GENETIC PATHWAYS UNDERLYING THE TRAITS OF SHELF LIFE AND FLOWERING TIME IN LEAFY CROPS AND PLANT MODEL SPECIES

Vegetable salad shelf life largely depends on leaf senescence and abiotic and biotic stress responses, both under control of the phytohormone cytokinin (CK). Flowering time (FT) diversity has adaptive value in natural populations and plays a major role in leafy crops production. Our studies aim at identifying molecular markers and hub/master gene regulators of these key agronomic traits in the Compositae (Asteraceae) family. This will produce novel genetic tools and strategies to improve leafy crops bel onging to this family. A de novo assembled Cichorium endivia transcriptome obtained in our lab was used for deep annotation and gene prediction. With the aim to dissect the genetic pathways of cytokinins and flowering time in this species, manual curation of the database was carried out to obtain high quality functional annotations based on knowledge acquired in plant model species. CK and FT genetic pathways were subdivided into functional modules for systematic bioinformatic analyses. Correlation analyse s of RNAseq and hormone metabolites data, obtained from edible leaves of four commercial cultivars, identified key genes involved in cytokinin nucleotide - nucleoside interconversion and O - glycosylation, and their relationships with other CK metabolism genes , CK transport and components of the signal transduction pathway. Cis - zeatin (cZ) was identified as the most abundant form of CK in C. endivia leaves, and functional gene modules connected to either cZ or trans - zeatin (tZ) pathways were characterized. Analysis of CK and flowering time gene RNAseq expression profiles over two production cycles allowed the identification of known and novel co - expression networks, giving new insights into CK connection with plant innate immune response and novel information on flowering time control in endive and escarole. A connection of both pathways with the T hree A mino acid L oop E xtension (TALE) superclass of homeobox transcription factors (TF) was revealed. Genome - wide in silico analyses of TALE binding sites in Arabidops is allowed us to predict that several TFs involved in the control of flowering time may be direct targets of TALEs. The 1135 sequenced genomes of A. thaliana natural accessions, available in the "1001 Genomes Project", were screened for SNPs/mutations in the core consensus region of the identified TALE binding sites, which may result in loss of transcriptional regulation. The screen identified several putative lost and some newly evolved TALE binding sites, some of them being excellent candidates for adapt ive mutations and diversity in the flowering time pathway.