Genetic diversity and phylogeographic structure of West African village chickens based on a 920bp segment of the mtDNA D-loop

Abstract

The West African village chicken characterised by small body size, low productivity, disease tolerance and strong links to local traditions is spread extensively within the sub-region especially in the rural settings. However, not much is known about its genetic diversity and population structure. In this study, the maternal genetic diversity and population structure of these chicken populations were characterised using sequence analysis of a 920-bp fragment of the mitochondrial DNA D-loop region. A total of 127 genomic samples were taken from the village chickens from four country populations (Gambia, Togo, Liberia and Nigeria). The mtDNA D-loop region was amplified following standard PCR protocols, using the primer pair of AV1F2: 5′-AGGACTACGGCTTGAAAAGC-3′ and 5′-TGCTTAAGGTTAATTACTGCTG-3′ based on complete mtDNA chicken genome. Sequencing was done using Sanger’s dideoxy chain termination method. In addition, 268 sequence samples harvested from Genbank representing Gallus gallus from Africa, Mediterranean and different regions of Asia, were included in the analysis, which brought the total sample size to 395. In all 24 polymorphic sites and 13 West African Chicken haplotypes (WAC1-13), were detected. Unbiased gene diversity (0.083±0.020) and haplotype diversity (0.43±0.29) further showed the genetic diversity of West African village chickens. The Analysis of Molecular Variance (AMOVA) revealed a maternal genetic sub-structuring of the populations (FST=0.213), with WAC8 and 10 haplotypes restricted to Nigeria. Mismatch distribution, Tests of goodness-of-fit and selective neutrality all indicated conformity with sudden demographic expansion model for Gambia, Togo and Liberia, suggestive of purifying selection, founder effect or genetic drift. On the other hand, Nigeria was indicative of a population under neutral selection, multiple parentage or bottleneck. The Nigerian and Liberian populations were the most genetically distant (pairwise FST=0.234). The study shows that the West African village chickens are genetically diverse; however, the Nigerian population was more diverse. The study concluded that understanding the genetic diversity of the African chicken can be exploited for genetic improvement.