Estimating the Genetic Situation of Native Upper Egypt Subpopulations of Rabbits Using Microsatellite Markers

This study aimed to explore genetic diversity in four native upper Egypt subpopulations of rabbits using microsatellite markers. A total of 247 biological samples were collected from unrelated individuals of native Upper Egypt rabbit (NUER) subpopulations across 77 rural villages and were genotyped via 31 microsatellite loci. Four hundred ninety-six alleles were recorded among the 4 NUER subpopulations, with about 43% being private. Luxor's subpopulation exhibited the most significant values of the mean number of alleles, which was 19.012, allelic richness was 8.009, and private alleles were 133. The negative values of the inbreeding coefficient were recorded in Qena and Luxor (-0.084 and -0.134, respectively). About 45% of loci gave highly polymorphic information content (PIC), and 58% were insignificant in Hardy –Weinberg equilibrium (HWE). The overlapping between Asyut and Sohag has appeared in the discriminant analysis of principal components (DAPC). Generally, we concluded that the classification is based on geographical directions to southern subpopulations (Qena and Luxor) and northern (Asyut and Sohag). Except that, the southern subpopulations (Qena and Luxor) showed high genetic variation. This study could be used as supporting documents for researchers in rabbit breeding and agriculture at national and regional levels.