Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.)

Network aggregation improves gene function prediction of grapevine gene co-expression networks

Aggregation across multiple networks highlights robust co-expression interactions and improves the functional connectivity of grapevine gene co-expression networks. In recent years, the rapid accumulation of transcriptome datasets from diverse experimental conditions has enabled the widespread use of gene co-expression network (GCN) analysis in plants. In grapevine, GCN analysis has shown great promise for gene function prediction, however, measurable progress is currently lacking. Using accumulated microarray datasets from the grapevine whole-genome array (33 experiments, 1359 samples), we explored how meta-analysis through aggregation influences the functional connectivity (performance) of derived networks using guilt-by-association neighbor voting. Two annotation schemes, i.e. MapMan BIN and Pfam, at two sparsity thresholds, i.e. top 100 (stringent) and 300 (relaxed) ranked genes were evaluated. We observed that aggregating across multiple networks improves performance dramatically, with the aggregate outperforming the majority of functional terms across individual networks. Network sparsity and size (i.e. the number of samples and aggregates) were key factors influencing performance while the choice of annotation scheme had little. Systematic comparison with various state-of-the-art microarray and RNA-seq networks was also performed, however, none outperformed the aggregate microarray network despite having good predictive performance. Repeating these series of tests using a functional enrichment-based performance metric also showed remarkably consistent findings with guilt-by-association neighbor voting. To demonstrate its functionality, we explore the function and transcriptional regulation of grapevine EXPANSIN genes. We envisage that network aggregation will offer new and unique opportunities for gene function prediction in future grapevine functional genomics studies. To this end, we make the aggregate networks and associated metadata publicly available at VTC-Agg (https://sites.google.com/view/vtc-agg).

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.

Oenological potential and health benefits of Chinese non-Vitis vinifera species: An opportunity to the revalorization and to breed new varieties

The wine industry is focused on the producing wine mostly from European grapevine varieties (Vitis vinifera L.). China has experienced a significant growth of the vineyard surface, based on the cultivation of these grapevine varieties. Currently, China has become one of the countries with the largest surface of planted vineyards in the world. In the last years, there has been a trend to oenologically and viticulturally revalorize certain autochthonous grapevine species. China holds a great diversity of Vitis species, which are being the focus of study. This could be an important alternative for the diversification of wine production, providing new products with a strong identity. Additionally, the varietal homogenization has increased the vineyard genetic vulnerability in relation to the emergence of grapevine diseases and their resistance to chemical fungicides. In this way, non-Vitis vinifera species are characterized by having a high resistance to a wide range of biotic and abiotic factors, which can bring an opportunity to breed new varieties. However, there is little available information about the oenological potential of these species, which makes it a current interesting topic. Therefore, this review aims to summarize the oenological potential of non-Vitis vinifera species found in China, discussing their potential effects on human health and thus, to propose some Chinese wild grapes for their use in breeding programs.

Characterization of Transcriptional Expression and Regulation of Carotenoid Cleavage Dioxygenase 4b in Grapes

Norisoprenoids are important aromatic volatiles contributing to the pleasant floral/fruity odor in grapes and wine. They are produced from carotenoids through the cleavage of carotenoid cleavage dioxygenases (CCDs). However, the underlying mechanisms regulating VvCCD expression remain poorly understood. In this study, we showed that VvCCD4b expression was positively correlated with the accumulation of β-damascenone, β-ionone, 6-methyl-5-hepten-2-one, geranylacetone, dihydroedulan I, and total norisoprenoids in developing grapes in two vintages from two regions. VvCCD4b was found to be principally expressed in flowers, mature leaves, and berries. Abscisic acid strongly induced the expression of this gene. Additionally, the present study preliminarily indicated that the activity of the VvCCD4b promoter was dropped under 37°C treatment and also responded to the illumination change. VvCCD4b was expressed in parallel with VvMADS4 in developing grape berries. The latter is a MADS family transcription factor and nucleus-localized protein that was captured by yeast one-hybrid. A dual-luciferase reporter assay in tobacco leaves revealed that VvMADS4 downregulated the activity of the VvCCD4b promoter. VvMADS4 overexpression in grape calli and Vitis quinquangularis Rehd. leaves repressed the VvCCD4b expression. In summary, this work demonstrates that VvCCD4b expression is positively correlated with the accumulation of norisoprenoids, and VvMADS4 is a potential negative regulator of VvCCD4b. Our results provide a new perspective for understanding the regulation of VvCCD4b expression and norisoprenoid accumulation in grapes.

A Review of the Potential Climate Change Impacts and Adaptation Options for European Viticulture

Viticulture and winemaking are important socioeconomic sectors in many European regions. Climate plays a vital role in the terroir of a given wine region, as it strongly controls canopy microclimate, vine growth, vine physiology, yield, and berry composition, which together determine wine attributes and typicity. New challenges are, however, predicted to arise from climate change, as grapevine cultivation is deeply dependent on weather and climate conditions. Changes in viticultural suitability over the last decades, for viticulture in general or the use of specific varieties, have already been reported for many wine regions. Despite spatially heterogeneous impacts, climate change is anticipated to exacerbate these recent trends on suitability for wine production. These shifts may reshape the geographical distribution of wine regions, while wine typicity may also be threatened in most cases. Changing climates will thereby urge for the implementation of timely, suitable, and cost-effective adaptation strategies, which should also be thoroughly planned and tuned to local conditions for an effective risk reduction. Although the potential of the different adaptation options is not yet fully investigated, deserving further research activities, their adoption will be of utmost relevance to maintain the socioeconomic and environmental sustainability of the highly valued viticulture and winemaking sector in Europe.

Identification of the gene network modules highly associated with the synthesis of phenolics compounds in barley by transcriptome and metabolome analysis

Phenolic compounds in barley grains have an important influence on beer flavor and stability. Drought condition enhances the content of phenolics in barley grains, leading to reduced malt quality. In this study, two barley genotypes, XZ20 and XZ25 with different total phenolics content were used to investigate the effect of drought on phenolic compounds during grain developing stage. Totally, 118 phenolic metabolites were affected by drought stress. A weighted gene co-expression network analysis (WGCNA) of 17,424 highly expressed genes uncovered black (two hub genes belonged to UGT family) and turquoise modules (three hub genes belonged to phenolics pathway) that are significantly associated with the variation of phenolics. All these results reveal the changes of phenolic metabolites during grain development and provide a new insight into the regulation network of phenolic compounds under drought stress.

Discovering the bacteriome of Vitis vinifera cv. Pinot Noir in a conventionally managed vineyard

The structure of the bacteriome associated with grapevine roots can affect plant development, health and grape quality. We previously investigated the bacterial biodiversity of the Vitis vinifera cv. Pinot Noir rhizosphere in a vineyard subjected to integrated pest management. The aim of this work is to characterize the bacteriome of V. vinifera cv. Pinot Noir in a conventionally managed vineyard using a metabarcoding approach. Comparisons between the microbial community structure in bulk soil and rhizosphere (variable space) were performed and shifts of bacteriome according to two sampling times (variable time) were characterized. Bacterial biodiversity was higher at the second than at the first sampling and did not differ according to the variable space. Actinobacteria was the dominant class, with Gaiella as the most represented genus in all the samples. Among Proteobacteria, the most represented classes were Alpha, Beta and Gamma-Proteobacteria, with higher abundance at the second than at the first sampling time. Bradyrhizobium was the most frequent genus among Alpha-Proteobacteria, while Burkholderia was the predominant Beta-Proteobacteria. Among Firmicutes, the frequency of Staphylococcus was higher than 60% in bulk soil and rhizosphere. Finally, the sampling time can be considered as one of the drivers responsible for the bacteriome variations assessed.

