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15 October 2025

Advancements in the Regulation of Flavonoid Compounds in Monocotyledons and Dicotyledons by Plant MYB Transcription Factors

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1
Hangzhou Lin’an District Agriculture and Rural Affairs Bureau, Hangzhou 311300, China
2
College of Horticulture Science, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
3
College of Agriculture and Biology, Liaocheng University, Liaocheng 252059, China
*
Author to whom correspondence should be addressed.
Horticulturae2025, 11(10), 1244;https://doi.org/10.3390/horticulturae11101244
This article belongs to the Special Issue Quality Control and Enhancement of Horticultural Crops in the Post-Genomic Era
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Abstract

Flavonoids are essential secondary metabolites in plants, predominantly found in flowers, leaves, and fruits. They mainly include anthocyanins, proanthocyanidins, and flavonols. Transcription factors are a crucial family of proteins in plants, playing a significant role in regulating the biosynthesis of secondary metabolites. This review introduces flavonoids and explores the characteristics and biological functions of MYB transcription factors. It establishes a phylogenetic tree using Arabidopsis thaliana MYB transcription factors as an example, which includes 17 subgroups (S1–S17). The subgroups related to flavonoids are primarily concentrated in S17, further classified into A, C, D, E, and F. The review also discusses the different regulatory roles of MYB transcription factors in flavonoid synthesis in monocotyledonous and dicotyledonous plants. This knowledge provides a theoretical foundation for further studies on the diverse regulatory functions of MYB transcription factors in flavonoid biosynthesis across the plant kingdom.

1. Introduction

During the long process of natural selection and evolution, plants have developed unique gene expression profiles and regulatory mechanisms to adapt to constantly changing environments []. Gene expression and silencing are tightly controlled to regulate diverse physiological processes throughout development, operating at multiple interdependent levels—including DNA modification, transcription, and translation []. Among these, transcriptional regulation is the most complex. It involves both cis-acting elements and trans-acting factors, which bind to specific nucleotide sequences and interact to precisely modulate the expression of structural genes, thereby executing regulatory functions []. MYB transcription factors represent one of the largest and most widespread families of regulatory proteins in plants and play key roles in the biosynthesis of numerous secondary metabolites. Recent genomic studies in safflower have shown that overexpression of R2R3-MYB genes significantly upregulates structural genes involved in flavonoid biosynthesis and enhances flavonol accumulation []; similarly, whole-genome identification in the medicinal orchid Dendrobium officinale revealed that certain R2R3-MYB members negatively regulate flavonoid synthesis by repressing key enzyme genes []. However, the field of MYB-mediated flavonoid regulation still faces considerable challenges. For instance, within a given species, multiple MYB homologs may regulate distinct branches of flavonoid metabolism or respond to different signals via functional differentiation. Moreover, understanding how epigenetic modifications of MYB genes and their target genes influence flavonoid synthesis and accumulation remains a major unresolved question. Flavonoids, an important class of plant secondary metabolites, are abundantly present in flowers, leaves, and fruits []. In Arabidopsis thaliana, early biosynthetic genes (EBGs) are activated by functionally redundant R2R3-MYB regulators (MYB11, MYB12, and MYB111), whereas late biosynthetic genes (LBGs) require the assembly of a ternary MYB–bHLH–WD40 (MBW) complex. In contrast, in monocot species such as maize (Zea mays), the MBW complex activates both EBGs and LBGs uniformly. Similar regulatory distinctions have been observed between other dicot and monocot species, suggesting fundamental differences in the flavonoid (particularly anthocyanin) regulatory networks between these two groups of plants []. By examining the characteristics and biological functions of MYB transcription factors, constructing a phylogeny of MYBs involved in flavonoid biosynthesis, and comparing their regulatory roles in monocots (e.g., rice and maize) and dicots (e.g., Arabidopsis thaliana), this study aims to provide a theoretical foundation for understanding the functional diversity and evolutionary divergence of MYB-mediated flavonoid regulation across the plant kingdom.

