Freitas Pedro H F, Wang Yachun, Yan Ping, Oliveira Hinayah R, Schenkel Flavio S, Zhang Yi, Xu Qing, Brito Luiz F
Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA - National Engineering Laboratory for Animal Breeding - College of Animal Science and Technology, China Agricultural University, Beijing, China.
Front Genet. 2021 Feb 3;12:604823. doi: 10.3389/fgene.2021.604823. eCollection 2021.
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (; YAK), and Bali () based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods ( , HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
了解气候适应的生物学机制对于优化育种计划和保护遗传资源至关重要。本研究的目的是基于密集的单核苷酸多态性（SNP）数据，调查32个全球牛品种的遗传多样性，并揭示可能在耐热和/或耐寒方面受到选择的基因组区域，重点关注适应不同气候条件的中国地方牛品种、大通牦牛（YAK）和巴厘牛（Bali）。总体而言，大多数牛群的遗传多样性水平适中。多态性SNP的比例范围从0.197（牦牛）到0.992（蒙古牛）。观察到的杂合度和预期杂合度分别从0.023（牦牛）到0.366（三河牛；SH），以及从0.021（牦牛）到0.358（三河牛）。基于观察到的与预期的纯合基因型数量、纯合度过高、联合配子之间的相关性以及纯合子片段（ROH），总体平均近亲繁殖（±标准差）分别为：0.118±0.028、0.228±0.059、0.194±0.041和0.021±0.004。基于多种情况和方法（如、HapFLK和ROH）的选择特征揭示了重要的基因组区域和候选基因。鉴定出的候选基因与各种生物学过程和途径相关，如热休克蛋白、氧气运输、解剖学特征、线粒体DNA维持、代谢活性、采食量、胴体形态、繁殖力和生殖。这突出了参与耐热性的大量生物学过程，因此也突出了气候适应能力的多基因性质。对中国牛和牦牛的遗传多样性指标进行了全面描述，并与24个全球牛品种进行了比较，以避免潜在偏差。使用三种选择特征方法检测到大量处于正选择的基因组区域，并鉴定出可能处于正选择的候选基因。富集功能分析确定了重要的生物学途径、分子功能和细胞成分，这有助于更好地理解牛耐热性的生物学机制。基于鉴定出的大量基因组区域，耐热性具有复杂的多基因遗传性质，考虑到热应激反应中涉及的各种机制，这是可以预期的。
