Transcriptional control of flavonoid biosynthesis by MYB-bHLH-WDR complexes

Phosphorylation of the strawberry MADS-box CMB1 regulates ripening via the catabolism of abscisic acid

Research on the ripening of fleshy fruits has relied on techniques that measure transcriptional changes. How ripening is linked to posttranslational modifications such as protein phosphorylation remains less studied. Here, we characterize the MADS-box SEPALLATA 4 (SEP4) subfamily transcription factor FaCMB1, a key negative regulator controlling strawberry ripening, whose transcript and protein abundance decrease progressively with fruit development and are repressed by abscisic acid (ABA). Transient RNAi or overexpression of FaCMB1 significantly altered the fruit ripening process and affected the content of endogenous ABA and ripening-related quality. Transcriptome sequencing (RNA-seq) analysis suggested that manipulation of FaCMB1 expression levels affected the transcription of FaASR (ABA-, stress-, ripening-induced), while FaCMB1 can repress the gene expression of FaASR by directly binding to its promoter. Furthermore, FaASR inhibited the transcriptional activity of FaCYP707A4, a key ABA 8'-hydroxylase enzyme involved in ABA catabolism. We show that FaCMB1 can be phosphorylated by the kinase FaSTPK, and Phos-tag assays indicated that the phosphorylation level of FaCMB1 increases during fruit ripening. This phosphorylation of FaCMB1 affects the binding ability of FaCMB1 to the FaASR promoter and alleviates its transcriptional repression. In conclusion, we elucidated a feedback regulatory path involving FaCMB1-FaASR-FaCYP707A4-ABA. During the fruit ripening process, an increase in ABA content led to a decrease in FaCMB1 transcript and protein levels, which, combined with increased phosphorylation levels, collectively impaired the transcriptional repression of FaASR by FaCMB1. Meanwhile, the increased transcriptional level of FaASR further repressed the expression level of FaCYP707A4, leading to ABA accumulation and fruit ripening.

Two tandem R2R3 MYB transcription factor genes cooperatively regulate anthocyanin accumulation in potato tuber flesh

Anthocyanin biosynthesis and accumulation determines the colour of tuber flesh in potato (Solanum tuberosum) and influences nutritional quality. However, the regulatory mechanism behind anthocyanin biosynthesis in potato tuber flesh remains unclear. In this study, we identified the Pigmented tuber flesh (Pf) locus through a genome-wide association study using 135 diploid potato landraces. Genome editing of two tandem R2R3 MYB transcription factor genes, StMYB200 and StMYB210, within the Pf locus demonstrated that both genes are involved in anthocyanin biosynthesis in tuber flesh. Molecular and biochemical assays revealed that StMYB200 promotes StMYB210 transcription by directly binding to a 1.7-kb insertion present in the StMYB210 promoter, while StMYB210 also regulates its own expression. Furthermore, StMYB200 and StMYB210 both activated the expression of the basic helix-loop-helix transcription factor gene StbHLH1 and interacted with StbHLH1 to regulate anthocyanin biosynthesis. An analysis of the StMYB210 promoter in different diploid potato accessions showed that the 1.7-kb insertion is associated with flesh colour in potato. These findings reveal the genetic and molecular mechanism by which the Pf locus regulates anthocyanin accumulation in tuber flesh and provide an important reference for breeding new potato varieties with colourful flesh.

Combined analysis of lncRNAs and mRNAs associated with coloration and wax formation during 'Fumei' Apple development

'Fumei' apple is characterized by high anthocyanin content and thick wax layer. Long non-coding RNAs (lncRNAs) play essential roles in the growth and development of various plants via regulation of gene expression. This study explored the potential mechanism underlying anthocyanin accumulation and cuticular wax formation during the development of 'Fumei' apple fruit. The results demonstrated that anthocyanin accumulation correlates with fruit coloration, while wax content drives wax layer formation. A total of 6039 and 3410 differentially expressed genes (DEGs), as well as 230 and 131 differentially expressed lncRNAs (DELs) were identified in the M1/M2 and M2/M3 pairs, respectively, by using RNA-seq. In the M1/M2 pair, the DEGs were mainly enriched in the 'photosynthesis' and 'flavonoid biosynthesis' pathways; in the M2/M3 pair, the DEGs were significantly enriched in the 'photosynthesis' and 'cutin, suberine and wax biosynthesis' pathways. Furthermore, the structural and regulatory genes involved in anthocyanin and cuticular wax biosynthesis were investigated, and the potential lncRNAs and genes that may control the anthocyanin and cuticular wax biosynthesis were identified. This study provides candidate lncRNAs and potential regulatory genes associated with both the regulation of anthocyanins and wax during apple development.

Selection of dysfunctional alleles of bHLH1 and MYB1 has produced white grain in the tribe Triticeae

Grain color is a key agronomic trait that greatly determines food quality. The molecular and evolutionary mechanisms that underlie grain-color regulation are also important questions in evolutionary biology and crop breeding. Here, we confirm that both bHLH and MYB genes have played a critical role in the evolution of grain color in Triticeae. Blue grain is the ancestral trait in Triticeae, whereas white grain caused by bHLH or MYB dysfunctions is the derived trait. HvbHLH1 and HvMYB1 have been the targets of selection in barley, and dysfunctions caused by deletion(s), insertion(s), and/or point mutation(s) in the vast majority of Triticeae species are accompanied by a change from blue grain to white grain. Wheat with white grains exhibits high seed vigor under stress. Artificial co-expression of ThbHLH1 and ThMYB1 in the wheat endosperm or aleurone layer can generate purple grains with health benefits and blue grains for use in a new hybrid breeding technology, respectively. Our study thus reveals that white grain may be a favorable derived trait retained through natural or artificial selection in Triticeae and that the ancient blue-grain trait could be regained and reused in molecular breeding of modern wheat.

BrGSTF12, an anthocyanin-related glutathione S-transferase gene, is essential for light-induced anthocyanin accumulation in zicaitai (Brassica Rapa Var. purpuraria)

BACKGROUND

Anthocyanins are a group of polyphenolic pigments that play essential biological roles and significantly influence the quality of agricultural produce. Bioinformatics approaches were employed to predict and identify potential genes involved in the sequestration of anthocyanins in Zicaitai (Brassica rapa var. purpuraria) utilizing data from the transcriptome database.

RESULTS

In this study 0-hour light (dark) and 8-hour light treatments of Zicaitai were examined using transcriptome analysis. RNA-seq analysis indicates that 24 important anthocyanin biosynthesis genes, including 5 PAL, 3 4CL, 3 CHS, 3 CHI, 2 F3H, 1 DFR, 2 ANS, and 5 UGFT were significantly differentially expressed between 0-hour and 8-hour light treatment. The transcript levels of the glutathione S-transferase gene, BrGSTF12, were significantly higher at 8 h compared to 0 h. BrGSTF12 expression level correlated with the patterns of anthocyanins content in each tissue of Zicaitai. Functional complementation in the Arabidopsis tt19 mutant further demonstrated that BrGSTF12 was involved in the transport of anthocyanins. Additionally, expression analysis showed that BrMYB114 levels were significantly elevated at 8 h, and dual-luciferase assays confirmed that BrMYB114 effectively trans-activated the promoter of the BrGSTF12 gene.

CONCLUSION

This study provides molecular evidence supporting the regulatory roles of BrGSTF12 and BrMYB114 in enhancing anthocyanin accumulation in Zicaitai under light induction. The findings contribute to a deeper understanding of the mechanisms behind anthocyanin biosynthesis and transport, offering valuable insights that could aid in breeding anthocyanin-rich crops, and paving the way for new opportunities in crop development.

AsNAC Genes: Response to High Mercury Concentrations in Allium sativum Seed Clove

Heavy metal contamination in soils is a growing concern due to anthropogenic activities, and Allium sativum (garlic) has shown tolerance to mercury pollution. We analyzed the physiological and molecular responses of garlic cloves exposed to HgCl2 at 0, 5000, 23,000, and 46,000 mg/kg for 2, 3, and 4 h. The germination percentage was lower than 46,000 mg/kg Hg for 4 h. We also analyzed the expression levels of NAC transcription factors and found that AsNAC11 had higher expression at 46,000 mg/kg at 2 h; AsNAC17 was underexpressed and the maximum was at 2 h at 23,000 mg/kg. AsNAC20 had the highest expression (30 times more than the control) at 3 and 4 h with 23,000 mg/Kg. AsNAC27 showed the highest expression at 3 h with 23,000 mg/kg. The tissues exhibited a maximum Hg bioconcentration factor of 0.037 at 23,000 mg/kg, indicating moderate mercury absorption. However, at a concentration of 46,000 mg/kg, the BCF decreased to 0.023. Our in-silico analysis revealed that the analyzed AsNACs are associated with various abiotic stress responses. This study provides valuable insights into genes that could be utilized for genetic improvement to enhance crop resistance to mercury soil contamination.

