Genetic Diversity and Selective Signature in Dabieshan Cattle Revealed by Whole-Genome Resequencing

SIMPLE SUMMARY: To protect the genetic resources of Chinese native cattle breeds, we investigated the genetic structure, genetic diversity and genetic signature from artificial or natural selection by sequencing 32 bovine genomes from the breeding farm of the Dabieshan population. We discovered that the ancestral contributions of Dabieshan originated from Chinese indicine and East Asian taurine on the autosomal genome, which had abundant genomic diversity. Some candidate genes associated with fertility, feed efficiency, fat deposition, immune response, heat resistance and the coat color were identified by a selective sweep. The SNPs data were based on genomics, which could establish a foundation for breed amelioration and support conservation for indigenous cattle breeds. ABSTRACT: Dabieshan cattle are a typical breed of southern Chinese cattle that have the characteristics of muscularity, excellent meat quality and tolerance to temperature and humidity. Based on 148 whole-genome data, our analysis disclosed the ancestry components of Dabieshan cattle with Chinese indicine (0.857) and East Asian taurine (0.139). The Dabieshan genome demonstrated a higher genomic diversity compared with the other eight populations, supported by the observed nucleotide diversity, linkage disequilibrium decay and runs of homozygosity. The candidate genes were detected by a selective sweep, which might relate to the fertility (GPX5, GPX6), feed efficiency (SLC2A5), immune response (IGLL1, BOLA-DQA2, BOLA-DQB), heat resistance (DnaJC1, DnaJC13, HSPA4), fat deposition (MLLT10) and the coat color (ASIP). We also identified the “East Asian taurine-like” segments in Dabieshan cattle, which might contribute to meat quality traits. The results revealed by the unique and valuable genomic data can build a foundation for the genetic improvement and conservation of genetic resources for indigenous cattle breeds.