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Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Identifieur interne : 002F38 ( Main/Exploration ); précédent : 002F37; suivant : 002F39

Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.

Auteurs : Amanda M. Hulse-Kemp [États-Unis] ; Jana Lemm [Allemagne] ; Joerg Plieske [Allemagne] ; Hamid Ashrafi [États-Unis] ; Ramesh Buyyarapu [États-Unis] ; David D. Fang [États-Unis] ; James Frelichowski [États-Unis] ; Marc Giband [France, Brésil] ; Steve Hague [États-Unis] ; Lori L. Hinze [États-Unis] ; Kelli J. Kochan [États-Unis] ; Penny K. Riggs [États-Unis] ; Jodi A. Scheffler [États-Unis] ; Joshua A. Udall [États-Unis] ; Mauricio Ulloa [États-Unis] ; Shirley S. Wang [États-Unis] ; Qian-Hao Zhu [Australie] ; Sumit K. Bag [Inde] ; Archana Bhardwaj [Inde] ; John J. Burke [États-Unis] ; Robert L. Byers [États-Unis] ; Michel Claverie [France] ; Michael A. Gore [États-Unis] ; David B. Harker [États-Unis] ; Md S. Islam [États-Unis] ; Johnie N. Jenkins [États-Unis] ; Don C. Jones [États-Unis] ; Jean-Marc Lacape [France] ; Danny J. Llewellyn [Australie] ; Richard G. Percy [États-Unis] ; Alan E. Pepper [États-Unis] ; Jesse A. Poland [États-Unis] ; Krishan Mohan Rai [Inde] ; Samir V. Sawant [Inde] ; Sunil Kumar Singh [Inde] ; Andrew Spriggs [Australie] ; Jen M. Taylor [Australie] ; Fei Wang [États-Unis] ; Scott M. Yourstone [États-Unis] ; Xiuting Zheng [États-Unis] ; Cindy T. Lawley [États-Unis] ; Martin W. Ganal [Allemagne] ; Allen Van Deynze [États-Unis] ; Iain W. Wilson [Australie] ; David M. Stelly [États-Unis]

Source :

RBID : PMC:4478548

Descripteurs français

English descriptors

Abstract

High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense L., G. tomentosum Nuttal × Seemann, G. mustelinum Miers × Watt, G. armourianum Kearny, and G. longicalyx J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F2 mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two G. hirsutum lines. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.


