Flavonoid Metabolism Research Articles

LC-MS/MS-based metabolic profiling: unraveling the impact of varying degrees of curing on metabolite transformations in tobacco

The curing process regulates metabolite transformations of leaves and significantly influences the formation of tobacco quality. This study investigated the major physicochemical compositions and metabolic profiles under normal curing (NC), excessive curing (EC), and insufficient curing (IC) treatments. The results indicated that the contents of nicotine, nitrogen, potassium, and chlorine remained stable among treatments, while the sugar content in EC was significantly lower than in IC. LC-MS/MS identified 845 metabolites, with flavonoids as the most abundant class. Comparative analyses identified a series of differentially expressed metabolites (DEMs) among fresh leaf, NC, EC, and IC leaves at the end of 42°C, 54°C, and 68°C, respectively. At the end of 68°C, 256 up-regulated and 241 down-regulated common DEMs across treatments were isolated in comparison to fresh leaf, underscoring the consistency of metabolic changes during curing. Notably, nonivamide varied markedly across treatments, suggesting its potential as a key curing indicator. NC_68°C displayed 11 up-regulated and 17 down-regulated unique DEMs, differing from EC_68°C and IC_68°C, suggesting their potential availability in evaluating tobacco leaf quality. KEGG pathway analysis revealed temporal shifts in metabolic pathways, particularly those involved in secondary metabolite biosynthesis (such as flavonoids, flavones, flavonols) and amino acid metabolism, during the transition from yellowing to color-fixing. Correlation analysis isolated the top 25 DEMs correlated with curing degree and stage, which might play pivotal roles in the curing process and could serve as potential biomarkers for assessing curing degree and stage. Specifically, D-(+)-cellobiose displayed the strongest negative correlation with curing degree, while 5,7-dihydroxychromone exhibited the highest positive correlation coefficient. Furthermore, curcurbitacin IIa showed the highest positive correlation with curing stage, followed by hesperetin and 8-shogaol. Additionally, random forest analysis emphasized morellic acid as a core molecular metabolite across curing degrees, suggesting its potential as a biomarker. Debiased sparse partial correlation (DSPC) network analysis further pinpointed hispidulin as a key metabolite, underscoring its significance in elucidating flavonoid metabolism during the curing process. Collectively, this study enhances the understanding of metabolite transformations underlying tobacco curing processes and provides a valuable reference for optimizing curing strategies to achieve desired outcomes.

Pre‐ADMET studies of 5‐(3′,4′‐dihydroxyphenyl)‐γ‐valerolactone, the bioactive intestinal metabolite of proanthocyanidins

Abstract5‐(3′,4′‐Dihydroxyphenyl)‐γ‐valerolactone (VL) is a bioactive metabolite resulting from the gut microbial metabolism of proanthocyanidins and flavonoids, known for its health‐promoting effects, including antidiabetic and anti‐inflammatory activities. Although VL has been observed in different in vivo studies, its pre‐absorption, distribution, metabolism, excretion, toxicity (ADMET) properties have rarely been investigated. This study aims to address this gap by evaluating the pre‐ADMET properties of VL for the first time. Also, the understanding of these properties is significant for correlating the encountered activities to this metabolite. In vitro absorption studies revealed that VL is rapidly metabolized and absorbed as its sulfate phase II conjugate (valerolactone sulfate), which enters systemic circulation and mildly activates the Breast Cancer Resistance Protein efflux transporter. In human S9 liver fraction, a mixture of liver enzymes used to simulate in vivo liver metabolism, VL is metabolized into glucuronic phase II conjugates (valerolactone glucuronide 1 [VLG1] and 2 [VLG2]) with a half‐life of 8.72 min and an 80% conversion rate. In human liver microsomes, VL is metabolized at a slower rate (half‐life of 23.08 min), suggesting that oxidative metabolism is secondary. Additionally, VL did not activate the pregnane X receptor or inhibit Cytochrome P3A4 (CYP3A4) and Cytochrome P1A2 (CYP1A2) enzymes, indicating no risk of herb–drug interactions with coadministered prescription drugs.

