水产学报2026，Vol.50Issue(7)：19-31,13.DOI:10.11964/jfc.20251115211
中华绒螯蟹基因组30 K液相芯片的开发与验证
Development and validation of the 30 K liquid chip for Chinese mitten crab(Eriocheir sinensis)
摘要
Abstract
The Chinese mitten crab(Eriocheir sinensis)is one of the most widely cultured aquatic species in China and has high economic and practical value.However,its development has been severely constrained by germplasm degradation and inbreeding caused by long-term unregulated breeding practices.Therefore,genetic improvement through selective breeding has become an effective approach to address these challenges.To improve the efficiency of genomic selection and germplasm resource evaluation in the E.sinensis,this study aimed to develop a medium-density and high-accuracy whole-genome single nucleotide polymorphism(SNP)liquid-phase genotyping chip.Based on whole-genome resequencing data from 136 E.sinen-sis individuals,high-quality SNPs were identified through parameter filtering and quality control and subsequently used for probe design and synthesis.In the preliminary validation of the SNP array,three resequenced individuals used in array develop-ment and ten individuals randomly selected from 96 genotyped samples were analyzed,including two technical replicates.Gen-otypes generated by the SNP array were compared with corresponding whole-genome resequencing results to assess concord-ance.A production-scale evaluation was then conducted using 96 E.sinensis individuals with two technical replicates,and the resulting genotyping data were used to assess chromosomal distribution and genotyping performance of SNP loci.Liquid-based SNP array was used to genotype 724 E.sinensis individuals.Genomic estimated breeding values for color traits were predicted using the BayesB model,and the prediction performance was assessed in terms of accuracy and bias.① In the preliminary val-idation experiment,the average call rate of 13 samples was 99.33%,with call rate differences between two technical replicates of 0.04%and 0.03%,respectively,and the average concordance rate between chip genotyping and resequencing results for three samples was 93.25%;② In the production-scale test,SNP call rates ranged from 98.61%to 99.54%,and genotype con-cordance rates between two technical replicates were 99.78%and 98.76%,respectively;③ SNP markers on the chip were evenly distributed across 72 chromosomes,with an average SNP density of 25.5 SNPs/Mb;SNP density across chromosomes ranged from 20 to 32 SNPs/Mb and showed a positive correlation with chromosome length;④ Quality control indicators,including minor allele frequency(MAF)and Hardy-Weinberg equilibrium(HWE),demonstrated the high quality of SNP markers on the chip,with a total of 21 680 high-quality polymorphic loci identified;⑤ The genomic selection results for color traits showed that the prediction accuracy of the four color parameters ranged from 0.153 5 to 0.557 6,while the prediction bias ranged from 0.691 7 to 1.0025.Among these traits,redness(a*)exhibited the highest prediction accuracy,indicating that the SNP array has good potential for practical application in breeding programs.The 30 K liquid-based SNP array developed in this study for the E.sinensis exhibits a high detection rate,high genotyping accuracy,and strong technical stability.It meets the requirements for genome-wide selection and germplasm resource evaluation in E.sinensis,and provides a reliable tool for molecular breeding,germplasm identification,and population genetic studies.关键词
中华绒螯蟹/单核苷酸多态性/液相芯片/基因组育种/种群遗传Key words
Eriocheir sinensis/single nucleotide polymorphism/liquid-phase chip/genomic selection/population genetics分类
农业科技引用本文复制引用
戎智超,姜晓东,唐美君,易鹏,赵翠,吴旭干..中华绒螯蟹基因组30 K液相芯片的开发与验证[J].水产学报,2026,50(7):19-31,13.基金项目
国家重点研发计划(2022YFD2400700) （2022YFD2400700）
江苏省农业农村厅种业振兴"揭榜挂帅"项目(JBGS[2021]127) （JBGS[2021]127）
东营市垦利区渔业高质量发展项目(KEHY2024001) （KEHY2024001）
山东省东营市黄河三角洲产业领军人才项目(DYRC202100215) National Key R&D Program of China(2022YFD2400700) （DYRC202100215）
An Open Competition Project from the Department of Agriculture and Rural Affairs of Jiangsu Province(JBGS[2021]127) （JBGS[2021]127）
High-quality Fishery Development Project from Marine Development and Fisheries Bureau of Kenli District of Dongying City(KEHY2024001) （KEHY2024001）
Leading Talent Project in Yellow River Delta from Dongying Municipal Government of Shandong Province(DYRC202100215) （DYRC202100215）