Effects of Vine Water Status and Exogenous Abscisic Acid on Berry Composition of Three Red Wine Grapes Grown under Mediterranean Climate

Beyond climatic conditions, qualitative performance is led by the intrinsic characteristics of the genotype. The aim of this study was to investigate the relationship between vine water status and exogenous abscisic acid (ABA) application on berry composition of the cultivars Cannonau, Merlot and Sangiovese. The experiment, carried out in 2016 and 2017, consisted of comparing two levels of irrigation treatments, full irrigation versus a non-irrigation treatment. Within each treatment, two sub-treatments were set up: (i) 4 mL L−1 of exogenous ABA applied at veraison to clusters only and subsequently repeated after six days; (ii) a control (untreated vines). The application of different irrigation regimes confirmed that the response to water stress is highly cultivar-dependent. Berry composition was influenced differently among cultivars by water stress. In terms of metabolites, positive influences were observed with Cannonau. No significant effects were observed by spraying exogenous ABA directly on grapes. Moreover, no significant interactions were found between the application of water stress and ABA. Exogenous ABA application did not appear to be a viticultural practice capable of influencing must composition in environments characterized by severe environmental conditions such as heat and drought.

Transcriptional changes during tomato ripening and influence of brackish water irrigation on fruit transcriptome and sugar content

Efficient management and utilization of brackish water irrigation help to minimize yield losses and promote fruit quality and sugar content in tomato fruit. However, the functional genes involved in sugar metabolic pathways and potential molecular pathways responsive to brackish water irrigation remain unknown. To this end, physiological responses and comparative transcriptional profiling was used to analyze the tomato fruit during the white-ripe period (CK1) and mature period (CK2) in plants grown under four water management strategies (rotating irrigation with brackish and fresh water during fruit development, T1; fresh water irrigation, T2; mixed brackish and fresh water irrigation, T3; mixed water and fresh water irrigation in sequence, T4). Comparative analysis revealed that during fruit development (CK2 cv CK1) differentially expressed genes (DEGs) involved in photosynthetic pathways and sucrose-starch metabolism were downregulated. However, two DEGs encoding putative beta-fructofuranosidases were significantly upregulated at the mature stage, which promoted the accumulation of glucose and fructose in CK2. Comparing four types of management strategies, rotating irrigation with brackish water and fresh water (T1) led to reprograming of global gene expression. Moreover, the upregulated DEGs in T1 were significantly enriched for signaling, hormone metabolism, and stress tolerance, suggesting the coordination of both stresses signaling as well as the plant hormone. These results provide a valuable reference for rational use of brackish water in the production of high-quality tomato in arid and semi-arid regions.

Transcriptomic and metabolomic analyses reveal several critical metabolic pathways and candidate genes involved in resin biosynthesis in Pinus massoniana

Pine resin, which typically consists of terpenoids, is a natural product used in various industrial applications. Oleoresin can be obtained from the xylem tissue by wounding the stem bark. Pinus massoniana (masson pine) is an important resin-tapping tree species that originated in southern China. Masson pines with different genetic backgrounds typically have different resin-yielding capacities (RYCs). However, the mechanisms underlying high resin yield in masson pines are unclear. The aim of this study was to identify the possible genetic regulation pathways and functional genes that influence the resin yield. In this study, we conducted transcriptomic and metabolomic studies of masson pine secondary xylem with high, medium, and low RYCs. A total of 230,068 unigenes and 3894 metabolites were identified from the tissue of the secondary xylem. Several differentially expressed regulation factors, including WRKY, bHLH, and ERF, and functional genes such as PKc and LRR-RLKs, were identified among these masson pines. The Kyoto Encyclopedia of Genes and Genomes pathways were mainly focused on diterpenoid biosynthesis, plant hormone signal transduction, and ABC transporters. Furthermore, integration of the transcriptomic and metabolomic data indicated that the PKc- and LRR-RLK-related regulatory and metabolic pathways may play critical roles in the biosynthesis of terpenoids. These above results improve our understanding of the biosynthesis mechanism of oleoresin in P. massoniana and facilitate further research work into the functional analysis of these candidate genes.

Study of must and wine amino acids composition after seaweed applications to Tempranillo blanco grapevines

Recently, A.O.C. Rioja have selected and enlisted the Tempranillo blanco as a new grapevine variety to be cultivated in this area. This is the first report that studies amino acid and ammonium composition of grape juice and wine from Tempranillo blanco. The aim was to study the effect of foliar application of a seaweed extract to a Tempranillo blanco vineyard on must and wine amino acids and ammonium content. The results suggested that Tempranillo blanco behaved as an arginine accumulator variety. Biostimulation after seaweed applications at a high dosage (Hd) to the grapevines increased the concentration of several amino acids in the 2017 season, while scarcely affected their content in 2018. Phenylalanine, precursor of several volatile and phenolic compounds, was increased in both seasons after Hd applications. Season was the most important factor in the variability of the must and wine amino acids concentration, followed by treatment and its interaction.

A leucine-rich repeat-receptor-like kinase gene SbER2-1 from sorghum (Sorghum bicolor L.) confers drought tolerance in maize

BACKGROUND

ERECTA (ER) is a leucine-rich repeat-receptor-like kinase gene (LRR-RLK) encoding a protein isolated from Arabidopsis. Although the regulatory functions of ER genes have been widely explored in plant development and disease resistance, their roles in drought stress responses remain to be clarified.

RESULTS

In this study, we cloned and characterized two ER genes, SbER1-1 and SbER2-1, from the drought-tolerant model plant sorghum (Sorghum bicolor L.). Under drought stress, the two genes were expressed in the leaves and stems but not in the roots, and SbER2-1 transcript accumulation in the stem was increased. SbER2-1 was localized both on the plasma membrane and in the chloroplast. Moreover, SbER2-1 expression in Arabidopsis and maize conferred increased drought tolerance, especially in regard to water-use efficiency, increasing the net photosynthetic rate in maize under drought stress. Based on RNA-Seq analysis together with the physiological data, we conclude that the transgenic maize plants have upregulated phenylpropanoid metabolism and increased lignin accumulation under drought stress.

CONCLUSIONS

Our results demonstrate that SbER2-1 plays an important role in response to drought stress. Furthermore, photosynthetic systems and phenylpropanoid metabolism are implicated in SbER2-1-mediated drought stress tolerance mechanisms. The use of genetic engineering to regulate SbER2-1 expression in plants and to breed new varieties tolerant to drought is a research field full of potential.

Regional Discrimination of Australian Shiraz Wine Volatome by Two-Dimensional Gas Chromatography Coupled to Time-of-Flight Mass Spectrometry

Shiraz wine volatomes from two Australian geographical indications (GIs), that is, Orange and Riverina, were compared using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry. Shiraz wines were made in triplicate from grapes harvested at two harvest dates from six vineyards in the two GIs. A total of 133 compounds showed a significant trend between wines from the cooler Orange GI and warmer Riverina. Compounds associated with wines from the cooler climate were grape-derived volatiles, such as monoterpenes, sesquiterpenes, green leaf volatiles, and some norisoprenoids. Fermentation-derived compounds, such as esters and S-containing compounds, showed no specific trend related to grape origin. In addition, wines could be also clearly separated according to the harvest date, irrespective of the climate, with C6 compounds, higher alcohol acetates, and other esters contributing utmost to the differentiation of samples, whereas terpenoids and norisoprenoids did not have an influence. This study demonstrated the plasticity of wine volatome related to grape origin and also the maturity level (harvest date), irrespective of climate.

