A Multimodal Study of Wild Tomato Species Introgressions Unravels the Genetic Basis of Transcriptome and Metabolome Variation in Important Fruit Traits

Here, we report RNAseq data from a Solanum lycopersicum-pennellii introgression population (IL) and a backcross introgression population (BIL), to establish the genetic basis of gene expression and chemical variation accompanying transfer of wild species-associated fruit traits. Transcriptome analysis of these lines resulted in the identification of genomic loci significantly linked with levels of hundreds of transcripts and metabolites. These associations occurred in functionally coherent hotspots that represent coordinated perturbation of metabolic pathways and ripening-related processes. We demonstrated the efficacy of our approach by discovering yet undisclosed components of the renowned Solanum alkaloids pathway and moreover, showing that fruit fungal resistance is associated with changes in the ripening regulatory network. 523 lines of IL and BIL population with introgression mapping provided in associated manuscript (Szymanski et al. 2020). Samples were collected in field conditions and skin tissue in a breaker stage of fruit ripening (~44 days post-anthesis) has been manually separated for further analysis.