Url:
DOI: 10.1534/g3.115.018416
PubMed: 25908569
PubMed Central: 4478548


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<name sortKey="Bag, Sumit K" sort="Bag, Sumit K" uniqKey="Bag S" first="Sumit K." last="Bag">Sumit K. Bag</name>
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<name sortKey="Byers, Robert L" sort="Byers, Robert L" uniqKey="Byers R" first="Robert L." last="Byers">Robert L. Byers</name>
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<name sortKey="Claverie, Michel" sort="Claverie, Michel" uniqKey="Claverie M" first="Michel" last="Claverie">Michel Claverie</name>
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<name sortKey="Islam, Md S" sort="Islam, Md S" uniqKey="Islam M" first="Md S." last="Islam">Md S. Islam</name>
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<region type="state">Louisiane</region>
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<name sortKey="Jenkins, Johnie N" sort="Jenkins, Johnie N" uniqKey="Jenkins J" first="Johnie N." last="Jenkins">Johnie N. Jenkins</name>
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<name sortKey="Jones, Don C" sort="Jones, Don C" uniqKey="Jones D" first="Don C." last="Jones">Don C. Jones</name>
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<nlm:aff id="aff19">Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513</nlm:aff>
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<region type="state">Caroline du Nord</region>
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<name sortKey="Lacape, Jean Marc" sort="Lacape, Jean Marc" uniqKey="Lacape J" first="Jean-Marc" last="Lacape">Jean-Marc Lacape</name>
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<name sortKey="Llewellyn, Danny J" sort="Llewellyn, Danny J" uniqKey="Llewellyn D" first="Danny J." last="Llewellyn">Danny J. Llewellyn</name>
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<name sortKey="Percy, Richard G" sort="Percy, Richard G" uniqKey="Percy R" first="Richard G." last="Percy">Richard G. Percy</name>
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<name sortKey="Pepper, Alan E" sort="Pepper, Alan E" uniqKey="Pepper A" first="Alan E." last="Pepper">Alan E. Pepper</name>
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<nlm:aff id="aff16">Department of Biology, Texas A&M University, College Station, Texas 77843</nlm:aff>
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<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Biology, Texas A&M University, College Station</wicri:cityArea>
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<name sortKey="Poland, Jesse A" sort="Poland, Jesse A" uniqKey="Poland J" first="Jesse A." last="Poland">Jesse A. Poland</name>
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<nlm:aff id="aff20">Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506</nlm:aff>
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<region type="state">Kansas</region>
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<name sortKey="Mohan Rai, Krishan" sort="Mohan Rai, Krishan" uniqKey="Mohan Rai K" first="Krishan" last="Mohan Rai">Krishan Mohan Rai</name>
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<title xml:lang="en" level="a" type="main">Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of
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<wicri:cityArea>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Harker, David B" sort="Harker, David B" uniqKey="Harker D" first="David B." last="Harker">David B. Harker</name>
<affiliation wicri:level="2">
<nlm:aff id="aff12">Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Utah</region>
</placeName>
<wicri:cityArea>Brigham Young University, Plant and Wildlife Science Department, Provo</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Islam, Md S" sort="Islam, Md S" uniqKey="Islam M" first="Md S." last="Islam">Md S. Islam</name>
<affiliation wicri:level="2">
<nlm:aff id="aff6">USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Louisiane</region>
</placeName>
<wicri:cityArea>USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Jenkins, Johnie N" sort="Jenkins, Johnie N" uniqKey="Jenkins J" first="Johnie N." last="Jenkins">Johnie N. Jenkins</name>
<affiliation wicri:level="2">
<nlm:aff id="aff18">USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">État du Mississippi</region>
</placeName>
<wicri:cityArea>USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Jones, Don C" sort="Jones, Don C" uniqKey="Jones D" first="Don C." last="Jones">Don C. Jones</name>
<affiliation wicri:level="2">
<nlm:aff id="aff19">Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Caroline du Nord</region>
</placeName>
<wicri:cityArea>Cotton Incorporated, Agricultural Research, Cary</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Lacape, Jean Marc" sort="Lacape, Jean Marc" uniqKey="Lacape J" first="Jean-Marc" last="Lacape">Jean-Marc Lacape</name>
<affiliation wicri:level="1">
<nlm:aff id="aff8">CIRAD, UMR AGAP, Montpellier, F34398, France</nlm:aff>
<country xml:lang="fr">France</country>
<wicri:regionArea>CIRAD, UMR AGAP, Montpellier, F34398</wicri:regionArea>
<wicri:noRegion>34398</wicri:noRegion>
<wicri:noRegion>34398</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Llewellyn, Danny J" sort="Llewellyn, Danny J" uniqKey="Llewellyn D" first="Danny J." last="Llewellyn">Danny J. Llewellyn</name>
