基于RAD-seq的大口黑鲈选育群体快长SNP挖掘及其与生长性状的关联分析  

Development of fast-growth SNP screening and association analysis with growth traits based on RAD-seq for largemouth bass(Micropterus salmoides)breeding populations

作　　者：华吉祥 陶易凡 李岩 王庆春 陈文华 诸葛燕[3] 张茂友[3] 董亚伦 路思琪 姜冰洁 强俊[1,2] HUA Jixiang;TAO Yifan;LI Yan;WANG Qingchun;CHEN Wenhua;ZHUGE Yan;ZHANG Maoyou;DONG Yalun;LU Siqi;JIANG Bingjie;QIANG Jun(Wuxi Fisheries College,Nanjing Agricultural University,Wuxi 214081,China;Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization,Ministry of Agriculture and Rural Affairs/Freshwater Fisheries Research Center,Chinese Academy of Fishery Sciences,Wuxi 214081,China;Suzhou Aquatic Technology Extension Station,Suzhou 215004,China)

机构地区：[1]南京农业大学无锡渔业学院,江苏无锡214081 [2]中国水产科学研究院淡水渔业研究中心,农业农村部淡水渔业与种质资源利用重点实验室,江苏无锡214081 [3]苏州市水产技术推广站,江苏苏州215004

出　　处：《中国水产科学》2024年第3期241-256,共16页Journal of Fishery Sciences of China

基　　金：国家重点研发计划项目(2022YFE0139600);科技创新2030-重大项目(2023ZD04065);苏州市科技计划项目(SNG2021009);江苏省种业振兴“揭榜挂帅”项目(JBGS[2021]130);加州鲈产业重大技术协同推广计划项目(2022-ZYXT-07);中国水产科学研究院淡水渔业研究中心基本科研业务费项目(2023JBFR02)。

摘　　要：大口黑鲈(Micropterussalmoides)生长性状是衡量品质与产量的重要标准,开发快长SNP标记与挖掘优势基因型及生长主效基因,有助于进一步解析其生长发育遗传机制,为选育优质高产新品系奠定基础。基于简化基因组测序技术(restriction-site associated DNA sequencing,RAD-seq),在大口黑鲈美国北方亚种F0生长性状极端群体(体重极大前1%和极小后1%)中,筛选了与生长性状存在潜在关联的SNP位点,利用一般线性模型(generalizedlinear model,GLM)将SNP位点基因型与230尾F0个体的体重、体长、体高和体厚进行相关性分析,此外通过基因注释信息预测生长候选基因,并结合优势基因型加性效应分析优势基因型聚合效果。在大口黑鲈23条染色体上发现了4196486个高质量SNPs,基于种群特异基因型频率阈值0.7,初步筛选出100个与生长性状潜在相关的SNP位点。关联性分析显示,有12个SNP标记存在显著关联,包括5个标记与体重显著关联,10个与体长显著关联,4个与体高显著关联,5个与体厚显著关联。其中标记SNP19140160、SNP24406191、SNP3355498和SNP9244620分别定位至生长候选基因fam174b、diaph2、kiaa1549lb和ppip5k1b上。富集6~10个优势基因型的群体较富集0~5个优势基因型的群体在平均体重、体长、体高和体厚上分别提高了32.07%、9.63%、9.96%和10.58%。本研究所鉴定的12个快长SNP标记和4个生长候选基因可助力大口黑鲈生长性状改良。Growth traits in largemouth bass(Micropterus salmoides)are crucial indicators of quality and yield.The development of growth single nucleotide polymorphism(SNP)markers and exploration of dominant genotypes and growth genes will enhance our understanding of the genetic mechanisms underlying growth and development.Moreover,this research will facilitate the selection and breeding of new populations with exceptional growth traits.Using restriction site-associated DNA sequencing(RAD-seq),we conducted SNP screening in the F0 generation of the northern subspecies of largemouth bass,focusing on extreme groups with very high body weights(top 1%)and very low body weights(bottom 1%).A general linear model(GLM)was applied to establish correlations between the SNP genotypes and four growth traits(body weight,body length,body height,and body thickness)in a cohort of 230 F0 individuals.Additionally,candidate genes associated with growth were predicted using gene annotation information,and the combined additive effects of the dominant genotypes were analyzed through examination of their aggregation.A total of 4196486 high-quality SNPs were identified across 23 chromosomes of the largemouth bass.Using a population-specific genotype frequency threshold of 0.7,we initially screened 100 potential SNP loci related to growth and identified 12 that were significantly associated with growth.Specifically,five SNPs were significantly associated with body weight,10 SNPs were significantly associated with body length,four SNPs were significantly associated with body height,and five SNPs were significantly associated with body thickness.Notably,the candidate growth genes fam174b,diaph2,kiaa1549lb,and ppip5k1b were linked to specific SNP markers including SNP19140160,SNP24406191,SNP3355498,and SNP9244620,respectively.The enrichment of 6−10 dominant genotypes resulted in an average increase of 32.07% in body weight,9.63% in body length,9.96% in body height,and 10.58% in body thickness compared to the enrichment of 0-5 dominant genotypes,sign

关 键 词：大口黑鲈 简化基因组测序 SNP 生长性状 优势基因型 

分 类 号：S917[农业科学—水产科学]