Rhizoctonia solani is the most important pathogen involved in cotton seedling disease in Egypt. Variations in the antagonistic activity of 20 isolates belonging to Trichoderma harzianum and T. longibrachiatum were evaluated in vitro, against three isolates of Rhizoctonia solani in dual culture. There was highly significant interaction between isolates of Trichoderma and R. solani. All isolates of Trichoderma spp. showed varying levels of antagonism against R. solani. Similarly, the interaction between Trichoderma isolates and R. solani was a highly significant source of variation in surviving seedlings under greenhouse conditions. In vitro and in vivo antagonism were not correlated, which indicated that, in vitro inhibition of the pathogen was not predictive of in vivo biocontrol by an individual antagonist. Microsatellite-primed PCR analysis was used to evaluate the genetic variation among Trichoderma isolates. The analysis divided the isolates into two main groups. Grouping the isolates based on cluster analysis of their DNA profiles matched that based on their morphological taxonomy. However, no congruency was found between cluster analyses obtained by PCR and cluster analysis by efficiency parameters of the biocontrol agents.
