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
Features
This publication contains information about 77,774 features:
Feature NameUniquenameType
NAU_TM13456NAU_TM13456genetic_marker
NAU_TM13457NAU_TM13457genetic_marker
NAU_TM13458NAU_TM13458genetic_marker
NAU_TM13459NAU_TM13459genetic_marker
NAU_TM13460NAU_TM13460genetic_marker
NAU_TM13461NAU_TM13461genetic_marker
NAU_TM13462NAU_TM13462genetic_marker
NAU_TM13463NAU_TM13463genetic_marker
NAU_TM13464NAU_TM13464genetic_marker
NAU_TM13465NAU_TM13465genetic_marker
NAU_TM13466NAU_TM13466genetic_marker
NAU_TM13467NAU_TM13467genetic_marker
NAU_TM13468NAU_TM13468genetic_marker
NAU_TM13469NAU_TM13469genetic_marker
NAU_TM13470NAU_TM13470genetic_marker
NAU_TM13471NAU_TM13471genetic_marker
NAU_TM13472NAU_TM13472genetic_marker
NAU_TM13473NAU_TM13473genetic_marker
NAU_TM13474NAU_TM13474genetic_marker
NAU_TM13475NAU_TM13475genetic_marker
NAU_TM13476NAU_TM13476genetic_marker
NAU_TM13477NAU_TM13477genetic_marker
NAU_TM13478NAU_TM13478genetic_marker
NAU_TM13479NAU_TM13479genetic_marker
NAU_TM13480NAU_TM13480genetic_marker

Pages

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