The anthocyanin reduced tomato mutant demonstrates the role of flavonols in tomato lateral root and root hair development

Flavonols improve thermotolerance in tomato pollen during germination and tube elongation by maintaining ROS homeostasis

Elevated temperatures impair pollen performance and reproductive success, resulting in lower crop yields. The Solanum lycopersicum anthocyanin reduced ( are ) mutant has a FLAVANONE 3 HYDROXYLASE ( F3H ) gene mutation resulting in impaired synthesis of flavonol antioxidants. The are mutant has reduced pollen performance and seed set relative to the VF36 parental line, which is accentuated at elevated temperatures. Transformation of are with the wild-type F3H gene, or chemical complementation with flavonols, prevented temperature-dependent ROS accumulation in pollen and reversed are's reduced viability, germination, and tube elongation to VF36 levels. VF36 transformed with an F3H overexpression construct prevented temperature driven ROS increases and impaired pollen performance, revealing thermotolerance results from elevated flavonol synthesis. Although stigmas of are had reduced flavonols and elevated ROS, the growth of are pollen tubes were similarly impaired in both are and VF36 pistils. RNA-Seq was performed at optimal and stress temperatures in are , VF36, and the VF36 F3H overexpression line at multiple timepoints across pollen tube elongation. Differentially expressed gene numbers increased with duration of elevated temperature in all genotypes, with the largest number in are . These findings suggest potential agricultural interventions to combat the negative effects of heat-induced ROS in pollen that leads to reproductive failure.

One sentence summary

Flavonol antioxidants reduce the negative impacts of elevated temperatures on pollen performance by reducing levels of heat induced reactive oxygen species and modulation of heat-induced changes in the pollen transcriptome.

Reactive oxygen species are signaling molecules that modulate plant reproduction

Reactive oxygen species (ROS) can serve as signaling molecules that are essential for plant growth and development but abiotic stress can lead to ROS increases to supraoptimal levels resulting in cellular damage. To ensure efficient ROS signaling, cells have machinery to locally synthesize ROS to initiate cellular responses and to scavenge ROS to prevent it from reaching damaging levels. This review summarizes experimental evidence revealing the role of ROS during multiple stages of plant reproduction. Localized ROS synthesis controls the formation of pollen grains, pollen-stigma interactions, pollen tube growth, ovule development, and fertilization. Plants utilize ROS-producing enzymes such as respiratory burst oxidase homologs and organelle metabolic pathways to generate ROS, while the presence of scavenging mechanisms, including synthesis of antioxidant proteins and small molecules, serves to prevent its escalation to harmful levels. In this review, we summarized the function of ROS and its synthesis and scavenging mechanisms in all reproductive stages from gametophyte development until completion of fertilization. Additionally, we further address the impact of elevated temperatures induced ROS on impairing these reproductive processes and of flavonol antioxidants in maintaining ROS homeostasis to minimize temperature stress to combat the impact of global climate change on agriculture.

The Characterization of R2R3-MYB Genes in Ammopiptanthus nanus Uncovers That the miR858-AnaMYB87 Module Mediates the Accumulation of Anthocyanin under Osmotic Stress

R2R3-MYB transcription factors (TFs) participate in the modulation of plant development, secondary metabolism, and responses to environmental stresses. Ammopiptanthus nanus, a leguminous dryland shrub, tolerates a high degree of environmental stress, including drought and low-temperature stress. The systematic identification, structural analysis, evolutionary analysis, and gene profiling of R2R3-MYB TFs under cold and osmotic stress in A. nanus were performed. Up to 137 R2R3-MYB TFs were identified and clustered into nine clades, with most A. nanus R2R3-MYB members belonging to clade VIII. Tandem and segmental duplication events drove the expansion of the A. nanus R2R3-MYB family. Expression profiling revealed that multiple R2R3-MYB genes significantly changed under osmotic and cold stress conditions. MiR858 and miR159 targeted 88 R2R3-MYB genes. AnaMYB87, an miR858-targeted clade VIII R2R3-MYB TF, was up-regulated under both osmotic and cold stress. A transient expression assay in apples showed that the overexpression of AnaMYB87 promoted anthocyanin accumulation. A luciferase reporter assay in tobacco demonstrated that AnaMYB87 positively affected the transactivation of the dihydroflavonol reductase gene, indicating that the miR858-MYB87 module mediates anthocyanin accumulation under osmotic stress by regulating the dihydroflavonol reductase gene in A. nanus. This study provides new data to understand the roles of R2R3-MYB in plant stress responses.

Ethylene inhibits ABA-induced stomatal closure via regulating NtMYB184-mediated flavonol biosynthesis in tobacco

Stomatal movement can be regulated by ABA signaling through synthesis of reactive oxygen species (ROS) in guard cells. By contrast, ethylene triggers the biosynthesis of antioxidant flavonols to suppress ROS accumulation and prevent ABA-induced stomatal closure; however, the underlying mechanism remains largely unknown. In this study, we isolated and characterized the tobacco (Nicotiana tabacum) R2R3-MYB transcription factor NtMYB184, which belongs to the flavonol-specific SG7 subgroup. RNAi suppression and CRISPR/Cas9 mutation (myb184) of NtMYB184 in tobacco caused down-regulation of flavonol biosynthetic genes and decreased the concentration of flavonols in the leaves. Yeast one-hybrid assays, transactivation assays, EMSAs, and ChIP-qPCR demonstrated that NtMYB184 specifically binds to the promoters of flavonol biosynthetic genes via MYBPLANT motifs. NtMYB184 regulated flavonol biosynthesis in guard cells to modulate ROS homeostasis and stomatal aperture. ABA-induced ROS production was accompanied by the suppression of NtMYB184 and flavonol biosynthesis, which may accelerate ABA-induced stomatal closure. Furthermore, ethylene stimulated NtMYB184 expression and flavonol biosynthesis to suppress ROS accumulation and curb ABA-induced stomatal closure. In myb184, however, neither the flavonol and ROS concentrations nor the stomatal aperture varied between the ABA and ABA+ethylene treatments, indicating that NtMYB184 was indispensable for the antagonism between ethylene and ABA via regulating flavonol and ROS concentrations in the guard cells.

An arginine-to-histidine mutation in flavanone-3-hydroxylase results in pink strawberry fruits

Fruit color is a very important external commodity factor for consumers. Compared to the most typical red octoploid strawberry (Fragaria × ananassa), the pink strawberry often sells for a more expensive price and has a higher economic benefit due to its outstanding color. However, few studies have examined the molecular basis of pink-colored strawberry fruit. Through an EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified a mutant with pink fruits and green petioles. Bulked-segregant analysis sequencing analysis and gene function verification confirmed that the responsible mutation resides in a gene encoding flavanone-3-hydroxylase (F3H) in the anthocyanin synthesis pathway. This nonsynonymous mutation results in an arginine-to-histidine change at position 130 of F3H. Molecular docking experiments showed that the arginine-to-histidine mutation results in a reduction of intermolecular force-hydrogen bonding between the F3H protein and its substrates. Enzymatic experiments showed a greatly reduced ability of the mutated F3H protein to catalyze the conversion of the substrates and hence a blockage of the anthocyanin synthesis pathway. The discovery of a key residue in the F3H gene controlling anthocyanin synthesis provides a clear target of modification for the molecular breeding of strawberry varieties with pink-colored fruits, which may be of great commercial value.

Metabolic characteristics of self-pollinated wheat seed under red and blue light during early development

MAIN CONCLUSION

Blue light has a greater effect on jasmonic acid and flavonoid accumulation in wheat seeds than red light; blue light reduces starch synthesis and the size of starch granules and seeds. This study sought to elucidate the effects of blue and red light on seed metabolism to provide important insights regarding the role of light quality in regulating seed growth and development. We used combined multi-omics analysis to investigate the impact of red and blue light (BL) on the induction of secondary metabolite accumulation in the hexaploid wheat Dianmai 3 after pollination. Flavonoids and alkaloids were the most differentially abundant metabolites detected under different treatments. Additionally, we used multi-omics and weighted correlation network analysis to screen multiple candidate genes associated with jasmonic acid (JA) and flavonoids. Expression regulatory networks were constructed based on RNA-sequencing data and their potential binding sites. The results revealed that BL had a greater effect on JA and flavonoid accumulation in wheat seeds than red light. Furthermore, BL reduced starch synthesis and stunted the size of starch granules and seeds. Collectively, these findings clarify the role of BL in the metabolic regulation of early seed development in wheat.