Integrated Metabolomics and Transcriptomics Provide Key Molecular Insights into Floral Stage-Driven Flavonoid Pathway in Safflower

Safflower (Carthamus tinctorius L.) is a traditional Chinese medicinal herb renowned for its high flavonoid content and significant medicinal value. However, the dynamic changes in safflower petal flavonoid profiles across different flowering phases present a challenge in optimizing harvest timing and medicinal use. To enhance the utilization of safflower, this study conducted an integrated transcriptomic and metabolomic analysis of safflower petals at different flowering stages. Our findings revealed that certain flavonoids were more abundant during the fading stage, while others peaked during full bloom. Specifically, seven metabolites, including p-coumaric acid, naringenin chalcone, naringenin, dihydrokaempferol, apigenin, kaempferol, and quercetin, accumulated significantly during the fading stage. In contrast, dihydromyricetin and delphinidin levels were notably reduced. Furthermore, key genes in the flavonoid biosynthesis pathway, such as 4CL, DFR, and ANR, exhibited up-regulated expression with safflower’s flowering progression, whereas CHI, F3H, and FLS were down-regulated. Additionally, exposure to UV-B stress at full bloom led to an up-regulation of flavonoid content and altered the expression of key flavonoid biosynthetic genes over time. This study not only elucidates the regulatory mechanisms underlying flavonoid metabolism in safflower but also provides insights for maximizing its medicinal and industrial applications.

Integrative Metabolomic and Transcriptomic Analysis Provides Novel Insights into the Effects of SO2 on the Postharvest Quality of ‘Munage’ Table Grapes

Postharvest grapes exhibit a limited shelf life due to susceptibility to rot and deterioration, significantly reducing their nutritional and economic value. Sulfur dioxide (SO2) is a widely recognized preservative for extending grape storage life. This study performed a detailed analysis of ‘Munage’ table grapes treated with SO2 fumigation, employing transcriptomic and metabolomic approaches. Results indicate that SO2 fumigation significantly extends the shelf life of grapes, as demonstrated by improved visual quality, reduced decay rates, and increased fruit firmness. We identified 309 differentially accumulated metabolites (DAMs) and 1906 differentially expressed genes (DEGs), including 135 transcription factors (TFs). Both DEGs and DAMs showed significant enrichment of flavonoid-related metabolism compared with the control, and the relative content of four flavonoid metabolites (Wogonin-7-O-glucuronide, Acacetin-7-O-glucuronide, Apigenin-7-O-glucuronide, and Baicalein 7-O-glucuronide) were significantly increased in grapes upon SO2 treatment, suggesting that SO2 treatment had a substantial regulatory effect on grape flavonoid metabolism. Importantly, we constructed complex regulatory networks by screening key enzyme genes (e.g., PAL, 4CLs, CHS, CHI2, and UGT88F3) related to the metabolism of target flavonoid, as well as potential regulatory transcription factors (TFs). Overall, our findings offer new insights into the regulatory mechanisms by which SO2 maintains the postharvest quality of table grapes.

Insights into physiological roles of flavonoids in plant coldacclimation.

Flavonoids represent a diverse group of plant specialised metabolites which are also discussed in the context of dietary health and inflammatory response. Numerous studies have revealed that flavonoids play a central role in plant acclimation to abiotic factors like low temperature or high light, but their structural and functional diversity frequently prevents a detailed mechanistic understanding. Further complexity in analysing flavonoid metabolism arises from the different subcellular compartments which are involved in biosynthesis and storage. In the present study, non-aqueous fractionation of Arabidopsis leaf tissue was combined with metabolomics and proteomics analysis to reveal the effects of flavonoid deficiencies on subcellular metabolism during cold acclimation. During the first 3 days of a 2-week cold acclimation period, flavonoid deficiency was observed to affect pyruvate, citrate and glutamate metabolism which indicated a role in stabilising C/N metabolism and photosynthesis. Also, tetrahydrofolate metabolism was found to be affected, which had significant effects on the proteome of the photorespiratory pathway. In the late stage of cold acclimation, flavonoid deficiency was found to affect protein stability, folding and proteasomal degradation, which resulted in a significant decrease in total protein amounts in both mutants. In summary, these findings suggest that flavonoid metabolism plays different roles in the early and late stages of plant cold acclimation and significantly contributes to establishing a new protein homeostasis in a changing environment.

Gene expression profiles and metabolic pathways responsible for male sterility in cybrid pummelo.

