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_TM28783NAU_TM28783genetic_marker
NAU_TM28784NAU_TM28784genetic_marker
NAU_TM28785NAU_TM28785genetic_marker
NAU_TM28786NAU_TM28786genetic_marker
NAU_TM28787NAU_TM28787genetic_marker
NAU_TM28788NAU_TM28788genetic_marker
NAU_TM28789NAU_TM28789genetic_marker
NAU_TM28790NAU_TM28790genetic_marker
NAU_TM28791NAU_TM28791genetic_marker
NAU_TM28792NAU_TM28792genetic_marker
NAU_TM28793NAU_TM28793genetic_marker
NAU_TM28794NAU_TM28794genetic_marker
NAU_TM28795NAU_TM28795genetic_marker
NAU_TM28796NAU_TM28796genetic_marker
NAU_TM28797NAU_TM28797genetic_marker
NAU_TM28798NAU_TM28798genetic_marker
NAU_TM28799NAU_TM28799genetic_marker
NAU_TM28800NAU_TM28800genetic_marker
NAU_TM28802NAU_TM28802genetic_marker
NAU_TM28803NAU_TM28803genetic_marker
NAU_TM28804NAU_TM28804genetic_marker
NAU_TM28805NAU_TM28805genetic_marker
NAU_TM28806NAU_TM28806genetic_marker
NAU_TM28807NAU_TM28807genetic_marker
NAU_TM28808NAU_TM28808genetic_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