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).

Genome diversity of Chinese indigenous chicken and the selective signatures in Chinese gamecock chicken

“…Except three breeds (BC, SK, and YOU) with muffs and beard phenotype, the other Chinese indigenous chickens have undergone much less intensive artificial selection compared with commercial chickens, which are basically consistent with previous findings 4 , 7 , 8 . Surprisingly, as one of the earliest recorded chicken populations in China 3 , Chinese gamecock chickens have been supposed to be under strong artificial selection since they have been consistently selected for cockfighting.…”

“…China as a possible origin of domestic chickens and a vast country with abundant diversities in geography and culture 1 , 2 , it has accumulated the most abundant genetic resources in Chinese indigenous chickens under extensive natural and artificial selections, with considerable genetic variations and phenotypic diversity in terms of morphology and physiology 3 – 8 . A comprehensive and deep understanding of the genome diversity of the Chinese indigenous breeds could reveal the population dynamics of the breeds, providing a theoretical basis for facilitating conservations and breeding programs.…”

“…In a previous pioneering study concerning selective signatures in BN gamecock chickens, Guo et al highlighted several numbers of candidate selective genes underlying signatures of gamecock chickens 11 , such as organ development-related genes: CBFB ( Core-binding factor beta subunit ), GRHL3 ( Grainyhead like transcription factor 3 ), Gli3 ( GLI family zinc finger 3 ), PTCH1 ( Patched 1 ) and EFNA5 ( EphrinA5 ), aggressive behavior related genes: BDNF ( Brain-derived neurotrophic factor ), NTS ( Neurotensin ) and GNAO1 ( G protein subunit alpha o1 ), energy metabolism-related genes: RICTOR ( RPTOR independent companion of MTOR complex 2 ) and SDHB ( Succinate dehydrogenase complex iron-sulfur subunit B ). However, this study is likely to be biased by genetic drift and confounded by potential artificial selection undergone in Chinese indigenous and commercial chickens, as this study just concerned one gamecock breed, and did not fully consider potential introgression from Chinese indigenous and commercial chickens into Chinese gamecock chickens because an introgression from commercial chickens into indigenous chickens seems common 7 , 8 , 12 . Incorporating more gamecock breeds and taking Chinese indigenous and commercial chickens into account in a subsequent whole genome re-sequencing study can help us totally reveal the pivotal variants/genes underlying signatures in gamecock chickens.…”

“…Similarly, the Chinese indigenous chickens from high-latitude zones have also evolutionarily adapted to the cold winter 3 , compared with the wild ancestor red jungle fowls 20 , which inhabit in tropical areas. Distinct from commercial chickens, Chinese indigenous chickens are less intensively selected 8 , decreasing the possibility of those genomic footprints left by natural selection are to be obscured by strong artificial selection. Aside from a potential introgression from commercial chickens into indigenous chickens, the Chinese indigenous chickens from low-latitude to high-latitude zones are likely to be a good model for exploring the genetic mechanisms underlying rapid adaptation to cold weather in birds within a short period of time.…”

Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data

“…In the poultry industry, most local breeds are seriously threatened by the impacts of commercial lines (Blackburn, 2006;Nie et al, 2019); only a few breeds, which match economic demands, are reared on a large scale. The use of a limited number of breeds is likely to cause a decrease in the genetic diversity of chickens, as commercial breeds and their hybrids are generated within a considerably shorter time to yield economic Abbreviations: BY, Beijing You; HS, Hongshan; SG, Shouguang; SK, Silkie; TB, Tibet; HD, Houdan; RIR, Rhode Island Red; WL, White Leghorn; Cor, Cornish; LX-G, Luxi gamecock; HN-G, Henan gamecock; XS-G, Xishuangbanna gamecock; ZZ-G, Zhangzhou gamecock; Tur-G, Turfan gamecock; RJF, red junglefowl; PCA, principal component analysis; ESR, effective sex ratio; LD, linkage disequilibrium; ROH, run of homozygosity; Ne, effective population size.…”