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

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).

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

Fig. 1.

—Population genetic structure of the eight chicken breeds. (A) Eight different chicken breeds with distinct phenotypes (Chen et al. 2004). (B) The PCA plot of chicken populations. PCA1 and PCA2 explained 13.06% and 8.36% of the observed variance, respectively. (C) Neighbor-joining tree constructed using MEGA. (D) The admixture plot for breeds analyzed based on different number of assumed ancestors (K). (E) Linkage disequilibrium (LD) decay for the eight breeds. LD decay determined by r² against distance between polymorphic sites.

Fig. 2.

—Scatterplots show that pairwise genetic distance is associated with geographic distance. (A) Eurasian breeds and (B) eight domesticated breeds.

Fig. 3.

—Phylogenetic network of the inferred relationships between the eight chicken breeds. Breeds were colored according to their geographic origin: green, Asia; orange, North America; red, Europe. Migration edge a signals introgression of White Leghorn chicken into Tibetan chicken.