A negative MYB regulator of proanthocyanidin accumulation, identified through expression quantitative locus mapping in the grape berry

A chromosome-scale genome of Rhus chinensis Mill. provides new insights into plant-insect interaction and gallotannins biosynthesis

Rhus chinensis Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid Schlechtendalia chinensis, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal-level genome assembly of R. chinensis, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of R. chinensis to S. chinensis by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase-like (SCPL) and their homologs involved in HT production were determined as specific to HT-rich species. The functional differentiation of DQD/SDH tandem duplicate genes and the significant contraction in the phenylalanine ammonia-lyase (PAL) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (UGT84A), three carboxylesterase (CXE), and six SCPL genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co-expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant-galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites.

The Transcription Factor MiMYB8 Suppresses Peel Coloration in Postharvest 'Guifei' Mango in Response to High Concentration of Exogenous Ethylene by Negatively Modulating MiPAL1

Anthocyanin accumulation is regulated by specific genes during fruit ripening. Currently, peel coloration of mango fruit in response to exogenous ethylene and the underlying molecular mechanism remain largely unknown. The role of MiMYB8 on suppressing peel coloration in postharvest 'Guifei' mango was investigated by physiology detection, RNA-seq, qRT-PCR, bioinformatics analysis, yeast one-hybrid, dual-luciferase reporter assay, and transient overexpression. Results showed that compared with the control, low concentration of exogenous ethylene (ETH, 500 mg·L-1) significantly promoted peel coloration of mango fruit (cv. Guifei). However, a higher concentration of ETH (1000 mg·L-1) suppressed color transformation, which is associated with higher chlorophyll content, lower a* value, anthocyanin content, and phenylalanine ammonia-lyase (PAL) activity of mango fruit. M. indica myeloblastosis8 MiMYB8 and MiPAL1 were differentially expressed during storage. MiMYB8 was highly similar to those found in other plant species related to anthocyanin biosynthesis and was located in the nucleus. MiMYB8 suppressed the transcription of MiPAL1 by binding directly to its promoter. Transient overexpression of MiMYB8 in tobacco leaves and mango fruit inhibited anthocyanin accumulation by decreasing PAL activity and down-regulating the gene expression. Our observations suggest that MiMYB8 may act as repressor of anthocyanin synthesis by negatively modulating the MiPAL gene during ripening of mango fruit, which provides us with a theoretical basis for the scientific use of exogenous ethylene in practice.

New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS

Lysine is an essential amino acid that cannot be synthesized in humans. Rice is a global staple food for humans but has a rather low lysine content. Identification of the quantitative trait nucleotides (QTNs) and genes underlying lysine content is crucial to increase lysine accumulation. In this study, five grain and three leaf lysine content datasets and 4,630,367 single nucleotide polymorphisms (SNPs) of 387 rice accessions were used to perform a genome-wide association study (GWAS) by ten statistical models. A total of 248 and 71 common QTNs associated with grain/leaf lysine content were identified. The accuracy of genomic selection/prediction RR-BLUP models was up to 0.85, and the significant correlation between the number of favorable alleles per accession and lysine content was up to 0.71, which validated the reliability and additive effects of these QTNs. Several key genes were uncovered for fine-tuning lysine accumulation. Additionally, 20 and 30 QTN-by-environment interactions (QEIs) were detected in grains/leaves. The QEI-sf0111954416 candidate gene LOC_Os01g21380 putatively accounted for gene-by-environment interaction was identified in grains. These findings suggested the application of multi-model GWAS facilitates a better understanding of lysine accumulation in rice. The identified QTNs and genes hold the potential for lysine-rich rice with a normal phenotype.

Metabolite and transcriptome analyses reveal the effects of salinity stress on the biosynthesis of proanthocyanidins and anthocyanins in grape suspension cells

Proanthocyanidins (PAs) and anthocyanins are flavonoids that contribute to the quality and health benefits of grapes and wine. Salinity affects their biosynthesis, but the underlying mechanism is still unclear. We studied the effects of NaCl stress on PA and anthocyanin biosynthesis in grape suspension cells derived from berry skins of Vitis vinifera L. Cabernet Sauvignon using metabolite profiling and transcriptome analysis. We treated the cells with low (75 mM NaCl) and high (150 mM NaCl) salinity for 4 and 7 days. High salinity inhibited cell growth and enhanced PA and anthocyanin accumulation more than low salinity. The salinity-induced PAs and anthocyanins lacked C5'-hydroxylation modification, suggesting the biological significance of delphinidin- and epigallocatechin-derivatives in coping with stress. The genes up-regulated by salinity stress indicated that the anthocyanin pathway was more sensitive to salt concentration than the PA pathway, and WGCNA analysis revealed the coordination between flavonoid biosynthesis and cell wall metabolism under salinity stress. We identified transcription factors potentially involved in regulating NaCl dose- and time-dependent PA and anthocyanin accumulation, showing the dynamic remodeling of flavonoid regulation network under different salinity levels and durations. Our study provides new insights into regulator candidates for tailoring flavonoid composition and molecular indicators of salt stress in grape cells.

Integrated Transcriptomic and Proteomic Analysis Identifies Novel Regulatory Genes Associated with Plant Growth Regulator-Induced Astringency in Grape Berries

Astringency influences the sensory characteristics and flavor quality of table grapes. We tested the astringency sensory attributes of berries and investigated the concentration of flavan-3-ols/proanthocyanidins (PAs) in skins after the application of the plant growth regulators CPPU and GA3 to the flowers and young berries of the "Summer Black" grape. Our results showed that CPPU and GA3 applications increase sensory astringency perception scores and flavan-3-ol/proanthocyanidin concentrations. Using integrated transcriptomic and proteomic analysis, differentially expressed transcripts and proteins associated with growth regulator treatment were identified, including those for flavonoid biosynthesis that contribute to the changes in sensory astringency levels. Transient overexpression of candidate astringency-related regulatory genes in grape leaves revealed that VvWRKY71, in combination with VvMYBPA1 and VvMYC1, could promote the biosynthesis of proanthocyanidins, while overexpression of VvNAC83 reduced the accumulation of proanthocyanidins. However, in transient promoter studies in Nicotiana benthamiana, VvWRKY71 repressed the promoter of VvMYBPA2, while VvNAC83 had no significant effect on the promoter activity of four PA-related genes, and VvMYBPA1 was shown to activate its own promoter. This study provides new insights into the molecular mechanisms of sensory astringency formation induced by plant growth regulators in grape berries.

Non-Mature miRNA-Encoded Micropeptide miPEP166c Stimulates Anthocyanin and Proanthocyanidin Synthesis in Grape Berry Cells

The phenylpropanoid and flavonoid pathways exhibit intricate regulation, not only influenced by environmental factors and a complex network of transcription factors but also by post-transcriptional regulation, such as silencing by microRNAs and miRNA-encoded micropeptides (miPEPs). VviMYBC2-L1 serves as a transcriptional repressor for flavonoids, playing a crucial role in coordinating the synthesis of anthocyanin and proanthocyanidin. It works in tandem with their respective transcriptional activators, VviMYBA1/2 and VviMYBPA1, to maintain an equilibrium of flavonoids. We have discovered a miPEP encoded by miR166c that appears to target VviMYBC2-L1. We conducted experiments to test the hypothesis that silencing this transcriptional repressor through miPEP166c would stimulate the synthesis of anthocyanins and proanthocyanidins. Our transcriptional analyses by qPCR revealed that the application of exogenous miPEP166c to Gamay Fréaux grape berry cells resulted in a significant upregulation in flavonoid transcriptional activators (VviMYBA1/2 and VviMYBPA1) and structural flavonoid genes (VviLDOX and VviDFR), as well as genes involved in the synthesis of proanthocyanidins (VviLAR1 and VviANR) and anthocyanins (VviUFGT1). These findings were supported by the increased enzyme activities of the key enzymes UFGT, LAR, and ANR, which were 2-fold, 14-fold, and 3-fold higher, respectively, in the miPEP166c-treated cells. Ultimately, these changes led to an elevated total content of anthocyanins and proanthocyanidins.

