Publications by authors named "Zhanwu Dai"

33 Publications

Data Comparison and Software Design for Easy Selection and Application of CRISPR-based Genome Editing Systems in Plants.

Genomics Proteomics Bioinformatics 2021 Jul 16. Epub 2021 Jul 16.

Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, the Innovative Academy of Seed Design, Chinese Academy of Science, Beijing 100093, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China. Electronic address:

CRISPR-based genome editing systems have been successfully and effectively used in many organisms. However, only a few studies have reported the comparison between CRISPR/Cas9 and CRISPR/Cpf1 systems in the whole-genome applications. Although many web-based toolkits are available, there is still a shortage of comprehensive, user-friendly, and plant-specific CRISPR databases and desktop software. In this study, we identified and analyzed the similarities and differences between CRISPR/Cas9 and CRISPR/Cpf1 systems by considering the abundance of proto-spacer adjacent motif (PAM) sites, effects of GC content, optimal proto-spacer length, potential universality within the plant kingdom, PAM-rich region (PARR) inhibiting ratio, and effects of G-quadruplex (G-Q) structures. Using this information, we built a comprehensive CRISPR database (including 138 plant genome data sources, www.grapeworld.cn/pc/index.html), which provides search tools for the identification of CRISPR editing sites in both CRISPR/Cas9 and CRISPR/Cpf1 systems. We also developed a desktop software on the basis of Perl/TK tool, which facilitates and improves the detection and analysis of CRISPR editing sites at the whole-genome level on Linux and/or Windows platform. Therefore, this study provides helpful data and software for easy selection and application of CRISPR-based genome editing systems in plants.
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http://dx.doi.org/10.1016/j.gpb.2019.05.008DOI Listing
July 2021

Characterization of Chromatin Accessibility and Gene Expression Upon Cold Stress Reveals the Transcription Factor RAV1 Functions in Cold Response in Vitis amurensis.

Plant Cell Physiol 2021 Jul 19. Epub 2021 Jul 19.

Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.

Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. A number of 9 TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde (MDA) content and high peroxidase (POD) activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for rapid identification of TFs in response to cold stress in grapevine. The VaRAV1 may play an important role in adaption to cold stress.
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http://dx.doi.org/10.1093/pcp/pcab115DOI Listing
July 2021

Genome-wide identification of B-box proteins and VvBBX44 involved in light-induced anthocyanin biosynthesis in grape (Vitis vinifera L.).

Planta 2021 May 1;253(5):114. Epub 2021 May 1.

Beijing Key Laboratory of Grape Science and Enology, and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.

Main Conclusion: Genome-wide identification, analysis and functional characterization of an unreported VvBBX gene showed a response to light and positive correlation with anthocyanin content, but also inhibition of light-induced anthocyanin synthesis. B-box (BBX) proteins are a class of zinc (Zn) finger transcription factors or regulators characterized by the presence of one or two BBX domains and play important roles in plant growth and development. However, the BBX genes' potential functions are insufficiently characterized in grape, a globally popular berry with high economic value. Here, 25 BBX family genes including a novel member (assigned VvBBX44) were identified genome widely in grape. The expression level of these VvBBXs were analyzed in 'Cabernet Sauvignon' (V. vinifera) stem, flower, leaf, tendril, petiole, and developing berries. The expression of VvBBX44 increased in developing 'Cabernet Sauvignon' berries. Its expression was inhibited in 'Jingxiu' and 'Muscat Hamburg' berry skin without sunlight. Furthermore, overexpression of VvBBX44 decreased the expression of LONG HYPOCOTYL 5 (VvHY5) and UDP-glucose flavonoid 3-O-glucosyltransferase (VvUFGT), and reduced the anthocyanin content in grape calli. Our results suggest that VvBBX44 may play an important role in grape berry coloring by directly repressing VvHY5 expression. This study provides new insights into the potential role of VvBBXs in berry development and light response and contributes to the understanding on the regulation mechanism of VvBBX44 in anthocyanin biosynthesis.
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http://dx.doi.org/10.1007/s00425-021-03618-zDOI Listing
May 2021

Metabolite analysis reveals distinct spatio-temporal accumulation of anthocyanins in two teinturier variants of cv. 'Gamay' grapevines (Vitis vinifera L.).

Planta 2021 Mar 31;253(4):84. Epub 2021 Mar 31.

Beijing Key Laboratory of Grape Science and Enology, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.

