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

Abstract

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 véraison, 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.

Proteins involved in biotic and abiotic stress responses as the most significant biomarkers in the ripening of Pinot Noir skins

“…In the past, it was proposed that glycolysis was inhibited after véraison (Famiani et al 2000). Then, through some microarray analyses, it was reported that some glycolytic enzymes were up regulated during ripening (da Silva et al 2005;Terrier et al 2005). In the present work, we observed that among the characterized spots, there are some enzymes relative to glycolysis and Krebs cycle, indicating that also in Pinot skins, primary metabolism undergoes some modulations during ripening.…”

“…As reported in many papers, grape ripening affects the expression of many enzymes involved in metabolic pathways of the primary metabolism such as those related to glycolysis/gluconeogenesis, pentose-phosphate pathway and Krebs cycle (Giribaldi et al 2007;Negri et al 2008a;Robinson et al 1997;Pilati et al 2007;Ruffner and Hawker 1977;Famiani et al 2000;da Silva et al 2005;Terrier et al 2005). In the past, it was proposed that glycolysis was inhibited after véraison (Famiani et al 2000).…”

“…The other two groups, RS35 and RS37, appear instead quite overlapped showing that the main differences in 2-DE patterns regarded the last ripening period. This result was quite surprising because some oligo/ microarray analyses (Waters et al 2005;Terrier et al 2005) indicated that most changes in mRNA profiles characterized the first ripening phases in cv. Shiraz berries immediately after véraison while no significant variations were observed towards maturity.…”

Ecophysiological, Genetic, and Molecular Causes of Variation in Grape Berry Weight and Composition: A Review

“…The genomic information has significantly increased in the last 10 years, from expressed sequence tag (EST) sequencing programs (Iandolino et al 2004) to the release of the Pinot noir genome sequence and annotation (Jaillon et al 2007). Several generations of microarrays have been created and used, from the first 3,500 unigene Qiagen/Operon chips (Terrier et al 2005) to the newly developed genomewide slides bearing up to 30,000 unigenes (Bellin et al 2009). Most recently, the grapevine research community gained access to massive parallel signature sequencing-based transcriptome analysis, the so-called deep RNA sequencing approach (Zenoni et al 2010).…”

Generation and Analysis of ESTs in <i>V. amurensis</i> Grapevine Pericarp at Veraison

“…ADH plays a central role in stress-response and could be a fruit-ripening related marker on grapevine. The up-regulation of some ADH genes for fruit-ripening implies that ethanol fermentation is a normal development response in grapes (Sarni-Manchado et al, 1997;Sweetman et al, 2009;Terrier et al, 2005). And Tesniere et al (2009) found that over-expression or down-regulation of VvADH resulted in unexpected responses at the primary and secondary metabolism levels in leaves and berries.…”