Transcriptomics integrated with metabolomics reveals the effect of regulated deficit irrigation on anthocyanin biosynthesis in Cabernet Sauvignon grape berries

Different frequencies of water deficit irrigation treatments improve fruit quality of Zitian seedless grapes under on-tree storage

In this study, we assessed the impact of varied water deficit irrigation frequencies (T1: 2.5 L/4 days; T2: 5 L/8 days; CK: 5 L/4 days) on Zitian Seedless grapes from veraison to post-ripening. Notably, total soluble solids increased during on-tree storage compared to at maturity, while total anthocyanin content decreased, particularly in CK (60.16%), T1 (62.35%), and less in T2 (50.54%). Glucose and fructose levels increased significantly in T1 and T2, more so in T2, but slightly declined in CK. Tartaric acid content increased by 41.42% in T2. Moreover, compared to regular irrigation, water deficit treatments enhanced phenolic metabolites and volatile compounds, including chlorogenic acid, various flavonoids, viniferin, hexanal, 2-nonenal, 2-hexen-1-ol, (E)-, 3-hydroxy-dodecanoic acid, and 1-hexanol, etc. Overall, the T2 treatment outperformed T1 and CK in maintaining grape quality. This study reveals that combining on-tree storage with water deficit irrigation not only improves grape quality but also water efficiency.

Multi-omics analysis reveals key regulatory defense pathways and genes involved in salt tolerance of rose plants

Salinity stress causes serious damage to crops worldwide, limiting plant production. However, the metabolic and molecular mechanisms underlying the response to salt stress in rose (Rosa spp.) remain poorly studied. We therefore performed a multi-omics investigation of Rosa hybrida cv. Jardin de Granville (JDG) and Rosa damascena Mill. (DMS) under salt stress to determine the mechanisms underlying rose adaptability to salinity stress. Salt treatment of both JDG and DMS led to the buildup of reactive oxygen species (H2O2). Palisade tissue was more severely damaged in DMS than in JDG, while the relative electrolyte permeability was lower and the soluble protein content was higher in JDG than in DMS. Metabolome profiling revealed significant alterations in phenolic acid, lipids, and flavonoid metabolite levels in JDG and DMS under salt stress. Proteome analysis identified enrichment of flavone and flavonol pathways in JDG under salt stress. RNA sequencing showed that salt stress influenced primary metabolism in DMS, whereas it substantially affected secondary metabolism in JDG. Integrating these datasets revealed that the phenylpropane pathway, especially the flavonoid pathway, is strongly enhanced in rose under salt stress. Consistent with this, weighted gene coexpression network analysis (WGCNA) identified the key regulatory gene chalcone synthase 1 (CHS1), which is important in the phenylpropane pathway. Moreover, luciferase assays indicated that the bHLH74 transcription factor binds to the CHS1 promoter to block its transcription. These results clarify the role of the phenylpropane pathway, especially flavonoid and flavonol metabolism, in the response to salt stress in rose.

Dietary Sources, Stabilization, Health Benefits, and Industrial Application of Anthocyanins-A Review

Natural phytochemicals are well known to protect against numerous metabolic disorders. Anthocyanins are vacuolar pigments belonging to the parent class of flavonoids. They are well known for their potent antioxidant and gut microbiome-modulating properties, primarily responsible for minimizing the risk of cardiovascular diseases, diabetes, obesity, neurodegenerative diseases, cancer, and several other diseases associated with metabolic syndromes. Berries are the primary source of anthocyanin in the diet. The color and stability of anthocyanins are substantially influenced by external environmental conditions, constraining their applications in foods. Furthermore, the significantly low bioavailability of anthocyanins greatly diminishes the extent of the actual health benefits linked to these bioactive compounds. Multiple strategies have been successfully developed and utilized to enhance the stability and bioavailability of anthocyanins. This review provides a comprehensive view of the recent advancements in chemistry, biosynthesis, dietary sources, stabilization, bioavailability, industrial applications, and health benefits of anthocyanins. Finally, we summarize the prospects and challenges of applications of anthocyanin in foods.

Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars

BACKGROUND

Drought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that 'ZC9-3' is a strong drought-resistant rootstock, whereas 'Jizhen-2' is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear.

RESULTS

In this study, the physiological and molecular mechanisms underlying differences in the drought resistance of 'Jizhen-2' (drought-sensitive) and 'ZC9-3' (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in 'ZC9-3' than in 'Jizhen-2', and the photosynthetic, antioxidant, and osmoregulatory capacities of 'ZC9-3' were stronger than those of 'Jizhen-2'. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in 'Jizhen-2' and 'ZC9-3' under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in 'ZC9-3' than in 'Jizhen-2' throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between 'ZC9-3' and 'Jizhen-2'. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of 'ZC9-3' to drought stress.

CONCLUSIONS

This study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.

Transcriptomics and metabolomics reveal the underlying mechanism of drought treatment on anthocyanin accumulation in postharvest blood orange fruit

BACKGROUND

Anthocyanins are the most important compounds for nutritional quality and economic values of blood orange. However, there are few reports on the pre-harvest treatment accelerating the accumulation of anthocyanins in postharvest blood orange fruit. Here, we performed a comparative transcriptome and metabolomics analysis to elucidate the underlying mechanism involved in seasonal drought (SD) treatment during the fruit expansion stage on anthocyanin accumulation in postharvest 'Tarocco' blood orange fruit.

RESULTS

Our results showed that SD treatment slowed down the fruit enlargement and increased the sugar accumulation during the fruit development and maturation period. Obviously, under SD treatment, the accumulation of anthocyanin in blood orange fruit during postharvest storage was significantly accelerated and markedly higher than that in CK. Meanwhile, the total flavonoids and phenols content and antioxidant activity in SD treatment fruits were also sensibly increased during postharvest storage. Based on metabolome analysis, we found that substrates required for anthocyanin biosynthesis, such as amino acids and their derivatives, and phenolic acids, had significantly accumulated and were higher in SD treated mature fruits compared with that of CK. Furthermore, according to the results of the transcriptome data and weighted gene coexpression correlation network analysis (WGCNA) analysis, phenylalanine ammonia-lyase (PAL3) was considered a key structural gene. The qRT-PCR analysis verified that the PAL3 was highly expressed in SD treated postharvest stored fruits, and was significantly positively correlated with the anthocyanin content. Moreover, we found that other structural genes in the anthocyanin biosynthesis pathway were also upregulated under SD treatment, as evidenced by transcriptome data and qRT-PCR analysis.

CONCLUSIONS

The findings suggest that SD treatment promotes the accumulation of substrates necessary for anthocyanin biosynthesis during the fruit ripening process, and activates the expression of anthocyanin biosynthesis pathway genes during the postharvest storage period. This is especially true for PAL3, which co-contributed to the rapid accumulation of anthocyanin. The present study provides a theoretical basis for the postharvest quality control and water-saving utilization of blood orange fruit.