Main Conclusion: White-fleshed grape cv. 'Gamay' and its two teinturier variants presented distinct spatial-temporal accumulation of anthocyanins, with uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. In most red grape cultivars, anthocyanins accumulate exclusively in the berry skin, while 'teinturier' cultivars also accumulate anthocyanins in the pulp. Here, we investigated the teinturier cvs. 'Gamay de Bouze' and 'Gamay Fréaux' (two somatic variants of the white-fleshed cv. 'Gamay') through metabolic and transcript analysis to clarify whether these two somatic variants have the same anthocyanin accumulation pattern in the skin and pulp, and whether primary metabolites are also affected. The skin of the three cultivars and the pulp of 'Gamay de Bouze' begun to accumulate anthocyanins at the onset of berry ripening. However, the pulp of 'Gamay Fréaux' exhibited a distinct anthocyanin accumulation pattern, starting as early as fruit set with very low level of sugars. The highest level of anthocyanins was found in 'Gamay Fréaux' skin, followed by 'Gamay de Bouze' and 'Gamay'. Consistently, the transcript abundance of genes involved in anthocyanin biosynthesis were in line with the anthocyanin levels in the three cultivars. Despite no evident differences in pulp sugar content, the concentration of glucose and fructose in the skin of 'Gamay Fréaux' was only half of those in the skin of 'Gamay' and 'Gamay de Bouze' throughout all berry ripening, suggesting an uncoupled accumulation of sugars and anthocyanins in 'Gamay Fréaux'. The study provides a comprehensive view of metabolic consequences in grape somatic variants and the three almost isogenic genotypes can serve as ideal reagents to further uncover the mechanisms underlying the linkage between sugar and anthocyanin accumulation.
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http://dx.doi.org/10.1007/s00425-021-03613-4DOI Listing
March 2021

Adapting Wine Grape Ripening to Global Change Requires a Multi-Trait Approach.

Front Plant Sci 2021 5;12:624867. Epub 2021 Feb 5.

EGFV, Univ. Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, F-33882, Villenave d'Ornon, France.

In winegrowing regions around the world increasing temperature associated with climate change is responsible for earlier harvests and is implicated in undesirably high sugar concentrations at harvest. Determining the suitability of grapevine varieties in existing or new winegrowing areas has often been based on temperature, without considering other factors. The purpose of this study was to quantify key berry sugar accumulation traits and characterize their plasticity in response to several climate variables. Data was collected from 36 different cultivars over 7 years (2012-2018) from an experimental vineyard in Bordeaux, France. Sugar amounts were obtained through weekly berry sampling starting at mid-veraison and continuing until after technological maturity. The variation in sugar accumulation traits for all cultivars, when considered together, were well explained by cultivar, year, and their interaction, highlighting the relative roles of genetic variation and phenotypic plasticity. Sugar accumulation traits were affected by antecedent and concurrent climate factors such as photosynthetically active radiation, temperature, and vine water status, whether before, or after mid-veraison. In addition, other traits such as berry weight at mid-veraison and date of mid-veraison had an important influence on sugar accumulation traits. More notably, the relative importance of these factors varied significantly by cultivar. The specific physiological mechanisms driving the plasticity of these traits remain to be identified. Adaptation to climate change cannot be based on temperature alone and crop responses cannot be generalized across genotypes, even within species.
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http://dx.doi.org/10.3389/fpls.2021.624867DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893094PMC
February 2021

Modelling predicts tomatoes can be bigger and sweeter if biophysical factors and transmembrane transports are fine-tuned during fruit development.

New Phytol 2021 05 2;230(4):1489-1502. Epub 2021 Mar 2.

INRAE, Bordeaux Science Agro, EGFV, UMR 1287, Univ. Bordeaux, Villenave d'Ornon, F-33140, France.

The trade-off between yield and quality, a major problem for the production of fleshy fruits, involves fruit expansive growth and sugar metabolism. Here we developed an integrative model by coupling a biophysical model of fleshy fruit growth processes, including water and carbon fluxes and organ expansion, with an enzyme-based kinetic model of sugar metabolism to better understand the interactions between these two processes. The integrative model was initially tested on tomato fruit, a model system for fleshy fruit. The integrative model closely simulated the biomass and major carbon metabolites of tomato fruit developing under optimal or stress conditions. The model also performed robustly when simulating the fruit size and sugar concentrations of different tomato genotypes including wild species. The validated model was used to explore ways of uncoupling the size-sweetness trade-off in fruit. Model-based virtual experiments suggested that larger sweeter tomatoes could be obtained by simultaneously manipulating certain biophysical factors and transmembrane transports. The integrative fleshy fruit model provides a promising tool to facilitate the targeted bioengineering and breeding of tomatoes and other fruits.
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http://dx.doi.org/10.1111/nph.17260DOI Listing
May 2021

Nighttime transpiration represents a negligible part of water loss and does not increase the risk of water stress in grapevine.

Plant Cell Environ 2021 02 5;44(2):387-398. Epub 2020 Nov 5.

EGFV, Bordeaux Sciences Agro, INRAE, Univ. Bordeaux, ISVV, Villenave d'Ornon, France.

Nighttime transpiration has been previously reported as a significant source of water loss in many species; however, there is a need to determine if this trait plays a key role in the response to drought. This study aimed to determine the magnitude, regulation and relative contribution to whole plant water-use, of nighttime stomatal conductance (g ) and transpiration (E ) in grapevine (Vitis vinifera L.). Our results showed that nighttime water loss was relatively low compared to daytime transpiration, and that decreases in soil and plant water potentials were mainly explained by daytime stomatal conductance (g ) and transpiration (E ). Contrary to E , E did not respond to VPD and possible effects of an innate circadian regulation were observed. Plants with higher g also exhibited higher daytime transpiration and carbon assimilation at midday, and total leaf area, suggesting that increased g may be linked with daytime behaviors that promote productivity. Modeling simulations indicated that g was not a significant factor in reaching critical hydraulic thresholds under scenarios of either extreme drought, or time to 20% of soil relative water content. Overall, this study suggests that g is not significant in exacerbating the risk of water stress and hydraulic failure in grapevine.
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http://dx.doi.org/10.1111/pce.13923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7894480PMC
February 2021

Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species.

