Integration of omics and system biology approaches to study grapevine ( Vitis vinifera L.) response to salt stress: a perspective for functional genomics - A review

摘要

The ability of plants to modify their behavior appropriately in response to salt stress is a major factor in their adaptation to this specific constraint. To date, environmental constraints, including salinity, become more and more unfavorable especially for glycophytes such as grapevines. Salt tolerance is a complex physiological and multigenic trait. Studying the functional networks of transcriptome, proteome and metabolome of grapevine plants subjected to salinity may help to identify candidate genes associated with salt tolerance mechanisms. Thus, the integration of omics tools (i.e., genomics, proteomics and metabolomics) with physiological approaches allows better understanding of the grapevine plant response and developing efficient markerassisted selection strategies in order to generate salt stress resistant grapevine varieties. In this review, research progress in grapevine responses to salt stress is discussed, highlighting the importance of the system biology approach for identifying molecular regulatory networks leading to a better adaptation ability of grapevine to salt stress. IntroductionPlants are permanently subjected to various types of stresses: osmotic, ionic, water and salt (Munns et al., 2006; Chadli and Belkhodja, 2007). Salinity affects about 10% of the land in the world (Cheong and Yun, 2007). The salinization registered in the arid and semi-arid ecosystems results from high soil water evaporation (Munns et al., 2006), irregular and insufficient rainfall (Mezni et al., 2002), as well as the use of poor quality water. Consequently, crop production with an appreciable yield becomes a challenge under these conditions. Therefore, a global understanding of plant mechanisms involved in salt stress adaptation is required. Plant response to salt stress occurs at various levels: molecular, cellular and physiological (Yamaguchi-Shinozaki et al., 2002). Tolerance to abiotic stresses is a complex feature influenced by the coordinated and differential expression of a group of genes (Chen et al., 2002). In general, several modifications are expected to be activated as a response to abiotic stresses (Jain et al., 2001). Recently, progress has been made in the functional genomics of grapevine following the whole genome sequencing and assembling of Vitis vinifera PN40024 reference genome (Jaillon et al., 2007). Global analyses have become possible with the development of high throughput genomic technologies which facilitated the identification of putative gene function. In parallel, methods have been developed for quantitative data acquisition: microarrays are used to quantitatively assess the transcriptome (Schena et al., 1995). However, the recent advent of high throughput-based sequencing technologies has revolutionized the analysis of transcriptomes (Morozova and Marra, 2008). In fact, RNA sequencing (RNA-Seq) involves direct sequencing of complementary DNAs (cDNAs) followed by mapping of the sequencing reads to the reference genome. It allows for the precise quantification of exon expression, generating absolute rather than relative gene expression measurements, providing greater insight and accuracy than microarrays (Cloonan et al., 2008; Mortazavi et al., 2008; Wang et al., 2009). Furthermore, it can detect and measure rare transcripts with frequencies as low as 1 to 10 RNA molecules per cell (Mortazavi et al., 2008). In this context, Next-Gen sequencing technologies have emerged, such as 454 (Margulies et al., 2005) or Illumina (Bennett, 2004) technologies. For example, the Illumina RNA-Seq method was successfully used by Zenoni et al. (2010) to analyze the global grapevine transcriptome during berry development. In proteomics, two-dimensional gels have routinely been used for proteome studies (O’Farrell, 1975). Recently, gel-free technologies have emerged, such as ICAT (Gygi et al., 1999) or iTRAQ (Ross et al., 2004). Metabolome studies are performed with a variety of tools such as gas chromatography or high performance liquid chromatography for the separation of the metabolites and mass spectrometry and nuclear magnetic resonance for the identification and quantification of the metabolites (Fiehn, 2002). This progress opened up a new investigation field, omics, from which many transcriptomic (Tattersall et al., 2007; Daldoul et al., 2010), proteomic (Vincent et al., 2007; Jellouli et al., 2008; Grimplet et al., 2009a; Cramer, 2010; Cramer et al., 2013), interactomic (?arná et al., 2012), metabolomic (Cramer et al., 2007; Deluc et al., 2009; Hochberg et al., 2013) and candidate gene approaches (Hanana et al., 2007; Hanana et al., 2008) were developed. The present review underlines the integration of the different omics tools with physiological and eco-physiological approaches and their subsequent incorporation into functional networks in order to better understand the mechanisms involved in grapevine salt tolerance.Physiological responses of grapevine to salt stressGrapevine (Vitis vinife