Genomic Selection Signatures in Two French and Swedish Holstein Cattle Breeds Provide Evidence for Several Potential Candidate Genes Linked to Economic Traits

The genomes of domestic animals have been artificially selected during long periods of domestication and have led to many significant changes in their economic traits. Exploring these changes is useful to expand our knowledge about the domestication process, understand the complexity of genetic diversity in livestock, and make an appropriate breeding decision. The genotypic information of 23 individuals representing French and Swedish Holsteins was used to detect signature signs between these two breeds. Quality control and data filtering were performed using PLINK software. The principal component analysis was performed to determine genetic diversity. In addition, linkage disequilibrium (LD), ancestral, and recent effective population size (Ne) were separately estimated for each breed. The signature of selection was determined by the fixation index (FST) statistic. The corrected r2 (calculated statistics for LD) between single nucleotide polymorphisms (SNPs) decreased with increasing the physical distance from 100 Kb to 7.5 Mb (from about 0.3 to 0.09 in both breeds). These values were slightly smaller for the French breed. The effective population size was estimated at 1775 and 2120 individuals for French and Swedish Holsteins 900 generations ago to 31 and 39 in the recent generation, respectively. Overall, three regions with outlier FST values were identified as the signature of selection. The flanking SNP was mostly located on BTA2, BTA16, and BTA19. Candidate genes were found to be associated with SERTAD (liver metabolism and health), SYT14 (meat yield and marble levels), IRF6 (immune system), HSD11B19 (heat stress), LAMB3, and (fat deposition). Therefore, these potential genes can be considered invaluable genetic resources for future research to attempt to create generations of commercial breeds of cattle.