Pinoresinol rescues developmental phenotypes of Arabidopsis phenylpropanoid mutants overexpressing FERULATE 5-HYDROXYLASE

Most phenylpropanoid pathway flux is directed toward the production of monolignols, but this pathway also generates multiple bioactive metabolites. The monolignols coniferyl and sinapyl alcohol polymerize to form guaiacyl (G) and syringyl (S) units in lignin, components that are characteristic of plant secondary cell walls. Lignin negatively impacts the saccharification potential of lignocellulosic biomass. Although manipulation of its content and composition through genetic engineering has reduced biomass recalcitrance, in some cases, these genetic manipulations lead to impaired growth. The reduced-growth phenotype is often attributed to poor water transport due to xylem collapse in low-lignin mutants, but alternative models suggest that it could be caused by the hyper- or hypoaccumulation of phenylpropanoid intermediates. In Arabidopsis thaliana, overexpression of FERULATE 5-HYDROXYLASE (F5H) shifts the normal G/S lignin ratio to nearly pure S lignin and does not result in substantial changes to plant growth. In contrast, when we overexpressed F5H in the low-lignin mutants cinnamyl dehydrogenase c and d (cadc cadd), cinnamoyl-CoA reductase 1, and reduced epidermal fluorescence 3, plant growth was severely compromised. In addition, cadc cadd plants overexpressing F5H exhibited defects in lateral root development. Exogenous coniferyl alcohol (CA) and its dimeric coupling product, pinoresinol, rescue these phenotypes. These data suggest that mutations in the phenylpropanoid pathway limit the biosynthesis of pinoresinol, and this effect is exacerbated by overexpression of F5H, which further draws down cellular pools of its precursor, CA. Overall, these genetic manipulations appear to restrict the synthesis of pinoresinol or a downstream metabolite that is necessary for plant growth.

From Nature to Lab: A Review of Secondary Metabolite Biosynthetic Pathways, Environmental Influences, and In Vitro Approaches

Secondary metabolites are gaining an increasing importance in various industries, such as pharmaceuticals, dyes, and food, as is the need for reliable and efficient methods of procuring these compounds. To develop sustainable and cost-effective approaches, a comprehensive understanding of the biosynthetic pathways and the factors influencing secondary metabolite production is essential. These compounds are a unique type of natural product which recognizes the oxidative damage caused by stresses, thereby activating the defence mechanism in plants. Various methods have been developed to enhance the production of secondary metabolites in plants. The elicitor-induced in vitro culture technique is considered an efficient tool for studying and improving the production of secondary metabolites in plants. In the present review, we have documented various biosynthetic pathways and the role of secondary metabolites under diverse environmental stresses. Furthermore, a practical strategy for obtaining consistent and abundant secondary metabolite production via various elicitation agents used in culturing techniques is also mentioned. By elucidating the intricate interplay of regulatory factors, this review paves the way for future advancements in sustainable and efficient production methods for high-value secondary metabolites.

Fine mapping of the flavonoid 3',5'-hydroxylase gene controlling anthocyanin biosynthesis in pepper anthers and stems

Pepper (Capsicum annuum L) is one of the most important vegetables grown worldwide. Nevertheless, the key structural and regulatory genes involved in anthocyanin accumulation in pepper have not been well understood or fine mapped yet. In this study, F1, F2, BC1P1, and BC1P2 pepper populations were analyzed and these populations were derived from a cross between line 14-Z4, which has yellow anthers and green stems, and line 14-Z5, which has purple anthers and stems. The results showed that the yellow anthers and green stems were determined by a single recessive locus called to as ayw. While, using preliminary and fine mapping techniques, ayw locus was located between markers aywSNP120 and aywSNP124, with physical distance of 0.2 Mb. The CA11g18550 gene was identified as promising candidate for the ayw locus, as it co-segregated with the yellow anthers and green stems phenotypes. CA11g18550 encodes a homolog of the F3'5'H (flavonoid 3',5'-hydroxylase) anthocyanin synthesis structure gene. The missense mutation of CA11g18550 possibly resulted in a loss-of-function. The expression analysis showed that CA11g18550 was significantly expressed in the stems, leaves, anthers and petals in 14-Z5, and it's silencing caused the stems changing from purple to green. This study provides a theoretical basis for using yellow anthers and green stems in pepper breeding and helps to advance the understanding of anthocyanin synthesis.

Anthocyanins and reactive oxygen species: a team of rivals regulating plant development?

Anthocyanins are a family of water-soluble vacuolar pigments present in almost all flowering plants. The chemistry, biosynthesis and functions of these flavonoids have been intensively studied, in part due to their benefit for human health. Given that they are efficient antioxidants, intense research has been devoted to studying their possible roles against damage caused by reactive oxygen species (ROS). However, the redox homeostasis established between antioxidants and ROS is important for plant growth and development. On the one hand, high levels of ROS can damage DNA, proteins, and lipids, on the other, they are also required for cell signaling, plant development and stress responses. Thus, a balance is needed in which antioxidants can remove excessive ROS, while not precluding ROS from triggering important cellular signaling cascades. In this article, we discuss how anthocyanins and ROS interact and how a deeper understanding of the balance between them could help improve plant productivity, nutritional value, and resistance to stress, while simultaneously maintaining proper cellular function and plant growth.

Thermosensitivity of pollen: a molecular perspective

A current trend in climate comprises adverse weather anomalies with more frequent and intense temperature events. Heatwaves are a serious threat to global food security because of the susceptibility of crop plants to high temperatures. Among various developmental stages of plants, even a slight rise in temperature during reproductive development proves detrimental, thus making sexual reproduction heat vulnerable. In this context, male gametophyte or pollen development stages are the most sensitive ones. High-temperature exposure induces pollen abortion, reducing pollen viability and germination rate with a concomitant effect on seed yield. This review summarizes the ultrastructural, morphological, biochemical, and molecular changes underpinning high temperature-induced aberrations in male gametophytes. Specifically, we highlight the temperature sensing cascade operating in pollen, involving reactive oxygen species (ROS), heat shock factors (HSFs), a hormones and transcriptional regulatory network. We also emphasize integrating various omics approaches to decipher the molecular events triggered by heat stress in pollen. The knowledge of genes, proteins, and metabolites conferring thermotolerance in reproductive tissues can be utilized to breed/engineer thermotolerant crops to ensure food security.

Tomato defence against Meloidogyne incognita by jasmonic acid-mediated fine-tuning of kaempferol homeostasis

Jasmonic acid (JA) is involved in the modulation of defence and growth activities in plants. The best-characterized growth-defence trade-offs stem from antagonistic crosstalk among hormones. In this study, we first confirmed that JA negatively regulates root-knot nematode (RKN) susceptibility via the root exudates (REs) of tomato plants. Omics and toxicological analyses implied that kaempferol, a type of flavonol, from REs has a negative effect on RKN infection. We demonstrated that SlMYB57 negatively regulated kaempferol contents in tomato roots, whereas SlMYB108/112 had the opposite effect. We revealed that JA fine-tuned the homeostasis of kaempferol via SlMYB-mediated transcriptional regulation and the interaction between SlJAZs and SlMYBs, thus ensuring a balance between lateral root (LR) development and RKN susceptibility. Overall, this work provides novel insights into JA-modulated LR development and RKN susceptibility mechanisms and elucidates a trade-off model mediated by JA in plants encountering stress.

The SPL transcription factor genes are potential targets for epigenetic regulation in response to drought stress in chickpea (C. arietinum L.)

BACKGROUND

Crop improvement for tolerance to various biotic and abiotic stress factors necessitates understanding the key gene regulatory mechanisms. One such mechanism of gene regulation involves changes in cytosine methylation at the gene body and flanking regulatory sequences. The present study was undertaken to identify genes which might be potential targets of drought-induced DNA methylation in chickpea.