Integrated Transcriptomics and Metabolomics Reveal Key Genes and Metabolic Pathway in Flower and Fruit Color Formation of Cerasus humilis (Bge.) Sok

Anthocyanins play a pivotal role in determining the color diversity in the flowers and fruits of Cerasus humilis (Bge.) Sok. This study performed a metabolomic analysis of the flowers and fruits of two varieties differing in pigmentation phenotypes ('Jinou 1' and 'Nongda 5'), and the results indicated that the cyanidin, pelargonidin, paeonidin, and delphinidin were the main substances serving as the primary pigments contributing to their striking chromatic divergence between two varieties. Transcriptome profiling revealed that several key structural genes (ChCHS1, ChDFR, ChF3H, and ChF3'H) in the anthocyanin biosynthesis pathway exhibited significantly elevated expression levels in 'Jinou 1' compared to 'Nongda 5'. Further metabolomic and transcriptomic correlation analyses identified that ChMYB9 and ChMYB12 exhibited strong positive associations with anthocyanin pathway metabolites in both floral and fruit tissues. Notably, ChMYB9 displayed the strongest correlation with the metabolite profiles, suggesting it may serve as a core regulatory component of the anthocyanin biosynthesis. This research provides new insights into the regulatory mechanisms of anthocyanin biosynthesis in C. humilis.

The regulatory module MdCPCL-MdILR3L mediates the synthesis of ascorbic acid and anthocyanin in apple

Apple (Malus domestica Borkh.) is one of the most economically valuable fruit crops globally and a key dietary source for various nutrients. However, the levels of ascorbic acid (AsA) and anthocyanin, essential micronutrients for human health, are extremely low in the pulp of commonly cultivated apple varieties. In the present study, the second-generation hybrid strain of Xinjiang red-fleshed apple ('Zihong No. 1' × 'Gala') was used as the test material. The results revealed that AsA content was significantly higher in red-fleshed apple pulp than in non-red-fleshed varieties, and the expression of MdGLDH, a key gene in the D-mannose/L-galactose pathway, correlated strongly with AsA levels. Using the promoter of MdGLDH as bait, an R3-type MYB transcription factor (TF), MdCPC-like, was identified through yeast one-hybrid screening. Further analysis revealed that the overexpression of MdCPCL increased the AsA and anthocyanin levels in both callus and fruits, whereas MdCPCL knockdown led to a reduction in their levels. Moreover, the interaction between MdCPCL and the bHLH TF MdILR3-like was confirmed, forming the MdCPCL-MdILR3L complex. This complex significantly enhanced the transcription of downstream target genes MdGLDH and MdANS, promoting the synthesis of AsA and anthocyanins. This study contributes to further enrich the anabolic pathways of AsA and anthocyanin in apples and provides a theoretical foundation for the quality breeding of red-fleshed apple varieties.

Genetic basis of camouflage in an alpine plant and its long-term co-evolution with an insect herbivore

Camouflage through colour change can involve reversible or permanent changes in response to cyclic predator or herbivore pressures. The evolution of background matching in camouflaged phenotypes partly depends on the genetics of the camouflage trait, but this has received little attention in plants. Here we clarify the genetic pathway underlying the grey-leaved morph of fumewort, Corydalis hemidicentra, of the Qinghai-Tibet Plateau that by being camouflaged escapes herbivory from caterpillars of host-specialized Parnassius butterflies. Field experiments show that camouflaged grey leaves matching the surrounding scree habitat experience reduced oviposition by female butterflies and herbivory by caterpillars, resulting in higher fruit set than that achieved by green-leaved plants. The defence is entirely visual. Multi-omics data and functional validation reveal that a 254-bp-inserted transposon causes anthocyanin accumulation in leaves, giving them a rock-like grey colour. Demographic analyses of plant and butterfly effective population sizes over the past 500 years indicate that plant populations have been more stable at sites with camouflage than at sites with only green-leaved plants. In the recent past, populations of Parnassius butterflies have declined at sites with camouflaged plants. These findings provide insights into the genetics of a plant camouflage trait and its potential role in the rapidly changing dynamics of plant-herbivore interactions.

Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement

The tea plant stands as a globally cherished nonalcoholic beverage crop, but the genetic underpinnings of important agronomic and metabolomic traits remain largely unexplored. Here we de novo deep resequenced 802 tea plants and their relative accessions globally. By integrating public Camellia accessions, we constructed a comprehensive genome-wide genetic variation map and annotated deleterious mutations for 1,325 accessions. Population genetic analyses provided insights into genetic divergence from its relatives, different evolutionary bottlenecks, interspecific introgression and conservation of wild relatives. Our findings suggest the pivotal role of southwest China as the origin of tea plants, revealing the genetic diversity and domestication status of ancient tea plants. Genome-wide association studies herein identified thousands of substantial associations with leaf shape and metabolite traits, pinpointing candidate genes for crucial agronomic and flavor traits. This study illuminates the tea plant's evolution and provides references for tea plant design breeding.

LcbHLH107 actively suppresses the expression of LcDFR to repress anthocyanin biosynthesis in Litchi chinensis Sonn

Basic helix-loop-helix (bHLH) proteins have been recognized as activators of anthocyanin in many plant species, but their role as inhibitors of anthocyanin is seldom reported. In this study, LcbHLH107 was identified as a transcription repressor regulating anthocyanin biosynthesis in litchi. LcbHLH107 was up-regulated in the red hairy roots overexpressing LcMYB1, which was the key transcription activator in litchi anthocyanin biosynthesis. Dual luciferase assay and yeast one-hybrid assay confirmed that LcbHLH107 was regulated by LcMYB1. LcbHLH107 could suppresses anthocyanin accumulation through transient transformation in petunia leaves and overexpression in litchi callus. Moreover, LcbHLH107 directly bound to the promoter of LcDFR, and inhibited its expression. Furthermore, protein sequence mutation and functional verification revealed that the EAR motif was essential for the inhibitory function of LcbHLH107. In summary, LcbHLH107 is a repressor that inhibits anthocyanin biosynthesis in litchi, providing a negative feedback mechanism to regulate anthocyanin accumulation at transcriptional level.

Comprehensive analysis of the physiological, metabolome, and transcriptome provided insights into anthocyanin biosynthesis and degradation of Malus crabapple

Malus crabapple is highly regarded for its ornamental and garden applications, with leaf color changes serving as an essential indicator of aesthetic appeal. Despite this significance, studies focusing on crabapple leaf color transformations, particularly the fading of purplish-red hues, remain limited. This research investigates the physiological and molecular mechanisms driving leaf color changes in crabapple through physiological, transcriptional, and metabolic assays. Leaf color was analyzed across 86 crabapple varieties, with three representative varieties in different color development paths (the color change from young to mature stage) selected for detailed examination of gene expression and metabolite accumulation within the flavonoid biosynthetic pathway. Our findings revealed greater variation in young leaves compared to mature ones, along with higher stability in the 'Purple to Purple' (P-P) color path compared to the 'Green to Green' (G-G) and 'Purple to Green' (P-G) paths. The comprehensive analysis highlighted anthocyanins, particularly pelargonidin and peonidin 3-glucoside in green crabapple leaves and cyanidin in purplish-red crabapple leaves, as central to leaf color regulation. Transcriptomic analysis revealed that the fading of purplish-red is attributable to decreased accumulation of total anthocyanin and degradation of cyanidin. This process is governed by the down-regulation of anthocyanidin synthase (ANS) gene and the up-regulation of the anthocyanin degradation gene, peroxidase (PRX). Additionally, two transcription factors potentially involved in the regulation of cyanidin biosynthesis and two transcription factors regulating pelargonidin biosynthesis were identified. This study identifies candidate genes influencing anthocyanin accumulation in purplish-red leaves, providing a foundation for future investigations into leaf coloration mechanisms and crabapple breeding efforts.