Transcriptomic and Gas Chromatography-Mass Spectrometry Metabolomic Profiling Analysis of the Epidermis Provides Insights into Cuticular Wax Regulation in Developing 'Yuluxiang' Pear Fruit

The layer of cuticular wax covering fruits plays important roles in protecting against disease, preventing non-stomatal water loss, and extending shelf life. However, the molecular basis of cuticular wax biosynthesis in pear (Pyrus) fruits remains elusive. Our study thoroughly investigates cuticular wax biosynthesis during pear fruit development from morphologic, transcriptomic, and gas chromatography-mass spectrometry metabolomic perspectives. Our results showed that cuticular wax concentrations increased during the early stage [20-80 days after full bloom (DAFB)] from 0.64 mg/cm² (50 DAFB) to 1.75 mg/cm² (80 DAFB) and then slightly decreased to 1.22 mg/cm² during the fruit ripening period (80-140 DAFB). Scanning electron microscopy imaging indicated that wax plate crystals increased and wax structures varied during the pear fruit development. The combined transcriptomic and metabolomic profiling analysis revealed 27 genes, including 12 genes encoding transcription factors and a new structural gene (Pbr028523) encoding β-amyrin synthase, participating in the biosynthesis, transport, and regulation of cuticular wax according to their expression patterns in pear fruit. The quantitative real-time polymerase chain reaction experiments of 18 differentially expressed genes were performed and confirmed the accuracy of the RNA-Seq-derived transcript expression. A model of VLCFAs and cuticular wax synthesis and transport in pear fruit is proposed, providing a mechanistic framework for understanding cuticular wax biosynthesis in pear fruit. These results and data sets provide a foundation for the molecular events related to cuticular wax in 'Yuluxiang' pear fruit and may also help guide the functional analyses of candidate genes important for improving the cuticular wax of pear fruit in the future.

Time-series transcriptome provides insights into the gene regulation network involved in the volatile terpenoid metabolism during the flower development of lavender

BACKGROUND

Essential oils (EOs) of Lavandula angustifolia, mainly consist of monoterpenoids and sesquiterpenoids, are of great commercial value. The multi-flower spiciform thyrse of lavender not only determines the output of EOs but also reflects an environmental adaption strategy. With the flower development and blossom in turn, the fluctuation of the volatile terpenoids displayed a regular change at each axis. However, the molecular mechanism underlying the regulation of volatile terpenoids during the process of flowering is poorly understood in lavender. Here, we combine metabolite and RNA-Seq analyses of flowers of five developmental stages at first- and second-axis (FFDSFSA) and initial flower bud (FB0) to discover the active terpenoid biosynthesis as well as flowering-related genes.

RESULTS

A total of 56 mono- and sesquiterpenoids were identified in the EOs of L. angustifolia 'JX-2'. FB0' EO consists of 55 compounds and the two highest compounds, β-trans-ocimene (20.57%) and (+)-R-limonene (17.00%), can get rid of 74.71 and 78.41% aphids in Y-tube olfactometer experiments, respectively. With sequential and successive blossoms, temporally regulated volatiles were linked to pollinator attraction in field and olfaction bioassays. In three characteristic compounds of FFDSFSA' EOs, linalyl acetate (72.73%) and lavandulyl acetate (72.09%) attracted more bees than linalool (45.35%). Many transcripts related to flowering time and volatile terpenoid metabolism expressed differently during the flower development. Similar metabolic and transcriptomic profiles were observed when florets from the two axes were maintained at the same maturity grade. Besides both compounds and differentially expressed genes were rich in FB0, most volatile compounds were significantly correlated with FB0-specific gene module. Most key regulators related to flowering and terpenoid metabolism were interconnected in the subnetwork of FB0-specific module, suggesting the cross-talk between the two biological processes to some degree.

CONCLUSIONS

Characteristic compounds and gene expression profile of FB0 exhibit ecological value in pest control. The precise control of each-axis flowering and regular emissions at transcriptional and metabolic level are important to pollinators attraction for lavender. Our study sheds new light on lavender maximizes its fitness from "gene-volatile terpenoid-insect" three layers.

ABA Alleviates Uptake and Accumulation of Zinc in Grapevine (Vitis vinifera L.) by Inducing Expression of ZIP and Detoxification-Related Genes

Abscisic acid (ABA) is a plant hormone that can mitigate heavy metal toxicity. Exogenous ABA and ABA mimic 1 (AM1) were applied to study the influence on Zn uptake and accumulation in Vitis vinifera L. cv. Merlot seedlings exposed to excess Zn. The seedlings were treated with either normal or excess levels of Zn in combination with applications of ABA and AM1. Excess Zn exposure resulted in decreased lateral root length, decreased photosynthesis, elevated uptake, and accumulation of Zn in roots, trunks, and stems, decreased jasmonic acid content in roots and leaves, and induced the expression of Zn transportation- and detoxification-related genes. Remarkably, in the presence of toxic amounts of Zn, the exogenous application of ABA, but not of AM1, reduced the uptake and accumulation of Zn in roots and induced higher expression of both ZIP genes and detoxification-related genes in root and leaf. These results indicate that exogenous ABA enhances the tolerance of grape seedlings to excess Zn and that AM1 is not a suitable ABA mimic compound for Zn stress alleviation in grapes.

ERF109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) contributes to cold tolerance by directly regulating expression of Prx1 involved in antioxidative process

Ethylene-responsive factors (ERFs) have been revealed to play essential roles in a variety of physiological and biological processes in higher plants. However, functions and regulatory pathways of most ERFs in cold stress remain largely unclear. Here, we identified PtrERF109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) and deciphered its role in cold tolerance. PtrERF109 was drastically up-regulated by cold, ethylene and dehydration, but repressed by salt. PtrERF109 was localized in the nucleus and displayed transcriptional activity, and the C terminus is required for the activation. Overexpression of PtrERF109 conferred enhanced cold tolerance in transgenic tobacco and lemon plants, whereas VIGS (virus-induced gene silencing)-mediated suppression of PtrERF109 in trifoliate orange led to increased cold susceptibility. PtrERF109 overexpression caused extensive transcriptional reprogramming of several suites of stress-responsive genes. Prx1 encoding class III peroxidase (POD) was one of the antioxidant genes exhibiting the greatest induction. PtrERF109 was shown to directly bind to the promoter of PtrPrx1 (trifoliate orange Prx1 homologue) and positively activated its expression. In addition, the PtrERF109-overexpressing plants exhibited significantly higher POD activity and accumulated dramatically less H₂ O₂ and were more tolerant to oxidative stress, whereas the VIGS plants exhibited opposite trends, in comparison with wild type. Taken together, these results indicate that PtrERF109 as a positive regulator contributes to imparting cold tolerance by, at least partly, directly regulating the POD-encoding gene to maintain a robust antioxidant capacity for effectively scavenging the reactive oxygen species. Our findings gain insight into better understanding of transcriptional regulation of antioxidant genes in response to cold stress.

