Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on evidence from mtDNA analysis, MC1R, and Y-chromosome haplotypes

Abstract

19 The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease 20 resistant traits. Characterisation of animal genetic resources provides relevant data for their 21 conservation and sustainable use for food security and economic development. We 22 investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses 23 with modern commercial breeds based on mtDNA, MC1R and Y-chromosome sequence 24 polymorphisms, as well as genome-wide SNP genotyping. 25 26 The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. 27 Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both 28 European and Asian genetic signatures, with differences between the geographical zones. 29 Black coat colour is the most predominant within the breed, with dominant black MC1R 30 alleles of both Asian and European origin contributing. European alleles for spotting are 31 present at a low frequency in the sample set, and may account for the occurrence of spotted 32 piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed 33 effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster 34 closely with European pigs of commercial origin, such as the Large White. 35 36 The presence of both European and Asian contributions, with differences between 37 geographical zones probably reflects trading and colonial influences.. Understanding the 38 effects of admixture on important adaptive and economic traits of the ADP and other local 39 breeds in Africa is critical for developing sustainable conservation programmes to prevent 40 the decline of these genetic resources. 41 2 bioRxiv preprint doi: https://doi.org/10.1101/066209; this version posted July 27, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. 42