藏鸡高原极端环境下的基因组变异及其低氧适应的分子机制

The Tibet chicken (Gallus gallus) is a distinctive indigenous breed native to Tibet Plateau. The chicken that has genetic mechanism of adaptation to extreme environment of plateau is a good model for research of adaptive evolution in high-altitude as well as mechanism. In this project, base on microevolution theory and previous evidences on genome-wide scan of human and our previous results about hypoxic physiology, candidate genes and regulating network in Tibet chicken, we hypothesis that the extreme environment of plateau have selected DNA variation and changed epigenetic pattern on functional genes of altitude adaptation in the Tibet chicken, which regulate gene expression in key tissue and coordinatively contribute to adaptation to high-altitude extreme environments in Tibet chicken. Through genome-wide scanning, we survey the DNA variation patterns of Tibet and lowland chicken breeds, and analysis the DNA mutations selective for adaptation to high-altitude environment. By measuring epigenome, transcriptome and proteome of heart tissue of chicken hypoxic embryo, we identify the genes that contribute to high-altitude adaptation and the regulating models by DNA variation and epigenetic, and clone and locate the key genes of hypoxic adaptation, then identify and verify in vitro the pathways and molecular mechanism of the genes controlled physiological phenotypes of adaptation, and finally reveal the microevolution mechanism of adaptation to high-altitude extreme environment in Tibet chicken.

藏鸡是青藏高原特有的原始小型地方鸡种，具有适应高原极端环境的遗传机制，是研究动物高原适应进化及其机制的模式动物。本项目根据微进化理论和近年来高原人群的全基因扫描结果，在前期对藏鸡低氧适应生理特征、候选基因、调控网络等研究的基础上，提出假设，藏鸡高原适应基因功能突变在高原极端环境中受到选择，频率发生变化，同时表观遗传修饰发生改变，调控关键组织中基因表达，特有的DNA变异与表观遗传共同使藏鸡适应高原极端环境。本项目采用全基因组扫描，研究藏鸡和低地鸡种的DNA多态性模式，分析适应高海拔环境的DNA变异，并通过表观组学、转录组学、蛋白组学鉴定高海拔适应相关基因，鉴定高海拔低氧适应基因和表观遗传调控模式，定位和克隆与低氧环境适应相关的关键基因，体外验证基因功能及其作用途径，确定适应性生理表型形成的分子机制，最终揭示藏鸡适应高原极端环境的微进化机制。

藏鸡是青藏高原特有的原始小型地方鸡种，具有适应高原极端环境的遗传机制，是研究动物高原适应进化及其机制的模式动物。基于微进化理论和高原人群的基因组研究，本项目采用高通量测序分析藏鸡群体全基因组、表观组、转录组、蛋白组，鉴定高海拔低氧适应相关基因和相关通路，探讨基因对适应生理表型的作用途径和分子机制。采用DNA-seq技术对4个高海拔鸡群和4个低海拔鸡群进行基因组重测序，鉴定高海拔低氧适应的选择位点及基因。结果表明正选择基因主要涉及脂肪酸代谢、呼吸器官和心血管系统发育、免疫反应、DNA修复和辐射反应等有关。采用MeDIP-seq技术建立了鸡胚胎心脏组织DNA甲基化图谱，分析了低氧孵化条件下与对照品种的差异甲基化区域和相关基因，研究了藏鸡高海拔环境适应的表观遗传进化模式。采用RNA-seq和iTRAQ技术测定了藏鸡低氧胚胎心肌组织转录组和蛋白组，获得差异表达基因62个和差异表达蛋白118个，主要富集在心脏发育、血管发育等，其中EGLN1、MAP2K2、RAB5C对藏鸡高原低氧适应起重要作用，为鸟类高原适应性研究提供了候选基因和新的方向。