The main objectives of this study were to assess the genetic diversity and phylogenetic relationship among three Egyptian rabbit breeds (Gabali, Baladi Red and Baladi Black) along with New Zealand White breed as a reference breed by using two different molecular markers (RAPD markers and microsatellite markers ).
A total of one hundred and twenty animals were used in this study, 30 animals from each breed. The samples were taken randomly from pedigreed animals with the least relationship (avoiding full-sib and half-sibs mating) to decrease the genetic similarity between the genotyped animals. Genomic DNA was extracted from leukocytes and PCR amplification was performed. The amplification products were resolved by electrophoresis; Images were captured and analyzed, then the results were statistically analyzed.
In the present study, RAPD technique was used to assess the genetic variability and phylogenetic relationship among the four rabbit breeds. Fourteen random primers were tested to amplify pooled genomic DNA from these breeds. Ten of them were chosen for further analysis, on the basis of the presence of reproducible and distinct RAPD profiles in one or more rabbit breeds. Out of 131 bands scored using these primers, 74(56.48%) were recognized as Polymorphic and 57 (43.52%) as monomorphic bands. The highest percentage of polymorphic bands was recognized for primers OPB-02 (94%) and OPB-07 (92%). While, the lowest percentage of polymorphic bands was recognized for primers OPA-02(16%) and OPF-12 (28%). The band sharing frequencies (BSF) was found higher between Baladi Red -Baladi Black (0.80± 0.038) , followed by Gabali - Baladi Black (0.71±0.079 ), New Zealand White- Baladi Black (0.70±0.096), New Zealand White- Baladi Red (0.69±0.088) and the least BSF was found between New Zealand White- Gabali (0.64±0.081). Overall, there was no significant difference (P>0.05) in BSF values between breeds. The highest genetic distance was found between Baladi Red - Baladi Black (0.87) followed by Gabali - Baladi Red (0.86), Gabali, Baladi Black (0.82), New Zealand White - Gabali (0.80), New Zealand White - Baladi Red (0.75) and the lowest genetic distance was found between New Zealand White - Baladi Black(0.73). One primer (OPA-20) in Gabali, two primers (OPA-02, OPB-14) in Baladi Red, three primers (OPA-02, OPB-14, OPA-20) in New Zealand White and Baladi Black were found to be specific for these breeds. The study suggests that RAPD can be successfully utilized for detecting genetic variation among the studied rabbit breeds.
Also, microsatellite markers were used in the present study to investigate the genetic diversity of three native rabbit breeds; Gabali (G), Baladi Red (BR) and Baladi Black (BB) in addition to New Zealand White (NZW) as a reference population by using twelve microsatellite markers. All microsatellite loci typed were polymorphic. The average number of alleles per locus was 5.250 ± 0.232 and ranging from 4 in SAT2 to 9 in SAT4 and SAT16. Mean observed heterozygosity was 0.616 ± 0.021 and that was ranged from 0.358 in SAT2 to 0.725 in SOL33.While, the mean expected heterozygosity was 0.682± 0.021 and that was ranged from 0.372 in SAT2 to 0.864 in SAT16. The average PIC was 0.7096 and found to be ranged from 0.351 at locus SAT2 to 0.846 at locus SOL33. All studied loci except SAT7 and SAT2 showed deviation from Hardy-Weinberg Equilibrium with high significant level. The inbreeding coefficient of individuals relative to the total population (FIT) was 0.071. The overall within-population heterozygote deficit (FIS) was 0.068±0.035, and ranging from 0.141±0.068 in Baladi Red to 0.015±0.084 in Baladi Black breed. The overall variation between populations (FST) was 0.138, The highest pairwise FST value was recorded between Baladi black and New Zealand white (0.071) while, the lowest pairwise FST value was recorded between Baladi Red and both of Gabali (0.038) and Black Baladi (0.039). The Neighbour-Joining tree showed close relation between Baladi Red and Baladi Black breeds. The close relation between Baladi Red and Baladi Black breeds may be explained as they had a common ancestor. Also, the three Egyptian breeds (BR, BB and G) are separated from the NZW breed. Analysis of population structure indicated that the New Zealand White and Baladi Black were assigned independently into their respective clusters while the remaining two populations (Baladi Red and Gabali) were clustered together forming admixed mosaic cluster.