GSE116238
Clone-specific transcript profiling of 'Nebbiolo' grape berries unveils environmental responses mediated by sugar and secondary metabolite signalling
Goal: In the last years, many research efforts were addressed to uncover how grapevine cultivars respond to environment, nevertheless little is known on the molecular processes underlying the interplay between clones (vegetatively propagated lines of selected mother plants) of the same cultivar and environment. The goal of this study was to explore the whole complexity of the clone x environment (C x E) interaction through the identification of molecular changes controlled by clone, vineyard, phenological phase or a combination of them. Methods: We analyzed the transcriptome of berries collected over the ripening period from three Vitis vinifera cv Nebbiolo clones (CVT 71, CVT 423, CVT 185) grown in different vineyards, in two vegetative seasons. A multidisciplinary approach was adopted by implementing RNA-seq data with: i) expression analysis of candidate genes; ii) quantification of abscisic acid, flavonoids and stilbenoids; iii) agronomical parameters; and iv) climatic data. Results: Transcripts involved in sugar signalling, anthocyanin biosynthesis and transport were differently modulated among diverse clones, accordingly to berry agronomical features. Conversely, genes linked to the production of secondary metabolites enhancing defence responses, such as stilbene synthase genes, were significantly affected by vineyard location, consistently with stilbenoid accumulation patterns. Conclusion: The collected results attest that clone-specific metabolic responses do play a key role in shaping agronomic performances of a grape variety in different environments, thus providing valuable indications for orienting viticultural practices. Overall design: mRNA profiles of berries collected from 3 clones (CVT 71, CVT 423, CVT 185) of Vitis vinifera cv Nebbiolo in 3 vineyards (V1, V2, V3) at 3 developmental stages (E-L31, E-L35, E-L38) were generated by Illumina deep sequencing. Three biological replicates were processed for each thesis.