Transcript and metabolite analysis in Trincadeira cultivar reveals novel information regarding the dynamics of grape ripening

Abstract

BackgroundGrapes (Vitis vinifera L.) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to the onset of ripening of nonclimacteric fruits is not fully understood which is further complicated in grapes due to seasonal and cultivar specific variation. The Portuguese wine variety Trincadeira gives rise to high quality wines but presents extremely irregular berry ripening among seasons probably due to high susceptibility to abiotic and biotic stresses.ResultsRipening of Trincadeira grapes was studied taking into account the transcriptional and metabolic profilings complemented with biochemical data. The mRNA expression profiles of four time points spanning developmental stages from pea size green berries, through véraison and mature berries (EL 32, EL 34, EL 35 and EL 36) and in two seasons (2007 and 2008) were compared using the Affymetrix GrapeGen® genome array containing 23096 probesets corresponding to 18726 unique sequences. Over 50% of these probesets were significantly differentially expressed (1.5 fold) between at least two developmental stages. A common set of modulated transcripts corresponding to 5877 unigenes indicates the activation of common pathways between years despite the irregular development of Trincadeira grapes. These unigenes were assigned to the functional categories of "metabolism", "development", "cellular process", "diverse/miscellanenous functions", "regulation overview", "response to stimulus, stress", "signaling", "transport overview", "xenoprotein, transposable element" and "unknown". Quantitative RT-PCR validated microarrays results being carried out for eight selected genes and five developmental stages (EL 32, EL 34, EL 35, EL 36 and EL 38). Metabolic profiling using 1H NMR spectroscopy associated to two-dimensional techniques showed the importance of metabolites related to oxidative stress response, amino acid and sugar metabolism as well as secondary metabolism. These results were integrated with transcriptional profiling obtained using genome array to provide new information regarding the network of events leading to grape ripening.ConclusionsAltogether the data obtained provides the most extensive survey obtained so far for gene expression and metabolites accumulated during grape ripening. Moreover, it highlighted information obtained in a poorly known variety exhibiting particular characteristics that may be cultivar specific or dependent upon climatic conditions. Several genes were identified that had not been previously reported in the context of grape ripening namely genes involved in carbohydrate and amino acid metabolisms as well as in growth regulators; metabolism, epigenetic factors and signaling pathways. Some of these genes were annotated as receptors, transcription factors, and kinases and constitute good candidates for functional analysis in order to establish a model for ripening control of a non-climacteric fruit.

Developmental and metabolic plasticity of white-skinned grape berries in response to Botrytis cinerea during noble rot

“…Although the grapevine genome contains at least 22 putative UF3GTs (Grimplet et al, 2009), only VvUF3GT (VIT_16s0039g02230) has been widely studied. Even though this UF3GT was not significantly up-regulated, the expression of six putative UF3GTs increased in response to noble rot (Table I) and during ripening in redskinned berries (Ali et al, 2011;Palumbo et al, 2014). The up-regulation of these genes resulted in enhanced UF3GT activity in the noble-rotted berries across all three growing seasons.…”

“…Candidate master regulators of véraison were also up-regulated by noble rot, such as VvNAC33 (VIT_19s0027g00230), VvNAC60 (VIT_08s0007g07670), a zinc-finger transcription factor (VIT_08s0040g01950), and a MYB transcription factor (VIT_07s0005g02730; Palumbo et al, 2014). Noble rot triggered the expression of 55 AP2/ERFs, most of which have been associated with the ripening of healthy red-skinned berries from cv Corvina, cv Cabernet Sauvignon, and cv Trincadeira (Deluc et al, 2007;Licausi et al, 2010;Fortes et al, 2011;Cramer et al, 2014). The expression of other potential berry-ripening and plant senescence regulators, such as the putative ortholog of SlNAC-NONRIPENING (VIT_19s0014g03300) and all WRKY53 genes annotated in the grape genome (VIT_02s0025g01280, VIT_15s0046g01140, and VIT_16s0050g02510), was also induced in noble-rotted berries.…”

The Evolution of Total Phenolic Compounds and Antioxidant Activities during Ripening of Grapes (Vitis vinifera L., cv. Tempranillo) Grown in Semiarid Region: Effects of Cluster Thinning and Water Deficit

“…One response to stressors during ripening is an increase in the amount of phenolic compounds. These include flavonoids and phenylpropanoid glycosides [31,33]. The latter form part of the cell’s antioxidant system [34], and, together with flavonoids, participate in protecting against oxidative stress by eliminating ROS [32].…”

Integrative Comparative Analyses of Transcript and Metabolite Profiles from Pepper and Tomato Ripening and Development Stages Uncovers Species-Specific Patterns of Network Regulatory Behavior

“…Integration of genomics, gene expression, and chemical composition data during fruit development and ripening can give important insights into gene-regulatory and metabolic events associated with these processes. In recent years, a number of studies on fruits have begun to integrate these extensive data sets, and while a number of them focused on the nonclimacteric grape and strawberry systems, most used the climacteric model of tomato fruit Deluc et al, 2007;Grimplet et al, 2007;Enfissi et al, 2010;Zamboni et al, 2010;Fortes et al, 2011;Osorio et al, 2011).…”