Exogenous Calcium Alleviates Oxidative Stress Caused by Salt Stress in Peanut Seedling Roots by Regulating the Antioxidant Enzyme System and Flavonoid Biosynthesis

Soil salinity is one of the adversity stresses plants face, and antioxidant defense mechanisms play an essential role in plant resistance. We investigated the effects of exogenous calcium on the antioxidant defense system in peanut seedling roots that are under salt stress by using indices including the transcriptome and absolute quantitative metabolome of flavonoids. Under salt stress conditions, the antioxidant defense capacity of enzymatic systems was weakened and the antioxidant capacity of the linked AsA-GSH cycle was effectively inhibited. In contrast, the ascorbate biosynthesis pathway and its upstream glycolysis metabolism pathway became active, which stimulated shikimate biosynthesis and the downstream phenylpropanoid metabolism pathway, resulting in an increased accumulation of flavonoids, which, as one of the antioxidants in the non-enzymatic system, provide hydroxyl radicals to scavenge the excess reactive oxygen species and maintain the plant's vital activities. However, the addition of exogenous calcium caused changes in the antioxidant defense system in the peanut root system. The activity of antioxidant enzymes and the antioxidant capacity of the AsA-GSH cycle were enhanced. Therefore, glycolysis and phenylpropanoid metabolism do not exert antioxidant function, and flavonoids were no longer synthesized. In addition, antioxidant enzymes and the AsA-GSH cycle showed a trade-off relationship with sugars and flavonoids.

Effects of water stress on endogenous hormones and free polyamines in different tissues of grapevines (Vitis vinifera L. cv. 'Merlot')

Water stress can affect plant ecological distribution, crop growth and carbohydrate distribution, impacting berry quality. However, previous studies mainly focused on short-term water stress or osmotic stress and few studies paid attention to the responses of grape to long-term water stresses. Grapevines were subjected to no water stress (CK), mild water stress (T1) and moderate water stress (T2). Hundred-berry weight and malic acid content were reduced under T1 and T2; however, glucose and fructose content showed the opposite trend. Endogenous hormones and polyamines (PAs) can regulate plant growth and development as well as physiological metabolic processes. T1 and T2 could increase abscisic acid content, however, indole-3-acetic acid, jasmonate, gibberellins 3 and 4, cytokinin and trans -zeatin contents were slightly decreased. Three species of PAs (putrescine, spermidine and spermine) were detected, presenting obvious tissue specificity. Furthermore, there was a statistically positive correlation relating spermidine content in the pulp with glucose and fructose contents of grape berries; and a negative correlation with organic acid. In summary, water stress had a profound influence on hormonally-driven changes in physiology and berry quality, indicating that endogenous hormones and the PAs play a critical role in the development and ripening of grape berries under water stress.

Metabolome and Transcriptome Analyses Reveal Flower Color Differentiation Mechanisms in Various Sophora japonica L. Petal Types

Sophora japonica L. is an important landscaping and ornamental tree species throughout southern and northern parts of China. The most common color of S. japonica petals is yellow and white. In this study, S. japonica flower color mutants with yellow and white flag petals and light purple-red wing and keel petals were used for transcriptomics and metabolomics analyses. To investigate the underlying mechanisms of flower color variation in S. japonica 'AM' mutant, 36 anthocyanin metabolites were screened in the anthocyanin-targeting metabolome. The results demonstrated that cyanidins such as cyanidin-3-O-glucoside and cyanidin-3-O-rutinoside in the 'AM' mutant were the key metabolites responsible for the red color of the wing and keel petals. Transcriptome sequencing and differentially expressed gene (DEG) analysis identified the key structural genes and transcription factors related to anthocyanin biosynthesis. Among these, F3'5'H, ANS, UFGT79B1, bHLH, and WRKY expression was significantly correlated with the cyanidin-type anthocyanins (key regulatory factors affecting anthocyanin biosynthesis) in the flag, wing, and keel petals in S. japonica at various flower development stages.

Combinatorial transcriptomics and metabolomics analysis reveals the effects of the harvesting stages on the accumulation of phenylpropanoid metabolites in Lonicera japonica

The flower buds of Lonicera japonica are widely used for its high medicinal value. It is reported that the accumulation of phenylpropanoids in the buds of L. japonica is affected by the stage at which it is harvested. However, the changes of active components and the underlying mechanisms in flower buds at different harvesting stages have not been reported. Integrative analyses of transcriptomics and metabolomics was used to explore the underlying mechanism of harvesting stages (green bud, GB; and white bud, WB) on the phenylpropanoids metabolites accumulation in L. japonica . The result showed that 3735 differentially expressed genes were identified, and the genes related to glycolysis/gluconeogenesis and phenylalanine biosynthesis pathway were significantly upregulated in GB stage. A total of 510 differential metabolites were identified in GB stage. Among them, 14 phenylpropanoids were changed during the GB and WB, seven of which increased in GB, including caffeic acid, sauchinone, coniferin, secoisolariciresinol diglucoside, scopolin, methyl cinnamate, chlorogenic acid, 7-hydroxycoumarin, while others such as sibiricose A6, coumarin, eleutheroside E decreased. Further correlation analysis showed that the unigenes for CSE, CAD, bg1, ADH, ALDH, DLAT and ENO significantly correlated with the 10 phenylpropanoid. The above results would provide basic data for the selection of harvesting stages in the production of L. japonica .

Revealing the Mechanistic Basis of Regulation of Phosphorus Uptake in Soybean (Glycine max) Roots by Molybdenum: An Integrated Omics Approach

While molybdenum (Mo) application can improve phosphorus (P) availability to plants by changing P speciation in the rhizosphere, the mechanistic basis of this process remains unclear. This work investigated the impact of various combinations of Mo and P treatments on root morphology, P and Mo uptake, and root transcriptome and metabolome. Mo application significantly increased soybean biomass and the number of lateral roots at both low (5 μmol) or normal (500 μmol) P levels and significantly improved P concentration and accumulation in Normal P treatment. Compared with the Normal P treatment, Low P significantly increased the number of roots, root surface area, and root acid phosphatase secretion. A total of 6811 Mo-responsive differentially expressed genes and 135 differential metabolites were identified at two P levels. At Low P, transcriptional changes significantly increased root synthesis and secretion of succinic acid, methylmalonic acid, and other organic acids as well as acid phosphatase, thereby increasing the conversion of soil aluminum-bound P and organic P into available P. At Normal P, Mo application increased P uptake mainly by increasing the number of lateral roots. Thus, Mo helps crops adapt to different P levels by regulating root anatomy and transcriptional and metabolic profiles of their roots.

Transcriptomics integrated with metabolomics to characterize key pigment compounds and genes related to anthocyanin biosynthesis in Zanthoxylum bungeanum peel

Zanthoxylum bungeanum is an important condiment with high economic value and its peel color is one of the main quality indexes. However, the key pigment compounds and related genes are still unclear affecting the quality control of the plants. In this study, the contents of four types of pigments were measured in Z. bungeanum and flavonoids were identified as the most important pigments. Based on the targeted flavonoid metabolomics of Z. bungeanum peels, 14 key pigment compounds were screened out from 152 flavonoids, among which cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside were the most critical compounds for peel color. They were further verified to be present in nine varieties of Z. bungeanum by HPLC fingerprints. The 14 compounds were all associated with flavonoid and anthocyanin biosynthesis pathways and the 39 differentially expressed genes related to these pathways were annotated and screened based on transcriptomics. The genes ZbDFR, ZbANS, and ZbUFGT were identified as three key genes for anthocyanin synthesis in Z. bungeanum peels. Further qRT-PCR results confirmed the reliability of transcriptomics and the accuracy of gene screening. Subsequent protein induced expression demonstrated that ZbANS and ZbUFGT were expressed after 12 h induced by IPTG while ZbDFR was expressed after 15 h. Further transient and stable transformation analysis confirmed that both anthocyanin content and the expression of ZbDFR were significantly increased in overexpression Z. bungeanum leaves and Nicotiana benthamiana. The functional effect of stable transformation of ZbDFR was more significant than that of transient transformation with a 7.67-fold/1.49-fold difference in total anthocyanin content and a 42.37-fold/12.32-fold difference in the expression of ZbDFR. This study provides new insights into the chemical composition and the molecular mechanisms of Z. bungeanum peel color and lays an effective foundation for the color quality control, multi-purpose utilization of Z. bungeanum and the creation of new germplasm.

