Data from: Genetic diversity, breed composition and admixture of Kenyan domestic pigs

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.