Methods And Compositions To Select Cotton Plants Resistant To Cotton Root Knot Nematode

Abstract

The present invention is in the field of plant breeding and disease resistance. More specifically, the invention provides a method for breeding cotton plants containing one or more quantitative trait loci that are associated with resistance to Root Knot Nematode(RKN), a disease associated with Meloidogyne incognita. The invention further provides germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease resistance for introgression into elite germplasm in a breeding program, thus producing novel elite germplasm comprising one or more RKN resistance QTL.

Description

CROSS-REFERENCES TO RELATED APPLICATIONS

[0001] This application claims the benefit under 35 U.S.C. .sctn.119(e) of U.S. Provisional Application No. 61/092,649 filed on 28 Aug. 2008. The entirety of the application is hereby incorporated by reference.

INCORPORATION OF SEQUENCE LISTING

[0002] A sequence listing containing the file named "pa.sub.--53664.txt" which is 70.5 kilobytes (measured in MS-Windows.RTM.) and created on Aug. 25, 2009, comprises 103 nucleotide sequences, and is herein incorporated by reference in its entirety.

FIELD OF INVENTION

[0003] The present invention is in the field of plant breeding and disease resistance. More specifically, the invention includes a method for breeding cotton plants containing quantitative trait loci that are associated with resistance to cotton root knot nematode (RKN), a disease associated with Meloidogyne incognita (Kofoid and White) Chitwood. The invention further includes germplasm and the use of germplasm containing quantitative trait loci (QTL) conferring disease resistance for introgression into elite germplasm in a breeding program thus producing novel elite germplasm comprising one or more cotton RKN resistance QTL.

BACKGROUND OF THE INVENTION

[0004] Cotton root knot nematode (RKN) is a destructive nematode which forms galls on the roots of cotton plants. The causative agent is Meloidogyne incognita (Kofoid and White) Chitwood, a nematode which can infect a variety of plant species. Nutrient and water uptake are decreased in infected plants, and plants may become susceptible to other pathogens, especially Fusarium wilt (Minton, N. A. and Minton E. B., Phytopathology 56:319-322 (1966)). Consequently, yield is decreased in plants infected with RKN. In the USA alone, an estimated 10.93% of cotton yield loss in 2004 was attributed to RKN (Blasingame and Patel, 2005). RKN is wide-spread throughout the US Cotton Belt. Methods to mitigate RKN damage include rotating cotton crops with non-susceptible crops and application of costly nematicides. However, the most effective way for cotton growers to reduce yield loss and crop damage due to RKN is to grow RKN resistant cotton cultivars. Therefore, a need exists for development of such RKN resistant cotton varieties and for methods to accelerate development of such varieties. Genetic markers can be used by plant breeders as an indirect means to select plants with favorable alleles. A major RKN resistance locus has been reported on Chromosome A11 (Kai, W. et al. Theor. Appl. Genet. 113:73-80 (2006)). Breeding for RKN resistant cotton varieties can be greatly facilitated by the use of marker-assisted selection for RKN resistance alleles. RKN resistance in cotton has been reported in different germplasm lines such as Auburn 623 RNR and Acala NemX. However, commercial cultivars with RKN resistance are limited. Identification of genetic markers associated with RKN resistance is of great value in a cotton breeding program. RAPD, AFLP, and RGA markers for identifying RKN resistant plants have been identified in a study using near-isogenic lines (NILs) (Niu, C. et al., Crop Science 47:951-960 (2007)). Genetic markers associated with RKN resistance in plants have also included SSR markers (Wang, C. et al. Theor. Appl. Genet. 112:770-777 (2006)).

[0005] Of the classes of markers, SNPs have characteristics which make them preferential to other genetic markers in detecting, selecting for, and introgressing RKN resistance in a cotton plant. SNPs are preferred because technologies are available for automated, high-throughput screening of SNP markers, which can decrease the time to select for and introgress RKN resistance in soybean plants. Further, SNP markers are ideal because the likelihood that a particular SNP allele is derived from independent origins in the extant population of a particular species is very low. As such, genetically linked SNP markers are useful for tracking and assisting introgression of RKN resistance alleles, particularly in the case of RKN resistance haplotypes validated to exist in the resistant donor parent. A need exists for a SNP based marker set for identifying cotton plants resistant to RKN. The present invention provides a SNP based marker for identifying plants resistant to RKN.

BRIEF SUMMARY OF THE INVENTION

[0006] The present invention provides a method of introgressing an allele associated with Root Knot Nematode (RKN) resistance into a cotton plant comprising the steps of: (A) providing a population of cotton plants; B) genotyping at least one cotton plant in the population with respect to a cotton genomic nucleic acid marker selected from the group comprising SEQ ID NOs: 1-38 and C) selecting from the population at least one cotton plant comprising at least one allele associated with RKN resistance. The population provided may be derived by crossing at least one RKN resistant cotton plant with at least one RKN sensitive plant to form a population.

[0007] In one aspect, the cotton plants selected by the methods of the present invention exhibit a resistant reaction rating to RKN of no worse than about 2.0 using indexing scale of 0-5, where 0 is nematode free plant and 5=100% roots with galls.

[0008] In one aspect, the method of the present invention further comprises the step (d) of assaying the selected cotton plant for resistance to a RKN disease inducing pathogen. In a further aspect, the genotype is determined by an assay which is selected from the group consisting of single base extension (SBE), allele-specific primer extension sequencing (ASPE), DNA sequencing, RNA sequencing, microarray-based analyses, universal PCR, allele specific extension, hybridization, mass spectrometry, ligation, extension-ligation, and Flap Endonuclease-mediated assays. In a further aspect, the cotton genomic nucleic acid marker is SEQ ID NO: 33.

[0009] The present invention also provides for an elite cotton plant produced by: a) providing a population of cotton plants; b) genotyping at least one cotton plant in the population with respect to a cotton genomic nucleic acid marker selected from the group comprising SEQ ID NOs: 1-38; and c) selecting from the population at least one cotton plant comprising at least one allele associated with RKN resistance. The elite cotton plant of the present invention can exhibit a transgenic trait. The transgenic trait is selected from the group consisting of herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma disease resistance, modified oils production, high oil production, high protein production, germination and/or seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistance, increased digestibility, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, and reduced allergenicity. The herbicide tolerance can be selected from the group consisting of glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil, 2,4, Dichlorophenoxyacetic acid, and norflurazon herbicides.

[0010] The present invention further provides a method of introgressing at least one RKN resistance allele into a cotton plant comprising a) providing a population of cotton plants, b) screening the population with at least one nucleic acid marker, c) selecting from the population one or more cotton plants comprising one or more alleles associated with RKN resistance. In one aspect, the selected cotton plants exhibit a resistant reaction rating to RKN of no worse than about 2.0. The present invention further provides for a cotton plant produced by a) providing a population of cotton plants, b) screening the population with at least one nucleic acid marker, c) selecting from the population one or more cotton plants comprising one or more alleles associated with RKN resistance.

[0011] The invention further provides a substantially purified nucleic acid molecule for the detection of loci related to RKN resistance comprising a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 1-62 and complements thereof. The invention further provides an isolated nucleic acid molecule for detecting a molecular marker representing a polymorphism in cotton DNA, wherein the nucleic acid molecule comprises at least 15 nucleotides that include or are adjacent to the polymorphism, wherein the nucleic acid molecule is at least 90 percent identical to a sequence of the same number of consecutive nucleotides in either strand of DNA that include or are adjacent to the polymorphism, and wherein the molecular marker is selected from the group consisting of SEQ ID NOs: 1-38. In one aspect, the isolated nucleic acid further comprises a detectable label or provides for incorporation of a detectable label. In a further aspect, the detectable label is selected from the group consisting of an isotope, a fluorophore, an oxidant, a reductant, a nucleotide and a hapten.

[0012] The present invention further provides a set of oligonucleotides comprising a) a pair of oligonucleotide primers wherein each of the primers comprises at least 12 contiguous nucleotides and wherein the pair of primers permit PCR amplification of a DNA segment comprising a molecular marker selected from the group consisting of SEQ ID NOs: 1-38 and b) at least one detector oligonucleotide that permits detection of a polymorphism in the amplified segment, wherein the sequence of the detector oligonucleotide is at least 95 percent identical to a sequence of the same number of consecutive nucleotides in either strand of a segment of cotton DNA that include or are adjacent to the polymorphism of step (a).

BRIEF DESCRIPTION OF THE NUCLEIC ACIDS

[0013] SEQ ID NO: 1 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0014] SEQ ID NO: 2 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0015] SEQ ID NO: 3 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0016] SEQ ID NO: 4 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0017] SEQ ID NO: 5 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0018] SEQ ID NO: 6 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0019] SEQ ID NO: 7 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0020] SEQ ID NO: 8 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0021] SEQ ID NO: 9 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0022] SEQ ID NO: 10 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0023] SEQ ID NO: 11 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0024] SEQ ID NO: 12 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0025] SEQ ID NO: 13 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0026] SEQ ID NO: 14 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0027] SEQ ID NO: 15 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0028] SEQ ID NO: 16 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0029] SEQ ID NO: 17 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0030] SEQ ID NO: 18 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0031] SEQ ID NO: 19 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0032] SEQ ID NO: 20 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0033] SEQ ID NO: 21 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0034] SEQ ID NO: 22 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0035] SEQ ID NO: 23 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0036] SEQ ID NO: 24 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0037] SEQ ID NO: 25 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0038] SEQ ID NO: 26 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0039] SEQ ID NO: 27 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0040] SEQ ID NO: 28 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0041] SEQ ID NO: 29 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0042] SEQ ID NO: 30 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0043] SEQ ID NO: 31 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0044] SEQ ID NO: 32 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0045] SEQ ID NO: 33 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0046] SEQ ID NO: 34 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0047] SEQ ID NO: 35 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0048] SEQ ID NO: 36 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0049] SEQ ID NO: 37 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0050] SEQ ID NO: 38 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 11.

[0051] SEQ ID NO: 39 is a forward PCR primer for the amplification of SEQ ID NO: 33.

[0052] SEQ ID NO: 40 is a reverse PCR primer for the amplification of SEQ ID NO: 33.

[0053] SEQ ID NO: 41 is a forward PCR primer for the amplification of SEQ ID NO: 36.

[0054] SEQ ID NO: 42 is a reverse PCR primer for the amplification of SEQ ID NO: 36.

[0055] SEQ ID NO: 43 is a forward PCR primer for the amplification of SEQ ID NO: 9.

[0056] SEQ ID NO: 44 is a reverse PCR primer for the amplification of SEQ ID NO: 9.

[0057] SEQ ID NO: 45 is a probe for detecting the RKN resistance locus of SEQ ID NO: 33.

[0058] SEQ ID NO: 46 is a second probe for detecting the RKN resistance locus of SEQ ID NO: 34.

[0059] SEQ ID NO: 47 is a probe for detecting the RKN resistance locus of SEQ ID NO: 36.

[0060] SEQ ID NO: 48 is a second probe for detecting the RKN resistance locus of SEQ ID NO: 36.

[0061] SEQ ID NO: 49 is a probe for detecting the RKN resistance locus of SEQ ID NO: 9.

[0062] SEQ ID NO: 50 is a second probe for detecting the RKN resistance locus of SEQ ID NO: 9.

[0063] SEQ ID NO: 51 is a forward single base extension probe for detecting the RKN resistance locus of SEQ ID NO: 33.

[0064] SEQ ID NO: 52 is a reverse single base extension probe for detecting the RKN resistance locus of SEQ ID NO: 33.

[0065] SEQ ID NO: 53 is a forward single base extension probe for detecting the RKN resistance locus of SEQ ID NO: 36.

[0066] SEQ ID NO: 54 is a reverse single base extension probe for detecting the RKN resistance locus of SEQ ID NO: 36.

[0067] SEQ ID NO: 55 is a forward single base extension probe for detecting the RKN resistance locus of SEQ ID NO: 9.

[0068] SEQ ID NO: 56 is a reverse single base extension probe for detecting the RKN resistance locus of SEQ ID NO: 9.

[0069] SEQ ID NO: 57 is a hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 33.

[0070] SEQ ID NO: 58 is a second hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 33.

[0071] SEQ ID NO: 59 is a hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 36.

[0072] SEQ ID NO: 60 is a second hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 36.

[0073] SEQ ID NO: 61 is a hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 9.

[0074] SEQ ID NO: 62 is a second hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 9.

[0075] SEQ ID NO: 63 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0076] SEQ ID NO: 64 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0077] SEQ ID NO: 65 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0078] SEQ ID NO: 66 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0079] SEQ ID NO: 67 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0080] SEQ ID NO: 68 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0081] SEQ ID NO: 69 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0082] SEQ ID NO: 70 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0083] SEQ ID NO: 71 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0084] SEQ ID NO: 72 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0085] SEQ ID NO: 73 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0086] SEQ ID NO: 74 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0087] SEQ ID NO: 75 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0088] SEQ ID NO: 76 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0089] SEQ ID NO: 77 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0090] SEQ ID NO: 78 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0091] SEQ ID NO: 79 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0092] SEQ ID NO: 80 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0093] SEQ ID NO: 81 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0094] SEQ ID NO: 82 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0095] SEQ ID NO: 83 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0096] SEQ ID NO: 84 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0097] SEQ ID NO: 85 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0098] SEQ ID NO: 86 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0099] SEQ ID NO: 87 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0100] SEQ ID NO: 88 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0101] SEQ ID NO: 89 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0102] SEQ ID NO: 90 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0103] SEQ ID NO: 91 is a genomic sequence derived from Gossypium hirsutum associated with RKN resistance locus on Chromsome 7.

[0104] SEQ ID NO: 92 is a forward PCR primer for the amplification of SEQ ID NO: 73.

[0105] SEQ ID NO: 93 is a reverse PCR primer for the amplification of SEQ ID NO: 73.

[0106] SEQ ID NO: 94 is a forward PCR primer for the amplification of SEQ ID NO: 74.

[0107] SEQ ID NO: 95 is a reverse PCR primer for the amplification of SEQ ID NO: 74.

[0108] SEQ ID NO: 96 is a forward PCR primer for the amplification of SEQ ID NO: 75.

[0109] SEQ ID NO: 97 is a reverse PCR primer for the amplification of SEQ ID NO: 75.

[0110] SEQ ID NO: 98 is a hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 73.

[0111] SEQ ID NO: 99 is a second hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 73.

[0112] SEQ ID NO: 100 is a hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 74.

[0113] SEQ ID NO: 101 is a second hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 74.

[0114] SEQ ID NO: 102 is a hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 75.

[0115] SEQ ID NO: 103 is a second hybridization probe for detecting the RKN resistance locus of SEQ ID NO: 75.

DETAILED DESCRIPTION OF THE INVENTION

[0116] The definitions and methods provided define the present invention and guide those of ordinary skill in the art in the practice of the present invention. Unless otherwise noted, terms are to be understood according to conventional usage by those of ordinary skill in the relevant art. Definitions of common terms in molecular biology may also be found in Alberts et al., Molecular Biology of The Cell, 5.sup.th Edition, Garland Science Publishing, Inc.: New York, 2007; Rieger et al., Glossary of Genetics: Classical and Molecular, 5th edition, Springer-Verlag: New York, 1991; King et al, A Dictionary of Genetics, 6th ed, Oxford University Press: New York, 2002; and Lewin, Genes IX, Oxford University Press: New York, 2007. The nomenclature for DNA bases as set forth at 37 CFR .sctn.1.822 is used.

[0117] An "allele" refers to an alternative sequence at a particular locus; the length of an allele can be as small as 1 nucleotide base, but is typically larger.

[0118] A "locus" is a position on a genomic sequence that is usually found by a point of reference; e.g., a DNA sequence that is a gene, or part of a gene or intergenic region. The loci of this invention comprise one or more polymorphisms in a population; i.e., alternative alleles are present in some individuals.

[0119] As used herein, "polymorphism" means the presence of two or more variations of a nucleic acid sequence or nucleic acid feature at one or more loci in a population of one or more individuals. The variation may comprise but is not limited to one or more base changes, the insertion of one or more nucleotides or the deletion of one or more nucleotides. A polymorphism may arise from random processes in nucleic acid replication, through mutagenesis, as a result of mobile genomic elements, from copy number variation and during the process of meiosis, such as unequal crossing over, genome duplication and chromosome breaks and fusions. The variation can be commonly found or may exist at low frequency within a population, the former having greater utility in general plant breeding and the latter may be associated with rare but important phenotypic variation. Useful polymorphisms may include single nucleotide polymorphisms (SNPs), insertions or deletions in DNA sequence (Indels), simple sequence repeats of DNA sequence (SSRs), a restriction fragment length polymorphism, and a tag SNP. A genetic marker, a gene, a DNA-derived sequence, a haplotype, a RNA-derived sequence, a promoter, a 5' untranslated region of a gene, a 3' untranslated region of a gene, microRNA, siRNA, a QTL, a satellite marker, a transgene, mRNA, ds mRNA, a transcriptional profile, and a methylation pattern may also comprise polymorphisms. In addition, the presence, absence, or variation in copy number of the preceding may comprise polymorphisms.

