Horses are one of the early domesticated animals in the world that changed societies and civilizations on a continent-wide scale. Due to the rare information about the genetic characterization of different horse populations in Egypt, this study aimed to identify the genetic biodiversity and relationships between four horse populations reared in Egypt. Genomic DNA was extracted and mtDNA region was amplified using polymerase chain reaction (PCR). The alignment of 384-bp amplified fragments showed the presence of 41 polymorphic sites resulting in 29 haplotypes which their sequences were submitted to GenBank under the accession numbers: KX909898-KX909926. The phylogeny tree for tested horses declared the presence of mixing maternal lineages between the four tested populations but still there are some separated lineages especially for Arabian and Thoroughbred horses. The sequences of 72 tested sequences were aligned with 13 published sequences as references, 11 of them for different Equus caballus whereas the other two reference sequences for Equus burchellii and Equus asinus. The results showed that all tested horses from the four populations are grouped with reference sequences of Equus caballus and separated from the other two reference sequences of Equus burchellii and Equus asinus. It is concluded that sequence analysis of mtDNA control region is still the most informative tool for the identification of genetic biodiversity and phylogeny of different horse breeds and populations. The horse populations reared in Egypt possess low genetic diversity and all of them are belonged to Equus caballus breed.
Keywords: Arabian; Baladi; Genetic variations; Horse populations; MtDNA; Sports; Thoroughbred.