RAPD based molecular variability of different isolates of Alternaria burnsii (Uppal, Patel and Kamat) causing blight of cumin

Abstract

Molecular variability in cumin blight pathogen (Alternaria burnsii) was analyzed using fifteen isolates collected from major cumin growing regions of Gujarat. The genomic DNA extracted from each isolates of Alternaria burnsii was subjected to polymerase chain reaction using 15 random decamer primers from OPA and OPE series. Only 10 of the 40 RAPD primers were selected based on repeatability. The 10 RAPD primers produced 622 bands and 84 loci. Among them, 77 loci were found polymorphic with an average of 91.51 per cent polymorphism. The average polymorphic information content value was 0.8473. As much as six primers out of the selected 10 primers viz., OPA 8, OPA 9, OPA 18, OPE 4, OPE 13 and OPE 10 were showed 100% polymorphism. However OPA 10 and OPE 3 showed (83.33%) polymorphism. Primer OPA 13 showed (81.81%) polymorphism. The lowest polymorphism (66.66%) was found in the primer OPE 7. The molecular weight of the amplicons ranged from 139.79 to 2319.40 bp. Dendrogram formed three clusters namely ‘C1’, ‘C2’ and ‘C3’. The cluster ‘C1’ included Ab-15, Ab-13, Ab-11, Ab-9, Ab-5, Ab-4, Ab-2, Ab-7, Ab-3 and Ab-1 isolates. The cluster ‘C2’ included Ab-8, and Ab-6 while, cluster ‘C3’ included Ab-12, Ab-10 and Ab-14 isolates. The maximum similarity index value of 0.767 was observed between the isolates Banaskantha (Ab-5) and Morbi (Ab-4) and the least similarity index value of 0.160 was found between the isolates Ahmedabad (Ab-8) and Surendranagar (Ab-14). The molecular characterization of fifteen isolates of A. burnsii by RAPD revealed existence of variations. Therefore, the primer OPA 8, OPA 9, OPA 18, OPE 4, OPE 13 and OPE 10 were could be very useful for ascertaining variability among the population of other species of Alternaria.