Mitochondrial D-loop nucleotide sequences of Egyptian river buffalo: Variation and phylogeny studies

The complete mitochondrial D-loop region of 48 Egyptian buffalo representing the two main subpopulations from Northern-Egypt and Southern-Egypt was sequenced and analyzed. To the best of our knowledge this is the first published data on the complete mitochondrial D-loop sequences of Egyptian river buffalo. Analysis of D-loop sequences revealed 28 different haplotypes resulting from 77 polymorphic sites. Two major haplotypes are shared by the two subpopulations which indicate the presence of similar founding populations in the north and south of Egypt. In addition, 16 haplotypes (14 of which are singletons) are present in the Northern subpopulation, whereas 10 haplotypes (8 of which are singletons) are present in the Southern subpopulation. The presence of the high number of haplotypes is due to the high substitution rate detected in the D-loop region. The 28 haplotypes are rich in A/T content, as seen in other mammals, with a mean value of 60 ± 0.358%. The A/T contents in the hypervariable regions ETSA1, ETSA2 and CSB1 are found to be higher than in the entire D-loop. The ratio of nucleotide transitions to transversions in the haplotypes is 4.8:1 demonstrating bias towards transitions. Only transitions are found in the hypervariable regions and their percentages at ETSA1, CSB1 and CSB2 regions are higher than in the entire D-loop. Results of the phylogenetic analysis of the two Egyptian buffalo subpopulations could be interpreted as showing the mixed origin of the two subpopulations and probably indicating the presence of many ancient maternal lineages for the Egyptian buffalo with high diversity in mtDNA sequences. The phylogenetic tree constructed from the Egyptian buffalo haplotypes and representatives of published haplotypes of river and swamp buffaloes shows two distinct clades: one comprises the Egyptian buffalo and all the other river buffaloes indicating that they have common origin, whereas the other clade comprises the swamp buffalo. This confirms that Egyptian buffalo are similar to domesticated river buffalo in other regions of the world.