J Exp Bot 2020 10;71(19):5823-5836

UMR 1332 Biologie du Fruit et Pathologie, INRAE, Univ. Bordeaux, INRAE Nouvelle Aquitaine - Bordeaux, Avenue Edouard Bourlaux, Villenave d'Ornon, France.

Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.
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http://dx.doi.org/10.1093/jxb/eraa302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7540837PMC
October 2020

Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species.

Ann Bot 2020 08;126(3):455-470

INRAE, UR1115, Unité Plantes et Systèmes de Culture Horticoles, Avignon, France.

Background And Aims: Sugar concentration is a key determinant of fruit quality. Soluble sugars and starch concentrations in fruits vary greatly from one species to another. The aim of this study was to investigate similarities and differences in sugar accumulation strategies across ten contrasting fruit species using a modelling approach.

Methods: We developed a coarse-grained model of primary metabolism based on the description of the main metabolic and hydraulic processes (synthesis of compounds other than sugar and starch, synthesis and hydrolysis of starch, and water dilution) involved in the accumulation of soluble sugars during fruit development.

Key Results: Statistical analyses based on metabolic rates separated the species into six groups according to the rate of synthesis of compounds other than sugar and starch. Herbaceous species (cucumber, tomato, eggplant, pepper and strawberry) were characterized by a higher synthesis rate than woody species (apple, nectarine, clementine, grape and kiwifruit). Inspection of the dynamics of the processes involved in sugar accumulation revealed that net sugar importation, metabolism and dilution processes were remarkably synchronous in most herbaceous plants, whereas in kiwifruit, apple and nectarine, processes related to starch metabolism were temporally separated from other processes. Strawberry, clementine and grape showed a distinct dynamic compared with all other species.

Conclusions: Overall, these results provide fresh insights into species-specific regulatory strategies and into the role of starch metabolism in the accumulation of soluble sugars in fleshy fruits. In particular, inter-specific differences in development period shape the co-ordination of metabolic processes and affect priorities for carbon allocation across species. The six metabolic groups identified by our analysis do not show a clear separation into climacteric and non-climacteric species, possibly suggesting that the metabolic processes related to sugar concentration are not greatly affected by ethylene-associated events.
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http://dx.doi.org/10.1093/aob/mcaa082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424760PMC
August 2020

The sequence and thresholds of leaf hydraulic traits underlying grapevine varietal differences in drought tolerance.

J Exp Bot 2020 07;71(14):4333-4344

EGFV, Bordeaux-Sciences Agro, INRA, Université de Bordeaux, ISVV, Villenave d'Ornon, France.

Adapting agriculture to climate change is driving the need for the selection and breeding of drought-tolerant crops. The aim of this study was to identify key drought tolerance traits and determine the sequence of their water potential thresholds across three grapevine cultivars with contrasting water use behaviors, Grenache, Syrah, and Semillon. We quantified differences in water use between cultivars and combined this with the determination of other leaf-level traits (e.g. leaf turgor loss point, π TLP), leaf vulnerability to embolism (P50), and the hydraulic safety margin (HSM P50). Semillon exhibited the highest maximum transpiration (Emax), and lowest sensitivity of canopy stomatal conductance (Gc) to vapor pressure deficit (VPD), followed by Syrah and Grenache. Increasing Emax was correlated with more negative water potential at which stomata close (Pgs90), π TLP, and P50, suggesting that increasing water use is associated with hydraulic traits allowing gas exchange under more negative water potentials. Nevertheless, all the cultivars closed their stomata prior to leaf embolism formation. Modeling simulations demonstrated that despite a narrower HSM, Grenache takes longer to reach thresholds of hydraulic failure due to its conservative water use. This study demonstrates that the relationships between leaf hydraulic traits are complex and interactive, stressing the importance of integrating multiple traits in characterizing drought tolerance.
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http://dx.doi.org/10.1093/jxb/eraa186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337184PMC
July 2020

Knockout of VvCCD8 gene in grapevine affects shoot branching.

BMC Plant Biol 2020 Jan 29;20(1):47. Epub 2020 Jan 29.

Institute of Botany, the Chinese Academy of Sciences, Nanxin Village 20, Xiangshan, Haidian District, Beijing, 100093, China.

Background: Shoot branching is an important trait of plants that allows them to adapt to environment changes. Strigolactones (SLs) are newly identified plant hormones that inhibit shoot branching in plants. The SL biosynthesis genes CCD7 (carotenoid cleavage dioxygenase 7) and CCD8 have been found to regulate branching in several herbaceous plants by taking advantage of their loss-of-function mutants. However, the role for CCD7 and CCD8 in shoot branching control in grapevine is still unknown due to the lack of corresponding mutants.

