Abstract
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 FST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise FST analysis 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.
Highlights
Pigs were domesticated over 5,000 years ago, leading to the gradual and cumulative development of modern pig breeds with very distinctive phenotypes and production abilities (Zeder et al, 2006; Rothschild and Ruvinsky, 2010)
The Kolbroek, which is of Chinese origin, is speculated to have pigs that ended up in the hands of South African farmers when a sailing ship wrecked at the Cape Hangklip (Ramsay et al, 1994)
About 31,705 SNPs were removed leaving 30,458 polymorphic SNPs of the loci distributed over 18 autosomal chromosomes, which were used for analysis of molecular variance (AMOVA) and FST analysis
Summary
Pigs were domesticated over 5,000 years ago, leading to the gradual and cumulative development of modern pig breeds with very distinctive phenotypes and production abilities (Zeder et al, 2006; Rothschild and Ruvinsky, 2010). Village production system is characterized by non-descript populations raised under extensive low-input management Commercial breeds such as the Large White, Landrace and Duroc have worldwide distribution in modern commercial farming systems including South Africa and are widely used (Amills et al, 2010). The origin of the Windsnyer is unknown, there are observed similarities to Chinese breeds (Nicholas, 1999) thereby suggesting that it is of Chinese origin Regardless of their origins and domestication routes, pig breeds in South Africa have become closed genetic pools restricted to specific farming systems and molded by artificial selection and possibly genetic drift (Amills et al, 2010). The existence of hybrids is a concern, as they could become asymptomatic carriers of diseases such African swine fever (Jori and Bastos, 2009)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
