SNP-based genetic diversity of South African commercial dairy and fiber goat breeds

Abstract Goats ( Capra aegagrus hircus ) have not been a prioritized livestock species with regards to molecular research. The genetic characterization of commercial South African (SA) goat breeds should contribute to improving the management of available animal genetic resources. The aim of this study was to investigate genetic diversity within and among SA commercial goat breeds utilizing the 50 k goat beadchip. 88 goats originating from four breeds (dairy: British Alpine, Saanen, Toggenburg; fiber: Angora) were genotyped with the goat SNP50 beadchip. Average MAF values ranged from 0.25 for the Angora to 0.29 for the Saanen, with 46 983 and 50 368 polymorphic SNPs obtained for the respective breeds. Observed heterozygosity values ranged from 0.365 for the Angora to 0.431 for the Toggenburg breed. Linkage disequilibrium (LD) estimation revealed average r 2 values of 0.12 and 0.15 for dairy and fiber breeds, respectively. LD decay was shown to occur after a distance interval of 20–40 KB and 40–60 KB for dairy and Angora breeds, respectively. Principal component analysis (PCA) produced clusters corresponding to the different production types (dairy and fiber). The Angora, British Alpine and Saanen breeds showed high proportions of membership to respective inferred ancestral populations with ADMIXTURE (97%, 84% and 92%, respectively). The results obtained in this study indicated genetic uniformity within dairy and fiber goats due to production-specific trait selection. Sufficient levels of genetic variation was, however, observed to allow genetic progress for SA commercial goat breeds pending the improved management of these goat genetic resources.