Results: Here we employed the CRISPR/Cas9 system to edit the VvCCD7 and VvCCD8 genes in the grape hybrid 41B. The 41B embryogenic cells can easily be transformed and used for regeneration of the corresponding transformed plants. Sequencing analysis revealed that gene editing has been used successfully to target both VvCCD genes in 41B embryogenic cells. After regeneration, six 41B plantlets were identified as transgenic plants carrying the CCD8-sgRNA expression cassette. Among these, four plants showed mutation in the target region and were selected as ccd8 mutants. These ccd8 mutants showed increased shoot branching compared to the corresponding wild-type plants. In addition, no off-target mutation was detected in the tested mutants at predicted off-target sites.

Conclusions: Our results underline the key role of VvCCD8 in the control of grapevine shoot branching.
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http://dx.doi.org/10.1186/s12870-020-2263-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6990564PMC
January 2020

Modeling Stem Water Potential by Separating the Effects of Soil Water Availability and Climatic Conditions on Water Status in Grapevine ( L.).

Front Plant Sci 2019 22;10:1485. Epub 2019 Nov 22.

EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, F-33882 Villenave d'Ornon, France.

Measuring seasonal plant water status is critical in choosing appropriate management strategies to ensure yields and quality of agricultural products, particularly in a context of climate change. Water status of grapevines is known to be a key factor for yield, grape composition, and wine quality. Predawn leaf water potential (PLWP) and stem water potential (SWP) proved to be simple and precise indicators for assessing grapevine water status and subsequent same-day spatial comparisons. A drawback of SWP is that it does not allow for temporal comparisons, because the measured value is impacted both by soil water availability and climatic conditions on the day of measurement. The objectives of this study are i) to provide a model that separates the effect of soil water content from the effect of climatic conditions on the SWP value and ii) to standardize the SWP value to a value under predefined reference climatic conditions in order to compare SWP values collected under different climatic conditions. SWP and PLWP were temporally assessed on three soil types in Saint-Émilion (Bordeaux, France) in 2015 and on five soil types in Margaux (Bordeaux, France) in 2018 using a pressure chamber. SWP measurements on two consecutive days with contrasting climatic conditions allowed to assess the impact of these conditions on SWP values. A large portion of the variability in SWP values was explained by PLWP. Model selection further showed that the addition of maximum air temperature and seasonality explained a significant amount of the remaining variability in SWP values. SWP values could be successfully standardized to a theoretical value under reference climatic conditions, which allows for temporal comparisons of SWP values. A plant-based measurement, such as the water potential, can be considered as the most straightforward indicator of plant water status as it integrates the effects of soil, plant, and atmospheric conditions. More precise interpretation of SWP values provides winegrowers with a tool to more adequately implement short- and long-term management strategies to adapt to drought in order to ensure yield and grape quality.
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http://dx.doi.org/10.3389/fpls.2019.01485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883387PMC
November 2019

Fruit Salad in the Lab: Comparing Botanical Species to Help Deciphering Fruit Primary Metabolism.

Front Plant Sci 2019 9;10:836. Epub 2019 Jul 9.

UMR1332 Biologie du Fruit et Pathologie, Centre INRA de Bordeaux, INRA, Université de Bordeaux, Bordeaux, France.

Although fleshy fruit species are economically important worldwide and crucial for human nutrition, the regulation of their fruit metabolism remains to be described finely. Fruit species differ in the origin of the tissue constituting the flesh, duration of fruit development, coordination of ripening changes (climacteric vs. non-climacteric type) and biochemical composition at ripeness is linked to sweetness and acidity. The main constituents of mature fruit result from different strategies of carbon transport and metabolism. Thus, the timing and nature of phloem loading and unloading can largely differ from one species to another. Furthermore, accumulations and transformations of major soluble sugars, organic acids, amino acids, starch and cell walls are very variable among fruit species. Comparing fruit species therefore appears as a valuable way to get a better understanding of metabolism. On the one hand, the comparison of results of studies about species of different botanical families allows pointing the drivers of sugar or organic acid accumulation but this kind of comparison is often hampered by heterogeneous analysis approaches applied in each study and incomplete dataset. On the other hand, cross-species studies remain rare but have brought new insights into key aspects of primary metabolism regulation. In addition, new tools for multi-species comparisons are currently emerging, including meta-analyses or re-use of shared metabolic or genomic data, and comparative metabolic flux or process-based modeling. All these approaches contribute to the identification of the metabolic factors that influence fruit growth and quality, in order to adjust their levels with breeding or cultural practices, with respect to improving fruit traits.
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http://dx.doi.org/10.3389/fpls.2019.00836DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6632546PMC
July 2019

VvWRKY8 represses stilbene synthase genes through direct interaction with VvMYB14 to control resveratrol biosynthesis in grapevine.

J Exp Bot 2019 01;70(2):715-729

Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, China.

