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Population structure, demographic history and local adaptation of the grass carp

文献类型： 外文期刊

作者： Shen, Yubang 1 ; Wang, Le 2 ; Fu, Jianjun 3 ; Xu, Xiaoyan 1 ; Yue, Gen Hua 2 ; Li, Jiale 1 ;

作者机构： 1.Shanghai Ocean Univ, Minist Agr, Key Lab Freshwater Aquat Genet Resources, Shanghai 201306, Peoples R China

2.Natl Univ Singapore, Temasek Life Sci Lab, Mol Populat Genet & Breeding Grp, 1 Res Link, Singapore 117604, Singapore

3.Chinese Acad Fishery Sci, Freshwater Fisheries Res Ctr, Minist Agr, Key Lab Freshwater Fisheries & Germplasm Resource, Wuxi 214081, Jiangsu, Peoples R China

4.Natl Univ Singapore, Dept Biol Sci, 14 Sci Dr 4, Singapore 117543, Singapore

5.Nanyang Technol Univ, Sch Biol Sci, 60 Nanyang Dr, Singapore 637551, Singapore

6.Shanghai Ocean Univ, Minist Educ, Key Lab Explorat & Utilizat Aquat Genet Resources, Shanghai 201306, Peoples R China

关键词： Grass carp; Diversity; Population structure; Evolution; Aquaculture; SNP

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2019 年 20 卷

页码：

收录情况： SCI

摘要： BackgroundGenetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture.ResultsWe used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow.ConclusionsThis study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.

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