2. Flavonoid Biosynthetic Pathways

Flavonoids, which represent one of the primary classes of secondary metabolites in plants, mainly comprise anthocyanins, proanthocyanidins, and flavonols []. Among these, flavonols are the earliest evolved flavonoids, with their biosynthetic origins traceable to bryophytes, such as physcomitrium patens and marchantia polymorpha []. Proanthocyanidins have been identified in ferns, whereas anthocyanins are believed to have originated prior to the divergence of gymnosperms and angiosperms [].
Anthocyanins are one of the principal pigments found in flowers, leaves, stems, fruits, and other tissues and organs of plants. Their primary function is to impart diverse colors, contributing to the vibrant pigmentation observed in various plant species. Stable anthocyanins are typically localized within vesicles of epidermal cells []. The coloration of anthocyanins is determined by the number of hydroxyl groups on the B-ring; an increased number of hydroxyl groups results in a bluer hue. Proanthocyanidins are widely distributed in various plant tissues, including tree bark, flowers, seeds, and fruit peels. Maynard et al. (1967) first isolated four polyphenolic compounds from grape skin and grape seed extracts that yielded red anthocyanidins upon acid hydrolysis under heating; these were subsequently designated collectively as proanthocyanidins []. The regulation of proanthocyanidin biosynthesis in plants is more complex than that of anthocyanins. Nevertheless, their synthesis is primarily controlled by MYB transcription factors. In most species, proanthocyanidin accumulation is regulated by multiple MYB transcription factors that exhibit functional divergence or act in concert through specific regulatory sequences []. Flavonols represent the most abundant and ubiquitous subclass of flavonoid compounds. Common examples include quercetin, kaempferol, isorhamnetin, and myricetin, which are present in various plant organs such as roots, stems, leaves, flowers, and fruits []. They often co-localize with anthocyanins and contribute to color development in plant tissues while also acting as a defense mechanism against environmental stressors such as insect herbivory, UV radiation, and bacterial infection [].
In current horticultural crop studies focusing on secondary metabolism, the metabolic pathways underlying flavonoid biosynthesis have been characterized in greater detail (Figure 1). As a conserved and pivotal component of the phenylpropanoid pathway across plant taxa, flavonoid biosynthesis is governed by two primary gene categories: structural genes, further classified into early and late subsets []. In the anthocyanin branch, enzymes such as CHS, CHI, F3H, F3′H, and F3′5′H constitute the EBGs, while DFR, ANS/LDOX, and UFGT are designated as LBGs []; regulatory genes exemplified by transcription factors (Table 1). Key enzymes in the anthocyanin pathway are coordinately regulated by the MBW transcriptional activation complex, comprising members from the MYB, bHLH, and WD40 repeat protein families, as well as additional TFs such as WRKY and NAC []. The synthesis of flavonoids begins with phenylalanine within the phenylalanine pathway, where phenylalanine aminolyase serves as the initial enzyme. Phenylalanine Ammonia-Lyase (PAL)catalyzes the conversion of phenylalanine into cinnamic acid, subsequently processed by cinnamic acid-4-hydroxylase and 4CL4-coumarate coenzyme A ligase to yield 4-coumaroyl coenzyme A. Chalcone synthase then acts on malonyl coenzyme A and 4-coumaroyl coenzyme A, producing chalcone. While chalcone isomerase (CHI) is not mandatory for this reaction in plants, its absence slows down the process significantly, showcasing tissue-specific expression. Dihydroflavonols are generated from 4,5,7-trihydroxyflavanones catalyzed by flavanone 3-hydroxylase, a common substrate for flavonoid 3′-hydroxylase and flavonoid 3′,5′-hydroxylase. F3H plays a regulatory role in the synthesis of flavonols and anthocyanin products and is a key enzyme in the metabolic pathway of flavonoid substances with a central position in the whole flavonoid metabolism process. Dihydroxyflavonol reductase, reliant on NADPH, catalyzes the formation of colorless anthocyanins from flavonols. Its expression varies across species and tissues. These colorless anthocyanins are later oxidized by anthocyanin synthase into colored anthocyanins. Anthocyanins, inherently unstable, undergo modification by uridine diphosphate glucosyltransferase, leading to glycosylation, hydroxylation, and methylation, ultimately producing stable, colored anthocyanins. Alternatively, anthocyanin reductase and colorless anthocyanin reductase facilitate the conversion of unmodified colorless anthocyanins or anthocyanins into proanthocyanidins [] (Figure 1).
Figure 1. Simplified model for the flavonoid biosynthetic pathway and the function of MYB transcription factors.
Table 1. Classification and functions of EBGs and LBGs.
Abbreviations are as follows: EBGs, early biosynthetic genes; LBGs, late biosynthetic genes; PAL, phenylalanine ammonium lyase; C4H, cinnamate-4-hydroxylase; 4CL, 4-coumaroyl-CoA synthase; CHS, chalcone synthase; CHI, chalcone isomerase; F3H, flavanone 3-hydroxylase; F3′H, flavonoid 3′-hydroxylase; F3′5′H, flavonoid 3′5′-hydroxylase; FLS, flavonol synthase; DFR, dihydroflavonol reductase; ANS, anthocyanindin synthase; LDOX, leucoanthocyanidin dioxygenase; LAR, leucoanthocyanidin reductase; ANR, anthocyanidin reductase; UFGT, UDP-Glc:flavonoid 3-O-glucosyltransferase; OMT, O-methyl transferase.
Biosynthetic pathways exhibit considerable taxonomic variation across plant lineages, reflecting divergent evolutionary trajectories and ecological adaptations. Although core enzymatic mechanisms are often conserved, key differences emerge through gene family expansion, alterations in enzyme substrate specificity, and lineage-specific transcriptional regulation—particularly involving MYB transcription factors []. These variations give rise to distinct profiles of specialized metabolites, such as differences in flavonoid composition between monocots and dicots [].
Although monocots and dicots share the core biochemical pathway for flavonoid biosynthesis, significant divergences exist between them in terms of metabolic profile, regulatory mechanisms, and compound specificity. With regard to product accumulation, dicots produce a wide diversity of anthocyanins, such as pelargonidin, cyanidin, and delphinidin, resulting in a broad spectrum of flower colors []. In contrast, monocots—particularly those in the Poaceae family—exhibit more conservative floral pigmentation, predominantly accumulating cyanidin-3-glucoside, which confines their coloration to red and purple hues []. At the molecular regulatory level, although both groups rely on the MYB-bHLH-WD40 (MBW) transcriptional complex to control gene expression in this pathway, key MYB transcription factors in monocots show low homology to those in dicots, indicating distinct evolutionary trajectories []. Furthermore, monocots are notably specialized in the accumulation of characteristic metabolites such as C-glycosyl flavonoids (e.g., orientin and isoorientin), which are less common in dicots and contribute to enhanced antioxidant capacity and stress adaptation []. These differences collectively reflect the metabolic diversity that has emerged through adaptation to distinct ecological and developmental constraints during the evolution of these two major plant groups.