METHODS AND RESULTS

Two chickpea genotypes, which contrast for drought tolerance, were subjected to drought stress conditions and their differential response was studied by analysing different morpho-physiological traits. Utilizing the in-house, high throughput sequencing data, the SQUAMOSA promoter-binding (SBP) protein-like (SPL) transcription factor genes were identified to be differentially methylated and expressed amongst the two genotypes, in response to drought stress. The methylation status of one of these genes was examined and validated through bisulfite PCR (BS-PCR). The identified genes could be possible homologs to known epialleles and can therefore serve as potential epialleles which can be utilized for crop improvement in chickpea.

CONCLUSION

The SPL TF genes are potential targets of epigenetic regulation in response to drought stress in chickpea. Since these are TFs, they might play important roles in controlling the expression of other genes, thus contributing to differential drought response of the two genotypes.

Novel players in organogenesis and flavonoid biosynthesis in cucumber glandular trichomes

Glandular trichomes (GTs) are outgrowths of plant epidermal cells that secrete and store specialized secondary metabolites that protect plants against biotic and abiotic stresses and have economic importance for human use. While extensive work has been done to understand the molecular mechanisms of trichome organogenesis in Arabidopsis (Arabidopsis thaliana), which forms unicellular, non-glandular trichomes (NGTs), little is known about the mechanisms of GT development or regulation of secondary metabolites in plants with multicellular GTs. Here, we identified and functionally characterized genes associated with GT organogenesis and secondary metabolism in GTs of cucumber (Cucumis sativus). We developed a method for effective separation and isolation of cucumber GTs and NGTs. Transcriptomic and metabolomic analyses showed that flavonoid accumulation in cucumber GTs is positively associated with increased expression of related biosynthesis genes. We identified 67 GT development-related genes, the functions of 7 of which were validated by virus-induced gene silencing. We further validated the role of cucumber ECERIFERUM1 (CsCER1) in GT organogenesis by overexpression and RNA interference transgenic approaches. We further show that the transcription factor TINY BRANCHED HAIR (CsTBH) serves as a central regulator of flavonoid biosynthesis in cucumber glandular trichomes. Work from this study provides insight into the development of secondary metabolite biosynthesis in multi-cellular glandular trichomes.

Flavonols modulate plant development, signaling, and stress responses

Flavonols are plant-specialized metabolites with important functions in plant growth and development. Isolation and characterization of mutants with reduced flavonol levels, especially the transparent testa mutants in Arabidopsis thaliana, have contributed to our understanding of the flavonol biosynthetic pathway. These mutants have also uncovered the roles of flavonols in controlling development in above- and below-ground tissues, notably in the regulation of root architecture, guard cell signaling, and pollen development. In this review, we present recent progress made towards a mechanistic understanding of flavonol function in plant growth and development. Specifically, we highlight findings that flavonols act as reactive oxygen species (ROS) scavengers and inhibitors of auxin transport in diverse tissues and cell types to modulate plant growth and development and responses to abiotic stresses.

Metabolomics Analysis Reveals Metabolites and Metabolic Pathways Involved in the Growth and Quality of Water Dropwort [Oenanthe javanica (Blume) DC.] under Nutrient Solution Culture

Water dropwort (Oenanthe javanica (Blume) DC.) is an important vegetable crop. Nutrient liquid culture has become an important cultivation method in the production of water dropwort. However, the effects of different nutrient solution cultivation methods on the growth and quality of water dropwort remains unclear. In this study, to screen the most suitable nutrient solution formula for the cultivation of water dropwort, the effects of different nutrient solution formulas (Hoagland, Cooper, Dutch greenhouse, Garden-style, Yamasaki and SCAU) on plant physiological and quality characteristics are investigated. The plant height, root length, water content (%), distribution rate of dry matter (%), chlorophyll, VC, flavonoid, total phenolic, DPPH and dietary fiber of water dropwort under different nutrient solutions were determined. According to the analytic hierarchy process (AHP) of the growth index and quality index of water dropwort under different nutrient solutions, the Yamazaki nutrient solution was considered to be the most suitable nutrient solution formula for water dropwort. To further confirm the differences of water dropwort under nutrient solution culture and soil culture, the broadly targeted metabolomics were performed. A total of 485 metabolites were detected in water dropwort under optimal nutrient solution and soil cultivation. Metabolomics analysis showed that flavonoids were the most abundant differential accumulated metabolites, and most flavonoids were up-regulated. A qRT-PCR assay indicated that the structural genes of the flavonoid biosynthesis pathway (PAL, C4H, CHS, CHI, F3H, DFR, UFGT) were significantly higher under the Yamasaki nutrient solution treatment. The current study provided a theoretical basis and technical guidance for the nutrient solution cultivation of water dropwort. Meanwhile, this study provides new insights into the study of flavonoids in water dropwort.

Flavonoids promote Rhizophagus irregularis spore germination and tomato root colonization: A target for sustainable agriculture

The use of arbuscular mycorrhizal (AM) fungi has great potential, being used as biostimulants, biofertilizers and bioprotection agents in agricultural and natural ecosystems. However, the application of AM fungal inoculants is still challenging due to the variability of results when applied in production systems. This variability is partly due to differences in symbiosis establishment. Reducing such variability and promoting symbiosis establishment is essential to improve the efficiency of the inoculants. In addition to strigolactones, flavonoids have been proposed to participate in the pre-symbiotic plant-AM fungus communication in the rhizosphere, although their role is still unclear. Here, we studied the specific function of flavonoids as signaling molecules in AM symbiosis. For that, both in vitro and in planta approaches were used to test the stimulatory effect of an array of different subclasses of flavonoids on Rhizophagus irregularis spore germination and symbiosis establishment, using physiological doses of the compounds. We show that the flavone chrysin and the flavonols quercetin and rutin were able to promote spore germination and root colonization at low doses, confirming their role as pre-symbiotic signaling molecules in AM symbiosis. The results pave the way to use these flavonoids in the formulation of AM fungal-based products to promote the symbiosis. This can improve the efficiency of commercial inoculants, and therefore, help to implement their use in sustainable agriculture.

CmHY5 functions in apigenin biosynthesis by regulating flavone synthase II expression in chrysanthemum flowers

The predominant flavones in the ray florets of chrysanthemum flowers are apigenin and its derivatives. CmHY5 participates in apigenin biosynthesis by directly regulating the expression of FNSII-1 in chrysanthemum. Chrysanthemum (Chrysanthemum morifolium) flowers have been used for centuries as functional food and in herbal tea and traditional medicine. The chrysanthemum flower contains significant amounts of the biologically active compound flavones, which has medicinal properties. However, the mechanism regulating flavones biosynthesis in chrysanthemum flowers organs is still unclear. Here, we compared the transcriptomes and metabolomes of different floral organs between two cultivars with contrasting flavone levels in their flowers. We identified 186 flavonoids by metabolome analysis. The predominant flavones in the ray florets of chrysanthemum flowers are apigenin and its derivatives, of which the contents are highly correlated with the expression of flavones synthase II gene CmFNSII-1. We also determined that CmHY5 is a direct upstream regulator of CmFNSII-1 transcription. We showed that CmHY5 RNAi interference lines in chrysanthemum have lower contents of apigenin compared to wild-type chrysanthemum. Our results demonstrated that CmHY5 participates in flavone biosynthesis by directly regulating the expression of FNSII-1 in chrysanthemum.

