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
De Li Nong 5Gossypium hirsutumaccession
J02-508Gossypium hirsutumaccession
E Mian 12Gossypium hirsutumaccession
Su Mian 2Gossypium hirsutumaccession
Xiang Mian 11Gossypium hirsutumaccession
Yan 1113Gossypium hirsutumaccession
Liao Mian 1Gossypium hirsutumaccession
Keyi 2Gossypium hirsutumaccession
Lu Mian 11Gossypium hirsutumaccession
Jin Mian 36Gossypium hirsutumaccession
NC20BGossypium hirsutumaccession
Jinyu 5Gossypium hirsutumaccession
Esha28Gossypium hirsutumaccession
Yu Mian 8Gossypium hirsutumaccession
Shan Nong Feng Kang Mian 6Gossypium hirsutumaccession
Handan 109Gossypium hirsutumaccession
Yin Shan 6Gossypium hirsutumaccession
Liao Mian 16Gossypium hirsutumaccession
ZhongArc-308Gossypium hirsutumaccession
Zhong Zi 4480Gossypium hirsutumaccession
MSCO-12Gossypium hirsutumaccession
Xin Lu Zao 30Gossypium hirsutumaccession
Si Mian 1Gossypium hirsutumaccession
Siyang-331Gossypium hirsutumaccession
Xiang Mian 12Gossypium hirsutumaccession

Pages

Features
This publication contains information about 77,774 features:
Feature NameUniquenameType
NAU_TM81047NAU_TM81047genetic_marker
NAU_TM81048NAU_TM81048genetic_marker
NAU_TM81049NAU_TM81049genetic_marker
NAU_TM81050NAU_TM81050genetic_marker
NAU_TM81051NAU_TM81051genetic_marker
NAU_TM81053NAU_TM81053genetic_marker
NAU_TM81054NAU_TM81054genetic_marker
NAU_TM81055NAU_TM81055genetic_marker
NAU_TM81056NAU_TM81056genetic_marker
NAU_TM81057NAU_TM81057genetic_marker
NAU_TM81059NAU_TM81059genetic_marker
NAU_TM81060NAU_TM81060genetic_marker
NAU_TM81061NAU_TM81061genetic_marker
NAU_TM81062NAU_TM81062genetic_marker
NAU_TM81063NAU_TM81063genetic_marker
NAU_TM81065NAU_TM81065genetic_marker
NAU_TM81066NAU_TM81066genetic_marker
NAU_TM81067NAU_TM81067genetic_marker
NAU_TM81068NAU_TM81068genetic_marker
NAU_TM81069NAU_TM81069genetic_marker
NAU_TM81070NAU_TM81070genetic_marker
NAU_TM81071NAU_TM81071genetic_marker
NAU_TM81072NAU_TM81072genetic_marker
NAU_TM81073NAU_TM81073genetic_marker
NAU_TM81074NAU_TM81074genetic_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