Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.
Identifieur interne : 002D52 ( PubMed/Curation ); précédent : 002D51; suivant : 002D53Development 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 [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 :
- G3 (Bethesda, Md.) [ 2160-1836 ] ; 2015.
Descripteurs français
- KwdFr :
- Bases de données génétiques, Cartographie chromosomique (), Chromosomes de plante (génétique), Crossing-over, Fréquence d'allèle (génétique), Gossypium (génétique), Génotype, Liaison génétique, Marqueurs génétiques, Polymorphisme de nucléotide simple (génétique), Polyploïdie, Reproductibilité des résultats, Spécificité d'espèce, Synténie (génétique), Techniques de génotypage.
- MESH :
- génétique : Chromosomes de plante, Fréquence d'allèle, Gossypium, Polymorphisme de nucléotide simple, Synténie.
- Bases de données génétiques, Cartographie chromosomique, Crossing-over, Génotype, Liaison génétique, Marqueurs génétiques, Polyploïdie, Reproductibilité des résultats, Spécificité d'espèce, Techniques de génotypage.
English descriptors
- KwdEn :
- Chromosome Mapping (methods), Chromosomes, Plant (genetics), Crossing Over, Genetic, Databases, Genetic, Gene Frequency (genetics), Genetic Linkage, Genetic Markers, Genotype, Genotyping Techniques, Gossypium (genetics), Polymorphism, Single Nucleotide (genetics), Polyploidy, Reproducibility of Results, Species Specificity, Synteny (genetics).
- MESH :
- chemical : Genetic Markers.
- genetics : Chromosomes, Plant, Gene Frequency, Gossypium, Polymorphism, Single Nucleotide, Synteny.
- methods : Chromosome Mapping.
- Crossing Over, Genetic, Databases, Genetic, Genetic Linkage, Genotype, Genotyping Techniques, Polyploidy, Reproducibility of Results, Species Specificity.
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.
DOI: 10.1534/g3.115.018416
PubMed: 25908569
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Burke</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock</wicri:cityArea></affiliation></author><author><name sortKey="Byers, Robert L" sort="Byers, Robert L" uniqKey="Byers R" first="Robert L" last="Byers">Robert L. Byers</name><affiliation wicri:level="2"><nlm:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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="Claverie, Michel" sort="Claverie, Michel" uniqKey="Claverie M" first="Michel" last="Claverie">Michel Claverie</name><affiliation wicri:level="1"><nlm:affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR AGAP, Montpellier, F34398</wicri:regionArea></affiliation></author><author><name sortKey="Gore, Michael A" sort="Gore, Michael A" uniqKey="Gore M" first="Michael A" last="Gore">Michael A. Gore</name><affiliation wicri:level="2"><nlm:affiliation>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><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:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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:affiliation>USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.</nlm:affiliation><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:affiliation>USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762.</nlm:affiliation><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:affiliation>Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513.</nlm:affiliation><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:affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR AGAP, Montpellier, F34398</wicri:regionArea></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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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:affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</nlm:affiliation><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:affiliation>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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, Texas 77843 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:affiliation>Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506.</nlm:affiliation><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:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></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:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></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:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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:affiliation>Illumina Inc., San Francisco, California 94158.</nlm:affiliation><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:affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>TraitGenetics GmbH, 06466 Gatersleben</wicri:regionArea></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:affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.</nlm:affiliation><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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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="1"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 stelly@tamu.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2015">2015</date><idno type="RBID">pubmed:25908569</idno><idno type="pmid">25908569</idno><idno type="doi">10.1534/g3.115.018416</idno><idno type="wicri:Area/PubMed/Corpus">002E28</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002E28</idno><idno type="wicri:Area/PubMed/Curation">002D52</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002D52</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.</title><author><name sortKey="Hulse Kemp, Amanda M" sort="Hulse Kemp, Amanda M" uniqKey="Hulse Kemp A" first="Amanda M" last="Hulse-Kemp">Amanda M. Hulse-Kemp</name><affiliation wicri:level="2"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station</wicri:cityArea></affiliation></author><author><name sortKey="Lemm, Jana" sort="Lemm, Jana" uniqKey="Lemm J" first="Jana" last="Lemm">Jana Lemm</name><affiliation wicri:level="1"><nlm:affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>TraitGenetics GmbH, 06466 Gatersleben</wicri:regionArea></affiliation></author><author><name sortKey="Plieske, Joerg" sort="Plieske, Joerg" uniqKey="Plieske J" first="Joerg" last="Plieske">Joerg Plieske</name><affiliation wicri:level="1"><nlm:affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>TraitGenetics GmbH, 06466 Gatersleben</wicri:regionArea></affiliation></author><author><name sortKey="Ashrafi, Hamid" sort="Ashrafi, Hamid" uniqKey="Ashrafi H" first="Hamid" last="Ashrafi">Hamid Ashrafi</name><affiliation wicri:level="2"><nlm:affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.