title: Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis.
abstract: The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping.
  
  
  
  The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FSTanalyses that may elucidate loci for ADP specific traits.
  
  
  
  The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.
authors.affiliation: Animal Breeding and Genetics Research Group, Department of Animal Science, University of Ghana, P. O. Box LG 226, Legon-ACCRA, Ghana.|Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Osei-Amponsah
authors.affiliation: Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Skinner
authors.affiliation: Animal Breeding and Genetics Research Group, Department of Animal Science, University of Ghana, P. O. Box LG 226, Legon-ACCRA, Ghana.
authors.forename: Dennis O
authors.initials: DO
authors.lastname: Adjei
authors.affiliation: Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK.
authors.forename: Julien
authors.initials: J
authors.lastname: Bauer
authors.affiliation: Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK.
authors.forename: Greger
authors.initials: G
authors.lastname: Larson
authors.affiliation: Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK.
authors.forename: Nabeel A
authors.initials: NA
authors.lastname: Affara
authors.affiliation: Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK. cas1001@cam.ac.uk.
authors.forename: Carole A
authors.initials: CA
authors.lastname: Sargent
mesh_terms: D000818:Animals; D060005:Genotyping Techniques; D005869:Ghana; D006239:Haplotypes / Q000235:genetics; D008928:Mitochondria / Q000235:genetics; D010802:Phylogeny; D010858:Pigmentation / Q000235:genetics; D013552:Swine / Q000235:genetics*; D014998:Y Chromosome / Q000235:genetics
keywords: D-Loop; Gene sequencing; Local pigs; SNP genotyping