Abnormal expression of genes regulating anther and pollen development and insufficient accumulation of male sterility (MS)- related metabolites lead to MS in cybrid pummelo Male sterility (MS) is a major cause of seedlessness in citrus, which is an important trait for fresh fruit. Understanding the mechanism of MS is important for breeding seedless citrus cultivars. In this study, we dissected the transcriptional, metabolic and physiological mechanisms of MS in somatic cybrid of pummelo (G1 + HBP). G1 + HBP exhibited severe male sterility, manifesting as retarded anther differentiation, abnormal anther wall development (especially tapetum and endothecium), and deficient pollen wall formation. In the anthers of G1 + HBP, the expression of genes regulating anther differentiation and tapetum development was abnormal, and the expression of genes regulating endothecium secondary lignification thickening and pollen wall formation was down-regulated. The transcription of genes involved in MS-related biological processes, such as jasmonic acid (JA) signaling pathway, primary metabolism, flavonoid metabolism, and programmed cell death, was altered in G1 + HBP anthers, and the accumulation of MS-associated metabolites, including fatty acids, amino acids, sugars, ATP, flavonols and reactive oxygen species (ROS), was down-regulated in G1 + HBP anthers. In summary, abnormal expression of key genes regulating anther and pollen development, altered transcription of key genes involved in MS-related metabolic pathways, and insufficient accumulation of MS-related metabolites together lead to MS in G1 + HBP. The critical genes and the metabolism pathways identified herein provide new insights into the formation mechanism of MS in citrus and candidate genes for breeding seedless citrus.

Crystal structure and function of a phosphate starvation responsive protein phosphatase, GmHAD1-2 regulating soybean root development and flavonoid metabolism.

Phosphate (Pi) availability is well known to regulate plant root growth. However, it remains largely unknown how flavonoid synthesis participates in affecting plant root growth in response to Pi starvation. In the study, the crystal structure of a plant protein phosphatase, GmHAD1-2, was dissected using X-ray crystallography for the first time. It was revealed that GmHAD1-2 contained a modified Rossmannoid class of α/β folds with three layered α/β sandwich. Transcripts of GmHAD1-2 were increased by Pi starvation in soybean roots, especially in lateral root tips. GmHAD1-2 suppression or overexpression significantly influenced soybean lateral root length and number, as well as phosphorus (P) content. Furthermore, GmHAD1-2 was found to interact with a chalcone reductase, GmCHR1. Suppression of GmHAD1-2 significantly changed the flavonoid biosynthesis pathway in soybean roots. Taken together, the results highlight that GmHAD1-2 can regulate soybean root growth by influencing flavonoid metabolism.

Synergistic variation in abscisic acid and brassinolide treatment signaling component alleviates fruit quality of ‘Shine Muscat’ grape during cold storage

Grape fruit are harvested in the late summer or early fall and need to be stored at low temperatures to prevent enfeeblement and prolong their shelf-life. This study aimed to determine the effects of abscisic acid (ABA), brassinolide (BR) and ABA + BR (ABR) treatment on the berry quality of ‘Shine Muscat’ under low temperatures. ABA and BR maintained fruit appearance, cellular structure, weight, firmness. ABR treatments reduced the loss of fruit aroma. Furthermore, the transcriptome and metabolome analysis revealed that ABA, BR, and ABR treatments maintained the quality of fruits during the low temperatures period by influencing chlorophyll metabolism, carotenoid metabolism, flavonoid metabolism, unsaturated fatty acid, and terpene metabolism. These findings identify key genes and metabolites for ABA and BR-induced maintenance of grape fruit quality during cold storage, expanding our understanding of postharvest storage quality maintenance of grape fruit at the transcript and metabolic levels.

Metabolite concentrations and the expression profiles of the corresponding metabolic pathway genes in eggplant (Solanum melongena L.) fruits of contrasting colors.