3. Structural Characteristics and Origin of MYB Transcription Factors

The functional diversification of transcription factors is primarily driven by gene duplication and subsequent functional divergence []. Duplicated paralogs may undergo subfunctionalization—where ancestral functions are partitioned among copies—or neofunctionalization, in which one copy acquires a novel function, thereby expanding functional diversity. Additionally, mutations in cis-regulatory elements, alterations in protein interaction interfaces, and structural domain rearrangements further promote functional innovation in DNA-binding specificity, regulatory activity, and signal responsiveness []. These evolutionary mechanisms ultimately enable transcription factors to regulate a broader array of biological processes and enhance organismal adaptability to environmental challenges []. Dedicated databases have been developed to catalog transcription factors across species—examples include the Plant Transcription Factor Database (PlantTFDB) and the Grass Transcription Factor Database (Grassius)—with well-characterized families such as MYB, WRKY, NAC, and AP2/ERF being widely recognized as key regulators of these metabolic pathways [].

3.1. Structural Characteristics and Classification of MYB Transcription Factors

MYB transcription factors are named after their highly conserved DNA-binding domain, the MYB domain, which typically comprises 1–4 tandem and partially repeated R units (R1, R2, R3, and in rare cases R4). Each R unit consists of approximately 50–53 amino acids that form a helix-turn-helix (HTH) motif capable of binding DNA. Key tryptophan residues—spaced at roughly 18-amino acid intervals—form a hydrophobic core essential for stabilizing the HTH conformation. Substitutions of these tryptophans, particularly the first tryptophan in the R3 repeat, with other aromatic or hydrophobic residues such as phenylalanine or leucine, are often observed and may influence DNA-binding specificity [].
Based on the number and arrangement of R repeats, MYB proteins are classified into four major categories: (1) 1R-MYB (MYB-related) proteins contain a single R repeat and are subdivided into R3-type, R1/R2-type, and other variants. R3-type members—such as CAPRICE (CPC), TRIPTYCHON (TRY), and MYBL2—participate in cell fate determination and secondary metabolism. R1/R2-type proteins, including LHY and CCA1, play key roles in circadian rhythm regulation [].
(2) R2R3-MYB proteins contain two adjacent R repeats and represent the largest MYB subfamily in plants. They feature a conserved N-terminal DNA-binding domain and a divergent C-terminal region that often contains transcriptional activation or repression domains, enabling diverse regulatory functions [].
(3) R1R2R3-MYB (3R-MYB) proteins comprise three R repeats and form an evolutionarily ancient group with limited membership. For instance, only five 3R-MYB genes are found in Arabidopsis and tobacco, and four to five in rice [].
(4) 4R-MYB proteins, containing four R repeats, are the rarest class. These proteins consist of four tandem R1/R2-like repeats and are encoded by very few genes across plant species. Their functional roles remain poorly characterized [].
Among these, R2R3-MYB and R3-MYB family members are notably involved in the regulation of anthocyanin biosynthesis, with many R3-MYBs acting as transcriptional repressors in this pathway [].