Designing plant flavonoids: harnessing transcriptional regulation and enzyme variation to enhance yield and diversity

Plant synthetic biology has emerged as a powerful and promising approach to enhance the production of value-added metabolites in plants. Flavonoids, a class of plant secondary metabolites, offer numerous health benefits and have attracted attention for their potential use in plant-based products. However, achieving high yields of specific flavonoids remains challenging due to the complex and diverse metabolic pathways involved in their biosynthesis. In recent years, synthetic biology approaches leveraging transcription factors and enzyme diversity have demonstrated promise in enhancing flavonoid yields and expanding their production repertoire. This review delves into the latest research progress in flavonoid metabolic engineering, encompassing the identification and manipulation of transcription factors and enzymes involved in flavonoid biosynthesis, as well as the deployment of synthetic biology tools for designing metabolic pathways. This review underscores the importance of employing carefully-selected transcription factors to boost plant flavonoid production and harnessing enzyme promiscuity to broaden flavonoid diversity or streamline the biosynthetic steps required for effective metabolic engineering. By harnessing the power of synthetic biology and a deeper understanding of flavonoid biosynthesis, future researchers can potentially transform the landscape of plant-based product development across the food and beverage, pharmaceutical, and cosmetic industries, ultimately benefiting consumers worldwide.

The complexities of proanthocyanidin biosynthesis and its regulation in plants

Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.

Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs

Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.

QTL mapping and identification of candidate genes linked to red rot resistance in sugarcane

Sugarcane (Saccharum species hybrid) is one of the most important commercial crops cultivated worldwide for products like white sugar, bagasse, ethanol, etc. Red rot is a major sugarcane disease caused by a hemi-biotrophic fungus, Colletotrichum falcatum Went., which can potentially cause a reduction in yield up to 100%. Breeding for red rot-resistant sugarcane varieties has become cumbersome due to its complex genome and frequent generation of new pathotypes of red rot fungus. In the present study, a genetic linkage map was developed using a selfed population of a popular sugarcane variety CoS 96268. A QTL linked to red rot resistance (qREDROT) was identified, which explained 26% of the total phenotypic variation for the trait. A genotype-phenotype network analysis performed to account for epistatic interactions, identified the key markers involved in red rot resistance. The differential expression of the genes located in the genomic region between the two flanking markers of the qREDROT as well as in the vicinity of the markers identified through the genotype-phenotype network analysis in a set of contrasting genotypes for red rot infection further confirmed the mapping results. Further, the expression analysis revealed that the plant defense-related gene coding 26S protease regulatory subunit is strongly associated with the red rot resistance. The findings can help in the screening of disease resistant genotypes for developing red rot-resistant varieties of sugarcane.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03481-7.

Interplay between R2R3 MYB-type activators and repressors regulates proanthocyanidin biosynthesis in banana (Musa acuminata)

Proanthocyanidins are oligomeric flavonoids that promote plant disease resistance and benefit human health. Banana is one of the world's most extensively farmed crops and its fruit pulp contain proanthocyanidins. However, the transcriptional regulatory network that fine tunes proanthocyanidin biosynthesis in banana remains poorly understood. We characterised two proanthocyanidin-specific R2R3 MYB activators (MaMYBPA1-MaMYBPA2) and four repressors (MaMYBPR1-MaMYBPR4) to elucidate the mechanisms underlying the transcriptional regulation of proanthocyanidin biosynthesis in banana. Heterologous expression of MaMYBPA1 and MaMYBPA2 partially complemented the Arabidopsis thaliana proanthocyanidin-deficient transparent testa2 mutant. MaMYBPA1 and MaMYBPA2 interacted physically with MaMYCs to transactivate anthocyanin synthase, leucoanthocyanidin reductase, and anthocyanidin reductase genes in vitro and form functional MYB-bHLH-WD Repeat (MBW) complexes with MaTTG1 to transactivate these promoters in vivo. Overexpression of MaMYBPAs alone or with MaMYC in banana fruits induced proanthocyanidin accumulation and transcription of proanthocyanidin biosynthesis-related genes. MaMYBPR repressors are also shown to interact with MaMYCs forming repressing MBW complexes, and diminished proanthocyanidin accumulation. Interestingly overexpression of MaMYBPA induces the expression of MaMYBPR, indicating an agile regulation of proanthocyanidin biosynthesis through the formation of competitive MBW complexes. Our results reveal regulatory modules of R2R3 MYB- that fine tune proanthocyanidin biosynthesis and offer possible targets for genetic manipulation for nutritional improvement of banana.

An R2R3-MYB transcription factor VyMYB24, isolated from wild grape Vitis yanshanesis J. X. Chen., regulates the plant development and confers the tolerance to drought

In grapevines, the MYB transcription factors play an important regulatory role in the phenylpropanoid pathway including proanthocyanidin, anthocyanin, and flavonoid biosynthesis. However, the role of MYB in abiotic stresses is not clear. In this study, an R2R3-MYB transcription factor, VyMYB24, was isolated from a high drought-tolerant Chinese wild Vitis species V. yanshanesis. Our findings demonstrated that it was involved in plant development and drought tolerance. VyMYB24 is a nuclear protein and is significantly induced by drought stress. When over-expressed in tobacco, VyMYB24 caused plant dwarfing including plant height, leaf area, flower size, and seed weight. The GA1+3 content in transgenic plants was reduced significantly, and spraying exogenous gibberellin could recover the dwarf phenotype of VyMYB24 transgenic plants, suggesting that VyMYB24 might inhibit plant development by the regulation of gibberellin (GA) metabolism. Under drought stress, the VyMYB24 transgenic plants improved their tolerance to drought with a lower wilting rate, lower relative electrical conductivity, and stronger roots. Compared to wild-type tobacco plants, VyMYB24 transgenic plants accumulated less reactive oxygen, accompanied by increased antioxidant enzyme activity and upregulated gene expression levels of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) genes. In addition, transgenic plants accumulated more proline, and their related synthetic genes NtP5CR and NtP5CS genes were significantly upregulated when exposed to drought. Besides, abiotic stress-responsive genes, NtDREB, NtERD10C, NtERD10D, and NtLEA5, were upregulated significantly in VyMYB24 transgenic plants. These results indicate that VyMYB24 plays a positive regulatory role in response to drought stress and also regulates plant development, which provides new evidence to further explore the molecular mechanism of drought stress of the MYB gene family.

