College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China.
Int J Mol Sci. 2024 Oct 21;25(20):11303. doi: 10.3390/ijms252011303.
The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (, , , , , , and ) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs.
青藏高原独特的高海拔环境，以极寒和低氧水平为特征，对人类和哺乳动物都构成了巨大的生存挑战。自然选择导致了藏猪积累了适应性突变，使它们形成了独特的适应性表型。在这里，我们旨在揭示藏猪适应高原低氧的遗传机制。因此，我们对来自不同代表猪群体的 140 个全基因组测序（WGS）数据点进行了系统分析。我们的分析总共鉴定出 27614561 个突变，包括 22386319 个单核苷酸变异（SNVs）和 5228242 个插入/缺失（INDELs，大小<50bp）。我们项目中总共鉴定出 11%（2678569）的 SNVs 是新的，极大地扩展了藏猪遗传变异数据集。与其他猪品种相比，藏猪独特地适应了高海拔环境，表现出最高的遗传多样性和最低的近交系数。采用复合多信号（CMS）方法，我们扫描了全基因组达尔文正选择信号，鉴定出 32499 个藏猪正选择 SNVs（TBPSSs）和 129 个选择基因（TBPSGs），其中包括 213 个新发现的基因。值得注意的是，我们鉴定出了 8 个具有强烈自然选择信号的基因（、、、、、、和）。它们可能改善心肺功能和脂肪代谢，帮助藏猪适应高海拔环境。这些发现为高原适应的遗传机制和藏猪的适应性表型提供了新的见解。
