Data from: Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa

Genetic diversity is of great importance and a prerequisite for genetic
improvement and conservation programs in pigs and other livestock
populations. The present study provides a genome wide analysis of the
genetic variability and population structure of pig populations from
different production systems in South Africa relative to global
populations. A total of 234 pigs sampled in South Africa and consisting of
village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5)
and wild (n = 38) populations were genotyped using Porcine SNP60K
BeadChip. In addition, 389 genotypes representing village and commercial
pigs from America, Europe and Asia were accessed from a previous study and
used to compare population clustering and relationships of South African
pigs with global populations. Moderate heterozygosity levels, ranging from
0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn
municipality in Eastern Cape province of South Africa were observed.
Principal Component Analysis of the South African pigs resulted in four
distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and
Warthog and (iv) a cluster with the rest of the commercial (SA Large White
and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and
Windsnyer. The clustering demonstrated alignment with genetic
similarities, geographic location and production
systems.  The PCA with the global populations also
resulted in four clusters that where populated with (i) all the village
populations, wild boars, SA indigenous and the large white and landraces;
(ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush
pig. K= 10 (The number of population units) was the most probable
ADMIXTURE based clustering, which grouped animals according to their
populations with the exception of the village pigs that showed presence of
admixture. AMOVA reported 19.92% – 98.62% of the genetic variation to be
within populations. Sub structuring was observed between South African
commercial populations as well as between Indigenous and commercial
breeds. Population pairwise FSTanalysis showed genetic
differentiation (P < 0.05)between the village, commercial
and wild populations. A per marker per population
pairwise FSTanalysis revealed SNPs associated with QTLs for
traits such as meat quality, cytoskeletal and muscle development, glucose
metabolism processes and growth factors between both domestic populations
as well as between wild and domestic breeds. Overall, the study provided a
baseline understanding of porcine diversity and an important foundation
for porcine genomics of South African populations.