Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.
Identifieur interne : 000E16 ( PubMed/Checkpoint ); précédent : 000E15; suivant : 000E17Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.
Auteurs : Lori L. Hinze [États-Unis] ; Amanda M. Hulse-Kemp [États-Unis] ; Iain W. Wilson [Australie] ; Qian-Hao Zhu [Australie] ; Danny J. Llewellyn [Australie] ; Jen M. Taylor [Australie] ; Andrew Spriggs [Australie] ; David D. Fang [États-Unis] ; Mauricio Ulloa [États-Unis] ; John J. Burke [États-Unis] ; Marc Giband [France] ; Jean-Marc Lacape [France] ; Allen Van Deynze [États-Unis] ; Joshua A. Udall [États-Unis] ; Jodi A. Scheffler [États-Unis] ; Steve Hague [États-Unis] ; Jonathan F. Wendel [États-Unis] ; Alan E. Pepper [États-Unis] ; James Frelichowski [États-Unis] ; Cindy T. Lawley [États-Unis] ; Don C. Jones [États-Unis] ; Richard G. Percy [États-Unis] ; David M. Stelly [États-Unis]Source :
- BMC plant biology [ 1471-2229 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- chemical : Genetic Markers.
- classification : Gossypium.
- genetics : Gossypium.
- Alleles, Genetic Variation, Genome, Plant, Genotype, Microsatellite Repeats, Phylogeny, Polymorphism, Single Nucleotide.
Abstract
Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.
DOI: 10.1186/s12870-017-0981-y
PubMed: 28158969
Affiliations:
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Fang</name><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124</wicri:regionArea><wicri:noRegion>70124</wicri:noRegion></affiliation></author><author><name sortKey="Ulloa, Mauricio" sort="Ulloa, Mauricio" uniqKey="Ulloa M" first="Mauricio" last="Ulloa">Mauricio Ulloa</name><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415</wicri:regionArea><wicri:noRegion>79415</wicri:noRegion></affiliation></author><author><name sortKey="Burke, John J" sort="Burke, John J" uniqKey="Burke J" first="John J" last="Burke">John J. 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Scheffler</name><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS, 38776, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS, 38776</wicri:regionArea><wicri:noRegion>38776</wicri:noRegion></affiliation></author><author><name sortKey="Hague, Steve" sort="Hague, Steve" uniqKey="Hague S" first="Steve" last="Hague">Steve Hague</name><affiliation wicri:level="1"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843</wicri:regionArea><wicri:noRegion>77843</wicri:noRegion></affiliation></author><author><name sortKey="Wendel, Jonathan F" sort="Wendel, Jonathan F" uniqKey="Wendel J" first="Jonathan F" last="Wendel">Jonathan F. Wendel</name><affiliation wicri:level="4"><nlm:affiliation>Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011</wicri:regionArea><orgName type="university">Université d'État de l'Iowa</orgName><placeName><settlement type="city">Ames (Iowa)</settlement><region type="state">Iowa</region></placeName></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="1"><nlm:affiliation>Department of Biology, Texas A&M University, College Station, TX, 77843, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Texas A&M University, College Station, TX, 77843</wicri:regionArea><wicri:noRegion>77843</wicri:noRegion></affiliation></author><author><name sortKey="Frelichowski, James" sort="Frelichowski, James" uniqKey="Frelichowski J" first="James" last="Frelichowski">James Frelichowski</name><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845</wicri:regionArea><wicri:noRegion>77845</wicri:noRegion></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="1"><nlm:affiliation>Illumina Inc., 499 Illinois Street, San Francisco, CA, 94158, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Illumina Inc., 499 Illinois Street, San Francisco, CA, 94158</wicri:regionArea><wicri:noRegion>94158</wicri:noRegion></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="1"><nlm:affiliation>Cotton Incorporated, Agricultural Research, Cary, NC, 27513, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cotton Incorporated, Agricultural Research, Cary, NC, 27513</wicri:regionArea><wicri:noRegion>27513</wicri:noRegion></affiliation></author><author><name sortKey="Percy, Richard G" sort="Percy, Richard G" uniqKey="Percy R" first="Richard G" last="Percy">Richard G. 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Stelly</name><affiliation wicri:level="1"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA. stelly@tamu.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843</wicri:regionArea><wicri:noRegion>77843</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:28158969</idno><idno type="pmid">28158969</idno><idno type="doi">10.1186/s12870-017-0981-y</idno><idno type="wicri:Area/PubMed/Corpus">001077</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001077</idno><idno type="wicri:Area/PubMed/Curation">001074</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001074</idno><idno type="wicri:Area/PubMed/Checkpoint">001074</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001074</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.