Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp.
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.
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Biblioteca del CIRAD Francia |
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eng |
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F30 - Génétique et amélioration des plantes Gossypium Gossypium barbadense Gossypium tomentosum Gossypium hirsutum carte génétique amélioration des plantes génomique hybridation interspécifique hybridation intraspécifique génotype polymorphisme génétique marqueur génétique génétique des populations http://aims.fao.org/aos/agrovoc/c_3335 http://aims.fao.org/aos/agrovoc/c_3337 http://aims.fao.org/aos/agrovoc/c_3340 http://aims.fao.org/aos/agrovoc/c_3339 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_34298 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_34326 F30 - Génétique et amélioration des plantes Gossypium Gossypium barbadense Gossypium tomentosum Gossypium hirsutum carte génétique amélioration des plantes génomique hybridation interspécifique hybridation intraspécifique génotype polymorphisme génétique marqueur génétique génétique des populations http://aims.fao.org/aos/agrovoc/c_3335 http://aims.fao.org/aos/agrovoc/c_3337 http://aims.fao.org/aos/agrovoc/c_3340 http://aims.fao.org/aos/agrovoc/c_3339 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_34298 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_34326 |
spellingShingle |
F30 - Génétique et amélioration des plantes Gossypium Gossypium barbadense Gossypium tomentosum Gossypium hirsutum carte génétique amélioration des plantes génomique hybridation interspécifique hybridation intraspécifique génotype polymorphisme génétique marqueur génétique génétique des populations http://aims.fao.org/aos/agrovoc/c_3335 http://aims.fao.org/aos/agrovoc/c_3337 http://aims.fao.org/aos/agrovoc/c_3340 http://aims.fao.org/aos/agrovoc/c_3339 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_34298 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_34326 F30 - Génétique et amélioration des plantes Gossypium Gossypium barbadense Gossypium tomentosum Gossypium hirsutum carte génétique amélioration des plantes génomique hybridation interspécifique hybridation intraspécifique génotype polymorphisme génétique marqueur génétique génétique des populations http://aims.fao.org/aos/agrovoc/c_3335 http://aims.fao.org/aos/agrovoc/c_3337 http://aims.fao.org/aos/agrovoc/c_3340 http://aims.fao.org/aos/agrovoc/c_3339 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_34298 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_34326 Hulse-Kemp, Amanda M. Lemm, Jana Plieske, Joerg Ashrafi, Hamid Buyyarapu, Ramesh Fang, David D. Frelichowski, James Giband, Marc Hague, Steve Hinze, Lori L. Kochan, Kelli J. Riggs, Penny K. Scheffler, Jodi Udall, Joshua Ulloa, Mauricio Wang, Shirley S. Zhu, Qian-Hao Bag, Sumit K. Bhardwaj, Archana Burke, John Byers, Robert L. Claverie, Michel Gore, Michael A. Harker, David B. Islam, Md S. Jenkins, Johnie N. Jones, Don C. Lacape, Jean-Marc Llewellyn, Danny Percy, Richard Pepper, Alan Poland, Jesse A. Mohan Rai, Krishan Sawant, Samir V. Singh, Sunil Kumar Spriggs, Andrew Taylor, Jen M. Wang, Fei Yourstone, Scott M. Zheng, Xiuting Lawley, Cindy T. Ganal, Martin W. Van Deynze, Allen Wilson, Iain W. Stelly, David M. Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. |
description |
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. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes Gossypium Gossypium barbadense Gossypium tomentosum Gossypium hirsutum carte génétique amélioration des plantes génomique hybridation interspécifique hybridation intraspécifique génotype polymorphisme génétique marqueur génétique génétique des populations http://aims.fao.org/aos/agrovoc/c_3335 http://aims.fao.org/aos/agrovoc/c_3337 http://aims.fao.org/aos/agrovoc/c_3340 http://aims.fao.org/aos/agrovoc/c_3339 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_34298 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_34326 |
author |
Hulse-Kemp, Amanda M. Lemm, Jana Plieske, Joerg Ashrafi, Hamid Buyyarapu, Ramesh Fang, David D. Frelichowski, James Giband, Marc Hague, Steve Hinze, Lori L. Kochan, Kelli J. Riggs, Penny K. Scheffler, Jodi Udall, Joshua Ulloa, Mauricio Wang, Shirley S. Zhu, Qian-Hao Bag, Sumit K. Bhardwaj, Archana Burke, John Byers, Robert L. Claverie, Michel Gore, Michael A. Harker, David B. Islam, Md S. Jenkins, Johnie N. Jones, Don C. Lacape, Jean-Marc Llewellyn, Danny Percy, Richard Pepper, Alan Poland, Jesse A. Mohan Rai, Krishan Sawant, Samir V. Singh, Sunil Kumar Spriggs, Andrew Taylor, Jen M. Wang, Fei Yourstone, Scott M. Zheng, Xiuting Lawley, Cindy T. Ganal, Martin W. Van Deynze, Allen Wilson, Iain W. Stelly, David M. |
