Transcriptomic exploration of Solanum spp. resistance upon early-stage broomrape parasitism

Tomato (Solanum lycopersicum) is a major crop of high economic value. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild tomato species, has been used as breeding material for S. lycopersicum. In the present study a commercial tomato hybrid and two Introgression Lines (ILs), (S. lycopersicum X S. pennellii), were employed to identify genes and metabolic pathways associated with resistance against broomrape. Comparative transcriptomic analysis revealed a multitude of differentially expressed genes (DEGs) in roots, especially in the resistant genotype IL6-3, several of which were validated by quantitative PCR. DEG and pathway enrichment analysis (PEA), revealed diverse molecular mechanisms that can potentially be implicated in the host's defense response and the establishment of resistance. Further research into these genes and associated metabolic pathways will contribute to our understanding of host-parasite interactions and resistance to broomrapes. Findings will be valuable in molecular breeding for generating resistant genotypes, ultimately providing alternative solutions for weed management in tomato and other valuable crops. Overall design: To investigate potential resistant mechanisms of tomato againt broomrape species we used one commercial hybrid: Formula (S.lycopersicum) and two introgression lines: IL6-2 &IL6-3 (S.lycopersicum x S. pennellii). For each genotype we had both control plants (no treatment) and inoculated plants with broomrape seeds with three replicates for each treatment. The total number sent for RNA-seq was 18 samples. Then we performed gene expression profiling analysis, using data obtained from RNA-seq and bibliography for 14 DEGs. Finally we carried out PEA to reveal molecular mechanisms potentially implicated in the host defense against broomrape parasitism.