Population genomics identifies patterns of genetic diversity and selection in chicken

作者：Diyan Li, Yán Li, Miao Li, Miao Li, Tiandong Che, Shilin Tian, Binlong Chen, Xuming Zhou, Guolong Zhang, Uma Gaur, Majing Luo, Kai Tian, Shen He, Shen He, Zhongxian Xu, Long Jin, Qianzi Tang, Yifei Dai, Yaodong Hu, Yaodong Hu, Xiaoling Zhao, Huadong Yin, Yan Wang, Rongjia Zhou, Chaowu Yang, Huarui Du, Xiaosong Jiang, Qing Zhu, Mingzhou Li, Mingzhou Li · 发表于：BMC Genomics · 年份：2019 · DOI：10.1186/s12864-019-5622-4 · 被引用次数：78 · 研究领域：Livestock and Poultry Management、Genetic and phenotypic traits in livestock、Genetic diversity and population structure

BACKGROUND: There are hundreds of phenotypically distinguishable domestic chicken breeds or lines with highly specialized traits worldwide, which provide a unique opportunity to illustrate how selection shapes patterns of genetic variation. There are many local chicken breeds in China. RESULTS: Here, we provide a population genome landscape of genetic variations in 86 domestic chickens representing 10 phenotypically diverse breeds. Genome-wide analysis indicated that sex chromosomes have less genetic diversity and are under stronger selection than autosomes during domestication and local adaptation. We found an evidence of admixture between Tibetan chickens and other domestic population. We further identified strong signatures of selection affecting genomic regions that harbor genes underlying economic traits (typically related to feathers, skin color, growth, reproduction and aggressiveness) and local adaptation (to high altitude). By comparing the genomes of the Tibetan and lowland fowls, we identified genes associated with high-altitude adaptation in Tibetan chickens were mainly involved in energy metabolism, body size maintenance and available food sources. CONCLUSIONS: The work provides crucial insights into the distinct evolutionary scenarios occurring under artificial selection for agricultural production and under natural selection for success at high altitudes in chicken. Several genes were identified as candidates for chicken economic traits and other phenotypic tra...