Impact of heat stress, water stress, and their combined effects on the metabolism and transcriptome of grape berries

Recurring heat and drought episodes present challenges to the sustainability of grape production worldwide. We investigated the impacts of heat and drought stress on transcriptomic and metabolic responses of berries from two wine grape varieties. Cabernet Sauvignon and Riesling grapevines were subjected to one of four treatments during early fruit ripening: (1) drought stress only, (2) heat stress only, (3) simultaneous drought and heat stress, (4) no drought or heat stress (control). Berry metabolites, especially organic acids, were analyzed, and time-course transcriptome analysis was performed on samples before, during, and after the stress episode. Both alone and in conjunction with water stress, heat stress had a much more significant impact on berry organic acid content, pH, and titratable acidity than water stress. This observation contrasts with previous reports for leaves, which responded more strongly to water stress, indicating that grape berries display a distinct, organ-specific response to environmental stresses. Consistent with the metabolic changes, the global transcriptomic analysis revealed that heat stress had a more significant impact on gene expression in grape berries than water stress in both varieties. The differentially expressed genes were those associated with the tricarboxylic acid cycle and glyoxylate cycle, mitochondrial electron transport and alternative respiration, glycolysis and gluconeogenesis, carbohydrate allocation, ascorbate metabolism, and abiotic stress signaling pathways. Knowledge regarding how environmental stresses, alone and in combination, impact the berry metabolism of different grape varieties will form the basis for developing recommendations for climate change mitigation strategies and genetic improvement.

Suitable crop loading: An effective method to improve "Shine Muscat" grape quality

Berry thinning was applied to control crop load of "Shine Muscat" grape variety. Primary and secondary metabolites released during berries development were monitored, and the correlation between physicochemical parameters and core aroma compounds was analyzed. Results revealed a significant increase in single-berry weight and sugar-acid ratio of berries under low crop load conditions. Furthermore, phenolic content and antioxidant activity under low crop load were significantly higher than those of the other groups. Grapes with low crop loads also exhibited better aroma characteristics and higher sensory scores than those of the other groups, chiefly due to significantly increased terpene and C₁₃-norisoprenoid contents and substantially decreased C₆ compound and aldehyde contents. Moreover, correlation analysis revealed total soluble solid accumulation was positively correlated to terpene accumulation, while hexanal, 2-hexanal, (E)-2-hexanal, and (E)-2-octenal were positively correlated with titratable acidity content. Thus, better grape quality could be achieved by precisely controlling berry crop load.

Characterization of anthocyanin accumulation, nutritional properties, and postharvest attributes of transgenic purple tomato

Anthocyanins are natural pigments with diverse physiological roles and protective effects, but most tomatoes produce little. In this study, the anthocyanin characteristics, nutritional properties, and postharvest attributes of purple tomato (SlMYB75-OE) obtained by overexpression of SlMYB75 gene were first analyzed. Compared to wild-type (WT), eight monomeric anthocyanins were newly produced by overexpression of SlMYB75, and further study demonstrated the expression of dihydroflavonol-4-reductase (SlDFR) and two UDP-glycosyltransferase (SlUGTs) genes was activated by SlMYB75. The contents of sugars (sucrose, glucose, and fructose) and citric acid content in SlMYB75-OE were higher and lower, respectively, than in WT. In addition, FRAP and DPPH assays indicated SlMYB75-OE had higher antioxidant capacity, when compared to WT. Moreover, SlMYB75-OE exhibited a longer shelf life and stronger resistance to Botrytis cinerea than WT, and this characteristic was positively correlated with anthocyanin content. These results help to clarify the function of SlMYB75 and provide a reference for tomato breeding.

Combined Metabolome and Transcriptome Analysis Elucidates Sugar Accumulation in Wucai (Brassica campestris L.)

Wucai (Brassica campestris L.) is a leafy vegetable that originated in China, its soluble sugars accumulate significantly to improve taste quality during maturation, and it is widely accepted by consumers. In this study, we investigated the soluble sugar content at different developmental stages. Two periods including 34 days after planting (DAP) and 46 DAP, which represent the period prior to and after sugar accumulation, respectively, were selected for metabolomic and transcriptomic profiling. Differentially accumulated metabolites (DAMs) were mainly enriched in the pentose phosphate pathway, galactose metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, and fructose and mannose metabolism. By orthogonal projection to latent structures-discriminant s-plot (OPLS-DA S-plot) and MetaboAnalyst analyses, D-galactose and β-D-glucose were identified as the major components of sugar accumulation in wucai. Combined with the transcriptome, the pathway of sugar accumulation and the interact network between 26 DEGs and the two sugars were mapped. CWINV4, CEL1, BGLU16, and BraA03g023380.3C had positive correlations with the accumulation of sugar accumulation in wucai. The lower expression of BraA06g003260.3C, BraA08g002960.3C, BraA05g019040.3C, and BraA05g027230.3C promoted sugar accumulation during the ripening of wucai. These findings provide insights into the mechanisms underlying sugar accumulation during commodity maturity, providing a basis for the breeding of sugar-rich wucai cultivars.

High temperature inhibited the accumulation of anthocyanin by promoting ABA catabolism in sweet cherry fruits

Color is an essential appearance characteristic of sweet cherry (Prunus avium L.) fruits and mainly determined by anthocyanin. Temperature plays an important role in the regulation of anthocyanin accumulation. In this research, anthocyanin, sugar, plant hormone and related gene expression were analyzed using physiological and transcriptomic methods in order to reveal the effects of high temperature on fruit coloring and the related mechanism. The results showed that high temperature severely inhibited anthocyanin accumulation in fruit peel and slowed the coloring process. The total anthocyanin content in fruit peel increased by 455% and 84% after 4 days of normal temperature treatment (NT, 24°C day/14°C night) and high temperature treatment (HT, 34°C day/24°C night), respectively. Similarly, the contents of 8 anthocyanin monomers were significantly higher in NT than in HT. HT also affected the levels of sugars and plant hormones. The total soluble sugar content increased by 29.49% and 16.81% in NT and HT, respectively, after 4 days of treatment. The levels of ABA, IAA and GA20 also increased in both the two treatments but more slowly in HT. Conversely, the contents of cZ, cZR and JA decreased more rapidly in HT than in NT. The results of the correlation analysis showed that the ABA and GA20 contents were significantly correlated with the total anthocyanin contents. Further transcriptome analysis showed that HT inhibited the activation of structural genes in anthocyanin biosynthesis as well as the repression of CYP707A and AOG, which dominated the catabolism and inactivation of ABA. These results indicate that ABA may be a key regulator in the high-temperature-inhibited fruit coloring of sweet cherry. High temperature induces higher ABA catabolism and inactivation, leading to lower ABA levels and finally resulting in slow coloring.