3.2. Origin and Differentiation of MYB Transcription Factors

Two principal models have been proposed to explain the evolution of MYB genes in plants. The first model posits that the MYB DNA-binding domain originated over a billion years ago. According to this view, MYB proteins containing two or three repeats emerged through sequence duplication and amplification events. Differential expansion of these genes across lineages accounts for the striking abundance of MYB transcription factors in plants—for example, the hundreds of R2R3-MYB genes found in Arabidopsis—compared to the more limited repertoires in animals and bacteria. This model further suggests that R2R3-MYB genes arose through the evolutionary loss of the R1 repeat from ancestral R1R2R3-MYB genes []. An alternative model proposes that R1R2R3-MYB transcription factors evolved through the acquisition of an additional R1 repeat, forming three-repeat proteins from simpler precursors []. Despite their differences, both models agree that MYB genes originated from single-repeat ancestral genes prior to the evolutionary divergence of plants and animals.
We generated a phylogenetic tree utilizing Arabidopsis MYB transcription factors as a model. The Arabidopsis MYB transcription factor family members were sourced from TAIR (https://www.Arabidopsis.org/, accessed on 5 February 2024), while those specifically associated with flavonoid biosynthesis were retrieved from the NCBI website (https://www.ncbi.nlm.nih.gov/, accessed on 8 February 2024). A total of 126 Arabidopsis R2R3-MYBs and 93 R2R3-MYBs linked to flavonoid biosynthesis were aligned using MAFFT, and subsequently, an ML tree was constructed employing IQ-TREE 2. This analysis delineated a significant Arabidopsis MYB family comprising 17 subgroups that regulate diverse metabolic pathways. In this study, the MYB transcription factors of primary interest, which are involved in the regulation of flavonoid biosynthesis, were positioned on Section S17 in Figure 2 to facilitate more detailed and focused analysis. R2R3 MYBs, which control flavonoids, have been discovered in an increasing variety of plants, and these gene homologs are frequently believed to control the same pathway []. In order to analyze the MYB gene related to flavonoids more clearly, we have subdivided it according to its different functions []. Flavonoid-related MYBs are divided into five clades, containing flavonol-related, proanthocyanin-related, anthocyanin-related, and repressor (Figure 2). While some R2R3 MYBs specifically control the expression of a single gene, others influence multiple genes and aspects of the flavonoid pathway.
Figure 2. Phylogenetic tree of the R2R3-MYB genes in Arabidopsis thaliana [] and functionally characterized genes related to flavonoid biosynthesis in plants. The tree was constructed by the maximum likelihood (ML) method using IQ-TREE 2, and ModelFinder was used to choose the best model. The tree was rooted using AtCDC5 as the outgroup. Bootstrap values ≥ 50% are shown as dark blue dots in the phylogenetic tree. The candidate R2R3-MYB proteins are clustered into 17 subfamilies (designated as S1 to S17). And the S17 subfamily is further divided into six groups, namely A (anthocyanin activators), B (proanthocyanidin activators), C (trichomes), D (general flavonoid activators), E (flavonol activators), and F (flavonoid repressors).
To enable a more precise investigation of the S17 subgroup, we performed correlation analyses of key parameters, yielding the following technical data. Multiple sequence alignment was performed with MAFFT v7.525 (129 sequences (S17), 1131 sites), comprising 277 conserved sites (24.5%), 298 singleton sites (26.4%), and 556 parsimony-informative sites (49.1%). AliStat v1.16 analysis indicated an average p-distance of 0.543, corresponding to ~45.7% mean identity. Phylogenetic inference was conducted in IQ-TREE v3.0.1 under the best-fit substitution model JTT+R7 selected by ModelFinder (BIC). Branch support was assessed with 1000 ultrafast bootstrap replicates, and values are shown on the consensus ML tree.
MYB transcription factors exhibit both evolutionary convergence and divergence in their functions. Evolutionary convergence refers to the process whereby MYB genes from distinct evolutionary lineages and independent origins gradually develop similar molecular functions through long-term natural selection and adaptation to shared physiological demands, such as responses to environmental stress or regulation of specific branches of flavonoid metabolism. For example, OsMYB12 in monocot rice and AtMYB12 in dicot Arabidopsis thaliana, despite belonging to divergent plant clades without direct evolutionary connections, both activate key promoters of flavonoid biosynthesis genes to regulate the accumulation of flavonols, demonstrating functional convergence [,]. In contrast, evolutionary divergence occurs when MYB genes derived from a common ancestor acquire functional specificity over time in different species or lineages due to accumulated genetic variations, ecological niche differentiation, and distinct selective pressures. For instance, an ancestral MYB gene initially involved in basal flavonoid regulation may have diverged in gymnosperms to control defensive flavonoid compounds in conifer needles, while in angiosperms, it further specialized into subtypes regulating distinct metabolites such as anthocyanins or proanthocyanidins []. Some MYBs even evolved from transcriptional activators into repressors, fine-tuning the balance of flavonoid metabolic networks. This dynamic interplay of convergence and divergence not only shapes the functional diversity of the MYB family but also underpins plants’ adaptation to varied ecological environments and enables precise regulation of metabolic pathways []. It is central to understanding the widespread yet functionally specialized distribution of key secondary metabolic pathways, such as flavonoid biosynthesis, across the plant kingdom.

4. The Regulation of Flavonoid Synthesis by MYB Transcription Factors

The evolutionary divergence between monocots and dicots is characterized by several distinct genomic and phenotypic patterns, driven by mechanisms such as lineage-specific whole-genome duplications, differential expansion of gene families, and functional diversification of key regulatory components []. For example, subfunctionalization of MADS-box genes has led to profound differences in floral architecture, while divergent expansion and expression of transcription factor families—including MYB and NAC—underpin variations in stress adaptation and secondary metabolism []. Structural innovations, such as the scattered vascular bundles characteristic of monocots and the robust secondary growth typical of many dicots, further illustrate how developmental and ecological constraints have shaped independent evolutionary trajectories. Together, these patterns highlight the deep phylogenetic and adaptive changes that have generated the morphological, physiological, and molecular distinctions defining these two major angiosperm groups.
MYB transcription factors in plants stand out from their animal and yeast counterparts due to their remarkable structural and functional conservation. They serve as pivotal players in a diverse array of biological processes, exerting a unique influence on plant growth. Engaging in multiple facets of plant development, MYB transcription factors govern cell fate, morphogenesis, and various developmental stages. They also oversee primary and specialized metabolic pathways, as well as orchestrate responses to both biotic and abiotic stresses. Notably, MYB transcription factors are actively involved in plant flavonoid metabolic pathways, regulating flower, fruit, and seed color, among others, in monocotyledonous plants such as rice and maize, and in dicotyledonous plants such as Arabidopsis thaliana. EBGs in Arabidopsis are activated by functionally redundant R2R3MYB regulatory genes (MYB11, MYB12, and MYB111), and the initiation of LBGs requires the MYB regulatory factor and bHLH factor, as well as the WD40 protein to make up the ternary MBW complex. In contrast, in monocotyledonous maize and rice, the MBW complex can activate both EBGs and LBGs as a single unit; therefore, we suggest that the regulatory mechanism of flavonoid synthesis in dicotyledons is different from that in monocotyledons (Figure 3). In Arabidopsis, the early synthetic genes EBGs associated with flavonoid synthesis are regulated by AtMYB12/PFG1 [], and the late synthetic genes, LBGs, are mainly regulated by AtMYB75/PAP1, AtMYB90/PAP2, AtMYB5, AtMYB123/AtTT2, AtMYB113, AtMYB114 [,,,], AtMYB3, AtMYB4, AtMYB7, and MYB32 overexpression inhibited both early synthesis genes EBGs and late synthesis genes, LBGs [,,], AtMYBL2 and AtCPC also inhibited the control of flavonoid production [,]. In monocotyledonous plants, of all the MYB genes present in the model plant rice, OsP1 (PERICARP COLOUR1) and OsMYB3/Kala3 are overexpressed to increase the transcriptional level of EBGs, and OsC1 (COLOURESS1) is overexpressed to increase the transcriptional level of LBGs, promoting the production of anthocyanins [,,]. In another model plant, maize, ZmP1 is overexpressed to increase the transcriptional level of EBG [], and ZMC1 and ZMPL are overexpressed to increase the transcriptional level of EBGs and LBGs, which promote the production of flavonoids [,].
Figure 3. MYB regulation of the flavonoid biosynthetic pathway in monocotyledons and dicotyledons.
Activation-type and repression-type MYB transcription factors can exhibit both functional paralogy and convergent evolution, enhancing the complexity and adaptability of regulatory networks in plants. Functional paralogy often arises from gene duplication events, where paralogous genes diverge to assume opposing roles—one activating and one repressing the same pathway—as observed in anthocyanin biosynthesis regulators such as AtMYB75 and AtMYB27 in Arabidopsis []. Meanwhile, convergent evolution is reflected in the independent emergence of repressive motifs in non-homologous MYB repressors across distantly related species, enabling analogous suppression of flavonoid biosynthesis in both monocots and eudicots []. These evolutionary mechanisms collectively fine-tune metabolic responses and contribute to phenotypic diversity under environmental constraints.

