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. Development of a 63K SNP array for cotton and high-density mapping of intraspecific and interspecific populations of Gossypium spp.. G3 - Genes Genomes Genetics, 5 (6) : pp. 1187-1209.

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Quartile : Q2, Sujet : GENETICS & HEREDITY

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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. (Résumé d'auteur)

Mots-clés Agrovoc : 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

Mots-clés complémentaires : Gossypium mustelinum

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • Hulse-Kemp Amanda M., Texas A & M University (USA)
  • Lemm Jana, TraitGenetics GmbH (DEU)
  • Plieske Joerg, TraitGenetics GmbH (DEU)
  • Ashrafi Hamid, UC (USA)
  • Buyyarapu Ramesh, Dow Agrosciences (USA)
  • Fang David D., USDA (USA)
  • Frelichowski James, USDA (USA)
  • Giband Marc, CIRAD-BIOS-UMR AGAP (BRA)
  • Hague Steve, Texas A & M University (USA)
  • Hinze Lori L., USDA (FRA)
  • Kochan Kelli J., Texas A & M University (USA)
  • Riggs Penny K., Texas A & M University (USA)
  • Scheffler Jodi, USDA (USA)
  • Udall Joshua, Brigham Young University (USA)
  • Ulloa Mauricio, USDA (USA)
  • Wang Shirley S., USDA (FRA)
  • Zhu Qian-Hao, CSIRO (AUS)
  • Bag Sumit K., National Botanical Research Institute (IND)
  • Bhardwaj Archana, National Botanical Research Institute (IND)
  • Burke John, USDA (USA)
  • Byers Robert L., Brigham Young University (USA)
  • Claverie Michel
  • Gore Michael A., Cornell University (USA)
  • Harker David B., Brigham Young University (USA)
  • Islam Md S., USDA (USA)
  • Jenkins Johnie N., USDA (USA)
  • Jones Don C., Cotton Incorporated (USA)
  • Lacape Jean-Marc, CIRAD-BIOS-UMR AGAP (FRA)
  • Llewellyn Danny, CSIRO (AUS)
  • Percy Richard, USDA (USA)
  • Pepper Alan, Texas A & M University (USA)
  • Poland Jesse A., Kansai University (JPN)
  • Mohan Rai Krishan, National Botanical Research Institute (IND)
  • Sawant Samir V., National Botanical Research Institute (IND)
  • Singh Sunil Kumar, National Botanical Research Institute (IND)
  • Spriggs Andrew, CSIRO (AUS)
  • Taylor Jen M., CSIRO (AUS)
  • Wang Fei, Texas A & M University (USA)
  • Yourstone Scott M., Brigham Young University (USA)
  • Zheng Xiuting, Texas A & M University (USA)
  • Lawley Cindy T., Illumina Inc. (USA)
  • Ganal Martin W., Texas A & M University (USA)
  • Van Deynze Allen, UC (USA)
  • Wilson Iain W., CSIRO (AUS)
  • Stelly David M., Texas A & M University (USA)

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