Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds

文献类型： 外文期刊

第一作者： Nie, Changsheng

作者： Nie, Changsheng;Ning, Zhonghua;Qu, Lujiang;Almeida, Pedro;Jia, Yaxiong;Bao, Haigang

作者机构：

关键词： admixture; Chinese indigenous chicken; genetic diversity; genome-wide single-nucleotide polymorphism; population structure

期刊名称：GENOME BIOLOGY AND EVOLUTION （ 影响因子：3.416； 五年影响因子：4.079 ）

ISSN： 1759-6653

年卷期： 2019 年 11 卷 7 期

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收录情况： SCI

摘要： The conservation and development of chicken have received considerable attention, but the admixture history of chicken breeds, especially Chinese indigenous breeds, has been poorly demonstrated. In this study, we aimed to evaluate the genetic diversity and population structure of eight chicken breeds (including conserved chicken breeds) from different geographic origin and to identify admixture within these breeds using a 600-K single-nucleotide polymorphism panel for genotyping. Using the genotype of 580,961 single-nucleotide polymorphism markers scored in 1,200 animals, we evaluated the genetic diversity (heterozygosity and proportion of polymorphic markers), linkage disequilibrium decay, population structure (principal component analysis and neighbor-joining tree), genetic differentiation (F-ST and genetic distance), and migration events (TreeMix and f-statistics) of the eight domesticated chicken breeds. The results of population analytical methods revealed patterns of hybridization that occurred after divergence in Tibetan chicken. We argue that chicken migration and admixture, followed by trade, have been important forces in shaping the genomic variation in modern Chinese chicken. Moreover, isolation by distance might play a critical role in shaping the genomic variation within Eurasia continent chicken breeds. Moreover, genetic information provided in this study is valuable resources for production applications (genomic prediction, and breeding strategy) and scientific research (genetic basis detection, studying evolution, or domestication).

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