Population history and genomic signatures for high-altitude adaptation in Tibetan pigs.
Population history and genomic signatures for high-altitude adaptation in Tibetan pigs.
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DOI：
10.1186/1471-2164-15-834
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发表时间：
2014-10-01
期刊：
影响因子：
4.4
通讯作者：
Ren J
中科院分区：
文献类型：
--
作者：
Ai H;Yang B;Li J;Xie X;Chen H;Ren J
藏猪是青藏高原特有的家畜之一。几个地理隔离的猪群分布在整个高原。这仍然是一个悬而未决的问题，如果这些人口经历了不同的人口历史，并已演变为高原的恶劣环境的独立适应位点。为了解决这些问题，我们在此研究了来自5个西藏地理种群和34个低地品种的678个个体的猪基因组中的约40，000个遗传变异。通过一系列群体遗传分析，我们发现藏猪群体存在显著的遗传分化。藏猪似乎是3个独立的群体，分别对应于西藏、甘肃和川滇地区。每一个人口在遗传上与其地理上的邻居比其他任何一个藏族人口都更相似。应用位点特异性分支长度检验，我们在藏猪中鉴定了群体特异性和群体共享的候选基因。这些基因，如PLA 2G 12 A、RGCC、C9 ORF 3、GRIN 2B、GRID 1和EPAS 1，参与高原生理学，包括血管生成、肺动脉高压、氧摄取、防御反应和红细胞生成。这些基因中的大多数在以前对高地人和高海拔动物的研究中没有涉及。藏猪群体经历了显著的遗传分化。从历史上看，藏猪可能与邻近的低地猪种混种。在长期的高原定居历史中，藏猪发展出了一种复杂的生物适应机制，可能与藏人和其他动物不同。不同藏猪群体对高原恶劣环境的适应性位点既有明显的差异，也有趋同的特点。本文的在线版本（doi：10.1186/1471-2164-15-834）包含补充材料，可供授权用户使用。
The Tibetan pig is one of domestic animals indigenous to the Qinghai-Tibet Plateau. Several geographically isolated pig populations are distributed throughout the Plateau. It remained an open question if these populations have experienced different demographic histories and have evolved independent adaptive loci for the harsh environment of the Plateau. To address these questions, we herein investigated ~ 40,000 genetic variants across the pig genome in a broad panel of 678 individuals from 5 Tibetan geographic populations and 34 lowland breeds. Using a series of population genetic analyses, we show that Tibetan pig populations have marked genetic differentiations. Tibetan pigs appear to be 3 independent populations corresponding to the Tibetan, Gansu and Sichuan & Yunnan locations. Each population is more genetically similar to its geographic neighbors than to any of the other Tibetan populations. By applying a locus-specific branch length test, we identified both population-specific and -shared candidate genes under selection in Tibetan pigs. These genes, such as PLA2G12A, RGCC, C9ORF3, GRIN2B, GRID1 and EPAS1, are involved in high-altitude physiology including angiogenesis, pulmonary hypertension, oxygen intake, defense response and erythropoiesis. A majority of these genes have not been implicated in previous studies of highlanders and high-altitude animals. Tibetan pig populations have experienced substantial genetic differentiation. Historically, Tibetan pigs likely had admixture with neighboring lowland breeds. During the long history of colonization in the Plateau, Tibetan pigs have developed a complex biological adaptation mechanism that could be different from that of Tibetans and other animals. Different Tibetan pig populations appear to have both distinct and convergent adaptive loci for the harsh environment of the Plateau. The online version of this article (doi:10.1186/1471-2164-15-834) contains supplementary material, which is available to authorized users.
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