作物学报2025，Vol.51Issue(5)：1178-1188,中插1-中插2,13.DOI:10.3724/SP.J.1006.2025.44146
棉花60K功能位点基因芯片的制备及应用
Preparation of cotton 60K functional locus gene chip and its application to genetic research
摘要
Abstract
Cotton is the leading source of natural textile fiber and an important source of oil.However,functional locus gene chips,which can significantly improve the accuracy of breeding value assessments and breeding efficiency,remain underutilized in cot-ton research.In this study,we developed a 60K functional locus gene chip for cotton,leveraging high-throughput sequencing datasets,including Assay for Transposase Accessible Chromatin with high-throughput sequencing(ATAC-seq),Chromatin Im-munoprecipitation sequencing(ChIP-seq)and High-throughput Chromosome Conformation Capture(Hi-C)data from diverse cotton varieties.Compared to existing cotton gene chips,this newly developed chip incorporates a higher number of functionally annotated loci with genetic variations derived from multi-dimensional data,offering richer insights into gene function.Using this gene chip in a genome-wide association study(GWAS)of cotton fiber quality traits,we identified 40 significant single nucleotide polymorphisms(SNPs)linked to fiber quality.These include twenty-five SNPs associated with fiber elongation rate(FE),five with fiber micronaire value(FM),two with fiber strength(FS),four with fiber length(FL),and four with fiber uniformity(FU).The 60K functional locus gene chip provides a powerful tool for the evaluation of cotton germplasm resources,genetic mapping,and genome-wide selection breeding.This advancement holds great promise for accelerating genomic breeding efforts,ultimately driving improvements in cotton production and quality.关键词
棉花育种/基因芯片/棉花60K功能位点基因芯片/全基因组关联分析/驯化选择Key words
cotton breeding/gene chip/cotton 60K functional locus gene chip/genome-wide association analysis/domestication selection引用本文复制引用
王亚雯,戚正阳,尤佳琦,聂新辉,曹娟,杨细燕,涂礼莉,张献龙,王茂军..棉花60K功能位点基因芯片的制备及应用[J].作物学报,2025,51(5):1178-1188,中插1-中插2,13.基金项目
本研究由湖北省支持种业高质量发展专项课题项目(HBZY2023B002-5)和农业生物育种国家科技重大专项(2023ZD0403801,2023ZD0403901)资助. This study was supported by the Special Project for Supporting High Quality Development of Seed Industry in Hubei Province(HBZY2023B002-5)and the National Science and Technology Major Project of Agricultural Biological Breeding in China(2023ZD0403801,2023ZD0403901). （HBZY2023B002-5）
