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Title: Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.)

Author
item HULSE-KEMP, AMANDA - Texas A&M University
item LEMM, JANA - Traitgenetics
item PLIESKE, JOERG - Traitgenetics
item ASHRAFI, HAMID - University Of California
item BUYYARAPU, RAMESH - Dow Agro Sciences
item Fang, David
item Frelichowski, James - Jim
item GIBAND, MARC - Centre National De La Recherche Scientifique
item HAGUE, STEVE - Texas A&M University
item Hinze, Lori
item KOCHAN, KELLI - Texas A&M University
item RIGGS, RENNY - Texas A&M University
item Scheffler, Jodi
item UDALL, JOSHUA - Brigham Young University
item Ulloa, Mauricio
item Wang, Shizhou
item ZHU, QIAN-HAO - Csiro European Laboratory
item BAG, SUMIT - National Botanical Research Institute - India
item BHARDWAJ, ARCHANA - National Botanical Research Institute - India
item Burke, John
item BYERS, ROBERT - Brigham Young University
item CLAVERIE, MICHEL - Centre National De La Recherche Scientifique
item GORE, MICHAEL - Cornell University
item HARKER, DAVID - Csiro European Laboratory
item Islam, Md
item Jenkins, Johnie
item JONES, DON - Cotton, Inc
item LACAPE, JEAN-MARC - Centre National De La Recherche Scientifique
item LLEWELLYN, DANNY - Csiro European Laboratory
item Percy, Richard
item PEPPER, ALAN - Texas A&M University
item POLAND, JESSE - Kansas State University
item RAI, KRISHAN MOHAN - National Botanical Research Institute - India
item SAWANT, SAMIR - National Botanical Research Institute - India
item SINGH, SUNIL KUMAR - National Botanical Research Institute - India
item SPRIGGS, ANDREW - Csiro European Laboratory
item TAYLOR, JEN - Csiro European Laboratory
item WANG, FEI - Texas A&M University
item YOURSTONE, SCOTT - Brigham Young University
item ZHENG, XIUTING - Texas A&M University
item LAWLEY, CINDY - Illumina, Inc
item GANAL, MARTIN - Traitgenetics
item VAN DEYNZE, ALLEN - University Of California
item WILSON, LAIN - Csiro European Laboratory
item STELLY, DAVID - Texas A&M University

Submitted to: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/13/2015
Publication Date: 4/20/2015
Citation: Hulse-Kemp, A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J.E., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, R., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S., Zhu, Q., Bag, S.K., Bhardwaj, A., Burke, J.J., Byers, R.L., Claverie, M., Gore, M.A., Harker, D.B., Islam, M.S., Jenkins, J.N., Jones, D.C., Lacape, J., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K., Sawant, S.V., Singh, S., Spriggs, A., Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X., Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, L.W., Stelly, D.M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). Genes, Genomes, Genetics. 5:1187-1209. doi:10.1534/g3.115.018416.

Interpretive Summary: High-throughput DNA marker chips provide a standardized resource for crop research communities that are useful for a breadth of applications including marker-assisted selection. Through an international cooperation, we have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intra-specific single nucleotide polymorphism (SNP) markers for use within the cultivated cotton species Gossypium hirsutum and 17,954 putative inter-specific SNP markers for use with crosses of other cotton species with Upland cotton. The SNPs on the array are developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 10,314 monomorphic probes and for 38,822 polymorphic markers on the array. Two high-density genetic maps for one intra-specific and one inter-specific F2 mapping population containing a total of 22,829 SNPs with 3,533 SNP markers occurring in both maps were generated. The developed CottonSNP63K array and cluster file along with the marker sequences will be a valuable resource for cotton breeding and the cotton research community.

Technical Abstract: High-throughput genotyping arrays provide a standardized resource for crop research communities that are useful for a breadth of applications including high-density genetic mapping, genome-wide association studies (GWAS), genomic selection (GS), candidate marker and quantitative trait loci (QTL) identification and studying genomic patterns of diversity among cotton cultivars and wild accessions. We have developed the CottonSNP63K, an Illumina Infinium array containing assays for 45,104 putative intra-specific SNP markers for use within the cultivated cotton species Gossypium hirsutum and 17,954 putative inter-specific SNP markers for use with crosses of other cotton species with G. hirsutum. The SNPs on the array are developed from 13 different discovery sets that represent a diverse range of G. hirsutum germplasm and five other species: G. barbadense, G. tomentosum, G. mustelinum, G. armourianum, and G. longicalyx. The array was validated with 1,156 samples to generate cluster positions to facilitate automated analysis of 10,314 monomorphic probes and for 38,822 polymorphic markers on the array. Two high-density genetic maps for one intra-specific and one inter-specific F2 mapping population containing a total of 22,829 SNPs with 3,533 SNP markers occurring in both maps were generated. The linkage maps were shown to have high levels of collinearity to the JGI G. raimondii reference genome sequence. The developed CottonSNP63K array and cluster file along with the marker sequences will be a valuable resource for cotton breeding and the cotton research community.