363-2 An Overview of Diversity in US and Global Cotton Using the CottonSNP63K Array.

See more from this Division: C08 Plant Genetic Resources
See more from this Session: Plant Genetic Resources: I

Wednesday, November 18, 2015: 10:20 AM
Minneapolis Convention Center, 103 F

Amanda M. Hulse-Kemp1, Lori Hinze2, Iain W. Wilson3, Qian-Hao Zhu3, Danny J. Llewellyn3, Jen M. Taylor3, Andrew Spriggs3, David Fang4, Mauricio Ulloa5, John J. Burke6, Marc Giband7, Jean-Marc Lacape7, Allen Van Deynze8, Joshua A. Udall9, Jodi A. Scheffler10, Steve Hague1, Alan E. Pepper11, James Frelichowski2, Cindy T. Lawley12, Donald C. Jones13, Richard G. Percy2 and David M. Stelly1, (1)Soil and Crop Sciences Department, Texas A&M University, College Station, TX
(2)USDA-ARS, College Station, TX
(3)CSIRO Agriculture Flagship, ACT, Australia
(4)Cotton Fiber Bioscience Research Unit, USDA-ARS, New Orleans, LA
(5)USDA-ARS, Lubbock, TX
(6)Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, TX
(7)CIRAD, Montpellier, France
(8)Plant Reproductive Biology, Rm 1103, University of California, Davis, CA
(9)Brigham Young University, Provo, UT
(10)USDA-ARS, Stoneville, MS
(11)Texas A&M University, College Station, TX
(12)Illumina Inc., San Francisco, CA
(13)Agricultural & Environmental Research, Cotton Incorporated, Cary, NC
Abstract:
A CottonSNP63K array and accompanying cluster file has been developed for the 45,104 intra-specific SNPs and the 17,954 inter-specific SNPs included in the fixed content of the array which allows for automated genotyping of cotton (Gossypium spp.) samples.  Development of the cluster file included genotyping of 1,156 samples, a subset of which were inbred lines of cultivated varieties and wild accessions.  Our diversity study was based on 402 Gossypium samples genotyped with the CottonSNP63K array.  Over half (38,822) of the SNPs were polymorphic in this dataset.  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 cultivated G. hirsutum. The polymorphism profiles and distribution results have significant implications for breeding and utilizing the CottonSNP63K array in the US and worldwide.

See more from this Division: C08 Plant Genetic Resources
See more from this Session: Plant Genetic Resources: I