Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

Abstract

BACKGROUND: China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and population structure of Chinese indigenous cattle, a population genetic analysis at both the individual and population levels was conducted and the admixture analysis was performed. We genotyped 572 samples from 20 Chinese indigenous cattle breeds using GeneSeek Genomic Profiler Bovine LD (GGP-LD, 30 K) and downloaded the published data of 77 samples from 4 worldwide commercial breeds genotyped with Illumina BovineSNP50 Beadchip (SNP50, 50 K). RESULTS: In principal component analysis (PCA) and neighbour-joining (NJ) tree analysis, samples of the same breeds were grouped together, leading to clear separation from other breeds. And Chinese indigenous cattle were clustered into two groups of southern and northern breeds, originated from Asian Bos indicus lineage and Eurasian Bos taurus lineage, respectively. In STRUCTURE K = 2, a clear transition occurred from the northern breeds to the southern breeds. Additionally, the northern breeds contained a smaller Eurasian taurine (62.5%) descent proportion than that reported previously (more than 90%). In STRUCTURE K = 3, a distinct descent was detected in the southern Chinese breeds, which could reflect a long-term selection history of Chinese indigenous cattle. The results from TreeMix and f3 statistic provided the evidence of an admixture history between southern breeds and northern breeds. CONCLUSIONS: Consistent with the observed geographical distributions, Chinese indigenous cattle were divided into two genetic clusters, northern indigenous cattle and southern indigenous cattle. Three improved breeds in the northern area also exhibited northern indigenous ancestry. We found that the breeds distributed in the northern China showed more southern lineage introgression than previously reported. Central-located populations appeared to the admixture between southern and northern lineages, and introgression events from European cattle were observed in Luxi Cattle, Qinchuan Cattle and Jinnan Cattle. The study revealed the population structures and levels of admixture pattern among Chinese indigenous cattle, shedding light on the origin and evolutionary history of these breeds.