Assessment of genetic diversity among Egyptian and Saudi chicken ecotypes and local Egyptian chicken breeds using microsatellite markers

<jats:p>Aim: To assess genetic diversity of two chicken ecotypes from Egypt and Saudi Arabia and compare these ecotypes to six local Egyptian and two exotic pure chicken breeds using 14 microsatellite markers. Methodology: Dataset consisted of two subsets. First subset represented two ecotypes from Saudi Arabia and Egypt. Second dataset consisted birds six Egyptian native chicken strains: Fayoumi (FAY), Dandarawy (DAN), Baladi (BAL), Sinai (Sini), El-Salam (Els) and Golden Montazah (GG), and two commercial strains: White Leghorn (WL) and Rhode Island Red (RIR). fourteen microsatellites markers were utilized to assess DNA polymorphism. Data analyses of the results were carried out using R statistical environment. Results: The obtained results indicated that number of alleles per locus averaged 11.4 ± 5.0. Polymorphic information content was informative (> 50%) for the local breeds, but not for two ecotypes. The observed and expected heterozygosity averaged 0.46 and 0.75, both ecotypes had the lowest estimates. All breeds showed significant deviation from Hardy–Weinberg equilibrium expectation. The average population differentiation index (FST) was 0.143, overall heterozygosity deficiency (FIT) was 0.156, and global inbreeding of individuals within breeds (FIS) was 0.319. Interpretation: This study revealed that both Egyptian and Saudi ecotypes have an endangered status. Lower genetic distances and lower FST values were reported for the Egyptian indigenous breeds. Phylogenetic and principle components showed that both ecotypes were genetically closer to each other when compared with other breeds. It also showed that the Dandarawy native Egyptian chicken breed was genetically the closest breed to both the Egyptian and Saudi ecotypes. Key words: Chicken, Ecotypes, Genetic diversity, Microsatellites, Phylogenetics</jats:p>