Isogene specific oligo arrays reveal multifaceted changes in gene expression during grape berry (Vitis vinifera L.) development.

The transition from a green, hard, and acidic pericarp to a sweet, soft, coloured, and sugar-rich ripe fruit occurs in many unrelated fruit species. High throughput identification of differentially expressed genes in grape berry has been achieved by the use of 50-mers oligoarrays bearing a set of 3,200 Unigenes from Vitis vinifera to compare berry transcriptome at nine developmental stages. Analysis of transcript profiles revealed that most activations were triggered simultaneously with softening, occurring within only 24 h for an individual berry, just before any change in colouration or water, sugar, and acid content can be detected. Although most dramatically induced genes belong to unknown functional categories, numerous changes occur in the expression of isogenes involved in primary and secondary metabolism during ripening. Focusing on isogenes potentially significant in development regulation (hormonal control of transcription factor) revealed a possible role for several hormones (cytokinin, gibberellin, or jasmonic acid). Transcription factor analysis revealed the induction of RAP2 and WRKY genes at veraison, suggesting increasing biotic and abiotic stress conditions during ripening. This observation was strengthened by an increased expression of multiple transcripts involved in sugar metabolism and also described as induced in other plant organs during stress conditions. This approach permitted the identification of new isogenes as possible control points: a glutathione S-transferase exhibits the same expression profile as anthocyanin accumulation and a new putative sugar transporter is induced in parallel with sugar import. Berries, collected from nine development stages (green to overripe) of the cv Shiraz (Vitis vinifera) and from two development stages (half-green and half-ripe) of the cvs Chardonnay and Cabernet Sauvignon, were used to detect differentially expressed genes; it was achieved by micro-array analysis developing 50-mer oligo arrays representing a set of 3,175 Unigenes from EST 3' sequencing of seven different libraries. Analysis of transcript profiles revealed a simultaneous activation of hundreds of genes at the berry softening, occurring within a shorter period of 48 h, and just before any change in color, water, sugar, and acid content. Although most induced genes belong to unknown functions, numerous changes occur in the expression of isogenes involved in primary and secondary ripening metabolism, in biotic and abiotic stress conditions and in hormonal control.