Genetic Diversity and Population Structure of South Ethiopian Arabica Coffee [Coffea arabica L.] Genotypes Using ISSR Markers

Arabica coffee originated and diversified in Ethiopia, yet its considerable genetic diversity remains underutilized. This study assessed the genetic diversity and population structure of 50 Arabica coffee genotypes representing five populations (Sidama, Amaro, Jinka, Guji, and improved varieties) using inter-simple sequence repeat (ISSR) markers. The populations produced 74 distinct bands, with improved varieties showing the highest number of private bands (8) and lowest common bands (≤50%) at 6. Band frequency ranged from 8.62% (Guji) to 25.86% (improved varieties), averaging 17.93%. Genetic diversity parameters, including number of alleles per population, effective alleles, Shannon’s information index, observed diversity, and unbiased diversity, ranged from 0.276-0.672, 1.063-1.149, 0.052-0.12, 0.036-0.082, and 0.039-0.092, respectively. AMOVA revealed significant genetic variability, with 67% among populations and 33% within. Principal coordinate analysis explained 42.96% of total variation across three axes. UPGMA cluster analysis grouped the genotypes into four clusters (I-IV) containing 20%, 28%, 12%, and 40% of the genotypes, respectively, with genotypes from the same populations clustering together. Overall, the study demonstrated substantial genetic variation and population structure among South Ethiopian Arabica coffee genotypes, highlighting the potential for conservation and breeding efforts. Future studies should incorporate high-resolution markers and broader accession sets to better capture the genetic landscape of Ethiopian Arabica coffee.