<affiliation wicri:level="1">
<nlm:aff id="aff14">CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea>
<wicri:noRegion>ACT 2601</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Percy, Richard G" sort="Percy, Richard G" uniqKey="Percy R" first="Richard G." last="Percy">Richard G. Percy</name>
<affiliation wicri:level="2">
<nlm:aff id="aff7">USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Pepper, Alan E" sort="Pepper, Alan E" uniqKey="Pepper A" first="Alan E." last="Pepper">Alan E. Pepper</name>
<affiliation wicri:level="2">
<nlm:aff id="aff2">Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station</wicri:cityArea>
</affiliation>
<affiliation wicri:level="2">
<nlm:aff id="aff16">Department of Biology, Texas A&M University, College Station, Texas 77843</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Biology, Texas A&M University, College Station</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Poland, Jesse A" sort="Poland, Jesse A" uniqKey="Poland J" first="Jesse A." last="Poland">Jesse A. Poland</name>
<affiliation wicri:level="2">
<nlm:aff id="aff20">Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Kansas</region>
</placeName>
<wicri:cityArea>Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Mohan Rai, Krishan" sort="Mohan Rai, Krishan" uniqKey="Mohan Rai K" first="Krishan" last="Mohan Rai">Krishan Mohan Rai</name>
<affiliation wicri:level="1">
<nlm:aff id="aff15">CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India</nlm:aff>
<country xml:lang="fr">Inde</country>
<wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea>
<wicri:noRegion>UP</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Sawant, Samir V" sort="Sawant, Samir V" uniqKey="Sawant S" first="Samir V." last="Sawant">Samir V. Sawant</name>
<affiliation wicri:level="1">
<nlm:aff id="aff15">CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India</nlm:aff>
<country xml:lang="fr">Inde</country>
<wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea>
<wicri:noRegion>UP</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Singh, Sunil Kumar" sort="Singh, Sunil Kumar" uniqKey="Singh S" first="Sunil Kumar" last="Singh">Sunil Kumar Singh</name>
<affiliation wicri:level="1">
<nlm:aff id="aff15">CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India</nlm:aff>
<country xml:lang="fr">Inde</country>
<wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea>
<wicri:noRegion>UP</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Spriggs, Andrew" sort="Spriggs, Andrew" uniqKey="Spriggs A" first="Andrew" last="Spriggs">Andrew Spriggs</name>
<affiliation wicri:level="1">
<nlm:aff id="aff14">CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea>
<wicri:noRegion>ACT 2601</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Taylor, Jen M" sort="Taylor, Jen M" uniqKey="Taylor J" first="Jen M." last="Taylor">Jen M. Taylor</name>
<affiliation wicri:level="1">
<nlm:aff id="aff14">CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea>
<wicri:noRegion>ACT 2601</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Wang, Fei" sort="Wang, Fei" uniqKey="Wang F" first="Fei" last="Wang">Fei Wang</name>
<affiliation wicri:level="2">
<nlm:aff id="aff1">Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Soil & Crop Sciences, Texas A&M University, College Station</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Yourstone, Scott M" sort="Yourstone, Scott M" uniqKey="Yourstone S" first="Scott M." last="Yourstone">Scott M. Yourstone</name>
<affiliation wicri:level="2">
<nlm:aff id="aff12">Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Utah</region>
</placeName>
<wicri:cityArea>Brigham Young University, Plant and Wildlife Science Department, Provo</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Zheng, Xiuting" sort="Zheng, Xiuting" uniqKey="Zheng X" first="Xiuting" last="Zheng">Xiuting Zheng</name>
<affiliation wicri:level="2">
<nlm:aff id="aff1">Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Soil & Crop Sciences, Texas A&M University, College Station</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Lawley, Cindy T" sort="Lawley, Cindy T" uniqKey="Lawley C" first="Cindy T." last="Lawley">Cindy T. Lawley</name>
<affiliation wicri:level="2">
<nlm:aff id="aff21">Illumina Inc., San Francisco, California 94158</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>Illumina Inc., San Francisco</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Ganal, Martin W" sort="Ganal, Martin W" uniqKey="Ganal M" first="Martin W." last="Ganal">Martin W. Ganal</name>
<affiliation wicri:level="1">
<nlm:aff id="aff3">TraitGenetics GmbH, 06466 Gatersleben, Germany</nlm:aff>
<country xml:lang="fr">Allemagne</country>
<wicri:regionArea>TraitGenetics GmbH, 06466 Gatersleben</wicri:regionArea>
<wicri:noRegion>06466 Gatersleben</wicri:noRegion>
<wicri:noRegion>06466 Gatersleben</wicri:noRegion>
<wicri:noRegion>06466 Gatersleben</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Van Deynze, Allen" sort="Van Deynze, Allen" uniqKey="Van Deynze A" first="Allen" last="Van Deynze">Allen Van Deynze</name>
<affiliation wicri:level="2">
<nlm:aff id="aff4">Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Californie</region>
</placeName>
<wicri:cityArea>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis</wicri:cityArea>
</affiliation>
</author>
<author>