MYB transcription factors and their role in Medicinal plants

Transcription factors are multi-domain proteins that regulate gene expression in eukaryotic organisms. They are one of the largest families of proteins, which are structurally and functionally diverse. While there are transcription factors that are plant-specific, such as AP2/ERF, B3, NAC, SBP and WRKY, some transcription factors are present in both plants as well as other eukaryotic organisms. MYB transcription factors are widely distributed among all eukaryotes. In plants, the MYB transcription factors are involved in the regulation of numerous functions such as gene regulation in different metabolic pathways especially secondary metabolic pathways, regulation of different signalling pathways of plant hormones, regulation of genes involved in various developmental and morphological processes etc. Out of the thousands of MYB TFs that have been studied in plants, the majority of them have been studied in the model plants like Arabidopsis thaliana, Oryza sativa etc. The study of MYBs in other plants, especially medicinal plants, has been comparatively limited. But the increasing demand for medicinal plants for the production of biopharmaceuticals and important bioactive compounds has also increased the need to explore more number of these multifaceted transcription factors which play a significant role in the regulation of secondary metabolic pathways. These studies will ultimately contribute to medicinal plants' research and increased production of secondary metabolites, either through transgenic plants or through synthetic biology approaches. This review compiles studies on MYB transcription factors that are involved in the regulation of diverse functions in medicinal plants.

Signal transduction in non-climacteric fruit ripening

Fleshy fruit ripening involves changes in numerous cellular processes and metabolic pathways, resulting from the coordinated actions of diverse classes of structural and regulatory proteins. These include enzymes, transporters and complex signal transduction systems. Many aspects of the signaling machinery that orchestrates the ripening of climacteric fruits, such as tomato (Solanum lycopersicum), have been elucidated, but less is known about analogous processes in non-climacteric fruits. The latter include strawberry (Fragaria x ananassa) and grape (Vitis vinifera), both of which are used as non-climacteric fruit experimental model systems, although they originate from different organs: the grape berry is a true fruit derived from the ovary, while strawberry is an accessory fruit that is derived from the floral receptacle. In this article, we summarize insights into the signal transduction events involved in strawberry and grape berry ripening. We highlight the mechanisms underlying non-climacteric fruit ripening, the multiple primary signals and their integrated action, individual signaling components, pathways and their crosstalk, as well as the associated transcription factors and their signaling output.

Transcription factor VvibHLH93 negatively regulates proanthocyanidin biosynthesis in grapevine

Proanthocyanidins (PAs) derived from grape berries determine the astringency and bitterness of red wines. The two leucoanthocyanidin reductases (VviLAR1 and VviLAR2) are crucial for PA accumulation in grapevine. Our previous studies show that the promoter of VviLAR1 contains multiple proposed bHLH transcription factor binding sites, but the corresponding bHLH family regulators remain unknown. Here we identified and functionally characterized VvibHLH93 as a new bHLH transcription factor in PA pathway. Yeast one-hybrid and electrophoretic mobility shift assays showed that VvibHLH93 bound the E/G-box in VviLAR1 promoter. And VvibHLH93 gene was mainly expressed in grape flowers, tendrils, stems and berries at PA active stages. Overexpression of VvibHLH93 suppressed PA accumulation in grape callus, which was linked to the repression of the transcript levels of two VviLARs. The gene expression analysis in transgenic grape callus and the dual-luciferase assay in tobacco leaves together revealed that VvibHLH93 targeted a broad set of structural genes and transcription factors in flavonoid pathway. This research enriches the regulatory mechanism of the two VviLAR genes, and provides new insights into regulating PA content in grape berries.

Hairy Root Cultures as a Source of Polyphenolic Antioxidants: Flavonoids, Stilbenoids and Hydrolyzable Tannins

Due to their chemical properties and biological activity, antioxidants of plant origin have gained interest as valuable components of the human diet, potential food preservatives and additives, ingredients of cosmetics and factors implicated in tolerance mechanisms against environmental stress. Plant polyphenols are the most prominent and extensively studied, albeit not only group of, secondary plant (specialized) metabolites manifesting antioxidative activity. Because of their potential economic importance, the productive and renewable sources of the compounds are desirable. Over thirty years of research on hairy root cultures, as both producers of secondary plant metabolites and experimental systems to investigate plant biosynthetic pathways, brought about several spectacular achievements. The present review focuses on the Rhizobium rhizogenes-transformed roots that either may be efficient sources of plant-derived antioxidants or were used to elucidate some regulatory mechanisms responsible for the enhanced accumulation of antioxidants in plant tissues.

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.)

Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.

Regulation of Plant Tannin Synthesis in Crop Species

Plant tannins belong to the antioxidant compound family, which includes chemicals responsible for protecting biological structures from the harmful effects of oxidative stress. A wide range of plants and crops are rich in antioxidant compounds, offering resistance to biotic, mainly against pathogens and herbivores, and abiotic stresses, such as light and wound stresses. These compounds are also related to human health benefits, offering protective effects against cardiovascular and neurodegenerative diseases in addition to providing anti-tumor, anti-inflammatory, and anti-bacterial characteristics. Most of these compounds are structurally and biosynthetically related, being synthesized through the shikimate-phenylpropanoid pathways, offering several classes of plant antioxidants: flavonoids, anthocyanins, and tannins. Tannins are divided into two major classes: condensed tannins or proanthocyanidins and hydrolysable tannins. Hydrolysable tannin synthesis branches directly from the shikimate pathway, while condensed tannins are derived from the flavonoid pathway, one of the branches of the phenylpropanoid pathway. Both types of tannins have been proposed as important molecules for taste perception of many fruits and beverages, especially wine, besides their well-known roles in plant defense and human health. Regulation at the gene level, biosynthesis and degradation have been extensively studied in condensed tannins in crops like grapevine (Vitis vinifera), persimmon (Diospyros kaki) and several berry species due to their high tannin content and their importance in the food and beverage industry. On the other hand, much less information is available regarding hydrolysable tannins, although some key aspects of their biosynthesis and regulation have been recently discovered. Here, we review recent findings about tannin metabolism, information that could be of high importance for crop breeding programs to obtain varieties with enhanced nutritional characteristics.

VvANR silencing promotes expression of VvANS and accumulation of anthocyanin in grape berries

Virus-induced gene silencing (VIGS) technology was applied to silence VvANR in cv. Zaoheibao grape berries, and the effects of VvANR silencing on berries phenotype; gene expression level of ANS, LAR1, LAR2, and UFGT; enzyme activity of ANS; and accumulations of anthocyanin and flavan-3-ol were investigated. At the third day after treatment, the VvANR silenced grape berries began to turn red slightly, which was 2 days earlier than that of the control group. And the flavan-3-ol content in VvANR-silenced grape berries had been remarkable within 1 to 5 days, the ANR enzyme activity in VvANR-silenced grapes extremely significantly decreased in 3 days, and LAR enzyme activity also decreased, but the difference was not striking. The ANS enzyme activity of the transformed berries was significantly higher than that of the control after 3 days of infection, and it was exceedingly significantly higher than that of the control after 5 to 10 days. The content of anthocyanin in transformed berries increased of a very marked difference within 3 to 15 days. pTRV2-ANR infection resulted in an extremely significant decrease in the expression of VvANR gene, and the expression of VvLAR1, VvLAR2, VvMYBPA1, VvMYBPA2, and VvDFR were also down-regulated. However, the expression of VvANS and VvUFGT was up-regulated significantly. After VvANR silencing via VIGS, VvANR expression in grape berries was extremely significantly decreased, resulting in decreased ANR enzyme activity and flavan-3-ol content; berries turned red and deeper in advance. In addition, VvANR silencing can induce up-regulation of VvANS and VvUFGT expression, significantly increase ANS enzyme activity, and increase of anthocyanin accumulation.

