Morphological and molecular diversity of Ganoderma spp. causal agent of basal stem rot of coconut in Southern dry tracts of Karnataka

Abstract

Morphological and molecular diversity of Ganoderma species causing basal stem rot of coconut in Southern dry tracts of Karnataka, India was carried out during 2016-17. A total of 20 isolates were isolated from Chitradurga, Chikamagalore, Hassan and Tumkur districts of Karnataka and were identified based on morphological and molecular characteristics. Sporocarps and diseased root bits were found as good source for isolation of Ganoderma. In all the isolates there were high variability in cultural, morphological and molecular characteristics. The dendrogram generated from the cultural and morphological characteristics showed clear variations among Ganoderma isolates and formed two main clusters, one cluster consisted of 13 isolates and another cluster consisted of 7 isolates. Several isolates showed 100 per cent similarity in the morphological characters regardless of their geographical origin. All the Ganoderma isolates amplified a fragment of 650 bp with fungal universal primers (ITS1 and ITS4). The ITS gene sequences of five isolates viz., CG1 (MK 681870), CG7 (MK681871), CG11 (MK681872), CG14 (MK681873) and CG20 (MK681874) were deposited in NCBI gene bank. Taxonomic comparison of the isolates with NCBI database proved that the isolates were genetically related to Ganoderma spp. with 80-100 per cent identity. However, all the tested isolates could not amplify G. lucidum species specific markers which indicate its absence in the region. The phylogenetic analysis of the Ganoderma isolates (ITS1 and ITS4) of coconut with other known species of Ganoderma from GenBank emphasized the close relationship with India, China and Sri Lanka isolates. The isolate CG1 grouped with Ganoderma carnosum (KR 733545.1) with 98.97 per cent identity which is isolated from Sri Lanka and CG14 and CG20 grouped with G. applanatum (MF 072395.1) and G. gibbosum (OM 350473.1) with 98 to 99 per cent identity and CG7 and CG11 isolates of coconut grouped into distinct sub cluster and clearly indicated the species diversity in Ganoderma infecting coconut in Southern Karnataka.