[0120] As used herein, "marker" means a detectable characteristic that can be used to discriminate between organisms. Examples of such characteristics may include genetic markers, protein composition, protein levels, oil composition, oil levels, carbohydrate composition, carbohydrate levels, fatty acid composition, fatty acid levels, amino acid composition, amino acid levels, biopolymers, pharmaceuticals, starch composition, starch levels, fermentable starch, fermentation yield, fermentation efficiency, energy yield, secondary compounds, metabolites, morphological characteristics, and agronomic characteristics. As used herein, "genetic marker" means polymorphic nucleic acid sequence or nucleic acid feature. A genetic marker may be represented by one or more particular variant sequences, or by a consensus sequence. In another sense, a "genetic marker" is an isolated variant or consensus of such a sequence.

[0121] As used herein, "marker assay" means a method for detecting a polymorphism at a particular locus using a particular method, e.g. measurement of at least one phenotype (such as seed color, flower color, or other visually detectable trait), restriction fragment length polymorphism (RFLP), single base extension, electrophoresis, sequence alignment, allelic specific oligonucleotide hybridization (ASO), random amplified polymorphic DNA (RAPD), microarray-based technologies, and nucleic acid sequencing technologies, etc.

[0122] As used herein, "typing" refers to any method whereby the specific allelic form of a given cotton genomic polymorphism is determined. For example, a single nucleotide polymorphism (SNP) is typed by determining which nucleotide is present (i.e. an A, G, T, or C). Insertion/deletions (Indels) are determined by determining if the Indel is present. Indels can be typed by a variety of assays including, but not limited to, marker assays.

[0123] As used herein, the phrase "adjacent", when used to describe a nucleic acid molecule that hybridizes to DNA containing a polymorphism, refers to a nucleic acid that hybridizes to DNA sequences that directly abut the polymorphic nucleotide base position. For example, a nucleic acid molecule that can be used in a single base extension assay is "adjacent" to the polymorphism.

[0124] As used herein, "interrogation position" refers to a physical position on a solid support that can be queried to obtain genotyping data for one or more predetermined genomic polymorphisms.

[0125] As used herein, "consensus sequence" refers to a constructed DNA sequence which identifies SNP and Indel polymorphisms in alleles at a locus. Consensus sequence can be based on either strand of DNA at the locus and states the nucleotide base of either one of each SNP in the locus and the nucleotide bases of all Indels in the locus. Thus, although a consensus sequence may not be a copy of an actual DNA sequence, a consensus sequence is useful for precisely designing primers and probes for actual polymorphisms in the locus.

[0126] As used herein, the term "single nucleotide polymorphism," also referred to by the abbreviation "SNP," means a polymorphism at a single site wherein the polymorphism constitutes a single base pair change, an insertion of one or more base pairs, or a deletion of one or more base pairs.

[0127] As used herein, the term "haplotype" means a chromosomal region within a haplotype window defined by at least one polymorphic molecular marker. The unique marker fingerprint combinations in each haplotype window define individual haplotypes for that window. Further, changes in a haplotype, brought about by recombination for example, may result in the modification of a haplotype so that it comprises only a portion of the original (parental) haplotype operably linked to the trait, for example, via physical linkage to a gene, QTL, or transgene. Any such change in a haplotype would be included in our definition of what constitutes a haplotype so long as the functional integrity of that genomic region is unchanged or improved.

[0128] As used herein, the term "haplotype window" means a chromosomal region that is established by statistical analyses known to those of skill in the art and is in linkage disequilibrium. Thus, identity by state between two inbred individuals (or two gametes) at one or more molecular marker loci located within this region is taken as evidence of identity-by-descent of the entire region. Each haplotype window includes at least one polymorphic molecular marker. Haplotype windows can be mapped along each chromosome in the genome. Haplotype windows are not fixed per se and, given the ever-increasing density of molecular markers, this invention anticipates the number and size of haplotype windows to evolve, with the number of windows increasing and their respective sizes decreasing, thus resulting in an ever-increasing degree confidence in ascertaining identity by descent based on the identity by state at the marker loci.

[0129] As used herein, "genotype" means the genetic component of the phenotype, and it can be indirectly characterized using markers or directly characterized by nucleic acid sequencing. Suitable markers include a phenotypic character, a metabolic profile, a genetic marker, or some other type of marker. A genotype may constitute an allele for at least one genetic marker locus or a haplotype for at least one haplotype window. In some embodiments, a genotype may represent a single locus and in others it may represent a genome-wide set of loci. In another embodiment, the genotype can reflect the sequence of a portion of a chromosome, an entire chromosome, a portion of the genome, and the entire genome.

[0130] As used herein, "genotyping" means the process of assaying the alleles present at one or more specific loci in an attempt to measure the genetic variation between members of a species. Current methods of genotyping include PCR, DNA sequencing, and probe hybridization. SNPs are the most common type of genetic variation. A SNP is a single base pair mutation at a specific locus, usually consisting of two alleles

[0131] As used herein, "phenotype" means the detectable characteristics of a cell or organism which can be influenced by genotype.

[0132] As used herein, "linkage" refers to relative frequency at which types of gametes are produced in a cross. For example, if locus A has genes "A" or "a" and locus B has genes "B" or "b" and a cross between parent I with AABB and parent B with aabb will produce four possible gametes where the genes are segregated into AB, Ab, aB and ab. The null expectation is that there will be independent equal segregation into each of the four possible genotypes, i.e. with no linkage 1/4 of the gametes will of each genotype. Segregation of gametes into a genotypes differing from 1/4 are attributed to linkage.

[0133] As used herein, "linkage disequilibrium" is defined in the context of the relative frequency of gamete types in a population of many individuals in a single generation. If the frequency of allele A is p, a is p', B is q and b is q', then the expected frequency (with no linkage disequilibrium) of genotype AB is pq, Ab is pq', aB is p'q and ab is p'q'. Any deviation from the expected frequency is called linkage disequilibrium. Two loci are said to be "genetically linked" when they are in linkage disequilibrium.

[0134] As used herein, "chromosomal position" means a linear designation of sites within a chromosome or genome, based upon the various frequencies of recombination between genetic markers

[0135] As used herein, "quantitative trait locus (QTL)" means a locus that controls to some degree numerically representable traits that are usually continuously distributed.

[0136] As used herein, "resistance allele" means the isolated nucleic acid sequence that includes the polymorphic allele associated with resistance to root knot nematode.

[0137] As used herein, "cotton" means Gossypium hirsutum and includes all plant varieties that can be bred with cotton, including wild cotton species. More specifically, cotton plants from the species Gossypium hirsutum and the subspecies Gossypium hirsutum L. can be genotyped using these compositions and methods. In an additional aspect, the cotton plant is from the group Gossypium arboreum L., otherwise known as tree cotton. In another aspect, the cotton plant is from the group Gossypium barbadense L., otherwise known as American pima or Egyptian cotton. In another aspect, the cotton plant is from the group Gossypium herbaceum L., otherwise known as levant cotton. Gossypium or cotton plants can include hybrids, inbreds, partial inbreds, or members of defined or undefined populations.

[0138] As used herein, the term "comprising" means "including but not limited to".

[0139] As used herein, the term "elite line" means any line that has resulted from breeding and selection for superior agronomic performance. Non-limiting examples of elite lines that are commercially available include DP 555 BG/RR, DP 445 BG/RR, DP 444 BG/RR, DP 454 BG/RR, DP 161 B2RF, DP 141 B2RF, DP 0924 B2RF, DP 0935 B2RF, DP 121 RF, DP 174 RF (Deltapine); ST5599BR, ST5242BR, ST4554B2RF, ST4498B2RF, ST5458B2RF (Stoneville); FM9058F, FM9180B2F, FM1880B2F, FM1740B2F (FiberMax); PHY485WRF, PHY375WRF, PHY745WRF (Acala)(PhytoGen); and MCS0423B2RF, MCS0508B2RF (Cotton States).

[0140] In the present invention, an RKN resistant locus is located on Chromosome A11 (RKN-1). SNP markers used to monitor the introgression of RKN-1 include those selected from the group consisting of SEQ ID NOs: 1-38. Illustrative RKN-1 SNP marker DNA sequence SEQ ID NO: 33 can be amplified using the primers indicated as SEQ ID NOs: 39 through 40 and detected with probes indicated as SEQ ID NOs: 45 through 46. Illustrative RKN-1 SNP marker DNA sequence SEQ ID NO: 36 can be amplified using the primers indicated as SEQ ID NOs: 41 through 42 and detected with probes indicated as SEQ ID NOs: 47 through 48. Illustrative RKN-1 SNP marker DNA sequence SEQ ID NO: 9 can be amplified using the primers indicated as SEQ ID NOs: 43 through 44 and detected with probes indicated as SEQ ID NOs: 49 through 50.

[0141] In the present invention an RKN resistant locus is located on Chromosome A07 (RKN-2). SNP markers used to monitor the introgression of RKN-2 include those selected from the group consisting of SEQ ID NOs: 63-91. Illustrative RKN-2 SNP marker DNA sequence SEQ ID NO: 73 can be amplified using the primers indicated as SEQ ID NOs: 92 through 93 and detected with probes indicated as SEQ ID NOs: 98 through 99. Illustrative RKN-2 SNP marker DNA sequence SEQ ID NO: 74 can be amplified using the primers indicated as SEQ ID NOs: 94 through 95 and detected with probes indicated as SEQ ID NOs: 100 through 101. Illustrative RKN-2 SNP marker DNA sequence SEQ ID NO: 75 can be amplified using the primers indicated as SEQ ID NOs: 96 through 97 and detected with probes indicated as SEQ ID NOs: 102 through 103.

[0142] The present invention also provides a cotton plant comprising a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 1-38, fragments thereof, and complements of both. The present invention also provides a cotton plant comprising a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 39 through 50, fragments thereof, and complements of both.

[0143] The present invention also provides a cotton plant comprising at least one RKN resistance loci. In one aspect, a cotton plant is provided comprising an RKN resistant locus of chromosome A11 (RKN-1). In an additional aspect, a cotton plant is provided comprising an RKN resistant locus of chromosome A07 (RKN-2). In a further aspect, a cotton plant is provided comprising both resistant alleles, RKN-1 and RKN-2, respectively. In all aspects such alleles may be homozygous or heterozygous.

[0144] As used herein, RKN refers to any RKN variant or isolate. A cotton plant of the present invention can be resistant to one or more nematodes capable of causing or inducing galls similar to RKN. In one aspect, the present invention provides plants resistant to RKN as well as methods and compositions for screening cotton plants for resistance or susceptibility to RKN, caused by the genus Meloidogyne. In a preferred aspect, the present invention provides methods and compositions for screening cotton plants for resistance or susceptibility to Meloidogyne incognita.

[0145] In one aspect, the plant is selected from the genus Gossypium. In another aspect, the plant is selected from the species Gossypium hirsutum. In a further aspect, the plant is selected from the subspecies Gossypium hirsutum L. In an additional aspect, the plant is from the group Gossypium arboreum L., otherwise known as tree cotton. In another aspect, the plant is from the group Gossypium barbadense L., otherwise known as American pima or Egyptian cotton. In another aspect, cotton plant is from the group Gossypium herbaceum L., otherwise known as levant cotton. Gossypium or cotton plants can include hybrids, inbreds, partial inbreds, or members of defined or undefined populations.

[0146] Plants of the present invention can be a cotton plant that is very resistant, resistant, substantially resistant, moderately-resistant, comparatively resistant, partially resistant, moderately susceptible, or susceptible.

[0147] In a preferred aspect, the present invention provides a cotton plant to be assayed for resistance or susceptibility to RKN by any method to determine whether a cotton plant is very resistant, resistant, substantially resistant, moderately resistant, comparatively resistant, partially resistant, moderately susceptible, or susceptible.

[0148] A galling index scale is used to rate plants as resistant or susceptible to RKN. Roots of plants are examined for number and size of galls and rated according to a 0 (no galls) to 5 (100% roots with galls) scale. The detailed description of indexing is as follows: 0 (no visible galls, healthy root system); 1 (1-2 galls, healthy root system); 2 (3-12 galls, small size galls more visible); 3 (13-30 galls, large size galls more visible on tap root); 4 (31-60 galls, severe galling with large gall size); 5 (over 60 galls, >75% roots with large galls, root system non-functional). In this aspect, the plants with a rating below 2 were considered as resistant plants.

[0149] In another aspect, the cotton plant can show a comparative resistance compared to a non-resistant control cotton plant. In this aspect, a control cotton plant will preferably be genetically similar except for the RKN resistance allele or alleles in question. Such plants can be grown under similar conditions with equivalent or near equivalent exposure to the pathogen. In this aspect, the resistant plant or plants has less than 25%, 15%, 10%, 5%, 2% or 1% of leaf area infected.

[0150] A disease resistance QTL of the present invention may be introduced into an elite cotton inbred line. An "elite line" is any line that has resulted from breeding and selection for superior agronomic performance.

[0151] An RKN resistance QTL of the present invention may also be introduced into an elite cotton plant comprising one or more transgenes conferring herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma disease resistance, modified oils production, high oil production, high protein production, germination and seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistant, increased digestibility, industrial enzymes, pharmaceutical proteins, peptides and small molecules, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, reduced allergenicity, biopolymers, and biofuels among others. In one aspect, the herbicide tolerance is selected from the group consisting of glyphosate, dicamba, glufosinate, sulfonylurea, bromoxynil and norflurazon herbicides. These traits can be provided by methods of plant biotechnology as transgenes in cotton.

[0152] A disease resistant QTL allele or alleles can be introduced from any plant that contains that allele (donor) to any recipient cotton plant. In one aspect, the recipient cotton plant can contain additional RKN resistant loci. In another aspect, the recipient cotton plant can contain a transgene. In another aspect, while maintaining the introduced QTL, the genetic contribution of the plant providing the disease resistant QTL can be reduced by back-crossing or other suitable approaches. In one aspect, the nuclear genetic material derived from the donor material in the cotton plant can be less than or about 50%, less than or about 25%, less than or about 13%, less than or about 5%, 3%, 2% or 1%, but that genetic material contains the cotton resistant locus or loci of interest.

[0153] It is further understood that a cotton plant of the present invention may exhibit the characteristics of any relative maturity group. In an aspect, the maturity group is selected from the group consisting of early maturing varieties, mid season maturing varieties, and full season varieties.

[0154] An allele of a QTL can, of course, comprise multiple genes or other genetic factors even within a contiguous genomic region or linkage group, such as a haplotype. As used herein, an allele of a disease resistance locus can therefore encompass more than one gene or other genetic factor where each individual gene or genetic component is also capable of exhibiting allelic variation and where each gene or genetic factor is also capable of eliciting a phenotypic effect on the quantitative trait in question. In an aspect of the present invention the allele of a QTL comprises one or more genes or other genetic factors that are also capable of exhibiting allelic variation. The use of the term "an allele of a QTL" is thus not intended to exclude a QTL that comprises more than one gene or other genetic factor. Specifically, an "allele of a QTL" in the present in the invention can denote a haplotype within a haplotype window wherein a phenotype can be disease resistance. A haplotype window is a contiguous genomic region that can be defined, and tracked, with a set of one or more polymorphic markers wherein the polymorphisms indicate identity by descent. A haplotype within that window can be defined by the unique fingerprint of alleles at each marker. As used herein, an allele is one of several alternative forms of a gene occupying a given locus on a chromosome. When all the alleles present at a given locus on a chromosome are the same, that plant is homozygous at that locus. If the alleles present at a given locus on a chromosome differ, that plant is heterozygous at that locus. Plants of the present invention may be homozygous or heterozygous at any particular RKN locus or for a particular polymorphic marker.

[0155] The present invention also provides for parts of the plants of the present invention. Plant parts, without limitation, include seed, endosperm, ovule and pollen. In a particularly preferred aspect of the present invention, the plant part is a seed.

[0156] The present invention also provides a container of cotton in which greater than 50%, 60%, 70%, 80%, 90%, 95%, or 99% of the seeds comprising RKN resistance loci.

