A New GeneChip for Grapevine Transcriptomic Analyses

LIJAVETZKY, D; FRANCISCO, R; LUND, ST; MARTINEZ-ZAPATER, JM

Adelaide

Simposio; Eighth International Symposium on Grapevine Physiology and Biotechnology; 2008

Australian Society of Viticulture and Oenology

Background and AimsDue to its economic importance, grape berry development has been a major target for expression profiling analyses during the last years. Crucial information has been generated through several studies regarding tissue specific expression in (Grimplet et al., 2007) and expression profiles either around veraison (Pilati et al., 2007) or during several stages of berry development (Deluc et al., 2007). All these works were performed with the commercial 14K Affymetrix GeneChip and obtained sorted Unigene catalogues according to the classically studied biochemical events taking place during berry development. In this work we develop a new and more complete GeneChip together with additional tools designed to facilitate functional analysis of the hybridization results. These tools have been used to follow berry development and ripening in a more comprehensive approach.Methods and ResultsA 23K custom Affymetrix GeneChip was developed as a result of the Spanish-Canadian GRAPEGEN project. All probe-sets were manually re-annotated and classified in order to perform functional analyses with state-of-the-art tools like MapMan (Thimm et al., 2004) or Babelomics (Al-Shahrour et al., 2008). Additionally, a web-based application was developed to display all the information associated with a probe-set list (including external dbase links). This GeneChip was used to analyze ten different berry development stages of the cultivar Muscat Hamburg during two seasons and dissecting skin and flesh from the pre-veraison stage. Analyses were sub-divided in green stages, veraison (skin/flesh) and ripening (skin/flesh). Differentially expressed genes were clustered using k-means and significant functional groups were identified within each cluster using Babelomics and graphically represented by means of MapMan.ConclusionsThe results of these experiments validate previous indications regarding the involvement of functional groups like stress responses, photosynthesis, cell wall metabolism and plant hormones metabolism and response during berry development and ripening. Furthermore, there are additional hints on the start of oxidative stress at the green stages, the down-regulation of the phenylpropanoid metabolism and auxins before ripening or the involvement of ethylene during ripening,. These phenomena were examined both in skin and flesh.Significance of StudyWe present and validate a new custom made Affymetrix GeneChip (representing a 70% probe-set increment respect to the commercial one) together with a suite of functional analysis tools. These tools allowed us to perform an unbiased functional classification of the genes involved in grape berry development, veraison and ripening.