</nlm:affiliation><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="Buyyarapu, Ramesh" sort="Buyyarapu, Ramesh" uniqKey="Buyyarapu R" first="Ramesh" last="Buyyarapu">Ramesh Buyyarapu</name><affiliation wicri:level="2"><nlm:affiliation>Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Indiana</region></placeName><wicri:cityArea>Dow AgroSciences, Trait Genetics and Technologies, Indianapolis</wicri:cityArea></affiliation></author><author><name sortKey="Fang, David D" sort="Fang, David D" uniqKey="Fang D" first="David D" last="Fang">David D. Fang</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.</nlm:affiliation><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="Frelichowski, James" sort="Frelichowski, James" uniqKey="Frelichowski J" first="James" last="Frelichowski">James Frelichowski</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</nlm:affiliation><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="Giband, Marc" sort="Giband, Marc" uniqKey="Giband M" first="Marc" last="Giband">Marc Giband</name><affiliation wicri:level="1"><nlm:affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil.</nlm:affiliation><country xml:lang="fr">Brésil</country><wicri:regionArea>CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO</wicri:regionArea></affiliation></author><author><name sortKey="Hague, Steve" sort="Hague, Steve" uniqKey="Hague S" first="Steve" last="Hague">Steve Hague</name><affiliation wicri:level="2"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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="Hinze, Lori L" sort="Hinze, Lori L" uniqKey="Hinze L" first="Lori L" last="Hinze">Lori L. Hinze</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</nlm:affiliation><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="Kochan, Kelli J" sort="Kochan, Kelli J" uniqKey="Kochan K" first="Kelli J" last="Kochan">Kelli J. Kochan</name><affiliation wicri:level="2"><nlm:affiliation>Department of Animal Science, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>Department of Animal Science, Texas A&M University, College Station</wicri:cityArea></affiliation></author><author><name sortKey="Riggs, Penny K" sort="Riggs, Penny K" uniqKey="Riggs P" first="Penny K" last="Riggs">Penny K. Riggs</name><affiliation wicri:level="2"><nlm:affiliation>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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, Texas 77843 Department of Animal Science, Texas A&M University, College Station</wicri:cityArea></affiliation></author><author><name sortKey="Scheffler, Jodi A" sort="Scheffler, Jodi A" uniqKey="Scheffler J" first="Jodi A" last="Scheffler">Jodi A. Scheffler</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État du Mississippi</region></placeName><wicri:cityArea>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville</wicri:cityArea></affiliation></author><author><name sortKey="Udall, Joshua A" sort="Udall, Joshua A" uniqKey="Udall J" first="Joshua A" last="Udall">Joshua A. Udall</name><affiliation wicri:level="2"><nlm:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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="Ulloa, Mauricio" sort="Ulloa, Mauricio" uniqKey="Ulloa M" first="Mauricio" last="Ulloa">Mauricio Ulloa</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock</wicri:cityArea></affiliation></author><author><name sortKey="Wang, Shirley S" sort="Wang, Shirley S" uniqKey="Wang S" first="Shirley S" last="Wang">Shirley S. Wang</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</nlm:affiliation><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="Zhu, Qian Hao" sort="Zhu, Qian Hao" uniqKey="Zhu Q" first="Qian-Hao" last="Zhu">Qian-Hao Zhu</name><affiliation wicri:level="1"><nlm:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></affiliation></author><author><name sortKey="Bag, Sumit K" sort="Bag, Sumit K" uniqKey="Bag S" first="Sumit K" last="Bag">Sumit K. Bag</name><affiliation wicri:level="1"><nlm:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></affiliation></author><author><name sortKey="Bhardwaj, Archana" sort="Bhardwaj, Archana" uniqKey="Bhardwaj A" first="Archana" last="Bhardwaj">Archana Bhardwaj</name><affiliation wicri:level="1"><nlm:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></affiliation></author><author><name sortKey="Burke, John J" sort="Burke, John J" uniqKey="Burke J" first="John J" last="Burke">John J. Burke</name><affiliation wicri:level="2"><nlm:affiliation>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Texas</region></placeName><wicri:cityArea>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock</wicri:cityArea></affiliation></author><author><name sortKey="Byers, Robert L" sort="Byers, Robert L" uniqKey="Byers R" first="Robert L" last="Byers">Robert L. Byers</name><affiliation wicri:level="2"><nlm:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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="Claverie, Michel" sort="Claverie, Michel" uniqKey="Claverie M" first="Michel" last="Claverie">Michel Claverie</name><affiliation wicri:level="1"><nlm:affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR AGAP, Montpellier, F34398</wicri:regionArea></affiliation></author><author><name sortKey="Gore, Michael A" sort="Gore, Michael A" uniqKey="Gore M" first="Michael A" last="Gore">Michael A. Gore</name><affiliation wicri:level="2"><nlm:affiliation>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">État de New York</region></placeName><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:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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:affiliation>USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.</nlm:affiliation><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:affiliation>USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762.</nlm:affiliation><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:affiliation>Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513.