Zhanwu Dai

Transcriptomic analysis of grape (Vitis vinifera L.) leaves during and after recovery from heat stress

BackgroundGrapes are a major fruit crop around the world. Heat stress can significantly reduce grape yield and quality. Changes at the molecular level in response to heat stress and subsequent recovery are poorly understood. To elucidate the effect of heat stress and subsequent recovery on expression of genes by grape leaves representing the classic heat stress response and thermotolerance mechanisms, transcript abundance of grape (Vitis vinifera L.) leaves was quantified using the Affymetrix Grape Genome oligonucleotide microarray (15,700 transcripts), followed by quantitative Real-Time PCR validation for some transcript profiles.ResultsWe found that about 8% of the total probe sets were responsive to heat stress and/or to subsequent recovery in grape leaves. The heat stress and recovery responses were characterized by different transcriptional changes. The number of heat stress-regulated genes was almost twice the number of recovery-regulated genes. The responsive genes identified in this study belong to a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, transcription factors, signal transduction, and development. We have identified some common genes and heat shock factors (HSFs) that were modulated differentially by heat stress and recovery. Most HSP genes were upregulated by heat stress but were downregulated by the recovery. On the other hand, some specific HSP genes or HSFs were uniquely responsive to heat stress or recovery.ConclusionThe effect of heat stress and recovery on grape appears to be associated with multiple processes and mechanisms including stress-related genes, transcription factors, and metabolism. Heat stress and recovery elicited common up- or downregulated genes as well as unique sets of responsive genes. Moreover, some genes were regulated in opposite directions by heat stress and recovery. The results indicated HSPs, especially small HSPs, antioxidant enzymes (i.e., ascorbate peroxidase), and galactinol synthase may be important to thermotolerance of grape. HSF30 may be a key regulator for heat stress and recovery, while HSF7 and HSF1 may only be specific to recovery. The identification of heat stress or recovery responsive genes in this study provides novel insights into the molecular basis for heat tolerance in grape leaves.

Anthocyanin biosynthesis is differentially regulated by light in the skin and flesh of white-fleshed and teinturier grape berries

AbstractMain conclusionLight exclusion reduces the concentration and modifies the composition of grape anthocyanins, by altering the expression of genes involved in anthocyanin biosynthesis and transport, in a cultivar- and tissue-specific manner. Unlike most grapes, teinturier grapes accumulate anthocyanins both in skin and flesh. However, the concentration and composition of anthocyanins in both tissues differ, providing a valuable system to study tissue-specific regulation of anthocyanin synthesis. Furthermore, little is known about the mechanisms controlling the sensitivity of anthocyanin accumulation to light. Here, light was excluded from Gamay (white-fleshed) and Gamay Fréaux (teinturier mutant) berries throughout berry development. Under light-exposed conditions, the skin of Gamay Fréaux accumulated the highest level of anthocyanins, followed by the skin of Gamay, while the pulp of Gamay Fréaux had much lower anthocyanins than the skins. Network analysis revealed the same order on the number of significant correlations among metabolites and transcripts in the three colored tissues, indicating a higher connectivity that reflects a higher efficiency of the anthocyanin pathway. Compared to light conditions, light exclusion reduced the total amount of anthocyanins, most severely in the skin of Gamay and to a lesser extent in the flesh and skin of Gamay Fréaux. Coordinated decrease in the transcript abundance of structural, regulatory and transporter genes by light exclusion correlated with the reduced anthocyanin concentration in a cultivar- and tissue-specific manner. Moreover, light exclusion increased the ratio of dihydroxylated to trihydroxylated anthocyanins, in parallel with F3′H and F3′5′H transcript amounts. Sugars and ABA only play a limited role in the control of anthocyanin synthesis in the berries, in contrast with what has been described in cell suspensions. This study provides novel insights into the regulation of anthocyanin in wild type and teinturier cultivars.

