Unveiling genetic diversity in Egyptian Arabian horses (Equus caballus) through cytogenetic and ISSR marker analysis

This study combined classical cytogenetics and ISSR molecular markers to characterize genetic diversity in 24 Egyptian Arabian horses. Karyotyping revealed the standard equine chromosome number (2n = 64) with no numerical or structural abnormalities. Chromosome measurements were consistent with ISCN Equine standards: autosomal relative lengths (RL%) followed the expected size hierarchy, biarmed chromosomes displayed metacentric to submetacentric morphology (CI = 37-50%), and recalculated centromeric indices confirmed the presence of measurable p-arms on all acrocentric chromosomes. ISSR analysis using nine informative primers generated 117 bands, of which 104 were polymorphic (88.89%). Highly polymorphic primers included (AGC)₆G (95.24%) and (GAG)₆C (93.75%), demonstrating broad genome coverage. Population-level parameters indicated moderate genetic diversity (P% = 88.89%, H = 0.32, I = 0.48). Pairwise Dice similarities (0.70-0.98) reflected moderate to high inter-individual relatedness without clear subgroup separation. Overall, the findings confirm cytogenetic stability within the cohort and highlight ISSR markers as an effective tool for assessing diversity in Egyptian Arabian horses. These results provide a foundational reference for conservation, breeding strategies, and future genomic studies.