凡纳滨对虾全基因组SSR标记开发及不同养殖群体的遗传多样性  

Development of SSR markers from genomic data for Litopenaeus vannamei and analysis of genetic diversity in different cultured populations

作　　者：王佳佳[1,2] 王琼 秦桢 陈耀辉 李健 李吉涛[1,2] WANG Jiajia;WANG Qiong;QIN Zhen;CHEN Yaohui;LI Jian;LI Jitao(Key Laboratory for Sustainable Utilization of Marine Fisheries Resources,Ministry of Agriculture and Rural Affairs,Yellow Sea Fisheries Research Institute,Chinese Academy of Fishery Sciences,Qingdao 266071,China;Function Laboratory for Marine Fisheries Science and Food Production Processes,Qingdao National Laboratory for Marine Science and Technology,Qingdao 266071,China)

机构地区：[1]中国水产科学研究院黄海水产研究所,农业农村部海洋渔业可持续发展重点实验室,山东青岛266071 [2]青岛海洋科学与技术国家试点实验室,海洋渔业科学与食物产出过程功能实验室,山东青岛266071

出　　处：《水产学报》2023年第6期62-72,共11页Journal of Fisheries of China

基　　金：国家虾蟹产业技术体系专项(CARS-48);中国水产科学研究院基本科研业务费专项(2021GH05,2020TD46)。

摘　　要：为了探究SSR标记对凡纳滨对虾养殖群体的遗传多样性和群体遗传结构的影响,为凡纳滨对虾种质资源的遗传改良提供基础信息。实验利用MISA软件对凡纳滨对虾全基因组SSR位点进行搜索,通过聚丙烯酰胺凝胶电泳获得多态性高的SSR标记,基于POPGENE 1.32、PIC-CALC和Mega 6.0软件分析6个不同来源的凡纳滨对虾养殖群体的遗传多样性和群体结构特征。在凡纳滨对虾全基因组数据中共鉴定出10 453 975个微卫星,约占基因组序列总长度的18.56%,其中,二碱基微卫星最丰富,占总数的82.15%。利用具有多态性的14个SSR标记分析3个国内群体[桂海1号(CG)、海兴农2号(CH)和山东养殖群体(CT)],及3个国外群体[厄瓜多尔1号(FO)、厄瓜多尔2号(FT)和墨西哥群体(FM)]的遗传特征。结果显示,14个SSR标记在6个群体中共检测到208个等位基因变异,等位基因数、观测杂合度、期望杂合度和多态性信息含量的范围分别为6~25、0.112~0.994、0.234~0.925和0.226~0.918;遗传多样性丰富程度为CH>FO>FM>CT>FT>CG。桂海1号与山东养殖群体、3个国外群体间属于中等程度的遗传分化。聚类分析结果显示,国内群体桂海1号和海兴农2号聚为一大类,山东养殖群体与国外群体厄瓜多尔1号、厄瓜多尔2号和墨西哥群体聚为一大类。研究表明,筛选的14个SSR标记可用于凡纳滨对虾群体遗传多样性的评估;3个国外群体的遗传多样性相对较高,且与国内群体桂海1号和海兴农2号的亲缘关系较远。本研究对凡纳滨对虾种质资源的开发利用与新品种选育具有十分重要的意义。Litopenaeus vannamei is a major cultured shrimp,accounting for 70%of the total output of mariculture shrimp in China.Genetic improvement is an essential measure for improving the important economic traits in shrimp aquaculture.Understanding the genetic diversity and population structure of different populations using molecular markers is considered as a prerequisite for efficient germplasm exploitation and utilization to deploy suitable breeding program for genetic improvement.Using the criteria of motif repeats,a total of 10453975 potential SSRs with a minimum of five repetitions were identified from the 1663588777 bp genome sequence by Perl script of MISA,which accounts for 18.56%of the total length of the genome sequence with a distribution density of 6589.25 loci/Mb.A total of 42 SSR primer pairs were randomly selected for validation,and 14 SSR loci had allelic polymorphism.The genetic characteristics of three representative domestic populations including Guihai No.1(CG),Haixingnong No.2(CH)and Shandong population,and three foreign populations including Ecuador No.1(FO),Ecuador No.2(FT)and Mexico(FM)were evaluated using 14 polymorphic microsatellite markers.The results showed that 208 alleles were detected in six populations,the average allele number,average expected heterozygosity,average observed heterozygosity and polymorphism information content were 14.9,0.462,0.736 and 0.7411,respectively.The genetic diversity of six populations ranged from high to low:CH>FO>FM>CT>FT>CG.There was medium genetic differentiation between the Guihai No.1 and three foreign populations.The analysis showed that Guihai No.1 and Haixingnong No.2 clustered into one branch,while Shandong population and three foreign populations including Ecuador No.1,Ecuador No.2 and Mexico clustered into another branch.In conclusion,the 14 polymorphic markers could be used as efficient markers to analyze the genetic diversity of L.vannamei population,and the furthest distance was found between Guihai No.1 and three foreign populations.This study

关 键 词：凡纳滨对虾 养殖群体 遗传多样性 基因组 微卫星标记 

分 类 号：Q348[生物学—遗传学] S968.22[农业科学—水产养殖]