Application of the Randomly Amplified Polymorphic DNA (RAPD) Markers to Analyze the Genetic Variability in Species of the Fungus Alternaria

The PCR-based technique of randomly amplified polymorphic DNA (RAPD) was used to fingerprint and assess the genetic relatedness among nine species of the fungus Alternaria isolated from various crop plants showing the leaf spot disease in Mosul, Iraq. Genomic DNA of each species was extracted at a final concentration of 300 - 400 g / 2-3 g of wet mycelium , and at a purity of 1.6-1.8. Each DNA sample was amplified with each of 22 primers and the products were resolved electrophoretically on 1.2% agarose gel, stained with ethidium bromide and photographed under UV. One Primer failed to support amplification but the remaining 21 (95.5%) primers produced a total of 112 bands (2-10 per primer) across the nine species. Of these bands, 100 (1-10 per primer ) were polymorphic. The least efficient primer was OP-H01 (1.79%), while the most efficient one weas OP-M05 (8.93 %). Primers OP-C05, OP-E20 and OP-T20 had the lowest (0.1%) discriminatory power while primer OP-M05 had the highest (10 %) power and identified all 9 species through unique patterns of banding. RAPD analysis fingerprinted eight of the nine isolates through marker bands with one or more of the 21 primers. Cluster analysis based on the genetic distances split the nine species into three distinct clusters with no obvious association between the pattern of clustering of the species and their host specificities.