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This study defined the population structure and phylogenetic relationship among the commonest breeds of rabbit in Nigeria. A total of 100 genomic DNA isolated from New Zealand White, Californian White, New Zealand Red and Chinchilla rabbit breeds in Nigeria were used with seven microsatellite markers in order to assess the genetic diversity, phylogenetic relationships and population structure of these rabbit breeds. Genomic DNA was extracted, amplification was done using PCR with each microsatellite marker, the products generated were subjected to 12 % polyacrylamide gel electrophoresis on an ABI 3730 DNA Sequencer. Bands on gels were scored based on size of ladder with Gene Scan 3.1.2. and designated as alleles on an Excel Worksheet. Allele frequencies were generated with Microsatellite Analyzer version 4.05 and further used in determining other population genetic parameters such as the genetic differentiation and genetic distance. The genetic sub-structuring carried out basing on the Evanno's method revealed 2 clusters, which are the New Zealand White (cluster 1) and the New Zealand Red, Chinchilla and Californian White (cluster 2) having a high degree of admixture and interbreeding with no significant gene pool variation between rabbit individual in cluster 2. Conclusively, these findings show that, in spite of the high level of genetic variation among the rabbit breeds, the breeding strategies adopted could have led to genetic admixture among the breeds as a result of relatively high gene-flow among the breeds.
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