利用“黄海芯1号”55K SNP芯片评估凡纳滨对虾选育群体的遗传多样性与基因组近交水平  

GENETIC DIVERSITY AND GENOMIC INBREEDING ANALYSIS IN TWO SELECTED POPULATIONS OF LITOPENAEUS VANNAMEI USING THE LIQUID CHIP OF“YELLOW SEA CHIP NO.1”(55K SNP)

作　　者：刘丹阳 孔杰[2] 王平 陈荣坚 傅强 罗坤[2] 陈宝龙[2] 隋娟[2] 孟宪红[2] 代平[2] 谭建 曹家旺 李旭鹏[2] 康子仪 刘绵宇 强光峰[2] 迟长凤 栾生[2] LIU Dan-Yang;KONG Jie;WANG Ping;CHEN Rong-Jian;FU Qiang;LUO Kun;CHEN Bao-Long;SUI Juan;MENG Xian-Hong;DAI Ping;TAN Jian;CAO Jia-Wang;LI Xu-Peng;KANG Zi-Yi;LIU Mian-Yu;QIANG Guang-Feng;CHI Chang-Feng;LUAN Sheng(National Engineering Research Center For Marine Aquaculture,Zhejiang Ocean University,Zhoushan 316022,China;Key Laboratory for Sustainable Development of Marine Fisheries,Ministry of Agriculture and Rural Affairs,Laboratory for Marine Fisheries Science and Food Production Processes,Qingdao Marine Science and Technology Center,Yellow Sea Fisheries Research Institute,Chinese Academy of Fishery Sciences,Qingdao 266071,China;Hainan Zhongzheng Technology Aquatic Products Co.,Ltd.,Dongfang 572633,China;Guangdong Hisenor Group Co.,Ltd.,Guangzhou 511400,China)

机构地区：[1]浙江海洋大学国家海洋设施养殖工程技术研究中心,浙江舟山316022 [2]中国水产科学研究院黄海水产研究所、青岛海洋科技中心海洋渔业科学与食物产出过程功能实验室、农业农村部海洋渔业可持续发展重点实验室,山东青岛266071 [3]海南中正水产科技有限公司,海南东方572633 [4]广东海兴农集团有限公司,广东广州511400

出　　处：《海洋与湖沼》2024年第2期479-488,共10页Oceanologia Et Limnologia Sinica

基　　金：国家重点研发计划课题,2022YFD2400202号;中国水产科学研究院科技创新团队项目,2020TD26号;海南省院士创新平台科研专项,YSPTZX202104号;湛江市海洋装备与海洋生物揭榜挂帅制人才团队项目,2021E05032号;国家虾蟹产业技术体系,CARS-48号;广东省“十四五”广东省农业科技创新十大主攻方向“揭榜挂帅”项目,2022SDZG01号。

摘　　要：凡纳滨对虾的主要选育目标分为两个方面:一是培育具有较强抗病、抗逆性的“高抗系”(GK),二是培育具有快速生长特性的“快大系”(KD)。然而,国内缺少针对这两个选育群体的遗传多样性特别是基因组近交水平的调查分析研究。基于液相芯片“黄海芯1号”(55 K SNP)的基因分型数据,首次分析了GK(1064尾个体)和KD(564尾个体)选育群体的遗传结构和遗传多样性,调查了连续性纯合片段(ROH)的基因组分布特征,并重点评估了两个群体的基因组近交水平。PCA及进化树分析表明GK及KD群体可明确分层,亲缘关系热图表明KD群体内个体间的亲缘关系比GK群体更近。GK群体包括的家系数量更多,导致其遗传多样性高于KD群体;两群体间的F_(st)为0.09,存在中等遗传分化。GK和KD群体每个ROH的平均长度分别为(1.70±0.34)Mb和(1.65±0.38)Mb,每个样本ROH的平均数量分别为1.98±1.30和2.07±1.37。GK和KD群体0.8~1.25 Mb长度的ROH占比分别为11.41%和19.17%,表明KD群体的选育历史比GK群体更长。两个群体>2.25 Mb长度的ROH片段占比分别为10.26和9.74%,表明两个群体短期内未发生近亲交配。七种基因组近交系数评估结果表明,KD群体的近交水平高于GK群体。不依赖基础群体等位基因频率的F_(ROH)和F_(HOM)方法可准确地评价育种群体的真实近交水平,而F_(VR1)、F_(YA1)和F_(LH1)等依赖基础群体等位基因频率的方法可以用来比较群体及个体间的相对近交水平。上述结果为准确地评估育种群体的近交水平和优化育种方案提供了重要参考依据。The main breeding objectives of Penaeus vannamei are divided into two aspects:one is to cultivate the selection line with high resistance(GK)and the other is to cultivate the selection line with fast growth rate(KD).However,there is a lack of investigation and analysis on the genetic diversity of these two selected populations,especially the level of genomic inbreeding.Based on the liquid chip of“Yellow Sea Chip No.1”(55K SNP),the genetic structure and genetic diversity of GK(1064 individuals)and KD(564 individuals)populations were analyzed for the first time.The genome distribution of runs of homozygosity(ROH)was investigated and the genomic inbreeding level of the two populations was mainly evaluated.The PCA and phylogenetic tree showed that GK and KD could be clearly stratified,and the kinship heatmap showed that individuals in KD were more closely related than those in GK.GK had a larger number of families,resulting in a higher genetic diversity than KD,the F_(st) between the two populations was 0.09,indicating moderate genetic differentiation.The average length of each ROH in GK and KD was(1.70±0.34)Mb and(1.65±0.38)Mb,respectively,and the average number of ROH in each sample was 1.98±1.30 and 2.07±1.37,respectively.The proportion of ROH with a length of 0.8~1.25 Mb in GK and KD was 11.41%and 19.17%,respectively,indicating that the selection history of KD was longer than that of GK.The proportion of ROH with a length of>2.25 Mb in the two populations was 10.26%and 9.74%,respectively,indicating that inbreeding events did not occur in the two populations in recent generations.The results of seven genomic inbreeding coefficients showed that the inbreeding level of KD was higher than that of GK.F_(ROH) and F_(HOM) methods which are independent of base population allele frequency could accurately evaluate the true inbreeding level of two selected populations,while F_(VR1),F_(YA1) and F_(LH1) methods which are dependent of the base population allele frequency can be used to compare the relative inbreeding

关 键 词：凡纳滨对虾 “黄海芯1号” 遗传多样性 连续性纯合片段 基因组近交系数 

分 类 号：Q953[生物学—动物学] Q789[农业科学—水产养殖] S968[农业科学—水产科学]