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_TM31287NAU_TM31287genetic_marker
NAU_TM31288NAU_TM31288genetic_marker
NAU_TM31289NAU_TM31289genetic_marker
NAU_TM31290NAU_TM31290genetic_marker
NAU_TM31291NAU_TM31291genetic_marker
NAU_TM31292NAU_TM31292genetic_marker
NAU_TM31293NAU_TM31293genetic_marker
NAU_TM31294NAU_TM31294genetic_marker
NAU_TM31295NAU_TM31295genetic_marker
NAU_TM31296NAU_TM31296genetic_marker
NAU_TM31297NAU_TM31297genetic_marker
NAU_TM31298NAU_TM31298genetic_marker
NAU_TM31299NAU_TM31299genetic_marker
NAU_TM31300NAU_TM31300genetic_marker
NAU_TM31301NAU_TM31301genetic_marker
NAU_TM31302NAU_TM31302genetic_marker
NAU_TM31303NAU_TM31303genetic_marker
NAU_TM31304NAU_TM31304genetic_marker
NAU_TM31305NAU_TM31305genetic_marker
NAU_TM31306NAU_TM31306genetic_marker
NAU_TM31307NAU_TM31307genetic_marker
NAU_TM31308NAU_TM31308genetic_marker
NAU_TM31309NAU_TM31309genetic_marker
NAU_TM31310NAU_TM31310genetic_marker
NAU_TM31311NAU_TM31311genetic_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