Institute of Animal Husbandry and Veterinary Research, Hainan Academy of Agricultural Sciences, Key Laboratory of Tropical Animal Breeding and Epidemic Disease Research, Haikou 571100, China.
School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
Int J Mol Sci. 2024 Nov 6;25(22):11919. doi: 10.3390/ijms252211919.
Copy number variation (CNV) serves as a crucial source of genomic variation and significantly aids in the mining of genomic information in cattle. This study aims to analyze re-sequencing data from Chinese Hainan yellow cattle, to uncover breed CNV information, and to elucidate the resources of population genetic variation. We conducted whole-genome sequencing on 30 Chinese Hainan yellow cattle, thus generating 814.50 Gb of raw data. CNVs were called using CNVnator software, and subsequent filtering with Plink and HandyCNV yielded 197,434 high-quality CNVs and 5852 CNV regions (CNVRs). Notably, the proportion of deleted sequences (81.98%) exceeded that of duplicated sequences (18.02%), with the lengths of CNVs predominantly ranging between 20 and 500 Kb This distribution demonstrated a decrease in CNVR count with increasing fragment length. Furthermore, an analysis of the population genetic structure using CNVR databases from Chinese, Indian, and European commercial cattle breeds revealed differences between Chinese Bos indicus and Indian Bos indicus. Significant differences were also observed between Hainan yellow cattle and European commercial breeds. We conducted gene annotation for both Hainan yellow cattle and European commercial cattle, as well as for Chinese Bos indicus and Indian Bos indicus, identifying 206 genes that are expressed in both Chinese and Indian Bos indicus. These findings may provide valuable references for future research on Bos indicus. Additionally, selection signatures analysis based on Hainan yellow cattle and three European commercial cattle breeds identified putative pathways related to heat tolerance, disease resistance, fat metabolism, environmental adaptation, candidate genes associated with reproduction and the development of sperm and oocytes (, , , , ), environmental adaptation (, , , , , , ), oxidative stress anti-inflammatory response (, , disease resistance (, , ), and meat quality (, , , ). This study provides a comprehensive exploration of CNVs at the molecular level in Chinese Hainan yellow cattle, offering theoretical support for future breeding and selection programs aimed at enhancing qualities of this breed.
拷贝数变异（CNV）是基因组变异的重要来源，极大地帮助了牛基因组信息的挖掘。本研究旨在分析中国海南黄牛的重测序数据，揭示品种 CNV 信息，阐明群体遗传变异的资源。我们对 30 头中国海南黄牛进行了全基因组测序，产生了 814.50 Gb 的原始数据。使用 CNVnator 软件对 CNVs 进行了调用，然后使用 Plink 和 HandyCNV 进行过滤，得到了 197,434 个高质量的 CNVs 和 5852 个 CNV 区域（CNVRs）。值得注意的是，缺失序列的比例（81.98%）超过了重复序列的比例（18.02%），CNVs 的长度主要在 20 到 500 Kb 之间。这种分布表明，随着片段长度的增加，CNVR 的数量减少。此外，使用中国、印度和欧洲商业牛品种的 CNVR 数据库分析群体遗传结构表明，中国瘤牛和印度瘤牛之间存在差异。海南黄牛和欧洲商业品种之间也存在显著差异。我们对海南黄牛和欧洲商业牛进行了基因注释，以及对中国瘤牛和印度瘤牛进行了基因注释，鉴定了 206 个在中印瘤牛中表达的基因。这些发现可能为未来对瘤牛的研究提供有价值的参考。此外，基于海南黄牛和三个欧洲商业牛品种的选择信号分析，确定了与耐热性、抗病性、脂肪代谢、环境适应、与繁殖和精子及卵母细胞发育相关的候选基因（，，，，）、环境适应（，，，，，，）、氧化应激抗炎反应（，，抗病性（，，）和肉质（，，，，）相关的潜在途径。本研究在分子水平上对中国海南黄牛的 CNVs 进行了全面探索，为未来的繁殖和选育计划提供了理论支持，以提高该品种的品质。
