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

作　　者：王亚雯 戚正阳 尤佳琦 聂新辉 曹娟 杨细燕[1] 涂礼莉[1] 张献龙[1] 王茂军[1,2] WANG Ya-Wen;QI Zheng-Yang;YOU Jia-Qi;NIE Xin-Hui;CAO Juan;YANG Xi-Yan;TU Li-Li;ZHANG Xian-Long;WANG Mao-Jun(National Key Laboratory of Crop Genetic Improvement,Huazhong Agricultural University,Wuhan 430070,Hubei,China;Shihezi University,Shihezi 832000,Xinjiang,China;Xinjiang Tarim River Seed Industry Co.,Ltd.,Alar 843300,Xinjiang,China)

机构地区：[1]华中农业大学作物遗传改良全国重点实验室,湖北武汉430070 [2]石河子大学,新疆石河子832000 [3]新疆塔里木河种业股份有限公司,新疆阿拉尔843300

出　　处：《作物学报》2025年第5期1178-1188,共11页Acta Agronomica Sinica

基　　金：湖北省支持种业高质量发展专项课题项目(HBZY2023B002-5);农业生物育种国家科技重大专项(2023ZD0403801,2023ZD0403901)资助。

摘　　要：棉花是最重要的天然纺织纤维来源,同时是重要的油料来源。功能位点基因芯片作为一种可以提高育种值评估准确性和育种效率的工具,在棉花中应用较少。本研究制备了一款棉花60K功能位点基因芯片。该芯片制备基于已获得的棉花不同品种的Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq)、Chromatin Immunoprecipitation sequencing (ChIP-seq)、High-throughput Chromosome Conformation Capture (Hi-C)等组学数据,相较棉花领域已有的基因芯片,包含了更多经过多维组学数据注释的功能遗传变异的位点,所携带的有效功能信息更多。本研究将该芯片应用于棉花群体的全基因组关联分析中,鉴定到40个与棉花纤维品质性状相关的显著SNP位点,其中与纤维伸长率(FE)相关的显著位点共25个,与马克隆值(FM)相关的显著位点共5个,与纤维强度(FS)相关的显著位点共2个,与纤维长度(FL)相关的显著位点共4个,与纤维整齐度(FU)相关的显著位点共4个。本研究中棉花60K功能位点基因芯片可应用于棉花种质资源评价、遗传定位及全基因组选择育种等方面,助力棉花基因组育种。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 

分 类 号：S562[农业科学—作物学]