Wang Zhen, Song Bangmin, Yao Jianyu, Li Xingzheng, Zhang Yan, Tang Zhonglin, Yi Guoqiang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan, 528226, China.
J Anim Sci Biotechnol. 2024 Jul 10;15(1):97. doi: 10.1186/s40104-024-01053-0.
Long-term natural and artificial selection has resulted in many genetic footprints within the genomes of pig breeds across distinct agroecological zones. Nevertheless, the mechanisms by which these signatures contribute to phenotypic diversity and facilitate environmental adaptation remain unclear.
Here, we leveraged whole-genome sequencing data from 82 individuals from 6 domestic pig breeds originating in tropical, high-altitude, and frigid regions. Population genetic analysis suggested that habitat isolation significantly shaped the genetic diversity and contributed to population stratification in local Chinese pig breeds. Analysis of selection signals revealed regions under selection for adaptation in tropical (55.5 Mb), high-altitude (43.6 Mb), and frigid (17.72 Mb) regions. The potential functions of the selective sweep regions were linked to certain complex traits that might play critical roles in different geographic environments, including fat coverage in frigid environments and blood indicators in tropical and high-altitude environments. Candidate genes under selection were significantly enriched in biological pathways involved in environmental adaptation. These pathways included blood circulation, protein degradation, and inflammation for adaptation to tropical environments; heart and lung development, hypoxia response, and DNA damage repair for high-altitude adaptation; and thermogenesis, cold-induced vasodilation (CIVD), and the cell cycle for adaptation to frigid environments. By examining the chromatin state of the selection signatures, we identified the lung and ileum as two candidate functional tissues for environmental adaptation. Finally, we identified a mutation (chr1: G246,175,129A) in the cis-regulatory region of ABCA1 as a plausible promising variant for adaptation to tropical environments.
In this study, we conducted a genome-wide exploration of the genetic mechanisms underlying the adaptability of local Chinese pig breeds to tropical, high-altitude, and frigid environments. Our findings shed light on the prominent role of cis-regulatory elements in environmental adaptation in pigs and may serve as a valuable biological model of human plateau-related disorders and cardiovascular diseases.
长期的自然选择和人工选择在不同农业生态区的猪品种基因组中留下了许多遗传印记。然而，这些特征如何导致表型多样性并促进环境适应的机制仍不清楚。
在此，我们利用了来自6个原产于热带、高海拔和寒冷地区的家猪品种的82个个体的全基因组测序数据。群体遗传分析表明，栖息地隔离显著塑造了遗传多样性，并导致了中国地方猪品种的群体分层。选择信号分析揭示了在热带（55.5 Mb）、高海拔（43.6 Mb）和寒冷（17.72 Mb）地区受到选择以适应环境的区域。选择性清除区域的潜在功能与某些复杂性状相关，这些性状可能在不同地理环境中发挥关键作用，包括寒冷环境中的脂肪覆盖以及热带和高海拔环境中的血液指标。受到选择的候选基因在参与环境适应的生物学途径中显著富集。这些途径包括适应热带环境的血液循环、蛋白质降解和炎症；适应高海拔环境的心肺发育、缺氧反应和DNA损伤修复；以及适应寒冷环境的产热、冷诱导血管舒张（CIVD）和细胞周期。通过检查选择特征的染色质状态，我们确定肺和回肠是环境适应的两个候选功能组织。最后，我们确定ABCA1顺式调控区域中的一个突变（chr1: G246,175,129A）是适应热带环境的一个可能的有前景的变异。
在本研究中我们对中国地方猪品种适应热带、高海拔和寒冷环境的遗传机制进行了全基因组探索。我们的发现揭示了顺式调控元件在猪环境适应中的重要作用，并可能成为人类高原相关疾病和心血管疾病的有价值的生物学模型。
