Song Xingya, Zhang Zijing, Xing Shengyan, Liu Xian, Zhang Yuqiao, Wang Jiamei, Lyu Shijie, Wang Xiangnan, Qi Xingshan, Ma Weidong, Lei Chuzhao, Wang Eryao, Huang Yongzhen
College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi, 712100, People's Republic of China.
Institute of Animal Husbandry, Henan Academy of Agricultural Sciences, Zhengzhou, Henan, 450002, People's Republic of China.
BMC Genomics. 2025 May 14;26(1):480. doi: 10.1186/s12864-025-11626-6.
Pinan cattle, as the progeny of crossbreeding improvement between Nanyang cattle and Piedmontese, have attracted attention for their excellent growth performance. In this study, we constructed a copy number variation map by whole genome resequencing of 132 Pinan cattle. In the genome of Pinan cattle, deletion-type copy number variants occupied a higher proportion and only 3.31% of CNVRs overlapped with exonic regions. It showed that Pinan cattle was clearly distinguishable from other breeds and Pinan cattle was closer to Nanyang cattle by population genetic structure analysis based on CNVRs. The degree of inbreeding in the Pinan cattle population was explored by ROH analysis, which showed that the degree of inbreeding in Pinan cattle was lower than that in European beef cattle, suggesting that the risk of inbreeding was low. Candidate genes related to muscle development (CADM3, CNTFR, DOCK3), reproductive traits (SCAPER), embryonic development (RERE) and immune traits (CD84) were identified by V selection analysis, ROH islands and iHS selection analysis, which provided a new scientific basis for the genetic basis of the excellent traits in Pinan cattle.
皮南牛作为南阳牛与皮埃蒙特牛杂交改良的后代，因其优异的生长性能而备受关注。在本研究中，我们通过对132头 皮南牛进行全基因组重测序构建了拷贝数变异图谱。在皮南牛基因组中，缺失型拷贝数变异占比较高，且只有3.31%的拷贝数变异区域（CNVRs）与外显子区域重叠。基于CNVRs的群体遗传结构分析表明，皮南牛与其他品种明显不同，且皮南牛与南阳牛的亲缘关系更近。通过回归同祖片段（ROH）分析探究了皮南牛群体的近交程度，结果表明皮南牛的近交程度低于欧洲肉牛，这表明其近交风险较低。通过V选择分析、ROH岛分析和iHS选择分析，鉴定出了与肌肉发育（CADM3、CNTFR、DOCK3）、繁殖性状（SCAPER）、胚胎发育（RERE）和免疫性状（CD84）相关的候选基因，这为皮南牛优良性状的遗传基础提供了新的科学依据。
