Whole-genome resequencing of Dulong Chicken reveal signatures of selection

1. Dulong Chickens (DLCs) live at high altitude (~3000 m) and humidity (~90%), are endemic to the Yunnan province, and have gradually developed unique physiological characteristics, but their genetic basis is still unclear. Using the fixation index (<i>F_ST</i>) approach, based on whole-genome resequencing, DLCs were analysed to uncover the genomic architecture of the population and candidate genes involved in selection during domestication. 2. A total of 469 candidate genes were obtained to be putatively under selection in DLCs. Further investigations revealed the genic footprint for local adaptation (high-altitude and high-humidity) as the genic signatures that are involved in economic traits (related to egg production). 3. Candidate genes were identified that may be associated with disease resistance, aggressiveness, small body size and positive selection of vision in DLCs. 4. These data revealed loci of selective signals that operate during selection for production at high altitude and humidity.

1. 独龙鸡（Dulong Chickens, DLCs）栖息于海拔约3000米、相对湿度约90%的高海拔区域，为云南省特有地方鸡种，经长期演化已形成独特的生理适应性特征，但其遗传基础仍未明确。本研究基于全基因组重测序（whole-genome resequencing）数据，采用固定指数（fixation index, F_ST）分析方法对独龙鸡开展基因组解析，以揭示该种群的基因组结构及其驯化过程中受选择的候选基因。
2. 本研究共筛选得到469个在独龙鸡中推定受选择的候选基因。进一步分析显示，独龙鸡适应高海拔与高湿度环境的局部适应性基因足迹，同时包含与产蛋相关经济性状相关的基因标记。
3. 本研究还鉴定出一批与独龙鸡抗病性、攻击性、体型偏小以及视觉正向选择相关的候选基因。
4. 本研究所得数据揭示了独龙鸡在高海拔高湿度环境下生产选育过程中发挥作用的选择信号位点。