[0157] The container of cotton seeds can contain any number, weight, or volume of seeds. For example, a container can contain at lest, or greater than, about 10, 25, 50, 100, 200, 300, 400, 500, 600, 700, 80, 90, 1000, 1500, 2000, 2500, 3000, 3500, 4000 or more seeds. In another aspect, a container can contain about, or greater than about, 1 gram, 5 grams, 10 grams, 15 grams, 20 grams, 25 grams, 50 grams, 100 grams, 250 grams, 500 grams, or 1000 grams of seeds. Alternatively, the container can contain at least, or greater than, about 0 ounces, 1 ounce, 5 ounces, 10 ounces, 1 pound, 2 pounds, 3 pounds, 4 pounds, 5 pounds, 10 pounds, 15 pounds, 20 pounds, 25 pounds, or 50 pounds or more seeds.

[0158] Containers of cotton seeds can be any container available in the art. For example, a container can be a box, a bag, a can, a packet, a pouch, a tape roll, a pail, or a tube.

[0159] In another aspect, the seeds contained in the containers of cotton seeds can be treated or untreated cotton seeds. In one aspect, the seeds can be treated to improve germination, for example, by priming the seeds, or by disinfection to protect against seed-born pathogens. In another aspect, seeds can be coated with any available coating to improve, for example, plantability, seed emergence, and protection against seed-born pathogens. Seed coating can be any form of seed coating including, but not limited to, pelleting, film coating, and encrustments.

[0160] Various patent and non-patent publications are cited herein, the disclosures of each of which are incorporated herein by reference in their entireties.

[0161] As various modifications could be made in the constructions and methods herein described and illustrated without departing from the scope of the invention, it is intended that all matter contained in the foregoing description or shown in the accompanying drawings shall be interpreted as illustrative rather than limiting. The breadth and scope of the present invention should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the following claims appended hereto and their equivalents.

EXAMPLES

[0162] The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims.

Example 1

Phenotypic Rating Scale

[0163] To asses the reaction of plants to RKN, cotton plants were grown in growth chambers and artificially inoculated with 2,500 nematode eggs approximately 7 days after emergence. Plant roots were examined for galling 45-50 days after inoculation. A galling index of 0 (no galls) to 5 (100% roots with galls) was used to rate the plants. Table 1 provides the phenotypic rating scale used to identify RKN reaction in cotton plants.

TABLE-US-00001 TABLE 1 Phenotypic Rating Scale Used for RKN Reaction Rating Phenotypic Description 0 No visible galls; healthy root system 1 1-2 galls; healthy root system 2 3-12 galls; small gall size 3 13-30 galls; large size galls more visible on tap root 4 31-60 galls; severe galling with large gall size 5 >60 galls; severe galling with >75% roots with large galls; root system non-functional

Example 2

Identification of SNP Markers Associated with RKN Resistance

[0164] A mapping population was developed from the cross of the RKN resistant parent M240 with RKN susceptible parent 33B. A total of 250 near-isogenic lines (NILs) were developed for the mapping population. Ten replicates of each line were evaluated for reaction to RKN as described in Example 1.

[0165] Eleven SNP markers located on Chromosome A11 were used to screen the NIL mapping population. Of these, SNP marker NG0204877 was found to be highly associated with RKN resistance. Of 248 lines screened, the mean galling index of lines with the TT genotype was significantly lower than those with the AA genotype. Table 2 provides the mean galling index for lines with the genotype AA, AT, and TT. A t-test analysis was performed and the p-value for no mean difference between AA and TT genotypes on the galling index was 3.84.times.10.sup.-82. The marker NG0204877 is on Chromosome A11 at position 181.1.

TABLE-US-00002 TABLE 2 Marker NG0204877 (SEQ ID NO. 31) is Associated with RKN Resistance in Cotton. Genotype Mean Galling Index Number of Lines AA 4.5 78 AT 3.0 37 TT 1.1 133

Example 3

Use of SNP markers for Monitoring RKN Resistance

[0166] Additional SNP markers are located on Chromosome A11. Table 3 provides the marker names, chromosome position, and the position of the polymorphism in the marker, and alleles.

[0167] In a breeding program, one or more markers provided in Table 3 can be used to select for and to introgress RKN resistance into a cotton plant. A cotton breeder can select one or more markers which are polymorphic between parents in a breeding cross to select progeny with the genotype of the RKN resistant parent.

TABLE-US-00003 TABLE 3 SNP Markers on Chromosome A11 for Detecting RKN Resistance. SEQ ID Chromosome SNP Marker NO: Position Position.sup.1 Allele 1 Allele 2 NG0204212 1 142.5 303 A C NG0204865 2 143 367 A G NG0203354 3 145 253 A G NG0207959 4 145.9 333 A T NG0204475 5 147 382 A G NG0210892 6 150.7 323 C T NG0206447 7 150.7 447 A G NG0209829 8 150.7 149 A C NG0210628 9 150.7 171 A G NG0203550 10 152.2 253 G T NG0204129 11 158.4 325 C G NG0209314 12 159.2 272 A T NG0209936 13 159.8 62 A G NG0207838 14 160.1 385 A G NG0209012 15 160.1 59 A T NG0209914 16 160.1 520 A T NG0210596 17 160.1 107 A C NG0207455 18 160.8 220 G * NG0203802 19 163.6 122 A G NG0207423 20 163.9 449 C T NG0206483 21 165.5 209 A G NG0209848 22 165.7 310 C G NG0204309 23 166.4 125 A C NG0206578 24 169.8 254 A T NG0211496 25 171.2 188 A G NG0206531 26 171.3 354 C T NG0204091 27 172.2 143 C T NG0210467 28 174.4 381 A G NG0209154 29 178.5 221 C T NG0210828 30 180.1 356 A G NG0208423 31 180.1 166 A T NG0208500 32 180.1 219 C T NG0204877 33 181.1 409 A T NG0210025 34 181.2 255 A G NG0210010 35 182.2 192 G T NG0209086 36 182.4 525 C G NG0206691 37 183.5 218 A T NG0208147 38 183.5 322 A G "*" Indicates a single nucleotide Deletion .sup.1SNP Position: refers to the position of the SNP polymorphism in the indicated SEQ ID NO.

TABLE-US-00004 TABLE 3A SNP Markers on Chromosome A07 for Detecting RKN Resistance. SEQ ID Chromosome SNP Marker NO: Position Position.sup.1 Allele 1 Allele 2 NG0203799 63 32.2 268 T A NG0210921 64 33.1 190 G A NG0210441 65 34.7 356 G A NG0210456 66 35.2 139 T G NG0204031 67 40.3 50 G A NG0207405 68 41.1 143 T C NG0210569 69 45.3 443 T G NG0206553 70 45.7 194 G C NG0210273 71 46.0 359 T C NG0208436 72 46.6 85 G C NG0206957 73 47.5 384 T G NG0207837 74 47.5 142 G A NG0207518 75 47.8 506 T C NG0211237 76 47.8 439 T C NG0210755 77 48.1 173 T A NG0208863 78 48.5 348 T A NG0203306 79 49.0 376 G A NG0210314 80 49.5 489 G A NG0208128 81 50.3 180 G A NG0209149 82 50.8 108 T A NG0209751 83 52.7 64 G A NG0204353 84 53.2 338 T C NG0209136 85 58.8 563 C A NG0207947 86 62.2 554 T C NG0204860 87 64.6 540 C A NG0207151 88 64.6 148 G A NG0208606 89 64.6 150 G A NG0206706 90 68.6 487 G A NG0207731 91 71.6 169 T C .sup.1SNP Position: refers to the position of the SNP polymorphism in the indicated SEQ ID NO.

Example 4

Exemplary Marker Assays for Detecting RKN Resistance

[0168] In one embodiment, the detection of polymorphic sites in a sample of DNA, RNA, or cDNA may be facilitated through the use of nucleic acid amplification methods. Such methods specifically increase the concentration of polynucleotides that span the polymorphic site, or include that site and sequences located either distal or proximal to it. Such amplified molecules can be readily detected by gel electrophoresis, fluorescence detection methods, or other means. Exemplary primers and probes for amplifying and detecting genomic regions associated with cotton RKN resistance are given in Table 4.

TABLE-US-00005 TABLE 4 Exemplary Assays for Detecting RKN Resistance SEQ ID SEQ ID Marker SNP Forward Reverse SEQ ID SEQ ID Marker SEQ ID Position Primer Primer Probe 1 Probe 2 NG0204877 33 409 39 40 45 46 NG0208147 36 322 41 42 47 48 NG0204129 9 325 43 44 49 50

Example 5

Oligonucleotide Probes Useful for Detecting Cotton Plants with RKN Resistance Loci by Single Base Extension Methods

[0169] Oligonucleotides can also be used to detect or type the polymorphisms associated with RKN resistance disclosed herein by single base extension (SBE)-based SNP detection methods. Exemplary oligonucleotides for use in SBE-based SNP detection are provided in Table 5. SBE methods are based on extension of a nucleotide primer that is hybridized to sequences adjacent to a polymorphism to incorporate a detectable nucleotide residue upon extension of the primer. It is also anticipated that the SBE method can use three synthetic oligonucleotides. Two of the oligonucleotides serve as PCR primers and are complementary to the sequence of the locus which flanks a region containing the polymorphism to be assayed. Exemplary PCR primers that can be used to type polymorphisms disclosed in this invention are provided in Table 4 in the columns labeled "Forward Primer SEQ ID" and "Reverse Primer SEQ ID". Following amplification of the region containing the polymorphism, the PCR product is hybridized with an extension primer which anneals to the amplified DNA adjacent to the polymorphism. DNA polymerase and two differentially labeled dideoxynucleoside triphosphates are then provided. If the polymorphism is present on the template, one of the labeled dideoxynucleoside triphosphates can be added to the primer in a single base chain extension. The allele present is then inferred by determining which of the two differential labels was added to the extension primer. Homozygous samples will result in only one of the two labeled bases being incorporated and thus only one of the two labels will be detected. Heterozygous samples have both alleles present, and will thus direct incorporation of both labels (into different molecules of the extension primer) and thus both labels will be detected. Exemplary forward and reverse SBE probes are provided in Table 5.

TABLE-US-00006 TABLE 5 Probes (Extension Primers) for Single Base Extension (SBE) Assays Marker SEQID SNP ProbeSEQ Marker NO. Position Probe (SBE) ID NO. NG0204877 33 409 TGATAACGGGATTTATT 51 NG0204877 33 409 GATCAATCCGATGAACA 52 NG0208147 36 322 ATTAAATGAAAAACGGG 53 NG0208147 36 322 GAGGTTTTATTACAACA 54 NG0204129 9 325 TACTGTCTCCTTGTAGA 55 NG0204129 9 325 TAGAGGCAATTAAAGAA 56

Example 6

Oligonucleotide Hybridization Probes Useful for Detecting Cotton Plants with Rkn Resistance Loci

[0170] Oligonucleotides can also be used to detect or type the polymorphisms associated with RKN resistance disclosed herein by hybridization-based SNP detection methods. Oligonucleotides capable of hybridizing to isolated nucleic acid sequences which include the polymorphism are provided. It is within the skill of the art to design assays with experimentally determined stringency to discriminate between the allelic states of the polymorphisms presented herein. Exemplary assays include Southern blots, Northern blots, microarrays, in situ hybridization, and other methods of polymorphism detection based on hybridization. Exemplary oligonucleotides for use in hybridization-based SNP detection are provided in Table 6. These oligonucleotides can be detectably labeled with radioactive labels, fluorophores, or other chemiluminescent means to facilitate detection of hybridization to samples of genomic or amplified nucleic acids derived from one or more cotton plants using methods known in the art.

TABLE-US-00007 TABLE 6 Oligonucleotide hybridization probes Marker Probe SEQ SNP Hybridization SEQ ID Marker ID NO. Position Probe NO. NG0204877 33 409 TTTATTAGTGTTCATC 57 NG0204877 33 409 TTTATTTGTGTTCATC 58 NG0208147 36 322 AACGGGGATGTTGTAA 59 NG0208147 36 322 AACGGGAATGTTGTAA 60 NG0204129 9 325 TGTAGAGCTTCTTTAA 61 NG0204129 9 325 TGTAGACCTTCTTTAA 62

Example 7

Prophetic Example of Introgression of RKN Resistance Using SNP Markers

[0171] A plant breeder can use SNP markers to facilitate the introgression of the RKN resistance locus on Chromosome A11 and to select for lines carrying the favorable alleles for one or more of said SNP markers. In this example, the cotton line M240 is used as a donor of RKN resistance. The SNP marker NG0204877 (SEQ ID NO: 31) is used to monitor the introgression of the RKN resistance locus. A plant breeder can select the favorable genotype as provided in Table 2 to select plants for RKN resistance arising from the donor while selecting for the recipient genome in adjacent chromosome regions. In practice, this reduces the amount of linkage drag from the donor genome that maybe associated with undesirable agronomic or fiber quality properties.

[0172] The introgression of one or more resistance loci is achieved via repeated backcrossing to a recurrent parent accompanied by selection to retain one or more RKN resistance loci from the donor parent. This backcrossing procedure is implemented at any stage in line development and occurs in conjunction with breeding for superior agronomic characteristics or one or more traits of interest, including transgenic and nontransgenic traits.

[0173] Alternatively, a forward breeding approach is employed wherein one or more RKN resistance loci can be monitored for successful introgression following a cross with a susceptible parent with subsequent generations genotyped for one or more RKN resistance loci and for one or more additional traits of interest, including transgenic and nontransgenic traits.

Example 8

Introgression of RKN-1 and RKN-2 Using SNP markers to Produce a Cotton Plant Resistant to Root Knot Nematode

[0174] A plant breeder can use SNP markers to facilitate the introgression of the RKN-1 resistant locus on Chromosome A07 and the RKN-2 resistant locus on Chromosome A11 to select for lines carrying the favorable alleles for one or more of said SNP markers. In this example, the cotton line M-315 is used as a donor of RKN resistance. The SNP marker NG0204877 (SEQ ID NO: 31) was used to monitor the introgression of the RKN-1 resistant locus and the SNP markers NG0206957 (SEQ ID NO: 73), NG0207837 (SEQ ID NO: 74), and NG0207518 (SEQ ID NO: 75) were used to monitor the introgression of the RKN-2 resistance locus. A plant breeder can select the favorable polymorphic genotype as provided in to select plants for RKN resistance arising from the donor while selecting for the recipient genome in adjacent chromosome regions. In practice, this reduces the amount of linkage drag from the donor genome that maybe associated with undesirable agronomic or fiber quality properties.

[0175] The introgression of one or more resistance loci is achieved via repeated backcrossing to a recurrent parent accompanied by selection to retain one or more RKN resistance loci from the donor parent. This backcrossing procedure is implemented at any stage in line development and occurs in conjunction with breeding for superior agronomic characteristics or one or more traits of interest, including transgenic and nontransgenic traits.

[0176] Alternatively, a forward breeding approach is employed wherein one or more RKN resistance loci can be monitored for successful introgression following a cross with a susceptible parent with subsequent generations genotyped for one or more RKN resistance loci and for one or more additional traits of interest, including transgenic and nontransgenic traits.

[0177] In view of the foregoing, it will be seen that the several advantages of the invention are achieved and attained. The embodiments were chosen and described in order to best explain the principles of the invention and its practical application to thereby enable others skilled in the art to best utilize the invention in various embodiments and with various modifications as are suited to the particular use contemplated.

[0178] Various patent and non-patent publications are cited herein, the disclosures of each of which are, to the extent necessary, incorporated herein by reference in their entireties. As various modifications could be made in the constructions and methods herein described and illustrated without departing from the scope of the invention, it is intended that all matter contained in the foregoing description or shown in the accompanying drawings shall be interpreted as illustrative rather than limiting. The breadth and scope of the present invention should not be limited by any of the above-described exemplary embodiments, but should be defined only in accordance with the following claims appended hereto and their equivalents.