Metabolomic and Transcriptome Analysis of the Inhibitory Effects of Bacillus subtilis Strain Z-14 against Fusarium oxysporum Causing Vascular Wilt Diseases in Cucumber

Controlling cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum (FOC) with Bacillus strains is a hot research topic. However, the molecular mechanism of Bacillus underlying the biocontrol of cucumber wilt is rarely reported. In this study, B. subtilis strain Z-14 showed significant antagonistic activity against FOC, and the control effect reached 88.46% via pot experiment. Microscopic observations showed that strain Z-14 induced the expansion and breakage of FOC hyphae. The cell wall thickness was uneven, and the organelle structure was degraded. The combined analysis of metabolome and transcriptome showed that strain Z-14 inhibited the FOC infection by inhibiting the synthesis of cell wall and cell membrane, energy metabolism, and amino acid synthesis of FOC mycelium, inhibiting the clearance of reactive oxygen species (ROS) and the secretion of cell wall-degrading enzymes (CWDEs), thereby affecting mitogen-activated protein kinase (MAPK) signal transduction and inhibiting the transport function.

Novel insight into anthocyanin metabolism and molecular characterization of its key regulators in Camellia sasanqua

Flower color is a trait that affects the ornamental value of a plant. Camellia sasanqua is a horticultural plant with rich flower color, but little is known about the regulatory mechanism of color diversity in this plant. Here, the anthocyanin profile of 20 C. sasanqua cultivars revealed and quantified 11 anthocyanin derivatives (five delphinidin-based and six cyanidin-based anthocyanins) for the first time. Cyanidin-3-O-(6-O-(E)-p-coumaroyl)-glucoside was the main contributor to flower base color, and the accumulation of cyanidin and delphinidin derivatives differed in the petals. To further explore the molecular mechanism of color divergence, a transcriptome analysis was performed using C. sasanqua cultivars 'YingYueYe', 'WanXia', 'XueYueHua', and'XiaoMeiGui'. The co-expression network related to differences in delphinidin and cyanidin derivatives accumulation was identified. Eleven candidate genes encoding key enzymes (e.g., F3H, F3'H, and ANS) were involved in anthocyanin biosynthesis. Moreover, 27 transcription factors were screened as regulators of the two types of accumulating anthocyanins. The association was suggested by correlation analysis between the expression levels of the candidate genes and the different camellia cultivars. We concluded that cyanidin and delphinidin derivatives are the major drivers of color diversity in C. sasanqua. This finding provides valuable resources for the study of flower color in C. sasanqua and lays a foundation for genetic modification of anthocyanin biosynthesis.

Integrating transcriptomic and metabolomic analysis to understand muscle qualities of red swamp crayfish (Procambarus clarkii) under transport stress

This study investigated the transport stress (crowding stress and duration) on the physicochemical properties, energy metabolism and antioxidant enzyme activities of the red swamp crayfish (Procambarus clarkii) tail muscle (CTM). Besides, transcriptomic and metabolomic were conducted to elucidate the possible mechanism of CTM alternations during transport stress. The survival rate of crayfish gradually decreased with the external crowding stress and crowding time increasing. The transport stress also led to the increased distance among muscle fibers, water mobility and energy consumption, and the decreased of water holding capacity (WHC), hardness of CTM. The hepatopancreas exhibited more sensitive to crowding stress than muscle. The multi-omics analysis revealed that transport stress could interfere the translation and protein folding functions of ribosomal proteins, fatty acid metabolism and degradation, physiological functions of mitochondria in CTM. This study could provide critical information to increase the understanding of the regulation mechanism of crayfish when subjected to transport stress.

Chromosome-scale genomics, metabolomics, and transcriptomics provide insight into the synthesis and regulation of phenols in Vitis adenoclada grapes

Vitis adenoclada is a wild grape unique to China. It exhibits well resistance to heat, humidity, fungal disease, drought, and soil infertility. Here, we report the high-quality, chromosome-level genome assembly of GH6 (V. adenoclada). The 498.27 Mb genome contained 221.78 Mb of transposable elements, 28,660 protein-coding genes, and 481.44 Mb of sequences associated with 19 chromosomes. GH6 shares a common ancestor with PN40024 (Vitis vinifera) from approximately 4.26-9.01 million years ago, whose divergence occurred later than Vitis rotundifolia and Vitis riparia. Widely-targeted metabolome and transcriptome analysis revealed that the profiles and metabolism of phenolic compounds in V. adenoclada varieties significantly were differed from other grape varieties. Specifically, V. adenoclada varieties were rich in phenolic acids and flavonols, whereas the flavan-3-ol and anthocyanin content was lower compared with other varieties that have V. vinifera consanguinity in this study. In addition, ferulic acid and stilbenes content were associated with higher expressions of COMT and STSs in V. adenoclada varieties. Furthermore, MYB2, MYB73-1, and MYB73-2 were presumably responsible for the high expression level of COMT in V. adenoclada berries. MYB12 (MYBF1) was positively correlated with PAL, CHS, FLS and UFGT.Meanwhile, MYB4 and MYBC2-L1 may inhibit the synthesis of flavan-3-ols and anthocyanins in two V. adenoclada varieties (YN2 and GH6). The publication of the V. adenoclada grape genome provides a molecular foundation for further revealing its flavor and quality characteristics, is also important for identifying favorable genes of the East Asian species for future breeding.

Molecular and Metabolic Insights into Anthocyanin Biosynthesis for Spot Formation on Lilium leichtlinii var. maximowiczii Flower Petals

Plants exhibit remarkable diversity in their petal colors through biosynthesis and the accumulation of various pigments. Lilium, an important cut and potted flower, has many coloring pattern variations, including bicolors and spots. To elucidate the mechanisms regulating spot formation in Lilium leichtlinii var. maximowiczii petals, we used multiple approaches to investigate the changes in petal carotenoids, spot anthocyanins, and gene expression dynamics. This included green petals without spots (D1-Pe and D1-Sp), yellow-green petals with purple spots (D2-Pe and D2-Sp), light-orange petals with dark-purple spots (D3-Pe and D3-Sp), and orange petals with dark-purple spots (D4-Pe and D4-Sp). D3-Pe and D4-Pe contained large amounts of capsanthin and capsorubin and small amounts of zeaxanthin and violaxanthin, which contributed to the orange color. In addition to cyanidin-3-O-glucoside, pelargonidin-3-O-rutinoside, cyanidin-3-O-rutinoside, and peonidin-3-O-rutinoside may also contribute to L. leichtlinii var. maximowiczii's petal spot colors. KEGs involved in flavonoid biosyntheses, such as CHS, DFR, and MYB12, were significantly upregulated in D2-Sp and D3-Sp, compared with D1-Sp, as well as in spots, compared with petals. Upregulated anthocyanin concentrations and biosynthesis-related genes promoted spot formation and color transition. Our results provide global insight into pigment accumulation and the regulatory mechanisms underlying spot formation during flower development in L. leichtlinii var. maximowiczii.

