Abstract
Poultry farming plays a vital role in rural livelihoods and is a primary source of animal protein in Burkina Faso. However, the increasing introduction of fast-growing exotic breeds threatens the genetic integrity of local chicken populations. This study aimed to assess the genetic diversity and structure of local chickens using 27 microsatellite markers, of which 23 were selected and 19 polymorphic markers were retained for analysis. A total of 116 individuals from local populations were genotyped, along with 20 individuals of the exotic broiler breed Cobb 500 for comparison. Genetic diversity, Hardy-Weinberg equilibrium, genetic distances, and population structure were evaluated using Bayesian and multivariate approaches. Results showed that 19 loci were polymorphic, revealing high allelic diversity with 117 alleles and a mean of 6.16 alleles per locus. The overall heterozygosity deficit (FIS) was low (0.04). Genetic differentiation among all populations was moderate (FST = 0.10), with higher differentiation between local populations and the exotic breed (FST = 0.19) and very low differentiation among local subpopulations (maximum FST = 0.04). Phylogenetic and Bayesian analyses indicated high admixture among local chickens, suggesting a largely homogeneous genetic structure, although the Sahelian population appeared slightly distinct. Evidence of introgression from exotic breeds was also observed, particularly in the Sudanian and Sudano-Sahelian zones. In conclusion, the local chickens of Burkina Faso form a single, weakly structured genetic pool characterized by high allelic diversity and a low heterozygosity deficit.