A novel system for evaluating drought–cold tolerance of grapevines using chlorophyll fluorescence

BackgroundGrape production in continental climatic regions suffers from the combination of drought and cold stresses during winter. Developing a reliable system to simulate combined drought–cold stress and to determine physiological responses and regulatory mechanisms is important. Evaluating tolerance to combined stress at germplasm level is crucial to select parents for breeding grapevines.ResultsIn the present study, two species, namely, Vitis amurensis and V. vinifera cv. ‘Muscat Hamburg’, were used to develop a reliable system for evaluating their tolerance to drought–cold stress. This system used tissue −cultured grapevine plants, 6% PEG solution, and gradient cooling mode to simulate drought–cold stress. V. amurensis had a significantly lower LT50 value (the temperature of 50% electrolyte leakage) than ‘Muscat Hamburg’ during simulated drought–cold stress. Thus, the former had higher tolerance than the latter to drought–cold stress based on electrolyte leakage (EL) measurements. Moreover, the chlorophyll fluorescence responses of V. amurensis and ‘Muscat Hamburg’ were also analyzed under drought–cold stress. The maximum photochemical quantum yield of PS II (Fv/Fm) exhibited a significant linear correlationship with EL. The relationship of EL with Fv/Fm in the other four genotypes of grapevines under drought–cold stress was also detected.ConclusionsA novel LT50 estimation model was established, and the LT50 values can be well calculated based on Fv/Fm in replacement of EL measurement. The Fv/Fm–based model exhibits good reliability for evaluating the tolerance of different grapevine genotypes to drought–cold stress.

Differential responses of sugar, organic acids and anthocyanins to source-sink modulation in Cabernet Sauvignon and Sangiovese grapevines

Grape berry composition mainly consists of primary and secondary metabolites. Both are sensitive to environment and viticultural management. As a consequence, climate change can affect berry composition and modify wine quality and typicity. Leaf removal techniques can impact berry composition by modulating the source-to-sink balance and, in turn, may mitigate some undesired effects due to climate change. The present study investigated the balance between technological maturity parameters such as sugars and organic acids, and phenolic maturity parameters such as anthocyanins in response to source-sink modulation. Sugar, organic acid, and anthocyanin profiles were compared under two contrasting carbon supply levels in berries of cv. Cabernet Sauvignon and Sangiovese collected at 9 and 14 developmental stages respectively. In addition, whole-canopy net carbon exchange rate was monitored for Sangiovese vines and a mathematic model was used to calculate the balance between carbon fixation and berry sugar accumulation. Carbon limitation affected neither berry size nor the concentration of organic acids at harvest. However, it significantly reduced the accumulation of sugars and total anthocyanins in both cultivars. Most interestingly, carbon limitation decreased total anthocyanin concentration by 84.3% as compared to the non source-limited control, whereas it decreased sugar concentration only by 27.1%. This suggests that carbon limitation led to a strong imbalance between sugars and anthocyanins. Moreover, carbon limitation affected anthocyanin profiles in a cultivar dependent manner. Mathematical analysis of carbon-balance indicated that berries used a higher proportion of fixed carbon for sugar accumulation under carbon limitation (76.9%) than under carbon sufficiency (48%). Thus, under carbon limitation, the grape berry can manage the metabolic fate of carbon in such a way that sugar accumulation is maintained at the expense of secondary metabolites.

Sensitivity of Grapevine Phenology to Water Availability, Temperature and CO2 Concentration