Transcriptomics of the grape berry shrivel ripening disorder

KEY MESSAGE

The lower expression at veraison of several ripening master regulators "switch genes" can play a central role in the induction of the berry shrivel ripening physiological disorder in grapevine. Berry shrivel (BS) is a ripening physiological disorder affecting grape berry with visible symptoms appearing after veraison. Berry shrivel leads to shrinking berries with a reduced weight and a lower content of sugars and anthocyanins. In this study, for the first time a transcriptomic analysis coupled with selected metabolites quantification was undertaken to understand the metabolic modifications induced by the disorder. Different stages of berry development were considered including pre- and symptomatic berries. No metabolic alterations in the berry transcriptome and in the metabolite content was observed in pre-symptomatic and pre-veraison samples. Interestingly, at veraison, with still not visible symptoms appearing on the berry, a subset of genes, called switch genes previously suggested as master regulators of the ripening onset in grape berries, were strongly lower expressed in BS. Later during the ripening phase and with visible symptoms of the disorder, more than 3000 genes were differentially expressed. The genes up-regulated were related to hormone biosynthesis, response to stress and the phenylpropanoid pathway, while the genes down-regulated during ripening belonged mainly to the flavonoid pathway, and the sugar metabolism. In agreement, BS berries showed lower content of sugars and anthocyanins from the onset of veraison onward, while the amount of acids was not significantly affected. In conclusion, these results highlight a pivotal role of the switch genes in grapevine ripening, as well as their possible contribution to induce the ripening disorder berry shrivel, although it remains unclear whether this is part of the cause or consequences of the BS disorder.

Grapevine trunk diseases under thermal and water stresses

Heat and water stresses, individually or combined, affect both the plant (development, physiology, and production) and the pathogens (growth, morphology, dissemination, distribution, and virulence). The grapevine response to combined abiotic and biotic stresses is complex and cannot be inferred from the response to each single stress. Several factors might impact the response and the recovery of the grapevine, such as the intensity, duration, and timing of the stresses. In the heat/water stress-GTDs-grapevine interaction, the nature of the pathogens, and the host, i.e., the nature of the rootstock, the cultivar and the clone, has a great importance. This review highlights the lack of studies investigating the response to combined stresses, in particular molecular studies, and the misreading of the relationship between rootstock and scion in the relationship GTDs/abiotic stresses. Grapevine trunk diseases (GTDs) are one of the biggest threats to vineyard sustainability in the next 30 years. Although many treatments and practices are used to manage GTDs, there has been an increase in the prevalence of these diseases due to several factors such as vineyard intensification, aging vineyards, or nursery practices. The ban of efficient treatments, i.e., sodium arsenite, carbendazim, and benomyl, in the early 2000s may be partly responsible for the fast spread of these diseases. However, GTD-associated fungi can act as endophytes for several years on, or inside the vine until the appearance of the first symptoms. This prompted several researchers to hypothesise that abiotic conditions, especially thermal and water stresses, were involved in the initiation of GTD symptoms. Unfortunately, the frequency of these abiotic conditions occurring is likely to increase according to the recent consensus scenario of climate change, especially in wine-growing areas. In this article, following a review on the impact of combined thermal and water stresses on grapevine physiology, we will examine (1) how this combination of stresses might influence the lifestyle of GTD pathogens, (2) learnings from grapevine field experiments and modelling aiming at studying biotic and abiotic stresses, and (3) what mechanistic concepts can be used to explain how these stresses might affect the grapevine plant status.

Optimization of Photosynthetic Photon Flux Density and Root-zone Temperature for Enhancing Secondary Metabolite Accumulation and Production of Coriander in Plant Factory

Coriander is an important aromatic plant, and contains abundant secondary metabolites that are considered to be beneficial for health. The demand for high-quality and fresh coriander in large cities has been growing rapidly. Plant factories are advanced indoor cultivation systems that can produce high-quality plants inside cities with a high productivity. This study aimed to maximize plant growth and the secondary metabolites production of coriander, by regulating photosynthetic photon flux density (PPFD) and root-zone temperature (RZT). Three PPFDs (100, 200, and 300 µmol m−2 s−1) and three RZTs (20, 25, and 30 °C) were applied on coriander plants grown hydroponically in a plant factory. The plant biomass and water content of leaf and stem were highest under RZT of 25 °C with a PPFD of 300 µmol m−2 s−1. However, chlorogenic acid, rutin, trans-2-decenal, total phenolic concentrations and the antioxidant capacity of the coriander plant were greatest under the combination of PPFD (300 µmol m−2 s−1) and RZT (30 °C). Chlorogenic acid in leaves responded more sensitively to PPFD and RZT than rutin. Controlling PPFD and RZT is effective in optimizing the yield and quality of coriander plants. The findings are expected to be applied to commercial plant production in plant factories.

Conserved MicroRNA Act Boldly During Sprout Development and Quality Formation in Pingyang Tezaocha (Camellia sinensis)

Tea tree [Camellia sinensis (L.) O. Kuntze] is an important leaf (sometimes tender stem)-using commercial plant with many medicinal uses. The development of newly sprouts would directly affect the yield and quality of tea product, especially significant for Pingyang Tezaocha (PYTZ) which takes up a large percent in the early spring tea market. MicroRNA (miRNA), particularly the conserved miRNAs, often position in the center of subtle and complex gene regulatory systems, precisely control the biological processes together with other factors in a spatio-temporal pattern. Here, quality-determined metabolites catechins, theanine and caffeine in PYTZ sprouts including buds (sBud), different development stages of leaves (sL1, sL2) and stems (sS1, sS2) were quantified. A total of 15 miRNA libraries of the same tissue with three repetitions for each were constructed to explore vital miRNAs during the biological processes of development and quality formation. We analyzed the whole miRNA profiles during the sprout development and defined conserved miRNA families in the tea plant. The differentially expressed miRNAs related to the expression profiles buds, leaves, and stems development stages were described. Twenty one miRNAs and eight miRNA-TF pairs that most likely to participate in regulating development, and at least two miRNA-TF-metabolite triplets that participate in both development and quality formation had been filtered. Our results indicated that conserved miRNA act boldly during important biological processes, they are (i) more likely to be linked with morphological function in primary metabolism during sprout development, and (ii) hold an important position in secondary metabolism during quality formation in tea plant, also (iii) coordinate with transcription factors in forming networks of complex multicellular organism regulation.

Drying the leaves of Perilla frutescens increases their content of anticancer nutraceuticals

A regular intake of plant-derived bioactive agents has gained popularity because of the health benefits. Fresh leafy greens, however, normally have a low concentration of such bioactive agents. In this study, we found that drying markedly affected the accumulation of secondary metabolites and that dried leaves of Perilla frutescens L. (perilla) contained more anticancer flavonoids than fresh leaves. Drying is a major method of food preparation, particularly for plant-based foods, but the quality of the bioactive agents contained in the fresh and dried leaves of perilla has received only scant attention. Quantitative analysis of the concentrations of perillaldehyde, rosmarinic acid, apigenin, luteolin, 4-hydroxyphenyllactic acid, and 4-coumaric acid, some of which are known as nutraceuticals, revealed that the effect of drying significantly increased apigenin (28-fold) and luteolin (86-fold), but decreased rosmarinic acid in all leaf stages. We examined the positive effect on flavonoid levels on perilla leaves and confirmed that, by comparison with fresh perilla leaves, the dried leaves contained greater concentrations of anticancer flavonoids regardless of variety, form, or manner of cultivation. This indicates that drying can significantly increase the level of flavonoids in perilla leaves without a loss of flavor. Therefore, drying is a simple and effective method to improve the concentrations of bioactive agents, which increases the intake of beneficial substances derived from herbs and edible plants. This finding serves as a method for the supply of raw plant materials rich in bioactive agents that are suitable for labeling as edible nutraceuticals.