Resveratrol (Res) is a stilbenoid, a group of plant phenolic metabolites derived from stilbene that possess activities against pests, pathogens, and abiotic stresses. Only a few species, including grapevine (Vitis), synthesize and accumulate Res. Although stilbene synthases (STSs) have been isolated and characterized in several species, the gene regulatory mechanisms underlying stilbene biosynthesis are still largely unknown. Here, we characterize a grapevine WRKY transcription factor, VvWRKY8, that regulates the Res biosynthetic pathway. Transient and stable overexpression of VvWRKY8 in grapevine results in decreased expression of VvSTS15/21 and VvMYB14, as well as in a reduction of Res accumulation. VvWRKY8 does not bind to or activate the promoters of VvMYB14 and VvSTS15/21; however, it physically interacts with VvMYB14 proteins through their N-terminal domains to prevent them from binding to the VvSTS15/21 promoter. Application of exogenous Res results in the stimulation of VvWRKY8 expression and in a decrease of VvMYB14 and VvSTS15/21 expression in grapevine suspension cells, and in the activation of the VvWRKY8 promoter in tobacco leaves. These results demonstrate that VvWRKY8 represses VvSTS15/21 expression and Res biosynthesis through interaction with VvMYB14. In this context, the VvMYB14-VvSTS15/21-Res-VvWRKY8 regulatory loop may be an important mechanism for the fine-tuning of Res biosynthesis in grapevine.
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http://dx.doi.org/10.1093/jxb/ery401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322584PMC
January 2019

Modelling grape growth in relation to whole-plant carbon and water fluxes.

J Exp Bot 2019 04;70(9):2505-2521

EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Villenave d'Ornon, France.

The growth of fleshy fruits is still poorly understood as a result of the complex integration of water and solute fluxes, cell structural properties, and the regulation of whole plant source-sink relationships. To unravel the contribution of these processes to berry growth, a biophysical grape (Vitis vinifera L.) berry growth module was developed and integrated with a whole-plant functional-structural model, and was calibrated on two varieties, Cabernet Sauvignon and Sangiovese. The model captured well the variations in growth and sugar accumulation caused by environmental conditions, changes in leaf-to-fruit ratio, plant water status, and varietal differences, with obvious future application in predicting yield and maturity under a variety of production contexts and regional climates. Our analyses illustrated that grapevines strive to maintain proper ripening by partially compensating for a reduced source-sink ratio, and that under drought an enhanced berry sucrose uptake capacity can reverse berry shrinkage. Sensitivity analysis highlighted the importance of phloem hydraulic conductance, sugar uptake, and surface transpiration on growth, while suggesting that cell wall extensibility and the turgor threshold for cell expansion had minor effects. This study demonstrates that this integrated model is a useful tool in understanding the integration and relative importance of different processes in driving fleshy fruit growth.
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http://dx.doi.org/10.1093/jxb/ery367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487596PMC
April 2019

Correction to: A molecular perspective on starch metabolism in woody tissues.

Planta 2018 09;248(3):569

Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.

The original article was corrected.
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http://dx.doi.org/10.1007/s00425-018-2963-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096776PMC
September 2018

A molecular perspective on starch metabolism in woody tissues.

Planta 2018 Sep 18;248(3):559-568. Epub 2018 Jul 18.

Centre of Molecular and Environmental Biology (CBMA), University of Minho, Braga, Portugal.

Main Conclusion: The elucidation of the molecular mechanisms of starch synthesis and mobilization in perennial woody tissues is of the utmost scientific and agricultural importance. Starch is the main carbohydrate reserve in plants and is fundamental in human nutrition and several industrial processes. In leaves, starch accumulated during the day is degraded throughout the night and the resulting sugars, glucose and maltose, are exported to the cytosol by the specialized transmembrane translocators pGT and MEX, respectively. Nevertheless, the degradation of the starch granule is a complex process not completely elucidated. While the mechanisms of starch mobilization during germination in the dead endosperm of cereal seeds are well described, the molecular and biochemical mechanisms involved in starch storage in the heterotrophic tissues of woody plants and its utilization in spring and winter are still puzzling. It is known that some biochemical steps of starch synthesis are conserved in heterotrophic tissues and in the leaves, but some aspects are particular to sink organs. From an agronomic standpoint, the knowledge on starch storage and mobilization in woody tissues is pivotal to understand (and to optimize) some common practices in the field that modify source-sink relationships, such as pruning and defoliation. Soluble sugars resulting from starch are also pivotal to cold adaptation, and in several fruits, such as banana and kiwifruit, starch may provide soluble sugars during ripening. In this review, we explore the recent advances on the molecular mechanisms and regulations involved in starch synthesis and mobilization, with a focus on perennial woody tissues.
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http://dx.doi.org/10.1007/s00425-018-2954-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096779PMC
September 2018

Constraint-Based Modeling Highlights Cell Energy, Redox Status and α-Ketoglutarate Availability as Metabolic Drivers for Anthocyanin Accumulation in Grape Cells Under Nitrogen Limitation.

Front Plant Sci 2018 17;9:421. Epub 2018 May 17.

UMR 1287 Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, Institut des Sciences de la Vigne et du Vin, Bordeaux, France.

