R2R3 MYB transcription factors: key regulators of the flavonoid biosynthetic pathway in grapevine

Analysis of rabbiteye blueberry metabolomes and transcriptomes reveals mechanisms underlying potassium-induced anthocyanin production

Environmental factors play an important role in anthocyanin biosynthesis, and potassium, an essential nutrient for blueberry growth, can act as an enzyme activator. However, few reports exist on the transcriptional and anthocyanin metabolic changes in blueberries regulated by potassium. The results indicated that potassium treatment significantly increased the contents of malvidin, petunidin, and delphinidin in blueberry fruits and accelerated early color development, particularly favoring the accumulation of darker pigments such as malvidin, petunidin, and delphinidin when applied at the young fruit stage. Transcriptome analysis identified 102 glucose metabolism-related genes and 12 differential potassium transport genes potentially involved in potassium-mediated anthocyanin synthesis and accumulation, with AKT1 and KUP potassium transporters being upregulated under potassium fertilization. In the anthocyanin biosynthesis pathway, 13 genes, including UFGT, F3H, CHI, HCT, C12RT1, DFR, and F3'5'H, were closely linked to flavonoid and anthocyanin metabolite synthesis regulated by potassium. Furthermore, potassium treatment markedly enhanced the activities of key enzymes, F3H, F3'5'H, and UFGT, in the anthocyanin synthesis pathway of blueberry fruits. Overall, these findings elucidate the influence of potassium application timing on anthocyanin synthesis and provide valuable insights into the molecular mechanisms governing anthocyanin biosynthesis in blueberries.

Proteome and Metabolome Analyses of Albino Bracts in Davidia involucrata

Although the mechanisms underlying albino phenotypes have been examined in model plants and major crops, our knowledge of bract albinism is still in its infancy. Davidia involucrata, a relic plant called dove tree, is best known for the intriguing trait with a pair of white bracts covering the capitula. Here, comparative physiological, cytological, proteomic, and metabolomic analyses were performed to dissect the albinism mechanism of D. involucrata bracts. The bracts exhibited low chlorophyll and carotenoid contents, reduced photosynthetic efficiency, and impaired chloroplast structure. The severe deficiency of photosynthetic pigments and the substantial decrease in cuticle thickness made the bracts light-sensitive. In total, 1134 differentially expressed proteins (DEPs) were obtained between bracts and leaves. Pathway enrichment analysis of DEPs revealed that photosynthetic pigment biosynthesis and photosynthesis were suppressed, whereas protein processing in endoplasmic reticulum, flavonoid biosynthesis, and the ubiquitin-proteasome system (UPS) were activated in bracts. Strikingly, DEPs implicated in chloroplast development, including PPR and AARS proteins, were mainly down-regulated in bracts. We further investigated albinism-induced metabolic changes and detected 412 differentially abundant metabolites (DAMs). Among them, enhanced flavonoids accumulation can plausibly explain the role of bracts in pollinator attraction. Amino acids and their derivatives in bracts showed remarkably increased abundance, which might be causally linked to enhanced UPS function. Our work could lay foundations for understanding albinism mechanisms and adaptive significance of plant bracts and facilitate future utilization of D. involucrata resources.

Exploring the differences in traits and genes between brown cotton and white cotton hybrid offspring (Gossypium hirsutum L.)

Brown cotton and white cotton are two important raw materials used in the cotton fiber industry. Clarifying the differences in morphology, agronomic traits, and fiber pigments between these varieties can facilitate the implementation of corresponding cultivation and breeding techniques. Therefore, we obtained F2 generation brown cotton plants through hybridization and compared them with their parents. In terms of agronomic traits, plant morphology and leaf shape were similar, but brown cotton presented more villi on the main stem. The first fruiting branch node was within the range of 4-6 cm, and the first fruiting branch node height was greater than that of TM-1, i.e., between 13.25 cm and 22.79 cm, with no difference compared with that of P26. The plant height was greater than that of the parents, and the number of bolls was essentially the same as that in TM-1 and greater than that in P26. The lint percentage and average fiber length were lower in TM-1 than in P26, and the seed index was greater than that in TM-1 and P26. Pigment measurements revealed that the chlorophyll a content in brown cotton during the boll stage was lower than that in white cotton, and the content of proanthocyanidin in the cotton fibers was greater in brown cotton than in white cotton. At 15 days after pollination, the highest content was 159.8 mg/g. To determine the differences in gene expression levels, we conducted transcriptome sequencing. Gene Ontology (GO) analysis revealed that the differentially expressed genes (DEGs) were enriched in pathways related to the cell wall and enzyme activity, whereas Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were enriched in flavonoid synthesis pathways. Transcription factor analysis revealed that the expression of the MYB3 transcription factor (Ghir_D07G002110) was higher in brown cotton, and bioinformatics analysis revealed that this gene has regulatory effects on the CHS, CHI1, and F3H genes.