4.1. Involvement of MYB Transcription Factors in Monocotyledonous Plants in Flavonoid Metabolism, Regulating the Color of Flowers, Fruits, etc.

In monocotyledonous plants, MYB transcription factors regulate flavonoid biosynthesis, which is more typical of rice and maize. Among all MYB genes present in rice, an R2R3 type (C1) regulates anthocyanin biosynthesis, OsC1(COLOURLESS1), OsP1(PERICARP COLOUR1), and OsMYB3/Kala3 overexpressed in rice plants trigger anthocyanin production through augmentation of the transcript level of late ABP genes [,,] (Table 2). The maize ZmMYBC1 gene, which is the first MYB-like gene to be discovered in plants, is ectopically expressed in tissue cells and interacts with the bHLH protein to jointly elicit the manifestation of the structural enzyme genes DFR and 3GT in the anthocyanin synthesis pathway, leading to massive synthesis and accumulation of anthocyanin in pigment-free maize tissue cells []. ZMP1 and ZMPL bind to and activate transcription of the A1 gene required for 3-deoxy flavonoid to promote the production of flavonoid compounds [,] (Table 2).
In other monocotyledons, MYB transcription factors promote or inhibit flavonoid production (Table 3). In lily, LhMYB6 and LhMYB12 interact with bHLH transcription factors to activate the expression of DFR and the formation of spots on tepals [], LhMYB12-Lat promotes anthocyanin synthesis [], overexpression of LhR3MYB1 and LhR3MYB2 actually inhibits anthocyanin biosynthesis []; In orchids, the OgMYB1 was associated with anthocyanin synthesis in the flowers of Mandarin orchids []; In Tulip, TfMYB3, TfMYB4 and TfMYB5 interact with TfbHLH1, TfMYB5 activates the promoter of TfCHS1, while TfMYB3 and TfMYB4 promote the promoter activity of TfANS1 were participated in the regulating of anthocyanin biosynthesis []; In Phalaenopsis, PeMYB2, PeMYB11 and PeMYB12 regulate the anthocyanin synthesizing Enzymes F3′5′H, DFR1, and ANS3 to accumulate anthocyanin synthesis []; In Bananas, MaMYBPA1 and MaMYBPA2 interact with MaANS to promote flavonoid synthesis [,], MaMYBA1 and MaMYBA2 function as components of transcription factor complexes with bHLH and WD40 proteins to activate anthocyanin biosynthesis [], while MaMYBPR1/MaMYB4, MaMYBPR2, MaMYBPR3 and MaMYBPR4 inhibit the synthesis of anthocyanins [,]; In Onions, AcMYB1 bounds to the promoters of anthocyanidin synthase (AcANS) and flavonoid 3-hydroxylase 1 (AcF3H1) and activates their expression []; In Dendrobium officinale, DhMYB2 and DhbHLH1 interact and are expressed together with DhDFR and DhANS, promote anthocyanin accumulation []. In Freesia hybrida, the R2R3-MYB factor FhMYB5 regulates the biosynthesis of anthocyanins and proanthocyanidins, FhMYB27 and FhMYBx inhibit anthocyanin synthesis by activating MBW; in contrast, FhPAP1 promotes anthocyanin synthesis []. In Daffodils, the NtMYB2 and NtMYB3 from Narcissus R2R3-MYB inhibit the biosynthesis of anthocyanin and flavonoids [].
Table 2. MYB transcription factors involved in the regulation of flavonoid compounds in model plants.
Table 2. MYB transcription factors involved in the regulation of flavonoid compounds in model plants.
Species (Family)GeneTypeMetabolismFunctionAccessionReference
Arabidopsis thaliana (Brassicaceae)AtMYB5R2R3-MYBFlavonoids, ProanthocyanidinsActivationAT3G13540.1[]