Anthocyanin biosynthesis is regulated by environmental factors (such as light, temperature, and water availability) and nutrient status (such as carbon, nitrogen, and phosphate nutrition). Previous reports show that low nitrogen availability strongly enhances anthocyanin accumulation in non carbon-limited plant organs or cell suspensions. It has been hypothesized that high carbon-to-nitrogen ratio would lead to an energy excess in plant cells, and that an increase in flavonoid pathway metabolic fluxes would act as an "energy escape valve," helping plant cells to cope with energy and carbon excess. However, this hypothesis has never been tested directly. To this end, we used the grapevine L. cultivar Gamay Teinturier (syn. Gamay Freaux or Freaux Tintorier, VIVC #4382) cell suspension line as a model system to study the regulation of anthocyanin accumulation in response to nitrogen supply. The cells were sub-cultured in the presence of either control (25 mM) or low (5 mM) nitrate concentration. Targeted metabolomics and enzyme activity determinations were used to parametrize a constraint-based model describing both the central carbon and nitrogen metabolisms and the flavonoid (phenylpropanoid) pathway connected by the energy (ATP) and reducing power equivalents (NADPH and NADH) cofactors. The flux analysis (2 flux maps generated, for control and low nitrogen in culture medium) clearly showed that in low nitrogen-fed cells all the metabolic fluxes of central metabolism were decreased, whereas fluxes that consume energy and reducing power, were either increased (upper part of glycolysis, shikimate, and flavonoid pathway) or maintained (pentose phosphate pathway). Also, fluxes of flavanone 3β-hydroxylase, flavonol synthase, and anthocyanidin synthase were strongly increased, advocating for a regulation of the flavonoid pathway by alpha-ketoglutarate levels. These results strongly support the hypothesis of anthocyanin biosynthesis acting as an energy escape valve in plant cells, and they open new possibilities to manipulate flavonoid production in plant cells. They do not, however, support a role of anthocyanins as an effective mechanism for coping with carbon excess in high carbon to nitrogen ratio situations in grape cells. Instead, constraint-based modeling output and biomass analysis indicate that carbon excess is dealt with by vacuolar storage of soluble sugars.
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http://dx.doi.org/10.3389/fpls.2018.00421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5966944PMC
May 2018

Putting primary metabolism into perspective to obtain better fruits.

Ann Bot 2018 06;122(1):1-21

UMR 1332 BFP, INRA, Univ. Bordeaux, Villenave d'Ornon, France.

Background: One of the key goals of fruit biology is to understand the factors that influence fruit growth and quality, ultimately with a view to manipulating them for improvement of fruit traits.

Scope: Primary metabolism, which is not only essential for growth but is also a major component of fruit quality, is an obvious target for improvement. However, metabolism is a moving target that undergoes marked changes throughout fruit growth and ripening.

Conclusions: Agricultural practice and breeding have successfully improved fruit metabolic traits, but both face the complexity of the interplay between development, metabolism and the environment. Thus, more fundamental knowledge is needed to identify further strategies for the manipulation of fruit metabolism. Nearly two decades of post-genomics approaches involving transcriptomics, proteomics and/or metabolomics have generated a lot of information about the behaviour of fruit metabolic networks. Today, the emergence of modelling tools is providing the opportunity to turn this information into a mechanistic understanding of fruits, and ultimately to design better fruits. Since high-quality data are a key requirement in modelling, a range of must-have parameters and variables is proposed.
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http://dx.doi.org/10.1093/aob/mcy057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6025238PMC
June 2018

A 3-D functional-structural grapevine model that couples the dynamics of water transport with leaf gas exchange.

Ann Bot 2018 04;121(5):833-848

EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, Villenave d'Ornon, France.

Background And Aims: Predicting both plant water status and leaf gas exchange under various environmental conditions is essential for anticipating the effects of climate change on plant growth and productivity. This study developed a functional-structural grapevine model which combines a mechanistic understanding of stomatal function and photosynthesis at the leaf level (i.e. extended Farqhuhar-von Caemmerer-Berry model) and the dynamics of water transport from soil to individual leaves (i.e. Tardieu-Davies model).

Methods: The model included novel features that account for the effects of xylem embolism (fPLC) on leaf hydraulic conductance and residual stomatal conductance (g0), variable root and leaf hydraulic conductance, and the microclimate of individual organs. The model was calibrated with detailed datasets of leaf photosynthesis, leaf water potential, xylem sap abscisic acid (ABA) concentration and hourly whole-plant transpiration observed within a soil drying period, and validated with independent datasets of whole-plant transpiration under both well-watered and water-stressed conditions.

Key Results: The model well captured the effects of radiation, temperature, CO2 and vapour pressure deficit on leaf photosynthesis, transpiration, stomatal conductance and leaf water potential, and correctly reproduced the diurnal pattern and decline of water flux within the soil drying period. In silico analyses revealed that decreases in g0 with increasing fPLC were essential to avoid unrealistic drops in leaf water potential under severe water stress. Additionally, by varying the hydraulic conductance along the pathway (e.g. root and leaves) and changing the sensitivity of stomatal conductance to ABA and leaf water potential, the model can produce different water use behaviours (i.e. iso- and anisohydric).

