基于简化基因组测序宽鳍鱲的微卫星分子标记及遗传多样性分析  

Microsatellite Markers and Genetic Diversity Analysis of Zacco platypus Based on Simplified Genome Sequencing

作　　者：覃宁 张桂蓉[2] 马徐发[2] 魏开建[2] QIN Ning;ZHANG Guirong;MA Xufa;WEI Kaijian(Guizhou Fisheries Research Institute,Guiyang,Guizhou 550025;College of Fisheries,Huazhong Agricultural University,Wuhan,Hubei 430070,China)

机构地区：[1]贵州省水产研究所,贵州贵阳550025 [2]华中农业大学水产学院,湖北武汉430070

出　　处：《贵州农业科学》2024年第8期78-83,共6页Guizhou Agricultural Sciences

基　　金：生态环境部生物多样性调查评估项目(2019HJ2096001006);贵州省农业科学院青年基金项目“从肌肉层面解析从江田鱼的‘座田’机制研究”(黔农科院青年基金〔2022〕25号);国家农业农村部项目“国家特色淡水鱼产业技术体系”(CARS-46);贵州省农业科学院种质资源专项“鱼类(含麻鱼)资源收集保护、鉴定评价和创新利用”(黔农科种质资源〔2023〕10号)。

摘　　要：【目的】建立基于简化基因组测序(2b-RAD)宽鳍鱲(Zacco platypus)的微卫星分子标记,并进行遗传多样性分析,为有效开展宽鳍鱲品种间遗传多样性分析和分子育种,挖掘和利用宽鳍鱲种质资源提供参考。【方法】利用限制性内切酶EcoRⅠ打断基因组DNA,每个样本分别进行物理打碎,选取300~700 bp插入片段文库,利用Illumina HiSeq PE150测序平台进行双末端(Paired-End)测序获得海量遗传多态性标签序列。【结果】2b-RAD筛选宽鳍鱲的微卫星位点得到两端各留100 bp作为引物的SSR数量为41018个,带有引物片段的SSR数量为1522个,片段引物的设计率为37.1%,构建的文库质量较高,测序深度达高准确度下的分型标准。在筛选的64个微卫星位点中,有14个位点(21.88%)具有多态性,由于存在无效等位基因,有3个位点(Zpla08、Zpla09和Zpla10)显著偏离Hardy-Weinberg平衡(P<0.05),因此选用其中的11个微卫星位点分析宽鳍鱲群体遗传多样性。基于11个微卫星DNA位点的分析表明,宽鳍鱲7个群体的平均等位基因数(N_(A))为3.66,平均Shannon;s信息指数(I)为0.689,平均观测杂合度(H_(O))为0.315,平均期望杂合度(H_(E))为0.354,平均多态信息含量(PIC)为0.409。【结论】基于简化基因组测序(2b-RAD)开发宽鳍鱲的微卫星分子标记可用于评估野生宽鳍鱲种群的遗传多样性、遗传结构和物种鉴定。宽鳍鱲基因组DNA 14个微卫星位点中有11个微卫星位点具有中高多态性,3个位点(Zpla08、Zpla09、Zpla10)偏离Hardy-Weinberg平衡,在群体遗传研究中应慎用。【Objective】The microsatellite molecular markers of Zacco platypus based on simplified genome sequencing(2b-RAD) were established and the genetic diversity analysis were carried out to effectively carry out the analysis of genetic diversity and molecular breeding among Z.platypus varieties,and to provide the reference for excavating and utilizing the Z.platypus germplasm resources.【Method】Genomic DNA was interrupted by the restriction endonuclease EcoR Ⅰ,and each sample was physically broken,and a library of 300–700 bp insert fragments was selected to obtain a large amount of genetic polymorphism tags by paired-end sequencing through the Illumina HiSeq PE150 sequencing platform.【Result】2b-RAD screening of microsatellite loci in Z.platypus obtained 41 018 SSRs with 100 bp left at each end as primers,and 1 522 SSRs with primer fragments,with a fragment primer design rate of 37.1%.The constructed libraries were of high quality,with sequencing depths meeting the typing standard at high accuracy.Among the 64 screened microsatellite loci,14 loci(21.88%) were polymorphic,and 3 loci(Zpla08,Zpla09 and Zpla10) deviated obviously from Hardy-Weinberg equilibrium due to the presence of null alleles(P<0.05),so 11 of them were selected for analyzing the genetic diversity of Z.platypus populations.Analysis of the 11 microsatellite DNA loci showed that the mean number of alleles(N_(A)) of the seven populations of Z.platypus was 3.66,the mean Shannon's information index(I) was 0.689,the mean observed heterozygosity(H_(O)) was 0.315,the mean expected heterozygosity(H_(E)) was 0.354,and the mean polymorphic information content(PIC) was 0.409.【Conclusion】The development of microsatellite molecular markers for Z.platypus based on 2b-RAD can be used to assess genetic diversity,genetic structure and species identification of wild Z.platypus populations.11 of the 14 microsatellite loci in the genomic DNA of Z.platypus are moderately to highly polymorphic,and 3 loci(Zpla08,Zpla09,Zpla10) deviated from Hardy-Weinberg equ

关 键 词：宽鳍鱲 简化基因组测序 微卫星分子标记 微卫星位点 遗传多样性 等位基因 

分 类 号：S917.4[农业科学—水产科学]