Sequence CWU 1

1

1031643DNAGossypium hirsutumn = a, t, c, or g(1)..(643)n = a, t, c, or g 1gttncncctt cctacctcct gttacaattt ttggtacttt ctcttcaatt cccttgagtt 60ctgaaatata gttattgatg aaacttgcta tctctttccc ggtcctgttg gccttcttat 120gaactctctt gtttctttct tcccagattg cccaaagagc gcagcaaaag atcctacacc 180gcgaagaagt gttctgttca aaaacccagg tgagccactg ttgaaactcc atctgagata 240cgtgtaataa ctccaaaaat gataattctt tccatactga tattgagaca gggcattcac 300ggaatagatg attcgtggtt tctgctgctc ttccacaccc agaacagagt gcattgtgta 360atagcctttt atgtagcaag gtagtcattg taggtagata attccatgat attctccaaa 420ctataatttt tatcttagaa gatagattaa gtagccaaag atttttgtaa aaattcctat 480agtcggtctg taaagcataa gctttaggat caatttcatt gccctgtaat agtttatagg 540cactatgcac cgtgaattct cctgaaggca ctctgctcca ggccaaaaaa tcatcgtgga 600cctcttttgc taacggaata tagagaatct tctcagttac atc 6432599DNAGossypium hirsutum 2tcggacaaag ataattagat gcagaaaaaa caattcacct tgaagagaac atgaaagaaa 60caagtcttgg ggttggcata attttcaaca ggaggctgca caagaacaaa aacatttaaa 120atcaatatat aagcaatcaa accagtaccc caagtacaaa ataaacagct ggatctgaaa 180ttagtaacat ttctatctaa ttttcatgtt ccgaacaagt atacaatggc catataagca 240aatgggaact ctattttgtt caatttcatc atctttcttc aaccaaaaca ttgaggaaaa 300cataaagttg aaatctttac cggctaaagt tggatcttgg gatctaattt gaataaccca 360gagttgacta ttgaaattgt gtttagaaat ggttagtttt catctgtttt atcaaaaacc 420aatcaaaagg gtaccgttca aaatcgaaat ctctcacaaa aaactcagat ctaccagtca 480aacagtccaa tacgtagaac aaatagttac aaatttgata aaccagcaaa aggaaactga 540agggaaggag aaacagagag agggatcaac tcacctgact aaaatccatt acgggaaga 5993960DNAGossypium hirsutum 3tgcagagatc ttcttcagcc attcaatcca gttccaaagt ttatcatcat aaaatctgtg 60gttttcttaa cctattggca ggtaaaatct tgtgtgcctg ttatttcctc tcatactcat 120gcatgcaaaa agaagacaaa tcctttgttt ttggctttta gatactttta tctttccttc 180tatttcattg catcaccctt ttgttgcttt ttggtgataa tcatcattta gaaatcttgt 240tagtatcttt atagcaaacc ttggggatgg tgaattctgg ttactggaat gcaatctttc 300ctaacctgtt tgctgtccac attgatatca tcttcatgtt ttgttttata ggggaggctg 360tttttctata ttttgctttc cctttttata ctgatgtcta atcataagac agcagttcga 420agttccggaa gtgctgtgac ggcattgtac aatgtattaa accctgtaaa atagaatgca 480tgcctatatt gatggttatc cataacatct tgtgttgtga tggcattgta ctgtttgtaa 540acctcatcta gttgcatagg tgctaaataa actcaaaaca tccttttctt ttatttcctt 600ttgcagggtg ttatgttttt tcttgctgca aaatctggat ttattaagga tgctgatgca 660gcagctcaat ttcaaaactt cattatatgt gttgagatgc ttctagctgc tctaggtcat 720ctttatgcat ttccatataa ggagtatgct ggtgcaaata ttggtatgtc tcgtggtttt 780acacgaagcc ttgcacatgc cttgatgttg aatgacttct atcatgatac tgttcaccag 840gtgaccctta cttctgttgc catttcccaa aggttcctct actggattct tcttcttttg 900tttagggtta tttatggttt ttatcatatt cgcagtttgc acctacgtat catgattatg 9604654DNAGossypium hirsutum 4aatctgaaat atgtgacatg cccagatgag atagtatatc attcatactc taccaagtca 60tggttccctt aaaaaataat ataggaaacc atttttgtac ctgatcagat catgagtccc 120accagatata gcatttgaga tggcttgtgt agcttgtatc caaatatcat atttatcatc 180attttgaagc aaatgaagta gaggagcaat aatattagct tcaattatag cctgtaaaat 240tcataccatt acccatcgtt tcattgcaca agtcaacgca gataaaacct taggttcaaa 300attgatactt gtacctttat ttcctgttgt gatacttgag attgtccaac aagcaaactt 360attgattctc ttttcataat tatttttcaa aggtttaaaa ggcatgggaa tgcctgatga 420ttaatgatac actttgtagc aacaagattt gcccataaat aagaaaataa atcatcttta 480acaactaaac ctaaaaaaat ctttagtcta attaagaggg ggtataaatg tgattttagt 540gagaaaatta gttattaaaa gaaaatgata tgataaatgg aaagagatac atattctagt 600aagatcattt aaaaggaaaa gcaaattaaa taaagtgcct gatacctgaa tttg 6545503DNAGossypium hirsutum 5cacaagggca ggctcactag gaatactaca gtactgaagt attctctcaa cagatataat 60tttattctcc atactgcaaa tattccatac cacccaagcc agcaacatat ttagattgag 120tccatacgtc acagctaaac cggcaatagc taaacaaaag aaaaatgcat aaagtcattc 180tcctagaaca tttgctatct agtagtcaat aaagctgcca atatgaatct gcatttactt 240accaggatcg ataattccct caggtataga gattaaaaag aataaagaga aggcaaacat 300aacagaagac agtaagtcca ggcggaagca cagccattcc attgcaccgc aaacatggaa 360ttttggacga gaatacgagt cagtcagcac catattggtg tcttggaacc ttttctcttg 420atcaaagctc cttatagttg ttgctcctaa aattgtttca gcaaaattct ggattactgg 480agctttgcat actccaacca acc 5036591DNAGossypium hirsutum 6gaatgcctca cttgcctaat ttattgcttt gactctttgt tgtatgctat ttgactttta 60accaccatcg aatataaata tataattatt acaaatagtt tagaagatta aataattata 120tttatattca acccttttga atattcctcg gaaagttctt tgaacaaagc acaaaccatg 180aaggttacct gtgctcgtca agaagaaacc acgaaatttc actgtttcac accaaagctc 240caccaccaag tttcccaatt ctaaccaatt ttgattaaac tgagattttc ccaatgcaag 300tgacccaatt ctaaatggtc tttttatgtt ttcaagccaa gctccgagca gcaaggttgg 360tggtccaagt tcagacccta accaaaacag ctacccgagg ggctctatcg atcggaatgg 420acacactcat tcgtagacgc agaaggtctc gttgtcatct tcgctttcct attctacttc 480tgctactttc attgatcgga agggttatcg gagtcgtact tggattgttg atcaccagaa 540tgttgatgag aaggcaataa tctacatacc ataggttgga aattgtatta g 5917501DNAGossypium hirsutum 7agatgctatt tggacatatg gtgactttac taaaagatta tcatcaggtc agcttcttct 60tcttcttcat ttatcttaaa tgtggcaaat ggtttatatg ctgaataatc gagcatgttt 120ctaataattg taactgacca ggaattccct aaaataaaca aggtgattac atgtgtccct 180ggaagtgaga tcccggaatg gtttgatttc aaaagctcag gatcttccat aaacatccaa 240ttgccttcaa agtggtacta caatagcagc aaaaactttc caactttcgt tgtttccact 300gttgtttctt tccaagacta ttctggcgac agagaaattc tcattagatg taaatgtcgt 360ctaaaatccc gtaatggcga ctgtcatgac cttagttgtt ctttcttaac ttggacaaaa 420cgaattcctg gaagcgaatt gactggatcg aatcacttgt tcctcttata taaaacttgt 480ttctgtgatg aggatgatga g 5018673DNAGossypium hirsutum 8catcttctgc aatgatgata gtcaactttg gtactcgatt caggtgctac aaaccacatc 60accaatgatg tctcgacact cagtcatctt actgaataaa caggtatgag ccaacttttg 120atcggcaatg gtgctcctgt tcctattgat catgtaggga gatcctctat tggtacttgt 180agtaggatat tacatcttaa acatgttttt acatgttccc tatgtctgta aaaatttgat 240ttctgtagca cagtttactt gttttttgaa tttcatccct ctcgttgttt tgtgaaggac 300atcaagacag ggaaggtttt gctagtaggt cacattcata aagggttata tcgatttaac 360acatcaccac aacaaagaag ttttgctggc tttgatgagg gctttcaata tgcacatact 420actaagattc aagcttgaga caccttctgt tctgagttcg acttatggca caaaaggctt 480ggccatccct gcacaaaaat tctttttcaa gttcttcgaa gttgtaatat ttcactgaat 540aaattcacac cacctagagt gtgtgttcct cgtcagctag gaaagtctca taagctggtg 600tttgataatt ctaagactgt atatacttcc ccttttcaac ttgttgtgtc tgatttgtgg 660ggacaatcac cta 6739748DNAGossypium hirsutumn = a, t, c, or g(1)..(748)n = a, t, c, or g 9aaagaggaga aaagagcctc ggccttctcc ttgcgtcgat tctaacgatg ggaaagaata 60tcccggcgac gcaacccccg ggtttgggta agttttcctt ctttctcctt ttatttattt 120tgttgaaaaa taaatttaaa agagcagaaa aataaataaa aaagaaaacc gaaagaaaaa 180agagaaccca aaaatgagat ttaaaatcaa ctttttattt ttttgctttt tacttctgaa 240aaaatttgcc tgtaatacaa tttttttttg tataccgaaa tcccctctta cattcggttc 300ttccctcggc ttatatagcc gaatacatag aaaatatttt ctgctctctt ctattgtttg 360ttgtttttcg ctctctttcc ttctgctttg tgtgcttctc ctttgttttg caggtaacgt 420cagagtaggt gagcagaggc gatgggacgg gcgtctgttc gggcgcaaaa tgcgctgaca 480ccacgtgggg gagggaggta cagcgcctag cataggaacc ctagggtttt ttcttttttt 540ctgataaatt tgggctttgg gttaggttta gttgggcttt ggattgggtc atagttcggg 600ctttgtattt gggctgtgaa ttgtaaaagg tatgggttga gcctgttttg tttgttcatt 660gggcccggtc taatttgggc atttacaata tgtatgatgc aaatttcctg annnnnatnn 720nnntagannn tagtatgcaa nnnnngct 74810615DNAGossypium hirsutum 10tttgaaaaat tttatgcaac tgctccacct acaaaataga aagcagatct caatcatttc 60atttttgcag caaatatgta ttttaagggt cttaaagcca tgttatatgc atggacatgt 120cattactcag tttatttgca caaatatgta tatatgtttt ggcttagaac tctaaaattc 180tacatgcttt gtaggaaatc tttcatttaa atgataaaaa cacacctcag ttcttcctgg 240cataataggc tttccagcat ataactcagc aagtatgcaa cctgtactcc atagatccac 300agcggtacca tagtaagtgg ctccaagtaa aagttctggt ggtctatacc aaagggttac 360gacacggctt gtcatgggtt gactttgatg gggatcataa aagctagcca gaccaaagtc 420tgcaatcttc aagatgccat tattgtcgat tagaaggttt gaacccttta tgtcacgatg 480taggacacca cggctgtgac aatgatcaag accacacaaa agttgttgta tgtaacactt 540cacctgcaca atagatcaat aaattaaacg tcaggataac ctttcaatgg aaagtgcaaa 600attctgtatt tgcag 61511635DNAGossypium hirsutum 11gttactagct gtttagctaa tggattgctt gaagccgttg tgaagaaaag gtaactgagg 60aggctcaaag agcaatggtt atggcttttt cttccccctg cattggactt agtactatgc 120atatgcttta agcatgagtt tagaaaaggt gaatatccaa cttgatattt aatgaatctg 180ctacttttgg aatcaatgaa atagatttgt cttatttttg aaatcaaata gttggtatta 240tatttttttt tgttgaaata taaaacaaaa aattacataa acttattcat aaacagaatg 300cctctagtac tgtctccttg tagagcttct ttaattgcct ctagaaattc ttcgaacata 360tgcaaatagt cgtcatcatc tgttcgagct actgccttat taaattctct agggacatat 420ttcaagaact actttttttc atttgataaa atctattaaa ttcgtctaac cagagtggaa 480tttaatcttt caattttact gtcttcaata atttttacaa cctcaaaatt atttttttgg 540ataacgaact catcataatc ttgtttatta atcaattaaa ccatccaaaa tgtcccaaaa 600ttcctcaagg aatacaggac acttcccaaa aaaaa 63512598DNAGossypium hirsutum 12tgggaacaat cgtaagagga tggcatcctt agtaacgcca ttgatcttga aagtgtcgca 60aatctctaga aagttatcca aatgggcatt caaatcttta tcttgcaacc catcaaactt 120aacatattat tgtatcattt gaattgtgtt cagatttagc taaaaattgt ttacagcaac 180agtcgatctg acgatactcg attcagcccc aattcaagtg tgcttagcat aatcatacat 240agtacgaaga gcaggagttg caagaagcag ttgattattt tgattaccac tcatctccat 300ggtaatatca ttttttttct tgatcatcta ctatatttgt tgattttgcc ttacttctct 360aaccttttta tgatttttgc gagcaatctt ttcaacttca ctataaaaaa ttaatgattc 420caacgagttt cctctagtca taaaccaaaa gaacctgtca gaatcaaacg aatgaacaaa 480tttagaatgt aaaaattaaa ttaaaaacaa aaatattaaa attaaaaaat agctaaatta 540atagaaataa aattttccta atattttagt ccctgtcaat agtggcaaac acttaatg 59813585DNAGossypium hirsutumn = a, t, c, or g(1)..(585)n = a, t, c, or g 13gcgccgatct acgtctatca gcagagacga acagccccgg gcttcaaagg atgaccattt 60cagtcgtggg atcccttcta aaccccgatt tcgacgaaat gaaggggata cgacggccaa 120ctcgcaaggt aaacctctct tttgctttct ttttttgttt ttgagataga tttcaaaata 180aaaagaaaat agaggcgtaa aaatgaaaac agggaacaac ctttgcagaa tattcaactt 240ctttgtattt gattcctctt ttttttgtgt aatctgttcg tagtcgtatt acaatcgaaa 300atcaaaggct tnatagccga ataactaaag aaaacaacaa tttttgtcct ctgcttttgt 360attggcttgt tgctgctttc gtttgttttc ttttgcaggt acggagcacg gggctgtgcg 420ttggcgctcg ggtacgggtc taggctaggg tacggaggtg gtacggtcgt tgcgaggctg 480ttgcggcgca agagggtgac ctagggttcc cgaaagtgtt gaagtttttg ggcttnttgg 540gctattcggg attgggctta ttgggctagg atattaagtt tggtt 58514530DNAGossypium hirsutum 14gatagcttgg aaggatctct ctcttatatg taagagcaga gaactttgga ttatataaat 60attaaaatag taaaaattta tattatattt taattattac tttttcataa tcatgctaat 120ctataattct taagtgcata aaacacaaac cgtccgacac attaattaaa gtaggctcca 180ctttgtcaac tctcaccttc ttgattcctt ttgggaaaag catcactgct catctatgac 240ctcatgcgtt attattggaa aaagaaaaag tgggaaatgc atagagaaat tgcttagaaa 300cctttgctgt tccctggaaa tttgagctgt ttttctttct tgttgcttat atacttattg 360tttctcgttt ctttctgggg tattaggtgg tttgttttct ggttttgaac accaaactga 420gatacctttt ttcttgtcgt acgttgtcat gttgtcgtta ccttcaactt cctcatctat 480ttctaaaatg aaatattgta gagctgttat ccaccgtaga cattctagac 53015699DNAGossypium hirsutumn = a, t, c, or g(1)..(699)n = a, t, c, or g 15ctaatcactt acctacctcc attaattaca ttgaaacttg ataacctata ctagcacaat 60ttgtaaagct gatttatcag ctcaaatgtc aacaaaatta catcaagtac attaccaacc 120tagttctaaa caaaccaagt tacaaaatgt taatttaaag taacaaaatt agcagcattg 180tcttcaactg cgacctgcat ggctcgggca gcttgttctt cttcttggct gcttcatgtg 240ctgcatgaag gccaacttca acactcctct ttggcctgca tactgcatac ttccagctta 300gctcgcaaat ccataaacct tgacacacaa agaggctttg tcaagatgta agcaagttga 360tcctctaaac tgcaatgaat cagtttcact tcttgtgctt gtttcatttc tctaacaaaa 420tgaagcttaa tgttgaagtg atttgtcctt ccatggaata ctggattctt tgcaattgca 480acatcagatt ggttgtcaca cataatctct gttgcttccc tttagtgaag attcaaatca 540gctaagattt tccttagcca antggcttgg ttgacaactc ctgcagctgc cacatattct 600gcctctactg tcgattgagn aanaacaaat tgctcctttt cactcnaaca aaaaatngat 660gaaccaagag taaaaacata tcctgaggta ctcttcatg 69916560DNAGossypium hirsutumn = a, t, c, or g(1)..(560)n = a, t, c, or g 16ctggctgttg gcctccagcg ttggtggccg ccgtatatgg tggtcggagt aatacgaaaa 60gaggtctttt tgaccgtttg gttctcccca accctgattt aaaacctaaa attctagaaa 120aagcctttta aaagtaaaan aaaacaaaca aacccttggt tcccctctcc gatctcagaa 180aggtaacttt ttttctttga atatctatat atgcatgttc tttattcgaa aataaacttg 240caaaggaaat aaaagaacag aacgaaagac caccttgatt ctttttttat ccgattgcta 300ttttttttgt gtctccttct aaaaaaatta caatgaaaaa tgtttatggc tttgtagccg 360agtgattaca gttttttttt gttctttttt gctgctattt cttgctgttg tgtggccttt 420tcttgtaggt ataaggctgg atgcaagtgt ggcatgctag tacgcggacg tggaggccgt 480tcggaggttg cgctgtaggc tgggggctgc gacgcgccta aacaaaccct agggtttctt 540attttttaat tttcgggcca 56017738DNAGossypium hirsutumn = a, t, c, or g(1)..(738)n = a, t, c, or g 17tatattcccg aaatctcttt tactttcnca gtaaaccttt aaaaaaccga aatttacaaa 60tcaaaactct gaacaaaatt acttaaatgc taagaaaatg agccaaaaac aaccggagag 120gccccaagag ccaatcaatt acggagatat cttctccgga aaaggcgagc ttgccgagaa 180gacagtggca cctaaagatg ttgccatgat gcagaaggcg gggaactccg tgattggtca 240aacccagaag ggtggtgtcg atgcatctat gcaatttgca acgtcgaaga atgagagttc 300gggattggtt ggccgcgaaa gagtcagtgc tgattctggt gtttatatta aagagaccga 360gtcccctaga aaacgtgtaa tctcggagta ctttggtaaa gaggtaagag gagcaatcta 420tagagagagc tctaatttaa tatttgttac cgctttttaa ttatagttaa tatatcaaaa 480aattattctn atattataga aatgtctgtt tgaattaggt tgagctgagc ctaagtactg 540agtctatact tagtaccaag tattaattta tttatgtttg tcaaaattcg atctaattca 600acatataaat tttaaatttt actcaaattt actataatat ttatatgact aacttaaata 660tgtttacatc atccattttt taaaatttaa tttatctttt tttattaatt tttaaacata 720aacaacatta aaatattt 73818557DNAGossypium hirsutum 18aaacacgaaa ggttgttgat ttgttttatt cctttctttg aaactacgca tatattcata 60catatttcat ttttatttgt gttctatgta tatatataag atatattaat aagttttttt 120taaaaaaaag aaaaaagcga aaaaactaaa atttttacct ttttcgaaaa tccggccacc 180gtgtacggtg gtcggcggcg gtggcgcatg gcggtgctgg agtctcaccg gaaatcccca 240ggctgagaga gagagagaga gagagagctt ttttgaagag aaagaaagaa aaaatgaatt 300tttttacaaa tttttttgct tttataacaa tatgaaatga cgccgttttg cattaaagac 360ccagggcata aaatgacgtc gttttgtcct gggtcggatt gacctgaccc atactcgctt 420agaatccgcg tgtttttgac ggaagggcta attgcacttg tagcccttcc gcttttttat 480agctttgtaa tttaattttt tgtattttta attttgccca aaaattttat ttttgtttca 540ttttggtcct ctgctgc 55719450DNAGossypium hirsutum 19cgctgctcta attgtgtcca gctcaaccac aacaatatga tttgagctgt caccgttgtt 60tgattgattg aaaagaccaa gatactggct gggaagagct ccaggaattc tattattagg 120cgagattaaa aaggctaatc catggccaga caaagtaggg tattcctccg gtacaattgc 180aaaaaagaat gtggtcgaaa aagagaaaac actaccattt gtggagttct tgaattggat 240tggattcttg tagaagatgt gacctgttga ttggattgta gaattagtca gttttaagag 300cccacttgaa tctacgcctg caactccatc aacattcaag taaccattga aactgaactg 360accctgattg atatctgaag atgcaaggtt caggaggaaa agcaacacaa gcatgatcaa 420gcaagacatc attacacaca caaaaaaaaa 45020548DNAGossypium hirsutum 20tgcgtgataa attatatcca ttttccttga aagataaata tggtggctgt gaaaccaata 60atttacggac aacagattgc ttagatcata aacgtgatgg gcttcatgtg tatttcaatg 120ggcatagcct taaggtgaag aagtgtggtg ttagaatagt gtatgagaaa gatttggaag 180aaataaaaga gttgcagtgc catacccctc aatcttcacc aaattttgaa cacatccacc 240aacactctgc tcacaacgat ggatcagtag gtagcacttc tgacattaaa caagaacgta 300atatctccga ggaagcggag gaagaggggc agcaaccaaa actgttgcaa aaaattttca 360attttataat gggccaatca gggaagaagc attaactgtg gtaaactact taaccaatct 420tgtcctatta actttttttc acatctttca tttaatgtga tcaatctaga cttacttacg 480atccttctta cataccacaa agttataaat cttttactca tattcaacag gagctcatat 540tccgtaaa 54821415DNAGossypium hirsutum 21gcccttgatt cggtttgtat tatcttctaa tccaatctat ttgctatctc cgaagtttgt 60tgggagaaaa gcttgaccgt attatgcgaa cgttttggtg gggtcatgat ccgaatcaga 120ggaaacttca ctttgggaaa ccgaaaacca atggtggact tagtattcac agcatggagt 180gatgcattac ttagtaagca ggcctggagg ttactgactg aaccccaaca cttcgccata 240taggaaaata tcatcgacac caacatttct ttaatggaag agtttagttg aaggagacga 300gatggttgtt tgagtggtat tgatatctaa atttgcaagg tgcaaacaac tctttttaag 360tgactaggtg atggatgatg ggtagacaaa ctttctaacc cacgcttctc acact 41522646DNAGossypium hirsutum 22ttctggagcc ttctctggat attccctcca ggtacttctt taaataaggt tatttgtttt 60ggaagtgctt gaaaaaacaa tatttcaaat taggctgatt aggtataacc aataatgtta 120ttacttgtaa acaattgagg ctgcaaaata caactgtttg aagcaatatc aagaagccgg 180tttgatacat tgtgaagaaa taacacgact tggagcagtt aagttttgga tcttgcattt 240gtggatggac ttatccatta gtgtttacat accataggga atttgtttgt aacaagtttt 300cttgggcttg tgtttacagt tgcttatctt ggtctttgga tatgatagtc ctttgggatg 360cctccttttc ttaaatatta tttataataa gttttcttag gcaccatctt tagtgttttg 420tcatattggt tgcatattgc taatcttcat taatcttgat taggtgatgg agtcccatca 480agcaggcaaa ttggacactt ctggtactgc taaggctatt atttcttgct ttcagaaatt 540gggggtgtca tttgacatgg atcaggtgtg tggctcttac atattcttaa ttgtaattga 600aagagaaatc aagttctttt ttcttattgg ttaggggctg gggagg 64623645DNAGossypium hirsutum 23taacattttg attgctctaa ctttaaaaaa ttctaaaata ctcattaaat tatttcaaaa 60tttttatttt tatttcaaaa agaaaagcat aatgccttgt tgtttaacaa taatgccaaa 120atctaattag catgcagtag aagtagaggt gtttaggttg gagtctagct caattaaaat 180tttaggaatg tttgttaagt ttggatttga

