Data from: Genetic diversity and population structure in South African, French and Argentinian Angora Goats from genome-wide SNP data

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.