Genetic diversity, breed composition and admixture of Kenyan domestic pigs

dc.contributor.author Mujibi, Fidalis Denis
dc.contributor.author Okoth, Edward
dc.contributor.author Rothschild, Max
dc.contributor.author Cheruiyot, Evans
dc.contributor.author Onzere, Cynthia
dc.contributor.author Bishop, Richard
dc.contributor.author Fèvre, Eric
dc.contributor.author Thomas, Lian
dc.contributor.author Masembe, Charles
dc.contributor.author Plastow, Graham
dc.contributor.author Rothschild, Max
dc.contributor.department Animal Science
dc.date 2018-03-05T22:34:39.000
dc.date.accessioned 2020-06-29T23:40:14Z
dc.date.available 2020-06-29T23:40:14Z
dc.date.issued 2018-01-22
dc.description.abstract <p>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 (<em>Potamochoerus larvatus</em>) and warthogs (<em>Phacochoerus spp</em>.) 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.</p>
dc.description.comments <p>This article is published as Mujibi, Fidalis Denis, Edward Okoth, Evans K. Cheruiyot, Cynthia Onzere, Richard P. Bishop, Eric M. Fèvre, Lian Thomas, Charles Masembe, Graham Plastow, and Max Rothschild. "Genetic diversity, breed composition and admixture of Kenyan domestic pigs." <em>PloS one</em> 13, no. 1 (2018): e0190080. doi: <a href="https://doi.org/10.1371/journal.pone.0190080">10.1371/journal.pone.0190080</a>. </p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/ans_pubs/364/
dc.identifier.articleid 1367
dc.identifier.contextkey 11702183
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath ans_pubs/364
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/9785
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/ans_pubs/364/2018_Rothschild_GeneticDiversity.pdf|||Fri Jan 14 23:47:58 UTC 2022
dc.source.uri 10.1371/journal.pone.0190080
dc.subject.disciplines Animal Sciences
dc.subject.disciplines Genetics and Genomics
dc.subject.disciplines Veterinary Microbiology and Immunobiology
dc.subject.disciplines Veterinary Pathology and Pathobiology
dc.subject.disciplines Veterinary Physiology
dc.title Genetic diversity, breed composition and admixture of Kenyan domestic pigs
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication a5915699-0c8a-411e-a601-1564d7090ab9
relation.isOrgUnitOfPublication 85ecce08-311a-441b-9c4d-ee2a3569506f
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