Dissection of graft-tomato interactions upon PVYc-to infection through multi-omics approaches

Grafting improves plant pathogen tolerance, including viruses, but its molecular mechanisms are not fully understood. This study investigated how grafting affects tomato responses to a recombinant potato virus Y (PVYc-to) using multi-omics, combining high-throughput phenotyping (HTP) and RNA sequencing (RNA-seq). Two tomato varieties, Manduria (Ma) and UC82 (UC), tolerant and susceptible to PVYc-to, served as rootstock and scion in UC/UC and UC/Ma combinations. Plants, grown in greenhouses, were mechanically inoculated with PVYc-to. Data on canopy morphology and surface temperature were collected at 9 time points up to 36 days post-inoculation (dpi) from infected, mock-inoculated, nongrafted, self-grafted (UC/UC), and hetero-grafted (UC/Ma) plants. In parallel, RNA from plants at 14 and 28 dpi was used to estimate viral loads and perform small RNA and mRNA sequencing. HTP showed that UC/Ma plants exhibited enhanced growth performance and reduced viral symptoms, and PVYc-to RNA accumulation compared to UC controls. Thermography at 28 dpi indicated higher canopy temperatures in infected plants, implying impaired transpiration. Transcriptomic and small-RNA analyses at 14 dpi revealed that grafting mainly affects gene expression during infection: PVYc-to suppresses photosynthesis genes, whereas in the UC/Ma combination, metabolic reprogramming and the activation of systemic defenses were observed. These results highlight the value of transcriptomics and HTP in studying tomato responses to viruses and grafting.