</nlm:affiliation><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:affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR AGAP, Montpellier, F34398</wicri:regionArea></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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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:affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</nlm:affiliation><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:affiliation>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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, Texas 77843 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:affiliation>Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506.</nlm:affiliation><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:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></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:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></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:affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</nlm:affiliation><country xml:lang="fr">Inde</country><wicri:regionArea>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP</wicri:regionArea></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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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:affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</nlm:affiliation><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:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</nlm:affiliation><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:affiliation>Illumina Inc., San Francisco, California 94158.</nlm:affiliation><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:affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>TraitGenetics GmbH, 06466 Gatersleben</wicri:regionArea></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:affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.</nlm:affiliation><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:affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601</wicri:regionArea></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="1"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 stelly@tamu.edu.</nlm:affiliation><country wicri:rule="url">États-Unis</country><wicri:regionArea>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station</wicri:regionArea></affiliation></author></analytic><series><title level="j">G3 (Bethesda, Md.)</title><idno type="eISSN">2160-1836</idno><imprint><date when="2015" type="published">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></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25908569</PMID><DateCreated><Year>2015</Year><Month>06</Month><Day>13</Day></DateCreated><DateCompleted><Year>2016</Year><Month>03</Month><Day>07</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">2160-1836</ISSN><JournalIssue CitedMedium="Internet"><Volume>5</Volume><Issue>6</Issue><PubDate><Year>2015</Year><Month>Apr</Month><Day>22</Day></PubDate></JournalIssue><Title>G3 (Bethesda, Md.)</Title><ISOAbbreviation>G3 (Bethesda)</ISOAbbreviation></Journal><ArticleTitle>Development of a 63K SNP Array for Cotton and High-Density Mapping of Intraspecific and Interspecific Populations of Gossypium spp.</ArticleTitle><Pagination><MedlinePgn>1187-209</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1534/g3.115.018416</ELocationID><Abstract><AbstractText>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.</AbstractText><CopyrightInformation>Copyright © 2015 Hulse-Kemp et al.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hulse-Kemp</LastName><ForeName>Amanda M</ForeName><Initials>AM</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9670-9433</Identifier><AffiliationInfo><Affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lemm</LastName><ForeName>Jana</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Plieske</LastName><ForeName>Joerg</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ashrafi</LastName><ForeName>Hamid</ForeName><Initials>H</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2094-2367</Identifier><AffiliationInfo><Affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Buyyarapu</LastName><ForeName>Ramesh</ForeName><Initials>R</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-5343-9960</Identifier><AffiliationInfo><Affiliation>Dow AgroSciences, Trait Genetics and Technologies, Indianapolis, Indiana 46268.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>David D</ForeName><Initials>DD</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-0036-5459</Identifier><AffiliationInfo><Affiliation>USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Frelichowski</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giband</LastName><ForeName>Marc</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO, Brazil.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hague</LastName><ForeName>Steve</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hinze</LastName><ForeName>Lori L</ForeName><Initials>LL</Initials><AffiliationInfo><Affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kochan</LastName><ForeName>Kelli J</ForeName><Initials>KJ</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8124-8283</Identifier><AffiliationInfo><Affiliation>Department of Animal Science, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Riggs</LastName><ForeName>Penny K</ForeName><Initials>PK</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-3296-320X</Identifier><AffiliationInfo><Affiliation>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Animal Science, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scheffler</LastName><ForeName>Jodi A</ForeName><Initials>JA</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-7897-2916</Identifier><AffiliationInfo><Affiliation>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, Mississippi 38776.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Udall</LastName><ForeName>Joshua A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ulloa</LastName><ForeName>Mauricio</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Shirley S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Qian-Hao</ForeName><Initials>QH</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-6505-7417</Identifier><AffiliationInfo><Affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bag</LastName><ForeName>Sumit K</ForeName><Initials>SK</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-8907-2841</Identifier><AffiliationInfo><Affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bhardwaj</LastName><ForeName>Archana</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Burke</LastName><ForeName>John J</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>USDA-ARS, PA, Plant Stress and Germplasm Development Research Unit, Lubbock, Texas 79415.