RNA-Seq Analysis Of Berry Development In Vitis vinifera

Grape berries function as a sophisticated biochemical factory that synthesizes flavour and aroma compounds. Many scientific advances have been achieved in understanding physiological, biochemical, and molecular aspects of grape berry maturation, but little is known about the regulatory circuits and the functional complexity of transcriptional changes underlying the biochemical and physical changes occurring during berry development. Deep sequencing has rapidly gained popularity for transcriptome analysis because of its ability to generate digital and quantitative information on annotated genes, and to detect transcripts and mRNA isoforms. We have carried out a global transcriptional analysis of berry development in Vitis vinifera cv. Corvina using high-throughput sequencing technology. We generated more than 59 million sequence reads, 36-44 bp in length, from three developmental stages: post-setting, véraison and ripening. The sequence reads were aligned onto the 8.4-fold draft sequence of the Pinot Noir 40024 genome and then analyzed to measure gene expression levels, to identify putative new genes and to detect alternative splicing events and expressed SNPs. Reads were then mapped to exons, introns or intergenic regions, hence identifying new exons or new genes. Then, we have adapted modules of the ERANGE program for digital gene expression analysis, detection of alternative splicing (annotated or new) and SNPs discovery. Expression values, calculated as reads per kilobase of exon model per million mapped reads (RPKM) were then used to monitor changes in gene expression. We are currently evaluating several statistical approaches to identify significantly modulated genes.