Multi-omics analyses reveal new insights into nutritional quality changes of alfalfa leaves during the flowering period

High-quality alfalfa is an indispensable resource for animal husbandry and sustainable development. Its nutritional quality changes dramatically during its life cycle and, at present, no molecular mechanisms for nutrient metabolic variation in alfalfa leaves at different growth stages have been clearly reported. We have used correlation and network analyses of the alfalfa leaf metabolome, proteome, and transcriptome to explore chlorophyll, flavonoid, and amino acid content at two development stages: budding stage (BS) and full-bloom stage (FBS). A high correlation between the expression of biosynthetic genes and their metabolites revealed significant reductions in metabolite content as the plant matured from BS to FBS. l-Glutamate, the first molecule of chlorophyll biosynthesis, decreased, and the expression of HemA, which controls the transformation of glutamyl-tRNA to glutamate 1-semialdehyde, was down-regulated, leading to a reduction in leaf chlorophyll content. Flavonoids also decreased, driven at least in part by increased expression of the gene encoding CYP75B1: flavonoid 3'-monooxygenase, which catalyzes the hydroxylation of dihydroflavonols and flavonols, resulting in degradation of flavonoids. Expression of NITRILASE 2 (NIT2) and Methyltransferase B (metB), which regulate amino acid metabolism and influence the expression of genes of the glycolysis-TCA pathway, were down-regulated, causing amino acid content in alfalfa leaves to decrease at FBS. This study provides new insights into the complex regulatory network governing the content and decrease of chlorophyll, amino acids, flavonoids, and other nutrients in alfalfa leaves during maturation. These results further provide a theoretical basis for the generation of alfalfa varieties exhibiting higher nutritional quality, high-yield cultivation, and a timely harvest.

Integrated metabolic, transcriptomic and chromatin accessibility analyses provide novel insights into the competition for anthocyanins and flavonols biosynthesis during fruit ripening in red apple

Fruit ripening is accompanied by a wide range of metabolites and global changes in gene expression that are regulated by various factors. In this study, we investigated the molecular differences in red apple 'Hongmantang' fruits at three ripening stages (PS1, PS5 and PS9) through a comprehensive analysis of metabolome, transcriptome and chromatin accessibility. Totally, we identified 341 and 195 differentially accumulated metabolites (DAMs) in comparison I (PS5_vs_PS1) and comparison II (PS9_vs_PS5), including 57 and 23 differentially accumulated flavonoids (DAFs), respectively. Intriguingly, among these DAFs, anthocyanins and flavonols showed opposite patterns of variation, suggesting a possible competition between their biosynthesis. To unveil the underlying mechanisms, RNA-Seq and ATAC-Seq analyses were performed. A total of 852 DEGs significantly enriched in anthocyanin metabolism and 128 differential accessible regions (DARs) significantly enriched by MYB-related motifs were identified as up-regulated in Comparison I but down-regulated in Comparison II. Meanwhile, the 843 DEGs significantly enriched in phenylalanine metabolism and the 364 DARs significantly enriched by bZIP-related motifs showed opposite trends. In addition, four bZIPs and 14 MYBs were identified as possible hub genes regulating the biosynthesis of flavonols and anthocyanins. Our study will contribute to the understanding of anthocyanins and flavonols biosynthesis competition in red apple fruits during ripening.

Exogenous Melatonin Improves Seed Germination of Wheat (Triticum aestivum L.) under Salt Stress

Melatonin (MT) can effectively reduce oxidative damage induced by abiotic stresses such as salt in plants. However, the effects of MT on physiological responses and molecular regulation during wheat germination remains largely elusive. In this study, the response of wheat seeds to MT under salt stress during germination was investigated at physiological and transcriptome levels. Our results revealed that application of MT significantly reduced the negative influence of salt stress on wheat seed germination. The oxidative load was reduced by inducing high activities of antioxidant enzymes. In parallel, the content of gibberellin A3 (GA₃) and jasmonic acid (JA) increased in MT-treated seedling. RNA-seq analysis demonstrated that MT alters oxidoreductase activity and phytohormone-dependent signal transduction pathways under salt stress. Weighted correlation network analysis (WGCNA) revealed that MT participates in enhanced energy metabolism and protected seeds via maintained cell morphology under salt stress during wheat seed germination. Our findings provide a conceptual basis of the MT-mediated regulatory mechanism in plant adaptation to salt stress, and identify the potential candidate genes for salt-tolerant wheat molecular breeding.

SlMYC2 mediates stomatal movement in response to drought stress by repressing SlCHS1 expression

Drought stress limits plant development and reproduction. Multiple mechanisms in plants are activated to respond to stress. The MYC2 transcription factor is a core regulator of the jasmonate (JA) pathway and plays a vital role in the crosstalk between abscisic acid (ABA) and JA. In this study, we found that SlMYC2 responded to drought stress and regulated stomatal aperture in tomato (Solanum lycopersicum). Overexpression of SlMYC2 repressed SlCHS1 expression and decreased the flavonol content, increased the reactive oxygen species (ROS) content in guard cells and promoted the accumulation of JA and ABA in leaves. Additionally, silencing the SlCHS1 gene produced a phenotype that was similar to that of the MYC2-overexpressing (MYC2-OE) strain, especially in terms of stomatal dynamics and ROS levels. Finally, we confirmed that SlMYC2 directly repressed the expression of SlCHS1. Our study revealed that SlMYC2 drove stomatal closure by modulating the accumulation of flavonol and the JA and ABA contents, helping us decipher the mechanism of stomatal movement under drought stress.

Kaempferol as a precursor for ubiquinone (coenzyme Q) biosynthesis: An atypical node between specialized metabolism and primary metabolism

Ubiquinone (coenzyme Q) is a vital respiratory cofactor and liposoluble antioxidant. Studies have shown that plants derive approximately a quarter of 4-hydroxybenzoate, which serves as the direct ring precursor of ubiquinone, from the catabolism of kaempferol. Biochemical and genetic evidence suggests that the release of 4-hydroxybenzoate from kaempferol is catalyzed by heme-dependent peroxidases and that 3-O-glycosylations of kaempferol act as a negative regulator of this process. These findings not only represent an atypical instance of primary metabolite being derived from specialized metabolism but also raise the question as to whether ubiquinone contributes to the ROS scavenging and signaling functions already established for flavonols.

Flavonoid deficiency disrupts redox homeostasis and terpenoid biosynthesis in glandular trichomes of tomato

Glandular trichomes (GTs) are epidermal structures that provide the first line of chemical defense against arthropod herbivores and other biotic threats. The most conspicuous structure on leaves of cultivated tomato (Solanum lycopersicum) is the type-VI GT (tVI-GT), which accumulates both flavonoids and volatile terpenoids. Although these classes of specialized metabolites are derived from distinct metabolic pathways, previous studies with a chalcone isomerase 1 (CHI1)-deficient mutant called anthocyanin free (af) showed that flavonoids are required for terpenoid accumulation in tVI-GTs. Here, we combined global transcriptomic and proteomic analyses of isolated trichomes as a starting point to show that the lack of CHI1 is associated with reduced levels of terpenoid biosynthetic transcripts and enzymes. The flavonoid deficiency in af trichomes also resulted in the upregulation of abiotic stress-responsive genes associated with DNA damage and repair. Several lines of biochemical and genetic evidence indicate that the terpenoid defect in af mutants is specific for the tVI-GT and is associated with the absence of bulk flavonoids rather than loss of CHI1 per se. A newly developed genome-scale model of metabolism in tomato tVI-GTs helped identify metabolic imbalances caused by the loss of flavonoid production. We provide evidence that flavonoid deficiency in this cell type leads to increased production of reactive oxygen species (ROS), which may impair terpenoid biosynthesis. Collectively, our findings support a role for flavonoids as ROS-scavenging antioxidants in GTs.

