Comparative analyses of copy number variations between swamp buffaloes and river buffaloes

文献类型： 外文期刊

第一作者： Yang, Lv

作者： Yang, Lv;Han, Jiazheng;Li, Fan;Han, Xiaotao;Xia, Han;Hua, Guohua;Yang, Liguo;Zhou, Yang;Yang, Lv;Han, Jiazheng;Li, Fan;Han, Xiaotao;Xia, Han;Hua, Guohua;Yang, Liguo;Zhou, Yang;Deng, Tingxian;Quan, Fanfan;Hua, Guohua;Yang, Liguo;Zhou, Yang

作者机构：

关键词： CNV; F-ST; population structure analysis; river buffalo; swamp buffalo

期刊名称：ANIMAL GENETICS （ 影响因子：2.4； 五年影响因子：2.8 ）

ISSN： 0268-9146

年卷期： 2023 年 54 卷 2 期

页码：

收录情况： SCI

摘要： As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating F-ST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.

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