Genome-wide scanning reveals genetic diversity and signatures of selection in Chinese indigenous cattle breeds

Chinese indigenous cattle exhibit abundant genetic resources and extensive gene pool, with 53 indigenous breeds generally classified into northern cattle breeds, central cattle breeds, and southern cattle breeds. To determine the population genetic diversity and signatures of selection of Chinese indigenous cattle, we collected 724 cattle from 20 geographically representative Chinese indigenous cattle breeds and genotyped all samples using GeneSeek Genomic Profiler Bovine LD (GGP-LD, n = 30,125). Runs of homozygosity (ROH) and identical by state (IBS) analyses were performed to investigate genetic diversity in Chinese indigenous cattle. Meanwhile, the integrated Haplotype Score (iHS) and FST-based di methods were used to reveal candidate selective sweeps. Our results showed that southern cattle breeds have abundant ROH segments and higher IBS values in comparison with northern and central cattle breeds. We also detected many potential selective sweeps in Chinese indigenous cattle. The genes within intervals spanning the candidate regions are associated with growth and development (NCAPG, LAP3, LCORL, IBSP and MEPE), fertility and reproduction (ABCG2, CATSPER4 and H1foo), immune functions (AZU1, PROC and LRP1) and environment adaption (RBFA, BARX2). Overall, these findings provide new insights into the level of genetic diversity of Chinese indigenous cattle, and suggest a role of natural/artificial selection in shaping their genome genetic variability.