SOLGENSYS · A Natural Variation-informed Systems Genetics Framework for Tomato Multi-Stress Tolerance

Climate change poses escalating threats to agriculture, with drought and salinity causing substantial yield losses in tomato, Europe’s most economically significant vegetable crop. SOLGENSYS addresses this urgent challenge by deploying an integrated, multi-disciplinary approach to identify, validate, and translate genetic and regulatory determinants of tomato tolerance to drought and salinity. Leveraging natural genetic diversity in a panel of tomato accessions and backcross lines, the project will combine genome-wide and transcriptome-wide association studies, and expression quantitative trait loci mapping to resolve the genetic and regulatory architecture of red-ripe fruit traits under water-limited and saline conditions. Multi-omics profiling, including ionomics, targeted metabolomics for lipids and vitamins, and transcriptomics, will be conducted on red-ripe fruit to capture trait expression at the critical sink stage. To probe regulatory plasticity, a seaweed-derived biostimulant will be applied at flowering and fruit set. Transcriptomic comparisons between treated and untreated genotypes will elucidate priming-induced reprogramming of hormonal networks and uncover stress mitigation mechanisms. The resulting multi-omics datasets will be integrated using machine learning frameworks. Top candidate genes and regulatory elements will undergo functional validation using CRISPR-based prime editing to introduce precise base edits or cis-regulatory motifs. Edited lines will be phenotyped for fruit yield, ion balance, and nutritional content. High-performing lines will be introgressed into elite cultivars through pre-breeding, delivering climate-tolerant germplasm aligned with EU Green Deal goals for sustainable, resource-efficient agriculture. SOLGENSYS exemplifies an end-to-end innovation pipeline, spanning from natural variation to gene discovery, genome editing, and breeding, and provides a scalable blueprint for enhancing crop tolerance under multiple stresses.