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

Publication Overview
TitleDiversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array.
AuthorsHinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski JF, Lawley CT, Jones DC, Percy RG, Stelly DM
TypeJournal Article
Journal NameBMC Plant Biology
Volume17
Issue1
Year2017
CitationHinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski JF, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC Plant Biology. 2017 Feb 3;17(1):37.
Publication CodeBMCPB-17-37

Abstract

Background: Cotton 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. Results: The 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. Conclusions: 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.
Germplasm
This publication contains information about 140 stocks:
Stock NameGRIN IDSpeciesType
Sicot 189 (IW-363 Wilson)Gossypium hirsutumaccession
Tamcot Sphinx (AH-247 Fang)Gossypium hirsutumaccession
Rogers GL-7 (AH-481 Giband)Gossypium hirsutumaccession
Riverina Paplar (IW-126 Wilson)Gossypium hirsutumaccession
Riverina Paplar (IW-447 Wilson)Gossypium hirsutumaccession
Siokra 1-4 (IW-376 Wilson)Gossypium hirsutumaccession
BRS 286 (AH-558 Giband)Gossypium hirsutumaccession
BRS 293 (AH-527 Giband)Gossypium hirsutumaccession
Namcala (IW-314 Wilson)Gossypium hirsutumaccession
Sicala 40 (IW-019 Wilson)Gossypium hirsutumaccession
Sicala 40 (Fibermax 966) (AH-217 Fang)Gossypium hirsutumaccession
Sicala 40 (Fibermax 966) (AH-524 Giband)Gossypium hirsutumaccession
Sicala 40 (Fibermax 966) (IW-087 Wilson)Gossypium hirsutumaccession
Sicot 81 (IW-340 Wilson)Gossypium hirsutumaccession
Sicala V-2 (Fibermax 989) (IW-139 Wilson)Gossypium hirsutumaccession
Sicala V-2 (Fibermax 989) (IW-351 Wilson)Gossypium hirsutumaccession
Sicot F-1 (IW-352 Wilson)Gossypium hirsutumaccession
Sicot 71 (IW-088 Wilson)Gossypium hirsutumaccession
Lu Mian 14 (IW-131 Wilson)Gossypium hirsutumaccession
Lu Mian 14 (IW-074 Wilson)Gossypium hirsutumaccession
BRS 335 (AH-542 Giband)Gossypium hirsutumaccession
08-WZ-51Gossypium hirsutumaccession
08-WZ-51 (AH-405 Hague)Gossypium hirsutumaccession
Acala Nem-X1Gossypium hirsutumaccession
Acala Nem-X1 (AH-406 Stelly - Ting)Gossypium hirsutumaccession

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
TAMU_SNP63K_genotype
Properties
Additional details for this publication include:
Property NameValue
DOI10.1186/s12870-017-0981-y
URLhttps://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-0981-y
Journal CodeBMCPB
Publication CodeBMCPB-17-37
KeywordsBreeding, Cotton, Diversity analysis, Genome-wide association analysis, Germplasm collection, Molecular markers, Seed protein content