Abstract
This chapter ascertains the variability in Trichoderma isolates, isolated from tomato plant is a challenging task, if based solely on morphological and cultural characters. In this perspective, the robustness of five different genetic marker viz., random amplified polymorphic DNA (RAPD), enterobacterial repetitive intergenic consensus (ERIC), BOX elements, and REP-markers were used to interpret intraspecific variability in Trichoderma isolates. All techniques significantly produced intraspecific polymorphism, but diverse levels of discrimination were obtained. PCA analysis explained genetic diversity among Trichoderma isolates based on RAPD, REP-, ERIC-, and BOX element analysis, respectively. In this study, first time ERG-1gene (encoding a squalene epoxidase) has been used for diversity analysis of antagonistic Trichoderma isolated from tomato rhizosphere. Phylogenetic analysis of ERG-1 gene sequences revealed close relatedness with earlier reported sequences of Hypocrea lixii, T. arundinaceum, and T. reesei. Molecular identification and phylogenetic analysis of Trichoderma species were performed using translation elongation factor alpha (Tef-α), internal transcribed spacer (ITS), and ergosterol (ERG) gene markers. However, ERG-1 gene also revealed heterogeneity among some antagonistic isolates and specified the prospect of occurrence of squalene epoxidase-driven triterpene biosynthesis as a substitute biocontrol mechanism in Trichoderma species. Information achieved from comparing results of diverse molecular marker systems should be useful to access the genetic variability and ideally, will improve disease management practices by identifying sources of inoculum and isolate characteristics.
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