Extensive Post-Transcriptional Regulation Revealed by Transcriptomic and Proteomic Integrative Analysis in Cassava under Drought

Cassava is a major tropical/subtropical food crop and its yield is greatly restrained by drought; however, the mechanism underlying the drought stress remains largely unknown. In this study, totally 1242 and 715 differentially expressed genes (DEGs), together with 237 and 307 differentially expressed proteins (DEPs), were respectively identified in cassava leaves and roots through RNA-seq and iTRAQ techniques. The majority of DEGs and DEPs were exclusively regulated at the mRNA and protein level, respectively, whereas only a few were commonly regulated, indicating the major involvement of post-transcriptional regulation under drought. Subsequently, the functions of these specifically or commonly regulated DEGs and DEPs were analyzed, and the post-transcriptional regulation of genes involved in heat shock protein, secondary metabolism biosynthesis, and hormone biosynthesis was extensively discussed. This is the first report on an integration of transcriptomic and proteomic analysis in cassava, and it provides new insights into the post-transcriptional regulation of cassava drought stress.

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.

Elevated atmospheric CO2 concentrations alter grapevine (Vitis vinifera) systemic transcriptional response to European grapevine moth (Lobesia botrana) herbivory

Atmospheric carbon dioxide (CO₂) concentrations are among the chief factors shaping the mode and magnitude of interactions between plants and herbivorous insects. Here, we describe the first global analysis of systemic transcriptomic responses of grapevine Vitis vinifera plants to feeding of European grapevine moth Lobesia botrana larvae at future elevated CO₂ concentrations. The study was conducted on mature, fruit-bearing grapevine plants under ambient and elevated CO₂ concentrations in a grapevine free-air carbon dioxide enrichment (FACE) facility. Grapevine transcriptional response to herbivory was clearly dependent on phenological stage, with a higher number of differentially expressed genes identified at fruit development compared to berry ripening. At fruit development, more transcripts were differentially expressed as a response to herbivory under elevated compared to ambient CO₂ concentrations. Classification of the respective transcripts revealed that in particular genes involved in metabolic pathways, biosynthesis of secondary metabolites and plant-pathogen interactions were significantly enriched. Most of these genes had similar expression patterns under both CO₂ concentrations, with a higher fold-change under elevated CO₂ concentrations. Differences in expression levels of a subset of herbivory responsive genes were further validated by RT-qPCR. Our study indicates that future elevated CO₂ concentrations will affect interactions between grapevine plants and one of its key insect pests, with consequences for future relevance of L. botrana in worldwide viticulture.

Transcriptomic and genomic structural variation analyses on grape cultivars reveal new insights into the genotype-dependent responses to water stress

Grapevine (Vitis vinifera L.) is importantly cultivated worldwide for table grape and wine production. Its cultivation requires irrigation supply, especially in arid and semiarid areas. Water deficiency can affect berry and wine quality mostly depending on the extent of plant perceived stress, which is a cultivar-specific trait. We tested the physiological and molecular responses to water deficiency of two table grape cultivars, Italia and Autumn royal, and we highlighted their different adaptation. Microarray analyses revealed that Autumn royal reacts involving only 29 genes, related to plant stress response and ABA/hormone signal transduction, to modulate the response to water deficit. Instead, cultivar Italia orchestrates a very broad response (we found 1037 differentially expressed genes) that modifies the cell wall organization, carbohydrate metabolism, response to reactive oxygen species, hormones and osmotic stress. For the first time, we integrated transcriptomic data with cultivar-specific genomics and found that ABA-perception and -signalling are key factors mediating the varietal-specific behaviour of the early response to drought. We were thus able to isolate candidate genes for the genotype-dependent response to drought. These insights will allow the identification of reliable plant stress indicators and the definition of sustainable cultivar-specific protocols for water management.

Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

BACKGROUND

Drought is an important constraint on grapevine sustainability. Vitis riparia, widely used in rootstock and scion breeding, has been studied in isolated leaf drying response studies; however, it is essential to identify key root and shoot water deficit signaling traits in intact plants. This information will aid improved scion and rootstock selection and management practices in grapevine. RNAseq data were generated from V. riparia roots and shoots under water deficit and well-watered conditions to determine root signaling and shoot responses to water deficit.

RESULTS

Shoot elongation, photosynthetic rate, and stomatal conductance were significantly reduced in water deficit (WD) treated than in well-watered grapevines. RNAseq analysis indicated greater transcriptional differences in shoots than in roots under WD, with 6925 and 1395 genes differentially expressed, respectively (q-value < 0.05). There were 50 and 25 VitisNet pathways significantly enriched in WD relative to well-watered treatments in grapevine shoots and roots, respectively. The ABA biosynthesis genes beta-carotene hydroxylase, zeaxanthin epoxidase, and 9-cis-epoxycarotenoid dioxygenases were up-regulated in WD root and WD shoot. A positive enrichment of ABA biosynthesis genes and signaling pathways in WD grapevine roots indicated enhanced root signaling to the shoot. An increased frequency of differentially expressed reactive oxygen species scavenging (ROS) genes were found in the WD shoot. Analyses of hormone signaling genes indicated a strong ABA, auxin, and ethylene network and an ABA, cytokinin, and circadian rhythm network in both WD shoot and WD root.

CONCLUSIONS

This work supports previous findings in detached leaf studies suggesting ABA-responsive binding factor 2 (ABF2) is a central regulator in ABA signaling in the WD shoot. Likewise, ABF2 may have a key role in V. riparia WD shoot and WD root. A role for ABF3 was indicated only in WD root. WD shoot and WD root hormone expression analysis identified strong ABA, auxin, ethylene, cytokinin, and circadian rhythm signaling networks. These results present the first ABA, cytokinin, and circadian rhythm signaling network in roots under water deficit. These networks point to organ specific regulators that should be explored to further define the communication network from soil to shoot.

Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress

BACKGROUND

Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest.

RESULTS

The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca²⁺ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened.

CONCLUSIONS

The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program.

From Flavanols Biosynthesis to Wine Tannins: What Place for Grape Seeds?

Phenolic compounds are among the most important quality factors of wines. They contribute to the organoleptic characteristics of wine such as color, astringency, and bitterness. Although tannins found in wine can come from microbial and oak sources, the main sources of polyphenols are grape skins and seeds. Since the 1960s, this subject has been widely studied by a large number of researchers covering different types of wine, climate conditions, growing practices, and grape varieties. As these works have been conducted under different conditions, the data collected can be conflicting. Moreover, even though the biosynthesis of the major proanthocyanidins units (+)-catechin and (-)-epicatechin is well-known, the mechanism of their polymerization remains unexplained. This is why the question remains: what factors influence the biosynthesis, the quantity, and the distribution of tannins in grape seeds and how can winemaking processes impact the extractability of seed tannins in wine?

