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

Authors: Hinze, Lori; HULSE-KEMP, AMANDA - University Of California; WILSON, IAIN - Commonwealth Scientific And Industrial Research Organisation (CSIRO); ZHU, QIAN-HAO - Commonwealth Scientific And Industrial Research Organisation (CSIRO); LLEWELLYN, DANNY - Commonwealth Scientific And Industrial Research Organisation (CSIRO); TAYLOR, JEN - Commonwealth Scientific And Industrial Research Organisation (CSIRO); SPRIGGS, ANDREW - Commonwealth Scientific And Industrial Research Organisation (CSIRO); Fang, David; Ulloa, Mauricio; Burke, John; GIBAND, MARC - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD); LACAPE, JEAN-MARC - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD); VAN DEYNZE, ALLEN - University Of California; UDALL, JOSHUA - Brigham Young University; Scheffler, Jodi; HAGUE, STEVE - Texas A&M University; PEPPER, ALAN - Texas A&M University; Frelichowski, James - Jim; LAWLEY, CINDY - Illumina, Inc; JONES, DON - Cotton, Inc; Percy, Richard; STELLY, DAVID - Texas A&M University

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2017
Publication Date: 2/3/2017
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. 2017. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. Biomed Central (BMC) Plant Biology. 17:37.

Interpretive Summary: Cotton grown throughout the world contains beneficial genetic variations that traditional and genomic breeding methods can exploit to develop cultivars adapted to emerging environmental and climate conditions. Germplasm resources from breeding programs as well as from the USDA National Cotton Germplasm Collection are often genotyped to enable molecular comparisons of cultivars, known pedigrees, and the respective resources available in specific countries and growing regions. However, unambiguous differentiation, categorization, and classification remain challenging for all cotton germplasm resources. For the Germplasm Collection, continual characterization and evaluation using the latest technologies are vital to accurately describe the resources and allow potential users to request the most relevant accessions for cotton research and improvement. Recently, the cotton community has established a high-throughput genotyping system, the CottonSNP63K array, which enables any researcher to simultaneously analyze large numbers of markers and obtain highly repeatable results. Cotton cultivars submitted by researchers as well as accessions from the Germplasm Collection were evaluated using this array to assess diversity and potential for improving the crop. The markers distinctly separated the most common species from other species and distinguished the wild from cultivated types. The markers also efficiently discerned differences among cultivars to provide other cotton researchers with a large genome-wide variation data set for cultivated cotton. Thousands of markers in representative genotypes provide an opportunity to finely discriminate among cultivated cotton to select those best suited for research programs and to avoid costly duplications within germplasm collections.

Technical Abstract: Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapting to emerging environmental and climate conditions, and this germplasm has commonly been characterized based on phenotypes. However, phenotypic profiles are limited by what can be observed and measured. Therefore, genotypic profiles are increasingly relevant for their greater power to identify differences due to the larger number of 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 enough SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to simultaneously 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. The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers were also able to efficiently discern 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 cottonseed protein content. Our 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.