Multiomic analysis reveals that the flavonoid biosynthesis pathway is associated with cold tolerance in Heracleum moellendorffii Hance

Heracleum moellendorffii Hance is a perennial herbaceous plant that is adaptable to cold environments and has both edible and medicinal value. Given that no reference genome for this species is available, we constructed a high-quality transcript isoform library using full-length transcriptome sequencing and conducted a comparative genomic analysis. Samples were obtained from plants that had been subjected to cold stress for 12, 24 and 36 hours (Cold_12, Cold_24, and Cold_36, respectively) and from control plants (Cold_0) that were not subjected to cold stress and used in transcriptome and nontargeted metabolome analyses. Compared with the genes expressed in CK (Cold_0), the number of differentially expressed genes (DEGs) in Cold 12, Cold_24, and Cold_36 increased gradually over time; plants subjected to 12, 24 and 36 hours of cold stress displayed 669, 6084, and 24,129 DEGs, respectively. The DEGs were clustered into 8 subclasses by k-means clustering; subclasses 2, 3, 4, and 7 were enriched in pathways related to "flavonoid biosynthesis". Nontargeted metabolome analysis revealed that 3719 annotated metabolites were shared by all four groups of samples. We identified 1186, 1087, and 1097 differentially accumulated metabolites (DAMs) in three comparisons: Cold_12 vs. CK, Cold_24 vs. CK, and Cold_36 vs. CK, respectively. The DAMs were predominantly enriched in the "flavonoid biosynthesis pathway". Through WGCNA, we obtained five modules and 29 flavonoid-related metabolites with extremely significant module-metabolite paired relationships (|correlation coefficient|> 0.9, P < 0.01). We analysed the DEGs and DAMs of the flavonoid biosynthetic pathway in H. moellendorffii Hance under cold stress and constructed a correlation network between transcription factors (TFs) and structural genes in the pathway. RT-qPCR was used to confirm the expression of four hub genes from the WGCNA, six TFs, and 15 structural genes of the flavonoid biosynthetic pathway. These data provide a foundation for functional genomics studies of H. moellendorffii Hance and contribute to the study of the molecular mechanisms and transcriptional regulation of flavonoid accumulation by TFs under cold stress conditions in plants.

Seed coat transcriptomic profiling of 5-593, a genotype important for genetic studies of seed coat color and patterning in common bean (Phaseolus vulgaris L.)

Common bean (Phaseolus vulgaris L.) market classes have distinct seed coat colors, which are directly related to the diverse flavonoids found in the mature seed coat. To understand and elucidate the molecular mechanisms underlying the regulation of seed coat color, RNA-Seq data was collected from the black bean 5-593 and used for a differential gene expression and enrichment analysis from four different seed coat color development stages. 5-593 carries dominant alleles for 10 of the 11 major genes that control seed coat color and expression and has historically been used to develop introgression lines used for seed coat genetic analysis. Pairwise comparison among the four stages identified 6,294 differentially expressed genes (DEGs) varying from 508 to 5,780 DEGs depending on the compared stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, and plant hormone signal transduction comprised the principal pathways expressed during bean seed coat pigment development. Transcriptome analysis suggested that most structural genes for flavonoid biosynthesis and some potential regulatory genes were significantly differentially expressed. Further studies detected 29 DEGs as important candidate genes governing the key enzymatic flavonoid biosynthetic pathways for common bean seed coat color development. Additionally, four gene models, Pv5-593.02G016100, 593.02G078700, Pv5-593.02G090900, and Pv5-593.06G121300, encode MYB-like transcription factor family protein were identified as strong candidate regulatory genes in anthocyanin biosynthesis which could regulate the expression levels of some important structural genes in flavonoid biosynthesis pathway. These findings provide a framework to draw new insights into the molecular networks underlying common bean seed coat pigment development.

Seasonal dynamics and molecular regulation of flavonoid biosynthesis in Cyclocarya paliurus (Batal.) Iljinsk

Introduction

Cyclocarya paliurus, an economically important species known for its high flavonoid content, has potential for industrial applications. Understanding the seasonal dynamics and molecular regulation of flavonoid biosynthesis in this species is crucial for optimizing its production.

Methods

We conducted an integrated analysis of transcriptomic and metabolomic data to identify key genes involved in flavonoid biosynthesis and regulation. Seasonal variation in flavonoid content and gene expression was examined, with a focus on the genes involved in the flavonoid synthesis pathway and their correlation with flavonoid levels.

Results

Flavonoid content peaked in August and declined towards November, with quercetin and kaempferol glycosides being the most abundant compounds. Pearson correlation analysis revealed significant relationships between the functional genes of the flavonoid synthesis pathway and flavonoid content. Seasonal variations in the expression of key biosynthetic genes (CHS, CHI, F3H, DFR, FLS) and regulatory transcription factors (MYB11, MYB12, MYB111, MYB75, MYB90, bHLH, WD40) were strongly correlated with flavonoid levels, particularly under environmental stress.

Discussion

These findings provide insights into the genetic regulation of flavonoid biosynthesis in C. paliurus and highlight the importance of seasonal and environmental factors. This knowledge has practical implications for industrial breeding and biotechnological applications, particularly in enhancing the functional properties of C. paliurus for industrial use. Our study establishes a foundation for future research aimed at optimizing flavonoid production in this species and exploring its potential for bioactive compound production.

Transcriptome analysis reveals potential medicinal ingredient synthesis in ornamental Dendrobium

Dendrobium is divided into ornamental and medicinal varieties due to ornamental and medicinal values. However, current research mainly focuses on medicinal Dendrobium, with less study on the medicinal value of ornamental Dendrobium. We analyzed the microstructures, active components of the stems from twelve ornamental Dendrobium, and explored the biosynthetic networks of these active components based on transcriptome sequencing. This study found the Dendrobium with the highest content of polysaccharide, alkaloid, and flavonoid was Dendrobium aphyllum (53.89 %), Dendrobium thyrsiflorum (2.11 %) and Dendrobium loddigesii (7.21 %). Further research revealed 9 DEGs associated with polysaccharide biosynthesis were highly expressed in D. aphyllum; 4 DEGs related to alkaloid biosynthesis were highly expressed in D. thyrsiflorum; 8 DEGs associated with flavonoid biosynthesis were highly expressed in D. loddigesii. This study revealed the potential medicinal value of ornamental Dendrobium and the synthetic mechanisms of its medicinal components, providing a foundation for the medical applications of ornamental Dendrobium.

Two glycoside hydrolase family 1 proteins mediate glycosylated modification at the 5-position of anthocyanin in grape hyacinth

Glycosylation modification of anthocyanins is important as a preceding step to acylation modification. Cyanidin-3-O-(p-coumaroyl)glucoside-5-O-malonylglucoside (Cy3pCG5MaG) is one of the major anthocyanin substances in blue-flowered grape hyacinth, but its 5-position glycosylation is unknown. Here, we identified two glycoside hydrolase family 1 genes, MaAGGT1 and MaAGGT5, which use acyl-glucose as a donor and are involved in the glycosylation modification of anthocyanins in grape hyacinth. MaAGGT1 and MaAGGT5 are localized in vacuoles and primarily expressed in the flowers, coinciding roughly with the accumulation of total anthocyanins and Cy3pCG5MaG. In vitro enzyme activity assays of recombinant proteins showed that MaAGGT1 is substrate-specific for Cy3G and Pt3G, while MaAGGT5 is substrate-specific for Mv3G. Suppressing the expression of MaAGGT1 or MaAGGT5 significantly inhibits the accumulation of total anthocyanins in blue-flowered grape hyacinth, but only MaAGGT1 affects the accumulation of Cy3pCG5MaG. Additionally, the anthocyanin activation factor MaMybA can bind to the promoters of MaAGGT1 and MaAGGT5, positively regulating their transcription, while MaAN2 binds only to the promoter of MaAGGT5, significantly enhancing its expression. In summary, our results provide evidence that two glycoside hydrolase family 1 proteins mediate the glycosylation modification at the 5-position of anthocyanins in grape hyacinth, with MaAGGT1 playing a key catalytic role in the formation of Cy3pCG5MaG.

Mutation in FvPAL2 leads to light red strawberry fruits and yellow-green petioles

In recent years, light red or white strawberries have attracted much attention because of their unusual color, however, the mechanism of strawberry color formation, especially light red strawberry color, is not well understood. By EMS mutagenesis of woodland strawberry (Fragaria vesca), we identified two mutants, rg40 and rg120, with light red fruit and yellow-green petiole, and allelic hybridization and BSA mixed-pool sequencing revealed that the phenotype was caused by mutation in the FvPAL2 protein in the anthocyanin synthesis pathway. Enzyme activity experiments showed that the mutant FvPAL2 protein barely catalyzed the substrate conversion normally, thus blocking anthocyanin synthesis, which in turn led to a decrease in anthocyanin accumulation in fruits and petioles. Analysis of the active pockets of the wild-type and mutant FvPAL2 proteins revealed that the mutant FvPAL2 could not bind to the substrate properly. The specific transcription factors FvMYB10 and FvMYB10L were further found to bind and activate the expression of FvPAL1 and FvPAL2 in both fruit and petiole. The discovery of the key site of FvPAL2 protein activity provides a clear modification target for the breeding of light red strawberry varieties, which has important application value.

