Abstract:
The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have
been kept geographically and genetically distinct. Due to country-specific selection and
breeding strategies, there is a need to characterize the populations on a genetic level. In
this study we analysed genetic variability of Angora goats from three distinct geographical
regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26;
SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all
autosomes per population were calculated. Diversity, as measured by expected heterozygosity
(HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA
goats were the only population with a positive average inbreeding coefficient value of 0.009.
After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for
further analyses. Principal component and clustering analyses were used to visualize individual
relationships within and between populations. All SA Angora goats were separated
from the others and formed a well-defined, unique cluster, while outliers were identified in
the FR and AR breeds. Apparent admixture between the AR and FR populations was
observed, while both these populations showed signs of having some common ancestry
with the SA goats. LD averaged over adjacent loci within the three populations per chromosome
were calculated. The highest LD values estimated across populations were observed
in the shorter intervals across populations. The Ne for the Angora breed was estimated to
be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness
between the populations.