In recent decades, mean global temperatures have increased in parallel with a sharp rise in atmospheric carbon dioxide (CO2) levels, with apparent implications for precipitation patterns. The aim of the present work is to assess the sensitivity of different phenological stages of grapevine to temperature and to study the influence of other factors related to climate change (water availability and CO2 concentration) on this relationship. Grapevine phenological records from 9 plantings between 42.75°N and 46.03°N consisting of dates for budburst, flowering and fruit maturity were used. In addition, we used phenological data collected from two years of experiments with grapevine fruit-bearing cuttings with two grapevine varieties under two levels of water availability, two temperature regimes and two levels of CO2. Dormancy breaking and flowering were strongly dependent on spring temperature, while neither variation in temperature during the chilling period nor precipitation significantly affected budburst date. The time needed to reach fruit maturity diminished with increasing temperature and decreasing precipitation. Experiments under semi-controlled conditions revealed great sensitivity of berry development to both temperature and CO2. Water availability had significant interactions with both temperature and CO2; however, in general, water deficit delayed maturity when combined with other factors. Sensitivities to temperature and CO2 varied widely, but higher sensitivities appeared in the coolest year, particularly for the late ripening variety, ‘White Tempranillo’. The knowledge gained in whole plant physiology and multi stress approaches is crucial to predict the effects of climate change and to design mitigation and adaptation strategies allowing viticulture to cope with climate change.

Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

Epigenetic variations are involved in the control of plant developmental processes and participate in shaping phenotypic plasticity to the environment. Intense breeding has eroded genetic diversity, and epigenetic diversity now emerge as a new source of phenotypic variations to improve adaptation to changing environments and ensure the yield and quality of crops. Here, we review how the characterization of the stability and heritability of epigenetic variations is required to drive breeding strategies, which can be assisted by process-based models. We propose future directions to hasten the elucidation of complex epigenetic regulatory networks that should help crop modelers to take epigenetic modifications into account and assist breeding strategies for specific agronomical traits.

Regulation of Anthocyanin Biosynthesis in Tissues of a Teinturier Grape Cultivar under Sunlight Exclusion

Yan-73 (Vitis vinifera) is a teinturier grape cultivar, which accumulates anthocyanins in skin, pulp, pedicels, and rachis. The effects of sunlight on anthocyanin biosynthesis and regulation in various tissues of this teinturier cultivar were investigated. Light transmission measurements showed that covering with opaque boxes substantially reduced light intensity around clusters; ≤0.25% of incident light reached the berry skin and <0.05% reached the pulp. The pulp naturally experiences increasing sunlight exclusion by skin during ripening. Sunlight exclusion reduced and delayed anthocyanin biosynthesis in skin and pulp during berry development, while both tissues nevertheless accumulated enough anthocyanins to turn dark red. No strong reduction of anthocyanin concentration was observed in pedicels or rachis. Sunlight exclusion decreased transcript abundance of VvUFGT, VvMybA1, VvMybA2, and VvMyc1 in both skin and pulp and also decreased transcript abundance of VvMycA1 in pulp. Sunlight exclusion differently influenced the anthocyanin components: it decreased the relative proportion of 3′,4′,5′-hydroxylated anthocyanins and increased that of 3′,4′-hydroxylated anthocyanins in berry skin and pulp, which corresponded to the change in the ratio of VvF3′H to VvF3′5′H. These results allow for insight on anthocyanin biosynthesis in various grape tissues in absence of sunlight.

Transcriptomic analysis of grape (Vitis vinifera L.) Leaves after exposure to ultraviolet C irradiation.

