Genome-wide characterization of South African pig breeds.
Loading...
Date
2022
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
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.
Description
Doctoral Degree. University of KwaZulu-Natal, Pietermaritzburg.