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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #323062

Research Project: Conservation, Genetic Analyses, and Utilization of Cotton Genetic Resources

Location: Crop Germplasm Research

Title: Measuring diversity in Gossypium hirsutum using the CottonSNP63K Array

Author
item Hinze, Lori
item Hulse-kemp, Amanda - Texas A&M University
item Wilson, Iain - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item Zhu, Qian-hao - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item Llewellyn, Danny - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item Taylor, Jen - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item Spriggs, Andrew - Commonwealth Scientific And Industrial Research Organisation (CSIRO)
item Fang, David
item Ulloa, Mauricio
item Burke, John
item Giband, Marc - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item Lacape, Jean-marc - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item Van Deynze, Allen - University Of California
item Udall, Joshua - Brigham Young University
item Scheffler, Jodi
item Hague, Steve - Texas A&M University
item Pepper, Alan - Texas A&M University
item Frelichowski, James - Jim
item Lawley, Cindy - Illumina, Inc
item Jones, Donald - Cotton, Inc
item Percy, Richard
item Stelly, David - Texas A&M University

Submitted to: National Cotton Council Beltwide Cotton Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/6/2016
Publication Date: 5/18/2016
Citation: Hinze, L.L., Hulse-Kemp, A., Wilson, I., Zhu, Q., Llewellyn, D., Taylor, J., Spriggs, A., Fang, D.D., Ulloa, M., Burke, J.J., Giband, M., Lacape, J., Van Deynze, A., Udall, J., Scheffler, J.A., Hague, S., Pepper, A., Frelichowski, J.E., Lawley, C., Jones, D., Percy, R.G., Stelly, D. 2016. Measuring diversity in Gossypium hirsutum using the CottonSNP63K Array. In: Proceedings of the Beltwide Cotton Conferences, January 5-7, 2016, New Orleans, Louisiana. 2016 CDROM.

Interpretive Summary:

Technical Abstract: A CottonSNP63K array and accompanying cluster file has been developed and includes 45,104 intra-specific SNPs and 17,954 inter-specific SNPs for automated genotyping of cotton (Gossypium spp.) samples. Development of the cluster file included genotyping of 1,156 samples, a subset of which were identified as improved or wild G. hirsutum. In our diversity study of 402 Gossypium samples genotyped with the CottonSNP63K array, over half (38,822) of the SNPs were polymorphic. The SNPs separated G. hirsutum samples from other tetraploids and diploids and distinguished between wild and improved types within G. hirsutum. Here we report the first diversity analysis with large numbers of SNP markers over a wide range of cotton germplasm, particularly within improved cultivars of G. hirsutum. The polymorphism profiles and distribution results have significant implications for breeding and utilizing the CottonSNP63K array in the US and worldwide.