Molecular basis of the formation and removal of fruit astringency

Astringency is a dry puckering mouthfeel mainly generated by the binding of tannins with proteins in the mouth. Tannins confer benefits such as resistance to biotic stresses and have antioxidant activity, and moderate concentrations of tannins can improve the flavor of fruits or their products. However, fruits with high contents of tannins have excessive astringency, which is undesirable. Thus, the balance of astringency formation and removal is extremely important for human consumption of fruit and fruit-based products. In recent years, the understanding of fruit astringency has moved beyond the biochemical aspects to focus on the genetic characterization of key structural genes and their transcriptional regulators that cause astringency. This article provides an overview of astringency formation and evaluation. We summarize the methods of astringency regulation and strategies and mechanisms for astringency removal, and discuss perspectives for future exploration and modulation of astringency for fruit quality improvement.

A Myb transcription factor, PgMyb308-like, enhances the level of shikimate, aromatic amino acids, and lignins, but represses the synthesis of flavonoids and hydrolyzable tannins, in pomegranate (Punica granatum L.)

Pomegranate fruit peels are highly abundant in metabolites derived from the shikimate pathway, such as hydrolyzable tannins (HTs) and flavonoids. These metabolites are beneficial to human health (commercial juice is enriched with peel metabolites), and also protect the fruit from environmental stresses. To understand the transcriptional control of shikimate pathway-related metabolites in pomegranate, we cloned and characterized a subgroup S4 R2R3 Myb transcription factor, PgMyb308-like. Overexpressing PgMyb308-like in pomegranate hairy roots increased the accumulation of shikimate, aromatic amino acids, isoferulic acid, and total lignins, but led to reduced gallic acid and its downstream products HTs, as well as multiple flavonoids. Changes in these metabolites are supported by the increased expression of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase and shikimate dehydrogenase 1 (PgSDH1) (the SDH isoform associated with shikimate biosynthesis), and the reduced expression of PgSDH4 (the SDH isoform suggested to produce gallic acid). Transcriptome analysis of PgMyb308-like-overexpressing hairy roots further revealed reprogramming of cell wall-related genes, while overexpression of PgMyb308-like in Arabidopsis thaliana plants uncovered its distinct role in a different genetic and metabolic background. These results together suggest that PgMyb308-like activates genes in the shikimate pathway and lignin biosynthesis, but suppresses those involved in the production of HTs and flavonoids.

Overexpression of VqWRKY31 enhances powdery mildew resistance in grapevine by promoting salicylic acid signaling and specific metabolite synthesis

Powdery mildew (PM), caused by the fungal pathogen Erysiphe necator, is one of the most destructive diseases of grapevine (Vitis vinifera and other Vitis spp). Resistance to PM is an important goal for cultivar improvement, and understanding the underlying molecular mechanisms conditioning resistance is critical. Here, we report that transgenic expression of the WRKY transcription factor gene VqWRKY31 from the PM-resistant species Vitis quinquangularis conferred resistance to powdery mildew in V. vinifera through promoting salicylic acid signaling and specific metabolite synthesis. VqWRKY31 belongs to the WRKY IIb subfamily, and expression of the VqWRKY31 gene was induced in response to E. necator inoculation. Transgenic V. vinifera plants expressing VqWRKY31 were substantially less susceptible to E. necator infection, and this was associated with increased levels of salicylic acid and reactive oxygen species. Correlation analysis of transcriptomic and metabolomic data revealed that VqWRKY31 promoted expression of genes in metabolic pathways and the accumulation of many disease resistance-related metabolites, including stilbenes, flavonoids, and proanthocyanidins. In addition, results indicated that VqWRKY31 can directly bind to the promoters of two structural genes in stilbene synthesis, STS9 and STS48, and activate their expression. Based on our results, we propose a model where VqWRKY31 enhances grapevine PM resistance through activation of salicylic acid defense signaling and promotion of specific disease resistance-related metabolite synthesis. These findings can be directly exploited for molecular breeding strategies to produce PM-resistant grapevine germplasm.

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

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

MYBA and MYBPA transcription factors co-regulate anthocyanin biosynthesis in blue-coloured berries

The regulatory network of R2R3 MYB transcription factors in anthocyanin biosynthesis is not fully understood in blue-coloured berries containing delphinidin compounds. We used blue berries of bilberry (Vaccinium myrtillus) to comprehensively characterise flavonoid-regulating R2R3 MYBs, which revealed a new type of co-regulation in anthocyanin biosynthesis between members of MYBA-, MYBPA1- and MYBPA2-subgroups. VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 expression was elevated at berry ripening and by abscisic acid treatment. Additionally, VmMYBA1 and VmMYBPA1.1 expression was strongly downregulated in a white berry mutant. Complementation and transient overexpression assays confirmed VmMYBA1 and VmMYBA2 to induce anthocyanin accumulation. Promoter activation assays showed that VmMYBA1, VmMYBPA1.1 and VmMYBPA2.2 had similar activity towards dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS), but differential regulation activity for UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT) and flavonoid 3'5'-hydroxylase (F3'5'H) promoters. Silencing of VmMYBPA1.1 in berries led to the downregulation of key anthocyanin and delphinidin biosynthesis genes. Functional analyses of other MYBPA regulators, and a member of novel MYBPA3 subgroup, associated them with proanthocyanidin biosynthesis and F3'5'H expression. The existence of 18 flavonoid-regulating MYBs indicated gene duplication, which may have enabled functional diversification among MYBA, MYBPA1 and MYBPA2 subgroups. Our results provide new insights into the intricate regulation of the complex anthocyanin profile found in blue-coloured berries involving regulation of both cyanidin and delphinidin branches.

Light Induced Regulation Pathway of Anthocyanin Biosynthesis in Plants

Anthocyanins are natural pigments with antioxidant effects that exist in various fruits and vegetables. The accumulation of anthocyanins is induced by environmental signals and regulated by transcription factors in plants. Numerous evidence has indicated that among the environmental factors, light is one of the most signal regulatory factors involved in the anthocyanin biosynthesis pathway. However, the signal transduction of light and molecular regulation of anthocyanin synthesis remains to be explored. Here, we focus on the research progress of signal transduction factors for positive and negative regulation in light-dependent and light-independent anthocyanin biosynthesis. In particular, we will discuss light-induced regulatory pathways and related specific regulators of anthocyanin biosynthesis in plants. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by transcription factors is discussed based on the significant progress.

Recent Advanced Metabolic and Genetic Engineering of Phenylpropanoid Biosynthetic Pathways

The MYB transcription factors (TFs) are evolving as critical role in the regulation of the phenylpropanoid and tanshinones biosynthetic pathway. MYB TFs relate to a very important gene family, which are involved in the regulation of primary and secondary metabolisms, terpenoids, bioactive compounds, plant defense against various stresses and cell morphology. R2R3 MYB TFs contained a conserved N-terminal domain, but the domain at C-terminal sorts them different regarding their structures and functions. MYB TFs suppressors generally possess particular repressive motifs, such as pdLNLD/ELxiG/S and TLLLFR, which contribute to their suppression role through a diversity of complex regulatory mechanisms. A novel flower specific "NF/YWSV/MEDF/LW" conserved motif has a great potential to understand the mechanisms of flower development. In the current review, we summarize recent advanced progress of MYB TFs on transcription regulation, posttranscriptional, microRNA, conserved motif and propose directions to future prospective research. We further suggest there should be more focus on the investigation for the role of MYB TFs in microalgae, which has great potential for heterologous protein expression system for future perspectives.

