基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构

Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing

利用基因组重测序的方法获取高通量SNP标记,分析了长江上游三峡大坝-白鹤滩大坝之间8个不同江段(太平溪、巴南、合川、岷江口、宜宾、邵女坪、桧溪、冯家坪)共136尾瓦氏黄颡鱼(Pelteobagrus vachelli)的遗传多样性和遗传分化水平,阐明了长江上游瓦氏黄颡鱼群体遗传结构。结果显示:(1)三峡库区太平溪群体和巴南群体具有较高的SNP(single nucleotide polymorphism)数量和核苷酸多样性指数,遗传来源丰富,其遗传多样性高于其他群体;上游的岷江口、宜宾、邵女坪和冯家坪群体遗传来源单一。(2)瓦氏黄颡鱼存在3个不同的遗传分支,且不同遗传分支之间存在较大的遗传分化。(3)群体SNP数量和核苷酸多样性指数与河流坡降呈显著负相关,群体遗传分化指数与地理距离和隔离时间无显著相关性。研究结果表明,在三峡大坝-白鹤滩大坝江段,瓦氏黄颡鱼上游群体具有更低的遗传多样性,更易发生遗传漂变作用,在鱼类遗传多样性保护中需要特别关注;瓦氏黄颡鱼存在3种显著的遗传结构,应视为3个不同遗传单元进行种质资源管理。

Aims:Pelteobagrus vachelli is an important economic fish in the Yangtze River.Nevertheless,it shows a trend of younger age and miniaturization,and the number of reproductive population above the third age was small,which is not benefit to the long-term maintenance of its resources.Therefore,more attention and conservation measure are needed for this species.The aim of this study is to clarify genetic diversity and genetic structure of P.vachelli.Methods:We collected 136 samples of eight different river sections(Taipingxi,Banan,Hechuan,Minjiangkou,Yibin,Shaonüping,Huixi,Fengjiaping)from the Three Gorges Dam to Baihetan Dam in the upper Yangtze River.High-throughput SNP(single nucleotide polymorphism)markers through genome re-sequencing method was used to study genetic diversity and genetic differentiation of P.vachelli populations.Results:The number of SNP and nucleotide diversity of Taipingxi and Banan populations in the Three Gorges Reservoir region were significantly higher than those in the other populations,and there were three genetic branches and abundant genetic sources in the two populations.However,there was only one genetic branch and single genetic source in Minjiangkou,Yibin,Shaonüping and Fengjiaping populations.The populations could be divided into three distinct genetic groups with great genetic differentiation.All individuals in Fengjiaping and Minjiangkou belonged to group 1,all individuals in Shaonüping and Yibin belonged to group 2,Huixi and Hechuan populations had two genetic branches(group 1 and group 2),and Banan and Taipingxi populations had three genetic branches(group 1,group 2 and group 3).The SNP number and nucleotide diversity were significantly affected by channel slope.The genetic differentiation was not related to geographical distance and isolated time.Conclusion:The upstream populations with lower genetic diversity are more prone to genetic drift and thus need more attention in the fish protection.There are three distinct genetic structures in the upper Yangtze River,which can be regarded as three different genetic units for management of germplasm resource.