A molecular analysis of the patterns of genetic diversity in local chickens from western Algeria in comparison with commercial lines and wild jungle fowls

The objectives of this study were to characterize the genetic variability of village chickens from three agro-ecological regions of western Algeria: coastal (CT), inland plains (IP) and highlands (HL), to reveal any underlying population structure, and to evaluate potential genetic introgression from commercial lines into local populations. A set of 233 chickens was genotyped with a panel of 23 microsatellite markers. Geographical coordinates were individually recorded. Eight reference populations were included in the study to investigate potential gene flow: four highly selected commercial pure lines and four lines of French slow-growing chickens. Two populations of wild red jungle fowls were also genotyped to compare the range of diversity between domestic and wild fowls. A genetic diversity analysis was conducted both within and between populations. Multivariate redundancy analyses were performed to assess the relative influence of geographical location among Algerian ecotypes. The results showed a high genetic variability within the Algerian population, with 184 alleles and a mean number of 8.09 alleles per locus. The values of heterozygosity (He and Ho) ranged from 0.55 to 0.62 in Algerian ecotypes and were smaller than values found in Jungle fowl populations and higher than values found in commercial populations. Although the structuring analysis of genotypes did not reveal clear subpopulations within Algerian ecotypes, the supervised approach using geographical data showed a significant (p < 0.01) differentiation between the three ecotypes which was mainly due to altitude. Thus, the genetic diversity of Algerian ecotypes may be under the influence of two factors with contradictory effects: the geographical location and climatic conditions may induce some differentiation, whereas the high level of exchanges and gene flow may suppress it. Evidence of gene flow between commercial and Algerian local populations was observed, which may be due to unrecorded crossing with commercial chickens. Chicken ecotypes from western Algeria are characterized by a high genetic diversity and must be safeguarded as an important reservoir of genetic diversity.