ctttacctta aaaattgatc taaaattttg 240gtcaagctcg atgtaaataa aaatattaaa atttcaagtt cggccggccc atattcaaat 300tttttatata atatttttat aaaaataata taatacataa aaaatactaa aaacattaaa 360ataaatgtct cccagcaatt tgaaaataaa ttttaaaaat atatgtgctt aaataacact 420gagataagtg caatttaaca gacaaatacc tttaaaatag taacaaaatt aacaataaaa 480taagaattat ataatatcca aacaataaga acaatatagt aacaaaataa tagtaaaatg 540atagcaaaat agtgagaaaa caataatata gcagcaaaac aataaaaaac aacaagaaaa 600caacattttt tttatttttg tagattcata cgagctgagc ttcag 64524611DNAGossypium hirsutum 24tcatgttaga gggtacacac ctggtatgat tttgatgtga aaccacacca gagaccacca 60gcacctaaaa gaatacccaa caccttttta gcaatcaaat tgcaaatcca tcaatactaa 120accgaacagc gtacacatac ttaccactat caaacccgat cacgcgcaca gattagactg 180attgagcgaa aactgcagtc tcaactcctt ctcctgcaca aaacgtttac agagaattat 240tttcccttac aacttacact aagaattcaa gtgaaaagga gaaaccccat agcttactga 300agatgaaacc tatcgacaag tgaaagcccc cacttatctg atcacacgaa aaacactgaa 360atcccaaatt gcatgtgaag aacaaaagga gagtacagat tgaaaaggga aaattgaaag 420aagaagagaa tagtggagaa aagcaaaaac gtacgtcaga aattttggaa gagagagaaa 480cgaaattaga aaaaaataaa ataaaataaa caacaatatc tatcctaacc tctcattctt 540tcccactcga actagtaagt ttattttaat atgagttaat aaagaatatt acataagcct 600acccagtaga g 61125300DNAGossypium hirsutum 25aagtttagtc aacttctaaa ccataaagaa cattagcata cttttcaatt gggtccccat 60ctgcaaaata cctttccttt atcttcaacc aagcgtgcaa tgtcaacaaa ctatcggaac 120cagcttgatg actcttccca attgcacgct ttactcccaa atctgtagac gcacgatcga 180gacctccatg taatccagcg cagaatttca tcaagtgttt gacgtcgtag attctgtctc 240cgaagaacac tcgcacgagt tccaaaaact cagtgagttg gtcaggcaat aacccaccgg 30026631DNAGossypium hirsutum 26atgttaattg ccataggctc aaaatgtgct ttgcatgctg ggtttcccat aacattgcac 60tgagttatga attttttatg gctaattgca tgttaaggat tgatgaaatt ttgtacaaaa 120tattaaatca aaacagataa aaacctttct atctgtaatg catgttttca tctgcacagc 180aggcatgtgc acagatcaca aaccatcaca acataaacct ttggtttgct attatctatg 240catttcccga ctgttcattt ttcttgaagt atttgtcttg cgattatgaa tatatgaccc 300ttcaatacat ggaaaaactt agaaaacaat taaacatacc cgtatctgaa actcgcccaa 360atccaagtaa catgggctcg aatatctctt attatattgg ttacttcccg ttggtcttcg 420taactctttc aagatatgct tttacttatg agattatgtt gttttagttg cttttcttag 480attttgatcc aacattaaat ggatgtttta tgtgtttcaa gggtgctttt tgagaaactg 540aatttaaatt acgaggaggg tgagagatgg attgtgaatc tcatccgaaa ctctaaactt 600gatgcaaaga ttgattcaaa gactggaacc g 63127658DNAGossypium hirsutum 27ccgatgggaa agccactgga gaggcatacg tggagtttgc ttccgtcgag gaagctaaaa 60gagcaatgtg caaggataag atgatgatag ggtctcgata tgtggagttg tttccttcaa 120caccagacga agctcgacga gccgaatcaa gatcgaggca gtgaagaggt cctgttatct 180gggtttttga tatgtagtct ttggtttgta tgtttgtcat tctagcctga agaaatgcat 240gtcaacccat atttaatggg ttaatcttct tcctatgtgt gtctctgctc tcaaaatata 300atctcctaat cctattaggt taaatatgat cagtatgttg ttgatgtact tttttttgtt 360tttcttttag atatttgaat tttggtttta aggatataaa atatatttta gataaatatg 420tagacttttt acctttcaaa ttcatgctca tggttgcctt cgggtggttt cattgttcat 480tttgcatgtt gtggtattgc catggcatta aatagagtcc ttcttgatcg aagattttaa 540agattattat ttgttacatt gggtggtttt aattccacaa ggttatttat tttttaaata 600ctagttaagg ataaaaaaat ccaaagggcc gatggattgg gtttcaatcg gattaaaa 65828578DNAGossypium hirsutum 28gaaaaattat ataaaaattt gtgtcggtat tatcttcact tgacccttgc tttaccattt 60tgattcgccg aacaatccaa gaatttaaca cccacaaggc cagaacaatc gcctatcacc 120gccgtagccg acacccaaaa tgaggaagga agcggcgccc tcctccgtcc cttccgccgc 180cgcaggcacc accactttgg ggaagctatt catttgcttc gagaccaaaa cattagtgac 240cacattgctg gcacttactt tagttacgtt cttatggaac ttacctcctt actaccaaaa 300cctcctctcc accacccgtc cttgctccgc tccgataacc tccgtttccg tcaccgcttc 360cgccgcatcc gtcaccgcca gtttgatctc caccaatgtc tcaatgcctt acaagccgaa 420tccggtagct aagaagtaca acacggcgac accacctaaa cccaaggacc caaacaagcg 480ggttttcgag tcgtacggga acgcggcggc tttgtttgta cagatgggtg cttacagagg 540aggaccgagg acgttcgcgg tggtgggatt agcttcca 57829652DNAGossypium hirsutum 29atgaatgctg acgacttgct cgatgatttc tctaccgaaa ctttgcggaa agatctaatg 60gctgggaaca agctgatgaa agaggtacgc cttttctttt caagctcaaa tcactttgct 120tacggtctca aaatgggtca gaaaattaag gccattaagg cgaggttagc ttcaattgaa 180agtgaggcca acacttttgg ctgcatggtg cgtgaccgcc cagtggaaac ctctttcatg 240attaaaaaga gacagcgaac acactctttt gtgagtaaag ataaaataat agggagggat 300gatgataaag cggctctttt aaaactcatg ttagagtttg aaagtgaaga gaacgtttac 360atcattccag ttgtggagtt tggaaggtta gggaagactg cattggcgca gtttgtttat 420aatgataaaa tggtctatga ttattttcaa ttgaggatgt gggtgtgtgt ttcagatgtt 480tttgatgtca aattaatttt agaaaacatt attaaatcta taactggcca agtaccagat 540caaaatctcg aaattgacca attgcaaaaa caacttcgag ataaaattgg tggaaaaaaa 600tatttgcttg ttttggatga catttagaat gaagagaggg aagaatgcgt ta 65230579DNAGossypium hirsutum 30tgcatcacag aacattgaat tttagggttg agagaagaaa gagtaaaaac caacaacgat 60tcctcaaccc atgtctttgc cttcgcctcc tatcgccatt ctctctacac ctttaagtcg 120cactttcagg agggagagat ctgtcattgt ttggcatccg gagagtgttt tcttccactt 180tctgagacgt gcattatatt actacagtag tcttgatcgt gaaattcagg taagttcttg 240gtattgtttt gttgagtcta atttgttatg gttttcgttg atcgaatcag ttatagacca 300tcagatttgg gattcaacaa agtacaagta ggacgtgcgc aatggacatt gacacggagt 360ttgagggtct gaatttgttg tttaagtctt aaactagtaa tggattttcc ttttgcctga 420gttctttgtt aacttaatta ttgtaaaatt gatgtaaact tatatgagaa gttgctgctg 480ttagctcttt ccataagcat tttccataag catcggaagc ttaaaaggtt acttttaacc 540tgtttatcat cttttctttt ggactgtaat tgtatgata 57931585DNAGossypium hirsutum 31tacctcccag ttacaaaagt cccaactttc catctcaacc gtccatcaat cttgatcatc 60aaaaaaacac tcccggccat ctattcagca cccaatgcga cggaatattc cggtgagatc 120ggtaccatag taccatatat tataggtgac caaatattga cctcaatatg gccttgtcca 180gagtgttatt tcttggttcc cgttagaagc gtaaacgtcg agccggtcgt aataaacacc 240gatatcgtcg tttgggttac gtgaacggac tgtgatttga aagtttgaag tgagggagtt 300gacggtggtg gcgttgaagg cgtagacggt ggtgtcgagg agagtgaagt tggatttgct 360gggaggaagg attgcccata tgagtaagat tgtgatgaga atgaggagga ttagaataca 420agcgatgact cggcgaaaaa atttctggcg ggatttgtgg tggtggccgc cgcagtctta 480gctaccagac atggtggatt tggaagttat tgggtttctt tttggtgatt gtgtgaggat 540ttagtgatgg aatagtattc agtgtgtgct attagctttc ttgtg 58532592DNAGossypium hirsutum 32acagaaatag aaatgattgc agtctgtcta ttttctttcc ttttattgga attaaatatt 60gatgtttttt ctcgaaataa agaaatttat gcatgtcata tgggctttga tatcttctca 120ttgttgagaa cttggttctg aaatggttac tatgttctaa ttgttttttt tttctgattt 180ttagggaaaa cacgggcaag agatgctgcg ctaaatgcta tccagtcgcc tttgttagat 240cttggtatag aaagggctac tggaattgtt tggaacataa ctggtggaag tcatttaacc 300ttgtttaagg taacgcgcca tctccgactc tctcagtgtg tctgcgtttt cttgcggaga 360ctttatatat tatcttgata ttgagcgcaa aattgttgat tattcgtaaa tggagcactt 420ccctgtagga gaagagtcat tgaagcccaa gcggccccac catatctgat acctgcattc 480ttgagtaaca gacaagtgaa taattggaaa tagtatagta atgaatacta ctttgtcatt 540gaaatgttat acatgggaaa ccttgattat attgactgat ccacttgggt tc 59233620DNAGossypium hirsutum 33tcaaagttcc atccaacata gaagttcaag cctgaaagtt ccaccattaa cgatttcttc 60ttgtcaaccc catcttcaac atcctgcaaa tgcatctgtt ccattgagct caattctatg 120ttggaagcac cattggctac tggacttcca ttaatttcaa gtccagacgt gtctacactt 180ccactcaatg tctccatccc aacactgtta ttttctcaat tttccaacct ttgtctaaag 240caaatttacc ctcctgtttg aaaactgacg atcttcatcg gttgattggg cttttgaaaa 300atatatcttt ttcttttttg gtacctttca aagtccattc aagcagcaaa gcaaacaagc 360aacttattca cagatattgg atcattacgc atgataacgg gatttattag tgttcatcgg 420attgatcatt tagcccaata gactttgagc ctaaacccaa gatctgtcct gaattaaaag 480aaataaaaat tggatttcaa tttccaaaat taaaaaacaa ctgaaattat aacatcaaat 540ttgcattact gccaccaagg caccaatcaa gatttgaacc cttcttcttt tgacatggag 600aaggatgact gttgcagtta 62034574DNAGossypium hirsutum 34ctttactatt cgcggtggct gcctcttttc ttctctacac gtgagcagta ctgaaatttg 60cagactttct tttcttcatt tcctagtcgt ttcgagtttc tttagtttat aattttctat 120cagttgtttg aagaaaacat ttcggtgttg ttgatttgct tgctctttat gttttttatt 180tgattattaa acgactcatc atctgatctg agttaaaatt ttcagatctg tacagttttt 240tttgaatagt ctccaagcaa ctatgggcca tcaacagctt gcgagggagg catcttaagc 300acaatatgac taaacgaacc tccattgttg gcaggaagca agaaaagaag tcgggagaga 360gttttcgatc ggttcccttt agcttctcaa aacttatctg aaattctttc ccggcttctt 420ttcttgcttt cgttttattg ttcgtttgcg ttgtgcttca gatgtcgcac atccaggctg 480tttgaagttg tttgtaggcc aacctaatct ccatggaaga aatccagtag ccgaagttga 540ggtgaagtgg agattgttcg aaaaaacact ataa 57435789DNAGossypium hirsutumn = a, t, c, or g(1)..(789)n = a, t, c, or g 35ttcttaaaca aaccctaaac cttaatttct ctcacatttt caatggaatt tnnngggtaa 60attttccttt acatcttaca tttctttcag ttaaaatttg ttctttgaat atttgtttca 120attgcgaaat tagttgaaat taataattat ttatgtttga ttatcgatta tttacgtttc 180tttgaaaatg ctaatcgtat gttcagatgc tgtcttctag taaggatttg atgtttcagg 240ctgtttcttt tgctaactat ttttctttta atatgatatt tttttatctt tgattttgta 300tgtaagagtg cggcatggaa ttatatatat atatacatgt tctcccagat agattcattc 360actcttttga attagaattt aggtttggta tttctattga ttttgttctt ttaaattgtt 420ttcttagttt catttcacgt ctgattaaag gaaaattact tatgttgtac aattttttct 480caagcatttc tctgtaaaat ttccctataa tttactcatt atgaatattg aagggaaaaa 540aagaaaatga tacctttttt tccttgttaa atcgtaattt ctttggacat tattaagggt 600ttgaaataat attttatagt ttgatgtttt gaattggatt accctgttgg aaacctttta 660gaatatgttc tatctgctac tactgttggt attgcgtttc atcatttggt gttattgtag 720ttttttacat ctcaatgatg attgcttgtc aaatattttt tgattgttac atattttgcg 780atttcatgt 78936687DNAGossypium hirsutum 36taaggctggt caagacacat tgatttcagt atataatata catcattcct cacaggtgct 60tgcttatttt catcatactc gtaatttttt ttctttgaat tttttcctgg ttattactcc 120tatgttgttc cgtttcttca tttttcttaa aatgcctgtg tttgatacct ttgtccgatg 180tatataacct aaaagacccc gccaaatata tgggaatact tagaaaaaat tttgaaaata 240tccaaatcct ctgtgaaata cctcattttc tgttgttcgc agcctacgta tcaaattgta 300catgcactat ctctatgctg aatttgctga ctgcataacc gatcaacgtt tggtttcctt 360caaatagaat attctaagtt tgaaaatagg gagttttacg attcctacca tttgttttct 420tggacagcaa taagcgatat tccgtctttt tcttctttcc aggtctggga aagagctgaa 480gagtttgtgc ccgagaggtt cgacttggaa agctcagtcc ctaaggaatc aaatacagat 540tacaggtacg aaaaacaacc gtgttttact agttttctcc ctgtccctga tatccttccc 600acatttgcat tacatactct tcatcatatt aatacggtag aacatcttca ggttcattcc 660gttcagcggg ggtcctcgta aatgtgt 68737620DNAGossypium hirsutum 37tagtgagggt atggtgaaac gtcaggatgt atgggtcacc tcaaaactat ggtttgcttt 60tgtgctttaa tacttttctt tataagttct tctcaatgga gtccgttact ttgcatatct 120aatatgtcat tgcgttgtac gtttaggtgt actgatcact tgcctgaaga tgtaccaaag 180gcattgcata aaactctgca ggatttgcaa cttgattatg ttgatctcta tctagtatgt 240cttaacactt actttattga aatgatatat atgtatatat gacatttgtg gtaactgcga 300tgaatgttga agatacattg gccagtgagt gcaaaaaggg gagcaattgc tgtgaagggt 360gaaagcctta cacaaccaga catcccagct acatggaaag caatggaggc actctacgat 420tccggtaagg ctaaagctat tggagtgagt aatttctcgg caaagaagct cagggatcta 480ttggaagtgg cacgtatacc gcctgcagtc aatcaagtgg aacttcaccc tgtatggcag 540cagccaaagc tgcatgaatt ttgtaaatcc aagggaattc acttgtcggt aagaaaacag 600gccgcttcag gttcatatca 62038669DNAGossypium hirsutum 38gggtgactaa tgaagaacat aggaagggga ttttcccaat ataaaaagaa aacaatgtaa 60tattgtggac caagtcaaat aaaaccccac aacatgtaac gtaatgcaca ctaccatcac 120aaccaccact aaaggcacgt caaaccgccc ccaaagcaca cgtatacgcg caatagaacc 180ggcgtttaaa gatgcatagc ctcggaagtg gtcgaccgat tccatgactc catcactatc 240ctttttacct tacctagtcc tcaccaaaat caatcattta aaagtataat aataatattc 300tgatattaaa tgaaaaacgg ggatgttgta ataaaacctc gttcatttca ttaacatttt 360cactttcaac aagatatatt tattcccaga ttaaaaaaga gtaacccctt cctatagctt 420taactggttt tccctaagcc caaagtaatg aacaaaatct ggctgcaacc ccatatatat 480atatcatcat cattcctgga aactagaaaa ttattgattt tcatctaaac ctaaccctaa 540aaacctatat atgtcttcta tactactaat atagtcaaca accatatgca aagttgagtc 600aataagtcca atcttgtggt aactggactt cacggttgat cccttgctga ggccttgagt 660tatgcttgt 6693930DNAArtificial SequenceDescription of artificial sequence synthetic primer 39caaacaagca acttattcac agatattgga 304025DNAArtificial SequenceDescription of artificial sequence synthetic primer 40cagatcttgg gtttaggctc aaagt 254134DNAArtificial SequenceDescription of artificial sequence synthetic primer 41cctagtcctc accaaaatca atcatttaaa agta 344232DNAArtificial SequenceDescription of artificial sequence synthetic primer 42aagtgaaaat gttaatgaaa tgaacgaggt tt 324332DNAArtificial SequenceDescription of artificial sequence synthetic primer 43cttattcata aacagaatgc ctctagtact gt 324427DNAArtificial SequenceDescription of artificial sequence synthetic primer 44tgatgacgac tatttgcata tgttcga 274518DNAArtificial SequenceDescription of artificial sequence synthetic probe 45cgatgaacac taataaat 184616DNAArtificial SequenceDescription of artificial sequence synthetic probe 46atgaacacaa ataaat 164717DNAArtificial SequenceDescription of artificial sequence synthetic probe 47acaacattcc cgttttt 174815DNAArtificial SequenceDescription of artificial sequence synthetic probe 48aacatccccg ttttt 154918DNAArtificial SequenceDescription of artificial sequence synthetic probe 49ctccttgtag accttctt 185016DNAArtificial SequenceDescription of artificial sequence synthetic probe 50ccttgtagag cttctt 165117DNAArtificial SequenceDescription of artificial sequence synthetic probe 51tgataacggg atttatt 175217DNAArtificial SequenceDescription of artificial sequence synthetic probe 52gatcaatccg atgaaca 175317DNAArtificial SequenceDescription of artificial sequence synthetic probe 53attaaatgaa aaacggg 175417DNAArtificial SequenceDescription of artificial sequence synthetic probe 54gaggttttat tacaaca 175517DNAArtificial SequenceDescription of artificial sequence synthetic probe 55tactgtctcc ttgtaga 175617DNAArtificial SequenceDescription of artificial sequence synthetic probe 56tagaggcaat taaagaa 175716DNAArtificial SequenceDescription of artificial sequence synthetic probe 57tttattagtg ttcatc 165816DNAArtificial SequenceDescription of artificial sequence synthetic probe 58tttatttgtg ttcatc 165916DNAArtificial SequenceDescription of artificial sequence synthetic probe 59aacggggatg ttgtaa 166016DNAArtificial SequenceDescription of artificial sequence synthetic probe 60aacgggaatg ttgtaa 166116DNAArtificial SequenceDescription of artificial sequence synthetic probe 61tgtagagctt ctttaa 166216DNAArtificial SequenceDescription of artificial sequence synthetic probe 62tgtagacctt ctttaa 1663658DNAGossypium hirsutumn = a, t, c, or g(1)..(658)n = a, t, c, or g 63attgagtctt acaatcccaa acaaggacat aatcatgtaa acaaaccaca ctatgtcaat 60actgatctct atctatgtcc acagccaagt cactactaaa tacttaacaa acctatgcaa 120taacataaga tgacaattcg tactaagctt ataatgcata tttgggtcna ttacagncat 180tgcgttttat gcntatattc agttgttgcc taaattgaag ttcatataaa gtcaagtcag 240ttgcctagat ggataaacac aagcaatncg gatcaacaca taaacagaaa taatgtcata 300ccaataggac attatagcag gctgatccac tatgctctca caaccaccaa atgatggagc 360aatgtatggt atctttaatg catcaacaaa cttgatggtg gtcatcaaat ctccatccac 420ctgaatgatt tagaatacat taatgtcaaa taatttttgc atcaataata ccaaatgaag 480taatagatac taaaggtgaa ttttccgagg tgcaaggttg aagtagttga agaaaacaaa 540cctcaaaact gaccacacca ccaaagccag tcatttgctg cttggcaatt tcatgttcag 600gatgacttgg caagcctgga taatagacgc gnctcacctg ccattgatat ttgataag 65864802DNAGossypium hirsutumn = a, t, c, or g(1)..(802)n = a, t, c, or g 64atacattgct cntcatttgg tggttgtgag agcatagtgg atcagcctgc tataatgtcc 60tattggtatg acattatttc tgtttatgtg ttgatccgaa ttgcttgtgt ttatccatct 120aggcaactga cttgacttta tatgaacttc aatttaggca acaactgaat atatgcataa 180aacgcaatgn ctgtaatnga cccaaatatg cattataagc ttagtacgaa ttgtcatctt 240atgttattgc ataggtttgt taagtattta gtagtgactt ggctgtggac atagatagag 300atcagtattg acatagtgtg gtttgtttac atgattatgt ccttgtttgg gattgtaaga 360ctcaataaat ttttccctct acgaaacagg gatcttagcc aagctgagag gcgcaagtat 420gggattgagg ataacttggt tcgtttcagc ttcggagtgg aagactttga agatttgaag 480gctgatgttc tgcaggcact ggagaccata taatggcgct aatctccgtc gtttgggttt 540gggtttaaat gaccggccta gttattttgg tgtttcaatt ggtatttgag ctctctgaag 600ttcgtgtttc attttaggtg gatcattgac