Dissecting the transcriptional regulation of proanthocyanidin and anthocyanin biosynthesis in soybean (Glycine max)

Proanthocyanidins (PAs), also known as condensed tannins, are plant natural products that are beneficial for human and livestock health. As one of the largest grown crops in the world, soybean (Glycine max) is widely used as human food and animal feed. Many cultivated soybeans with yellow seed coats lack PAs or anthocyanins, although some soybean cultivars have coloured seed coats that contain these compounds. Here, we analyse the transcriptional control of PA and anthocyanin biosynthesis in soybean. Ectopic expression of the transcription factors (TFs) GmTT2A, GmTT2B, GmMYB5A or R in soybean hairy roots induced the accumulation of PAs (primarily in phloem tissues) or anthocyanins and led to up-regulation of 1775, 856, 1411 and 1766 genes, respectively, several of which encode enzymes involved in PA biosynthesis. The genes regulated by GmTT2A and GmTT2B partially overlapped, suggesting conserved but potentially divergent roles for these two TFs in regulating PA accumulation in soybean. The two key enzymes anthocyanidin reductase and leucoanthocyanidin reductase were differentially upregulated, by GmTT2A/GmTT2B and GmMYB5A, respectively. Transgenic soybean plants overexpressing GmTT2B or MtLAP1 (a proven up-regulator of the upstream reactions for production of precursors for PA biosynthesis in legumes) showed increased accumulation of PAs and anthocyanins, respectively, associated with transcriptional reprogramming paralleling the RNA-seq data collected in soybean hairy roots. Collectively, our results show that engineered PA biosynthesis in soybean exhibits qualitative and spatial differences from the better-studied model systems Arabidopsis thaliana and Medicago truncatula, and suggest targets for engineering PAs in soybean plants.

DkMYB14 is a bifunctional transcription factor that regulates the accumulation of proanthocyanidin in persimmon fruit

Proanthocyanidins (PAs) are phenolic secondary metabolites that contribute to the protection of plant and human health. Persimmon (Diospyros kaki Thunb.) can accumulate abundant PAs in fruit, which cause a strong sensation of astringency. Proanthocyanidins can be classified into soluble and insoluble PAs; the former cause astringency but the latter do not. Soluble PAs can be converted into insoluble PAs upon interacting with acetaldehydes. We demonstrate here that DkMYB14, which regulates the accumulation of PA in persimmon fruit flesh, is a bifunctional transcription factor that acts as a repressor in PA biosynthesis but becomes an activator when involved in acetaldehyde biosynthesis. Interestingly, both functions contribute to the elimination of astringency by decreasing PA biosynthesis and promoting its insolubilization. We show that the amino acid Gly39 in the R2 domain and the ethylene response factor-associated amphiphilic repression-like motif in the C-terminal of DkMYB14 are essential for the regulation of both PA and acetaldehyde synthesis. The repressive function of DkMYB14 was lost after the mutation of either motif, and all activities of DkMYB14 were eliminated following the mutation of both motifs. Our results demonstrate that DkMYB14 functions as both a transcriptional activator and a repressor, directly repressing biosynthesis of PA and promoting its insolubilization, resulting in non-astringency in persimmon.

Comparative Metabolite and Gene Expression Analyses in Combination With Gene Characterization Revealed the Patterns of Flavonoid Accumulation During Cistus creticus subsp. creticus Fruit Development

Cistus creticus L. subsp. creticus (rockrose) is a shrub widespread in Greece and the Mediterranean basin and has been used in traditional medicine as herb tea for colds, for healing and digestive hitches, for the treatment of maladies, as perfumes, and for other purposes. Compounds from its flavonoid fraction have recently drawn attention due to antiviral action against influenza virus and HIV. Although several bioactive metabolites belonging to this group have been chemically characterized in the leaves, the genes involved in their biosynthesis in Cistus remain largely unknown. Flavonoid metabolism during C. creticus fruit development was studied by adopting comparative metabolomic and transcriptomic approaches. The present study highlights the fruit of C. creticus subsp. creticus as a rich source of flavonols, flavan-3-ols, and proanthocyanidins, all of which displayed a decreasing trend during fruit development. The majority of proanthocyanidins recorded in Cistus fruit are B-type procyanidins and prodelphinidins, while gallocatechin and catechin are the dominant flavan-3-ols. The expression patterns of biosynthetic genes and transcription factors were analyzed in flowers and throughout three fruit development stages. Flavonoid biosynthetic genes were developmentally regulated, showing a decrease in transcript levels during fruit maturation. A high degree of positive correlations between the content of targeted metabolites and the expression of biosynthetic genes indicated the transcriptional regulation of flavonoid biosynthesis during C. creticus fruit development. This is further supported by the high degree of significant positive correlations between the expression of biosynthetic genes and transcription factors. The results suggest that leucoanthocyanidin reductase predominates the biosynthetic pathway in the control of flavan-3-ol formation, which results in catechin and gallocatechin as two of the major building blocks for Cistus proanthocyanidins. Additionally, there is a decline in ethylene production rates during non-climacteric Cistus fruit maturation, which coincides with the downregulation of the majority of flavonoid- and ethylene-related biosynthetic genes and corresponding transcription factors as well as with the decline in flavonoid content. Finally, functional characterization of a Cistus flavonoid hydroxylase (F3'5'H) was performed for the first time.

Identification of gene co-expression networks and key genes regulating flavonoid accumulation in apple (Malus × domestica) fruit skin

Anthocyanin provides a red color for apple and health benefit for human. To better understand the molecular mechanisms of regulating apple color formation, we analyzed 27 transcriptomes of fruit skin from three cultivars 'Huashuo' (red-skinned), 'Hongcuibao' (red-skinned), and 'Golden Delicious' (yellow-skinned) at 0, 2, and 6 days after bag removal. Using pairwise comparisons and weighted gene co-expression network analyses (WGCNA), we constructed 17 co-expression modules. Among them, a specific module was negatively correlated to anthocyanin accumulation. The genes in the module are enriched in flavonoid biosynthesis pathways. These pathway genes were used to construct gene co-expression network of anthocyanin accumulation. Finally, a R2R3-MYB repressor designated MdMYB28 was identified as a key hub gene in the anthocyanin metabolism network. During the anthocyanin accumulation of apple fruit skin reaching a peak, MdMYB28 expression level was negatively correlated with the anthocyanin content. MdMYB28 was shown to directly bind to the promoter of MdMYB10 in yeast one-hybrid analyses. Over-expression of MdMYB28 decreased the anthocyanin biosynthesis in tobacco flower petals, suggesting that MdMYB28 acts as a negatively regulator of anthocyanin biosynthesis.

Molecular Tools for Adapting Viticulture to Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

MrMYB6 From Chinese Bayberry (Myrica rubra) Negatively Regulates Anthocyanin and Proanthocyanidin Accumulation

Anthocyanins and proanthocyanidins (PAs) are important flavonoids in Chinese bayberry (Morella rubra), which functions in fruit color and exhibits multiple health promoting and disease-preventing effects. To investigate the regulation of their biosynthesis in Chinese bayberries, we isolated and identified a subgroup 4 MYB transcription factor (TF), MrMYB6, and found MrMYB6 shared similar repressor domains with other MYB co-repressors of anthocyanin and PA biosynthesis after sequence analysis. Gene expression results revealed the transcripts of MrMYB6 were negatively correlated with the anthocyanin and insoluble PA contents and also with the gene expressions involved in anthocyanin biosynthesis and PA specific genes such as MrLAR and MrANR during the late ripening stages of bayberries. In addition, overexpression of MrMYB6 in tobacco inhibited the transcript levels of NtCHI, NtLAR, and NtANR2, resulting into a decline in the levels of anthocyanins and PAs in tobacco flowers. We further found that MrMYB6 interacted with MrbHLH1 and MrWD40-1 to form functional complexes that acted to directly repress the promoter activities of the PA-specific gene MrLAR and MrANR and the anthocyanin-specific gene MrANS and MrUFGT. Taken together, our results suggested that MrMYB6 might negatively regulate anthocyanin and PA accumulation in Chinese bayberry.

