Microsatellite markers application in the genetic survey of native rabbits in the Egyptian delta

The human interest in exotic animal breeds in the agricultural sector led to the deterioration of local breeds. The interest in national farm animal genetic studies is important for the agriculture ecosystems under climate change challenges. Microsatellite markers are important tools to determine the genetic status of breeds, populations, and subpopulations. In this study, 28 microsatellite loci were used to investigate the genetic situation among 274 biological samples collected from the native Delta Egypt rabbits (NDER) population in the north of Egypt. They belonged to eight subpopulations (Damietta, Dakahlia, Kafr El sheikh, Beheira, Gharbia, Menoufia, Sharqia, and Qalyubia). It was found that expected heterozygosity (He) values were greater than observed heterozygosity (Ho). A total of 184 alleles were identified, with a mean of 6.571 and 4.122 as effective alleles. About 89% of microsatellite markers expressed high informative values in the polymorphism information content (PIC). The comparison among 8 NDER subpopulations showed low genetic variability parameters with high inbreeding coefficient (FIS) values in the north (Damietta, Dakahlia, Kafr El sheikh, Beheira, and Gharbia). However, values of genetic variables increased with decreasing FIS in the middle (Menoufia), east (Sharqia), and south (Qalyubia) Delta. Furthermore, the discriminant analysis principal components (DAPC) showed overlaying in the north. In the same context, the neighbor-joining tree (NJ) and heatmap showed the genetic convergence among the northern subpopulations. The analysis of STRUCTURE found 4 clusters (K= 8). The north subpopulations were in one cluster, while others in the middle, east, and south were a separate cluster for each subpopulation. Our findings show that the NDER suffers from genetic drift in the northern Delta subpopulations. On the contrary, the south, east, and middle subpopulations showed more genetic variability. A strategy of correct mating should be fostered to improve the genetic traits of rabbits.