Transcriptomics and metabolomics reveal tolerance new mechanism of rice roots to Al stress

The prevalence of soluble aluminum (Al) ions is one of the major limitations to crop production worldwide on acid soils. Therefore, understanding the Al tolerance mechanism of rice and applying Al tolerance functional genes in sensitive plants can significantly improve Al stress resistance. In this study, transcriptomics and metabolomics analyses were performed to reveal the mechanism of Al tolerance differences between two rice landraces (Al-tolerant genotype Shibanzhan (KR) and Al-sensitive genotype Hekedanuo (MR) with different Al tolerance. The results showed that DEG related to phenylpropanoid biosynthesis was highly enriched in KR and MR after Al stress, indicating that phenylpropanoid biosynthesis may be closely related to Al tolerance. E1.11.1.7 (peroxidase) was the most significant enzyme of phenylpropanoid biosynthesis in KR and MR under Al stress and is regulated by multiple genes. We further identified that two candidate genes Os02g0770800 and Os06g0521900 may be involved in the regulation of Al tolerance in rice. Our results not only reveal the resistance mechanism of rice to Al stress to some extent, but also provide a useful reference for the molecular mechanism of different effects of Al poisoning on plants.

Brassinosteroid Promotes Grape Berry Quality-Focus on Physicochemical Qualities and Their Coordination with Enzymatic and Molecular Processes: A Review

Brassinosteroid (BR) is an important endogenous phytohormone that plays a significant role in fruit quality regulation. The regulation of BR biosynthesis and its physiological effects have been well-studied in various fruits. External quality (fruit longitudinal and transverse diameters, firmness, single berry weight, color) and internal quality (sugars, aroma, anthocyanin, stress-related metabolites) are important parameters that are modified during grape berry development and ripening. Grapevines are grown all over the world as a cash crop and utilized for fresh consumption, wine manufacture, and raisin production. In this paper, the biosynthesis and signaling transduction of BR in grapevine were summarized, as well as the recent developments in understanding the role of BR in regulating the external quality (fruit longitudinal and transverse diameters, firmness, single berry weight, and color) and internal quality (sugars, organic acids, aroma substances, anthocyanins, antioxidants) of grapes. Additionally, current advancements in exogenous BR strategies for improving grape berries quality were examined from the perspectives of enzymatic activity and transcriptional regulation. Furthermore, the interaction between BR and other phytohormones regulating the grape berry quality was also discussed, aiming to provide a reliable reference for better understanding the potential value of BR in the grape/wine industry.

Metabolomics Integrated with HPLC-MS Reveals the Crucial Antioxidant Compounds of Muscadine Wine

Wine is a kind of beverage with a variety of compounds beneficial to human health, which makes it popular all over the world and it contributes importantly to economics. The excessive oxidation of wine has always been a major problem in wine production and storage. Unlike traditional wines which are made from Eurasian grapes, wines made from muscadine grapes (Muscadinia rotundifolia Michx.) can maintain their sensory qualities under natural oxidation conditions for relatively long periods of time despite the insight mechanisms still being unclear. In this study, two muscadine wines, Carlos (CAL) and Noble (NOB), and two traditional wines, Chardonnay (CH) and Marselan (MAS), were chosen for comparison of their compositional alteration during oxidation, in order to analyze the principal components contributing to the antioxidant characteristics of muscadine wines. The DPPH, ORAC, color intensity, and total phenolic content changes during the natural oxidation process were analyzed. Six core significantly changed metabolites (SCMs, avicularin, beta-lactose, delphinidin-3-O-glucoside, ellagic acid, myricetin, and 4-methylcatechol [p < 0.05]) related to the oxidation process were determined. In addition, HPLC−MS was also used to identify pyrogallol which is a unique antioxidant compound in muscadine wine. The present work aims to reveal the crucial antioxidant compounds of muscadine wine and provide valuable information and a new platform for future research on wine oxidation.

Transcriptome and Metabolome Analysis Reveals the Effect of Nitrogen-Potassium on Anthocyanin Biosynthesis in "Fuji" Apple

Nitrogen (N) and potassium (K) have significant effects on apple peel color. To further understand the molecular mechanism of N-K regulation of apple color, we analyzed the apple peel under different N and K treatments using isotope labeling, transcriptomics, and metabolomics. Under high N treatments, fruit red color and anthocyanin content decreased significantly. High N decreased the ¹³C distribution rate and increased the Ndff values of fruits, while K increased the expression of MdSUTs and MdSOTs and promoted ¹³C transportation to fruits. Anthocyanin-targeted metabonomics and transcriptome analysis revealed that high N downregulated the expression of structural genes related to the anthocyanin synthesis pathway (MdPAL, Md4CL, MdF3H, MdANS, and MdUFGT) and their regulators (MdMYBs and MdbHLHs), and also decreased some metabolites contents. K alleviated this inhibition and seven anthocyanins were regulated by N-K. Our results improve the understanding of the synergistic regulation of apple fruit coloring by N-K.

Screening of cold hardiness-related indexes and establishment of a comprehensive evaluation method for grapevines (V. vinifera)

The goals of this work were to screen physiological and biochemical indexes to assess a set of V. vinifera germplasm resources, to compare evaluation methods for cold hardiness, and to establish a comprehensive method that can be used for more accurate screening for cold hardiness in V. vinifera. Four single methods were used to evaluate the cold hardiness of 20 germplasms resources and 18 physiological and biochemical indexes related to cold hardiness were determined. The LT₅₀ values determined by electrical conductivity (EL), 2,3,5-triphenyltetrazolium chloride staining (TTC), differential thermal analysis (DTA), and recovery growth (RG) methods showed extremely significant positive correlation. Bound water content (BW), proline content (Pro), total soluble sugar content (TSS), malondialdehyde content (MDA), catalase content (CAT), and ascorbic acid content (ASA) exhibited significant correlation with LT₅₀ values measured by different evaluation methods. The comprehensive cold hardiness index calculated by principal component analysis (PCA) combined with subordinate function (SF) was negatively correlated with LT₅₀ values measured by different evaluation methods. Meili and Ecolly exhibited the highest cold hardiness, indicating their potential for use as parents for cold hardiness breeding. EL, DTA, TTC, and RG methods successfully distinguished cold hardiness among different V. vinifera germplasm lines. Measurements of BW, Pro, TSS, MDA, CAT, and ASA in dormant shoots also can be used as main physiological and biochemical indexes related to cold hardiness of V. vinifera. Comprehensive evaluation by PCA combined with SF can accurately screen cold hardiness in V. vinifera. This study provides a reference and accurate identification method for the selection of cold hardiness parents and the evaluation of cold hardiness of germplasm of V. vinifera.

Berry flavonoids are differently modulated by timing and intensities of water deficit in Vitis vinifera L. cv. Sangiovese

In this work, we tested the effect of different regulated deficit irrigation (RDI) regimes on berry flavonoid content and its relative biosynthetic pathways. Vines were subjected to six irrigation regimes over two consecutive years: a) full irrigation during the entire irrigation period (FI); b) moderate (RDI-1M) or c) severe (RDI-1S) water deficit between berry pea-size and veraison; d) severe water deficit during the lag-phase (RDI-LS); and e) moderate (RDI-2M) or f) severe (RDI-2S) water deficit from veraison through harvest. Berries from both RDI-1 treatments showed the highest accumulation of anthocyanins, upregulating the expression of many genes of the flavonoid pathway since the beginning of veraison until harvest, far after the water deficit was released. Although to a lesser degree than RDI-1, both post-veraison water deficit treatments increased anthocyanin concentration, particularly those of the tri-substituted forms, overexpressing the F3'5'H hydroxylases. The moderate deficit irrigation treatments enhanced anthocyanin accumulation with respect to the severe ones regardless of the period when they were applied (pre- or post-veraison). The water deficit imposed during the lag-phase downregulated many genes throughout the flavonoid pathway, showing a slight reduction in anthocyanin accumulation. The measurements of cluster temperature and light exposure highlighted that under deficit irrigation conditions, the effects induced by water stress prevailed over that of light and temperature in regulating anthocyanin biosynthesis. Flavonol concentration was higher in RDI-1S berries due to the upregulation of the flavonol synthases and the flavonol-3-O-glycosyltransferases. In this case, the higher cluster light exposure induced by water deficit in RDI-1S berries had a major role in flavonol accumulation. We conclude that the timing and intensity of water stress strongly regulate the berry flavonoid accumulation and that proper management of deficit irrigation can modulate the phenylpropanoid and flavonoid pathways.

Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

Integrated metabolomic and transcriptomic analysis of the anthocyanin and proanthocyanidin regulatory networks in red walnut natural hybrid progeny leaves

Background

Walnuts are among the most important dry fruit crops worldwide, typically exhibiting green leaves and yellow-brown or gray-yellow seed coats. A specific walnut accession with red leaves and seed coats, 'RW-1', was selected for study because of its high anthocyanin and proanthocyanidin (PA) contents. Anthocyanins and PAs are important secondary metabolites and play key roles in plant responses to biotic and abiotic stresses. However, few studies have focused on the molecular mechanism of anthocyanin biosynthesis in walnuts.

Methods

In this study, we determined the anthocyanin and PA components and their contents in different color leaves of 'RW-1' natural hybrid progenies at various developmental stages. Integrated transcriptome and metabolome analyses were used to identify the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). We also performed conjoint analyses on DEGs and DAMs to ascertain the degree pathways, and explore the regulation of anthocyanin and PA biosynthesis.

Results

The results of widely targeted metabolome profiling and anthocyanin detection revealed 395 substances, including four PAs and 26 anthocyanins, in red (SR) and green leaves (SG) of 'RW-1' natural hybrid progenies. From the research, the contents of all anthocyanin components in SR were higher than that in SG. Among them, the contents of delphinidin 3-O-galactoside, cyanidin 3-O-galactoside, delphinidin 3-O-arabinoside and cyanidin 3-O-glucoside were significantly higher than others, and they were considered as the main types of anthocyanins. However, nine anthocyanins were detected only in SR. For PAs, the content of procyanidin C1 was higher in SR compared with SG, while procyanidin B1 and procyanidin B3 were higher in SR-1 and SR-3 but downregulated in SR-2 compared with the controls. Furthermore, transcriptome analysis revealed that the expressions of structural genes (C4H, F3H, F3'5'H, UFGT, LAR and ANR), three MYBs predicted as the activators of anthocyanin and PA biosynthesis, two MYBs predicted as the repressors of anthocyanin biosynthesis, and five WD40s in the anthocyanin and PA biosynthetic pathways were significantly higher in the SR walnuts. Gene-metabolite correlation analyses revealed a core set of 31 genes that were strongly correlated with four anthocyanins and one PA metabolites. The alteration of gene coding sequence altered the binding or regulation of regulatory factors to structural genes in different color leaves, resulting in the effective increase of anthocyanins and PAs accumulation in red walnut.

Conclusions

This study provides valuable information on anthocyanin and PA metabolites and candidate genes for anthocyanin and PA biosynthesis, yielding new insights into anthocyanin and PA biosynthesis in walnuts.

Melatonin enhances stress tolerance in pigeon pea by promoting flavonoid enrichment, particularly luteolin in response to salt stress

Melatonin improves plant resistance to multiple stresses by participating in the biosynthesis of metabolites. Flavonoids are an important family of plant secondary metabolites and are widely recognized to be involved in resistance; however, the crosstalk between melatonin and flavonoid is largely unknown. We found that the resistance of pigeon pea (Cajanus cajan) to salt, drought, and heat stresses were significantly enhanced by pre-treatment with melatonin. Combined transcriptome and LC-ESI-MS/MS metabolomics analyses showed that melatonin significantly induced the enrichment of flavonoids and mediated the reprogramming of biosynthetic pathway genes. The highest fold-increase in expression in response to melatonin treatment was observed for the CcF3´H family, which encodes an enzyme that catalyses the biosynthesis of luteolin, and the transcription factor CcPCL1 directly bonded to the CcF3´H-5 promoter to enhance its expression. In addition, salt stress also induced the expression of CcPCL1 and CcF3´H-5, and their overexpression in transgenic plants greatly enhanced salt tolerance by promoting the biosynthesis of luteolin. Overall, our results indicated that pre-treatment of pigeon pea with melatonin promoted luteolin biosynthesis through the CcPCL1 and CcF3´H-5 pathways, resulting in salt tolerance. Our study shows that melatonin enhances plant tolerance to multiple stresses by mediating flavonoid biosynthesis, providing new avenues for studying the crosstalk between melatonin and flavonoids.

Analysis of the different growth years accumulation of flavonoids in Dendrobium moniliforme (L.) Sw. by the integration of metabolomic and transcriptomic approaches

Dendrobium moniliforme (L.) Sw. is a valuable herbal crop, and flavonoids are primarily distributed as active ingredients in the stem, but the composition and synthesis mechanisms of flavonoids in different growth years are not clear. The accumulation of flavonoids in D. moniliforme from four different years was investigated, using a combined metabolomics and transcriptomics approach in this study. The phenylpropanoid and flavonoid biosynthetic pathways were significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). The widely targeted metabolomics technique revealed a total of 173 kinds of flavonoid metabolites. The metabolomics data confirmed the trend of total flavonoids (TF) content in stems of D. moniliforme, with chalcone, naringenin, eriodictyol, dihydroquercetin, and other flavonoids considerably up-accumulating in the third year. Twenty DEGs were detected that regulate flavonoid synthesis and the expression of these genes in different growth years was verified using real-time quantitative PCR (qRT-PCR). Furthermore, a comprehensive regulatory network was built for flavonoid biosynthesis and it was discovered that there is one FLS gene, one CCR gene and two MYB transcription factors (TFs) with a high connection with flavonoid biosynthesis by weighted gene co-expression network analysis (WGCNA). In this study, the correlation between genes involved in flavonoid biosynthesis and metabolites was revealed, and a new regulatory mechanism related to flavonoid biosynthesis in D. moniliforme was proposed. These results provide an important reference for the farmers involved in the cultivation of D. moniliforme.

Accumulation and regulation of anthocyanins in white and purple Tibetan Hulless Barley (Hordeum vulgare L. var. nudum Hook. f.) revealed by combined de novo transcriptomics and metabolomics

BACKGROUND

Colored barley, which may have associated human health benefits, is more desirable than the standard white variety, but the metabolites and molecular mechanisms underlying seedcoat coloration remain unclear.

