Yang Lv, Han Jiazheng, Deng Tingxian, Li Fan, Han Xiaotao, Xia Han, Quan Fanfan, Hua Guohua, Yang Liguo, Zhou Yang
Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, China.
National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Wuhan, Hubei, China.
Anim Genet. 2023 Apr;54(2):199-206. doi: 10.1111/age.13288. Epub 2023 Jan 22.
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 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.
作为基因组变异的重要来源，拷贝数变异（CNV）有助于全球水牛的环境适应。尽管具有这一重要性，但沼泽水牛和河流型水牛之间的CNV差异此前尚未得到研究。在此，我们报告了通过多种CNV检测策略在20个品种的141头水牛中检测到的21152个拷贝数变异区域（CNVR）。河流型水牛和沼泽水牛之间仅共享248个CNVR，这反映出两个亚种之间CNVR的巨大差异。基于CNV的群体结构分析成功地将两个水牛亚种区分开来。我们通过计算全基因组CNV的F值进一步评估了CNV差异。总体而言，我们在河流型水牛和沼泽水牛之间鉴定出110个显著分化的CNV片段和44个推定的选择基因。特别是，LALBA是控制奶牛产奶量的关键基因，其启动子区域呈现出高度分化的CNV，这使其成为沼泽水牛和河流型水牛在与产奶相关性状上存在差异的有力功能候选基因。我们的研究提供了水牛中CNV的有用信息，这可能有助于解释两个亚种之间的遗传差异。