Conclusions: The robust performance of this model allows for modelling climate effects from individual plants to fields, and for modelling plants with complex, non-homogenous canopies. In addition, the model provides a basis for future modelling efforts aimed at describing the physiology and growth of individual organs in relation to water status.
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http://dx.doi.org/10.1093/aob/mcx141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5906973PMC
April 2018

Dissecting the rootstock control of scion transpiration using model-assisted analyses in grapevine.

Tree Physiol 2018 07;38(7):1026-1040

EGFV, Bordeaux Sciences Agro, CNRS, INRA, ISVV, Université de Bordeaux, Villenave d'Ornon, France.

How rootstocks contribute to the control of scion transpiration under drought is poorly understood. We investigated the role of root characteristics, hydraulic conductance and chemical signals (abscisic acid, ABA) in the response of stomatal conductance (gs) and transpiration (E) to drought in Cabernet Sauvignon (Vitis vinifera) grafted onto drought-sensitive (Vitis riparia) and drought-tolerant (Vitis berlandieri × Vitis rupestris 110R) rootstocks. All combinations showed a concomitant reduction in gs and E, and an increase in xylem sap ABA concentration during the drought cycle. Cabernet Sauvignon grafted onto 110R exhibited higher gs and E under well-watered and moderate water deficit, but all combinations converged as water deficit increased. These results were integrated into three permutations of a whole-plant transpiration model that couples both chemical (i.e., ABA) and hydraulic signals in the modelling of stomatal control. Model comparisons revealed that both hydraulic and chemical signals were important for rootstock-specific stomatal regulation. Moreover, model parameter comparison and sensitivity analysis highlighted two major parameters differentiating the rootstocks: (i) ABA biosynthetic activity and (ii) the hydraulic conductance between the rhizosphere and soil-root interface determined by root system architecture. These differences in root architecture, specifically a higher root length area in 110R, likely explain its higher E and gs observed at low and moderate water deficit.
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http://dx.doi.org/10.1093/treephys/tpx153DOI Listing
July 2018

Root transcriptomic responses of grafted grapevines to heterogeneous nitrogen availability depend on rootstock genotype.

J Exp Bot 2017 07;68(15):4339-4355

EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 33140 Villenave d'Ornon, France.

In many fruit species, including grapevine, grafting is used to improve scion productivity and quality and to adapt the plant to environmental conditions. However, the mechanisms underlying the rootstock control of scion development are still poorly understood. The ability of rootstocks to regulate nitrogen uptake and assimilation may contribute to this control. A split-root system was used to grow heterografted grapevines and to investigate the molecular responses to changes in nitrate availability of two rootstocks known to affect scion growth differently. Transcriptome profiling by RNA sequencing was performed on root samples collected 3 and 24 h after nitrogen supply. The results demonstrated a common response involving nitrogen-related genes, as well as a more pronounced transcriptomic reprogramming in the genotype conferring the lower scion growth. A weighted gene co-expression network analysis allowed the identification of co-regulated gene modules, suggesting a role for nitrate transporter 2 family genes and some transcription factors as main actors controlling this genotype-dependent response to heterogeneous nitrogen supply. The relationship between nitrate, ethylene, and strigolactone hormonal pathways was found to differ between the two genotypes. These findings indicated that the genotypes responded differently to heterogeneous nitrogen availability, and this may contribute to their contrasting effect on scion growth.
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http://dx.doi.org/10.1093/jxb/erx224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854021PMC
July 2017

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

Food Res Int 2017 08 11;98:2-9. Epub 2017 Jan 11.

EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 33140 Villenave d'Ornon, France. Electronic address:

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.
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http://dx.doi.org/10.1016/j.foodres.2017.01.008DOI Listing
August 2017

Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues.

Trends Plant Sci 2017 07 3;22(7):610-623. Epub 2017 Jun 3.

EVA, Normandie Univ, UNICAEN, INRA, 14000, Caen, France. Electronic address:

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.
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http://dx.doi.org/10.1016/j.tplants.2017.04.009DOI Listing
July 2017

Low source-sink ratio reduces reserve starch in grapevine woody canes and modulates sugar transport and metabolism at transcriptional and enzyme activity levels.

Planta 2017 Sep 19;246(3):525-535. Epub 2017 May 19.

Centro de Investigação e de Tecnologias Agro-ambientais e Biológicas (CITAB), Vila Real, Portugal.