AtMYB11/PFG2R2R3-MYBFlavonolsActivationAT3G62610.1[]
AtMYB12/PFG1R2R3-MYBFlavonolsActivationAT2G47460.1[]
AtMYB75/PAP1R2R3-MYBAnthocyaninsActivationAT1G56650.1[]
AtMYB90/PAP2R2R3-MYBAnthocyaninsActivationAT1G66390.1[]
AtMYB111/PFG3R2R3-MYBFlavonolsActivationAT5G49330.1[]
AtMYB113R2R3-MYBAnthocyaninsActivationAT1G66370.1[]
AtMYB114R2R3-MYBAnthocyaninsActivationAT1G66380.1[]
AtMYB123/AtTT2R2R3-MYBProanthocyanidinsActivationAT5G35550.1[]
AtMYB3R2R3-MYBFlavonoidsInhibitionAT1G22640.1[]
AtMYB4R2R3-MYBFlavonoidsInhibitionAT4G38620.1[]
AtMYB7R2R3-MYBFlavonolsInhibitionAT2G16720.1[]
AtMYB32R2R3-MYBFlavonoidsInhibitionAT4G34990.1[]
AtMYBL2R3-MYBAnthocyaninsInhibitionAT1G71030.1[]
AtCPCR3-MYBAnthocyaninsInhibitionAT2G46410.1[]
Oryza sativa (Poaceae)OsC1(COLOURLESS1)R2R3-MYBAnthocyaninsActivationLOC_Os06g10350.1[]
OsP1(PERICARP COLOUR1)R2R3-MYBFlavonolsActivationLOC_Os03g19120.1[]
OsMYB3/Kala3R2R3-MYBAnthocyaninsActivationLOC_Os03g29614.1[]
Zea mays (Poaceae)ZmC1(COLOURLESS1)R2R3-MYBAnthocyaninsActivationZm00001d044975_P001[]
ZmPL(PURPLE LEAF)R2R3-MYBAnthocyaninsActivationZm00001d037118_P001[]
ZmP1(PERICARP COLOUR)R2R3-MYBFlavonolsActivationZm00001d028850_P001[]
Table 3. MYB transcription factors involved in the regulation of flavonoid compounds in monocotyledon plants.
Table 3. MYB transcription factors involved in the regulation of flavonoid compounds in monocotyledon plants.
Species (Family)GeneTypeMetabolismFunctionAccessionReference
Lilium spp. (Liliaceae)LhMYB6R2R3-MYBAnthocyaninsActivationBAJ05399.1[]
LhMYB12R2R3-MYBAnthocyaninsActivationBAJ05398.1[]
LhMYB12-LatR2R3-MYBAnthocyaninsActivationBAO04194.1[]
LhR3MYB1R3-MYBAnthocyaninsInhibitionBBG71951.1[]
LhR3MYB2R3-MYBAnthocyaninsInhibitionBBG71952.1[]
Oncidium spp. (Orchidaceae)OgMYB1R2R3-MYBAnthocyaninsActivationABS58501.1[]
Tulipa fosteriana (Liliaceae)TfMYB3R2R3-MYBAnthocyaninsActivationAHY20034.1[]
TfMYB4R2R3-MYBAnthocyaninsActivationAHY20035.1[]
TfMYB5R2R3-MYBAnthocyaninsActivationAHY20036.1[]
Phalaenopsis aphrodite (Orchidaceae)PeMYB2R2R3-MYBAnthocyaninsActivationAIS35919.1[]
PeMYB11R2R3-MYBAnthocyaninsActivationAIS35928.1[]
PeMYB12R2R3-MYBAnthocyaninsActivationAIS35929.1[]
Musa acuminata (Musaceae)MaMYBPA1R2R3-MYBProanthocyanidinsActivationMa03_g07840.1[]
MaMYBPA2R2R3-MYBAnthocyanins, ProanthocyanidinsActivationMa10_g17650.1[,]
MaMYBA1R2R3-MYBAnthocyaninsActivationMa06_g05960.1[]
MaMYBA2R2R3-MYBAnthocyaninsActivationMa09_g27990.1[]
MaMYBPR1/MaMYB4R2R3-MYBAnthocyanins, ProanthocyanidinsInhibitionMa03_g21920.1[]
MaMYBPR2R2R3-MYBAnthocyaninsInhibitionMa06_g11140.1[]
MaMYBPR3R2R3-MYBAnthocyaninsInhibitionMa08_g16760.1[]
MaMYBPR4R2R3-MYBAnthocyaninsInhibitionMa10_g19970.1[]
Allium cepa (Amaryllidaceae)AcMYB1R2R3-MYBAnthocyaninsActivationAQP25672.1[]
Dendrobium spp. (Orchidaceae)DhMYB2R2R3-MYBAnthocyaninsActivationAQS79852.1[]
Freesia hybrida (Iridaceae)FhMYB5R2R3-MYBAnthocyanins, ProanthocyanidinsActivationQAX87835.1[]
FhPAP1R2R3-MYBAnthocyaninsActivationQJW70307.1[]
FhMYB27R2R3-MYBAnthocyaninsInhibitionQJW70308.1[]
FhMYBxR3-MYBAnthocyaninsInhibitionQJW70309.1[]
Narcissus tazetta (Amaryllidaceae)NtMYB2R2R3-MYBAnthocyaninsInhibitionATO58377.1[]
NtMYB3R2R3-MYBFlavonoidsInhibitionAGO33166.1[]

4.2. Involvement of MYB Transcription Factors in Dicotyledonous Plants in Flavonoid Metabolism, Regulating the Color of Flowers, Fruits, etc.