A novel bHLH transcription factor, FabHLH110, is involved in regulation of anthocyanin synthesis in petals of pink-flowered strawberry

The pink-flowered strawberry is a kind of perennial herb that serves as both an ornamental plant with a range of red-colored petals and a food crop, which was produced by distant hybridization of Fragaria × Potentilla. Although there have been numerous reports on anthocyanin synthesis in strawberry fruits, the mechanism by which bHLH transcription factors regulate anthocyanin synthesis in strawberry red petals remains unclear. In this study, a total of 376 FabHLHs were finally identified, which were divided into 25 subfamilies. According to transcriptome sequencing, phylogenetic tree construction, correlation analysis and real-time fluorescence quantitative analysis, the differential gene FabHLH110 was screened out to regulate the synthesis of flower petal anthocyanin of pink-flowered strawberry. Specifically, transient overexpression of FabHLH110 in petals of pink-flowered strawberry increased anthocyanin accumulation, while virus-induced FabHLH110 gene silencing had the opposite effect, indicating FabHLH110 functioned as a positive regulator of anthocyanin biosynthesis. In addition, it was found that FabHLH110 could not bind to the promoter of FaDFR, FaANS, FaUGT and FaGST, which should interact with FaMYB10, FaMYB90 and FaMYB114 to form MBW complex to promote anthocyanin accumulation in fruit and petals of pink-flowered strawberry, respectively. Our findings provide new insight into the regulatory network of anthocyanin synthesis in petal of pink-flowered strawberry and a new strategy for breeding rich anthocyanin.

Multi-omics analysis of the accumulation mechanism of flavonoids in rice caryopsis under blue light

KEY MESSAGE

Blue light influences the MYB gene family, resulting in varying accumulations of different flavonoids in rice caryopsis at distinct developmental stages, with a higher concentration observed in the initial stage. The regulatory effect of blue light on plant flavonoids has been extensively documented; however, its influence on the development of rice caryopsis morphology remains unreported. Through the analysis of transcriptomes, proteomes, and metabolites, combined with Weighted Gene Co-expression Network Analysis (WGCNA), the accumulation of flavonoids in rice caryopsis under blue light at various developmental stages was thoroughly examined. Furthermore, four MYB family transcription factors (TFs) that significantly influence the structural genes involved in flavonoid biosynthesis were identified. The results indicate that the accumulation of flavonoids primarily occurs during the early stages of caryopsis development. Key structural genes, including PAL, 4CL, CHS, CHI, F3H, and FLS, are upregulated in both gene and protein expression when exposed to blue light. Moreover, the WGCNA analysis identified several TFs that may influence these genes, including Os08t0144000-01 and Os01t0695900-01, as well as the proteins Q7F3D6, Q2QM89, A0A0P0W9C3, and Q6ZDM0, all of which belong to the MYB family. The research has enhanced our understanding of flavonoid accumulation in rice caryopsis when exposed to blue light. It also establishes a framework for the synthesis of secondary metabolites induced by blue light, thereby creating more opportunities to enhance the quality of horticultural plants.

Pan-WD40ome analysis of 26 diverse inbred lines reveals the structural and functional diversity of WD40 proteins in maize

BACKGROUND

The WD40 repeat proteins are crucial components of eukaryotic genomes and contribute to a wide array of plant developmental processes and environmental interactions. However, the true extent of intraspecific WD40 diversity in plants is unclear.

RESULTS

We defined a nearly complete species-wide pan-WD40ome in maize based on the published genome sequences of 26 nested association mapping (NAM) population founders. The pan-WD40ome largely saturated with inclusion of approximately 20 inbred lines, with about 95% of the pan-WD40ome being present in at least two founders. The architectural diversity of the WD40 domains, additional domains, and consequent spatial protein structures suggested the functional diversity of the maize pan-WD40ome. This finding was supported by significant associations between 87 WD40 genes and 19 agronomic, 3 kernel-quality, and 3 biotic-stress traits, as well as the multiple molecular pathways through which the trait-associated WD40 genes were predicted to function. In addition, WD40 genes exhibited abundant genomic variations among the NAM founders. Sequence analysis indicated that gene duplications and gene translocations caused by Helitron transposons may play important roles in the amplification of WD40 genes during the evolution of the maize WD40 gene family.

CONCLUSIONS

In summary, this study provides a comprehensive framework for understanding the structural and functional diversity of the pan-WD40ome in maize and other agronomically important species with complex genomes, as well as excellent candidate genes/alleles for maize genetic improvement.

CsMYB308 as a repressive transcription factor inhibits anthocyanin biosynthesis in tea plants

Anthocyanins in tea (Camellia sinensis) leaves enhance tea quality due to their unique health benefits. MYB transcription factors are crucial in regulating anthocyanin biosynthesis in various plant species. In this research, a typical R2R3 repressive transcription factor CsMYB308 was identified which includes an EAR motif that belongs to the SG4 subfamily and was localized in the nucleus. Antisense oligonucleotide (asODN)-mediated CsMYB308 silencing revealed that the anthocyanin synthesis of structural genes was up-regulated. Furthermore, DNA affinity purification sequencing (DAP-seq) screened downstream genes regulated by CsMYB308. Dual-luciferase reporter (DLR) results showed that CsMYB308 suppressed anthocyanin biosynthesis by regulating the transcriptional activity of CsF3'5'H, CsDFR, and CsANS and electrophoretic mobility shift assay (EMSA) proved the concrete binding sites. In addition, we elucidated the molecular mechanism of Zijuan accumulating anthocyanin at an optimal concentration by shading experiment in summer. The results could provide an agronomic strategy to enhance the utilization of fresh leaves in summer. This study also presented a new insight of the regulatory pathway involved in anthocyanin biosynthesis in tea plants.

Identification of key genes controlling anthocyanin biosynthesis in the fruits of a bud variety of Tarocco blood-orange

Tarocco is a prevalent blood-orange variety in China, has a bud variant identified in Wenzhou City. To characterize the quality traits and molecular mechanisms underlying inhibition of anthocyanin synthesis in this variety, we collected fruits of Tarocco (WT) and the bud variant Ouya (MT) at nine developmental stages. Their anthocyanin, soluble sugar, and organic acid profiles were examined, and transcriptomes and metabolites were analyzed at three developmental stages. The results revealed that MT is a new blood orange variety with weak anthocyanins and a better sugar-acid ratio than the WT. The content of anthocyanin in MT fruits were significantly lower than those in WT fruits, especially cyanidin-like anthocyanins, while the flavone contents exhibited no remarkable variation. A total of 64 differentially expressed genes (DEGs), including five transcription factors (TFs), five methylation-related genes, and one flavonoid biosynthesis gene, were identified between WT and MT at three fruit developmental stages. The potential regulatory networks of these TFs were further constructed using weighted gene co-expression network analysis.Furthermore, in MT fruit treated with the 5-azacytidine, we observed hypomethylation of anthocyanins accumulated in the pulp and the promoters and genebodies of some anthocyanin synthesis-related genes. These results provide new insights into the influence of DNA methylation on anthocyanin accumulation in MT and also provide support for the promotion of MT as a new variety.

Transcriptome and Metabolome Analyses Reveal the Mechanism of Color Differences in Pomegranate (Punica granatum L.) Red and White Petals

Pomegranate (Punica granatum L.) is an important economic tree, possessing both edible and ornamental value. Flower color is an important ornamental trait of pomegranate, but the color formation pattern and related molecular mechanisms of pomegranate petals are still unclear. In this study, we conducted physiological, transcriptomic, and metabolomic studies on the petals of Tunisia and White pomegranate varieties during the blooming stage. The results showed that compared to White petals, the contents of anthocyanin, carotenoid, and sucrose in Tunisia petals were significantly increased, while the flavonoid content was significantly decreased. Through RNA-seq, 23 DEGs were identified in the anthocyanin synthesis, and 3 DEGs were identified in the carotenoid synthesis. Transcription factor genes such as MYB, bHLH, WRKY, and MADS were identified as key candidates for regulating anthocyanin metabolism. Metabolomic analysis revealed that eight DEMs are associated with anthocyanin synthesis and three DEMs are associated with carotenoid synthesis. In addition, caffeic acid and its derivatives were significantly upregulated in Tunisia petals. In summary, we propose the following hypothesis: the accumulation of anthocyanins and carotenoids is the reason for the red color of Tunisian petals, and the upregulation of structural genes, including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, DFR, ANS, PSY, and LCYB, leads to an increase in their content. Transcription factor genes such as MYB, bHLH, bZIP, MADS, and WRKY may also play a positive role in anthocyanin accumulation. The research results provide a basis for the theory of pomegranate petal color formation.

AoMYB114 transcription factor regulates anthocyanin biosynthesis in the epidermis of tender asparagus stems

Introduction

Asparagus is a valuable vegetable, and its edible part is a tender stem. The color of the tender stem epidermis is an important trait. In particular, purple asparagus is rich in anthocyanins. However, the molecular mechanisms underlying anthocyanin accumulation in purple asparagus remains unclear.

