Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation

文献类型： 外文期刊

第一作者： Zeng, Tao

作者： Zeng, Tao;Tian, Yong;Gu, Tiantian;Chen, Li;Xu, Wenwu;Cao, Yongqing;Li, Guoqin;Tao, Zhengrong;Shen, Junda;Lu, Lizhi;Yin, Jianmei;Li, Guohui;Qu, Liang;Xue, Qian;Zhang, Huiyong;Zhou, Chenghao;Han, Wei;Yin, Jianmei;Li, Guohui;Qu, Liang;Xue, Qian;Zhang, Huiyong;Zhou, Chenghao;Han, Wei;Feng, Peishi;Han, Feiran;Xu, Yuhui;Wang, Yuntong;Liu, Yali;Liu, Lijun;Gu, Lihong;Wei, Qingyu;Li, Peifeng

作者机构：

期刊名称：COMMUNICATIONS BIOLOGY （ 影响因子：6.548； 五年影响因子：6.816 ）

ISSN：

年卷期： 2022 年 5 卷 1 期

页码：

收录情况： SCI

摘要： Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments. Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation.

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