RESULTS

Here, the development of Tibetan hulless barley was monitored, and 18 biological samples at 3 seedcoat color developmental stages were analyzed by transcriptomic and metabolic assays in Nierumuzha (purple) and Kunlun10 (white). A total of 41 anthocyanin compounds and 4186 DEGs were identified. Then we constructed the proanthocyanin-anthocyanin biosynthesis pathway of Tibetan hulless barley, including 19 genes encoding structural enzymes in 12 classes (PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, DFR, ANS, ANR, GT, and ACT). 11 DEGs other than ANR were significantly upregulated in Nierumuzha as compared to Kunlun10, leading to high levels of 15 anthocyanin compounds in this variety (more than 25 times greater than the contents in Kunlun10). ANR was significantly upregulated in Kunlun10 as compared to Nierumuzha, resulting in higher contents of three anthocyanins compounds (more than 5 times greater than the contents in Nierumuzha). In addition, 22 TFs, including MYBs, bHLHs, NACs, bZips, and WD40s, were significantly positively or negatively correlated with the expression patterns of the structural genes. Moreover, comparisons of homologous gene sequences between the two varieties identified 61 putative SNPs in 13 of 19 structural genes. A nonsense mutation was identified in the coding sequence of the ANS gene in Kunlun10. This mutation might encode a nonfunctional protein, further reducing anthocyanin accumulation in Kunlun10. Then we identified 3 modules were highly specific to the Nierumuzha (purple) using WGCNA. Moreover, 12 DEGs appeared both in the putative proanthocyanin-anthocyanin biosynthesis pathway and the protein co-expression network were obtained and verified.

CONCLUSION

Our study constructed the proanthocyanin-anthocyanin biosynthesis pathway of Tibetan hulless barley. A series of compounds, structural genes and TFs responsible for the differences between purple and white hulless barley were obtained in this pathway. Our study improves the understanding of the molecular mechanisms of anthocyanin accumulation and biosynthesis in barley seeds. It provides new targets for the genetic improvement of anthocyanin content and a framework for improving the nutritional quality of barley.

Regulated deficit irrigation: an effective way to solve the shortage of agricultural water for horticulture

The deficient agricultural water caused by water shortage is a crucial limiting factor of horticultural production. Among many agricultural water-saving technologies, regulated deficit irrigation (RDI) has been proven to be one of the effective technologies to improve water use efficiency and reduce water waste on the premise of maintaining the quality of agricultural products. RDI was first reported more than 40 years ago, although it has been applied in some areas, little is known about understanding of the implementation method, scope of application and detailed mechanism of RDI, resulting in the failure to achieve the effect that RDI should have. This review refers to the research on RDI in different crops published in recent years, summarizes the definition, equipment condition, function, theory illumination, plant response and application in different crops of RDI, and looks forward to its prospect. We expect that this review will provide valuable guidance for researchers and producers concerned, and support the promotion of RDI in more horticultural crops.

Anti-osteoporosis effects and regulatory mechanism of Lindera aggregata based on network pharmacology and experimental validation

Osteoporosis (OP) is characterized by the flaccidity of bones or bone bi-disease caused by kidney deficiency. Lindera aggregate has been used to strengthen kidney function in China for thousands of years. It has been approved by Chinese Pharmacopoeia that the root of Lindera aggregata (RLA) can replenish and tonify the kidney, which is thought to be an effective way to alleviate OP. In this study, a network pharmacology approach was applied to explore the active components and potential mechanisms of RLA in osteoporosis treatment. Then, the ethanolic extract of the root of L. aggregata (EERL) was prepared and these predicted results were validated by prednisone-induced zebrafish embryos model. Moreover, the candidate compounds were identified by UPLC-ESI-MS/MS. The anti-OP results showed that EERL could significantly reverse the bone loss of zebrafish induced by prednisone. The mRNA expressions results showed that EERL decreased osteoclast bone resorption by regulating the RANK/RANKL/OPG system. Also, it increased bone formation by regulating the gene expressions of spp1, mmp2, mmp9, runx2b, alp, and entpd5a. Our results demonstrated the reliability of the network pharmacology method, and also revealed the anti-OP effect and potential mechanism of RLA.

A Feature Selection Approach Guided an Early Prediction of Anthocyanin Accumulation Using Massive Untargeted Metabolomics Data in Mulberry

Identifying the early predictive biomarkers or compounds represents a pivotal task for guiding a targeted agricultural practice. Despite the various available tools, it remains challenging to define the ideal compound combination and thereby elaborate an effective predictive model fitting that. Hence, we employed a stepwise feature selection approach followed by a maximum relevance and minimum redundancy (MRMR) on the untargeted metabolism in four mulberry genotypes at different fruit developmental stages (FDSs). Thus, we revealed that 7 out of 226 differentially abundant metabolites (DAMs) explained up to 80% variance of anthocyanin based on linear regression model and stepwise feature selection approach accompanied by an MRMR across the genotypes over the FDSs. Among them, the phosphoenolpyruvate, d-mannose and shikimate show the top 3 attribution indexes to the accumulation of anthocyanin in the fruits of these genotypes across the four FDSs. The obtained results were further validated by assessing the regulatory genes expression levels and the targeted metabolism approach. Taken together, our findings provide valuable evidences on the fact that the anthocyanin biosynthesis is somehow involved in the coordination between the carbon metabolism and secondary metabolic pathway. Our report highlights as well the importance of using the feature selection approach for the predictive biomarker identification issued from the untargeted metabolomics data.

Post-veraison different frequencies of water deficit strategies enhance Reliance grapes quality under root restriction

In this study, two water deficit treatments in the same amount of water but with different frequencies (T1: 2.5 L per 4 d and T2: 5 L per 8 d) were performed on Reliance grapevines from veraison until harvest to explore their effects on grape berries quality under root restriction. Results showed that glucose, fructose and sucrose contents were increased, while malic acid, tartaric acid and citric acid contents were decreased under two treatments. Meanwhile, water deficits also promoted the accumulation of phenylalanine and proline. For phenols, anthocyanins, resveratrol and flavonols contents in the water deficit groups were significantly higher than those in the control group. In addition, two water deficit treatments increased the characteristic aromas contents, especially the esters contents. Overall, T2 treatment had a better effect than T1 treatment. This study provided an idea for improving water use efficiency and grape quality.

Comparative analysis of flavonoids in white and red table grape cultivars during ripening by widely targeted metabolome and transcript levels

The flavonoid metabolites were compared between red 'Summer Black' (SB) and white 'Shine Muscat' (SM) table grapes during fruit development based on widely targeted metabolome. A total of 134 flavonoids were identified in two cultivars, including 37 flavones, 33 flavonols, and 11 anthocyanidins, and so on. From young to veraison, the composition and the content of most flavonoids were decreasing in both cultivars but increased at maturation in SB. In general, SB has higher flavonoid compositions and content than SM during the whole fruit development, especially the content of anthocyanin after veraison. While the SM had higher content of flavonols such as quercetin, kaempferol and their derivatives. The expression of anthocyanin-related genes such as UFGT, OMT, GST, MATE, MYBA1, and MYBA2 was remarkably higher in SB than those in SM, which may attribute to higher anthocyanin content, while the higher expression of F3H and FLS resulted higher level of flavonols in SM. These results improve our understanding of flavonoid profiles and molecular mechanism in table grape cultivars.

Enhancement of anthocyanin and chromatic profiles in 'Cabernet Sauvignon' (Vitis vinifera L.) by foliar nitrogen fertilizer during veraison

BACKGROUND

The influence of foliar nitrogen fertilizer during veraison (FNFV) on anthocyanin accumulation and chromatic characteristics of 'Cabernet Sauvignon' grapes over two seasons was investigated.

