Genetic diversity, clustering pattern and phylogenetic relationship between Moshtohor rabbits (M-line) as a new
synthetic line and their founder line of Spanish V-line and Sinai Gabali were assessed using sixteen microsatellite
markers. Moreover, polymorphism based on SNP G/A2464 located in the promoter region of progesterone
receptor gene (PGR) was evaluated based on PCR-RFLP method. The French Giant Papillon (FGP) was used as an
out-group breed. All the investigated microsatellite loci were polymorphic and the average NO, HO, He, FIS were
6.75, 0.65, 0.80 and 0,083 respectively. M-line rabbits recorded the highest values of NO (5.50), Ho (0.758) and
He (0.742). Three genotypes (GG, AA and GA) were detected by genotyping G/A2464 SNP located in the promoter
region of progesterone receptor (PGR) gene. M-line recorded the highest values of Ne (1.987), He (0.497) and
Polymorphic information content (PIC) (0.373) and showed high potentiality for litter traits improvement by
possessing the highest GG genotype frequency (0.120) among the studied populations. A close relationship
between M-line and V-line (0.18) was supported by their clustering in one phylogenetic clade and their
appearance as one admixed mosaic cluster in population structuring