Application of Sequence-Related Amplified Polymorphism (SRAP) Markers for Assessing Molecular Diversity of Trichoderma Associated with Biocontrol Potential Against Phytopathogen.

The genus Trichoderma comprises potent biocontrol fungi known for their antagonistic activity against diverse phytopathogens. Understanding the genetic diversity among Trichoderma isolates is essential for identifying strains with enhanced biocontrol potential. Sequence-related amplified polymorphism (SRAP) markers, which target open reading frames (ORFs) and associated regulatory regions, offer a robust and efficient molecular tool for diversity analysis. This chapter describes a detailed protocol for genomic DNA extraction, SRAP-PCR amplification, and data analysis for Trichoderma isolates. The approach enables reliable assessment of genetic variation and its correlation with biocontrol traits, such as antagonism against Sclerotium rolfsii and production of antifungal metabolites. Representative primer combinations and analytical strategies are provided to facilitate reproducibility and effective strain characterization for biocontrol applications.