In dicotyledonous plants, many R2R3 MYBs have been shown to play an important role in flavonoid biosynthesis, among which Arabidopsis is a very representative class and a focus of research (Table 2). In Arabidopsis, the early synthesis genes (EBGs) related to flavonoid synthesis are promoted and regulated by AtMYB12/PFG1, AtMYB11/PFG2, and AtMYB111/PFG3 [], and the LBGs related to flavonoid synthesis are promoted and regulated by AtMYB75/PAP1, AtMYB90/PAP2, AtMYB5, and AtMYB123/AtTT2 [,]. In the study of the synthesis pathways of flavonoids such as Arabidopsis anthocyanins, proanthocyanidins, and flavonols, some MYB transcription factors, AtMYB123/AtTT2 and AtMYB5 bind to the promoters of different key enzyme genes to promote flavonols synthesis [,], AtMYB11/PFG2 and AtMYB111/PFG3, three members of subfamily 7 of the MYB family in Arabidopsis, can activate structural enzyme genes related to flavonol synthesis in different plant parts of Arabidopsis to regulate flavonol synthesis and control the accumulation of flavonol analogs in various tissues or organs of the plant [], while AtMYB3 inhibits the synthesis of flavonoids in Arabidopsis thaliana [], AtMYB4 and AtMYB32 interact with the bHLH transcription factors TT8, GL3 and EGL3 and thereby interfere with the transcriptional activity of the MBW complexes to inhibit the synthesis of anthocyanins [,,], AtMYB7 inhibits the flavonol biosynthesis by controlling DFR and UGT [], ectopic expression of AtMYBL2 or of a chimeric repressor that is a dominant negative form of AtMYBL2 suppressed the expression of the biosynthesis of anthocyanin [,], anthocyanin synthesis genes are down-regulated in AtCPC overexpressing plants [].
In addition to its role in Arabidopsis, there is a large amount of new evidence indicating the role of R2R3 MYBs in transcriptional regulation of flavonoid metabolism in other aspects (Table 4). In grapes, the VvMYBF1 can directly activate the structural enzyme genes related to flavonol [], the VvMYBA1 and VvMYBA2 promote anthocyanin synthesis by activating UFGT, CHS3 and LDOX [], VvMYBPA1 and VvMYBPA2 activate the promoters of LAR and ANR to promote the synthesis of anthocyanins [,], VvMYB5a and VvMYB5b activate the grapevine promoters of several structural genes of the flavonoid pathway to regulate of the flavonoid [], VvMYBPAR induces proanthocyanidin synthase to promote proanthocyanidin accumulation [], VvMYBC2-L1, VvMYBC2-L2 and VvMYBC2-L3 inhibit anthocyanin synthesis by affecting PAL, C4H, CHS, DFR, and UFGT [,]. In poplar, PtrMYB134 and PtrMYB115 regulate proanthocyanidin biosynthesis by activating key flavonoid genes through a transcription factor complex composed of bHLH and WD-40 proteins [], whereas PtrMYB165 and PtrMYB194 inhibit the activation of flavonoid promoters and reduce anthocyanin and proanthocyanidin synthesis by interacting with bHLH131 [], overexpression of PtrMYB57 and PtrMYB182 led to a decrease in anthocyanin and PA accumulation in poplar, demonstrating that PtrMYB57 and PtrMYB182 play a negative role in the regulation of anthocyanin and PA biosynthesis in poplar [,], PtrRML1 controls inhibition of anthocyanins and synthesis such as DFR and UF3GT []. In Medicago truncatula, MtPAR and MtTT8 regulate genes encoding enzymes of the flavonoid–PA pathway via a activation of WD40-1 to regulate proanthocyanidin biosynthesis [,], MtMYB5 and MtMYB14 interact and activate the promoters of anthocyanidin reductase and leucoanthocyanidin reductase [], MtMYB134 activate AtCHS and AtFLS1 to promote flavonol biosynthesis [], ectopic expression of MtLAP1 transcription factor activates the anthocyanin [], overexpression of MtMYB2 abolishes anthocyanin and PA accumulation in Arabidopsis thaliana seeds []; In soybean, GmTT2A, GmTT2B and GmMYB5A induce the accumulation of proanthocyanidins and anthocyanins [], Ectopic expression of GmMYBA2 conferred the enhanced accumulation of delphinidin and cyanidin types of anthocyanins in W1t and w1T backgrounds, GmMYBR is an inhibitor of anthocyanins []. In strawberry, FaMYB123 interacts with FabHLH3 to regulate anthocyanin [], FaMYB5 is an R2R3-MYB activator involved in the composition of MBW to regulate the biosynthesis of anthocyanin and proanthocyanidin [], FaMYB9 and FaMYB11 activate the proanthocyanidin reductase gene promoter and promote proanthocyanidin accumulation [], FaMYB10 regulates the expression of most of the EBGs and the LBGs to involve in anthocyanin production [], the FaMYB1 of strawberry significantly inhibited the synthesis of anthocyanins and flavonols []. In rose, RcMYB1 activates its own gene promoter and those of other EBGs and LBGs; overexpression of RcMYB1 promotes anthocyanin accumulation []. In tea trees, CsMYB5a, CsMYB5b, and CsMYB5e promote the gene expression of CsLAR and CsANR, CsMYB5f and CsMYB5g only upregulate the gene expression of CsLAR but not CsANR to regulate proanthocyanidin biosynthesis [], CsMYB75 promotes the expression of CsGSTF1 to improve anthocyanin synthesis []. In apple, the MdMYB1 gene from apple and validated it in Arabidopsis and isolated grapevine somatic cells and found that MdMYB1 is capable of ectopic expression for the synthesis of anthocyanin and has abundant polymorphisms in its promoter region, overexpression of MdMYB3 has resulted in transcriptional activation of several anthocyanins and flavonol pathway genes, including CHS, CHI, UFGT and FLS [], MdMYB9, MdMYB10 and MdMYB11 interact with MdbHLH3, bind to the promoters of ANS, ANR, and LAR, and promote anthocyanin synthesis [,], MdMYB12 interacts with bHLH3 and bHLH33 and played an essential role in proanthocyanidin synthesis [], MdMYB22 activate flavonol pathways by combining directly with the flavonol synthase promoter. MdMYB24L positively regulates the transcription of MdDFR and MdUFGT and promotes anthocyanin accumulation [], MdWRKY11 binds to W-box cis-elements in the MdMYB10 and MdUFGT promoters and promotes anthocyanin synthesis in apple [], MdMYB110a binds to the promoter of CHS and promotes anthocyanin synthesis [], MdMYBA bound to an anthocyanidin synthase (MdANS) promoter region to control the increase in anthocyanins [], the interaction between MdMYBPA1 and MdbHLH33 forms a complex, promote the production of proanthocyanidin [], MdbHLH33 in callus overexpressing MdMYB16 and found that it weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis []. In kiwifruit, AcMYBF110 and AcbHLH1, AcbHLH4, AcbHLH5 and AcWDR1 together activate the kiwifruit anthocyanin synthesis promoter and regulate anthocyanin accumulation [], AcMYB123 activates promoters of AcANS and AcF3GT1 that encode the dedicated enzymes for anthocyanin biosynthesis to affect the accumulation of anthocyanins []. In tomato, the SlMYB75/AN2 regulates chlorophyll, carotenoids, and flavonoids [], and SlMYBATV plays a repressive role in anthocyanin biosynthesis in tomato []. In cucumber, CsMYB60 activates CsFLS and CsLAR to promote biosynthesis of flavonols and proanthocyanidins in cucumber []. In peony flowers, PsMYB58 interacted with PsbHLH1 and PsbHLH3 to enhance anthocyanin accumulation in various organs []. In carrot, DcMYB113 induces DcbHLH3, which controls anthocyanin biosynthesis gene expression and promotes anthocyanin biosynthesis [,].
Table 4. MYB transcription factors involved in the regulation of flavonoid compounds in dicotyledonous plants.