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Byers</LastName><ForeName>Robert L</ForeName><Initials>RL</Initials><AffiliationInfo><Affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Claverie</LastName><ForeName>Michel</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gore</LastName><ForeName>Michael A</ForeName><Initials>MA</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-6896-8024</Identifier><AffiliationInfo><Affiliation>Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Harker</LastName><ForeName>David B</ForeName><Initials>DB</Initials><AffiliationInfo><Affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Islam</LastName><ForeName>Md S</ForeName><Initials>MS</Initials><AffiliationInfo><Affiliation>USDA-ARS-SRRC, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana 70124.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jenkins</LastName><ForeName>Johnie N</ForeName><Initials>JN</Initials><AffiliationInfo><Affiliation>USDA-ARS, Genetics and Precision Agriculture Research, Mississippi State, Mississippi 39762.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Don C</ForeName><Initials>DC</Initials><AffiliationInfo><Affiliation>Cotton Incorporated, Agricultural Research, Cary, North Carolina 27513.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lacape</LastName><ForeName>Jean-Marc</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Llewellyn</LastName><ForeName>Danny J</ForeName><Initials>DJ</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Percy</LastName><ForeName>Richard G</ForeName><Initials>RG</Initials><AffiliationInfo><Affiliation>USDA-ARS-SPARC, Crop Germplasm Research Unit, College Station, Texas 77845.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pepper</LastName><ForeName>Alan E</ForeName><Initials>AE</Initials><AffiliationInfo><Affiliation>Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 Department of Biology, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Poland</LastName><ForeName>Jesse A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, Kansas 66506.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mohan Rai</LastName><ForeName>Krishan</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sawant</LastName><ForeName>Samir V</ForeName><Initials>SV</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-7635-5049</Identifier><AffiliationInfo><Affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Sunil Kumar</ForeName><Initials>SK</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-4897-8812</Identifier><AffiliationInfo><Affiliation>CSIR-National Botanical Research Institute, Plant Molecular Biology Division, Lucknow-226001, UP, India.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Spriggs</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>Jen M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Fei</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yourstone</LastName><ForeName>Scott M</ForeName><Initials>SM</Initials><AffiliationInfo><Affiliation>Brigham Young University, Plant and Wildlife Science Department, Provo, Utah 84602.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zheng</LastName><ForeName>Xiuting</ForeName><Initials>X</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-8574-4708</Identifier><AffiliationInfo><Affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawley</LastName><ForeName>Cindy T</ForeName><Initials>CT</Initials><AffiliationInfo><Affiliation>Illumina Inc., San Francisco, California 94158.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ganal</LastName><ForeName>Martin W</ForeName><Initials>MW</Initials><AffiliationInfo><Affiliation>TraitGenetics GmbH, 06466 Gatersleben, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Van Deynze</LastName><ForeName>Allen</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-2093-0577</Identifier><AffiliationInfo><Affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, California 95616.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wilson</LastName><ForeName>Iain W</ForeName><Initials>IW</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture Flagship, Black Mountain Laboratories, ACT 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stelly</LastName><ForeName>David M</ForeName><Initials>DM</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-3468-4119</Identifier><AffiliationInfo><Affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, Texas 77843 Interdisciplinary Degree Program in Genetics, Texas A&M University, College Station, Texas 77843 stelly@tamu.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>T32 GM067553</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, 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Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005787" MajorTopicYN="N">Gene Frequency</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008040" MajorTopicYN="N">Genetic Linkage</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D060005" MajorTopicYN="N">Genotyping Techniques</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003368" MajorTopicYN="N">Gossypium</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011123" MajorTopicYN="N">Polyploidy</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D026801" MajorTopicYN="N">Synteny</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC4478548</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">breeding</Keyword><Keyword MajorTopicYN="N">interspecific SNPs</Keyword><Keyword MajorTopicYN="N">intraspecific SNPs</Keyword><Keyword MajorTopicYN="N">linkage analysis</Keyword><Keyword MajorTopicYN="N">recombination</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>3</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25908569</ArticleId><ArticleId IdType="pii">g3.115.018416</ArticleId><ArticleId IdType="doi">10.1534/g3.115.018416</ArticleId><ArticleId IdType="pmc">PMC4478548</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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