Transcriptome analysis and metabolic profiling reveal the key role of α-linolenic acid in dormancy regulation of European pear

Deciduous trees require sufficient chilling during winter dormancy to grow. To decipher the dormancy-regulating mechanism, we carried out RNA sequencing (RNA-Seq) analysis and metabolic profiling of European pear (Pyrus communis L.) vegetative buds during the dormancy phases. Samples were collected from two cultivars that differed greatly in their chilling requirements: 'Spadona' (SPD), a low chilling requirement cultivar; and Harrow Sweet (HS), a high chilling requirement cultivar. Comparative transcriptome analysis revealed >8500 differentially expressed transcripts; most were related to metabolic pathways. Out of 174 metabolites, 44 displayed differential levels in both cultivars, 38 were significantly changed only in SPD, and 15 only in HS. Phospholipids were mostly accumulated at the beginning of dormancy, sugars between before dormancy and mid-dormancy, and fatty acids, including α-linolenic acid, at dormancy break. Differentially expressed genes underlying previously identified major quantitative trait loci (QTLs) in linkage group 8 included genes related to the α-linolenic acid pathway, 12-oxophytodienoate reductase 2-like, and the DORMANCY-ASSOCIATED MADS-BOX (DAM) genes, PcDAM1 and PcDAM2, putative orthologs of PpDAM1 and PpDAM2, confirming their role for the first time in European pear. Additional new putative dormancy-related uncharacterized genes and genes related to metabolic pathways are suggested. These results suggest the crucial role of α-linolenic acid and DAM genes in pear bud dormancy phase transitions.

Impact of agronomic practices on grape aroma composition: a review

Aroma compounds are secondary metabolites that play a key role in grape quality for enological purposes. Terpenes, C₁₃ -norisoprenoids, phenols, and non-terpenic alcohols are the most important aroma compounds in grapes and they can be found as free volatiles or glycoconjugated (bound) molecules. The non-volatile glycosylated group is the largest, and it is present in all varieties of Vitis vinifera (L.), the most widely used species for wine production. These aroma precursors represent the reserve of aroma molecules that can be released during winemaking. Their relative and absolute concentrations at fruit ripening determine the organoleptic value of the final product. A large range of biotic and abiotic factors can influence their biosynthesis in several ways. Agronomic practices such as irrigation, training systems, leaf removal, and bunch thinning can have an effect at plant level. The spraying of stimulatory compounds on fruit at different developmental stages has also been shown to modify metabolic pathways at fruit level with some impact on the aroma composition of the grapevine fruit. Viticulturists could act to promote aroma precursors to improve the aromatic profile of grapes and the wine ultimately produced. However, agronomic practices do not always have uniform results. The metabolic and physiological changes resulting from agronomic practices are unknown because there has not been sufficient research to date. This review presents the state of the art regarding the influences of vineyard agronomic management on the biosynthesis of grape aroma compounds. Although literature regarding the topic is abundant there are still many unknown biological mechanisms involved and/or that have been insufficiently studied. The aim of this work is therefore to find the gaps in scientific literature so that future investigations can focus on them. © 2018 Society of Chemical Industry.

Seasonal changes in amino acids and phenolic compounds in fruits from hybrid cross populations of American grapes differing in disease resistance

The production of wine grapes in upstate New York (USA) is limited by diseases that are promoted by the cool and sometimes rainy climate. A breeding program has been introducing disease resistance from related species into the cultivated stock. Previous work has indicated that such resistance may be based on biochemical reactions rather than on a hypersensitive reaction. We therefore undertook metabolic profiling of amino acids and phenolic compounds in berries from collections of susceptible and resistant hybrids over the course of berry development to determine whether any of these compounds could be causal in disease resistance. The most abundant amino acids were GLN, ARG, PRO and THR. The amount of amino acids in ripe berries was from 3 to 4.7-fold higher compared to earlier stages. The concentrations of total phenolics were variable through the season with no consistent trend between susceptible and resistant fruits. Notable changes in phenolic compounds, especially anthocyanins, were recorded, especially during the ripening phase, when phenolics and anthocyanins increased following veraison. The most abundant phenolic compounds were catechin and epi-catechin; the most abundant anthocyanin was delphinidin-3-glucoside, which had a slightly greater concentration in resistant fruit at harvest, followed by malvidin-3-glucoside and petunidin-3-glucoside. The content of both amino acids and phenolic compounds in white-fruited parent cv. Horizon was equal to several-fold lower than the progeny plants, whether susceptible or resistant, depending on the harvest time. While no major differences between susceptible and resistant lines were found, multivariate analyses showed that it is possible to discriminate the susceptibility or resistance of grapes by analyzing their combined concentrations of amino acids, polyphenols and anthocyanins. Therefore, these compounds are influenced by the resistance capacity of grapes and could be used as a chemical fingerprint of this ability. However, it is likely that these are associations with disease resistance rather than their cause as no major consistent differences were noted.

Comparative Transcriptome Analysis of the Skin-Specific Accumulation of Anthocyanins in Black Peanut ( Arachis hypogaea L.)

As an oil crop with good taste and profuse nutrition, peanut ( Arachis hypogaea L.) is grown worldwide, mainly for edible seeds. Black peanuts attract more attention for their appealing color and health-promoting anthocyanins. Here, two cyanidin-based anthocyanins and four quercetin-based flavonols were separated and identified from skins of two black cultivars (Zi Yu and Zi Guan) by HPLC-ESI-Q-TOF-MS. To study the anthocyanin accumulation, libraries constructed from the mRNA of skins of Zi Yu and white cultivar (Bai Yu) were sequenced, and 4042 differentially expressed genes were identified. Gene ontology and KEGG pathway analysis underlined the importance of the high expression of flavonoid biosynthetic and regulatory genes in seed skin of Zi Yu. Furthermore, expression profiles of these genes were analyzed carefully in four representative peanut cultivars. Altogether, these results strongly indicate that the up-regulation of transcriptional activators (AhMYB1, AhMYB2, and AhTT8) accounts for the skin-specific accumulation of anthocyanins in black peanut.

Comparative Metabolic Profiling of Grape Skin Tissue along Grapevine Berry Developmental Stages Reveals Systematic Influences of Root Restriction on Skin Metabolome

This research aimed to comparatively evaluate the influences of root restriction (RR) cultivation and traditional cultivation (RC) on grape berry skin metabolomics using a non-targeted metabolomics method. Two-hundred-and-ninety-one metabolites were annotated and the kinetics analyses showed that berry skin metabolome is stage- and cultivation-dependent. Our results showed that RR influences significantly the metabolomes of berry skin tissues, particularly on secondary metabolism, and that this effect is more obvious at pre-veraison stage, which was evidenced by the early and fast metabolic shift from primary to secondary metabolism. Altogether, this study provided an insight into metabolic adaptation of berry skin to RR stress and expanded general understanding of berry development.

Comparison of transcriptional expression patterns of phenols and carotenoids in 'Kyoho' grapes under a two-crop-a-year cultivation system

To fully utilize the characteristic climatic conditions in the southern region of China, a two-crop-a-year cultivation system technique for ‘Kyoho’ grape was developed during the past decade. After summer harvest in June, appropriate pruning and chemical treatments promote flowering and fruiting, which enables a second harvest in late December. Due to climatic differences between the two crop growing seasons, grape phenol and carotenoid metabolism differ greatly. The reported study analyzed the transcriptome of the carotenoid and phenylpropanoid/flavonoid pathways in grapes at four different stages during the two growing seasons. Compared with those in summer grapes, expression levels of the majority of genes involved in the carotenoid metabolic pathway in winter grapes were generally upregulated. This result was associated with lower rainfall and much more abundant sunlight during the second growing season. On the other hand, summer cropping strongly triggered the expression of upstream genes in the phenylpropanoid/flavonoid pathway at E-L 33 and E-L 35. Transcript levels of flavonoid 3’,5’-hydroxylase (F3’5’H), flavonoid 3’-hydroxylase (F3’H), flavonoid 3-hydroxylase (F3H) and glutathione S-transferase (GST) were upregulated in winter grapes at the mature stage. Together, these results might indicate that more flavonoids would be synthesized in ripe winter grapes during the mature stage of the second crop under much drier conditions, longer sunlight hours and lower temperature. These data provide a theoretical foundation for the secondary metabolism of berries grown under two-crop-a-year cultivation systems.