Methods

The white variety 'Jinguan' (JG), the green variety 'Fengdao 2' (FD), and the purple variety 'Jingzilu 2' (JZ) were compared using physiological and transcriptomic analysis. High-performance liquid chromatography and real-time quantitative polymerase chain reaction were employed to detect anthocyanins and validate gene expression.

Results

Cyanidin 3-glucoside and cyanidin 3-rutinoside were detected as the main anthocyanins in JZ. Transcriptome data demonstrated that 4,694 and 9,427 differentially expressed genes (DEGs) were detected in the JZ versus FD and JZ versus JG control groups, respectively. These DEGs were significantly enriched in pathways associated with anthocyanin accumulation, including phenylalanine metabolism, phenylpropanoid biosynthesis, and flavonoid biosynthesis. A total of 29 structural genes related to anthocyanin biosynthesis were identified. The expression of these structural genes was higher in JZ than in FD and JG, thereby activating the anthocyanin biosynthesis pathway. Additionally, a candidate gene, AoMYB114, was identified based on transcriptomic data. The expression of AoMYB114 was associated with anthocyanin accumulation in different tissues. Further research found that overexpression of AoMYB114 activated the anthocyanin biosynthesis pathway. It promoted leaf pigment accumulation in transgenic Arabidopsis.

Discussion

These findings demonstrate that AoMYB114 positively regulated anthocyanin biosynthesis. This study elucidates the molecular mechanism underlying purple coloration in asparagus. It provides important insights for improving asparagus quality and for breeding high-anthocyanin varieties.

Molecular mapping of candidate genes in determining red color of perilla leaf

Perilla frutescens is a traditional medicinal plant and functional food in Asian communities, characterized by distinct red and green leaf types that have significant phenotypic and medicinal implications. However, the genetic mechanisms controlling anthocyanin synthesis in this species remain unclear. Genetic analysis serves as a powerful tool for investigating the pivotal genes and regulatory mechanisms governing anthocyanin accumulation in red and green perilla. In this study, an F2 segregation population was constructed from a hybrid of red and green perilla, and representative samples were subjected to mix-sequencing using BSA-seq and BSR-seq. A 6.0 Mb candidate region on chromosome 8 was identified, pinpointing PfMYB113b, PfC4H1, and PfF3H as key genes involved in anthocyanin biosynthesis. The insertion of a repeat sequence in the promoter of PfMYB113b leads to alterations in gene expression levels. Furthermore, PfMYB113b regulates the transcription of PfC4H1 and PfF3H, thereby influencing anthocyanin synthesis. These findings enhance our understanding of the genetic regulatory mechanisms underlying leaf coloration in perilla.

Functional characterization in Chimonobambusa utilis reveals the role of bHLH gene family in bamboo sheath color variation

Introduction

The basic helix-loop-helix (bHLH) proteins are a large family of transcription factors that are essential to physiology, metabolism, and development. However, the available information is limited about the bHLH gene family in Chimonobambusa utilis, which is widely cultivated in China because of its high-quality and economic value. C. utilis cultivars exhibit five natural color variations in their shoot sheaths, but the molecular mechanism behind this color diversity remains unclear.

Methods

De novo assembly was employed to obtain gene sequences. To identify pathways related to color formation, GO enrichment analysis was performed on the 44,255 functionally annotated unigenes.

Results

The transcriptomic analysis of C. utilis yielded a total of 195,977 transcripts and 75,137 unigenes after removing redundancy. The enrichment results revealed that four pathways were most strongly associated with color formation. Phylogenetic, conserved motif, and protein-protein interaction analyses, along with qRT-PCR validation, confirmed CubHLH17's role in red sheath color.

Discussion

This research not only deepens insights into the functional roles of CubHLH genes but also lays the foundation for genetic improvement of bamboo species. We suggest that these findings will contribute to both scientific research and commercial bamboo cultivation through gene editing technology in the future.

MdZFP7 integrates JA and GA signals via interaction with MdJAZ2 and MdRGL3a in regulating anthocyanin biosynthesis and undergoes degradation by the E3 ubiquitin ligase MdBRG3

Jasmonic acid (JA) and gibberellin (GA) coordinate many aspects of plant growth and development, including anthocyanin biosynthesis. However, the crossover points of JA and GA signals and the pathways through which they interact to regulate anthocyanin biosynthesis are poorly understood. Here, we investigated the molecular mechanism by which the zinc finger protein (ZFP) transcription factor Malus domestica ZFP7 (MdZFP7) regulates anthocyanin biosynthesis by integrating JA and GA signals at the transcriptional and post-translational levels. MdZFP7 is a positive regulator of anthocyanin biosynthesis, which fulfills its role by directly activating the expression of MdMYB1 and enhancing the transcriptional activation of MdWRKY6 on the target genes MdDFR and MdUF3GT. MdZFP7 integrates JA and GA signals by interacting with the JA repressor apple JASMONATE ZIM-DOMAIN2 (MdJAZ2) and the GA repressor apple REPRESSOR-of-ga1-3-like 3a (MdRGL3a). MdJAZ2 weakens the transcriptional activation of MdMYB1 by MdZFP7 and disrupts the MdZFP7-MdWRKY6 interaction, thereby reducing the anthocyanin biosynthesis promoted by MdZFP7. MdRGL3a contributes to the stimulation of anthocyanin biosynthesis by MdZFP7 by sequestering MdJAZ2 from the MdJAZ2-MdZFP7 complex. The E3 ubiquitin ligase apple BOI-related E3 ubiquitin-protein ligase 3 (MdBRG3), which is antagonistically regulated by JA and GA, targets the ubiquitination degradation of MdZFP7. The MdBRG3-MdZFP7 module moves the crosstalk of JA and GA signals from the realm of transcriptional regulation and into the protein post-translational modification. In conclusion, this study not only elucidates the node-role of MdZFP7 in the integration of JA and GA signals, but also describes the transcriptional and post-translational regulatory network of anthocyanin biosynthesis with MdZFP7 as the hub.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Potential Molecular Mechanism Underlying Callus Browning in Paeonia ostii

Callus browning is a significant problem that hinders plant tissue regeneration in Paeonia ostii "Fengdan" by causing cell death and inhibiting growth. However, the molecular mechanism underlying callus browning in P. ostii remains unclear. In this study, we investigated the metabolites and potential regulatory genes involved in callus browning of P. ostii using metabolomic and transcriptomic analyses. We found a significant accumulation of phenolic compounds in the browned callus, represented by flavonoid compounds. Notably, the accumulations of luteotin and disomentin were higher in browning calli compared to non-browning calli. Transcriptomic analysis identified that candidate genes associated with flavonoid biosynthesis, including flavonoid 3-hydroxylase (PoF3H) and flavone synthase II (PoFNSII), were highly expressed in the browned callus of P. ostii "Fengdan". Weighted gene co-expression network analysis (WGCNA) further highlighted that polyphenol oxidase (PoPPO) which encoded polyphenol oxidase, together with flavonoid biosynthesis-related genes such as flavanone 3-hydroxylase (PoF3H) and flavonone Synthase II (PoFNSII), as well as cellular totipotency-related genes wuschel-related homeobox 4 (PoWOX4), were involved in callus browning. Based on these findings, we proposed the molecular mechanism by which flavonoid accumulation, polyphenol oxidation, and cellular totipotency pathways contribute to callus browning in P. ostii. Our study provides new insights into the molecular mechanism underlying callus browning and offers the foundations to facilitate the establishment of an efficient plant tissue regeneration system in P. ostii.

The transcription factor VvMYB44-1 plays a role in reducing grapevine anthocyanin biosynthesis at high temperature

High temperature reduces anthocyanin accumulation in various horticultural plants. However, the molecular mechanisms underlying the high-temperature-induced reduction of anthocyanin in grape (Vitis vinifera) remain poorly understood. In this study, VvMYB44-1 was identified as a transcriptional repressor of anthocyanin biosynthesis in grape berries, and its gene expression was strongly induced by high-temperature treatment. Overexpression of VvMYB44-1 inhibited anthocyanin accumulation in both grape berries and tobacco (Nicotiana tabacum) by repressing the transcription of the anthocyanin biosynthesis genes dihydroflavonol-4-reductase (VvDFR) and UDP-glucose flavonoid-3-O-glucosyltransferase (VvUFGT). Furthermore, the interaction between VvMYB44-1 and VvWDR2 competitively inhibited the formation of the MYB-bHLH-WD40 (MBW) activation complex and weakened the transcriptional activity of the complex, thereby decreasing anthocyanin accumulation. Additionally, VvMYB44-1 facilitated cytokinin (CK) accumulation by upregulating the expression of the CK synthesis gene lonely guy 8 (VvLOG8) and inhibiting the CK degradation gene CK oxidase 4(VvCKX4), thus contributing to CK-mediated anthocyanin inhibition in grape berries. Moreover, the inhibitory effect of VvMYB44-1 on anthocyanin biosynthesis and its downstream target genes was weakened with the deletion of the ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motif, indicating that the EAR motif is indispensable for the inhibitory effect of VvMYB44-1 on anthocyanin biosynthesis in grapes. These results provide insights into the regulatory network of VvMYB44-1 in high-temperature-mediated anthocyanin biosynthesis in grapes.