cccccggtaa taaattggaa ctttgtttgt 660aatcccatca atggggggat tgattttcaa tttttttatg agtgtttatc aggggattaa 720gcaaacaaaa ttagaaagaa gcctgnnnnn nattngnnnn nnggggnntt nnnnnccctn 780nnnnnggnnn ntggnntgta aa 80265624DNAGossypium hirsutumn = a, t, c, or g(1)..(624)n = a, t, c, or g 65cttctcaccg ctcttccgga aatcgtcact ctctntcacc aggtatgttt cttnctcttt 60ctttaaagct tcttctgcaa tcttatgggc aaaagcattt tctgttctgt ttataaactg 120gaagctaata tattcaaaac tagtcatctt actatggatg tctttaataa tcgcccctat 180gactgattta tcgttcttca tggcttgaca tttcttgatg attgtgcgag aatcccccat 240gatcgttact gagggaaaat ccattgcaat tcctagtttt aacgcctgta gacctgcaaa 300agcttctgca gcaaatggaa acgggacatt cctgtgtagc tgagtcttca tagccntaag 360tctccctgac cagccccaaa ccgccagtct cgatgcctat ttagagttcc ttttatcaaa 420agttgcatcg aactgaatcg tcactttggt ataaacctcc tgatgcctgt aactgctact 480cgtatttaag gtacttnctc tttcccgcaa cccttcaagt ttggctatgt acttttgaac 540nttgagtgtt aactccctcc ctgtctctgc tttctgttca tgtataaatt tattccttaa 600gctccaaata aaccacatac cgca 62466774DNAGossypium hirsutumn = a, t, c, or g(1)..(774)n = a, t, c, or g 66ctccctcgac accactattc tactagaaac ggtgaccgac gaagcgtaga ggtccgattt 60acaaccaaga ctcgaaggct gccaatttca gccttgaaat cccctccaga actccgattt 120gaaggagaag attccagcng cctatttgcg aatgtaaacc taatttgaag attttatgta 180aagagatttt taattatctg atctctgtct ctgctgctat attttatttt tggttttcta 240tcctactgct cgttattccg tctgtttact tcgttgagaa ggagaatttt ttttaaagct 300atcagtttag tgtcaatagc ggatttgcgg tcgacactgt gaattagcgg ctgcatcacc 360gctatttgaa actctgactt gctattaatt ttggatattt attgcagctt caaatggaag 420gattaagcgt agcagatgct aatttgttga tgtatttaca cccatcaaag agtaggaacg 480tgtctcagtc gattctccgt gagcttggct ctttgctatt caagttagtt cttttacttt 540cacttaaatt taatttttca tataactcaa aactcctgtt tttgtttatt attttttctt 600caccaaaagc tgttttgtgt tgatattgct tttgatttaa ataaagtata ccttaattta 660gtttggtctg ttttctagtt tagctgaaaa tttaacttct gatgatgaag ctaatgatac 720tgtggctcnn nttaaacaaa tggagaagtt tattactgtt gagaatataa gctt 77467170DNAGossypium hirsutumn = a, t, c, or g(1)..(170)n = a, t, c, or g 67ttagacattg gcgatctgct tcatttcttg cttcgtcgct ttggttatcn gatgcgagtt 60tcatctctct cagtctctct nagtgtcttt ctttttgtct tcatcttttc tttggaaaaa 120agttgcgtaa ttttgttgtg aatgttcaat tgttgtttcg cttttttttt 17068551DNAGossypium hirsutumn = a, t, c, or g(1)..(551)n = a, t, c, or g 68tttgggcctg gtttatccta tctaggtatt gggccctgtt gtaaatgggt attcgggttt 60gggcctattg taattgggtg tggtatttgg gttttgatng gctgtaaatg aactttatat 120tttggactat cgtttattgg gcnccgggct aaaattgggc cctacaacta taatgcatat 180tttattatat taaaaaccac aaataaatat aataaatatt tttattgtat taaatataat 240ttttaaaatt ttatactttg ggttcgatta tttattggat cnattttttt aagttttgga 300taatcgattt aattgttatt ggattaatna tttaatatat ataattattt aacatatata 360attaatataa tattttttat aacataatat attcgggcta ggtttgggtc aaaaaaatct 420tacccaatgc tcggctcata taaaaaatgg tcccaaattt tacaaaaaaa ttatttttta 480gattttgtat tttattcaaa cccttttatt ttttaggtaa attttnaaat ttataccgat 540gacccgatcc a 55169635DNAGossypium hirsutumn = a, t, c, or g(1)..(635)n = a, t, c, or g 69agttgctggc tggggactgg tcttangctc ggaagtgaat cctcangcat cacatattcc 60actcacagaa atattggaat tgcccttttc gttcttgcta ctgtgcaggt atttcttcaa 120ttactaaatc tttcatgccc ttttaacatt ttgggtcatt cttagaattg tgcgaatcaa 180gtttaattat ggtggtgtga cactgaaact tgggaactta ttgtgtcttt acttgttaga 240tttttgcctt gtttataagg cccaagaaag atcacaagta tagattctac tggaacgttt 300accaccacag ctttggatac gccatccttg tccttggcat cttcaatgta ttcaagggta 360tcaatatctt gaaacctgaa gacaaatgga aaacagctta tatgattgtg attattgcct 420tgggtggtat ttcattgctg ttngaagcca ttacttgggt tgtcgttttg aagagaaaat 480ctagaaagtc caccaaacct tgcgacggat acaacaatgg ccaaagttga tggcatcagc 540aagcctccaa ttgcagattt tgtaacaccc ttgtgctttc tcatccttgt tgggatgttc 600tatttcctat tttcagtgtc ttgtataatt gcttg 63570583DNAGossypium hirsutumn = a, t, c, or g(1)..(583)n = a, t, c, or g 70tggagggaca gagatcatct ggcacagcag gagaaacccg tcttggaagc atttgcccca 60tccttgacta gggtgacttt attcccagac aactcacctt tatatgaatc agagtttagg 120gcttttcggc ttacattgtt gtagatttcc cggataacga tctcnaaagc agtctgaacg 180ttagtagatt cganggcaga cgtttccagg aagaacangc cttcttcctc tgcgaggctt 240ttgccttcct ccacacttac atctcttatg ttctccaaat cacatttgtt ccccaccagc 300attcttgtca atgtagtntc acaatgagct gcaaggatta attacaataa ggttcaattt 360ttttnacttg aatnaaacaa angaatgtca tttaatttag tttcctagaa agtgaaaact 420tttctaggaa taaatttttt tctcatagct taaacaattc ctcttntccc tagaccaaga 480agaaccatgg gcaagtacta actttttgca cagaatctaa aaaaagagct ttttggtata 540aagatcataa atctaagaat agacaaagaa aatgtaaatc taa 58371572DNAGossypium hirsutumn = a, t, c, or g(1)..(572)n = a, t, c, or g 71taaggggcat acccttatta gatatttgct tgatctcata acccaacacc ccccaaaaag 60aaccctaatt tgttatcaac tttcatatct caataaatca tatagtatat cccccctccc 120catgaataac cctcaccatc tgaaccctac ttctctaaaa tccaggttca ccacgaggtt 180cctccgcgcc ctgactaaaa tccgtgctca aaaacctatc tcctcgtctt ctcccacaga 240gatcttccga cggtatcgaa ggatcaaggt tgcagctgac aagtccatgg cttactccgt 300taggtcgagg agaatttgga gtaaggcaat gctttggaag cttcgaagcc gatcttatng 360tcgtcaagac ccttgttcag gcagaagatc tgggaagact aatcaagcca tcatgaaaaa 420atcaagtaac gagaatacta caacaagaag ggaagatggg gttgggtttg ttgaagaggc 480agatgaacta agacagcttg ttccaggtgg tgaaaccatg aatttatgca acttgttgga 540tgagactgca cattacataa agtgtcttac ca 57272464DNAGossypium hirsutumn = a, t, c, or g(1)..(464)n = a, t, c, or g 72ataagccctt tagactccat cccattgcac catttaactt tcctcacgtg tctgtaaccg 60atacaatgga ccctcagtcg ggtanggctt ggtcagaacc ctaaagtttg ggaggagccg 120ggcaagttca agccagaacg tcacctccag catcgtaata aaggcaaaga agcggtgctt 180gctgagccag atttgttgtt attaacattc agtagaggaa agagtgggtg ccccggtgtg 240gtgcttggaa actcaatgac taccatgttt gcgaggcttt tgcaaggttt tgattggagc 300atcccggcta atctggcaag cattgatctt agtcaagaaa agggagagta atttctggct 360aaaccattgc ttgctattgc aaggccgcgg ttgccaccct ctgtctactc gttttctggg 420taaataaaag agagagaaag agaaagacag tgatgtttac agga 46473661DNAGossypium hirsutumn = a, t, c, or g(1)..(661)n = a, t, c, or g 73ctcaaccatc aggagtaagt ttggtcctaa aaacacactt cactccaatc acctttctgt 60ttgcaggtca cccaactagc tcccatatct ggtttttctt tatcatacct agctcttcct 120tcattgcctc catccattct tgatcatctt tggcttcntc atacccaaca agttcaagaa 180caaccacact acacctttga taaacttcat tcaatnatct tgtacctcta gttgatgtat 240catccaccaa tttattagna ctgagagata actcttgctt ctttacttca gtgtcacttg 300tccgatccca ctgttcatct tctgggaact agaaatctct acttccaatn attttccttg 360cctgaggtta atggattctg tagnctttta acaccaagtt ataactaaca aatatttcat 420gctcagatgt ctctcctaac ttgtccctct taacctgtgt aacatgacag aatcataaac 480aaccaaacat attcaaaatt ttcagagttg gtttcatctc aaaaatattt catgcttaga 540tttctctcct aacttgtccc tcttaacctg tgtaacatga caaaatcata aacaaccaaa 600catattcaag cttcataagg tgttttcttc tctaanatcc tcatagacag gctattcagc 660a 66174472DNAGossypium hirsutumn = a, t, c, or g(1)..(472)n = a, t, c, or g s 74nctngttcat ccgttgactt aatgaatgtt tttatcttag ctttccaata ctcataattt 60gttccacgat catagatcgg catgagacta aagatccttt cattacaagc aagcatatca 120accaagataa tcactattta tnttgagtaa gaggctctga taccaattat agaaaagagt 180gagtacttgt tttacaaaca taaactgtgg ctaaaatagt gcttngaatt atggtcacag 240tttcaaccac aaaattaaaa gtgcaaaaat gtaaanatga acattgagat tgtttacata 300gttcgacttc aatctacatc ttcanggcct tgcctagagc gatgatacac tatctttatc 360gcaatcaacc aattatttaa gtcttaacat caatataact cttacnaatt taacgacctc 420accattgtac aaagactaaa tcactctctc attaagcttc tgcctcaaaa aa 47275662DNAGossypium hirsutumn = a, t, c, or g(1)..(662)n = a, t, c, or g 75gatcgttata gcttaaccta gctagcgcgg ggactaantt gcaaaatgat tttaggtttt 60tgaagtttaa tggaagaaaa tgaatctttg ttgttagtta aacaactttt gttaagtgaa 120ttttaatgaa attgtcaatt aggggttaat ttgaaaaatg tgaaaattgt gtgttaaatg 180tgtgaaattg tgaaatgcat gggcttctat gagcatatag gatatttggc taggcttaga 240tgnggtgaaa ttgcatgaat ttcattttnn cgagcctaaa gactaaattg taaagaagtt 300aaaagtgtag gggtaaaata gtaattttgc caaaacatga attttggatt gaatagaata 360gaataaagat taaagtagtt aaatttgatt atatagatca agaaaagcaa cgtacagaat 420tagatcgagg aaaagataaa gtattggatt gaacgatcgt tttctgtcgt acgtgttcga 480ggtaagttcg tgtaattaaa ttgcgnattt gtatgattta attgaatata tgtatatgaa 540tggtttaatt attttgtata attatcaagc atataaccga cgacgtacga agaatactga 600gccccgtttg aaccttagga attcgtagga tacaaataac atgtcattag ggttaccgat 660tc 66276711DNAGossypium hirsutumn = a, t, c, or g(1)..(711)n = a, t, c, or g 76ctttttgcct gttgggtctt agtttaganc ancaagggtc gaaactgaat ttgggtttgt 60tgctccccca ttccccaccg ttgatgagtt gattgttttg ccgtttggga gctttccacc 120aagtgtcggt aatatcaatg gggttagttg atgacaacaa gaacaaggag aaggaggcaa 180gcgaggatga aggaggagct gcaaggggtg gtggcagaca aatgagtgat gattcctctt 240tctataccac tgatcaggag gaggataacg atgatgagag tgcacttcaa ttgggtcccc 300agtgtagtct caaggaacag cttgaaaaag ataaggttta aacttttcat ccnctttctt 360tcacttggat ttactcaaac tctcatgcat gtatagttgg aatttgtctt tttatcatca 420tttgcttgag ttgtaggang atgagagctt aaggaaatgg aaagaacagc ttctcggaag 480tgtggatatt aacaacattg gaggtaccgc tttcatttct tttttctttt ttttttaaat 540ccctttgaaa cataggtttc tgtataattc aattgtatgg catgtttcag tactattgct 600ctggctctgg gaaaattaaa acaaacaaat ctttcatgca agtcttaann natctgcnnn 660atttgacatg aatcaaaatn nntngaattt tggatgnngt tntnnnnntt g 71177592DNAGossypium hirsutumn = a, t, c, or g(1)..(592)n = a, t, c, or g 77tttttgaaga atctatgtgt ggagcangcg ccacagactg accatcactg ccatctttct 60tgtaaagatg gttcagcagc gtatgagaag gctttcgcaa ggaccgggga ttcctaacaa 120aaagtgattg ctcatctaat atctttgtcc gaagctgtgg aggcagttca ggnggaggct 180tgctgaaatc accatcattt agtggttgac tgtcatagct tgatatcgga gaaggtggag 240attcgaactc tgaaaggctt tcaggagctt ctggaacaaa ctcctgttac aacacaccaa 300gagagtctca tttttaatgt tggtattcaa gcaacaaatt aagtaaaatg catcaaagaa 360tcattacacc atagctactt aaatatatga agaatactct caacttccta gtcttgaaag 420ctgagaagat agcaatagag atgccatgaa cacttccaaa tcataattat gcgttataaa 480gtcttagcaa ctagcacgca tcatatacgg gctgatgtca ttgatatgta agtagcanat 540ttatatcaca ccattgaaaa cacaagcatg atagcagata tggagtcctt gc 59278610DNAGossypium hirsutumn = a, t, c, or g(1)..(610)n = a, t, c, or g 78atttataaac gacttccttg ttgtttgtaa atcatcctaa actgttgtta cttaataagt 60ctngaatnng tttggaaaac atattgatat aattanttag tttaaaattg ttgttcgttt 120acgtctttca aattcnatca aatgtcttac agcggngttt ctttggaaac ngttattttt 180ggaaaaaccg ttgccttcaa aattaccgtt ttatcagtca ctatgctaga aaccaaaatt 240aaagtttaaa cctaaaaaca atccaaaaag tttggagagt cccaaaatta caaaactctc 300aaaaatcata aagttaggta aattttatga aaatgaagtt tacagaanag tggtcacaac 360tgagctttcg tcgcaccaac ctgcctaagt ctgaaggtta cctaaacata atagacaaat 420agagaatgag tttttgacaa ctcagtgtgt aacgcattta tgtaaacaga attcaaattc 480aatcttttgc agaatcaaaa ttatacagat acagacatgt ctaatcctac cctcatcctc 540tacacaccaa ctctaaccat cctaacacac cacgtggggt ataaaacacc catccagccc 600tacacaccgc 61079608DNAGossypium hirsutumn = a, t, c, or g(1)..(608)n = a, t, c, or g 79caaaatatgt agaatttcac gcagttcaat agcaatataa tacttcaatt aatcaatctc 60aaaaacacac aagaaattgt cgaattccac aaaatccaac agcaatgcga taacaaaatt 120aaacagtttc ataacacaca ccttaaatan aaaccttgat gccaagactg atcgattcgc 180tcccactaaa ccattcnaaa acccgattta gaaagcaatt agacngaaca cacgaagatg 240actaaccctt aaccaatcga taagtaacat atatgtaaaa actaaaaaga ataagaaaag 300aattgaagaa cagaaggaac cccaacaaaa ttctaaaaat ttgggaaaca aaaggaaaca 360gtaagagaag aacgtnaaga gaaagtaatg gaaaaaaacg tgatatttgt tttatgagaa 420caacttcttt ttgtaaaaaa taaaataaca aatacttaaa tagtttaaca caaaatcaaa 480acataactta aaccaaaatt cgaataaaac caattattct ttaacacaca tgaggattca 540aacctgagac cngaaggtaa actaacacac atccaaccac cgaaccaaca atctcattcc 600gacattag 60880655DNAGossypium hirsutumn = a, t, c, or g(1)..(655)n = a, t, c, or g 80tggagactga cattccggtg tnaaaccgtt ttcattgcca tgagtcgtcc gcccctgccc 60cagaccacca ggctggatgc cgacttaaaa ttcctactat caaatgctgc gtcgaactga 120atcgtcacgc tggttcttcc ctcttgatac ctgtgactac tactcggttt taaggtattt 180cctttcatcc tcaacccttc gagttcagct atgtagtttc aaactttaag agataactcc 240ctccctgttt ctgttttctg ttcatgtatg aatttattcc ttgagttcca aataaaccac 300atgccacaac agtaaatctt acattgctca gaggtactcg ttctgaaaac ccaggtaatt 360cattcccaaa atccttgaat cgtactttca ctgatccacg acagatctaa taatggccac 420atttcaccta ttgcaggaca atacctaaag atgtgggtga tgtcttcttc ccctcttcca 480catcgaggnc atgccgcgtc attactcacc cgtttatgtt ttaaattagc tagagtaggg 540atatagttct aagatattct ccatattgta attgctatgt tggcaggcag ttgtaaattc 600catagcttgc cgtagaaatc ctttagatta gcctatatta aataaaaatt aggat 65581549DNAGossypium hirsutumn = a, t, c, or g(1)..(549)n = a, t, c, or g 81ctcgtcacct tcttccctgt taagtatttt ctttttggat aaattacatc tgtagtcact 60aaactattga taaatttatt ttttgatcac tcaactatga atagttacaa atagtcatcc 120aactatttga ttttttcttt tttagttact agttgttaaa tggctaacga aaagatgatn 180tggcagcttt cagaattgtc ataataataa ttttaaccct caacatttat anattgtttc 240aatttagtct tgatcataaa aatttaacac tcattggtct ttttctttca aaataaaata 300attgtccatg atctcggaac ttcattttca tccttttttg tctttgaaga cgaataagag 360catgtttctt tccaagtcan ggacttcaat aggtcatgcc ttcctcgnat gaaccattgg 420actcgtccgg acctatccaa catggctttc ttacgaatga tgttgcacaa atacgtttgt 480aaatccaatg tgacaagttc gtattctaaa tcacccacca cgatatcttt catggattct 540tcattgtcg 54982634DNAGossypium hirsutumn = a, t, c, or g(1)..(634)n = a, t, c, or g 82cacaaacata ggatataatg ccgatgccat atcccanaca tggtcttaca ctggctcatc 60catcaagtcg atgccatgtc gcagacatgg tctgacactg aaacctcnat atgtgccgat 120gcatgtccca gacatgtctc acagtagctc tcgtctcaat gcngatncca tgtcccanac 180atggtcttac actngctctc ataatatggt cgatgcatgt tctagacatt tcgtacactn 240gcacacaaat aacccgaatg tcatggcatg aatatttgat ttatttccta aggttcaaac 300aggagttcta ctgtaacatc ccgaatgagg gcctagtcag aatagtggtt ttgagaccac 360aaatatgatg ttaaaataat tgtttcatga tcattatgag gtctaggata tgaaaatgag 420catgtgttaa agtttcataa agaaattcta tgtgtaaggt gtcctattgg aaattaggga 480ctaaattgaa taaattgcaa aacttggatt ctagaagtaa tttgtatgaa attgctttgg 540aatgttaatt aggagtcctt aaagagtaat tttcccaatt tttaagtttt tggacaaaaa 600tgggcatgca tgaaaaattt tggaagttta gtag 63483681DNAGossypium hirsutumn = a, t, c, or g(1)..(681)n = a, t, c, or g 83tgtttctgaa accactcnga atgtcaatcc agcaggtgag atttcctttc ttttttcttg 60gttntgggga tgtcctgtac tatgtgaata tatggaattt aactgaagtg atataatggt 120gtatgtgtaa aactcgcact acttgtgcat tatgcaaaac gtgagtgtgg acatgcacga 180agctaatttg acaagcatgt gttctgtttc tcaagtattg tatcaaaata ggaaacagta 240gactggaact ttgagaactt ttgtaagtgt ttctctttta cgaatgttgt catgattttt 300gtgattagga tcaagggctc tagagcttgg tatgatgaac aaactaacaa gatcctcaaa 360actgctggat ggatcatctg attttgtgct cacttacgag gacaaggagg gggactggat 420gcttgttggg gatgttcctt ggaagtacgt atagtttcag ttatacgtgt tgctttacat 480tttcattttc ctatggtttt gctcacatga gatttataaa accaactact gttttgcttt 540atctccagtt aggaaaccaa atgtaggatc tccattagtt tcactttgcc tacatgtgtt 600gaatgaattt taaactatgg aagtgcatat tctcttttag ccgtatatat agttgcattt 660atnngannnn ctctgcggtt c 68184667DNAGossypium hirsutumn = a, t, c, or g(1)..(667)n = a, t, c, or g 84aactcagata ccgtccatta tttccttcac tgaagtggtg aagctgactt ttcttactat 60ttattttaaa acttaaaaca tattctaatt ttattaagta taaacttact acaatttaat 120tacgttaaaa ctttgttaaa tcatcaaaac tcttaagctt caacatcctt caaacattaa 180agtccttcag aaccaaatat agatattgcc aatcaaaagt gaacatgtat ttttttcctc 240tattctttat ctattctact atttgttttc tttttaattc attttctcca tgtgtaattt 300ttaactgatt tttgtaacag attagccagg gaagtagnga gctaatgtct aatgatgact 360tctcatttca aactttgttt tattttgaaa tagattagta agtgaattgt tagacttgaa 420caacaatttg agtttataaa acaaattata ttaaaattta tctaaagtaa ctatttatta 480tatattacat aaaatttcat ttatatttta catatatatt tttatatgca tgcgccttat 540tttactctgg cgagtgcttt tattttgtgt cttgtgcctt gggccataca gcagacttag 600agagtgcacc tagtgccttt gacaatggta gtttgaagat atagtcgtcg aatgctgttg 660aaatatc 66785648DNAGossypium hirsutumn = a, t, c, or g(1)..(648)n = a, t, c, or g 85gtcatctgca aagaacagat gcgaaagatt cggacctata cgngataaat gaataggact 60ccactcccct gcatagatgc ttcctgaaat ctatgtctca accattccat acagaaaaca 120aagaggtatg gtgacagtag nnatccttgt ngaatatccc ttactgacct aaacttttag 180gttggcacac cgttctatag tacctgcata gaagataaan atatagcatc nataataact 240ttaaccaaaa aaggangaat acctataaca tttagggagg cctcaataaa atcccatcta 300actctatcgt aagccttttc caaatcaata ttgactgcca tcnattggag tctcttctta 360gtcctcatac agtgtaaaac ttcctaagcg ataatgacgt tgtcaataat acttcttcta 420gctataaagc ctgctngctc ttggcctatg atcttcagaa aaatactctt aaatctatta 480gcaatgacct tcatgaccaa tttatacaac accgagcaaa gactaatagg cctaaattaa 540gaaaattttt tcgagttttg gantttgggt attaacacaa taagtgtatt attgaactct 600ggatcgatga ttcctccttc gaacactttc ttgacccact cacagatg 64886617DNAGossypium hirsutumn = a, t, c, or g(1)..(617)n = a, t, c, or g 86cctaaatgat accattgacc attccaacat ataatgaaac aaccatcgga aaattacaag 60gaaaaaagag aaactccagt ttacaaatta cccttaccca tttattggtg tggagaggac 120cgatgtttat tgctccattt tggtagacca caaggtcgan ccttgaatga aggccatcaa 180tgaggggacc taaaatgaaa ccacaaccaa aaagcgagag agagatggaa ggccatgagc 240tttttagact tctcttgcgc tgttttctta cagtgcaaca atttatagaa ggggaatgtt 300tgaaattaac atttagagga agtttaggaa gcagatgaga ggaacttaca gcgatgaggt 360tgggcatggt ttaccatccc ctcaagtttt