Eggplant (Solanum melongena L.) ranks fifth in importance among vegetable crops of the Solanaceae family, in part due to the high antioxidant properties and polyphenol content of the fruit. Along with the popular purple-fruited varieties of S. melongena, there are cultivars, the fruits of which are rich in phenolic compounds, but are white-colored due to the lack of anthocyanin biosynthesis. Determination of the amount of anthocyanins and other phenolic compounds, as well as carotenoids and sugars, is included in the assessment of the quality of eggplant fruits of commercial (technical) ripeness. In addition to antioxidant and taste properties, these metabolites are associated with fruit resistance to various stress factors. In this study, a comparative analysis of the content of anthocyanins, carotenoids and soluble sugars (sucrose, glucose, fructose) in the peel and pulp of the fruit of both technical and biological ripeness was carried out in purple-fruited (cv. Vlas) and white-fruited (cv. Snezhny) eggplant accessions of domestic selection. The peel and pulp of biologically ripe fruits of the cvs Vlas and Snezhny were used for comparative transcriptomic analysis. The key genes of the flavonoid and carotenoid metabolism, sucrose hydrolysis, and soluble sugar transport were shown to be differentially expressed between fruit tissues, both within each cultivar and between them. It has been confirmed that the purple color of the peel of the cv. Vlas fruit is due to substantial amounts of anthocyanins. Flavonoid biosynthesis genes showed a significantly lower expression level in the ripe fruit of the cv. Vlas in comparison with the cv. Snezhny. However, in both cultivars, transcripts of anthocyanin biosynthesis genes (DFR, ANS, UFGT) were not detected. Additionally, the purple fruit of the cv. Vlas accumulated more carotenoids and sucrose and less glucose and fructose than the white fruit of the cv. Snezhny. Biochemical data corresponded to the differential expression pattern of the key genes encoding the structural proteins of metabolism and transport of the compounds analyzed.

Comparative Analysis of Citrus Species' Flavonoid Metabolism, Gene Expression Profiling, and Their Antioxidant Capacity under Drought Stress.

Citrus species are widely cultivated across the globe and frequently encounter drought stress during their growth and development phases. Previous research has indicated that citrus species synthesize flavonoids as a response mechanism to drought stress. This study aimed to comprehensively quantify and analyze the presence of 85 distinct flavonoids in the leaf and root tissues of lemon (drought susceptible) and sour orange (drought tolerant). In drought-stressed sour orange roots, flavonoids, such as isosakuranin, mangiferin, trilobatin, liquiritigenin, avicularin, silibinin, and glabridin, were more elevated than control sour orange roots and drought-stressed lemon roots. Additionally, hydroxysafflor yellow A, cynaroside, tiliroside, and apigenin 7-glucoside were increased in drought-stressed sour orange leaves compared to drought-stressed lemon leaves. Under drought stress, flavonoids such as (-)-epigallocatechin, silibinin, benzylideneacetophenone, trilobatin, isorhamnetin, 3,7,4'-trihydroxyflavone, and liquiritigenin were significantly increased, by 3.01-, 3.01-, 2.59-, 2.43-, 2.07-, 2.05-, and 2.01-fold, in sour orange roots compared to control sour orange roots. Moreover, the total flavonoid content and antioxidant capacity were significantly increased in drought-stressed sour orange leaves and root tissues compared to drought-stressed lemon leaves and root tissues. The expression levels of genes involved in flavonoid biosynthesis were highly expressed in sour orange leaves and roots, compared to lemon leaves and root tissues, post-drought stress. These findings indicate that lemons fail to synthesize protective flavonoids under drought conditions, whereas sour orange leaves and root tissues enhance flavonoid synthesis, with higher antioxidant activities to mitigate the adverse effects of reactive oxygen species generated during drought stress.

Evolution and Domestication of a Novel Biosynthetic Gene Cluster Contributing to the Flavonoid Metabolism and High-Altitude Adaptability of Plants in the Fagopyrum Genus.

The diversity of secondary metabolites is an important means for plants to cope with the complex and ever-changing terrestrial environment. Plant biosynthetic gene clusters (BGCs) are crucial for the biosynthesis of secondary metabolites. The domestication and evolution of BGCs and how they affect plant secondary metabolites biosynthesis and environmental adaptation are still not fully understood. Buckwheat exhibits strong resistance and abundant secondary metabolites, especially flavonoids, allowing it to thrive in harsh environments. A non-canonical BGC named UFGT3 cluster is identified, which comprises a phosphorylase kinase (PAK), two transcription factors (MADS1/2), and a glycosyltransferase (UFGT3), forming a complete molecular regulatory module involved in flavonoid biosynthesis. This cluster is selected during Tartary buckwheat domestication and is widely present in species of the Fagopyrum genus. In wild relatives of cultivated buckwheat, a gene encoding anthocyanin glycosyltransferase (AGT), which glycosylates pelargonidin into pelargonidin-3-O-glucoside, is found inserted into this cluster. The pelargonidin-3-O-glucoside can help plants resist UV stress, endowing wild relatives with stronger high-altitude adaptability. This study provides a new research paradigm for the evolutionary dynamics of plant BGCs, and offers new perspectives for exploring the mechanism of plant ecological adaptability driven by environmental stress through the synthesis of secondary metabolites.