RNA-Seq analysis unveils gene regulation of fruit size cooperatively determined by velocity and duration of fruit swelling in peach

Fruit swelling determines fruit size and usually occurs in two distinct time periods in peach. However, little is known about the gene regulation of fruit swelling. In this study, measurements of longitudinal and transverse diameters in developing and ripening peach fruits unveiled two periods of fruit swelling: the first swelling ends at approximately 65 days after flower blooming (DAFB) and the second swelling starts at approximately 75 DAFB. Comparisons of diameters sizes and development periods among cultivars and accessions revealed a cooperative regulation of swelling velocity and swelling duration, which leads to final determination of fruit size. Furthermore, RNA-sequencing was conducted for fruits at the initial swelling, non-swelling interval between the two swellings (hereafter, 'the interval'), second swelling and ripening stages. A total of 110 and 128 differentially expressed genes were screened from fruits in the first and second swelling, respectively. Besides, the nine most differentially expressed genes located within the reported quantitative trait locations (QTLs) of fruit size in peach were detected in both the first and second swelling stages. Those genes have been reported to be involved in mediating cell size, which indicates the occurrence of both cell proliferation and cell expansion in each of the two major periods of fruit swelling. In addition, a potential gene regulation network is proposed herein and could be used to elucidate the molecular mechanism of peach fruit swellings mediated by multiple key genes.

Timing and Order of the Molecular Events Marking the Onset of Berry Ripening in Grapevine

Grapevine (Vitis vinifera) is a model for the investigation of physiological and biochemical changes during the formation and ripening of nonclimacteric fleshy fruits. However, the order and complexity of the molecular events during fruit development remain poorly understood. To identify the key molecular events controlling berry formation and ripening, we created a highly detailed transcriptomic and metabolomic map of berry development, based on samples collected every week from fruit set to maturity in two grapevine genotypes for three consecutive years, resulting in 219 samples. Major transcriptomic changes were represented by coordinated waves of gene expression associated with early development, veraison (onset of ripening)/midripening, and late-ripening and were consistent across vintages. The two genotypes were clearly distinguished by metabolite profiles and transcriptional changes occurring primarily at the veraison/midripening phase. Coexpression analysis identified a core network of transcripts as well as variations in the within-module connections representing varietal differences. By focusing on transcriptome rearrangements close to veraison, we identified two rapid and successive shared transitions involving genes whose expression profiles precisely locate the timing of the molecular reprogramming of berry development. Functional analyses of two transcription factors, markers of the first transition, suggested that they participate in a hierarchical cascade of gene activation at the onset of ripening. This study defined the initial transcriptional events that mark and trigger the onset of ripening and the molecular network that characterizes the whole process of berry development, providing a framework to model fruit development and maturation in grapevine.

iTRAQ-Based Quantitative Proteomic Analysis of Chemically Induced Aquilaria sinensis Provides Insights into Agarwood Formation Mechanism

Agarwood is a precious traditional Chinese medicine with a variety of pharmacological effects. Although efforts have been made in elucidating the mechanism of agarwood formation, little progress is obtained till now. Therefore, the molecular mechanism of agarwood formation needs to be further explored using different biological approaches. In this study, the quantitative proteomic analysis using iTRAQ technology combined with transcriptomic and metabolomic analyses on chemically induced Aquilaria sinensis is performed to elucidate the agarwood formation mechanism by formic acid stimulus. Data are available via ProteomeXchange with identifier PXD007586; 1884 proteins are detected, 504 differential proteins that show at least twofold differences in their expression levels are selected based on GO annotations, KEGG, STRING analysis, and quantitative RT-PCR analysis. The results indicate that sesquiterpene synthase, germin-like protein, pathogenesis-related protein, 6-phosphogluconate dehydrogenase, lipoyl synthase, and superoxide dismutase play important roles in the agarwood formation, suggesting that the proteins related to the plant defensive response, the removal of peroxide, the disease-resistance, the biosythesis of glycan, fatty acids, and sesquiterpene are crucial for agarwood formation.

Identification, characterization, and expression analysis of calmodulin and calmodulin-like genes in grapevine (Vitis vinifera) reveal likely roles in stress responses

Calcium (Ca²⁺) is an ubiquitous key second messenger in plants, where it modulates many developmental and adaptive processes in response to various stimuli. Several proteins containing Ca²⁺ binding domain have been identified in plants, including calmodulin (CaM) and calmodulin-like (CML) proteins, which play critical roles in translating Ca²⁺ signals into proper cellular responses. In this work, a genome-wide analysis conducted in Vitis vinifera identified three CaM- and 62 CML-encoding genes. We assigned gene family nomenclature, analyzed gene structure, chromosomal location and gene duplication, as well as protein motif organization. The phylogenetic clustering revealed a total of eight subgroups, including one unique clade of VviCaMs distinct from VviCMLs. VviCaMs were found to contain four EF-hand motifs whereas VviCML proteins have one to five. Most of grapevine CML genes were intronless, while VviCaMs were intron rich. All the genes were well spread among the 19 grapevine chromosomes and displayed a high level of duplication. The expression profiling of VviCaM/VviCML genes revealed a broad expression pattern across all grape organs and tissues at various developmental stages, and a significant modulation in biotic stress-related responses. Our results highlight the complexity of CaM/CML protein family also in grapevine, supporting the versatile role of its different members in modulating cellular responses to various stimuli, in particular to biotic stresses. This work lays the foundation for further functional and structural studies on specific grapevine CaMs/CMLs in order to better understand the role of Ca²⁺-binding proteins in grapevine and to explore their potential for further biotechnological applications.

Comparative analysis of root transcriptome profiles between drought-tolerant and susceptible wheat genotypes in response to water stress

Water deficit is one of the major factors limiting crop productivity worldwide. Plant roots play a key role in uptaking water, perceiving and transducing of water deficit signals to shoot. Although the mechanisms of drought-tolerance have been reported recently, the transcriptional regulatory network of wheat root response to water stress has not been fully understood. In this study, drought-tolerant cultivar JM-262 and susceptible cultivar LM-2 are planted to characterize the root transcriptional changes and physiological responses to water deficit. A total of 8197 drought tolerance-associated differentially expressed genes (DEGs) are identified, these genes are mainly mapped to carbon metabolism, flavonoid biosynthesis, and phytohormone signal transduction. The number and expression level of DEGs involved in antioxidative and antiosmotic stresses are more enhanced in JM-262 under water stress. Furthermore, we find the DEGs related to root development are much more induced in JM-262 in phytohormone signal transduction and carbon metabolism pathway. In conclusion, JM-262 may alleviate the damage of drought by producing more osmoprotectants, ROS scavengers, biomass and energy. Interestingly, hormone signaling and cross-talk probably play an important role in promoting JM-262 greater root systems to take up more water, higher capabilities to induce more drought-related DEGs and higher resisitance to oxidative stresse.

