Genome-wide characterization of South African pig breeds.

Abstract

South African pig production is dominated by the commercial sector with a small portion of the smallholder farmers. With an expected increase in pork consumption, commercial breeds such the Large White, South African Landrace and Duroc comes with proven growth potential. On the other hand, indigenous breeds like Kolbroek and Windsnyer have low growth potential, although they are well adapted to the hardy and harsh conditions of South Africa. Village pigs kept by communal farmers have potential to provide food security and assists in poverty alleviation. The free-roaming Warthogs, Bush Pigs and Wild Boars that are found in the villages and in national parks and zoos could be a contribution to the pig genetic resource of South Africa. However, the possibility of interactions of domestic and wild pigs is there and could be a concern to the pork industry, with potential challenges of indiscriminate crossbreeding and introgression. In addition, the zoos are home to some exotic and wild populations such as the Vietnamese Potbelly and Warthogs. Genetic diversity, history and relationships of pigs found in South Africa is poorly understood. Pigs are currently understudied in South Africa resulting in a poor understanding of (i) the genetic diversity and how it is distributed within and among breeds and populations, (ii) the effect of the current production systems on the genetic diversity and threat to populations that has a potential to cause inbreeding and extinction and (iii) the interactions within and between domestic and wild pig populations. This lack of research and information is to the detriment of the species and the pig sector and makes it difficult to implement successful genetic improvement programs further predisposing the unimproved and indigenous pig populations to genetic loss and risk of extinction. This study aimed to close the information gap through genomic characterisation of the pig populations that are within the borders of South Africa. The study sampled broadly from domestic pig populations consisting of villages (Mopani, Capricorn, Alfred Nzo and O.R. Tambo), commercial (Large White, South African Landrace and Duroc), indigenous (Kolbroek and Windsnyer) and Vietnamese Potbelly representing Asian ancestry and wild pig populations consisting of Wild Boars, Warthogs and Bush Pigs. The pigs were sampled from diverse production systems consisting of intensive, semi-intensive and free-range/scavenging as well as pigs in national parks and zoos. The Illumina Porcine SNP60K was used to genotype the pigs generating 62 163 genome-wide SNPs that were analysed to infer of a number of genomic parameters that included (i) within and between population genetic diversity and population structure, (ii) linkage disequilibrium, haplotype blocks and effective population size, (iii) population history, gene flow and introgression and finally (iv) genomic signatures of selection within and between populations. Genetic diversity levels ranged from 0.204 ± 0.151 forWarthog to 0.371 ± 0.126 for Capricorn village pigs. Clustering of South African populations was comparable to the genetic cluster using the worldwide genotypes from a deposited database. There were four major clusters consisting of (i) Duroc, (ii) Vietnamese Potbelly, (iii) Bush Pigs and Warthogs and (iv) a large cluster of commercial Large White and South African Landrace, indigenous Kolbroek and Windsnyer and village pigs of Mopani, Capricorn, Alfred Nzo and, O.R. Tambo (villages) as well as Wild Boar populations. The PCA clustering which included the global populations also displayed four clusters. Bush Pigs and Warthogs clustered together while the Durocs formed a separate cluster. The Vietnamese Potbelly clustered with Chinese populations. The South African villages, worldwide village dataset, Wild Boars, South African indigenous and all the Large Whites and Landraces constituted one major cluster. Admixture based population structure had K = 10 as the optimal which made up of eight distinct clusters of the Warthogs and Bush Pigs; Wild Boars; Vietnamese Potbelly; Kolbroek; Windsnyer; Large White; South African Landrace and Duroc, as well as admixed clusters of Alfred Nzo together with O.R. Tambo (Eastern Cape Province) and Mopani and Capricorn (Limpopo Province). Clustering of populations also depicted the production systems the pigs are reared under. Generally, the effective population sizes of all pig populations have been on the decrease since 12 to 22 generations ago. The effective population sizes of indigenous and commercial breeds were lower compared to that of village populations. Overall, linkage disequilibrium and haplotype blocks results reflected the differences between breeds and production systems. Average LD ranged from 0.18±0.22 for Mopani to 0.40±0.36 for Kolbroek. Most populations (Alfred Nzo, Mopani, South African Landrace, Duroc and Windsnyer) had a high LD on chromosome 14. The highest mean correlation was observed at 1 kb between Duroc and Large White at r = 0.79±0.73. A total of 23 969 haplotypes were observed across populations with Duroc having the highest number of haplotype blocks of 3 402 while Alfred Nzo had the least at 1 350. Duroc pigs had the most unique haplotype blocks 2 513 and associated QTLs 562. Mopani shared the most haplotype blocks with 10 other populations while Mopani and Capricorn shared the most (963) haplotypes. Three haplotype blocks were shared across populations and the corresponding genes were associated with carcass quality and growth, immune response, fertility, and milk production. There was a total of 910 genomic regions with high LD (LD > 0.80) and most QTLs were concentrated on chromosome 7 at 236.