Comparative Stem Transcriptome Analysis Reveals Pathways Associated with Drought Tolerance in Maritime Pine Grafts.

The maritime pine (Pinus pinaster Ait.) is a highly valuable Mediterranean conifer. However, recurrent drought events threaten its propagation and conservation. P. pinaster populations exhibit remarkable differences in drought tolerance. To explore these differences, we analyzed stem transcriptional profiles of grafts combining genotypes with contrasting drought responses under well-watered and water-stress regimes. Our analysis underscored that P. pinaster drought tolerance is mainly associated with constitutively expressed genes, which vary based on genotype provenance. However, we identified key genes encoding proteins involved in water stress response, abscisic acid signaling, and growth control including a PHD chromatin regulator, a histone deubiquitinase, the ABI5-binding protein 3, and transcription factors from Myb-related, DOF NAC and LHY families. Additionally, we identified that drought-tolerant rootstock could enhance the drought tolerance of sensitive scions by regulating the accumulation of transcripts involved in carbon mobilization, osmolyte biosynthesis, flavonoid and terpenoid metabolism, and reactive oxygen species scavenging. These included genes encoding galactinol synthase, CBL-interacting serine/threonine protein kinase 5, BEL1-like homeodomain protein, dihydroflavonol 4-reductase, and 1-deoxy-D-xylulose-5-phosphate. Our results revealed several hub genes that could help us to understand the molecular and physiological response to drought of conifers. Based on all the above, grafting with selected drought-tolerant rootstocks is a promising method for propagating elite recalcitrant conifer species, such as P. pinaster.

Investigation of the impact of papain on the volatile and non-volatile metabolites of soybean meal yogurt.

Soybean meal yogurt was prepared from soybean meal using papain and Bifidobacterium animalis subsp. lactis. A non-targeted metabolomics approach was employed to analyze the relevance of papain to the differences in volatile and non-volatile metabolites of soybean meal yogurt. The results showed that the main up-regulated metabolites and metabolic pathways after enzymatic digestion were dominated by amino acids and their derivatives. Conversely, the main down-regulated metabolites and pathways were predominantly associated with flavonoid metabolism. Amino acids and their derivatives, as well as flavonoids, were found to be highly correlated with the formation of sweet, umami, astringent, and bitterness. The addition of papain enriched the content of aromatic compounds in soybean meal yogurt. Aromatic components such as 2-heptanone, naphthalene, and p-xylene increased in concentration. Synthetic peptide of aspartate and serine, gramine, geissospermine, N-desmethyl vinblastine, and 3,7-dihydroxyflavone were the major non-volatile differential metabolites distinguishing the soybean meal yogurt. This study provided a comprehensive analysis of the metabolic traits of products co-fermented by papain and Bifidobacterium animalis subsp. lactis, offering insights for the application of papain in fermented goods. © 2024 Society of Chemical Industry.

Multi-omics analysis reveals the transcription factor AtuMYB306 improves drought tolerance by regulating flavonoid metabolism in Chinese chive (Allium tuberosum Rottler)

Drought is one of the most detrimental stresses that severely constrains plant growth and productivity. Although Chinese chive (Allium tuberosum Rottler) is a vegetable species that is cultivated and consumed worldwide, few studies have investigated how this species responds to drought. In this study, we conducted transcriptomics, metabolomics, and proteomics analyses on chive seedlings exposed to different water availability conditions (mild drought, moderate drought, severe drought, and re-watering) and found that the accumulation of flavonoids in chive leaves was substantially altered under drought stress. Gene co-expression regulatory network analysis, conducted by integrating transcriptome and metabolome data, revealed a chive R2R3-MYB transcription factor, AtuMYB306, as a central regulator of flavonoid synthesis. Overexpression of AtuMYB306 significantly improved osmotic stress tolerance and enhanced flavonoid content in Arabidopsis. We further demonstrated that AtuMYB306 directly binds to the promoters of three flavonoid biosynthetic genes (Atu4CL, AtuF3H, and AtuF3’H) and activates their expression. These results suggest that AtuMYB306 improves drought tolerance in Chinese chive by enhancing flavonoid biosynthesis to scavenge reactive oxygen species (ROS) generated under water-deficit conditions. Thus, our findings provide evidence that AtuMYB306 playing a pivotal role in improving drought resistance in Chinese chive.