RESULTS

Urea and phenylalanine fertilizers (TU and TP, respectively) and a control were sprayed three times at veraison. In 2018, TU displayed a significant enhancement in total individual anthocyanin content and a* and C_ab * profiles. In 2019, FNAV significantly improved the content of total non-acylated, acylated anthocyanin and total individual anthocyanin, and the profiles of L*, a* and C_ab *, except a* in TU. The whole process from phenylalanine variation to anthocyanin accumulation in grape skins was analyzed. On the whole, after the first FNFV to harvest, the increase in phenylalanine metabolism, abscisic acid content, effects of PAL (Phenylalanine ammonia lyase), UFGT (UDP glucose-flavonoid 3-O-glucosyltransferase) and transcript concentrations of VvPAL and VvUFGT involved in anthocyanin biosynthesis were also strong evidence explaining the increased anthocyanin and chromatic profiles in 2019.

CONCLUSION

Overall, FNFV for nitrogen-deficient grapevines could significantly improve grape color, especially in the 2019 veraison with a proper climate. © 2021 Society of Chemical Industry.

Multiomics Analyses of Two Sorghum Cultivars Reveal the Molecular Mechanism of Salt Tolerance

Sorghum [Sorghum bicolor (L.) Moench] is one of the most important cereal crops and contains many health-promoting substances. Sorghum has high tolerance to abiotic stress and contains a variety of flavonoids compounds. Flavonoids are produced by the phenylpropanoid pathway and performed a wide range of functions in plants resistance to biotic and abiotic stress. A multiomics analysis of two sorghum cultivars (HN and GZ) under different salt treatments time (0, 24, 48, and 72) was performed. A total of 45 genes, 58 secondary metabolites, and 246 proteins were recognized with significant differential abundances in different comparison models. The common differentially expressed genes (DEGs) were allocated to the "flavonoid biosynthesis" and "phenylpropanoid biosynthesis" pathways. The most enriched pathways of the common differentially accumulating metabolites (DAMs) were "flavonoid biosynthesis," followed by "phenylpropanoid biosynthesis" and "arginine and proline metabolism." The common differentially expressed proteins (DEPs) were mainly distributed in "phenylpropanoid biosynthesis," "biosynthesis of cofactors," and "RNA transport." Furthermore, considerable differences were observed in the accumulation of low molecular weight nonenzymatic antioxidants and the activity of antioxidant enzymes. Collectively, the results of our study support the idea that flavonoid biological pathways may play an important physiological role in the ability of sorghum to withstand salt stress.

Unraveling the Mechanism of Purple Leaf Formation in Brassica napus by Integrated Metabolome and Transcriptome Analyses

Brassica napus as both oilseed and vegetable, is widely cultivated in China. The purple leaf of B. napus is rich in anthocyanins and can provide valuable nutrients. Although several high-anthocyanin cultivars have been reported, the molecular mechanism underlying anthocyanin biosynthesis in B. napus remains lesser-known. Therefore, in this study, we conducted integrative metabolome and transcriptome analyses in three B. napus cultivars with different leaf colors. Overall, 39 flavonoids were identified (including 35 anthocyanins), and 22 anthocyanins were differentially accumulated in the leaves, contributing to the different leaf colors. Cyanidin-3,5,3'-O-triglucoside was confirmed as the main contributor of the purple leaf phenotype. Meanwhile, other anthocyanins may play important roles in deepening the color of B. napus leaves. A total of 5,069 differentially expressed genes (DEGs) and 32 overlapping DEGs were identified by RNA-sequencing; hence, the correlation between anthocyanin content and DEG expression levels was explored. Two structural genes (DFR and ANS), three GSTs (homologous to TT19), and 68 differentially expressed transcription factors (TFs), especially MYB-related TFs and WRKY44, were identified in three B. napus varieties characterized by different leaf color, thereby indicating that these genes may contribute to anthocyanin biosynthesis, transport, or accumulation in B. napus leaves. The findings of study provide important insights that may contribute to gaining a better understanding of the transcriptional regulation of anthocyanin metabolism in B. napus.

Metabolite Profiling and Transcriptome Analysis Unveil the Mechanisms of Red-Heart Chinese Fir [Cunninghamia lanceolata (Lamb.) Hook] Heartwood Coloration

Red-heart Chinese fir (Cunninghamia lanceolata) has the advantages of high density and attractive color, making it popular in the market. To date, most studies about stems of woody plants have only been reported at the cytological level because of few living cells. In this study, the xylem was successfully partitioned into three effective sampling areas: sapwood, transition zone, and heartwood. Secondary metabolites, cell survival, and differentially expressed genes in the three sampling areas were, respectively, investigated. First, we identified the phenylpropanoid and flavonoid pathways closely related to color. Based on the chemical structure of secondary metabolites in pathways, two notable directions had been found. Luteolin's glycosylation products might be the key substances that regulated the color of heartwood in red-heart Chinese fir because of the 1,000-fold difference between red-heart and white-heart. We also found pinocembrin and pinobanksin in Chinese fir, which were rarely reported before. At the cytological level, we believed that the transition zone of red-heart Chinese fir was a critical region for color production because of the fewer living ray parenchyma cells. In addition, transcriptome and quantitative reverse transcription PCR (qRT-PCR) proved that genes regulating the entire phenylpropanoid pathway, upstream of the flavonoid pathway, and some glycosyltransferases were significantly upregulated in the transition zone of red-heart and then colored the heartwood by increasing metabolites. This is the first report on the color-related secondary metabolites regulated by differential genes in red-heart Chinese fir. This study will broaden our knowledge on the effects of metabolites on coloring woody plant xylems.

The Impact of Elsinoë ampelina Infection on Key Metabolic Properties in Vitis vinifera 'Red Globe' Berries via Multiomics Approaches

Grape anthracnose caused by Elsinoë ampelina (Shear) is one of the most serious fungal diseases that lead to the quality reduction and yield losses of grape (Vitis vinifera 'Red Globe') berries. In the present study, metabolome and transcriptome analyses were conducted using grape berries in the field after infection with E. ampelina at 7, 10, and 13 days to identify the metabolic properties of berries. In total, 132 metabolites with significant differences and 6,877 differentially expressed genes were detected and shared by three comparisons. The analyses demonstrated that phenylpropanoid, flavonoid, stilbenoid, and nucleotide metabolisms were enriched in E. ampelina-infected grape berries but not amino acid metabolism. Phenolamide, terpene, and polyphenole contents also accumulated during E. ampelina infection. The results provided evidence of the enhancement of secondary metabolites such as resveratrol, α-viniferin, ε-viniferin, and lignins involved in plant defense. The results showed the plant defense-associated metabolic reprogramming caused by E. ampelina infection in grape berry and provided a global metabolic mechanism under E. ampelina stimulation.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Grape bioactive molecules, and the potential health benefits in reducing the risk of heart diseases

Grapes are a rich source of bioactive molecules including phenolic acids, flavonoids, anthocyanins, stilbenes, and lipids. These are the compounds which contribute to the health benefits of grape and grape-derived products. They possess antioxidant, antimicrobial, anti-inflammatory, and anti-carcinogenic activities and have wide applications in food and nutraceutical industries. Use of grape extracts rich in these bioactive compounds are linked to reduced incidence of cardiovascular disease and its major risk factors including hypertension (high blood pressure); a clinical condition associated with high mortality worldwide. Therefore, considerable attention has been given to grape-based products to alleviate and treat hypertension. The aim of this review is to summarize the bioactive compounds of grapes, composition changes in different grape extracts and the potential benefits in reducing hypertension.