Serratene triterpenoids from Lycopodium cernuum L. as α-glucosidase inhibitors: Identification, structure-activity relationship and molecular docking studies

Phytochemical investigation of Lycopodium cernuum L. afforded seven undescribed serratene triterpenoids named 3β, 21β-dihydroxyserra-14-en-24-oic acid-3β-(5'-hydroxybenzoate) (1), 3β, 21β, 24-trihydroxyserrat-14-en-3β-(5'-hydroxyl benzoate) (2), 3β, 14α, 15α, 21β-tetrahydroxyserratane-24-methyl ester (3), 3β, 14α, 21β-trihydroxyserratane-15α-(4'-methoxy-5'-hydroxybenzoate)-24-methyl ester (4), 3β, 14α, 21β-trihydroxyserratane-15α-(4'-methoxy-5'-hydroxybenzoate) (5), 3β-hydroxy-21β-acetate-16-oxoserrat-14-en-24-oic acid (6), 3β, 21β-dihydroxy-16α, 29-epoxyserrat-14-en-24-methyl ester (7), together with eleven known compounds (8-18), whose chemical structures were elucidated through spectroscopic analysis of HRESIMS, 1D NMR, 2D NMR and comparison between the literature. All compounds were evaluated for their α-glucosidase inhibitory activity for the first time. The results showed that compounds 1, 2, 4, 5, 6, 10, 13, 15, and 16 were among the most potent α-glucosidase inhibitors, with IC₅₀ values ranging from 23.22 ± 0.64 to 50.65 ± 0.82 μM. Structure-activity relationship (SAR) studies indicated that the combined properties of the 5-hydroxybenzoate moiety at C-3, β-OH at C-21, COOH- at C-24, and Δ^14,15 groups enabled an increase in the α-glucosidase inhibitory effect. In addition, molecular docking studies showed that the potential inhibitors mainly interact with key amino acid residues in the active site of α-glucosidase through hydrogen bonds and hydrophobic forces.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

Hydroxylation decoration patterns of flavonoids in horticultural crops: chemistry, bioactivity and biosynthesis

Flavonoids are the most widespread polyphenolic compounds and are important dietary constituents present in horticultural crops such as fruits, vegetables, and tea. Natural flavonoids are responsible for important quality traits, such as food colors and beneficial dietary antioxidants and numerous investigations have shown that intake of flavonoids can reduce the incidence of various non-communicable diseases (NCDs). Analysis of the thousands of flavonoids reported so far has shown that different hydroxylation modifications affect their chemical properties and nutritional values. These diverse flavonoids can be classified based on different hydroxylation patterns in the B, C, A rings and multiple structure-activity analyses have shown that hydroxylation decoration at specific positions markedly enhances their bioactivities. This review focuses on current knowledge concerning hydroxylation of flavonoids catalyzed by several different types of hydroxylase enzymes. Flavonoid 3'-hydroxylase (F3'H) and flavonoid 3'5'-hydroxylase (F3'5'H) are important enzymes for the hydroxylation of the B ring of flavonoids. Flavanone 3-hydroxylase (F3H) is key for the hydroxylation of the C ring, while flavone 6-hydroxylase (F6H) and flavone 8-hydroxylase (F8H) are key enzymes for hydroxylation of the A ring. These key hydroxylases in the flavonoid biosynthesis pathway are promising targets for the future bioengineering of plants and mass production of flavonoids with designated hydroxylation patterns of high nutritional importance. In addition, hydroxylation in key places on the ring may help render flavonoids ready for degradation, the catabolic turnover of which may open the door for new lines of inquiry.

Flavonoids are involved in phosphorus-deficiency-induced cluster-root formation in white lupin

BACKGROUND AND AIMS

Initiation of cluster roots in white lupin (Lupinus albus) under phosphorus (P) deficiency requires auxin signalling, whereas flavonoids inhibit auxin transport. However, little information is available about the interactions between P deficiency and flavonoids in terms of cluster-root formation in white lupin.

METHODS

Hydroponic and aeroponic systems were used to investigate the role of flavonoids in cluster-root formation, with or without 75 μm P supply.

KEY RESULTS

Phosphorus-deficiency-induced flavonoid accumulation in cluster roots depended on developmental stage, based on in situ determination of fluorescence of flavonoids and flavonoid concentration. LaCHS8, which codes for a chalcone synthase isoform, was highly expressed in cluster roots, and silencing LaCHS8 reduced flavonoid production and rootlet density. Exogenous flavonoids suppressed cluster-root formation. Tissue-specific distribution of flavonoids in roots was altered by P deficiency, suggesting that P deficiency induced flavonoid accumulation, thus fine-tuning the effect of flavonoids on cluster-root formation. Furthermore, naringenin inhibited expression of an auxin-responsive DR5:GUS marker, suggesting an interaction of flavonoids and auxin in regulating cluster-root formation.

CONCLUSIONS

Phosphorus deficiency triggered cluster-root formation through the regulation of flavonoid distribution, which fine-tuned an auxin response in the early stages of cluster-root development. These findings provide valuable insights into the mechanisms of cluster-root formation under P deficiency.

Root hair growth from the pH point of view

Root hairs are tubular outgrowths of epidermal cells that increase the root surface area and thereby make the root more efficient at absorbing water and nutrients. Their expansion is limited to the root hair apex, where growth is reported to take place in a pulsating manner. These growth pulses coincide with oscillations of the apoplastic and cytosolic pH in a similar way as has been reported for pollen tubes. Likewise, the concentrations of apoplastic reactive oxygen species (ROS) and cytoplasmic Ca²⁺ oscillate with the same periodicity as growth. Whereas ROS appear to control cell wall extensibility and opening of Ca²⁺ channels, the role of protons as a growth signal in root hairs is less clear and may differ from that in pollen tubes where plasma membrane H⁺-ATPases have been shown to sustain growth. In this review, we outline our current understanding of how pH contributes to root hair development.

Specialized metabolism and development: An unexpected friendship

Plants produce a myriad of metabolites. Some of them have been regarded for a long time as secondary or specialized metabolites and are considered to have functions mostly in defense and the adaptation of plants to their environment. However, in the last years, new research has shown that these metabolites can also have roles in the regulation of plant growth and development, some acting as signals, through the interaction with hormonal pathways, and some independently of them. These reports provide a glimpse of the functional possibilities that specialized metabolites present in the modulation of plant development and encourage more research in this direction.

Rejuvenation remodels transcriptional network to improve rhizogenesis in mature Juglans tree

Adventitious rooting of walnut species (Juglans L.) is known to be rather difficult, especially for mature trees. The adventitious root formation (ARF) capacities of mature trees can be significantly improved by rejuvenation. However, the underlying gene regulatory networks (GRNs) of rejuvenation remain largely unknown. To characterize such regulatory networks, we carried out the transcriptomic study using RNA samples of the cambia and peripheral tissues on the bottom of rejuvenated and mature walnut (Juglans hindsii × J. regia) cuttings during the ARF. The RNA sequencing data suggested that zeatin biosynthesis, energy metabolism and substance metabolism were activated by rejuvenation, whereas photosynthesis, fatty acid biosynthesis and the synthesis pathways for secondary metabolites were inhibited. The inter- and intra-module GRNs were constructed using differentially expressed genes. We identified 35 hub genes involved in five modules associated with ARF. Among these hub genes, particularly, beta-glucosidase-like (BGLs) family members involved in auxin metabolism were overexpressed at the early stage of the ARF. Furthermore, BGL12 from the cuttings of Juglans was overexpressed in Populus alba × P. glandulosa. Accelerated ARF and increased number of ARs were observed in the transgenic poplars. These results provide a high-resolution atlas of gene activity during ARF and help to uncover the regulatory modules associated with the ARF promoted by rejuvenation.

Elucidation of myricetin biosynthesis in Morella rubra of the Myricaceae

Flavonols are health-promoting bioactive compounds important for plant defense and human nutrition. Quercetin (Q) and kaempferol (K) biosynthesis have been studied extensively while little is known about myricetin (M) biosynthesis. The roles of flavonol synthases (FLSs) and flavonoid 3',5'-hydroxylase (F3'5'H) in M biosynthesis in Morella rubra, a member of the Myricaceae rich in M-based flavonols, were investigated. The level of MrFLS transcripts alone did not correlate well with the accumulation of M-based flavonols. However, combined transcript data for MrFLS1 and MrF3'5'H showed a good correlation with the accumulation of M-based flavonols in different tissues of M. rubra. Recombinant MrFLS1 and MrFLS2 proteins showed strong activity with dihydroquercetin (DHQ), dihydrokaempferol (DHK), and dihydromyricetin (DHM) as substrates, while recombinant MrF3'5'H protein preferred converting K to M, amongst a range of substrates. Tobacco (Nicotiana tabacum) overexpressing 35S::MrFLSs produced elevated levels of K-based and Q-based flavonols without affecting M-based flavonol levels, while tobacco overexpressing 35S::MrF3'5'H accumulated significantly higher levels of M-based flavonols. We conclude that M accumulation in M. rubra is affected by gene expression and enzyme specificity of FLS and F3'5'H as well as substrate availability. In the metabolic grid of flavonol biosynthesis, the strong activity of MrF3'5'H with K as substrate additionally promotes metabolic flux towards M in M. rubra.