A multiomics investigation into the evolution and specialized metabolisms of three Toxicodendron cultivars

Toxicodendron species are economically and medicinally important trees because of their rich sources of natural products. We present three chromosome-level genome assemblies of Toxicodendron vernicifluum 'Dali', Toxicodendron succedaneum 'Vietnam', and T. succedaneum 'Japan', which display diverse production capacities of specialized metabolites. Genome synteny and structural variation analyses revealed large genomic differences between the two species (T. vernicifluum and T. succedaneum) but fewer differences between the two cultivars within the species. Despite no occurrence of recent whole-genome duplications, Toxicodendron showed evidence of local duplications. The genomic modules with high expression of genes encoding metabolic flux regulators and chalcone synthase-like enzymes were identified via multiomics analyses, which may be responsible for the greater urushiol accumulation in T. vernicifluum 'Dali' than in other Toxicodendron species. In addition, our analyses revealed the regulatory patterns of lipid metabolism in T. succedaneum 'Japan', which differ from those of other Toxicodendron species and may contribute to its high lipid accumulation. Furthermore, we identified the key regulatory elements of lipid metabolism at each developmental stage, which could aid in molecular breeding to improve the production of urushiol and lipids in Toxicodendron species. In summary, this study provides new insights into the genomic underpinnings of the evolution and diversity of specialized metabolic pathways in three Toxicodendron cultivars through multiomics studies.

Metabolome and Transcriptome Joint Analysis Reveals That Different Sucrose Levels Regulate the Production of Flavonoids and Stilbenes in Grape Callus Culture

To reveal the effect of sucrose concentration on the production of secondary metabolites, a metabolome and transcriptome joint analysis was carried out using callus induced from grape variety Mio Red cambial meristematic cells. We identified 559 metabolites-mainly flavonoids, phenolic acids, and stilbenoids-as differential content metabolites (fold change ≥2 or ≤0.5) in at least one pairwise comparison of treatments with 7.5, 15, or 30 g/L sucrose in the growing media for 15 or 30 days (d). Resveratrol, viniferin, and amurensin contents were highest at 15 d of subculture; piceid, ampelopsin, and pterostilbene had higher contents at 30 d. A transcriptome analysis identified 1310 and 498 (at 15 d) and 1696 and 2211 (at 30 d) differentially expressed genes (DEGs; log2(fold change) ≥ 1, p < 0.05) in 7.5 vs. 15 g/L and 15 vs. 30 g/L sucrose treatments, respectively. In phenylpropane and isoflavone pathways, DEGs encoding cinnamic acid 4-hydroxylase, chalcone synthase, chalcone isomerase, and flavanone 3-hydroxylase were more highly expressed at 15 d than at 30 d, while other DEGs showed different regulation patterns corresponding to sucrose concentrations and cultivation times. For all three sucrose concentrations, the stilbene synthase (STS) gene exhibited significantly higher expression at 15 vs. 30 d, while two resveratrol O-methyltransferase (ROMT) genes related to pterostilbene synthesis showed significantly higher expression at 30 vs. 15 d. In addition, a total of 481 DEGs were annotated as transcription factors in pairwise comparisons; an integrative analysis suggested MYB59, WRKY20, and MADS8 as potential regulators responding to sucrose levels in flavonoid and stilbene biosynthesis in grape callus. Our results provide valuable information for high-efficiency production of flavonoids and stilbenes using grape callus.

