基于微卫星标记的鳜种质遗传多样性与群体遗传结构分析

Genetic diversity and population genetic structure of mandarin fish (Siniperca chuatsi) based on microsatellite markers

采用Illumina高通量测序技术对鳜(Siniperca chuatsi)性腺转录组进行分析,筛选获得可设计引物的微卫星序列4 986条。随机合成239对微卫星引物,其中27个微卫星标记(11.30%)在12个鳜群体中呈现多态性,等位基因数2~8(5.63±1.84),有效等位基因数1.86~6.80(3.99±1.56),观测杂合度0.21~0.78(0.49±0.16),期望杂合度0.46~0.85(0.71±0.12),平均多态信息量0.37~0.84(0.66±0.15),基因流0.11~2.14(0.67±0.45)。在12个鳜群体中,嘉鱼群体平均等位基因数和平均有效等位基因数最大;武汉群体平均观测杂合度、平均期望杂合度高;12个群体遗传距离为0.103 0~1.511 7,遗传相似系数为0.220 5~0.902 2;抚远群体和顺德群体间的遗传距离最大(1.511 7),遗传相似系数最小(0.220 5);韶关群体和顺德群体间的遗传距离最小(0.103 0),遗传相似系数最大(0.902 2);UPGMA聚类分析显示珠江水系一支与长江水系一支先聚集后再与黑龙江水体支汇聚;12个群体间的遗传分化系数F ST介于0.041 8~0.611 0,群体间的遗传分化达到了显著性水平(P<0.05),梁子湖群体与武汉群体间的F ST最小(0.041 8),顺德群体与抚远群体间的F ST最大(0.611 0);AMOVA分析表明:群体间的遗传变异占33.14%,群体内遗传变异占66.86%;Structure分析显示12个群体可分为5个亚群。

Microsatellites were firstly screened in the Siniperca chuatsi gonadal transcriptome obtained by high-throughput sequencing.A total of 4 986 sequences,which contained microsatellites and could be designed with primers were obtained.Twenty seven(11.30%)out of 239 microsatellite loci were proved to be polymorphic in 12 S.chuatsi populations.The number of alleles per locus ranged from 2 to 8(5.63±1.84),the effective number of alleles per locus ranged from 1.86 to 6.80(3.99±1.56),the observed heterozygosity per locus ranged from 0.21 to 0.78(0.49±0.16),the expected heterozygosity per locus ranged from 0.46 to 0.85(0.71±0.12),the polymorphic information content per locus ranged from 0.37 to 0.84(0.66±0.15),and the gene flow per locus ranged from 0.11 to 2.14(0.67±0.45).The number of alleles and the effective number of alleles per locus in the Jiayu population were the highest among 12 populations.The observed heterozygosity and the expected heterozygosity per locus in the Wuhan population were the highest.The Nei’s genetic distance ranged from 0.103 0 to 1.511 7,the Nei’s genetic identity ranged from 0.220 5 to 0.902 2.The maximum Nei’s genetic distance(1.511 7)and the minimum Nei’s genetic identity(0.220 5)were between the Fuyuan population and Shunde population.The minimum Nei’s genetic distance(0.103 0)and the maximum Nei’s genetic identity(0.902 2)were between the Fuyuan population and Shunde population.UPGMA cluster analysis showed that one branch of the Pearl River system and the other branch of the Yangtze River system gathered firstly and then converged with the branch of the Heilongjiang River.The genetic differentiation coefficient F ST among the 12 groups was 0.041 8-0.611 0,and the genetic differentiation among the groups reached the significant level(P<0.05).The minimum F ST(0.041 8)was between the Liangzihu population and Wuhan population,and the maximum F ST(0.611 0)between the Shunde population and Fuyuan population.AMOVA analysis showed that the genetic variation among populations accounted for 33.14%,and the genetic variation within populations was 66.86%.Structure analysis showed that 12 populations were divided into 5 subpopulations.This study could provide useful basic data for protection of germplasm resources and variety breeding in S.chuatsi.