基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构_熊飞.pdf

2023,31(4):22391,pages 110 doi:10.17520/biods.2022391 收稿日期:2022-07-09;接受日期:2022-11-14 基金项目:国家自然科学基金(51979123)、湖北省高等学校优秀中青年科技创新团队计划项目(T2020034)和江汉大学科技创新专项项目(2021kjzx006)*共同通讯作者 Co-authors for correspondence.E-mail:; https:/www.biodiversity-基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构 熊飞1,2,刘红艳1,2*,翟东东1,2,段辛斌3*,田辉伍3,陈大庆3 1.江汉大学生命科学学院,湖北省汉江流域特色生物资源保护开发与利用工程技术研究中心,武汉 430056;2.江汉大学持久性有毒污染物环境与健康危害湖北省重点实验室,武汉 430056;3.中国水产科学研究院长江水产研究所,武汉 430223 摘要: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。关键词:瓦氏黄颡鱼;长江上游;遗传分化;遗传多样性;基因组重测序 熊飞,刘红艳,翟东东,段辛斌,田辉伍,陈大庆(2023)基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构.生物多样性,31,22391.doi:10.17520/biods.2022391.Xiong F,Liu HY,Zhai DD,Duan XB,Tian HW,Chen DQ(2023)Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing.Biodiversity Science,31,22391.doi:10.17520/biods.2022391.Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing Fei Xiong1,2,Hongyan Liu1,2*,Dongdong Zhai1,2,Xinbin Duan3*,Huiwu Tian3,Daqing Chen3 1 School of Life Sciences,Jianghan University,Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin,Wuhan 430056 2 Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances,Jianghan University,Wuhan 430056 3 Yangtze River Fisheries Research Institute,Chinese Academy of Fishery Sciences,Wuhan 430223 ABSTRACT 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,Shaonping,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 研究报告 熊飞等:基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构研究 2023年|31卷|4期|22391|第2页 and abundant genetic sources in the two populations.However,there was only one genetic branch and single genetic source in Minjiangkou,Yibin,Shaonping 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 Shaonping 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.Key words:Pelteobagrus vachelli;the upper Yangtze River;genetic differentiation;genetic diversity;genome re-sequencing 瓦氏黄颡鱼(Pelteobagrus vachelli)隶属于鲿科 黄颡鱼属,广泛分布于长江及其支流,是长江常见的底栖定居性鱼类(丁瑞华,1994)。过度捕捞等人为因素导致其资源衰退,瓦氏黄颡鱼被认为是中度超额开发物种(陈大庆等,2002)。另外,水电工程的建设导致许多河段水位抬高,淹没大量砾石和水草等附着物,影响粘性卵的附着,造成瓦氏黄颡鱼等产粘性卵鱼类的产卵场消失(姚维志,2018)。虽然渔业资源调查显示,瓦氏黄颡鱼目前在长江渔获物中的占比仍处于优势地位,但是其群体呈现出低龄化和小型化的现象,渔获物中大部分个体未达到性成熟,3龄以上繁殖群体较少,不利于其资源的可持续利用(杨家云,1994;熊飞等,2015)。遗传多样性是物种进化和适应的基础,维持群体遗传多样性有利于物种长期的进化和生存(Nakajima et al,2020)。瓦氏黄颡鱼是长江重要的经济鱼类,探明其群体遗传多样性和遗传结构,对于评估其种质状况和制定合理的管理政策至关重要。长江上游是水电大坝梯级开发集中、河流生境破碎化严重的区域,已建成三峡、向家坝、溪洛渡等多座大型水电站(Cheng et al,2015)。关于长江上游鱼类的相关研究主要集中在特有鱼类和洄游性鱼类等方面(Song et al,2016;Liu et al,2017),而对于广布种及定居性鱼类的关注较少。关于瓦氏黄颡鱼群体遗传结构的研究,涉及长江上游区域的较少,且所用的分子标记多为线粒体DNA标记(Wang et al,2004),获得的遗传信息有限。单核苷酸多态性(single nucleotide polymorphism,SNP)是基因组变异的主要方式之一,其遗传稳定性好、通量高。重测序技术将新获得的序列与已知的参考基因组序列进行比对,获取大量的SNP位点,为群体遗传研究提供了重要手段(Kang et al,2017)。本研究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、