High-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis

Publication Overview
TitleHigh-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis
AuthorsCaiping Cai, Guozhong Zhu, Tianzhen Zhang, and Wangzhen Guo
TypeJournal Article
Journal NameBMC Genomics
Volume18
Year2017
Page(s)654
CitationCai C., Zhu G., Zhang T., Guo W. High-density 80 K SNP array is a powerful tool for genotyping G. hirsutum accessions and genome analysis BMC Genomics 2017 18:654

Abstract

Background: High-throughput genotyping platforms play important roles in plant genomic studies. Cotton (Gossypium spp.) is the world’s important natural textile fiber and oil crop. Upland cotton accounts for more than 90% of the world’s cotton production, however, modern upland cotton cultivars have narrow genetic diversity. The amounts of genomic sequencing and re-sequencing data released make it possible to develop a high-quality single nucleotide polymorphism (SNP) array for intraspecific genotyping detection in cotton. Results: Here we report a high-throughput CottonSNP80K array and its utilization in genotyping detection in different cotton accessions. 82,259 SNP markers were selected from the re-sequencing data of 100 cotton cultivars and used to produce the array on the Illumina Infinium platform. 77,774 SNP loci (94.55%) were successfully synthesized on the array. Of them, 77,252 (99.33%) had call rates of >95% in 352 cotton accessions and 59,502 (76.51%) were polymorphic loci. Application tests using 22 cotton accessions with parent/F1 combinations or with similar genetic backgrounds showed that CottonSNP80K array had high genotyping accuracy, good repeatability, and wide applicability. Phylogenetic analysis of 312 cotton cultivars and landraces with wide geographical distribution showed that they could be classified into ten groups, irrelevant of their origins. We found that the different landraces were clustered in different subgroups, indicating that these landraces were major contributors to the development of different breeding populations of modern G. hirsutum cultivars in China. We integrated a total of 54,588 SNPs (MAFs >0.05) associated with 10 salt stress traits into 288 G. hirsutum accessions for genome-wide association studies (GWAS), and eight significant SNPs associated with three salt stress traits were detected. Conclusions: We developed CottonSNP80K array with high polymorphism to distinguish upland cotton accessions. Diverse application tests indicated that the CottonSNP80K play important roles in germplasm genotyping, variety verification, functional genomics studies, and molecular breeding in cotton. Keywords: Single nucleotide polymorphism (SNP), Array, Upland cotton, Genotyping identification, Genome-wide association studies (GWAS), Molecular breeding
Germplasm
This publication contains information about 302 stocks:
Stock NameGRIN IDSpeciesType
W-7Gossypium hirsutumaccession
W-8Gossypium hirsutumaccession
Zhong Su 410408Gossypium hirsutumaccession
E Mian 13Gossypium hirsutumaccession
Gan Mian 8Gossypium hirsutumaccession
Russia 6036 wide crossGossypium hirsutumaccession
Russia 6108 wide crossGossypium hirsutumaccession
SuBR6109Gossypium hirsutumaccession
Stoneville 4Gossypium hirsutumaccession
E Mian 14Gossypium hirsutumaccession
Xuzhou 514Gossypium hirsutumaccession
Yan Mian 48Gossypium hirsutumaccession
Chuan Mian 239Gossypium hirsutumaccession
Chuan Mian 45Gossypium hirsutumaccession
Su Mian 20Gossypium hirsutumaccession
Chuan R128Gossypium hirsutumaccession
Zhong Zhi Mian 86-4Gossypium hirsutumaccession
Lu Mian 2Gossypium hirsutumaccession
Ji Mian 11Gossypium hirsutumaccession
Ji Mian 12Gossypium hirsutumaccession
Jin Mian 13Gossypium hirsutumaccession
Ji Mian 27Gossypium hirsutumaccession
Yu Mian 20Gossypium hirsutumaccession
Han 7860Gossypium hirsutumaccession
Zhong Zhi Mian 3Gossypium hirsutumaccession

Pages

Features
This publication contains information about 77,774 features:
Feature NameUniquenameType
NAU_TM15565NAU_TM15565genetic_marker
NAU_TM15566NAU_TM15566genetic_marker
NAU_TM15567NAU_TM15567genetic_marker
NAU_TM15568NAU_TM15568genetic_marker
NAU_TM15569NAU_TM15569genetic_marker
NAU_TM15570NAU_TM15570genetic_marker
NAU_TM15571NAU_TM15571genetic_marker
NAU_TM15572NAU_TM15572genetic_marker
NAU_TM15573NAU_TM15573genetic_marker
NAU_TM15574NAU_TM15574genetic_marker
NAU_TM15575NAU_TM15575genetic_marker
NAU_TM15576NAU_TM15576genetic_marker
NAU_TM15577NAU_TM15577genetic_marker
NAU_TM15578NAU_TM15578genetic_marker
NAU_TM15579NAU_TM15579genetic_marker
NAU_TM15580NAU_TM15580genetic_marker
NAU_TM15581NAU_TM15581genetic_marker
NAU_TM15582NAU_TM15582genetic_marker
NAU_TM15583NAU_TM15583genetic_marker
NAU_TM15584NAU_TM15584genetic_marker
NAU_TM15585NAU_TM15585genetic_marker
NAU_TM15586NAU_TM15586genetic_marker
NAU_TM15588NAU_TM15588genetic_marker
NAU_TM15589NAU_TM15589genetic_marker
NAU_TM15590NAU_TM15590genetic_marker

Pages

Projects
This publication contains information about 1 projects:
Project NameDescription
Salt-stress-test_NAU-Guo-2017
Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
NAU_CottonSNP80KNAU_CottonSNP80KGossypium hirsutum
Properties
Additional details for this publication include:
Property NameValue
DOI10.1186/s12864-017-4062-2
Journal AbbreviationBMC Genomics
KeywordsSingle nucleotide polymorphism (SNP), Array, Upland cotton, Genotyping identification, Genome-wide association studies (GWAS), Molecular breeding