Genetic Diversity and Population Structure of Nigerian Indigenous Chicken Populations Inferred from Microsatellite Markers

Knowledge of genetic diversity is a prerequisite for better utilization of any genetic resource. However, such information is insufficient for Nigerian indigenous chicken (NIC). Deoxyribonucleic acid (DNA) of NIC was extracted from FTA® paper and amplified with predefined microsatellite primer sets. A total of 180 chickens: northeast (NE; n=44), north[1]west (NW; n=25), north-central (NC; n=42) and southwest (SW; n=69) were genotyped along with 15 microsatellite markers to assess genetic diversity, demographic and population stratification. All microsatellites typed were found to be polymorphic (mean PIC = 0.53), and a total of 44 distinct alleles were detected. For all the loci, average inbreeding values (FIS) were ranged from -0.01 (NW chickens) to 0.17 (SW chickens), with an average value of 0.12, thus suggesting heterozygote excess. Most of the microsatellites deviated from Hardy[1]Weinberg equilibrium. SW and NC chickens related more closely having a genetic distance value of 0.02. The cluster analyses using STRUCTURE program indicated there were three primary populations, which provided evidence of extensive sharing of genetic variability, revealing varying levels of admixture among the studied population. The AMOVA analysis result indicated the proportion of genetic variation due to differences among populations and within populations was 5.46% and 96.56% respectively. Our results revealed multiple waves of introduction of diverse gene pools, and high panmixia has created and maintained a unique set of Gallus biodiversity in Nigeria