基于基因分型测序(GBS)技术分析鲂鲌鱼类及其杂交子代的遗传结构  

Genetic structure analysis of Megalobrama terminalis,Culter alburnus,Chanodichthys mongolicus and their hybrids based on genotyping by sequencing

作　　者：刘凯[1] 冯晓宇[1] 沈玉帮[2] 马恒甲[1] 李家乐[2] 郭炜 谢楠[1] LIU Kai;FENG Xiaoyu;SHEN Yubang;MA Hengjia;LI Jiale;GUO Wei;XIE Nan(Institute of Fishery Science,Hangzhou Academy of Agricultural Sciences,Hangzhou 310024,China;Key Laboratory of Freshwater Aquatic Genetic Resources,Ministry of Agriculture and Rural Affairs,Shanghai Ocean University,Shanghai 201306,China)

机构地区：[1]杭州市农业科学研究院,水产研究所,浙江杭州310024 [2]上海海洋大学,农业农村部淡水水产种质资源重点实验室,上海201306

出　　处：《水产学报》2021年第8期1307-1316,共10页Journal of Fisheries of China

基　　金：现代农业产业技术体系专项(CARS-45-39);杭州市农业科研主动设计项目(20162012A03);杭州市农科院创新基金(2019HNCT-01)。

摘　　要：为利用基因分型测序(GBS)技术对三角鲂、翘嘴鲌、蒙古鲌及其杂交子代的遗传结构进行分析。本研究采用GBS技术对三角鲂、翘嘴鲌、蒙古鲌及其杂交子代(F_(1))共6个个体的鳍条提取总DNA进行双酶切简化基因组测序,使用Stacks软件构建SNP比对参考基因组进行分析。结果显示,6个个体共产生clean data 7.01 GB,平均每个样品1.17 GB;将所有样本作为一个群体检测SNP变异,共检测出SNP位点399145个,质控过滤后得到SNP位点97911个。基于亲本及其子代的SNP位点分析表明,亲本及其子代的平均观测杂合度(H_(o))为0.3394,平均期望杂合度(H_(e))为0.2853,平均多态性信息含量(PIC)为0.2737,平均核苷酸多样性(P_(i))为0.3727,平均最小等位基因频率(MAF)为0.2472,平均可分型样品比例(genotype rate)为93.94%。遗传分化指数和遗传距离分析结果表明,三角鲂、翘嘴鲌、蒙古鲌及其杂交子代间的分化指数为0.3096~0.8940,遗传距离为0.3705~2.2443。使用最大似然(ML)法构建的系统进化树显示,三角鲂、翘嘴鲌、蒙古鲌及其杂交子代区分明显。本研究通过对三角鲂、翘嘴鲌、蒙古鲌及其杂交子代的遗传结构分析,将为鲂鲌鱼类的杂交选育提供更多的遗传学数据。Distant hybridization is an essential means of breeding among aquatic animal species,genera,subfamilies,and even families,combining parents’dominant traits to obtain excellent new hybrid varieties.Previous studies on Megalobrama and Culter’s distant hybridization show that Megalobrama and Culter’s hybrid offspring have significant heterosis.However,the analysis of the genetic structure of the fish hybridized from Megalobrama and Culter is still relatively limited,and there is little research on single nucleotide polymorphism markers(SNPs).This study aims to analyze the genetic structure of Megalobrama terminalis,Culter alburnus,Chanodichthys mongolicus,and their hybrids by high-quality SNPs obtained by genotyping by sequencing(GBS)technology.In the study,the total DNA extracted from the fin strips of 6 individuals that included M.terminalis,C.alburnus,C.mongolicus,and their hybrids(F_(1)),was double digested.Simplified genome sequencing was performed using Stacks software to construct a reference genome for SNP comparison.As a result,six individuals produced 7.01 GB of clean data,with an average of 1.17 GB per sample.All samples were used as a group to detect SNP mutations.A total of 399145 SNP sites were detected.After quality control filtering,97911 SNP sites were obtained.SNP analysis indicated that,of parents and their hybrids,the average observed heterozygosity was 0.3394.The average expected heterozygosity was 0.2853.The average polymorphic information content was 0.2737,average nucleotide diversity was 0.3727,the average minimum allele frequency was 0.2472,and the average genotyping rate was 93.94%.The principal component analysis(PCA)showed that M.terminalis,C.alburnus,C.mongolicus,and their hybrids clustered at different points,but the clustering points of the two hybrids of M.terminalis and C.alburnus were close.The PCA’s result indicated apparent genetic differentiation among M.terminalis,C.alburnus,C.mongolicus,and their hybrids.Based on the genetic differentiation index and genetic distance b

关 键 词：三角鲂 翘嘴鲌 蒙古鲌 杂交 单核苷酸多态性 基因结构 基因分型测序 

分 类 号：Q959.4[生物学—动物学] S917.4[农业科学—水产科学]