Genetic diversity and maternal ancestry of Liberian country chickens indicated at the hypervariable-1 section of the mitochondrial DNA D-loop.

Abstract

The vast majority of animal production in Africa, Liberia inclusive is in the hands of traditional operators based in the rural or countryside, upon which there is a general dearth of genetic information, especially at the molecular level regarding their origins and characterization. The study sought to evaluate the molecular genetic diversity and trace the evolutionary origins of the Liberian country chickens using the maternally inherited mitochondrial DNA as a profiling marker. The D-loop regions of the mtDNA of 34 Liberian country chickens sampled from four different locations were analysed following standard DNA isolation protocol (www.whatman.com) and polymerisation using AV1F2: 5′-AGGACTACGGCTTGAAAAGC-3′ and 5′-TGCTTAAGGTTAATTACTGCTG-3′ , as forward and reverse primers respectively. PCR amplicons were sequenced based on Sanger’s di-deoxy chain termination method at Stabvida genetic laboratories, Portugal and thereafter edited with BioEdit 7.0 and truncated to 490bp covering the hypervariable-1 segment, using MEGA 7. Genetic diversity indices and molecular variance were analysed using DnaSP V.5.10 and Arlequin 3.5.1.3 softwares respectively. The evolutionary relationships of the Liberian chickens with 268 global chicken mtDNA sequences from Mainland Asia, Pacific Asia, Mediterranean region and Africa extracted from Genbank depository (leading to a total sample size of 302), and their maternal origins were inferred following reconstruction of Neighbour-joining phylogenetic and Median-joining network analyses using MUSCLE software and NETWORK 4.6. Results from the study show no population structure (FST values not significant at P<0.05) and low genetic diversity (Haplotype diversity = 0.06±0.05, Nucleotide diversity = 0.002±0.006) among the Liberian chickens probably due to purifying selection and founder effect, possibly occasioned by genetic bottlenecks in the recent history of the country, like the prolonged civil war. One polymorphic site and two Liberian chicken haplotypes (LibE1 and LibE2) belonging to Clade E were detected. This evidence along with others overwhelmingly pointed to India as the ancestral root of the matriarch of the current populations of the Liberian country chickens. Findings from this study hold the potential for the genetic improvement of the Liberian country chickens and further understanding of the possible impact of human conflicts on animal genetic resources in Africa.