Beyond Purple Tomatoes: Combined Strategies Targeting Anthocyanins to Generate Crimson, Magenta, and Indigo Fruit

The range of colours of many flowers and fruits is largely due to variations in the types of anthocyanins produced. The degree of hydroxylation on the B-ring affects the hue of these pigments, causing a shift from the orange end of the visible spectrum to the blue end. Besides colour, this modification can also affect other properties of anthocyanins, including the ability to protect the plant against different stresses or, when included in the human diet, to provide benefits for disease prevention. The level of hydroxylation of the B-ring is determined by the activity of two key hydroxylases, F3′H and F3′5′H, and by the substrate preference of DFR, an enzyme acting downstream in the biosynthetic pathway. We show that, in tomato, a strategy based on fruit-specific engineering of three regulatory genes (AmDel, AmRos1, AtMYB12) and a single biosynthetic gene (AmDFR), together with the availability of a specific mutation (f3′5′h), results in the generation of three different varieties producing high levels of anthocyanins with different levels of hydroxylation. These tomatoes show distinctive colours and mimic the classes of anthocyanins found in natural berries, thus providing unique near-isogenic material for different studies.

Biosynthetic Pathway of Proanthocyanidins in Major Cash Crops

Proanthocyanidins (PAs) are a group of oligomers or polymers composed of monomeric flavanols. They offer many benefits for human fitness, such as antioxidant, anticancer, and anti-inflammatory activities. To date, three types of PA have been observed in nature: procyanidins, propelargonidins, and prodelphinidins. These are synthesized as some of the end-products of the flavonoid pathway by different consecutive enzymatic activities, from the same precursor—naringenin. Although the general biosynthetic pathways of PAs have been reported in a few model plant species, little is known about the species-specific pathways in major crops containing different types of PA. In the present study, we identified the species-specific pathways in 10 major crops, based on the presence/absence of flavanol-based intermediates in the metabolic pathway, and found 202 orthologous genes in the reference genomic database of each species, which may encode for key enzymes involved in the biosynthetic pathways of PAs. Parallel enzymatic reactions in the pathway are responsible for the ratio between PAs and anthocyanins, as well as among the three types of PAs. Our study suggests a promising strategy for molecular breeding, to regulate the content of PAs and anthocyanins and improve the nutritional quality of food sources globally.

McMYB4 improves temperature adaptation by regulating phenylpropanoid metabolism and hormone signaling in apple

Temperature changes affect apple development and production. Phenylpropanoid metabolism and hormone signaling play a crucial role in regulating apple growth and development in response to temperature changes. Here, we found that McMYB4 is induced by treatment at 28 °C and 18 °C, and McMYB4 overexpression results in flavonol and lignin accumulation in apple leaves. Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs) further revealed that McMYB4 targets the promoters of the flavonol biosynthesis genes CHS and FLS and the lignin biosynthesis genes CAD and F5H. McMYB4 expression resulted in higher levels of flavonol and lignin biosynthesis in apple during growth at 28 °C and 18 °C than during growth at 23 °C. At 28 °C and 18 °C, McMYB4 also binds to the AUX/ARF and BRI/BIN promoters to activate gene expression, resulting in acceleration of the auxin and brassinolide signaling pathways. Taken together, our results demonstrate that McMYB4 promotes flavonol biosynthesis and brassinolide signaling, which decreases ROS contents to improve plant resistance and promotes lignin biosynthesis and auxin signaling to regulate plant growth. This study suggests that McMYB4 participates in the abiotic resistance and growth of apple in response to temperature changes by regulating phenylpropanoid metabolism and hormone signaling.

EkFLS overexpression promotes flavonoid accumulation and abiotic stress tolerance in plant

Flavonoids with great medicinal value play an important role in plant individual growth and stress resistance. Flavonol synthetase (FLS) is one of the key enzymes to synthesize flavonoids. However, the role of the FLS gene in flavonoid accumulation and tolerance to abiotic stresses, as well as its mechanism has not yet been investigated systematically in plants. The aim of this research is to evaluate the effect of FLS overexpression on the accumulation of active ingredients and stress resistance in Euphorbia kansui Liou. The results showed that when the EkFLS gene was overexpressed in Arabidopsis thaliana, the accumulation of flavonoids was improved. In addition, when the wild-type and EkFLS overexpressed Arabidopsis plants were treated with ABA and MeJA, compared with WT Arabidopsis, EkFLS overexpressed Arabidopsis promoted stomatal aperture to influence photosynthesis of the plants, which in turn can promote stress resistance. Meanwhile, under MeJA, NaCl, and PEG treatment, EkFLS overexpressed in Arabidopsis induced higher accumulation of flavonoids, which significantly enhanced peroxidase (POD) and superoxide dismutase (SOD) activities that can scavenge reactive oxygen species in cells to protect the plant. These results indicated that EkFLS overexpression is strongly correlated to the increase of flavonoid synthesis and therefore the tolerance to abiotic stresses in plants, providing a theoretical basis for further improving the quality of medicinal plants and their resistance to abiotic stresses simultaneously.

Integrating transcriptome, co-expression and QTL-seq analysis reveals that primary root growth in maize is regulated via flavonoid biosynthesis and auxin signal transduction

The primary root is critical for early seedling growth and survival. To understand the molecular mechanisms governing primary root development, we performed a dynamic transcriptome analysis of two maize (Zea mays) inbred lines with contrasting primary root length at nine time points over a 12-day period. A total of 18 702 genes were differentially expressed between two lines or different time points. Gene enrichment, phytohormone content determination, and metabolomics analysis showed that auxin biosynthesis and signal transduction, as well as the phenylpropanoid and flavonoid biosynthesis pathways, were associated with root development. Co-expression network analysis revealed that eight modules were associated with lines/stages, as well as primary or lateral root length. In root-related modules, flavonoid metabolism accompanied by auxin biosynthesis and signal transduction constituted a complex gene regulatory network during primary root development. Two candidate genes (rootless concerning crown and seminal roots, rtcs and Zm00001d012781) involved in auxin signaling and flavonoid biosynthesis were identified by co-expression network analysis, QTL-seq and functional annotation. These results increase our understanding of the regulatory network controlling the development of primary and lateral root length, and provide a valuable genetic resource for improvement of root performance in maize.

Metabolomics and transcriptome analysis of the biosynthesis mechanism of flavonoids in the seeds of Euryale ferox Salisb at different developmental stages

Flavonoids belong to polyphenolic compounds, which are widely distributed in plants and have rich functions. Euryale ferox Salisb is an important medicinal and edible homologous plant, and flavonoids are its main functional substances. However, the biosynthesis mechanism of flavonoids in E. ferox is still poorly understood. To explore the dynamic changes of flavonoid biosynthesis during the development of E. ferox seeds, the targeted flavonoid metabolome was determined. A total of 129 kinds of flavonoid metabolites were characterized in the seeds of E. ferox, including 11 flavanones, 8 dihydroflavanols, 16 flavanols, 29 flavones, 3 isoflavones, 12 anthocyanins, 29 flavonols, 6 flavonoid carbonosides, 3 chalcones and 13 proanthocyanidins. The relative content of flavonoid metabolites accumulated continuously during the development of E. ferox seeds, and reached the highest at T30. In transcriptome, the expression of key genes in the flavonoid pathway, such as PAL, CHS, F3H, FLS, ANS, was highest in T30, which was consistent with the trend of metabolites. Six candidate transcription factors (R2R3MYBs and bHLHs) may affect the biosynthesis of flavonoids by regulating the expression of structural genes. Furthermore, transcriptome analysis and exogenous ABA and SA treatment demonstrated that ABA (PYR1, PP2Cs, SnRK2s) and SA (NPR1) are involved in the positive regulation of flavonoid biosynthesis. This study clarified the differential changes of flavonoid metabolites during the development of E. ferox seeds, confirmed that ABA and SA promote the synthesis of flavonoids, and found key candidate genes that are involved in the regulation of ABA and SA in the positive regulation of flavonoid biosynthesis.

