DNAArtificialMolecular markermisc_feature(251)..(251)n = a or gmisc_feature(317)..(318)n is a, c, g, or t 12aaggaacgcc gccgccggct tccgtccccg gcgcggtgtt caacgtggcc accagcatag 60tcggcgccgg aatcatgtcg attccggcga tcatgaaggt tctcggcgta gttcccgctt 120tcgcgatgat tctcgtggtg gccgtgctgg cggaactgtc cgtggacttc ctgatgcggt 180tcacgcactc cggcgaaacg acgacgtacg ctggcgtcat gagggaggcg ttcggatcgg 240gtggagcatt ngccgcgcaa gtttgcgtca tcatcaccaa cgttgggggt ttaattctct 300accttatcat catcggnnac gtaacggaac ttttcccttt ttttttaatt tcctttctac 360tgaattcgta aaaaaggaaa aaaaaatgta gattttttca tgtttttggt ttggtatgct 420tgttctgagt tttgccgggt tttcagtcag attcattttg attggtgaaa ttgttgctaa 480taataagtga aatttgtttt t 5011322DNAArtificialMolecular marker 13agcgaaagcc acttcatcaa tt 221430DNAArtificialMolecular marker 14tgcgatatgc tctatacact gtaactattc 301515DNAArtificialMolecular marker 15tgactcgtca cactt 151616DNAArtificialMolecular marker 16tgactcgtaa cacttt 161730DNAArtificialMolecular marker 17cactgaaata taaactcaag cactaattca 301824DNAArtificialMolecular marker 18cctcatccaa catctacaaa acgt 241920DNAArtificialMolecular marker 19tgaaaatgcg ttgtatgtac 202022DNAArtificialMolecular marker 20attgaaaatg cattgtatgt ac 222124DNAArtificialMolecular marker 21cggtatgtgc atgaaccatg atta 242222DNAArtificialMolecular marker 22ctgcaagctc tgcacaaaca ag 222316DNAArtificialMolecular marker 23aattggttcc tccatt 162417DNAArtificialMolecular marker 24taattggttc ctcgatt 172521DNAArtificialMolecular marker 25cagaggtttc tcttattttg a 212618DNAArtificialMolecular marker 26gggatggaga ttcagatg 182716DNAArtificialMolecular marker 27actaagccac cctttt 162817DNAArtificialMolecular marker 28atggactaag ccactct 172920DNAArtificialMolecular marker 29gttcagcttc cgtaaccgta 203021DNAArtificialMolecular marker 30tgcgaaagtg gtgaagtcca t 213114DNAArtificialMolecular marker 31ttaacgtcat cgtc 143214DNAArtificialMolecular marker 32ttaacgtcgt cgtc 143322DNAArtificialMolecular marker 33gaactgcaga atctcaggca ct 223422DNAArtificialMolecular marker 34cctggactgc tgttgacatc tc 223513DNAArtificialMolecular marker 35ctgccccgga ttg 133614DNAArtificialMolecular marker 36ttctgcccgg gatt 143719DNAArtificialMolecular marker 37ggagcttgtt ccggaggtt 193820DNAArtificialMolecular marker 38tccaaggaag ctggatcaca 203918DNAArtificialMolecular marker 39aatcaagtgt gctaaggg 184017DNAArtificialMolecular marker 40aatcaagtgt gctcagg 174118DNAArtificialMolecular marker 41aagccacggg ccaagtct 184221DNAArtificialMolecular marker 42tgcaggtggt ggaactgaaa c 214319DNAArtificialMolecular marker 43tgtgctattt tcatccttg 194419DNAArtificialMolecular marker 44tgtgctattt tcattcttg 194524DNAArtificialMolecular marker 45cctttgcttc agtctcttga cctc 244620DNAArtificialMolecular marker 46ttggtggaat tggcaaggct 204717DNAArtificialMolecular marker 47aacaacttgc tcacagg 174816DNAArtificialMolecular marker 48aacttgctca ccggag 164923DNAArtificialMolecular marker 49aaaccagtcc tggctcaata aga 235020DNAArtificialMolecular marker 50agcgggaacc acaccagtta 205115DNAArtificialMolecular marker 51accggttcca taccg 155214DNAArtificialMolecular marker 52cggttccatt ccgg 145324DNAArtificialMolecular marker 53tgcaggtaca gaaagccttt gatt 245424DNAArtificialMolecular marker 54gctgaacacc gaagcatgat attg 245517DNAArtificialMolecular marker 55agctgttggt tagtact 175619DNAArtificialMolecular marker 56tatagctgtt ggttattac 195719DNAArtificialMolecular marker 57cgttggtgat gatgacgca 195821DNAArtificialMolecular marker 58ctgtccgtgg acttcctgat g 215913DNAArtificialMolecular marker 59cgcggccaat gct 136016DNAArtificialMolecular marker 60acttgcgcgg ctaatg 16

