Identification of tissue-specific, abiotic stress-responsive gene expression patterns in wine grape (Vitis viniferaL.) based on curation and mining of large-scale EST data sets

Abstract

BackgroundAbiotic stresses, such as water deficit and soil salinity, result in changes in physiology, nutrient use, and vegetative growth in vines, and ultimately, yield and flavor in berries of wine grape, Vitis vinifera L. Large-scale expressed sequence tags (ESTs) were generated, curated, and analyzed to identify major genetic determinants responsible for stress-adaptive responses. Although roots serve as the first site of perception and/or injury for many types of abiotic stress, EST sequencing in root tissues of wine grape exposed to abiotic stresses has been extremely limited to date. To overcome this limitation, large-scale EST sequencing was conducted from root tissues exposed to multiple abiotic stresses.ResultsA total of 62,236 expressed sequence tags (ESTs) were generated from leaf, berry, and root tissues from vines subjected to abiotic stresses and compared with 32,286 ESTs sequenced from 20 public cDNA libraries. Curation to correct annotation errors, clustering and assembly of the berry and leaf ESTs with currently available V. vinifera full-length transcripts and ESTs yielded a total of 13,278 unique sequences, with 2302 singletons and 10,976 mapped to V. vinifera gene models. Of these, 739 transcripts were found to have significant differential expression in stressed leaves and berries including 250 genes not described previously as being abiotic stress responsive. In a second analysis of 16,452 ESTs from a normalized root cDNA library derived from roots exposed to multiple, short-term, abiotic stresses, 135 genes with root-enriched expression patterns were identified on the basis of their relative EST abundance in roots relative to other tissues.ConclusionsThe large-scale analysis of relative EST frequency counts among a diverse collection of 23 different cDNA libraries from leaf, berry, and root tissues of wine grape exposed to a variety of abiotic stress conditions revealed distinct, tissue-specific expression patterns, previously unrecognized stress-induced genes, and many novel genes with root-enriched mRNA expression for improving our understanding of root biology and manipulation of rootstock traits in wine grape. mRNA abundance estimates based on EST library-enriched expression patterns showed only modest correlations between microarray and quantitative, real-time reverse transcription-polymerase chain reaction (qRT-PCR) methods highlighting the need for deep-sequencing expression profiling methods.

Transcriptome pathways in leaf and root of grapevine genotypes with contrasting drought tolerance

“…In contrast to other studies (Cramer et al, 2007;Tillett et al, 2011), we did not consider responses to water stress that are common to susceptible and tolerant plants (e.g., genes involved in ABA metabolism or those responsible for ROS production and primary ROS scavenging), but rather focused on genes whose expression is strictly related to the tolerant genotype. From this point of view, the data suggest that M4 drought tolerance could be associated to enhanced scavenging capacity of secondary ROS.…”

“…Drought is associated with many morphological and physiological changes in plants, including reduced expansion of aerial organs (Cramer et al, 2007), lack of root growth (Sharp and Davies, 1979), decrease in transpiration rate and photosynthesis (Chaves et al, 2010), accumulation of osmolytes (Cramer et al, 2007), activation of detoxifying processes. Moreover, it affected the transcriptional regulation of a large number of genes (Cramer et al, 2007;Tillett et al, 2011). Grapevines are well adapted to semi-arid climates such as that of Mediterranean regions and are generally considered as relatively tolerant to water deficit.…”

Genetic diversity, variety identification and gene detection in some Egyptian grape varieties by SSR and SCoT markers

“…The retrotransposons are retrovirusrelated mobile sequences that have the potential to replicate via RNA intermediates and increase the genome size by insertion into new sites. Such elements have been reported in cultivated grapes as a key role in fruit colour variation and abiotic stresses (Cadle-Davidson and Owens 2008;Tillett et al, 2011). TSA is an archive of computationally assembled Primer name (PN), size of marker Band (MBS), total number of markers (TMC) and grand total markers (GT) identifying each variety.…”

Skin Browning and Expression of PPO, STS, and CHS Genes in the Grape Berries of ‘Shine Muscat’

“…In the context of biosynthesis progression, polyphenol oxidase, laccase, and peroxidase play important roles in metabolic pathways such as lignin biosynthesis and phenol compound polymerization (Pezet et al, 2003;Tavares et al, 2013;Zamboni et al, 2010). Recently, molecular bases for the regulation of these biosynthetic pathways have been researched intensively in grapevine (Czemmel et al, 2012;Tillett et al, 2011;Vannozzi et al, 2012). In the berry skin of 'Shine Muscat', similar induction and activation of those biosynthetic pathways could have been replaced by skin browning because increases in the expression levels of VvSTS type B and VvCHS1 were observed along with browning.…”

“…Biotic and abiotic stresses have been demonstrated to be responsible for polyphenol accumulation, such as anthocyanin accumulation (Winkel-Shirley, 2002). The expression levels of genes encoding enzymes involved in these biosynthetic pathways are correlated with the stress suffered (Tillett et al, 2011). Stilbenoids, including resveratrol and its derivatives, are classified as phytoalexins, which can inhibit the growth of fungi infecting the plant body.…”