Approfondimenti genetico-molecolari sulle risposte del pomodoro (Solanum lycopersicum L.) a stress ambientali

Tomato (Solanum lycopersicum L.) is one of the most important vegetable crops from the Solanaceae family extensively used across the globe for edible purposes. While with the rising population, agricultural demands have increased, recent climate changes have posed a huge threat to agricultural practices and food security. Major challenges include abiotic stress induced by rapid climate changes and biotic stress by a vast array of fast-evolving pathogens causing massive economic losses. Crop improvement using breeding and advancements in genomics and gene editing technologies is one of the most promising ways to overcome these challenges. Toward this goal, this thesis is aimed to explore the genetic aspects of important agronomic traits in tomato. The focus of the three thesis chapters was mainly on understanding genomic and transcriptomic characteristics and changes happening between varieties with contrasting traits. Further emphasis was given to exploring the molecular pathways, use of vastly available public genomic data and developing resources and understanding in the context of plant breeding. The first chapter was aimed at the genomic characterization of an important pre-breeding line A10 which carries many desirable traits like high anthocyanin content, tolerance to high pH, and resistance to blossom end rot. Genomic data from A10 was used to profile variants and their putative role in traits. Further, to understand the ancestry and introgressions from wild Solanum varieties, publicly available whole genome datasets of cultivars and wild lines were analysed and compared with A10. Results showing a close relationship of A10 with wild lines and characterization of introgressed genomic regions will further serve as a resource for the subsequent chapter exploring the genetic basis of blossom end rot. The second chapter focused on Blossom end rot (BER); a physiological disorder characterized by necrotic lesions at the blossom end of tomato fruit. A10, a pre-breeding line with resistance against BER was studied to understand transcriptomic changes in BER-resistant and susceptible lines under water stress and well-watered conditions. The resistant A10 line to BER showed changes in important Ca2+-related genes and stomatal density-related genes which can play an important role in BER resistance. Finally, the third chapter focused on the Late blight disease caused by the fungal agent Phytophthora infestans infecting tomato fruit and foliage. To understand disease dynamics, transcriptome sequencing was carried out to evaluate the gene expression dynamics of tomato varieties, resistant and susceptible to Phytophthora infection. Next, single nucleotide polymorphisms (SNPs) were studied by integrating the transcriptome dataset with large-scale public genomic data of varieties with known disease phenotypes. Subsequently, a panel of SNP markers correlated with disease resistance were identified and validated on multiple breeding lines with contrasting phenotypes for late blight resistance. The results generated by this study show a correlation with disease resistance across a broad set of plant materials that can be used as markers for molecular screening in tomato breeding.