5. Prospects

MYB transcription factors are central regulators of the flavonoid biosynthesis pathway in both monocot and dicot species. Comparative analyses between model monocots and the dicot Arabidopsis thaliana have revealed fundamental divergences in regulatory circuitry. In Arabidopsis, EBGs are primarily activated by functionally redundant R2R3-MYB proteins, while LBGs require the assembly of MBW complexes for transcriptional activation. In contrast, monocots exhibit a more integrated regulatory model in which the MBW complex directly coordinates both EBGs and LBGs. This functional plasticity suggests that the MBW module has undergone lineage-specific evolution, leading to distinct architectural logics in flavonoid pathway regulation. Despite progress in characterizing the MBW complex, major knowledge gaps persist regarding the evolutionary mechanisms and molecular determinants underlying these regulatory divergences. Key unanswered questions include how the MBW complex acquired extended target gene specificity in monocots, the role of cis-regulatory element evolution and chromatin accessibility in shaping regulatory divergence, and the contribution of non-MYB factors and post-translational modifications to pathway fine-tuning in a lineage-specific manner. Addressing these questions is critical not only for understanding the evolutionary rewiring of metabolic networks but also for harnessing MYB regulators in biotechnology. Targeted manipulation of MYBs—through overexpression, silencing, or genome editing—holds substantial promise for tailoring flavonoid profiles to enhance crop resilience, nutritional content, and visual traits. Examples include increasing antioxidant levels in food crops, modifying flower and fruit pigmentation, and reducing antinutrient accumulation. Thus, elucidating the mechanistic basis of MYB regulatory divergence offers a foundation for predictive metabolic engineering across economically important plant species.

Author Contributions

Z.S., H.L., Q.L., T.B. and J.N. conceived and designed the review. H.L. wrote the manuscript, and Z.S., H.L., Q.L., T.B. and J.N. proposed revisions to the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the National Natural Science Foundation of China (Grant No. 32071731), and the Personnel Startup Project of the Scientific Research and Development Foundation of Liaocheng University (Grant No. 318042402).

Institutional Review Board Statement

Not applicable.

Data Availability Statement

Not applicable.

Conflicts of Interest

The authors declare no conflicts of interest.

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Physiological and Biochemical Responses of Mentha spp. to Light Spectrum and Methyl Jasmonate in a Controlled Plant Factory Environment
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