The identification and characterization of wheat genes involved in compatibility with the biocontrol agent Clonostachys rosea and the pathogen Zymoseptoria tritici is crucial for enhancing disease resistance and biocontrol efficacy. We hypothesize that gene expression varies among plant genotypes in their interactions with BCA C. rosea and the pathogen Z. tritici. Additionally, we propose that C. rosea will induce distinct sets of defense-related genes in plant genotypes both directly and in the presence of Z. tritici. The aims of this study are to identify differentially expressed genes in wheat genotypes during interactions with the pathogen Z. tritici and BCA C. rosea, and to potentially functionally characterize the identified candidate genes. An RNA-Seq-based transcriptomic analysis will be conducted to study the three-way interaction between wheat, Z. tritici, and C. rosea. Two wheat genotypes with contrasting compatibility with C. rosea from previous work are selected and evaluated for gene expression at early stages (8h and 16h) post-inoculation with Z. tritici and C. rosea. Differentially expressed genes will undergo functional enrichment and network analysis. These identified genes will be cross-referenced with candidate genes detected in GWAS studies from previous related to biocontrol compatibility. Additionally, the gene expressions will be compared with other identified genes in the literature (e.g., Rudd et al. 2015). Transcriptional profiles, combined with haplotype analysis from previous will be utilized to identify and further characterize a selected number of wheat candidate genes. This research aims to enhance our understanding of the genetic basis of plant-BCA-pathogen interactions, paving the way for improved biocontrol strategies and disease-resistant wheat breeding programs.