<name sortKey="Wilson, Iain W" sort="Wilson, Iain W" uniqKey="Wilson I" first="Iain W." last="Wilson">Iain W. Wilson</name>
<affiliation wicri:level="1">
<nlm:aff id="aff14">CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea>
<wicri:noRegion>ACT 2601</wicri:noRegion>
</affiliation>
</author>
<author>
<name sortKey="Stelly, David M" sort="Stelly, David M" uniqKey="Stelly D" first="David M." last="Stelly">David M. Stelly</name>
<affiliation wicri:level="2">
<nlm:aff id="aff1">Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Department of Soil & Crop Sciences, Texas A&M University, College Station</wicri:cityArea>
</affiliation>
<affiliation wicri:level="2">
<nlm:aff id="aff2">Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<placeName>
<region type="state">Texas</region>
</placeName>
<wicri:cityArea>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station</wicri:cityArea>
</affiliation>
</author>
</analytic>
<series>
<title level="j">G3: Genes|Genomes|Genetics</title>
<idno type="eISSN">2160-1836</idno>
<imprint>
<date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc>
<textClass>
<keywords scheme="KwdEn" xml:lang="en">
<term>Chromosome Mapping (methods)</term>
<term>Chromosomes, Plant (genetics)</term>
<term>Crossing Over, Genetic</term>
<term>Databases, Genetic</term>
<term>Gene Frequency (genetics)</term>
<term>Genetic Linkage</term>
<term>Genetic Markers</term>
<term>Genotype</term>
<term>Genotyping Techniques</term>
<term>Gossypium (genetics)</term>
<term>Polymorphism, Single Nucleotide (genetics)</term>
<term>Polyploidy</term>
<term>Reproducibility of Results</term>
<term>Species Specificity</term>
<term>Synteny (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Bases de données génétiques</term>
<term>Cartographie chromosomique ()</term>
<term>Chromosomes de plante (génétique)</term>
<term>Crossing-over</term>
<term>Fréquence d'allèle (génétique)</term>
<term>Gossypium (génétique)</term>
<term>Génotype</term>
<term>Liaison génétique</term>
<term>Marqueurs génétiques</term>
<term>Polymorphisme de nucléotide simple (génétique)</term>
<term>Polyploïdie</term>
<term>Reproductibilité des résultats</term>
<term>Spécificité d'espèce</term>
<term>Synténie (génétique)</term>
<term>Techniques de génotypage</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en">
<term>Genetic Markers</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Chromosomes, Plant</term>
<term>Gene Frequency</term>
<term>Gossypium</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Synteny</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Chromosomes de plante</term>
<term>Fréquence d'allèle</term>
<term>Gossypium</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Synténie</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en">
<term>Chromosome Mapping</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Crossing Over, Genetic</term>
<term>Databases, Genetic</term>
<term>Genetic Linkage</term>
<term>Genotype</term>
<term>Genotyping Techniques</term>
<term>Polyploidy</term>
<term>Reproducibility of Results</term>
<term>Species Specificity</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Bases de données génétiques</term>
<term>Cartographie chromosomique</term>
<term>Crossing-over</term>
<term>Génotype</term>
<term>Liaison génétique</term>
<term>Marqueurs génétiques</term>
<term>Polyploïdie</term>
<term>Reproductibilité des résultats</term>
<term>Spécificité d'espèce</term>
<term>Techniques de génotypage</term>
</keywords>
</textClass>
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<front>
<div type="abstract" xml:lang="en">
<p>High-throughput genotyping arrays provide a standardized resource for plant breeding communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), complex trait dissection, and studying patterns of genomic diversity among cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intraspecific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species
<italic>Gossypium hirsutum</italic>
L. and 17,954 putative interspecific SNP markers for use with crosses of other cotton species with
<italic>G. hirsutum</italic>
. The SNPs on the array were developed from 13 different discovery sets that represent a diverse range of
<italic>G. hirsutum</italic>
germplasm and five other species:
<italic>G. barbadense</italic>
L.,
<italic>G. tomentosum</italic>
Nuttal × Seemann,
<italic>G. mustelinum</italic>
Miers × Watt,
<italic>G. armourianum</italic>
Kearny, and
<italic>G. longicalyx</italic>
J.B. Hutchinson and Lee. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 38,822 polymorphic markers. Two high-density genetic maps containing a total of 22,829 SNPs were generated for two F
<sub>2</sub>
mapping populations, one intraspecific and one interspecific, and 3,533 SNP markers were co-occurring in both maps. The produced intraspecific genetic map is the first saturated map that associates into 26 linkage groups corresponding to the number of cotton chromosomes for a cross between two
<italic>G. hirsutum</italic>
lines. The linkage maps were shown to have high levels of collinearity to the JGI
<italic>G. raimondii</italic>
Ulbrich reference genome sequence. The CottonSNP63K array, cluster file and associated marker sequences constitute a major new resource for the global cotton research community.</p>
</div>
</front>
<back>
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