5-Aminolevulinic acid activates the MdWRKY71-MdMADS1 module to enhance anthocyanin biosynthesis in apple

5-Aminolevulinic acid (ALA), as a natural plant growth regulator, is well known for promoting red fruit coloring by enhancing anthocyanin accumulation. However, the underlying mechanisms remain elusive. In this study, we firstly demonstrated that ALA upregulates gene expression of the transcription factor MdMADS1, which in turn directly binds to and activates transcription of the key anthocyanin biosynthetic genes, MdCHS and MdUFGT. Then, we identified a novel WRKY transcription factor, MdWRKY71, that interacts with MdMADS1. Through gene manipulation, we revealed that MdWRKY71 plays a pivotal role in ALA-induced anthocyanin accumulation, highlighting its regulatory significance in this process. Further investigation unveiled that MdWRKY71 not only activates MdMADS1 transcription but also enhances its transcriptional activation on its target genes, MdCHS and MdUFGT. Additionally, we discovered that MdWRKY71 independently binds to and activates the transcription of two other anthocyanin biosynthetic genes, MdANS and MdDFR. The protein-protein interaction between MdWRKY71 and MdMADS1 amplifies the transcriptional activation of these genes by MdWRKY71. These findings delineate a fine and complex regulatory framework where MdWRKY71 and MdMADS1 coordinately regulate anthocyanin biosynthesis in apples, providing new insights into the molecular control of fruit coloration and offering potential target genes for breeding aimed at enhancing fruit quality.

The nuclear and cytoplasmic colocalization of MdGST12 regulated by MdWRKY26 and MdHY5 promotes anthocyanin accumulation by forming homodimers and interact with MdUFGT and MdDFR under light conditions in Malus

The glutathione S-transferase (GST) gene family participates in the sequestration of anthocyanins into vacuoles. In this study, MdGST12 was identified as a candidate gene during light-induced anthocyanin accumulation. The methylation levels of the MdGST12 promoter exhibited marked differences among apple fruit treated with different light intensities. Interestingly, it was revealed that MdGST12 was localized in both the cytoplasm and nucleus. Moreover, MdHY5 and MdWRKY26 bind to the G-box and W-box cis-elements within the MdGST12 promoter, respectively. Instantaneous and stable transformation in plantlets, fruit, and calli, confirmed the role of MdGST12 and MdWRKY26 in promoting anthocyanin accumulation in apples. Moreover, the silencing of MdGST12 or MdWRKY26 by RNA interference significantly damaged the anthocyanin accumulation. Surprisingly, we found that MdGST12 could act as a transactivator and that the interaction between MdGST12 and MdDFR further enhances transcriptional activation of the MdDFR promoter. Moreover, MdGST12 also interacts with MdUFGT. Further study revealed that MdGST12 could interact with itself forming homodimers in the nucleus. Taken together, our study first revealed that MdGST12 regulated by MdWRKY26 and MdHY5 interacts with MdDFR and enters the nucleus, enhancing the transcriptional level of MdDFR and promoting anthocyanin accumulation in Malus under light conditions. It first revealed the complexity of GST's function in addition to the function of transferases and transporters in plants.

Metabolomics analysis reveals crucial effects of arbuscular mycorrhizal fungi on the metabolism of quality compounds in shoots and roots of Camellia sinensis L

Arbuscular mycorrhizal fungi (AMF) are known as plants' mutualists to enhance plant growth, but their impact on the quality-related metabolites in Camellia sinensis still needs to be studied. In this study, the 2-year-old potted C. sinensis cv. 'Longjing 43' was inoculated with AMF Rhizophagus irregularis to examine the effect of AMF colonization for 3 months on plant growth, photosynthesis, and changes in metabolomics and associated gene expression in the shoots and roots of tea plants. The results showed that AMF not only promoted the growth of tea plants but also significantly up-regulated the total contents of flavonoids and free amino acids, especially the anthocyanins, flavanols, GABA, and arginine. Consistently, the expression of genes such as F3H, DFR, LAR, ANR, UFGT, GDH, and GS in tea shoots was induced by AMF. Further studies found that transcription factors MYBs and HY5, as well as phytohormone strigolactones, were induced by AMF, which may participate in the regulatory mechanism controlling the metabolism of tea-quality compounds. These findings revealed regulatory mechanisms through which AMF affected tea quality and provided a theoretical basis for the application of AMF in tea gardens to improve the economic value and health benefits of tea.

Natural pigments derived from plants and microorganisms: classification, biosynthesis, and applications

Pigments, as coloured secondary metabolites, endow the world with a rich palette of colours. They primarily originate from plants and microorganisms and play crucial roles in their survival and adaptation processes. In this article, we categorize pigments based on their chemical structure into flavonoids, carotenoids, pyrroles, quinones, azaphilones, melanins, betalains, flavins, and others. We further meticulously describe the colours, sources, and biosynthetic pathways, including key enzymatic steps and regulatory networks that control pigment production, in both plants and microorganisms. In particular, we highlight the role of transport proteins and transcription factors in fine-tuning these pathways. Finally, we introduce the use of pigments in practical production and research, aiming to provide new insights and directions for the application of coloured compounds in diverse fields, such as agriculture, industry, and medicine.

Association analyses reveal both anthropic and environmental selective events during eggplant domestication

Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the genome-wide association of historical genebank phenotypic data on a genotyped worldwide collection of 3449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a genotype-environment association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.

Enrichment of rice endosperm with anthocyanins by endosperm-specific expression of rice endogenous genes

A diet rich in anthocyanins can benefit human health against a broad spectrum of human diseases due to the high antioxidant activities of anthocyanins. Enrichment of anthocyanins in the starchy endosperm of rice is an effective solution to provide nutritional food in human diets. However, previous attempts failed to engineer anthocyanin biosynthesis in the rice endosperm by transgenic expression of rice endogenous genes. In this study, four rice endogenous genes, OsDFR (encoding dihydroflavonol 4-reductase), OsRb (encoding a bHLH family transcription factor), OsC1 (encoding an R2R3-MYB-type transcription factor) and OsPAC1 (encoding a WD40 class protein), were employed to rebuild the anthocyanin biosynthesis pathway in the rice endosperm. Endosperm-specific expression of OsDFR-OsRb-OsC1 (DRC) or OsDFR-OsPAC1-OsRb-OsC1 (DPRC) resulted in transgenic rice germplasm with dark purple grains. The expression of endogenous anthocyanin biosynthesis-related genes was significantly upregulated in the transgenic lines. Metabolomics analysis revealed a substantial increase in flavonoids flux, including 12 anthocyanins, in the polished grains of these transgenic lines. Our findings demonstrated that ectopic expressing a minimal set of three rice endogenous genes enabled de novo anthocyanin biosynthesis in the rice endosperm. This study contributes valuable insights into the molecular mechanisms underlying rice organ coloration and provides valuable guidance for future anthocyanin biofortification in crops.

A genus-specific R2R3 MYB transcription factor, CsMYB34, regulates galloylated catechin biosynthesis in Camellia sinensis

Galloylated catechins are the dominant polyphenols in Camellia sinensis (L.) O. Kuntze. The mechanisms responsible for accumulation of these specialized metabolites in tea plants remains unclear. This paper presents an extended member of subgroup 5 of transcription factors R2R3-MYB, CsMYB34, as a critical gene specifically regulating galloylated catechin biosynthesis. CsMYB34 has a TT2-type motif [VIRTKATRCSKVFIP]. Its transcription levels were positively correlated with galloylated catechin content in 19 tea varieties, with correlation coefficients ≥0.79. Suppression of CsMYB34 expression caused a significant decrease in galloylated catechin content, as well as reduced expression levels of the key galloylated catechin biosynthesis gene CsSCPL4. Yeast one-hybrid (Y1H), electrophoretic mobile shift assay (EMSA) and dual-luciferase reporter system (DLR) showed that CsMYB34 interacts directly with the promoter region of CsSCPL4, thereby upregulating its transcription. This research indicates that the CsMYB34 transcription factor selectively modulates the biosynthetic pathway of galloylated catechins, thereby offering a plausible rationale for the observed elevated levels of these compounds in tea leaves.

