Whole-loop mitochondrial DNA D-loop sequence variability in Egyptian Arabian equine matrilines

Area of Science:

• Animal Genetics
• Equine Science
• Population Genetics

Background:

• Egyptian Arabian horses have been genetically isolated for over a century.
• Limited genetic evidence exists to validate the accuracy of their historical female lineage records.
• This study investigated the genetic signatures of 126 horses from 14 matrilines within the Egyptian Agricultural Organization (EAO) breeding program.

Purpose of the Study:

• To characterize the mitochondrial DNA (mtDNA) signatures of Egyptian Arabian horses.
• To assess the reliability of EAO studbook records for matrilineal ancestry.
• To explore the genetic diversity and origins of EAO horse populations.

Main Methods:

• Mitochondrial DNA (mtDNA) sequencing of the whole D-loop and hypervariable region-1 (HVR1).
• Analysis of polymorphic sites and haplotype diversity.
• Phylogenetic inference to determine ancestral relationships.

Main Results:

• Whole D-loop sequencing provided greater resolution than HVR1 analysis, identifying ten haplotypes versus nine.
• Most identified haplotypes belonged to ancient haplogroups, indicating diverse geographical origins over millennia.
• A novel haplotype was discovered, alongside shared haplotypes within historical families and across different strains.

Conclusions:

• The classical EAO strain designation does not consistently align with modern matrilineal genetic groupings.
• Phylogenetic analysis strongly supports the accuracy of EAO studbook records, with high probability (p > 0.998) that foundation mares share haplotypes with studied animals.
• These findings validate the reliability of EAO breeding records and offer breeders a tool to confirm equine ancestry.