基于2b-RAD简化基因组测序的半滑舌鳎群体遗传多样性分析

Analysis of Population Genetic Diversity of Cynoglossus cynoglossus Based on 2b-RAD Simplified Genome Sequencing

摘要: 以天津野生、天津养殖和海阳养殖群体三个半滑舌鳎群体为材料，利用2b-RAD测序筛选得到的32,746个SNP位点，利用SNP标记，进行群体遗传结构、遗传多样性和类群间遗传关系分析。每个SNP位点在所有群体内遗传变异(Fis)，群体间的遗传变异(Fst)，总变异(Fit)以及综合多位点的Fis，Fst和Fit估计值,表明3个群体两两群体间的Fst值从0.0731~0.1635不等。天津养殖群体和天津野生群体的遗传分化最小，天津养殖群体和海阳养殖群体以及天津野生群体和海阳养殖群体的遗传分化大。选择消除分析结果显示3个群体的θπ在0.118~0.206之间，Tajima’D值在0.448~1.457之间：天津野生群体种群多态程度最高，天津养殖群体次之，海阳养殖群体最低。分别统计海阳、天津、天津野生三个群体中每个SNP位点的多态信息含量(PIC)，天津野生最高为0.220，天津养殖次之，海阳养殖最低，为0.175，天津野生和天津养殖差异并不显著。利用软件GCTA进行主成分分析，PCA结果显示，前两个主成分PC1和PC2贡献率分别为16.25%和9.54%，累积贡献25.79%。二维聚类结果显示，天津野生少部分区域与天津养殖间隔较小，但是两个主成分大体上还是可以明显区分为两大类，且二者与海阳养殖群体分类界限明显。综合以上SNP位点多样性、多态性信息含量、群体遗传多样性比较结果，所取的半滑舌鳎天津群体较海阳群体具有较高的遗传多样性和种群多态程度，其中天津野生群体和天津养殖群体虽较海阳养殖群体有差异，但前两者之间差异并不显著，揭示天津野生和养殖群体可能有一定程度的混杂，不排除野生群体中混杂有经养殖放流的养殖个体的可能性。

Abstract: Taking the cultured and wild populations of Cynoglossus semilaevis in Tianjin coast and cultured populations in Haiyang as study objects, there were 32,746 SNP locis screened by 2b-RAD se-quencing. The genetic relationship, genetic structure, genetic diversity in these three groups were also analyzed by SNP markers. The genetic variation within populations (Fis), the genetic variation between groups (Fst), and total variation (Fit) in each SNP locus in these three groups were estimated, which shown that Fst value was ranged from 0.0731 - 0.1635. The genetic differentiation between Tianjin culture population and Tianjin wild population is the smallest, and the genetic differentiation between Tianjin and Haiyang culture populations, Tianjin wild population and Haiyang culture population is great. The results of selective sweep showed that the polymorphism of wild population was highest in Tianjin, followed by Tianjin culture population, and lowest in Haiyang breeding population. The polymorphism information content (PIC) statistics of Haiyang, Tianjin wild and Tianjin cultured populations respectively in each SNP site shown that Tianjin wild was up to 0.220, followed by Haiyang cultured and Tianjin breeding; the lowest is 0.175. The differentiation between Tianjin wild and Tianjin culture populations is not significant. Principal component analysis was carried out by using software GCTA, and PCA showed that the contribution rates of the first two principal components PC1 and PC2 were  16.25% and 9.54%, respectively, and the cumulative contribution was 25.79%. Two dimensional clustering results show that a small part of the region in Tianjin wild population had a small intervals with that of Tianjin cultured population, but the two principal components generally can be clearly divided into two categories, and these two populations had a clear boundaries with Haiyang cultured one. Based on the above SNP locus diversity, polymorphism information content, genetic diversity comparison, the genetic diversity of Tianjin wild population is higher than Haiyang farming groups, but not significant difference between wild and cultured populations in Tianjin. It revealed that Tianjin populations may have a certain extent mixture, which means the possibility of population mixture between wild and culture individuals may exist.