RG-I pectic polysaccharides and hesperidin synergistically modulate gut microbiota: An in vitro study targeting the proportional relationship

In this study, we investigated how different proportions blends of Rhamnogalacturonan-I pectic polysaccharides and hesperidin impact the gut microbiota and metabolites using an in vitro simulated digestion and fermentation model. The results indicated that both of them could modulate the gut microbiota and produce beneficial metabolites. However, their blends in particular proportions (such as 1:1) exhibited remarkable synergistic effects on modulating the intestinal microenvironment, surpassing the effects observed with individual components. Specifically, these blends could benefit the host by increasing short-chain fatty acids production (such as acetate), improving hesperidin bioavailability, producing more metabolites (such as hesperetin, phenolic acids), and promoting the growth of beneficial bacteria. This synergistic and additive effect was inseparable from the role of gut microbiota. Certain beneficial bacteria, such as Blautia, Faecalibacterium, and Prevotella, exhibited strong preferences for those blends, thereby contributing to host health through participating in carbohydrate and flavonoid metabolism.

Saline-alkali stress affects the accumulation of proanthocyanidins and sesquiterpenoids via the MYB5-ANR/TPS31 cascades in the rose petals

Abstract Rose (Rosa rugosa) petals are rich in diverse secondary metabolites, which have important physiological functions as well as great economic values. Currently, it remains unclear how saline and/or alkaline stress(es) influence the accumulation of secondary metabolites in rose. In this study, we analyzed the transcriptome and metabolite profiles of rose petals under aline–alkali stress and uncovered the induction mechanism underlying major metabolites. Dramatic changes were observed in the expression of 1363 genes and the abundances of 196 metabolites in petals in response to saline–alkali stress. These differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) are mainly associated with flavonoid and terpenoid metabolism and the reconstruction of cell walls. Of them, TERPENE SYNTHASE 31 (TPS31) overexpression in tobacco leaves driven by its own promoter resulted in significant alterations in the levels of diverse terpenoids, which were differentially influenced by saline–alkali stress. An integrated analysis of metabolomic and transcriptomic data revealed a high correlation between the abundances of flavonoids/terpenoids and the expression of the transcription factor MYB5. MYB5 may orchestrate the biosynthesis of sesquiterpenoids and proanthocyanidins through direct regulation of TPS31 and ANR expression under aline–alkali stress. Our finding facilitates improving the bioactive substance accumulation of rose petals by metabolic engineering.

Commonalities and Specificities in Wheat (Triticum aestivum L.) Responses to Aluminum Toxicity and Low Phosphorus Revealed by Transcriptomics and Targeted Metabolomics.

Aluminum (Al) toxicity and low phosphorus availability (LP) are the top two co-existing edaphic constraints limiting agriculture productivity in acid soils. Plants have evolved versatile mechanisms to cope with the two stresses alone or simultaneously. However, the specific and common molecular mechanisms, especially those involving flavonoids and carbohydrate metabolism, remain unclear. Laboratory studies were conducted on two wheat genotypes-Fielder (Al-tolerant and P-efficient) and Ardito (Al-sensitive and P-inefficient)-exposed to 50 μM Al and 2 μM Pi (LP) in hydroponic solutions. After 4 days of stress, wheat roots were analyzed using transcriptomics and targeted metabolomics techniques. In Fielder, a total of 2296 differentially expressed genes (DEGs) were identified under Al stress, with 1535 upregulated and 761 downregulated, and 3029 DEGs were identified under LP stress, with 1591 upregulated and 1438 downregulated. Similarly, 4404 DEGs were identified in Ardito under Al stress, with 3191 upregulated and 1213 downregulated, and 1430 DEGs were identified under LP stress, with 1176 upregulated and 254 downregulated. GO annotation analysis results showed that 4079 DEGs were annotated to the metabolic processes term. These DEGs were significantly enriched in the phenylpropanoid, flavonoid, flavone and flavonol biosynthesis, and carbohydrate metabolism pathways by performing the KEGG enrichment analysis. The targeted metabolome analysis detected 19 flavonoids and 15 carbohydrate components in Fielder and Ardito under Al and LP stresses. In Fielder, more responsive genes and metabolites were involved in flavonoid metabolism under LP than Al stress, whereas the opposite trend was observed in Ardito. In the carbohydrate metabolism pathway, the gene and metabolite expression levels were higher in Fielder than in Ardito. The combined transcriptome and metabolome analysis revealed differences in flavonoid- and carbohydrate-related genes and metabolites between Fielder and Ardito under Al and LP stresses, which may contribute to Fielder's higher resistance to Al and LP. The results of this study lay a foundation for pyramiding genes and breeding multi-resistant varieties.

Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana

AbstractLight/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. Those oscillations can persist under constant conditions due to regulation by the circadian oscillator. The response of the transcriptome to light regimes is dynamic and allows plants to adapt rapidly to changing environmental conditions. We compared the transcriptome of Arabidopsis under LD and constant light (LL) for 3 days and identified different gene co‐expression networks in the two light regimes. Our studies yielded unforeseen insights into circadian regulation. Intuitively, we anticipated that gene clusters regulated by the circadian oscillator would display oscillations under LD cycles. However, we found transcripts encoding components of the flavonoid metabolism pathway that were rhythmic in LL but not in LD. We also discovered that the expressions of many stress‐related genes were significantly increased during the dark period in LD relative to the subjective night in LL, whereas the expression of these genes in the light period was similar. The nocturnal pattern of these stress‐related gene expressions suggested a form of “skotoprotection.” The transcriptomics data were made available in a web application named Cyclath, which we believe will be a useful tool to contribute to a better understanding of the impact of light regimes on plants.

Integrated transcriptomic and metabolomic analysis reveals the effects and potential mechanism of hydrogen peroxide on pigment metabolism in postharvest broccoli.

To understand the effects and related potential mechanism of H2O2 on pigment metabolism in postharvest broccoli, an integrated analysis of transcriptome and metabolome was performed. Results suggested that 65 differentially expressed genes and 26 differentially accumulated metabolites involved in chlorophyll, carotenoid, and flavonoid metabolism were identified. H2O2 treatment delayed the decrease of chlorophyll content by upregulating the expressions of chlorophyll synthetic genes, thylakoid synthetic genes, and 15 light-harvesting complex genes compared with the control and diphenylene iodonium treatments. H2O2 treatment decreased the accumulation of 11 flavonoids and 5 flavonols by downregulating the flavonoid synthetic genes. In addition, H2O2 treatment promoted carotenoid biosynthesis to eliminate reactive oxygen species in thylakoids, thereby protecting chlorophyll molecules from degradation. The inhibition of flavonoids and flavonols accumulation and chlorophyll decrease was the crucial reason for the delayed yellowing in H2O2 treatment. This study provides a new method and theoretical support for delaying the yellowing process in postharvest broccoli.

Quantitative evaluation and genome-wide association studies of chrysanthemum flower color

Chrysanthemum, one of the economically most important and highly favored ornamental crops, exhibits a wide range of flower colors that are pivotal in determining its aesthetic value and market demand. However, probably due to the high genetic complexity of flower color traits, the progress in the dissection of genetic architecture and identification of quantitative trait nucleotides (QTNs) or candidate genes moves rather slowly. In this study, we systematically assessed the genetic variation of flower color phenotypes by integrating multiple color systems (RHSCC, CIELAB, and RGB) and four principal floral pigments (anthocyanins, chlorophylls, carotenoids, and flavonoids) in a diverse collection of 141 chrysanthemums. The results showed that the flower color traits exhibited a wide range of variations, with coefficients of variation (CV) varying from 26.00 % to 203.52 %. Among the 66 pairs of flower color traits, 48 exhibited highly significant correlations at p < 0.01 or p < 0.05 levels. Moreover, eight exponential regression models were established for predicting anthocyanin and carotenoid contents. Based on the 370,562 high-quality SNPs, genome-wide association studies (GWAS) revealed 36 QTNs significantly associated with flower color phenotype traits and 109 QTNs for pigment content traits. By integrating the functional annotation and expression profiles, a total of 809 candidate genes surrounding the QTNs were initially filtered out. The candidate genes encompassed multiple transcription factor families related to flavonoid metabolism pathways, including MYB, bHLH, WD40, NAC, and AP2/ERF transcription factors, as well as cytochrome P450-type enzyme genes. The current findings contribute to the accurate assessment of flower colors and provide valuable resources for the molecular breeding and functional analysis of flower color in chrysanthemums.