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.
Projects
This publication contains information about 1 projects:
Project NameDescription
TAMU_SNP63K_genotyping
Germplasm
This publication contains information about 140 stocks:
Stock NameUniquenameType
cdbgm_000956.x1Acala Maxxa (AH-407, Stelly/VanDeynze)cultivar
cdbgm_000956.x2Acala Maxxa (AH-485, Giband)cultivar
cdbgm_001000.x1BJA 592 (AH-560, Giband)breeding_germplasm
cdbgm_001217.x1Reba P279 (AH-531, Giband)obsolete_cultivar
cdbgm_001778.x1TX-2263 (AH-461, Wendel)wild_unimproved
cdbgm_003155.x1Deltapine 16 (IW-136, Wilson)obsolete_cultivar
cdbgm_003155.x2Deltapine 16 (IW-337, Wilson)obsolete_cultivar
cdbgm_003172.x1Coker 312 (AH-553, VanDeynze)cultivar
cdbgm_003199.x1Stoneville 256 (AH-P9-014, n/a)cultivar
cdbgm_003287.x1Deltapine 90 (IW-081, Wilson)obsolete_cultivar
cdbgm_003287.x2Deltapine 90 (IW-160, Wilson)obsolete_cultivar
cdbgm_003287.x3Deltapine 90 (IW-349, Wilson)obsolete_cultivar
cdbgm_003288.x1Coker 315 (IW-004, Wilson)cultivar
cdbgm_003288.x2Coker 315 (IW-368, Wilson)cultivar
cdbgm_003288.x3Coker 315 (IW-313, Wilson)cultivar
cdbgm_003391.x1Tamcot CAMD-E (AH-212, Stelly - Andrea)cultivar
cdbgm_003395.x1Tamcot SP37 (IW-142, Wilson)cultivar
cdbgm_005043.x1PD 1 (AH-403, VanDeynze)cultivar
cdbgm_005409.x1TM-1 (AH-712, Stelly)breeding_germplasm
cdbgm_005409.x2TM-1 (AH-213, Fang)breeding_germplasm
cdbgm_008306.x1Delta Opal (IW-124, Wilson)cultivar
cdbgm_008306.x2Delta Opal (IW-344, Wilson)cultivar
cdbgm_008306.x3Delta Opal (IW-325, Wilson)cultivar
cdbgm_008527.x1Sicot 53 (IW-375, Wilson)cultivar
cdbgm_008531.x1Sicot 189 (IW-363, Wilson)cultivar

Pages

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