gcgactgcta tatttcttca ttttcagatt 420gagctanngt taaatctcaa ccacataagc aattgtgttt ttgggtaaac tactagttgg 480tcacccaact tttagggtga ttttattttg gtcacccaaa atgaaatcct tgcaatttca 540tcattcaact tttntgacac gttcatttta gtcacacaac cgtttaattt ctaatggcag 600ttatcttgta catgtca 61787607DNAGossypium hirsutumn = a, t, c, or g(1)..(607)n = a, t, c, or g 87tctggtttgg tgnataatga ggtatttctg cttcatctgg ctttgcctga gggccgtcag 60ccggtattcc atcgaaacca tatttagatg aagcatcgct ataatcgcca gccgaagcaa 120taactagcaa tgaaagtaga agtaaggaga atggcaagga gagacgtggg agagccattg 180cgatgtagtt actatatgaa caaagaaagg aagatggtgg ctgaagaaat cggctcacaa 240cgttgcctat ttatagggaa atttgttacc aatgattatt gattatgatt agtagttagg 300aaataaaata aacaatgtag gaacattacg ttgggtgcac gatcccaacg tgatttgtag 360actggggtac cactacctaa ataatctata tctaatgtac atggacacct tttcctgcaa 420ccctaatgaa gatcgtcaaa tgctatgaaa atatatacta aaatcttgtt aaaaattaac 480cgtaaaaaaa ttatatgcct gaagttacat atctattaca ggcaaaaaag cgcatcaccn 540agaaggaaaa aaggaaatgt aataggcagc ttgaaacctg ccaggttaag gcaaggacac 600gtcatag 60788775DNAGossypium hirsutumn = a, t, c, or g(1)..(775)n = a, t, c, or g 88tttcattttt aatgtttaag tttgtattat aattaaaaat aataatttaa ttttttttaa 60aggttgatag tccaattcta cgccttttaa aaggttgaga actaaattta actaaaaaat 120aagtgcaagg ttgtttgaac cggatcgnat aaactaattg gattagttgg atcgagaacc 180cattggggta ctaattcgga gaaaggcatt gatctgtttt actcgagaac cagtatagat 240aagttgaata ggcaaaaatc gattgaacta ggcttttaat atatacattt tttnnnnnnn 300natgaatttt taaagattta tttaattgaa ccaaacggat cggttagatt gaaaaactgg 360tggtttaact gattcgacct ccggttcaat tttaaaaacc ttaaataagg gcttaatttg 420ataaaagatg taaatataaa gtgttaaatt tatcattact ctgtgtgaat aacttctaat 480atnctnngta aattttaatt aattaaaata tttataatat taactcaaat ttttttnnna 540aaatgacaaa aaaaaattac tatagaagtt aagggcaggt aatgaccttg gtaaaatgag 600ataactgtaa atttaggctt tttagaataa ttaattactt aatttaagtt ttttaacccc 660actaattatt gaaaaaatta tatagtcgac ccctccaaaa aataacattt taatttaaac 720cttttatttt tttaactaat ttaaaccgaa cttttacaaa atcgtattac actaa 77589585DNAGossypium hirsutumn = a, t, c, or g(1)..(585)n = a, t, c, or g 89ataatgaggc tcttgtcacc tgaatccaaa gagaatgaga tgaatgttag ctatctagaa 60tcccaaatga aatccaagga ggaacccaaa acagccaaga tagaaacata tcattatttg 120gctaaaacca agtttgacga aaagaagaan atagcaactg aggagcttgt cgtgatggat 180gttcgaaaac aacattcagc agcaaagaga cagatttggt tttggttagc tttggtggta 240ctgctgctag ctttgcttgc caattgctta ctccaatcta attatgtctc taacagtgtt 300tcttttgttt ttcccatgaa ataagaatag aatcatctgc accgatagac agctgccaga 360aaatttaatt aattaaataa ataaaccaag tttgtagatt tcatttaact gaagtatttt 420tgaacgttaa taaattcgcc accaacctta taaaaggcta caaatatggt tgaacggnga 480gaaattaggc ttagtttgna tgagcnataa atttacctct ggtgaggtta aaaatagtgg 540tggcggtgag attaattant gaancggtga gttagaaaca atgat 58590604DNAGossypium hirsutumn = a, t, c, or g(1)..(604)n = a, t, c, or g 90tatgcaagca cccgtttgcc aatgaacctt gacgagtttc acttgggaga ctgtttttta 60attaacatna catacggaga gggcgccatg ttcttcagaa gaatcagtcc caagtactaa 120caccattttg caactcagcc aatagagatt tcatcaactc ttgtggccac catattcgga 180cagacaggag ggatcgtctt acggcagaca tgacacctaa atccaataat cttgcttttg 240ttccctgaat taagcccata agcatctcca tgaaaccatt ctgcataaat taatttaaag 300gaatattatg aaaaagtata aaggaggaaa ttttttcaag catcagtagt cgatgtctat 360aataataggc agtcgcctac agtgaactga tataaaaatg ctgaaaacta attacctcca 420caaatttcac atgcaatata gcttgaatta gatgcatatc ctgattcaca acaaagaaaa 480catctgngtg gatcagggga gacaatctta tgctcggaag gatcaaaaac catttttctt 540tgaaattgca tcacccgctc atcatttggc ttactagaca accgaagacc attaagccag 600aaac 60491644DNAGossypium hirsutumn = a, t, c, or g(1)..(644)n = a, t, c, or g 91caatggaacc cattattatc aatcaaattg gattatgcta gcagtttgca cgataagttc 60cgcatgggac atggatggta tgatgacggg cgggaagccg ataagggtca cccattgctt 120caacataggc tttaatatga ttcttacgtt gtaatttata aatttaccng ccatgcattt 180aatttatcca tgttgggcca atttattttg gaggcctaaa ctttttattt cactattttg 240atcacgcagt gtttgttttt aatcctacat cttcaaattc tttctttttt gtaattgttc 300attataatca gttccccttt tttttncata ttaatttttt ttnataaaat gagatttatt 360ttgtnacttt taaatattat ttggtaaaat ttcaatgtct ttttcataaa tatttcttaa 420aaagttttca agaattttta attattttaa ctattttaaa tataaaatat ttatttatat 480cataaaaaat taacatcaat tatatattaa ataaaaaaac aaattcggta tggtttcaag 540taggcccgtc cgaaaaataa aaaagtttga ataaaaatat aggttcaaaa aatgggttta 600gacaaaaaaa ataatgccca ttttctaaat gggctgaacc ttga 6449225DNAArtificial SequenceDescription of artificial sequence synthetic primer 92tttccttgcc tgaggttaat ggatt 259325DNAArtificial SequenceDescription of artificial sequence synthetic primer 93agttaggaga gacatctgag catga 259428DNAArtificial SequenceDescription of artificial sequence synthetic primer 94cattacaagc aagcatatca accaagat 289535DNAArtificial SequenceDescription of artificial sequence synthetic primer 95acaagtactc actcttttct ataattggta tcaga 359625DNAArtificial SequenceDescription of artificial sequence synthetic primer 96cgtgttcgag gtaagttcgt gtaat 259733DNAArtificial SequenceDescription of artificial sequence synthetic primer 97gtcgtcggtt atatgcttga taattataca aaa 339822DNAArtificial SequenceDescription of artificial sequence synthetic probe 98acttggtgtt aaaagcctac ag 229921DNAArtificial SequenceDescription of artificial sequence synthetic probe 99cttggtgtta aaagactaca g 2110019DNAArtificial SequenceDescription of artificial sequence synthetic probe 100cctcttactc aatataaat 1910118DNAArtificial SequenceDescription of artificial sequence synthetic probe 101ctcttactca acataaat 1810219DNAArtificial SequenceDescription of artificial sequence synthetic probe 102atcatacaaa tgcgcaatt 1910323DNAArtificial SequenceDescription of artificial sequence synthetic probe 103ttaaatcata caaatacgca att 23