The candidate gene SibHLHA regulates anthocyanin-driven purple pigmentation in Sesamum indicum flowers

Anthocyanins not only serve as critical pigments determining floral hues but also play essential roles in attracting insects for pollination, feeding animals and mitigating abiotic stress. However, the molecular mechanisms underlying the regulation of flower color in sesame has not yet been reported. In this study, an F2 population was constructed by crossing 'Ganzhi 9' (purple-flowered) with 'BS377' (white-flowered). Genetic analysis revealed that purple flower is controlled by a single locus named as SiFC (Sesamum indicum flower color). Using the BSA-seq approach, SiFC was preliminarily identified on chromosome 6, which was further mapped to a 473 kb interval using Kompetitive Allele Specific PCR (KASP) marker analysis. Moreover, functional annotation, expression profiling, and sequence analyses confirmed that the SibHLHA (Sesame10992) was the most likely candidate gene for SiFC. In addition, SibHLHA, highly homologous to AtTT8 (a key regulator in the anthocyanin synthesis pathway), was found to interact with WER-like or TTG1 proteins, enhancing anthocyanin accumulation in tobacco leaves. Furthermore, an SNP in the second exon of Sibhlha (BS377 variant) was found to alter the encoding amino acids, which affected Sibhlha binding to MYB protein and showed low anthocyanin in tobacco leaves compared with SibHLHA binding with WER-like or TTG1 proteins. These findings not only deepen our understanding of the molecular mechanisms controlling sesame corolla color, but also provide valuable insights for developing ornamental and consumable sesame varieties.

Integrative analysis of the metabolome and transcriptome provides insights into the mechanisms of flavonoid biosynthesis in Polygonatum

A noteworthy group of culinary and medicinal plants is Polygonatum species. They are known for their abundant flavonoid compound-rich rhizomes, which have antioxidative and anticancer activities. Using Polygonatum sibiricum Red (SXHZ) and Polygonatum kingianum var. grandifolium (HBES), we conducted transcriptome and metabolomic investigations to look into the molecular processes that control the manufacture of these flavonoids in Polygonatum plants. Seven distinct flavonoid metabolites were identified by the analytical data, with phloretin exhibiting a notable differential expression in the biosynthetic pathway. 30 genes with differential expression were found in both plants after further investigation, five of which are members of the transcription factor family associated with MBW. Thus, we suggest that Phloretin and the genes belonging to the MYB-related transcription factor family play a crucial role in controlling the flavonoid biosynthesis pathway in Polygonatum. This work lays the groundwork for a deeper comprehension of the biosynthesis and metabolic processes of flavonoids in Polygonatum, serving as an invaluable resource for the development of the polygonatum-related pharmaceutical industries as well as for the future breeding of Polygonatum plants with higher flavonoid content.

Metabolomic and Transcriptomic Analyses Reveal the Factors Underlying Mature Fruit Pericarp Color Variations in the 'Xinli No. 7' Pear (Pyrus sinkiangensis)

Background/Objectives: The 'Xinli No. 7' pear is a new pear variety with the advantages of early ripening, high quality, high storage resistance, and a long shelf life. Peel color is an important appearance-related trait and an important indicator of fruit quality and commercial value. Methods: In this study, we investigated the polyphenol compound biosynthesis metabolic pathway in the fruit pericarp of 'Xinli No. 7' pear using metabolomic and transcriptomic approaches, and qRT-PCR was used for the relative expression analysis of 21 DEGs associated with flavonoid biosynthesis. Results: A total of 128 phenolic compounds were identified, along with 1850 differently expressed genes (DEGs) in peels of different colors. Caftaric acid, apigenin, astragalin, phlorizin, prunin, taxifolin, rutin, naringenin, and their derivatives were abundant in the peel of 'Xinli No. 7' pear. An integrated analysis of transcriptomic and metabolomic data revealed that one PGT1, one LAR, two ANS, three 4CL, one CHS, one DFR, and one CHI gene involved in flavonoid biosynthesis exhibited markedly different expression levels in the fruit pericarp of 'Xinli No. 7' pear. Metabolic profiling of pear skin led to the identification of polyphenol substances involved in the flavonoid biosynthetic process and revealed 16 flavonoid compounds with high accumulation in pear fruit with red skin (PR). Notably, MYBs (25), bHLHs (18), WRKYs (15), NACs (15), ERFs (15), and MADs (2) may also contribute to the accumulation of flavonoid metabolites and the biosynthesis of anthocyanins in the peel of 'Xinli No. 7'. Conclusions: Therefore, our results demonstrate the key role of phenolic compounds and candidate transcription factors involved in the peel color formation of 'Xinli No. 7' pear fruit.

Genome-Wide Identification of the WD40 Gene Family in Walnut (Juglans regia L.) and Its Expression Profile in Different Colored Varieties

The walnut (Juglans regia) is a woody oilseed crop with high economic and food value as its kernels are edible and its hulls can be widely used in oil extraction and plugging, chemical raw materials, and water purification. Currently, red walnut varieties have emerged, attracting consumer interest due to their high nutritional values as they are rich in anthocyanins. WD40 is a widespread superfamily in eukaryotes that play roles in plant color regulation and resistance to stresses. In order to screen for JrWD40 associated with walnut color, we identified 265 JrWD40s in walnuts by genome-wide identification, which were unevenly distributed on 16 chromosomes. According to the phylogenetic tree, all JrWD40s were classified into six clades. WGD (Whole genome duplication) is the main reason for the expansion of the JrWD40 gene family. JrWD40s were relatively conserved during evolution, but their gene structures were highly varied; lower sequence similarity may be the main reason for the functional diversity of JrWD40s. Some JrWD40s were highly expressed only in red or green walnuts. In addition, we screened 16 unique JrWD40s to walnuts based on collinearity analysis. By qRT-PCR, we found that JrWD40-133, JrWD40-150, JrWD40-155, and JrWD40-206 may regulate anthocyanin synthesis through positive regulation, whereas JrWD40-65, JrWD40-172, JrWD40-191, JrWD40-224, and JrWD40-254 may inhibit anthocyanin synthesis, suggesting that these JrWD40s are key genes affecting walnut color variation.

PSC1, a basic/helix-loop-helix transcription factor controlling the purplish-red testa trait in peanut

Seed color is a key agronomic trait in crops such as peanut, where it is a vital indicator of both nutritional and commercial value. In recent years, peanuts with darker seed coats have gained market attention due to their high anthocyanin content. Here, we used bulk segregant analysis to identify the gene associated with the purplish-red coat trait and identified a novel gene encoding a basic/helix-loop-helix transcription factor, PURPLE RED SEED COAT1 (PSC1), which regulates the accumulation of anthocyanins in the seed coat. Specifically, we found that a 35-bp insertion in the PSC1 promoter increased the abundance of PSC1 mRNA. Transcriptomic and metabolomic analyses indicated that the purplish-red color of the seed coat was the result of decreased expression of anthocyanidin reductase (ANR), leading to increased accumulation of delphinidin, cyanidin, and pelargonidin derivatives. Further analysis revealed that PSC1 interacts with AhMYB7 to form a complex that specifically binds to the ANR promoter to suppress its expression, resulting in increased anthocyanin accumulation. Moreover, overexpression of PSC1 increased anthocyanin content in Arabidopsis thaliana and peanut callus. Our study reveals a new gene that controls seed coat color by regulating anthocyanin metabolism and provides a valuable genetic resource for breeding peanuts with a purplish-red seed coat.

Comprehensive genomic analysis of SmbHLH genes and the role of SmbHLH93 in eggplant anthocyanin biosynthesis

KEY MESSAGE

SmbHLH93can activate the expression of SmCHS, SmANS, SmDFR and SmF3H.Overexpression of SmbHLH93promotes anthocyanin biosynthesis. SmbHLH93can interact with SmMYB1 to promote anthocyanin accumulation. As an outstanding source of anthocyanins, eggplant (Solanum melongena L.) is extremely beneficial for human health. In the process of anthocyanin biosynthesis in eggplant, the basic helix-loop-helix (bHLH) transcription factor family plays a crucial role. However, the bHLH gene family is extensive, making it difficult to systematically screen and analyze their functions using conventional methods. We studied the phylogeny, gene structure, conserved motifs, promoter element, and chromosomal location of the 166 SmbHLH genes in the recently released eggplant genome. Through the analysis of transcriptomic data of eggplant peel treated with light, it was found that SmbHLH93 was the most responsive to light among those of unknown function. Additionally, it was discovered that SmbHLH93 plays a positive regulatory role in anthocyanin synthesis through dual-luciferase reporter assay(dual-LUC) and genetic transformation in Arabidopsis (Arabidopsis thaliana). Furthermore, experiments involving yeast two-hybrid (Y2H), luciferase complementation assay (Split-LUC), and tobacco transient transformation demonstrated that SmbHLH93 has the ability to interact with SmMYB1 in order to enhance anthocyanin accumulation. This study will serve as a foundation for exploring the role of SmbHLH transcription factors in anthocyanin biosynthesis in the future.