Background Only a small amount of solar ultraviolet C (UV-C) radiation reaches the Earths surface. This is because of the filtering effects of the stratospheric ozone layer. Artificial UV-C irradiation is used on leaves and fruits to stimulate different biological processes in plants. Grapes are a major fruit crop and are grown in many parts of the world. Research has shown that UV-C irradiation induces the biosynthesis of phenols in grape leaves. However, few studies have analyzed the overall changes in gene expression in grape leaves exposed to UV-C. Methodology/Principal Findings In the present study, transcriptional responses were investigated in grape (Vitis vinifera L.) leaves before and after exposure to UV-C irradiation (6 W·m−2 for 10 min) using an Affymetrix Vitis vinifera (Grape) Genome Array (15,700 transcripts). A total of 5274 differentially expressed probe sets were defined, including 3564 (67.58%) probe sets that appeared at both 6 and 12 h after exposure to UV-C irradiation but not before exposure. A total of 468 (8.87%) probe sets and 1242 (23.55%) probe sets were specifically expressed at these times. The probe sets were associated with a large number of important traits and biological pathways, including cell rescue (i.e., antioxidant enzymes), protein fate (i.e., HSPs), primary and secondary metabolism, and transcription factors. Interestingly, some of the genes involved in secondary metabolism, such as stilbene synthase, responded intensely to irradiation. Some of the MYB and WRKY family transcription factors, such as VvMYBPA1, VvMYB14, VvMYB4, WRKY57-like, and WRKY 65, were also strongly up-regulated (about 100 to 200 fold). Conclusions UV-C irridiation has an important role in some biology processes, especially cell rescue, protein fate, secondary metabolism, and regulation of transcription.These results opened up ways of exploring the molecular mechanisms underlying the effects of UV-C irradiation on grape leaves and have great implications for further studies.

Inter-Species Comparative Analysis of Components of Soluble Sugar Concentration in Fleshy Fruits.

The soluble sugar concentration of fleshy fruit is a key determinant of fleshy fruit quality. It affects directly the sweetness of fresh fruits and indirectly the properties of processed products (e.g., alcohol content in wine). Despite considerable divergence among species, soluble sugar accumulation in a fruit results from the complex interplay of three main processes, namely sugar import, sugar metabolism, and water dilution. Therefore, inter-species comparison would help to identify common and/or species-specific modes of regulation in sugar accumulation. For this purpose, a process-based mathematical framework was used to compare soluble sugar accumulation in three fruits: grape, tomato, and peach. Representative datasets covering the time course of sugar accumulation during fruit development were collected. They encompassed 104 combinations of species (3), genotypes (30), and growing conditions (19 years and 16 nutrient and environmental treatments). At maturity, grape showed the highest soluble sugar concentrations (16.5–26.3 g/100 g FW), followed by peach (2.2 to 20 g/100 g FW) and tomato (1.4 to 5 g/100 g FW). Main processes determining soluble sugar concentration were decomposed into sugar importation, metabolism, and water dilution with the process-based analysis. Different regulation modes of soluble sugar concentration were then identified, showing either import-based, dilution-based, or import and dilution dual-based. Firstly, the higher soluble sugar concentration in grape than in tomato is a result of higher sugar importation. Secondly, the higher soluble sugar concentration in grape than in peach is due to a lower water dilution. The third mode of regulation is more complicated than the first two, with differences both in sugar importation and water dilution (grape vs. cherry tomato; cherry tomato vs. peach; peach vs. tomato). On the other hand, carbon utilization for synthesis of non-soluble sugar compounds (namely metabolism) was conserved among the three fruit species. These distinct modes appear to be quite species-specific, but the intensity of the effect may significantly vary depending on the genotype and management practices. These results provide novel insights into the drivers of differences in soluble sugar concentration among fleshy fruits.

Cluster shading modifies amino acids in grape (Vitis vinifera L.) berries in a genotype- and tissue-dependent manner

Amino acid composition of the grape berry at harvest is important for wine making. The present study investigates the complex interplay between tissue, cultivar and light conditions that determine berry amino acid content. Twenty amino acids were assessed in the berry skin and pulp of two grape cultivars (Gamay Noir and Gamay Fréaux), grown under either light exposure or cluster shading conditions. In all samples, cluster shading significantly reduced most amino acids, except gamma-aminobutyric acid (GABA) and phenylalanine. However, the magnitude of the decrease was stronger in the skin (67.0% decrease) than in the pulp (30.4%) and stronger in cv. Gamay Noir (69.7%) than in Gamay Fréaux (30.7%). Cluster shading also significantly modified amino acid composition by decreasing the proline content while increasing the GABA content. These results are of oenological interest for shaping the amino acid composition of the must and improving wine quality.