Genetic diversity, breed composition and admixture of Kenyan domestic pigs

Abstract

The genetic diversity of African pigs, whether domestic or wild has not been widely studied and there is very limited published information available. Available data suggests that African domestic pigs originate from different domestication centers as opposed to international commercial breeds. We evaluated two domestic pig populations in Western Kenya, in order to characterize the genetic diversity, breed composition and admixture of the pigs in an area known to be endemic for African swine fever (ASF). One of the reasons for characterizing these specific populations is the fact that a proportion of indigenous pigs have tested ASF virus (ASFv) positive but do not present with clinical symptoms of disease indicating some form of tolerance to infection. Pigs were genotyped using either the porcine SNP60 or SNP80 chip. Village pigs were sourced from Busia and Homabay counties in Kenya. Because bush pigs (Potamochoerus larvatus) and warthogs (Phacochoerus spp.) are known to be tolerant to ASFv infection (exhibiting no clinical symptoms despite infection), they were included in the study to assess whether domestic pigs have similar genomic signatures. Additionally, samples representing European wild boar and international commercial breeds were included as references, given their potential contribution to the genetic make-up of the target domestic populations. The data indicate that village pigs in Busia are a non-homogenous admixed population with significant introgression of genes from international commercial breeds. Pigs from Homabay by contrast, represent a homogenous population with a “local indigenous’ composition that is distinct from the international breeds, and clusters more closely with the European wild boar than African wild pigs. Interestingly, village pigs from Busia that tested negative by PCR for ASFv genotype IX, had significantly higher local ancestry (>54%) compared to those testing positive, which contained more commercial breed gene introgression. This may have implication for breed selection and utilization in ASF endemic areas. A genome wide scan detected several regions under preferential selection with signatures for pigs from Busia and Homabay being very distinct. Additionally, there was no similarity in specific genes under selection between the wild pigs and domestic pigs despite having some broad areas under similar selection signatures. These results provide a basis to explore possible genetic determinants underlying tolerance to infection by ASFv genotypes and suggests multiple pathways for genetically mediated ASFv tolerance given the diversity of selection signatures observed among the populations studied.

CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

“…Among the European commercial breeds Duroc, Landrace, and Yorkshire, two AHR gene copies were detected in 46.1, 67.0, and 66.9%, respectively, of the tested population. Previous studies indicated the Landrace and Large White were much more closely related than Duroc at the genome-wide level [54,55], thus the higher proportion in Landrace and Yorkshire compared to Duroc could be attributed to the differences in the genome level among the three breeds. Landrace and Yorkshire were commonly used as maternal pigs, which are selected in the artificial breeding process based on large litter size.…”

African swine fever: Update on Eastern, Central and Southern Africa

“…It is possible that a resource worth further investigation exists in the ECSA countries in the form of pig populations that have demonstrated a natural resistance to virulent ASF viruses. Greater resistance to the pathogenic effects of ASF virus in some populations of traditionally kept pigs has been investigated in Mozambique, Kenya and Uganda (Muhangi et al, ; Mujibi et al, ; Okoth et al, ; Penrith et al, ) and evidence for resistance based on healthy pigs with antibodies to ASF or lower than expected mortality has been reported in Angola, Malawi, Mozambique, Tanzania and Uganda (Allaway, Chinombo, Edelsten, Hutchings, & Sumption, ; Atuhaire, Afayoa, Ochwo, Mwesigwa, Mwiine, et al, ; Atuhaire et al, ; Haresnape, Lungu, & Mamu, , ; Nsalambi, ; Penrith et al, ; Uttenthal et al, ). Obtaining and managing wild African suids for experimental studies is challenging, but genetic and immunological studies on domestic pigs from populations with demonstrated resistance could provide vital information for vaccine development.…”

Domestic Free-Range Pig Genetic Resources in Southern Africa: Progress and Prospects

“…Sufficient genetic variation was, however, estimated for pig populations in Ghana and South Africa that can support genetic improvement for many growth and carcass traits in the breed [10,13]. Mujibi et al (2018) [14] observed a significant introgression of genes from international commercial breeds into the Busia pigs in Kenya. Following various periods of utilization in South Africa, molecular data describing levels of diversity in these breeds are not available.…”

“…The domestic free-range pigs in Southern Africa have a slower growth rate than exotics, their major strength being adaptive traits that give them an advantage in low-intensity management smallholder systems [9]. Invariably, the genetic heritage of domestic free-range pigs is constantly threatened by genetic erosion caused by some indiscriminate crossbreeding with exotic breeds [14]. There are a few pig genetic and phenotypic characterization studies.…”