Flavonols modulate lateral root emergence by scavenging reactive oxygen species in Arabidopsis thaliana

Flavonoids are a class of specialized metabolites with subclasses including flavonols and anthocyanins, which have unique properties as antioxidants. Flavonoids modulate plant development, but whether and how they impact lateral root development is unclear. We examined potential roles for flavonols in this process using Arabidopsis thaliana mutants with defects in genes encoding key enzymes in flavonoid biosynthesis. We observed the tt4 and fls1 mutants, which produce no flavonols, have increased lateral root emergence. The tt4 root phenotype was reversed by genetic and chemical complementation. To more specifically define the flavonoids involved, we tested an array of flavonoid biosynthetic mutants, eliminating roles for anthocyanins and the flavonols quercetin and isorhamnetin in modulating lateral root development. Instead, two tt7 mutant alleles, with defects in a branchpoint enzyme blocking quercetin biosynthesis, formed reduced numbers of lateral roots and tt7-2 had elevated levels of kaempferol. Using a flavonol-specific dye, we observed that in the tt7-2 mutant, kaempferol accumulated within lateral root primordia at higher levels than wild-type. These data are consistent with kaempferol, or downstream derivatives, acting as a negative regulator of lateral root emergence. We examined ROS accumulation using ROS-responsive probes and found reduced fluorescence of a superoxide-selective probe within the primordia of tt7-2 compared with wild-type, but not in the tt4 mutant, consistent with opposite effects of these mutants on lateral root emergence. These results support a model in which increased level of kaempferol in the lateral root primordia of tt7-2 reduces superoxide concentration and ROS-stimulated lateral root emergence.

SPX4 interacts with both PHR1 and PAP1 to regulate critical steps in phosphorus-status-dependent anthocyanin biosynthesis

Phosphate (Pi) is the plant-accessible form of phosphorus, and its insufficiency limits plant growth. The over-accumulation of anthocyanins in plants is often an indication of Pi starvation. However, whether the two pathways are directly linked and which components are involved in this process await identification. Here, we demonstrate that SPX4, a conserved regulator of the Pi response, transduces the Pi starvation signal to anthocyanin biosynthesis in Arabidopsis. When phr1spx4 plants were grown under low Pi conditions, DFR expression and anthocyanin biosynthesis were induced, which distinguished the plant from the behavior reported in the phr1 mutant. We also provide evidence that SPX4 interacts with PAP1, an MYB transcription factor that controls the anthocyanin biosynthetic pathway, in an inositol polyphosphate-dependent manner. Through a physical interaction, SPX4 prevented PAP1 from binding to its target gene promoter; by contrast, during Pi-deficient conditions, in the absence of inositol polyphosphates, PAP1 was released from SPX to activate anthocyanin biosynthesis. Our results reveal a direct link between Pi deficiency and flavonoid metabolism. This new regulatory module, at least partially independent from PHR1, may contribute to developing a strategy for plants to adapt to Pi starvation.

Rapid generation of tomato male-sterile lines with a marker use for hybrid seed production by CRISPR/Cas9 system

Owing to their superior agronomic performance, the hybrids of vegetable crops are currently applied extensively. However, effective hybrid production requires a laborious manual emasculation to ensure the purity of hybrid seeds in tomato because of the lack of an effective male sterility system. Here, we created two types of tomato nuclear male-sterile lines with different screening markers in a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system. Co-knockouts of male sterile 1035 (Ms1035) and glutathione S-transferase (GSTAA) created a male-sterile line marked by a green hypocotyl. The Ms1035 biallelic mutation was introduced into the woolly tomato background, resulting in the linkage of male sterility and a non-woolly phenotype. Two types of male-sterile lines were easily selected at the seedling stage by hypocotyl color or trichome density and further showed high seed purity during hybrid seed production. Our work established the procedure for a rapid transfer of the male-sterile phenotype to the parents of hybrids without extra-modification by the CRISPR/Cas9 system that can be practically applied to hybrid seed production in tomato. This method will be the basis and example for sterile parent creation of multiple crops for hybrid production with the CRISPR/Cas9 system.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01215-2.

Metabolome and Transcriptome Association Analysis Reveals Regulation of Flavonoid Biosynthesis by Overexpression of LaMIR166a in Larix kaempferi (Lamb.) Carr

Somatic embryogenesis is an ideal model process for studying early plant development. Embryonic cell lines of Larix kaempferi (Lamb.) Carr overexpressing LaMIR166a were obtained in our previous study. Here, a combination of de novo transcriptomics and extensively targeted metabolomics was used to study the transcriptional profiles and metabolic changes in wild-type and LaMIR166a-overexpressed embryonic cell lines. A total of 459 metabolites were found in the wild-type and transgenic cell lines. Compared to those in the wild-type cell lines, transcripts and metabolites were significantly altered in the LaMIR166a-overexpressed cell lines. Among differentially expressed genes (DEGs), phenylalanine and flavonoid synthesis genes were significantly enriched, and among differentially accumulated metabolites (DAMs), phenolic acids and flavonoids accumulated in particularly high amounts. Thus, the flavonoid biosynthetic pathway seems to be the most abundant pathway in response to LaMIR166a overexpression. Based on the Kyoto Encyclopedia of Genes and Genomes database, the association analysis of metabolome and transcriptome data showed that flavonoid biosynthesis and plant hormone signal transduction processes were significantly changed in miR166a-overexpression lines, suggesting that miR166 might be involved in these processes. The present study identified a number of potential metabolites associated with LaMIR166a overexpression, providing a significant foundation for a better understanding of the regulatory mechanisms underlying miR166.

Naringenin induces tolerance to salt/osmotic stress through the regulation of nitrogen metabolism, cellular redox and ROS scavenging capacity in bean plants

The present study was conducted to uncover underlying possible effect mechanisms of flavonoid naringenin (Nar, 0.1-0.4 mM) in nitrogen assimilation, antioxidant response, redox status and the expression of NLP7 and DREB2A, on salt (100 mM NaCl) and osmotic-stressed (10% Polyethylene glycol, -0.54 MPa) Phaseolus vulgaris cv. Yunus 90). Nar ameliorated salt/osmotic stresses-induced growth inhibition and improved the accumulation of proline, glycine betaine and choline. In response to stress, Nar increased endogenous content of nitrate (NO₃^-) and nitrite (NO₂^-) by regulating of nitrate reductase and nitrite reductase. Stress-triggered NH₄⁺ was eliminated with Nar through increases in glutamine synthetase and glutamate synthase. After NaCl or NaCl + PEG exposure, Nar utilized the aminating activity of glutamate dehydrogenase in the conversion of NH₄⁺. The stress-inducible expression levels of DREB2A were increased further by Nar, which might have affected stress tolerance of bean. Nar induced effectively the relative expression of NLP7 in the presence of the combination or alone of stress. Also, the impaired redox state by stress was modulated by Nar and hydrogen peroxide (H₂O₂) and TBARS decreased. Nar regulated the different pathways for scavenging of H₂O₂ under NaCl and/or PEG treatments. When Nar + NaCl exposure, the damage was removed by superoxide dismutase (SOD), catalase (CAT), POX (only at 0.1 mM Nar + NaCl) and AsA-GSH cycle. Under osmotic stress plus Nar, the protection was manifested by activated CAT and, glutathione S-transferase and the regeneration of ascorbate. 0.1 mM Nar could protect bean plant against salt/osmotic stresses, likely by regulating nitrogen assimilation pathways, improving expression levels of genes associated with tolerance mechanisms and modulating the antioxidant capacity and AsA-GSH redox-based systems.

