Ma Xiaohui, Cheng Haijian, Liu Yangkai, Sun Luyang, Chen Ningbo, Jiang Fugui, You Wei, Yang Zhangang, Zhang Baoheng, Song Enliang, Lei Chuzhao
Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250100, China.
College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China.
Animals (Basel). 2022 Mar 7;12(5):665. doi: 10.3390/ani12050665.
Bohai Black cattle are one of the well-known cattle breeds with black coat color in China, which are cultivated for beef. However, no study has conducted a comprehensive analysis of genomic diversity and selective pressures in Bohai Black cattle. Here, we performed a comprehensive analysis of genomic variation in 10 Bohai Black cattle (five newly sequenced and five published) and the published whole-genome sequencing (WGS) data of 50 cattle representing five "core" cattle populations. The population structure analysis revealed that Bohai Black cattle harbored the ancestry with European taurine, Northeast Asian taurine, and Chinese indicine. The Bohai Black cattle demonstrated relatively high genomic diversity from the other cattle breeds, as indicated by the nucleotide diversity (pi), the expected heterozygosity (H) and the observed heterozygosity (H), the linkage disequilibrium (LD) decay, and runs of homozygosity (ROH). We identified 65 genes containing more than five non-synonymous SNPs (nsSNPs), and an enrichment analysis revealed the "ECM-receptor interaction" pathways associated with meat quality in Bohai Black cattle. Five methods (CLR, θπ, F, θπ ratio, and XP-EHH) were used to find several pathways and genes carried selection signatures in Bohai Black cattle, including black coat color (), muscle development (, , , , and ), fat deposition (, , , and ), reproduction traits (, , and ), and immune system response (, , , and ). Taken together, our results provide a valuable resource for characterizing the uniqueness of Bohai Black cattle.
渤海黑牛是中国著名的黑色被毛肉牛品种之一。然而，尚未有研究对渤海黑牛的基因组多样性和选择压力进行全面分析。在此，我们对10头渤海黑牛（5头新测序和5头已发表）以及代表5个“核心”牛群的50头牛的已发表全基因组测序（WGS）数据进行了基因组变异的全面分析。群体结构分析表明，渤海黑牛具有欧洲牛、东北亚牛和中国瘤牛的血统。核苷酸多样性（pi）、期望杂合度（H）和观察杂合度（H）、连锁不平衡（LD）衰减和纯合子连续片段（ROH）表明，渤海黑牛与其他牛品种相比表现出相对较高的基因组多样性。我们鉴定出65个包含5个以上非同义单核苷酸多态性（nsSNPs）的基因，富集分析揭示了与渤海黑牛肉质相关的“细胞外基质受体相互作用”途径。使用五种方法（CLR、θπ、F、θπ比率和XP-EHH）来寻找渤海黑牛中带有选择印记的几个途径和基因，包括黑色被毛（）、肌肉发育（、、、、和）、脂肪沉积（、、、和）、繁殖性状（、、和）以及免疫系统反应（、、、和）。综上所述，我们的结果为表征渤海黑牛的独特性提供了宝贵资源。
