The Arabian;horse Equus caballus is belonging to family Equidae that all of its species are in danger of extinction. We sequenced 1059 nucleotides from three mitochondrial DNA protein coding genes for some breeds of the Arabian and English horses designated for race, productivity and longevity in order to investigate their genetic variation. The sequenced genes were NADH dehydrogenase subunit 2 (ND2), cyto-chrome C oxidase subunit 1 (CO1) and ATPase subunit 6 (ATP6). ATP6 discriminated among the different breeds where seven substitutions were recorded of which 2 were non-synonymous. The other loci recoded 8 synonymous substitutions of transitions most of which were among the breeds of longevity. The data of CO1 gene were used to construct the relationship of the Arabian horse to the thoroughbreds. Maximum-likelihood (ML) and Neighbor-joining (NJ) analytical methods were used. The two analytical methods showed clustering of the Arabian breeds in one group and the non-sister relationship within the thoroughbreds. One of the thoroughbreds clustered within the Arabian breeds suggesting the possibility of their out breeding. Increasing tendency in the variation of the studied genes was proportional to the utility of these genes in energy production within the mitochondria. The present study is therefore a preliminary step in the conservational efforts of the Arabian horse of equestrian..
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