Claims

1. A method of identifying or selecting an SCN tolerant soybean plant or part thereof, comprising the steps of a) Isolating a nucleic acid from a first soybean plant; b) Detecting in the nucleic acid of a) a molecular marker associated with increased SCN resistance wherein said molecular marker corresponds to any one of Chromosome 18 a G at position 1638718; Chromosome 18 a G at position 1690438; Chromosome 18 a C at position 1712035; Chromosome 18 a G at position 1712922; Chromosome 18 a C at position 1735950; Chromosome 18 a A at position 1736100; Chromosome 18 a G at position 1736136; Chromosome 19 a A at position 37734309; or Chromosome 19 a G at position 37877119. c) thereby identifying or selecting a SCN tolerant soybean plant or part thereof.

2. A method of producing a SCN resistant soybean plant, the method comprising the steps of: a) Crossing a first soybean plant with a second soybean plant wherein said first plant comprises in its genome a SCN resistance loci further wherein the SCN resistance loci comprises any one of any one of Chromosome 18 a G at position 1638718; Chromosome 18 a G at position 1690438; Chromosome 18 a C at position 1712035; Chromosome 18 a G at position 1712922; Chromosome 18 a C at position 1735950; Chromosome 18 a A at position 1736100; Chromosome 18 a G at position 1736136; Chromosome 19 a A at position 37734309; or Chromosome 19 a G at position 37877119 and wherein said second plant does not comprise said SCN resistance loci; b) producing a progeny seed from the cross of a); c) growing a progeny plant from the seed of b) wherein said progeny plant comprises in its genome the SCN resistance loci described in a) thereby producing a SCN resistant plant.

3. The method of claim 3, wherein the first soybean plant is CE1210290.

4. A plant produced by the method of claim 3.

5. A method of identifying or selecting an SCN tolerant soybean plant or part thereof, comprising the steps of a) Isolating a nucleic acid from a first soybean plant; b) Detecting in the nucleic acid of a) a molecular marker within a chromosomal interval associated with increased SCN resistance wherein said chromosomal interval is defined by and including Chromosome 19 position 37734309 to position 37877119. c) thereby identifying or selecting a SCN tolerant soybean plant or part thereof.

6. A method of producing a SCN resistant soybean plant, the method comprising the steps of: a) Crossing a first soybean plant with a second soybean plant wherein said first plant comprises in its genome a chromosomal interval wherein the chromosomal interval is defined by and including Chromosome 19 position 37734309 to position 37877119 and wherein said second plant does not comprise said chromosomal interval; b) producing a progeny seed from the cross of a); c) growing a progeny plant from the seed of b) wherein said progeny plant comprises in its genome the chromosomal interval of a) thereby producing a SCN resistant plant.

7. The method of claim 6, wherein the first soybean plant is CE1210290 or a progeny thereof.

8. The method of claim 7, wherein the progeny plant produced in c) shows increased resistance to SCN race 2.

9. A plant created by the method of claim 7.

10. A elite soybean plant having introgressed into its genome a chromosomal interval from CE1210290 or a progeny thereof wherein the chromosomal interval comprises at least one molecular marker associated with SCN resistance wherein the molecular marker corresponds to soybean chromosome 19 position 37734309 having a A or soybean chromosome position 37877119 having a G.