Comparison of SSR and AFLP analysis for genetic diversity assessment of Ethiopian arabica coffee genotypes

Knowledge of genetic diversity within and among genotypes of any crop is fundamental for estimation of the potential genetic gain in a breeding programme and effective conservation of available genetic resources. Currently, different molecular marker techniques are being developed for measuring genetic diversity. Comparison among molecular marker techniques is important for effective marker selection. However such types of efforts are rare for arabica coffee. This study was conducted to compare the efficiency of simple sequence repeat (SSR) analysis for determining genetic relationships of 28 Coffea arabica L genotypes collected from different parts of Ethiopia with work previously done using amplified fragment length polymorphism (AFLP) analysis. A total of 22 SSR fragments were amplified and compared with 712 previously amplified AFLP fragments. AFLP and SSR markers were positively and significantly correlated (0.217) in estimating genetic similarity among genotypes. The average genetic similarity coefficient calculated using SSR markers was much lower (0.560 with a range of 0.286-1.000) compared to AFLP markers (0.915 with a range of 0.860-0.982) indicating the higher information content of SSR markers. AFLP markers distinguished all genotypes, while SSR markers distinguished 64.3% of the genotypes. Results indicated that AFLP markers were more efficient compared to SSR markers for characterization of the evaluated coffee genotypes