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Title:   Author  item
                                            HULSE-KEMP, AMANDA - Texas A&M Universityitem
                                            LEMM, JANA - Traitgeneticsitem
                                            PLIESKE, JOERG - Traitgeneticsitem
                                            ASHRAFI, HAMID - University Of Californiaitem
                                            BUYYARAPU, RAMESH - Dow Agro Sciencesitem
                                            Fang, Daviditem
                                            Frelichowski, James

                                                         - *Jim*item
                                            GIBAND, MARC - Centre National De La Recherche Scientifiqueitem
                                            HAGUE, STEVE - Texas A&M Universityitem
                                            Hinze, Loriitem
                                            KOCHAN, KELLI - Texas A&M Universityitem
                                            RIGGS, RENNY - Texas A&M Universityitem
                                            Scheffler, Jodiitem
                                            UDALL, JOSHUA - Brigham Young Universityitem
                                            Ulloa, Mauricioitem
                                            Wang, Shizhouitem
                                            ZHU, QIAN-HAO - Csiro European Laboratoryitem
                                            BAG, SUMIT - National Botanical Research Institute - Indiaitem
                                            BHARDWAJ, ARCHANA - National Botanical Research Institute - Indiaitem
                                            Burke, Johnitem
                                            BYERS, ROBERT - Brigham Young Universityitem
                                            CLAVERIE, MICHEL - Centre National De La Recherche Scientifiqueitem
                                            GORE, MICHAEL - Cornell Universityitem
                                            HARKER, DAVID - Csiro European Laboratoryitem
                                            Islam, Mditem
                                            Jenkins, Johnieitem
                                            JONES, DON - Cotton, Incitem
                                            LACAPE, JEAN-MARC - Centre National De La Recherche Scientifiqueitem
                                            LLEWELLYN, DANNY - Csiro European Laboratoryitem
                                            Percy, Richarditem
                                            PEPPER, ALAN - Texas A&M Universityitem
                                            POLAND, JESSE - Kansas State Universityitem
                                            RAI, KRISHAN MOHAN - National Botanical Research Institute - Indiaitem
                                            SAWANT, SAMIR - National Botanical Research Institute - Indiaitem
                                            SINGH, SUNIL KUMAR - National Botanical Research Institute - Indiaitem
                                            SPRIGGS, ANDREW - Csiro European Laboratoryitem
                                            TAYLOR, JEN - Csiro European Laboratoryitem
                                            WANG, FEI - Texas A&M Universityitem
                                            YOURSTONE, SCOTT - Brigham Young Universityitem
                                            ZHENG, XIUTING - Texas A&M Universityitem
                                            LAWLEY, CINDY - Illumina, Incitem
                                            GANAL, MARTIN - Traitgeneticsitem
                                            VAN DEYNZE, ALLEN - University Of Californiaitem
                                            WILSON, LAIN - Csiro European Laboratoryitem
                                            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.


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