Identification of Transcription Factor Genes and Functional Characterization of PlMYB1 From Pueraria lobata

Kudzu, Pueraria lobata, is a traditional Chinese food and medicinal herb that has been commonly used since ancient times. Kudzu roots are rich sources of isoflavonoids, e.g., puerarin, with beneficial effects on human health. To gain global information on the isoflavonoid biosynthetic regulation network in kudzu, de novo transcriptome sequencings were performed using two genotypes of kudzu with and without puerarin accumulation in roots. RNAseq data showed that the genes of the isoflavonoid biosynthetic pathway were significantly represented in the upregulated genes in the kudzu with puerarin. To discover regulatory genes, 105, 112, and 143 genes encoding MYB, bHLH, and WD40 transcription regulators were identified and classified, respectively. Among them, three MYB, four bHLHs, and one WD40 gene were found to be highly identical to their orthologs involved in flavonoid biosynthesis in other plants. Notably, the expression profiles of PlMYB1, PlHLH3-4, and PlWD40-1 genes were closely correlated with isoflavonoid accumulation profiles in different tissues and cell cultures of kudzu. Over-expression of PlMYB1 in Arabidopsis thaliana significantly increased the accumulation of anthocyanins in leaves and proanthocyanidins in seeds, by activating AtDFR, AtANR, and AtANS genes. Our study provided valuable comparative transcriptome information for further identification of regulatory or structural genes involved in the isoflavonoid pathway in P. lobata, as well as for bioengineering of bioactive isoflavonoid compounds.

Grape Berry Secondary Metabolites and Their Modulation by Abiotic Factors in a Climate Change Scenario-A Review

Temperature, water, solar radiation, and atmospheric CO₂ concentration are the main abiotic factors that are changing in the course of global warming. These abiotic factors govern the synthesis and degradation of primary (sugars, amino acids, organic acids, etc.) and secondary (phenolic and volatile flavor compounds and their precursors) metabolites directly, via the regulation of their biosynthetic pathways, or indirectly, via their effects on vine physiology and phenology. Several hundred secondary metabolites have been identified in the grape berry. Their biosynthesis and degradation have been characterized and have been shown to occur during different developmental stages of the berry. The understanding of how the different abiotic factors modulate secondary metabolism and thus berry quality is of crucial importance for breeders and growers to develop plant material and viticultural practices to maintain high-quality fruit and wine production in the context of global warming. Here, we review the main secondary metabolites of the grape berry, their biosynthesis, and how their accumulation and degradation is influenced by abiotic factors. The first part of the review provides an update on structure, biosynthesis, and degradation of phenolic compounds (flavonoids and non-flavonoids) and major aroma compounds (terpenes, thiols, methoxypyrazines, and C13 norisoprenoids). The second part gives an update on the influence of abiotic factors, such as water availability, temperature, radiation, and CO₂ concentration, on berry secondary metabolism. At the end of the paper, we raise some critical questions regarding intracluster berry heterogeneity and dilution effects and how the sampling strategy can impact the outcome of studies on the grapevine berry response to abiotic factors.

Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective

In plants, fruit ripening is a coordinated developmental process that requires the change in expression of hundreds to thousands of genes to modify many biochemical and physiological signal cascades such as carbohydrate and organic acid metabolism, cell wall restructuring, ethylene production, stress response, and organoleptic compound formation. In Prunus species (including peaches, apricots, plums, and cherries), fruit ripening leads to the breakdown of complex carbohydrates into sugars, fruit firmness reductions (softening by cell wall degradation and cuticle properties alteration), color changes (loss of green color by chlorophylls degradation and increase in non-photosynthetic pigments like anthocyanins and carotenoids), acidity decreases, and aroma increases (the production and release of organic volatile compounds). Actually, the level of information of molecular events at the transcriptional, biochemical, hormonal, and metabolite levels underlying ripening in Prunus fruits has increased considerably. However, we still poorly understand the molecular switch that occurs during the transition from unripe to ripe fruits. The objective of this review was to analyze of the molecular bases of fruit quality in Prunus species through an integrated metabolic, genomic, transcriptomic, and epigenetic approach to better understand the molecular switch involved in the ripening process with important consequences from a breeding point of view.

Advances in Biosynthesis and Biological Functions of Proanthocyanidins in Horticultural Plants

Proanthocyanidins are colorless flavonoid polymers condensed from flavan-3-ol units. They are essential secondary plant metabolites that contribute to the nutritional value and sensory quality of many fruits and the related processed products. Mounting evidence has shown that the accumulation of proanthocyanidins is associated with the resistance of plants against a broad spectrum of abiotic and biotic stress conditions. The biosynthesis of proanthocyanidins has been examined extensively, allowing for identifying and characterizing the key regulators controlling the biosynthetic pathway in many plants. New findings revealed that these specific regulators were involved in the proanthocyanidins biosynthetic network in response to various environmental conditions. This paper reviews the current knowledge regarding the control of key regulators in the underlying proanthocyanidins biosynthetic and molecular mechanisms in response to environmental stress. Furthermore, it discusses the directions for future research on the metabolic engineering of proanthocyanidins production to improve food and fruit crop quality.

In Silico Identification of MYB and bHLH Families Reveals Candidate Transcription Factors for Secondary Metabolic Pathways in Cannabis sativa L

Plant secondary metabolic pathways are finely regulated by the activity of transcription factors, among which members of the bHLH and MYB subfamilies play a main role. Cannabis sativa L. is a unique officinal plant species with over 600 synthesized phytochemicals having diverse scale-up industrial and pharmaceutical usage. Despite comprehensive knowledge of cannabinoids' metabolic pathways, very little is known about their regulation, while the literature on flavonoids' metabolic pathways is still scarce. In this study, we provide the first genome-wide analysis of bHLH and MYB families in C. sativa reference cultivar CBDRx and identification of candidate coding sequences for these transcription factors. Cannabis sativa bHLHs and MYBs were then classified into functional subfamilies through comparative phylogenetic analysis with A. thaliana transcription factors. Analyses of gene structure and motif distribution confirmed that CsbHLHs and CsMYBs belonging to the same evolutionary clade share common features at both gene and amino acidic level. Candidate regulatory genes for key metabolic pathways leading to flavonoid and cannabinoid synthesis in Cannabis were also retrieved. Furthermore, a candidate gene approach was used to identify structural enzyme-coding genes for flavonoid and cannabinoid synthesis. Taken as a whole, this work represents a valuable resource of candidate genes for further investigation of the C. sativa cannabinoid and flavonoid metabolic pathways for genomic studies and breeding programs.

