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_TM51209NAU_TM51209genetic_marker
NAU_TM51210NAU_TM51210genetic_marker
NAU_TM51211NAU_TM51211genetic_marker
NAU_TM51212NAU_TM51212genetic_marker
NAU_TM51213NAU_TM51213genetic_marker
NAU_TM51214NAU_TM51214genetic_marker
NAU_TM51215NAU_TM51215genetic_marker
NAU_TM51216NAU_TM51216genetic_marker
NAU_TM51217NAU_TM51217genetic_marker
NAU_TM51218NAU_TM51218genetic_marker
NAU_TM51219NAU_TM51219genetic_marker
NAU_TM51220NAU_TM51220genetic_marker
NAU_TM51221NAU_TM51221genetic_marker
NAU_TM51222NAU_TM51222genetic_marker
NAU_TM51223NAU_TM51223genetic_marker
NAU_TM51224NAU_TM51224genetic_marker
NAU_TM51225NAU_TM51225genetic_marker
NAU_TM51226NAU_TM51226genetic_marker
NAU_TM51227NAU_TM51227genetic_marker
NAU_TM51228NAU_TM51228genetic_marker
NAU_TM51229NAU_TM51229genetic_marker
NAU_TM51230NAU_TM51230genetic_marker
NAU_TM51231NAU_TM51231genetic_marker
NAU_TM51232NAU_TM51232genetic_marker
NAU_TM51233NAU_TM51233genetic_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