1. Genome-Wide Single-Nucleotide Polymorphism Data Unveil Admixture of Chinese Indigenous Chicken Breeds with Commercial Breeds
- Author
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Lujiang Qu, Changsheng Nie, Zhonghua Ning, Haigang Bao, Pedro Almeida, and Yaxiong Jia
- Subjects
Chinese indigenous chicken ,Linkage disequilibrium ,animal structures ,Population ,Breeding ,Biology ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,03 medical and health sciences ,Genotype ,Genetics ,Animals ,education ,Domestication ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Isolation by distance ,0303 health sciences ,education.field_of_study ,Genetic diversity ,0402 animal and dairy science ,Genetic Variation ,population structure ,genetic diversity ,04 agricultural and veterinary sciences ,genome-wide single-nucleotide polymorphism ,040201 dairy & animal science ,Genetic distance ,Evolutionary biology ,Genetic marker ,admixture ,Chickens ,Research Article - Abstract
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 (FST 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).
- Published
- 2019