</title><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="1"><nlm:affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA. Lori.Hinze@ars.usda.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845</wicri:regionArea><wicri:noRegion>77845</wicri:noRegion></affiliation></author><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="1"><nlm:affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></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 & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></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 & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</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:affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>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:affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</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:affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</nlm:affiliation><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601</wicri:regionArea><wicri:noRegion>2601</wicri:noRegion></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="1"><nlm:affiliation>USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124</wicri:regionArea><wicri:noRegion>70124</wicri:noRegion></affiliation></author><author><name sortKey="Ulloa, Mauricio" sort="Ulloa, Mauricio" uniqKey="Ulloa M" first="Mauricio" last="Ulloa">Mauricio Ulloa</name><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415</wicri:regionArea><wicri:noRegion>79415</wicri:noRegion></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="1"><nlm:affiliation>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415</wicri:regionArea><wicri:noRegion>79415</wicri:noRegion></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.</nlm:affiliation><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="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><wicri:noRegion>34398</wicri:noRegion><wicri:noRegion>34398</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="1"><nlm:affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616</wicri:regionArea><wicri:noRegion>95616</wicri:noRegion></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="1"><nlm:affiliation>Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602</wicri:regionArea><wicri:noRegion>84602</wicri:noRegion></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="1"><nlm:affiliation>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS, 38776, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS, 38776</wicri:regionArea><wicri:noRegion>38776</wicri:noRegion></affiliation></author><author><name sortKey="Hague, Steve" sort="Hague, Steve" uniqKey="Hague S" first="Steve" last="Hague">Steve Hague</name><affiliation wicri:level="1"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843</wicri:regionArea><wicri:noRegion>77843</wicri:noRegion></affiliation></author><author><name sortKey="Wendel, Jonathan F" sort="Wendel, Jonathan F" uniqKey="Wendel J" first="Jonathan F" last="Wendel">Jonathan F. Wendel</name><affiliation wicri:level="4"><nlm:affiliation>Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011</wicri:regionArea><orgName type="university">Université d'État de l'Iowa</orgName><placeName><settlement type="city">Ames (Iowa)</settlement><region type="state">Iowa</region></placeName></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="1"><nlm:affiliation>Department of Biology, Texas A&M University, College Station, TX, 77843, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Texas A&M University, College Station, TX, 77843</wicri:regionArea><wicri:noRegion>77843</wicri:noRegion></affiliation></author><author><name sortKey="Frelichowski, James" sort="Frelichowski, James" uniqKey="Frelichowski J" first="James" last="Frelichowski">James Frelichowski</name><affiliation wicri:level="1"><nlm:affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845</wicri:regionArea><wicri:noRegion>77845</wicri:noRegion></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="1"><nlm:affiliation>Illumina Inc., 499 Illinois Street, San Francisco, CA, 94158, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Illumina Inc., 499 Illinois Street, San Francisco, CA, 94158</wicri:regionArea><wicri:noRegion>94158</wicri:noRegion></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="1"><nlm:affiliation>Cotton Incorporated, Agricultural Research, Cary, NC, 27513, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cotton Incorporated, Agricultural Research, Cary, NC, 27513</wicri:regionArea><wicri:noRegion>27513</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="1"><nlm:affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845</wicri:regionArea><wicri:noRegion>77845</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="1"><nlm:affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA. stelly@tamu.