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_TM56181NAU_TM56181genetic_marker
NAU_TM56183NAU_TM56183genetic_marker
NAU_TM56184NAU_TM56184genetic_marker
NAU_TM56185NAU_TM56185genetic_marker
NAU_TM56186NAU_TM56186genetic_marker
NAU_TM56187NAU_TM56187genetic_marker
NAU_TM56188NAU_TM56188genetic_marker
NAU_TM56189NAU_TM56189genetic_marker
NAU_TM56190NAU_TM56190genetic_marker
NAU_TM56191NAU_TM56191genetic_marker
NAU_TM56192NAU_TM56192genetic_marker
NAU_TM56193NAU_TM56193genetic_marker
NAU_TM56194NAU_TM56194genetic_marker
NAU_TM56195NAU_TM56195genetic_marker
NAU_TM56196NAU_TM56196genetic_marker
NAU_TM56197NAU_TM56197genetic_marker
NAU_TM56198NAU_TM56198genetic_marker
NAU_TM56199NAU_TM56199genetic_marker
NAU_TM56200NAU_TM56200genetic_marker
NAU_TM56201NAU_TM56201genetic_marker
NAU_TM56203NAU_TM56203genetic_marker
NAU_TM56204NAU_TM56204genetic_marker
NAU_TM56205NAU_TM56205genetic_marker
NAU_TM56206NAU_TM56206genetic_marker
NAU_TM56207NAU_TM56207genetic_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