Arbuscular Mycorrhizal Symbiosis as a Promising Resource for Improving Berry Quality in Grapevines Under Changing Environments

Climate change and their resulting impacts are becoming a concern for winegrowers due to the high socioeconomic relevance of the winemaking sector worldwide. In fact, the projected climate change is expected to have detrimental impacts on the yield of grapevines, as well as on the quality and properties of grapes and wine. It is well known that arbuscular mycorrhizal fungi (AMF) can improve the nutritional quality of edible parts of crops and play essential roles in the maintenance of host plant fitness under stressed environments, including grapevines. The future scenarios of climate change may also modify the diversity and the growth of AMF in soils as well as the functionality of the mycorrhizal symbiosis. In this review, we summarize recent research progress on the effects of climate change on grapevine metabolism, paying special attention to the secondary compounds involved in the organoleptic properties of grapes and wines and to the levels of the phytohormones implied in the control of berry development and fruit ripening. In this context, the potential role of AMF for maintaining fruit quality in future climate change scenarios is discussed.

Gene Discovery of Characteristic Metabolic Pathways in the Tea Plant (Camellia sinensis) Using 'Omics'-Based Network Approaches: A Future Perspective

Characteristic secondary metabolites, including flavonoids, theanine and caffeine, in the tea plant (Camellia sinensis) are the primary sources of the rich flavors, fresh taste, and health benefits of tea. The decoding of genes involved in these characteristic components is still significantly lagging, which lays an obstacle for applied genetic improvement and metabolic engineering. With the popularity of high-throughout transcriptomics and metabolomics, 'omics'-based network approaches, such as gene co-expression network and gene-to-metabolite network, have emerged as powerful tools for gene discovery of plant-specialized (secondary) metabolism. Thus, it is pivotal to summarize and introduce such system-based strategies in facilitating gene identification of characteristic metabolic pathways in the tea plant (or other plants). In this review, we describe recent advances in transcriptomics and metabolomics for transcript and metabolite profiling, and highlight 'omics'-based network strategies using successful examples in model and non-model plants. Further, we summarize recent progress in 'omics' analysis for gene identification of characteristic metabolites in the tea plant. Limitations of the current strategies are discussed by comparison with 'omics'-based network approaches. Finally, we demonstrate the potential of introducing such network strategies in the tea plant, with a prospects ending for a promising network discovery of characteristic metabolite genes in the tea plant.

Responses of grapevine rootstocks to drought through altered root system architecture and root transcriptomic regulations

Roots are the major interface between the plant and various stress factors in the soil environment. Alteration of root system architecture (RSA) (root length, spread, number and length of lateral roots) in response to environmental changes is known to be an important strategy for plant adaptation and productivity. In light of ongoing climate changes and global warming predictions, the breeding of drought-tolerant grapevine cultivars is becoming a crucial factor for developing a sustainable viticulture. Root-trait modeling of grapevine rootstock for drought stress scenarios, together with high-throughput phenotyping and genotyping techniques, may provide a valuable background for breeding studies in viticulture. Here, tree grafted grapevine rootstocks (110R, 5BB and 41B) having differential RSA regulations and drought tolerance were investigated to define their drought dependent root characteristics. Root area, root length, ramification and number of root tips reduced less in 110R grafted grapevines compared to 5BB and 41B grafted ones during drought treatment. Root relative water content as well as total carbohydrate and nitrogen content were found to be much higher in the roots of 110R than it was in the roots of other rootstocks under drought. Microarray-based root transcriptome profiling was also conducted on the roots of these rootstocks to identify their gene regulation network behind drought-dependent RSA alterations. Transcriptome analysis revealed totally 2795, 1196 and 1612 differentially expressed transcripts at the severe drought for the roots of 110R, 5BB and 41B, respectively. According to this transcriptomic data, effective root elongation and enlargement performance of 110R were suggested to depend on three transcriptomic regulations. First one is the drought-dependent induction in sugar and protein transporters genes (SWEET and NRT1/PTR) in the roots of 110R to facilitate carbohydrate and nitrogen accumulation. In the roots of the same rootstock, expression increase in osmolyte producer genes revealed another transcriptomic regulation enabling effective root osmotic adjustment under drought stress. The third mechanism was linked to root suberization with upregulation of transcripts functional in wax producing enzymes (Caffeic acid 3-O-methyltransferase, Eceriferum3, 3-ketoacyl-CoAsynthase). These three transcriptomic regulations were suggested to provide essential energy and water preservation to the roots of 110R for its effective RSA regulation under drought. This phenotypic and genotypic knowledge could be used to develop root-dependent drought tolerant grapevines in breeding programs and could facilitate elucidation of genetic regulations behind RSA alteration in other plants.

Grape Berry Acclimation to Excessive Solar Irradiance Leads to Repartitioning between Major Flavonoid Groups

Warm viticulture regions are associated with inferior wines, resulting from the interaction between microclimate and fruit biochemistry. Solar irradiance triggers biosynthetic processes in the fruit and dominates its thermal balance. Therefore, deciphering its impact on fruit metabolism is pivotal to develop strategies for fruit protection and ameliorate its quality traits. Here, we modified light quality and intensity in the fruit-zone and integrated micrometeorology with grape and wine metabolomics, allowing a complete assessment, from field to bottle. We analyzed the dynamics of fruit's adaptation to altered conditions during ripening and constructed temporal-based metabolic networks. Micrometeorological modifications shifted the balance between the major flavonoids, associating increased solar exposure with lower levels of anthocyanins and flavan-3-ols, and higher flavonols. Differences were fixed from 2 weeks postveraison until harvest, suggesting a controlled acclimation response rather than external modulation. Differences in grape composition manifested in the wine and resulted in higher color intensity and improved wine hue under partial shading.

Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases

Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset. This revealed strong correlations between ATL proteins and diverse signal transduction components and transcriptional regulators, in particular those involved in immunity. An enrichment analysis of cis-regulatory elements in ATL gene promoters and related co-expressed genes highlighted the importance of hormones in the regulation of ATL gene expression. Our work identified several ATL proteins as candidates for further studies aiming to decipher specific grapevine resistance mechanisms activated in response to pathogens.

Molecular Profiling of Pierce's Disease Outlines the Response Circuitry of Vitis vinifera to Xylella fastidiosa Infection

Pierce's disease is a major threat to grapevines caused by the bacterium Xylella fastidiosa. Although devoid of a type 3 secretion system commonly employed by bacterial pathogens to deliver effectors inside host cells, this pathogen is able to influence host parenchymal cells from the xylem lumen by secreting a battery of hydrolytic enzymes. Defining the cellular and biochemical changes induced during disease can foster the development of novel therapeutic strategies aimed at reducing the pathogen fitness and increasing plant health. To this end, we investigated the transcriptional, proteomic, and metabolomic responses of diseased Vitis vinifera compared to healthy plants. We found that several antioxidant strategies were induced, including the accumulation of gamma-aminobutyric acid (GABA) and polyamine metabolism, as well as iron and copper chelation, but these were insufficient to protect the plant from chronic oxidative stress and disease symptom development. Notable upregulation of phytoalexins, pathogenesis-related proteins, and various aromatic acid metabolites was part of the host responses observed. Moreover, upregulation of various cell wall modification enzymes followed the proliferation of the pathogen within xylem vessels, consistent with the intensive thickening of vessels' secondary walls observed by magnetic resonance imaging. By interpreting the molecular profile changes taking place in symptomatic tissues, we report a set of molecular markers that can be further explored to aid in disease detection, breeding for resistance, and developing therapeutics.