Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array

BMC Plant Biology

Research Article

Jean-Marc Lacape¹  Marc Giband²  Danny J. Llewellyn³  Iain W. Wilson³  Qian-Hao Zhu³  Jen M. Taylor³  Andrew Spriggs³  Don C. Jones⁴  Alan E. Pepper⁵  Jonathan F. Wendel⁶  Allen Van Deynze⁷  Amanda M. Hulse-Kemp⁷  Steve Hague⁸  David M. Stelly⁹  Cindy T. Lawley^1,10  Joshua A. Udall^1,11  David D. Fang^1,12  Richard G. Percy^1,13  Lori L. Hinze^1,13  James Frelichowski^1,13  Mauricio Ulloa^1,14  John J. Burke^1,14  Jodi A. Scheffler^1,15 

[1] CIRAD, UMR AGAP, F34398, Montpellier, France;CIRAD, UMR AGAP, F34398, Montpellier, France;EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000, Santo Antônio de Goias, GO, Brazil;CSIRO Agriculture & Food, Black Mountain Laboratories, 2601, Canberra, ACT, Australia;Cotton Incorporated, Agricultural Research, 27513, Cary, NC, USA;Department of Biology, Texas A&M University, 77843, College Station, TX, USA;Interdisciplinary Department of Genetics, Texas A&M University, 77843, College Station, TX, USA;Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 50011, Ames, IA, USA;Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, 95616, Davis, CA, USA;Department of Soil & Crop Sciences, Texas A&M University, 77843, College Station, TX, USA;Department of Soil & Crop Sciences, Texas A&M University, 77843, College Station, TX, USA;Interdisciplinary Department of Genetics, Texas A&M University, 77843, College Station, TX, USA;Illumina Inc., 499 Illinois Street, 94158, San Francisco, CA, USA;Plant and Wildlife Science Department, Brigham Young University, 84602, Provo, UT, USA;USDA-ARS, Cotton Fiber Bioscience Research Unit, 70124, New Orleans, LA, USA;USDA-ARS, Crop Germplasm Research Unit, 77845, College Station, TX, USA;USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, 79415, Lubbock, TX, USA;USDA-ARS, Jamie Whitten Delta States Research Center, 38776, Stoneville, MS, USA;

关键词: Breeding;    Cotton;    Diversity analysis;    Genome-wide association analysis;    Germplasm collection;    Molecular markers;    Seed protein content;   

DOI  :  10.1186/s12870-017-0981-y

 received in 2016-09-17, accepted in 2017-01-23,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundCotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits.ResultsThe SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content.ConclusionsOur results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.

【 授权许可】

CC BY   
© The Author(s). 2017