基于RAD-seq测序技术的墨西哥湾扇贝遗传改良后代及其双亲的遗传结构分析  

Genetic Structure Analysis of the Genetically Improved Progeny and Both Parents of Argopecten irradians concentricus Based on RAD-seq Sequencing Technology

作　　者：卢怡凝 张元 张柯馨 李腾 刘付少梅 方家熙 刘志刚[1,3] LU Yining;ZHANG Yuan;ZHANG Kexin;LI Teng;LIUFU Shaomei;FANG James Kar-Hei;LIU Zhigang(College of Fisheries,Guangdong Ocean University,Zhanjiang,524088;Zhanjiang Silverwave Marine Biotechnology Co.,Ltd.,Zhanjiang,524022;Guangdong Marine Invertebrate Science and Technology Innovation Center,Zhanjiang,524088;Department of Applied Biology and Chemical Technology,Hong Kong Polytechnic University,Hong Kong,999077,China)

机构地区：[1]广东海洋大学水产学院,湛江524088 [2]湛江银浪海洋生物技术有限公司,湛江524002 [3]广东省海产无脊椎动物科技创新中心,湛江524088 [4]香港理工大学应用生物及化学科技学系,中国香港999077

出　　处：《基因组学与应用生物学》2024年第9期1607-1619,共13页Genomics and Applied Biology

基　　金：2020广东省国际科技合作领域项目(2020A0505100057);广东省现代化海洋牧场适养品种核心技术攻关项目(2024-MRB-00-001);2019广东省重点领域研发计划项目(2019B020238002);2019广东省贝类产业技术体系创新团队项目(2023KJ146);南海经济动物种质创新与利用创新团队项目(2021KCXTD026)共同资助。

摘　　要：本研究旨在阐明遗传改良后代墨西哥湾扇贝(Argopecten irradians concentricus)“橙黄1号”杂交选育系F5与其双亲的遗传关系及遗传进展。运用RAD-seq测序技术,对4个群体共96份扇贝样本进行了主成分分析(principal component analysis,PCA)、系统进化树构建及群体结构分析。进一步对墨西哥湾扇贝“橙黄1号”F5的30份样本进行亲本基因型转化及遗传多样性分析。结果表明,96份扇贝样本与参考基因组的平均比对率为96.45%,平均覆盖度为13.89%,平均覆盖深度为5.62×,共获得116533个高质量单核苷酸多态性(single nucleotide polymorphism,SNP)位点。群体遗传结构分析表明,96份扇贝样本被明显划分为4个类群,墨西哥湾扇贝“橙黄1号”F5的遗传结构与其双亲相近,介于双亲之间,与外群华贵栉孔扇贝(Chlamys nobilis)遗传结构相距较远。遗传多样性分析结果表明,墨西哥湾扇贝“橙黄1号”F5的平均观测杂合度为0.1485,低于平均期望杂合度0.3781。说明经过5代选育,墨西哥湾扇贝“橙黄1号”F5的遗传基因获得纯化。研究结果为墨西哥湾扇贝“橙黄1号”的遗传背景、亲缘关系及遗传进展提供依据。This study aims to elucidate the genetic relationship and genetic progress of the genetically improved Argopecten irradians concentricus“Orange No.1”crossbreeding line F5 and its parents.RAD-seq sequencing technology was used to analyze the principal component analysis(PCA),phylogenetic tree construction,and population structure analysis of a total of 96 scallop samples from four populations.Furthermore,the parental genotypes and the genetic diversity analysis were conducted on the 30 samples of Argopecten irradians concentricus“Orange No.1”F5.The results showed that 96 scallop samples were matched to the reference genome at an average rate of 96.45%,with an average coverage of 13.89%and an average depth of coverage of 5.62×.A total of 116533 high-quality single nucleotide polymorphism(SNP)were obtained.Analysis of the population genetic structure showed that the 96 scallop samples were clearly divided into four taxa,with the genetic structure of Argopecten irradians concentricus“Orange No.1”F5 was similar to that of its parents,between the two parents,and far from the genetic structure of the outgroup of Chlamys nobilis.Genetic diversity analysis showed that the average observed heterozygosity of Argopecten irradians concentricus“Orange No.1”F5 was 0.1485,which was lower than the average expected heterozygosity of 0.3781.This study shows that the Argopecten irradians concentricus“Orange No.1”F5 gene has been purified after five generations of selection,and the results of the study provide a basis for the genetic background,parentage and genetic progression of Argopecten irradians concentricus“Orange No.1”.

关 键 词：墨西哥湾扇贝“橙黄1号” 单核苷酸多态性(SNP) 遗传结构 亲缘关系 遗传进展 

分 类 号：S917.4[农业科学—水产科学]