The Effect of Light Intensity on the Expression of Leucoanthocyanidin Reductase in Grapevine Calluses and Analysis of Its Promoter Activity

To investigate the effect of light intensity on flavonoid biosynthesis, grapevine calluses were subjected to high light (HL, 250 μmol m⁻² s⁻¹) and dark (0 μmol m⁻² s⁻¹) in comparison to 125 μmol m⁻² s⁻¹ under controlled conditions (NL). The alteration of flavonoid profiles was determined and was integrated with RNA sequencing (RNA-seq)-based transcriptional changes of the flavonoid pathway genes. Results revealed that dark conditions inhibited flavonoid biosynthesis. Increasing light intensity affected flavonoids differently—the concentrations of flavonols and anthocyanins as well as the expressions of corresponding genes were less affected, whereas flavan-3-ol concentrations were predominantly increased, which caused enhanced trans-flavan-3-ol concentrations. Moreover, genes encoding leucoanthocyanidin reductase (LAR) exhibited different response patterns to light intensity changes—VviLAR1 expression increased with an increased light intensity, whereas VviLAR2 expression was insensitive. We further confirmed that the known transcription factors (TFs) involved in regulating flavan-3-ol biosynthesis utilized VviLAR1 as a target gene in grapevine calluses. In addition, VviLAR1 promoter activity was more sensitive to light intensity changes than that of VviLAR2 as determined using a transgenic Arabidopsis leaf system. These results suggested that light intensity had the most prominent effect on trans-flavan-3-ols in grapevine calluses and demonstrated that the two LAR genes had different response patterns to light intensity changes.

A genome-wide association study uncovers a critical role of the RsPAP2 gene in red-skinned Raphanus sativus L

Radish (Raphanus sativus L.) taproot contains high concentrations of flavonoids, including anthocyanins (ATCs), in red-skinned genotypes. However, little information on the genetic regulation of ATC biosynthesis in radish is available. A genome-wide association study of radish red skin color was conducted using whole-genome sequencing data derived from 179 radish genotypes. The R2R3-MYB transcription factor production of anthocyanin pigment 2 (PAP2) gene was found in the region associated with a leading SNP located on chromosome 2. The amino acid sequence encoded by the RsPAP2 gene was different from those of the other published RsMYB genes responsible for the red skin color of radish. The overexpression of the RsPAP2 gene resulted in ATC accumulation in Arabidopsis and radish, which was accompanied by the upregulation of several ATC-related structural genes. RsPAP2 was found to bind the RsUFGT and RsTT8 promoters, as shown by a dual-luciferase reporter system and a yeast one-hybrid assay. The promoter activities of the RsANS, RsCHI, RsPAL, and RsUFGT genes could be strongly activated by coinfiltration with RsPAP2 and RsTT8. These findings showed the effectiveness of GWAS in identifying candidate genes in radish and demonstrated that RsPAP2 could (either directly or together with its cofactor RsTT8) regulate the transcript levels of ATC-related genes to promote ATC biosynthesis, facilitating the genetic enhancement of ATC contents and other related traits in radish.

New perspectives on the biosynthesis, transportation, astringency perception and detection methods of grape proanthocyanidins

Proanthocyanidins (PAs) are important secondary metabolites crucial for the quality of grape berry and wine. Despite important advances in our understanding of the structural and regulatory genes involved in the PAs biosynthesis pathway, our knowledge about the details of biosynthetic and regulatory networks, especially the mechanism of polymerization and transportation remains limited. We provided an overview of the latest discoveries related to the mechanisms of grape PAs structure, astringency properties, detection methods, biosynthesis and transportation. We also summarized the environmental influencing factors of PAs synthesis in grape. Future trends were discussed.

Transcriptional Factors Regulate Plant Stress Responses through Mediating Secondary Metabolism

Plants are adapted to sense numerous stress stimuli and mount efficient defense responses by directing intricate signaling pathways. They respond to undesirable circumstances to produce stress-inducible phytochemicals that play indispensable roles in plant immunity. Extensive studies have been made to elucidate the underpinnings of defensive molecular mechanisms in various plant species. Transcriptional factors (TFs) are involved in plant defense regulations through acting as mediators by perceiving stress signals and directing downstream defense gene expression. The cross interactions of TFs and stress signaling crosstalk are decisive in determining accumulation of defense metabolites. Here, we collected the major TFs that are efficient in stress responses through regulating secondary metabolism for the direct cessation of stress factors. We focused on six major TF families including AP2/ERF, WRKY, bHLH, bZIP, MYB, and NAC. This review is the compilation of studies where researches were conducted to explore the roles of TFs in stress responses and the contribution of secondary metabolites in combating stress influences. Modulation of these TFs at transcriptional and post-transcriptional levels can facilitate molecular breeding and genetic improvement of crop plants regarding stress sensitivity and response through production of defensive compounds.

Abnormal expression of bHLH3 disrupts a flavonoid homeostasis network, causing differences in pigment composition among mulberry fruits

Mulberry fruits with high concentrations of anthocyanins are favored by consumers because of their good taste, bright color, and high nutritional value. However, neither the regulatory mechanism controlling flavonoid biosynthesis in mulberry nor the molecular basis of different mulberry fruit colors is fully understood. Here, we report that a flavonoid homeostasis network comprising activation and feedback regulation mechanisms determines mulberry fruit color. In vitro and in vivo assays showed that MYBA-bHLH3-TTG1 regulates the biosynthesis of anthocyanins, while TT2L1 and TT2L2 work with bHLH3 or GL3 and form a MYB-bHLH-WD40 (MBW) complex with TTG1 to regulate proanthocyanidin (PA) synthesis. Functional and expression analyses showed that bHLH3 is a key regulator of the regulatory network controlling mulberry fruit coloration and that MYB4 is activated by MBW complexes and participates in negative feedback control of the regulatory network to balance the accumulation of anthocyanins and proanthocyanidins. Our research demonstrates that the interaction between bHLH3 and MYB4 in the homeostasis regulatory network ensures that the fruits accumulate desirable flavonoids and that this network is stable in pigment-rich mulberry fruits. However, the abnormal expression of bHLH3 disrupts the balance of the network and redirects flavonoid metabolic flux in pale-colored fruits, resulting in differences in the levels and proportions of anthocyanins, flavones, and flavonols among differently colored mulberry fruits (red, yellow, and white). The results of our study reveal the molecular basis of the diversity of mulberry fruit colors.

Transcription Factor VviMYB86 Oppositely Regulates Proanthocyanidin and Anthocyanin Biosynthesis in Grape Berries

Proanthocyanidins (PAs) and anthocyanins are two vital groups of flavonoid compounds for grape berries and red wines. Several transcription factors (TFs) have been identified to be involved in regulating PA and anthocyanin biosynthesis in grape berries. However, research on TFs with different regulatory mechanisms for these two biosynthesis branches in grapes remains limited. In this study, we identified an R2R3-MYB TF, VviMYB86, whose spatiotemporal gene expression pattern in grape berries coincided well with PA accumulation but contrasted with anthocyanin synthesis. Both in vivo and in vitro experiments verified that VviMYB86 positively regulated PA biosynthesis, primarily by upregulating the expression of the two leucoanthocyanidin reductase (LAR) genes in the Arabidopsis protoplast system, as well as in VviMYB86-overexpressing grape callus cultured under 24 h of darkness. Moreover, VviMYB86 was observed to repress the anthocyanin biosynthesis branch in grapes by downregulating the transcript levels of VviANS and VviUFGT. Overall, VviMYB86 is indicated to have a broad effect on flavonoid synthesis in grape berries. The results of this study will help elucidate the regulatory mechanism governing the expression of the two LAR genes in grape berries and provide new insights into the regulation of PA and anthocyanin biosynthesis in grape berries.

GbMYBR1 from Ginkgo biloba represses phenylpropanoid biosynthesis and trichome development in Arabidopsis

Main Conclusion

GbMYBR1, a new type of R2R3-MYB repressor from Ginkgo biloba, displayed pleiotropic effects on plant growth, phenylpropanoid accumulation, by regulating multiple related genes at different levels.

