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 50k
goat beadchip. 88 goats originating from four breeds (dairy: British Alpine, Saanen, Toggenburg;
fibre: 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 r2 values of 0.12
and 0.15 for dairy and fibre breeds, respectively. LD decay was shown to occur after a distance
interval of 20-40kb and 40-60kb for dairy and Angora breeds, respectively. Principal component
analysis (PCA) produced clusters corresponding to the different production types (dairy and fibre).
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 fibre goats due to productionspecific
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.
