Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa

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 F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose

Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle

“…The first suggestive pleiotropic region on BTA19 (27.0–28.0 Mb) contains four genes that may play important regulatory functions in metabolism and gene expression: Dynein Axonemal Heavy Chain 2 ( DNAH2 ), Chromodomain Helicase DNA Binding Protein 3 ( CHD3 ), Arachidonate 15-Lipoxygenase Type B ( ALOX15B ), and Phosphoribosylformylglycinamidine Synthase ( PFAS ). The DNAH2 gene codes for a motor protein found in cilia and flagella that was related to intramuscular fat content and carcass weight in pigs ( Hlongwane et al, 2020 ). The CHD3 protein deacetylates histones for chromatin remodeling and may have an important regulatory function.…”

Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

“…Similarly, the results reported in our study suggested that the explanatory power of the SNPs is slightly lower; this could be justified by the fact that local indigenous breeds have not been considered for design of commercial porcine chip. This could be indicated by the results of Hlongwane et al, who reported the genetic variation and population distinctiveness of three commercial, four village, two indigenous, three wild, and one Asian pig breeds [ 44 ].…”

A Mix of Old British and Modern European Breeds: Genomic Prediction of Breed Composition of Smallholder Pigs in Uganda

“…Using literature on East African pigs and phenotypic characteristics of pigs owned by the smallholder farmers in the study area (Figure 2), we chose as putative ancestral populations, Asian, Duroc, British, Iberian, and Continental European pig breeds. We explored the ancestry of Uganda pigs in global context by incorporating publicly or privately available genotypes from the putative ancestral populations (Cleveland et al, 2012;Yang et al, 2017;Pena et al, 2019;Pfeiffer et al, 2019;Hlongwane et al, 2020).The data were merged and manipulated in PLINK1.9 (Chang et al, 2015). Prior to merging the data, the SNP positions in each dataset were updated to the sus scrofa reference 11.1 genome build (Illumina, 2013).…”