DOI: 10.5061/dryad.b0t10b0
title: Data from: Genome wide assessment of genetic variation and population distinctiveness of the pig family in South Africa

description: 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 &lt; 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.
description: <b>Genome wide
 assessment of genetic variation and population distinctiveness of the pig
 family in South Africa</b> Hair and Tissue samples
 were collected and genotyped using the PorcineSNP60K beadChip with
 GenomeStudio version 2.0 was used to process the genotype data
  
description: Hair and Tissue samples were collected and genotyped using the
 PorcineSNP60K beadChip with GenomeStudio version 2.0 was used to process
 the genotype data