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Assessing the genetic diversity of the critically endangered Chinese sturgeon Acipenser sinensis using mitochondrial markers and genome-wide single-nucleotide polymorphisms from RAD-seq

文献类型： 外文期刊

作者： Liu, Jian 1 ; You, Xinxin 2 ; Xu, Pao 3 ; Zhuang, Ping 4 ; Zheng, Yueping 1 ; Zhang, Kai 2 ; Wang, Min 2 ; Lv, Yunyun 2 ; Xu 1 ;

作者机构： 1.Shanghai Yangtze Estuarine Nat Reserve Chinese St, Superintendency Dept, Shanghai 200092, Peoples R China

2.BGI, BGI Marine, Guangdong Prov Key Lab Mol Breeding Marine Econ A, Shenzhen Key Lab Marine Genom, Shenzhen 518083, Peoples R China

3.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Wuxi 214081, Peoples R China

4.Chinese Acad Fishery Sci, East China Sea Fisheries Res Inst, Key & Open Lab Marine & Estuarine Fisheries Resou, Shanghai 200090, Peoples R China

5.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China

6.BGI Zhenjiang Inst Hydrobiol, Zhenjiang 212000, Peoples R China

7.Shanghai Ocean Univ, Coll Marine Sci, Shanghai 201306, Peoples R China

8.Chinese Acad Fishery Sci, BGI Res Ctr Aquat Genom, Shenzhen 518083, Peoples R China

9.Shenzhen Univ, Coll Life Sci & Oceanog, Lab Aquat Genom, Shenzhen 518060, Peoples R China

关键词： Acipenser sinensis; genetic diversity; effective female population size; mtDNA; RAD-seq

期刊名称：SCIENCE CHINA-LIFE SCIENCES （ 影响因子：6.038； 五年影响因子：4.754 ）

ISSN： 1674-7305

年卷期： 2018 年 61 卷 9 期

页码：

收录情况： SCI

摘要： As a living fossil, the endangered Chinese sturgeon (Acipenser sinensis) has been considered a national treasure in China. Here, the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes. The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths (10-35 cm) were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA (mtDNA) D-loop region and 1,481,620 SNPs (single-nucleotide polymorphisms) generated by restriction site-associated DNA sequencing (RAD-seq). For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.

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