Main Conclusion: Severe leaf removal decreases storage starch and sucrose in grapevine cv. Cabernet Sauvignon fruiting cuttings and modulates the activity of key enzymes and the expression of sugar transporter genes. Leaf removal is an agricultural practice that has been shown to modify vineyard efficiency and grape and wine composition. In this study, we took advantage of the ability to precisely control the number of leaves to fruits in Cabernet Sauvignon fruiting cuttings to study the effect of source-sink ratios (2 (2L), 6 (6L) and 12 (12) leaves per cluster) on starch metabolism and accumulation. Starch concentration was significantly higher in canes from 6L (42.13 ± 1.44 mg g DW) and 12L (43.50 ± 2.85 mg g DW) than in 2L (22.72 ± 3.10 mg g DW) plants. Moreover, carbon limitation promoted a transcriptional adjustment of genes involved in starch metabolism in grapevine woody tissues, including a decrease in the expression of the plastidic glucose-6-phosphate translocator, VvGPT1. Contrarily, the transcript levels of the gene coding the catalytic subunit VvAGPB1 of the VvAGPase complex were higher in canes from 2L plants than in 6L and 12L, which positively correlated with the biochemical activity of this enzyme. Sucrose concentration increased in canes from 2L to 6L and 12L plants, and the amount of total phenolics followed the same trend. Expression studies showed that VvSusy transcripts decreased in canes from 2L to 6L and 12L plants, which correlated with the biochemical activity of insoluble invertase, while the expression of the sugar transporters VvSUC11 and VvSUC12, together with VvSPS1, which codes an enzyme involved in sucrose synthesis, increased. Thus, sucrose seems to control starch accumulation through the adjustment of the cane sink strength.
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http://dx.doi.org/10.1007/s00425-017-2708-6DOI Listing
September 2017

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

Front Plant Sci 2016 19;7:649. Epub 2016 May 19.

INRA, UR1115, Plantes et Systèmes de Culture Horticoles Avignon, France.

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.
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http://dx.doi.org/10.3389/fpls.2016.00649DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872523PMC
May 2016

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

Planta 2016 Jan 3;243(1):23-41. Epub 2015 Sep 3.

UMR 1287 EGFV, INRA, Univ. de Bordeaux, ISVV, 33882, Villenave d'Ornon, France.

Main Conclusion: Light 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.
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http://dx.doi.org/10.1007/s00425-015-2391-4DOI Listing
January 2016

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

Front Plant Sci 2015 29;6:382. Epub 2015 May 29.

INRA, ISVV, EGFV, UMR 1287, University of Bordeaux Villenave d'Ornon, France.

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.
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http://dx.doi.org/10.3389/fpls.2015.00382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4448006PMC
June 2015

Transcriptional and metabolic alternations rebalance wheat grain storage protein accumulation under variable nitrogen and sulfur supply.

Plant J 2015 Jul 8;83(2):326-43. Epub 2015 Jun 8.

INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 5 chemin de Beaulieu, Clermont-Ferrand, F-63 039, France.

Wheat (Triticum aestivum L.) grain storage proteins (GSPs) are major determinants of flour end-use value. Biological and molecular mechanisms underlying the developmental and nutritional determination of GSP accumulation in cereals are as yet poorly understood. Here we timed the accumulation of GSPs during wheat grain maturation relative to changes in metabolite and transcript pools in different conditions of nitrogen (N) and sulfur (S) availability. We found that the N/S supply ratio modulated the duration of accumulation of S-rich GSPs and the rate of accumulation of S-poor GSPs. These changes are likely to be the result of distinct relationships between N and S allocation, depending on the S content of the GSP. Most developmental and nutritional modifications in GSP synthesis correlated with the abundance of structural gene transcripts. Changes in the expression of transport and metabolism genes altered the concentrations of several free amino acids under variable conditions of N and S supply, and these amino acids seem to be essential in determining GSP expression. The comprehensive data set generated and analyzed here provides insights that will be useful in adapting fertilizer use to variable N and S supply, or for breeding new cultivars with balanced and robust GSP composition.
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http://dx.doi.org/10.1111/tpj.12881DOI Listing
July 2015

RulNet: A Web-Oriented Platform for Regulatory Network Inference, Application to Wheat -Omics Data.

PLoS One 2015 19;10(5):e0127127. Epub 2015 May 19.

Blaise Pascal University, UMR6158 CNRS LIMOS Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes, Aubière, F-63 173, France.

With the increasing amount of -omics data available, a particular effort has to be made to provide suitable analysis tools. A major challenge is that of unraveling the molecular regulatory networks from massive and heterogeneous datasets. Here we describe RulNet, a web-oriented platform dedicated to the inference and analysis of regulatory networks from qualitative and quantitative -omics data by means of rule discovery. Queries for rule discovery can be written in an extended form of the RQL query language, which has a syntax similar to SQL. RulNet also offers users interactive features that progressively adjust and refine the inferred networks. In this paper, we present a functional characterization of RulNet and compare inferred networks with correlation-based approaches. The performance of RulNet has been evaluated using the three benchmark datasets used for the transcriptional network inference challenge DREAM5. Overall, RulNet performed as well as the best methods that participated in this challenge and it was shown to behave more consistently when compared across the three datasets. Finally, we assessed the suitability of RulNet to analyze experimental -omics data and to infer regulatory networks involved in the response to nitrogen and sulfur supply in wheat (Triticum aestivum L.) grains. The results highlight putative actors governing the response to nitrogen and sulfur supply in wheat grains. We evaluate the main characteristics and features of RulNet as an all-in-one solution for RN inference, visualization and editing. Using simple yet powerful RulNet queries allowed RNs involved in the adaptation of wheat grain to N and S supply to be discovered. We demonstrate the effectiveness and suitability of RulNet as a platform for the analysis of RNs involving different types of -omics data. The results are promising since they are consistent with what was previously established by the scientific community.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0127127PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4437996PMC
April 2016
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