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843</wicri:regionArea><wicri:noRegion>77843</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles</term><term>Genetic Markers</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genotype</term><term>Gossypium (classification)</term><term>Gossypium (genetics)</term><term>Microsatellite Repeats</term><term>Phylogeny</term><term>Plant Proteins (genetics)</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Allèles</term><term>Gossypium ()</term><term>Gossypium (génétique)</term><term>Génome végétal</term><term>Génotype</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Polymorphisme de nucléotide simple</term><term>Protéines végétales (génétique)</term><term>Répétitions microsatellites</term><term>Variation génétique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Gossypium</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gossypium</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gossypium</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Genotype</term><term>Microsatellite Repeats</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Allèles</term><term>Gossypium</term><term>Génome végétal</term><term>Génotype</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Polymorphisme de nucléotide simple</term><term>Répétitions microsatellites</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28158969</PMID><DateCreated><Year>2017</Year><Month>02</Month><Day>04</Day></DateCreated><DateCompleted><Year>2017</Year><Month>10</Month><Day>23</Day></DateCompleted><DateRevised><Year>2017</Year><Month>10</Month><Day>23</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>Feb</Month><Day>03</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol.</ISOAbbreviation></Journal><ArticleTitle>Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.</ArticleTitle><Pagination><MedlinePgn>37</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12870-017-0981-y</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hinze</LastName><ForeName>Lori L</ForeName><Initials>LL</Initials><AffiliationInfo><Affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA. Lori.Hinze@ars.usda.gov.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hulse-Kemp</LastName><ForeName>Amanda M</ForeName><Initials>AM</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wilson</LastName><ForeName>Iain W</ForeName><Initials>IW</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Qian-Hao</ForeName><Initials>QH</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Llewellyn</LastName><ForeName>Danny J</ForeName><Initials>DJ</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Taylor</LastName><ForeName>Jen M</ForeName><Initials>JM</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Spriggs</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT, 2601, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>David D</ForeName><Initials>DD</Initials><AffiliationInfo><Affiliation>USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA, 70124, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ulloa</LastName><ForeName>Mauricio</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Burke</LastName><ForeName>John J</ForeName><Initials>JJ</Initials><AffiliationInfo><Affiliation>USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX, 79415, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Giband</LastName><ForeName>Marc</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>CIRAD, UMR AGAP, Montpellier, F34398, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000, Santo Antônio de Goias, GO, Brazil.</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>Van Deynze</LastName><ForeName>Allen</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA, 95616, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Udall</LastName><ForeName>Joshua A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>Plant and Wildlife Science Department, Brigham Young University, Provo, UT, 84602, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Scheffler</LastName><ForeName>Jodi A</ForeName><Initials>JA</Initials><AffiliationInfo><Affiliation>USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS, 38776, USA.</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, TX, 77843, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wendel</LastName><ForeName>Jonathan F</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pepper</LastName><ForeName>Alan E</ForeName><Initials>AE</Initials><AffiliationInfo><Affiliation>Department of Biology, Texas A&M University, College Station, TX, 77843, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX, 77843, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Frelichowski</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lawley</LastName><ForeName>Cindy T</ForeName><Initials>CT</Initials><AffiliationInfo><Affiliation>Illumina Inc., 499 Illinois Street, San Francisco, CA, 94158, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jones</LastName><ForeName>Don C</ForeName><Initials>DC</Initials><AffiliationInfo><Affiliation>Cotton Incorporated, Agricultural Research, Cary, NC, 27513, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Percy</LastName><ForeName>Richard G</ForeName><Initials>RG</Initials><AffiliationInfo><Affiliation>USDA-ARS, Crop Germplasm Research Unit, College Station, TX, 77845, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Stelly</LastName><ForeName>David M</ForeName><Initials>DM</Initials><AffiliationInfo><Affiliation>Department of Soil & Crop Sciences, Texas A&M University, College Station, TX, 77843, USA. stelly@tamu.edu.