AaMYB61-like and AabHLH137 jointly regulate anthocyanin biosynthesis in Actinidia arguta

BACKGROUND

Red Actinidia arguta has recently become highly popular because of its red appearance resulting from anthocyanin accumulation, and has gradually become an important breeding direction. However, regulators involved in anthocyanin biosynthesis have not been fully characterized in A. arguta.

RESULTS

Here, we demonstrated that a key R2R3-MYB transcription factor, AaMYB61-like, plays a crucial role in A. arguta anthocyanin biosynthesis. The RT-qPCR results revealed that transient overexpression of AaMYB61-like in A. arguta fruit at 90-100 DAFB significantly promoted anthocyanin biosynthesis, as did the gene expression levels of AaCHS, AaCHI, AaF3H, AaLDOX, and AaF3GT, whereas the result of VIGS revealed the opposite results in A. arguta fruit at 105-115 DAFB. A transcriptional activation assay indicated that AaMYB61-like exhibited transcriptional activation activity. Y1H and LUC assays revealed that AaMYB61-like activates the promoters of AaCHS, AaLDOX, and AaF3GT. In addition, AabHLH137 was found to be related to fruit color from the transcriptome data. We demonstrated that AaMYB61-like promotes anthocyanin biosynthesis by interacting with AabHLH137 via Y2H, BiFC, and Agrobacterium-mediated co-transformation.

CONCLUSIONS

Our study not only reveals the functions of AaMYB61-like and AabHLH137 in anthocyanin regulation, but also broadly enriches color regulation theory, establishing a foundation for clarifying the molecular mechanism of fruit coloration in kiwifruit.

Spatial and Temporal Regulation of Flower Coloration in Cymbidium lowianum

Flower color is a crucial trait that attracts pollinators and determines the ornamental value of floral crops. Cymbidium lowianum, one of the most important breeding parent of Cymbidium hybrids, has two flower morphs (normal and albino) that differ in flower lip color. However, the molecular mechanisms underlying flower color formation in C. lowianum are not well understood. In this study, comparative metabolomic analysis between normal and albino flower lip tissues indicated that cyanidin-3-O-glucoside content was significantly higher in red epichiles than in other lip tissues. This finding suggests that cyanidin-3-O-glucoside is responsible for color variation and differentiation in the lip in C. lowianum. We also found that red coloration in C. lowianum flower is correlated with high levels of F3'H expression; further, anthocyanins, carotenoids and chlorophyll coordinate to influence sepal and petal coloration during flower development. In transgenic Arabidopsis lines, overexpression of F3'H increased anthocyanin concentration, overexpression of BCH increased carotenoid concentration, whereas overexpression of HEMG and CHLI both increased chlorophyll concentration. Identification and assessment of several transcription factors revealed that MYB308-1 activates BCH, MYB111 and PIF4-2 activate HEMG and CHLI expression during flower development. Importantly, MYB14-1 shows interaction with PIF4-2, and appears to act as a connector between anthocyanin and chlorophyll biosynthesis by either activating F3'H expression or inhibiting CHLI expression. These results indicate that, in C. lowianum, variation in flower color and differentiation of lip color patterns are primarily regulated by the types and concentrations of flavonoids; further, carotenoids and chlorophyll also influence flower coloration during development.

Post-transcriptional and post-translational regulation of anthocyanin biosynthesis in sweetpotato by Ib-miR2111 and IbKFB: Implications for health promotion

INTRODUCTION

Sweetpotato (Ipomoea batatas (L.) Lam.) is a genetically intricate hexaploid crop. The purple-fleshed variety, enriched with anthocyanin pigments, is an outstanding source for creating high-value functional products. Previous research on anthocyanin biosynthesis has primarily focused on the above-ground plant parts at the transcriptional level. However, the regulatory mechanisms underlying anthocyanin accumulation in underground tuberous roots of sweetpotato remain largely unexplored.

OBJECTIVES

This study aimed to elucidate the post-transcriptional and post-translational mechanisms of Ib-miR2111 and its target gene IbKFB in anthocyanin synthesis in sweetpotato.

METHODS

Genetic manipulation techniques were used to validate the function of Ib-miR2111 and IbKFB in anthocyanin biosynthesis in sweetpotato. To investigate how IbKFB works, a series of protein interaction assays, including yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), GST pull-down, co-immunoprecipitation (Co-IP), and ubiquitination, were conducted. Additionally, the impact of anthocyanin extracts from the genetically modified sweetpotato lines on inflammatory cells morphology, cytokine expression, and cell proliferation were evaluated using in vitro assays.

RESULTS

Purple-fleshed sweetpotato (PFSP) varieties exhibited elevated Ib-miR2111 expression compared to white-fleshed sweetpotato (WFSP) varieties, with an inverse expression pattern in IbKFB. Genetic manipulations, including overexpression, CRISPR/Cas9 knockouts, and targeted mutations, confirmed their critical roles in anthocyanin modulation. Furthermore, IbKFB's interactions and ubiquitination with phenylalanine ammonia-lyase 1 (IbPAL1) and glyceraldehyde-3-phosphate dehydrogenase 1 (IbGAPCp1) were elucidated, revealing intricate regulatory mechanisms. Enhanced anthocyanin content showed significant effects on inflammatory cell morphology, cytokine expression, and cell proliferation.

CONCLUSION

This study provides new insights into the regulatory mechanisms of Ib-miR2111 and IbKFB in anthocyanin biosynthesis and suggests potential health benefits of anthocyanin-rich sweetpotatoes.

Integrated Transcriptomic and Metabolomic Analysis Revealed Regulatory Mechanisms on Flavonoids Biosynthesis in the Skin of Passion Fruit (Passiflora spp.)

Passion fruit is one of the most famous fruit crops in tropical and subtropical regions due to its high edible, medicinal, and ornamental value. Flavonoids, a class of plant secondary metabolites, have important health-related roles. In this study, a total of 151 flavonoid metabolites were identified, of which 25 key metabolites may be the main contributors to the purple phenotype. Using RNA sequencing, 11,180 differentially expressed genes (DEGs) were identified. Among these, 48 flavonoid biosynthesis genes (PAL, 4CL, C4H, CHS, CHI, F3H, DFR, ANS, and UFGT) and 123 transcription factors were identified. Furthermore, 12 distinct modules were identified through weighted gene coexpression network analysis, of which the brown module displays a robust positive correlation with numerous flavonoid metabolites. Overexpression of PeMYB114 significantly promoted flavonoids accumulation in tobacco leaves. Our study provided a key candidate gene for molecular breeding to improve color traits in passion fruit.

Comparative transcriptome analyses of different orthosiphon aristatus tissues reveal differentially expressed genes associated with flavonoid biosynthesis

Orthosiphon aristatus (O. aristatus) has been used as a popular traditional folk medicine for the treatment of kidney disease. Recent studies have shown that O. aristatus root contains more flavonoids and has higher antioxidant capacity compared to its medicinal parts. However, there is limited knowledge on the mechanisms behind the synthetic biology of flavonoid in all tissues of O. aristatus. Here, we performed high-performance liquid chromatography (HPLC) analysis and comparative transcriptome analyses of flavonoids in all tissues. The content of 4 major flavonoids is significantly higher in roots and leaves compared to stems in O. aristatus. Out of a total of 138,294 Unigenes, the KEGG pathway analysis identified 66 Unigenes encoding 8 key metabolic enzymes involved in the biosynthetic pathway of flavonoid compounds. Additionally, 5,154 on average DEGs involved in flavonoid biosynthesis could be categorised into 58 transcription factor (TF) families. Among the identified DEGs, a total of 5,897 were common to all tissues, with 212 DEGs strongly associated with flavonoid accumulation in root. Several of these key enzyme genes were further validated by quantitative real-time polymerase chain reaction (qRT-PCR). Our research provides novel insights into flavonoids synthetic biology, and highlights O. aristatus root may serve as a valuable resource for medicinal use.

A rare dominant allele DYSOC1 determines seed coat color and improves seed oil content in Brassica napus

Yellow seed coat color (SCC) is a valuable trait in Brassica napus, which is significantly correlated to high seed oil content (SOC) and low seed lignocellulose content (SLC). However, no dominant yellow SCC genes were identified in B. napus. In this study, a dominant yellow SCC B. napus N53-2 was verified, and then 58,981 eQTLs and 25 trans-eQTL hotspots were identified in a double haploid population derived from N53-2 and black SCC material Ken-C8. A rare dominant allele DYSOC1 (dominant gene of yellow seed coat color and improved seed oil content 1) was subsequently cloned in a trans-eQTL hotspot that colocated with SCC, SOC, and SLC QTL hotspot on ChrA09 through QTL fine mapping and multi-omics analysis. Transgenic experiments revealed that the expression of DYSOC1 produced yellow SCC seeds with significantly increased SOC and decreased SLC. Our result provides a rare dominant yellow SCC allele in B. napus, which has excellent potential for yellow SCC and high SOC rapeseed breeding.