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

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 and Y-chromosome sequence polymorphisms, as well as 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 dominant black MC1R alleles of both Asian and European origin contributing. 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, such as the Large White. 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.


Introduction 4
A number of approaches have been developed to study the origin, genetic variation and 68 unique attributes of animal genetic resources providing valuable information for their 69 conservation.. Mitochondrial DNA (mtDNA) has been used to produce phylogenetic trees at 70 several taxanomic levels, from within species to among orders (e.g., Larson et al., 2005; 71 Haile et al., 2010). MtDNA is maternally inherited, haploid, non-recombining and its 72 evolutionary rate of base substitution is much faster than that of nuclear DNA (Avise, 2000).

73
Thus it can be used to follow the maternal contributions within the porcine domestication 74 process (Kim et al., 2001. In contrast, fragments of sequence from the Y 75 chromosome have been analysed to study paternal lineages in domesticated pigs (Ramos et

85
Coat colour is another important trait in characterization of animal breeds (Switonski et al., 86 2013) and among the genes affecting this trait, the melanocortin receptor 1 (MC1R) locus is 87 the most consistently polymorphic (Margeta et al., 2013). MC1R is primarily expressed in 88 melanocytes and plays a key role in melanogenesis by determining the switch between 89 production of red/yellow pheomelanin and dark eumelanin (Robins et al., 1993). Mutations in 90 the MC1R gene affect coat colour in pigs (Kijas et al., 1998;2001); loss-of-function    gives the total for individuals that share the haplotype, and the bar shows the regional 137 distribution.

139
The clustering of haplotypes into European and Asian clades was confirmed using base 140 substitution data, with smaller genetic distances observed between the two major European 141 haplotypes identified in this study compared to the genetic distances between the major 142 Asian and European haplotypes (Table 1). Globally, the mitochondrial sequences from the 143 ADP of Ghana were closer to European than Asian sequences, as shown in Table 2

Coat Colour in Ghanaian local pigs 177
The ADP of Ghana, although predominantly black, displays other coat colours and patterns.

178
These can be observed even in the offspring of selected "purebred" black-coated ADPs,

206
As with the mitochondrial data, the occurrence of Asian alleles was higher in animals from 207 the Guinea Savannah zone than those from the other regions. Further discussion of the 208 distribution of alleles is given in Supplementary Information.

Genotyping Analysis 210
Genotyping data were used to perform comparisons using PCA analyses, genome wide 211 levels of homozygosity, and an F ST comparison of the ADPs against other world pig breeds.

213
The PCA analysis of local Ghanaian animals is shown in Supplementary_ Figure_6A.pdf.

214
ADPs form two main groups, based on geographical location: those from the Guinea 215 Savannah zone are the most tightly grouped, followed by those from the Coastal zone 216 (particularly GAR), with the Forest zone animals being more diffusely scatted across the 217 plot. In general, the crossbred pigs tended to be closer to the exotic (European breed) 218 animals, as might be predicted based on known introduction of European breed genetics.

219
When data from other world pig breeds are included, the Ghanaian pigs cluster more closely 220 with European commercial breeds than with Asian pig breeds (Supplementary_

228
The second subgroup came from the Coastal zone (Supplementary_ Figure_6A.pdf set 2).

229
The two major subgroups of ADPs (Guinea Savannah and Coastal) comprise 17 animals 230 each.

231
Genome averaged Fst values are consistent with the mitochondrial data: the ADPs are 232 genetically more similar to European Commercial breeds than to either Duroc or Chinese 233 breeds (Table 3) 234 235

493
The present raw dataset was also merged with data from a previous study using pig breeds