Abstract

Genetic characteristics and population structure within and among Egyptian indigenous chicken strains are important for identifying some genetic resources. The present study aimed to use microsatellite markers to determine similarity and genetic distance among different genotypes and their association with growth and production traits in Egyptian indigenous chicken strains. The current study included 800 chickens and 100 genomic DNA samples obtained from four Egyptian local chicken strains of four different areas (Dokki-4, Mandarah, Anshas, and Al-Salam) in Egypt. Their genetic characteristics, population structure, phylogenetic relationships, and their association with body weight were analyzed using seven microsatellite markers. The performance of 200 chicks from each strain was assessed in terms of individual body weight and growth rate. Al-Salam strain had a significantly higher body weight than the other strains up to 12 weeks of age among the four lines of Egyptian local chickens. Additionally, male chickens across all strains indicated significantly higher body weight than females from 2 weeks of age until the end of the experiment. The study revealed a total of 68 alleles from the 7 loci across 4 chicken strains, with an average of 9.71. The average of observed heterozygosity, expected heterozygosity, and polymorphism information content were 0.799, 0.358, and 0.707, respectively. The Mandarah strain had the highest observed allele number of 5.37; however, the lowest observed allele number was 3.12 for the Dokki strain. Analysis of population structure revealed that the four chicken strains should be divided into three clusters based on the highest log-likelihood values (�K value, 56.3). The results showed a degree of heterozygosity in the Mandara strain with 66.7 individual memberships, indicating a level of admixture. On the other hand, the Al-Salam strain indicated a high genetic diversity with 99 individual membership. The current study provides valuable insights for future genetic polymorphism studies, the advancement of breeding programs, and strategies for the conservation of the Egyptian local chicken strains. © The Author(s) 2023. All Rights Reserved.