TRANSCRIPTOME PROFILING OF SOLANUM LYCOPERSICUM ROOTS PROVIDES NOVEL INSIGHTS INTO THE PLANT RESPONSE TO BENEFICIAL FUNGUS

Rhizosphere supports the development and growth of diverse microbial communities. Among them, Plant-Growth-Promoting Fungi (PGPFs) are of great interest for their use in sustainable and eco-friendly agriculture. Many biochemical and physiological aspects of the interaction between plants and PGPFs have been characterized, including protection against plant diseases as well as stimulation of plant growth and fitness. Previous works on plant-beneficial fungi interaction have been mainly focused on the plant systemic response, while the molecular mechanisms underlying the early phases of the plant response, particularly at the root level, have not been investigated in depth. In the present work, for the first time, we analysed the global transcriptomic changes of tomato roots (cv Crovarese) to the beneficial rhizosphere fungus Trichoderma harzianum strain T22 after 24, 48 and 72 hours of interaction, using a RNA-seq approach. A total of 1,100 differentially expressed genes (DEGs) were identified, 85% of which involved in the response at 24 hrs, highlighting the rapid reaction of the plant to the interaction with T22. Gene Ontology (GO) annotations in the Biological Process (BP) ontology domain are enriched in GO terms related to stress response (mainly involving down-regulated genes) as well as transport and metabolism of macromolecules (up-regulated genes) after 24 hrs of interaction. Interestingly, after 72 hours, the macro-group of "macromolecule modification", mainly protein modification, is the most enriched. MapMan pathway analysis indicated that the DEGs were remarkably enriched in regulation of transcription, protein degradation, transport, stress, hormone and lipid metabolism, and signalling processes, along the three time points under investigation. An in-depth analysis on the transcriptional machinery revealed a total of 153 DEGs belonging to this category with a large presence of Transcription factors (TFs), in particular Myb TFs. Characterization of these genes will help elucidating the regulatory mechanisms underlying the response to beneficial rhizosphere microorganisms.