author_facet |
Hulse-Kemp, Amanda M. Lemm, Jana Plieske, Joerg Ashrafi, Hamid Buyyarapu, Ramesh Fang, David D. Frelichowski, James Giband, Marc Hague, Steve Hinze, Lori L. Kochan, Kelli J. Riggs, Penny K. Scheffler, Jodi Udall, Joshua Ulloa, Mauricio Wang, Shirley S. Zhu, Qian-Hao Bag, Sumit K. Bhardwaj, Archana Burke, John Byers, Robert L. Claverie, Michel Gore, Michael A. Harker, David B. Islam, Md S. Jenkins, Johnie N. Jones, Don C. Lacape, Jean-Marc Llewellyn, Danny Percy, Richard Pepper, Alan Poland, Jesse A. Mohan Rai, Krishan Sawant, Samir V. Singh, Sunil Kumar Spriggs, Andrew Taylor, Jen M. Wang, Fei Yourstone, Scott M. Zheng, Xiuting Lawley, Cindy T. Ganal, Martin W. Van Deynze, Allen Wilson, Iain W. Stelly, David M. |
author_sort |
Hulse-Kemp, Amanda M. |
title |
Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. |
title_short |
Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. |
title_full |
Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. |
title_fullStr |
Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. |
title_full_unstemmed |
Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. |
title_sort |
development of a 63k snp array for cotton and high-density mapping of intraspecific and interspecific populations of gossypium spp. |
url |
http://agritrop.cirad.fr/576372/ http://agritrop.cirad.fr/576372/1/Hulse-Kemp2015%20SNPchip.pdf |
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dig-cirad-fr-5763722024-01-28T22:45:39Z http://agritrop.cirad.fr/576372/ http://agritrop.cirad.fr/576372/ Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. Hulse-Kemp Amanda M., Lemm Jana, Plieske Joerg, Ashrafi Hamid, Buyyarapu Ramesh, Fang David D., Frelichowski James, Giband Marc, Hague Steve, Hinze Lori L., Kochan Kelli J., Riggs Penny K., Scheffler Jodi, Udall Joshua, Ulloa Mauricio, Wang Shirley S., Zhu Qian-Hao, Bag Sumit K., Bhardwaj Archana, Burke John, Byers Robert L., Claverie Michel, Gore Michael A., Harker David B., Islam Md S., Jenkins Johnie N., Jones Don C., Lacape Jean-Marc, Llewellyn Danny, Percy Richard, Pepper Alan, Poland Jesse A., Mohan Rai Krishan, Sawant Samir V., Singh Sunil Kumar, Spriggs Andrew, Taylor Jen M., Wang Fei, Yourstone Scott M., Zheng Xiuting, Lawley Cindy T., Ganal Martin W., Van Deynze Allen, Wilson Iain W., Stelly David M.. 2015. G3 - Genes Genomes Genetics, 5 (6) : 1187-1209.https://doi.org/10.1534/g3.115.018416 <https://doi.org/10.1534/g3.115.018416> Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp. Hulse-Kemp, Amanda M. Lemm, Jana Plieske, Joerg Ashrafi, Hamid Buyyarapu, Ramesh Fang, David D. Frelichowski, James Giband, Marc Hague, Steve Hinze, Lori L. Kochan, Kelli J. Riggs, Penny K. Scheffler, Jodi Udall, Joshua Ulloa, Mauricio Wang, Shirley S. Zhu, Qian-Hao Bag, Sumit K. Bhardwaj, Archana Burke, John Byers, Robert L. Claverie, Michel Gore, Michael A. Harker, David B. Islam, Md S. Jenkins, Johnie N. Jones, Don C. Lacape, Jean-Marc Llewellyn, Danny Percy, Richard Pepper, Alan Poland, Jesse A. Mohan Rai, Krishan Sawant, Samir V. Singh, Sunil Kumar Spriggs, Andrew Taylor, Jen M. Wang, Fei Yourstone, Scott M. Zheng, Xiuting Lawley, Cindy T. Ganal, Martin W. Van Deynze, Allen Wilson, Iain W. Stelly, David M. eng 2015 G3 - Genes Genomes Genetics F30 - Génétique et amélioration des plantes Gossypium Gossypium barbadense Gossypium tomentosum Gossypium hirsutum carte génétique amélioration des plantes génomique hybridation interspécifique hybridation intraspécifique génotype polymorphisme génétique marqueur génétique génétique des populations http://aims.fao.org/aos/agrovoc/c_3335 http://aims.fao.org/aos/agrovoc/c_3337 http://aims.fao.org/aos/agrovoc/c_3340 http://aims.fao.org/aos/agrovoc/c_3339 http://aims.fao.org/aos/agrovoc/c_24002 http://aims.fao.org/aos/agrovoc/c_5956 http://aims.fao.org/aos/agrovoc/c_92382 http://aims.fao.org/aos/agrovoc/c_26794 http://aims.fao.org/aos/agrovoc/c_34298 http://aims.fao.org/aos/agrovoc/c_3225 http://aims.fao.org/aos/agrovoc/c_24031 http://aims.fao.org/aos/agrovoc/c_24030 http://aims.fao.org/aos/agrovoc/c_34326 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. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/576372/1/Hulse-Kemp2015%20SNPchip.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1534/g3.115.018416 10.1534/g3.115.018416 info:eu-repo/semantics/altIdentifier/doi/10.1534/g3.115.018416 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1534/g3.115.018416 |