Abstract

Ginkgo biloba is a typical gymnosperm that has been thriving on earth for millions of years. MYB transcription factors (TFs) play important roles in diverse processes in plants. However, the role of MYBs remains largely unknown in Ginkgo. Here, an MYB TF gene from Ginkgo, designated as GbMYBR1, was found to act as a repressor in multiple processes. GbMYBR1 was mainly expressed in the leaves of Ginkgo. Over-expression of GbMYBR1 in Arabidopsis thaliana led to growth retardation, decreases in lignin content, reduced trichome density, and remarkable reduction in anthocyanin and flavonol contents in leaves. Proanthocyanidin content was decreased in the seeds of transgenic Arabidopsis, which led to light-brown seed color. Both qPCR and transcriptome sequencing analyses demonstrated that the transcript levels of multiple genes related to phenylpropanoid biosynthesis, trichome formation, and pathogen resistance were down-regulated in the transgenic Arabidopsis. In particular, we found that GbMYBR1 directly interacts with the bHLH cofactor GL3 as revealed by yeast two-hybrid assays. Our work indicated that GbMYBR1 has pleiotropic effects on plant growth, phenylpropanoid accumulation, and trichome development, mediated by interaction with GL3 or direct suppression of key pathway genes. Thus, GbMYBR1 represents a novel type of R2R3 MYB repressor.

Electronic supplementary material

The online version of this article (10.1007/s00425-020-03476-1) contains supplementary material, which is available to authorized users.

Transcriptome Analysis Identifies Two Ethylene Response Factors That Regulate Proanthocyanidin Biosynthesis During Malus Crabapple Fruit Development

Proanthocyanidins (PAs) are a class of flavonoid compounds in plants that play many important roles in pest and disease resistance and are beneficial components of the human diet. The crabapple (Malus) provides an excellent model to study PA biosynthesis and metabolism; therefore, to gain insights into the PA regulatory network in Malus plants, we performed RNA-seq profiling of fruits of the 'Flame' cultivar at five sequential developmental stages. KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that differentially expressed genes (DEGs) related to the functional category 'plant hormone signal transduction' were significantly enriched during fruit development. Further analysis showed that ethylene signal transduction pathway genes or response genes, such as ERS (ethylene response sensor), EIN3 (ETHYLENE INSENSITIVE 3) and ERFs (ethylene response factors), may play an important role in the regulatory network of PA biosynthesis. Additionally, 12 DEGs, including 10 ERFs, 1 MYB, and 1 bHLH transcription factor, associated with PA biosynthesis were identified using WGCNA. The expression patterns of these genes correlated with PA accumulation trends and transcriptome data from qRT-PCR analysis. The expression of RAP2-4 (RELATED TO APETALA 2-4) and RAV1 (related to ABI3/VP1), which belong to the ERF transcription factor family, showed the greatest correlations with PAs accumulation among the 12 identified TFs. Agrobacterium mediated-transient overexpression of the RAP2-4 led to an increase in PA abundance in crabapple leaves and apple fruits, and the opposite results were observed in RAV1-overexpressed crabapple leaves and apple fruits. Moreover, a yeast one-hybrid assay showed that RAP2-4 and RAV1 specifically bound the promoters of the PA biosynthetic genes McLAR1 and McANR2, respectively. These results indicate that RAP2-4 act as an inducer and RAV1 act as a repressor of PA biosynthesis by regulating the expression of the PA biosynthetic genes McLAR1 and McANR2. Taken together, we identified two potential regulators of PA biosynthesis and provide new insights into the ethylene-PA regulatory network.

Identification of novel MYB transcription factors involved in the isoflavone biosynthetic pathway by using the combination screening system with agroinfiltration and hairy root transformation

Soybean isoflavones are functionally important secondary metabolites that are mainly accumulated in seeds. Their biosynthetic processes are regulated coordinately at the transcriptional level; however, screening systems for key transcription factors (TFs) are limited. Here we developed a combination screening system comprising a simple agroinfiltration assay and a robust hairy root transformation assay. First, we screened for candidate MYB TFs that could activate the promoters of the chalcone synthase (CHS) gene GmCHS8 and the isoflavone synthase (IFS) genes GmIFS1 and GmIFS2 in the isoflavone biosynthetic pathway. In the agroinfiltration assay, we co-transformed a LjUbi (Lotus japonicus polyubiquitin gene) promoter-fused MYB gene with target promoter-fused GUS (β-glucuronidase) gene constructs, and identified three genes (GmMYB102, GmMYB280, and GmMYB502) as candidate regulators of isoflavone biosynthesis. We then evaluated the functional regulatory role of identified three MYB genes in isoflavone biosynthesis using hairy roots transformation assay in soybean for the accumulation of isoflavones. Three candidate MYB genes showed an increased accumulation of total isoflavones in hairy root transgenic lines. Accumulation of total isoflavones in the three MYB-overexpressing lines was approximately 2-to 4-folds more than that in the vector control, confirming their possible role to regulate isoflavone biosynthesis. However, the significant accumulation of authentic GmCHS8, GmIFS1, and GmIFS2 transcripts could not be observed except for the GmMYB502-overexpressing line. Therefore, the analysis of isoflavone accumulation in transgenic hairy root was effective for evaluation of transactivation activity of MYB TFs for isoflavone biosynthetic genes. Our results demonstrate a simple and robust system that can potentially identify the function of orphan TFs in diverse plant metabolic pathways.

Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data

BACKGROUND

High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates.

RESULTS

With the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition.

CONCLUSION

Integration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development.

Ectopic Expression of Multiple Chrysanthemum (Chrysanthemum × morifolium) R2R3-MYB Transcription Factor Genes Regulates Anthocyanin Accumulation in Tobacco

The generation of chrysanthemum (Chrysanthemum × morifolium) flower color is mainly attributed to the accumulation of anthocyanins. In the anthocyanin biosynthetic pathway in chrysanthemum, although all of the structural genes have been cloned, the regulatory function of R2R3-MYB transcription factor (TF) genes, which play a crucial role in determining anthocyanin accumulation in many ornamental crops, still remains unclear. In our previous study, four light-induced R2R3-MYB TF genes in chrysanthemum were identified using transcriptomic sequencing. In the present study, we further investigated the regulatory functions of these genes via phylogenetic and alignment analyses of amino acid sequences, which were subsequently verified by phenotypic, pigmental, and structural gene expression analyses in transgenic tobacco lines. As revealed by phylogenetic and alignment analyses, CmMYB4 and CmMYB5 were phenylpropanoid and flavonoid repressor R2R3-MYB genes, respectively, while CmMYB6 was an activator of anthocyanin biosynthesis, and CmMYB7 was involved in regulating flavonol biosynthesis. Compared with wild-type plants, the relative anthocyanin contents in the 35S:CmMYB4 and 35S:CmMYB5 tobacco lines significantly decreased (p < 0.05), while for 35S:CmMYB6 and 35S:CmMYB7, the opposite result was obtained. Both in the 35S:CmMYB4 and 35S:CmMYB5 lines, the relative expression of several anthocyanin biosynthetic genes in tobacco was significantly downregulated (p < 0.05); on the contrary, several genes were upregulated in the 35S:CmMYB6 and 35S:CmMYB7 lines. These results indicate that CmMYB4 and CmMYB5 negatively regulate anthocyanin biosynthesis in chrysanthemum, while CmMYB6 and CmMYB7 play a positive role, which will aid in understanding the complex mechanism regulating floral pigmentation in chrysanthemum and the functional divergence of the R2R3-MYB gene family in higher plants.