In silico characterization of new molecular actors involved in the tolerance to chilling injury in fruits

AIMARO N.; GISMONDI M.; MULLER G.; DRINCOVICH M.F.; BUSTAMANTE C.

Rosario

Congreso; LIX Reunión de la Sociedad Argentina de Investigación en Bioquímica y Biología Molecular (SAIB); 2023

Cold-induced damage (CI, chilling injury) is a problem arising from fruit refrigeration (CS, cold storage), significantly affecting its commercialization. Multiple strategies aimed atgenerating CI tolerance have proven to be efficient; one of them is heat treatment (HT).The molecular basis of CI, CS, HT, and other post-harvest conditions have beeninvestigated at the molecular level through several experimental designs and omicsapproaches, yielding a wide array of molecules as potential protectors against CI. However, thelack of detailed knowledge regarding fruit genomes, their molecular products, and theirfunctions suggests that further studies are needed to select genes of importance and varieties with desirable traits. The catalogue constructed in this work was compiled utilizing a wide variety of tools and available data in Solanum lycopersicum, including the evaluation of genomic data, transcriptional expression or transcriptomic data (including RNAseq and sequence-specific signal data), functional annotations, exon-intron architecture, gene ontology, physical interactions, as well as the presence or absence of cold-associated promoter regions. This compilation serves as a solid starting point for selecting genes potentially involved in the protection against CI in tomato fruit for further investigation, aiming to cover all possibilities, thereby enhancing the likelihood of getting interesting results. GO term searches yielded surprising results, demonstrating the lack of gene annotation related to this agronomically relevant fruit. Additionally, there is less annotation of low-temperaturebiological processes in this species compared to the model organism Arabidopsis thaliana.Conversely, the dataset and certain criteria related to future experiments allowed us toexplore different approaches and apply effective filters that aid in the desired selection,prioritizing accurate ortholog assignment, simplicity in UTR, exon and intron annotations, andvalidation with RNAseq data, few or only one transcriptional variant, the A. thaliana-S.lycopersicum conservation of cold-induced transcriptional expression, among others. Basedon our catalogue, we selected three genes for further experiments, REIL 1 and REIL2, both of them encoding zinc finger proteins, and HD2C, which encodes a histone deacetylase. This selection encourages the implementation of wet lab experiments to test the conservation of the response of these genes to cold stimulus in our system of interest, the tomato fruit. Our approach has not only yielded genes potentially involved in the tolerance to CI, but alsosystematically ordered strategies for other purposes.