Claims

1. A cotton plant comprising in its genome the root knot nematode resistance loci RKN-1 and RKN-2, produced by a method comprising the steps of: a. crossing at least one root knot nematode resistant cotton plant with at least one other cotton plant in order to form a population segregating for resistance to root knot nematode; b. genotyping at least one cotton plant from said population using at least one SNP marker selected from Table 3 and at least one SNP marker selected from Table 3A; and c. identifying a cotton plant comprising a desirable genotype at each of RKN-1 locus and RKN-2 locus, wherein said desirable genotype is capable of conferring resistance to root knot nematode in said identified cotton plant.

2. The cotton plant of claim 1, wherein said at least one SNP marker selected from Table 3 is NG0204877.

3. The cotton plant of claim 1, wherein said at least one SNP marker selected from Table 3A are NG0206957, NG0207837, and NG0207518.

4. The cotton plant of claim 1, wherein the cotton plant exhibits a transgenic trait.

5. The cotton plant of claim 4, wherein the transgenic trait is selected from the group consisting of herbicide tolerance, increased yield, insect control, fungal disease resistance, virus resistance, nematode resistance, bacterial disease resistance, mycoplasma diseaseresistance, modified oils production, high oil production, high protein production, germination and/or seedling growth control, enhanced animal and human nutrition, low raffinose, environmental stress resistance, increased digestibility, improved processing traits, improved flavor, nitrogen fixation, hybrid seed production, and reduced allergenicity.

6. A method of breeding a cotton plant capable of resisting root knot nematode, comprising the steps of: a. providing a population of cotton plants; b. genotyping at least one cotton plant from said population with respect to the RKN-1 locus using at least one SNP marker selected from Table 3; and c. identifying at least one cotton plant comprising a desirable genotype at the RKN-1 locus wherein said desirable genotype is capable of conferring resistance to root knot nematode in said identified cotton plants.

7. The method of claim 6, wherein the population of cotton plants is derived by crossing at least one root knot nematode resistant cotton plant with at least one other cotton plant to form a population.

8. The method of claim 6, further comprising exposing the identified at least one cotton plant to a root knot nematode inducing pathogen.

9. The method of claim 8, wherein the identified at least one cotton plant exhibits a root knot nematode resistance reaction rating of no worse than about 2.0.

10. The method of claim 6, wherein said at least one SNP marker selected from Table 3 is NG0204877.

11. A method for selecting a cotton plant comprising in its genome the root knot nematode resistance loci RKN-1 and RKN-2, compromising the steps of: a. providing a population of cotton plants; b. genotyping at least one cotton plant from said population using at least one SNP marker selected from Table 3 and at least one SNP marker selected from Table 3A; and c. selecting a cotton plant comprising a desirable genotype at each of RKN-1 locus and RKN-2 locus, wherein said desirable genotype is capable of conferring resistance to root knot nematode in said identified cotton plant.

12. The method of claim 11, wherein the population is derived by crossing at least one root knot nematode resistant cotton plant with at least one other cotton plant to form a population.

13. The method of claim 11, further comprising exposing the selected cotton plant to a root knot nematode inducing pathogen.

14. The method of claim 13, wherein the selected cotton plant exhibits a root knot nematode resistance reaction rating of no worse than about 2.0.

15. The method of claim 11, wherein said at least one SNP marker selected from Table 3 is NG0204877.

16. The method of claim 11, wherein said at least one SNP marker selected from Table 3A are NG0206957, NG0207837, and NG0207518.

17. A substantially purified nucleic acid molecule for the detection of loci related to root knot nematode resistance comprising a nucleic acid molecule selected from the group consisting of SEQ ID NOs: 6, 8, 9, 12, 13, 15-17, 22, 25, 28-32, 34-36, 64-66, 69, 71, 72, 76-78, 80-83, 85, 89.