Genome-wide SNP data unveil admixture of Chinese indigenous chicken breeds with commercial breeds v2

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 SNP (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 (LD) 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.