A quick protocol for the identification and characterization of early growth mutants in tomato

Root system architecture (RSA) manipulation may improve water and nutrient capture by plants under normal and extreme climate conditions. With the aim of initiating the genetic dissection of RSA in tomato, we established a defined ontology that allowed the curated annotation of the observed phenotypes on 12 traits at four consecutive growth stages. In addition, we established a quick approach for the molecular identification of the mutations associated with the trait-of-interest by using a whole-genome sequencing approach that does not require the building of an additional mapping population. As a proof-of-concept, we screened 4543 seedlings from 300 tomato M₃ lines (Solanum lycopersicum L. cv. Micro-Tom) generated by chemical mutagenesis with ethyl methanesulfonate. We studied the growth and early development of both the root system (primary and lateral roots) and the aerial part of the seedlings as well as the wound-induced adventitious roots emerging from the hypocotyl. We identified 659 individuals (belonging to 203 M₃ lines) whose early seedling and RSA phenotypes differed from those of their reference background. We confirmed the genetic segregation of the mutant phenotypes affecting primary root length, seedling viability and early RSA in 31 M₄ families derived from 15 M₃ lines selected in our screen. Finally, we identified a missense mutation in the SlCESA3 gene causing a seedling-lethal phenotype with short roots. Our results validated the experimental approach used for the identification of tomato mutants during early growth, which will allow the molecular identification of the genes involved.

GSM2, a transaldolase, contributes to reactive oxygen species homeostasis in Arabidopsis

Plants are exposed to various environmental cues that lead to reactive oxygen species (ROS) accumulation. ROS production and detoxification are tightly regulated to maintain balance. Although studies of glucose (Glc) are always accompanied by ROS in animals, the role of Glc in respect of ROS in plants is unclear. We isolated gsm2 (Glc-hypersensitive mutant 2), a mutant with a notably chlorotic-cotyledon phenotype. The chloroplast-localized GSM2 was characterized as a transaldolase in the pentose phosphate pathway. With 3% Glc treatment, fewer or no thylakoids were observed in gsm2 cotyledon chloroplasts than in wild-type cotyledon chloroplasts, suggesting that GSM2 is required for chloroplast protection under stress. gsm2 also showed evaluated accumulation of ROS with 3% Glc treatment and was more sensitive to exogenous H₂O₂ than the wild type. Gene expression analysis of the antioxidant enzymes in gsm2 revealed that chloroplast damage to gsm2 cotyledons results from the accumulation of excessive ROS in response to Glc. Moreover, the addition of diphenyleneiodonium chloride or phenylalanine can rescue Glc-induced chlorosis in gsm2 cotyledons. This work suggests that GSM2 functions to maintain ROS balance in response to Glc during early seedling growth and sheds light on the relationship between Glc, the pentose phosphate pathway and ROS.

Flavonols regulate root hair development by modulating accumulation of reactive oxygen species in the root epidermis

Reactive oxygen species (ROS) are signaling molecules produced by tissue-specific respiratory burst oxidase homolog (RBOH) enzymes to drive development. In Arabidopsis thaliana, ROS produced by RBOHC was previously reported to drive root hair elongation. We identified a specific role for one ROS, H₂O₂, in driving root hair initiation and demonstrated that localized synthesis of flavonol antioxidants control the level of H₂O₂ and root hair formation. Root hairs form from trichoblast cells that express RBOHC and have elevated H₂O₂ compared with adjacent atrichoblast cells that do not form root hairs. The flavonol-deficient tt4 mutant has elevated ROS in trichoblasts and elevated frequency of root hair formation compared with the wild type. The increases in ROS and root hairs in tt4 are reversed by genetic or chemical complementation. Auxin-induced root hair initiation and ROS accumulation were reduced in an rbohc mutant and increased in tt4, consistent with flavonols modulating ROS and auxin transport. These results support a model in which localized synthesis of RBOHC and flavonol antioxidants establish patterns of ROS accumulation that drive root hair formation.

Modulation of Arabidopsis Flavonol Biosynthesis Genes by Cyst and Root-Knot Nematodes

Although it is well established that flavonoid synthesis is induced in diverse plant species during nematode parasitism, little is known about the regulation of genes controlling flavonol biosynthesis during the plant–nematode interaction. In this study, expression of the Arabidopsis thaliana flavonol-specific transcription factor, AtMYB12, the flavonol synthase genes, AtFLS1, 2, 3, 4, and 5, and the gene encoding the central flavonoid enzyme, chalcone synthase (AtCHS), were examined in plant roots during infection by Heterodera schachtii (sugar beet cyst) and Meloidogyne incognita (root-knot) nematodes. These experiments showed that AtMYB12 was transiently upregulated at 9 dpi in syncytia associated with sugar beet cyst nematode infection and that an Atmyb12-deficient line was less susceptible to the parasite. This suggests that, rather than contributing to plant defense, this gene is essential for productive infection. However, the AtCHS and AtFLS1 genes, which are controlled by AtMYB12, did not exhibit a similar transient increase, but rather were expressly downregulated in syncytia relative to adjacent uninfected root tissue. Genetic analyses further indicated that AtFLS1 contributes to plant defense against Cyst nematode infection, while other AtFLS gene family members do not, consistent with prior reports that these other genes encode little or no enzyme activity. Together, these findings indicate a role of AtMyb12 in promoting the early stages of Cyst nematode infection, while flavonols produced through the action of AtFLS1 are essential for plant defense. On the other hand, a transient induction of AtMYB12 was not observed in galls produced during root-knot nematode infection, but this gene was instead substantially downregulated, starting at the 9 dpi sampling point, as were AtCHS and AtFLS1. In addition, both the AtMYB12- and AtFLS1-deficient lines were more susceptible to infection by this parasite. There was again little evidence for contributions from the other AtFLS gene family members, although an AtFLS5-deficient line appeared to be somewhat more susceptible to infection. Taken together, this study shows that sugar-beet cyst and root-knot nematodes modulate differently the genes involved in flavonol biosynthesis in order to successfully infect host roots and that AtFLS1 may be involved in the plant basal defense response against nematode infection.

The Evolution of Flavonoid Biosynthesis: A Bryophyte Perspective

The flavonoid pathway is one of the best characterized specialized metabolite pathways of plants. In angiosperms, the flavonoids have varied roles in assisting with tolerance to abiotic stress and are also key for signaling to pollinators and seed dispersal agents. The pathway is thought to be specific to land plants and to have arisen during the period of land colonization around 550-470 million years ago. In this review we consider current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornworts, and mosses. The pathway is less characterized for bryophytes than angiosperms, and the first genetic and molecular studies on bryophytes are finding both commonalities and significant differences in flavonoid biosynthesis and pathway regulation between angiosperms and bryophytes. This includes biosynthetic pathway branches specific to each plant group and the apparent complete absence of flavonoids from the hornworts.

Increased Flavonol Levels in Tobacco Expressing AcFLS Affect Flower Color and Root Growth

The onion (Allium cepa L.) flavonol synthase (AcFLS-HRB) gene, encoding an enzyme responsible for flavonol biosynthesis in yellow onion, was recently identified and enzymatically characterized. Here, we performed an in vivo feeding assay involving bacterial expression of AcFLS-HRB and observed that it exhibited both flavanone 3-hydroxylase (F3H) and FLS activity. Transgenic tobacco (Nicotiana tabacum) expressing AcFLS-HRB produced lighter-pink flowers compared to wild-type plants. In transgenic petals, AcFLS-HRB was highly expressed at the mRNA and protein levels, and most AcFLS-HRB protein accumulated in the insoluble microsomal fractions. High-performance liquid chromatography (HPLC) analysis showed that flavonol levels increased but anthocyanin levels decreased in transgenic petals, indicating that AcFLS-HRB is a functional gene in planta. Gene expression analysis showed the reduced transcript levels of general phenylpropanoid biosynthetic genes and flavonoid biosynthetic genes in AcFLS-HRB overexpressed tobacco petals. Additionally, transgenic tobacco plants at the seedling stages showed increased primary root and root hair length and enhanced quercetin signals in roots. Exogenous supplementation with quercetin 3-O-rutinoside (rutin) led to the same phenotypic changes in root growth, suggesting that rutin is the causal compound that promotes root growth in tobacco. Therefore, augmenting flavonol levels affects both flower color and root growth in tobacco.