Genetic Diversity and Structure of Local Chicken Populations Raised in Five Agroecological Zones of Togo

Abstract

Local chickens are the most commonly raised poultry breed in rural areas of Togo, where they help in alleviating poverty and food insecurity in households. The current study aimed to ensure the sustainable management of this genetic resource by evaluating the genetic diversity, phylogenetic relationships, and population structure of local chicken populations from five agroecological zones (Dry Savannah, Atakora, Forest, Wet Savannah, and Littoral) in Togo. Genotyping was carried out using 15 microsatellite markers on 30 unrelated individuals per agroecological zone. Genetic diversity was assessed by estimating the number of alleles per locus, observed heterozygosity, unbiased expected heterozygosity, and the polymorphic information content (PIC). The genetic structure of the populations was analyzed using a Bayesian-based approach. The results revealed a high genetic diversity but weak population structuring among local chickens. Moreover, 98 alleles were detected in all population groups, varying from 3 to 12 per locus, with an average of 6.53 ± 2.67 alleles per locus. The PIC values varied from 0.436 to 0.690, with an average of 0.550 ± 0.087. The mean number of alleles per population across all markers ranged from 4.4 ± 1.4 (Dry Savannah) to 5.4 ± 2.0 (Forest). The unbiased expected heterozygosity was high and varied from 0.58 ± 0.07 (Atakora) to 0.65 ± 0.11 (Forest), while that observed varied between 0.46 ± 0.09 (Dry Savannah) and 0.57 ± 0.14 (Forest). All populations deviated significantly from the Hardy-Weinberg equilibrium. Across populations, FIT, FIS, and FST fixation indices were 0.150, 0.132, and 0.021, respectively. The genetic distances were low and varied from 0.022 (between Atakora and Dry Savannah) to 0.045 (between Atakora and Forest). These results could be used in potential genetic improvement programs or the preservation of local chickens in Togo.