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX, 77843, USA. stelly@tamu.edu.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>02</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Plant Biol</MedlineTA><NlmUniqueID>100967807</NlmUniqueID><ISSNLinking>1471-2229</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic 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Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003368" MajorTopicYN="N">Gossypium</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Breeding</Keyword><Keyword MajorTopicYN="N">Cotton</Keyword><Keyword MajorTopicYN="N">Diversity analysis</Keyword><Keyword MajorTopicYN="N">Genome-wide association analysis</Keyword><Keyword MajorTopicYN="N">Germplasm collection</Keyword><Keyword MajorTopicYN="N">Molecular markers</Keyword><Keyword MajorTopicYN="N">Seed protein content</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>09</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2017</Year><Month>01</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>2</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>2</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>10</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">28158969</ArticleId><ArticleId IdType="doi">10.1186/s12870-017-0981-y</ArticleId><ArticleId IdType="pii">10.1186/s12870-017-0981-y</ArticleId><ArticleId IdType="pmc">PMC5291959</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Australie</li><li>France</li><li>États-Unis</li></country><region><li>Iowa</li></region><settlement><li>Ames (Iowa)</li></settlement><orgName><li>Université d'État de l'Iowa</li></orgName></list><tree><country name="États-Unis"><noRegion><name sortKey="Hinze, Lori L" sort="Hinze, Lori L" uniqKey="Hinze L" first="Lori L" last="Hinze">Lori L. Hinze</name></noRegion><name sortKey="Burke, John J" sort="Burke, John J" uniqKey="Burke J" first="John J" last="Burke">John J. Burke</name><name sortKey="Fang, David D" sort="Fang, David D" uniqKey="Fang D" first="David D" last="Fang">David D. Fang</name><name sortKey="Frelichowski, James" sort="Frelichowski, James" uniqKey="Frelichowski J" first="James" last="Frelichowski">James Frelichowski</name><name sortKey="Hague, Steve" sort="Hague, Steve" uniqKey="Hague S" first="Steve" last="Hague">Steve Hague</name><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><name sortKey="Jones, Don C" sort="Jones, Don C" uniqKey="Jones D" first="Don C" last="Jones">Don C. Jones</name><name sortKey="Lawley, Cindy T" sort="Lawley, Cindy T" uniqKey="Lawley C" first="Cindy T" last="Lawley">Cindy T. Lawley</name><name sortKey="Pepper, Alan E" sort="Pepper, Alan E" uniqKey="Pepper A" first="Alan E" last="Pepper">Alan E. Pepper</name><name sortKey="Percy, Richard G" sort="Percy, Richard G" uniqKey="Percy R" first="Richard G" last="Percy">Richard G. Percy</name><name sortKey="Scheffler, Jodi A" sort="Scheffler, Jodi A" uniqKey="Scheffler J" first="Jodi A" last="Scheffler">Jodi A. Scheffler</name><name sortKey="Stelly, David M" sort="Stelly, David M" uniqKey="Stelly D" first="David M" last="Stelly">David M. Stelly</name><name sortKey="Udall, Joshua A" sort="Udall, Joshua A" uniqKey="Udall J" first="Joshua A" last="Udall">Joshua A. Udall</name><name sortKey="Ulloa, Mauricio" sort="Ulloa, Mauricio" uniqKey="Ulloa M" first="Mauricio" last="Ulloa">Mauricio Ulloa</name><name sortKey="Van Deynze, Allen" sort="Van Deynze, Allen" uniqKey="Van Deynze A" first="Allen" last="Van Deynze">Allen Van Deynze</name><name sortKey="Wendel, Jonathan F" sort="Wendel, Jonathan F" uniqKey="Wendel J" first="Jonathan F" last="Wendel">Jonathan F. Wendel</name></country><country name="Australie"><noRegion><name sortKey="Wilson, Iain W" sort="Wilson, Iain W" uniqKey="Wilson I" first="Iain W" last="Wilson">Iain W. Wilson</name></noRegion><name sortKey="Llewellyn, Danny J" sort="Llewellyn, Danny J" uniqKey="Llewellyn D" first="Danny J" last="Llewellyn">Danny J. Llewellyn</name><name sortKey="Spriggs, Andrew" sort="Spriggs, Andrew" uniqKey="Spriggs A" first="Andrew" last="Spriggs">Andrew Spriggs</name><name sortKey="Taylor, Jen M" sort="Taylor, Jen M" uniqKey="Taylor J" first="Jen M" last="Taylor">Jen M. Taylor</name><name sortKey="Zhu, Qian Hao" sort="Zhu, Qian Hao" uniqKey="Zhu Q" first="Qian-Hao" last="Zhu">Qian-Hao Zhu</name></country><country name="France"><noRegion><name sortKey="Giband, Marc" sort="Giband, Marc" uniqKey="Giband M" first="Marc" last="Giband">Marc Giband</name></noRegion><name sortKey="Lacape, Jean Marc" sort="Lacape, Jean Marc" uniqKey="Lacape J" first="Jean-Marc" last="Lacape">Jean-Marc Lacape</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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