Identification of MYB Transcription Factor, a Regulator Related to Hydrolysable Tannin Synthesis in Canarium album L., and Functional Analysis of CaMYBR04

Hydrolysed tannins (HTs) are polyphenols, which are related to the astringency, flavour, colour, stability, medicinal value and other characteristics of many fruits and vegetables. The biosynthetic mechanism of the majority of HTs remains unknown, and many biosynthetic pathways of HTs are speculative conclusions that have not been confirmed. The fruit of Canarium album L. (Chinese olive), which is notable for its pharmacological and edible properties, is rich in HTs. The fruit has a distinctive bitter and astringent taste when initially consumed, which mellows to a sweet sensation upon chewing. HTs serve as the primary material basis for the formation of the Chinese olive fruit's astringent quality and pharmacological effects. In this study, the fruit of C. album Changying was utilised as the research material. The objective of this study was to provide a theoretical basis for the quality control of Chinese olive fruit and the application and development of its medicinal value. In addition, the study aimed to identify and screen related MYB transcription factors involved in the synthesis of HTs in the fruit and to clarify the mechanism of MYBs in the process of synthesis and regulation of HTs in Chinese olive fruit. The principal findings were as follows. A total of 83 differentially expressed Chinese olive MYB transcription factors (CaMYBs) were identified, including 54 1R-MYBs (MYB-related), 25 2R-MYBs (R2R3-MYBs), 3 3R-MYBs, and 1 4R-MYB. Through trend analysis and correlation analysis, it was found that CaMYBR04 (Isoform0032534) exhibited a significantly higher expression (FPKM) than the other CaMYBs. The full-length cDNA sequence of CaMYBR04 was cloned and transformed into strawberry. The results demonstrated that CaMYBR04 significantly enhanced the fruit's hydrolysable tannin content. Consequently, this study elucidated the function of CaMYBR04, a regulator of the Chinese olive fruit hydrolysable tannin synthesis pathway, and established a theoretical foundation for the synthesis and regulation of fruit HTs.

Unlocking Nature's Rhythms: Insights into Secondary Metabolite Modulation by the Circadian Clock

Plants, like many other living organisms, have an internal timekeeper, the circadian clock, which allows them to anticipate photoperiod rhythms and environmental stimuli to optimally adjust plant growth, development, and fitness. These fine-tuned processes depend on the interaction between environmental signals and the internal interactive metabolic network regulated by the circadian clock. Although primary metabolites have received significant attention, the impact of the circadian clock on secondary metabolites remains less explored. Transcriptome analyses revealed that many genes involved in secondary metabolite biosynthesis exhibit diurnal expression patterns, potentially enhancing stress tolerance. Understanding the interaction mechanisms between the circadian clock and secondary metabolites, including plant defense mechanisms against stress, may facilitate the development of stress-resilient crops and enhance targeted management practices that integrate circadian agricultural strategies, particularly in the face of climate change. In this review, we will delve into the molecular mechanisms underlying circadian rhythms of phenolic compounds, terpenoids, and N-containing compounds.

Regulatory Mechanism of Proanthocyanidins in Grape Peels Using vvi-miR828a and Its Target Gene VvMYBPA1

Anthocyanins and proanthocyanidins are considered to be essential secondary metabolites in grapes and are used to regulate metabolic processes, while miRNAs are involved in their synthesis of anthocyanins and proanthocyanidins to regulate metabolic processes. The present research work was carried out to investigate the underlying regulatory mechanism of target genes in the grape cultivars 'Italia' and 'Benitaka'. miRNA and transnscriptomic sequencing technology were employed to characterize both the profiles of miRNAs and the transcripts of grape peels at 10 and 11 weeks post flowering (10 wpf and 11 wpf). The results revealed that the expression level of vvi-miR828a in 'Italia' at 10 and 11 wpf was significantly higher than that in 'Benitaka'. miRNA-seq analysis predicted MYBPA1 to be the target gene of vvi-miR828a. In transcriptome analysis, the expression level of the VvMYBPA1 gene in 'Benitaka' was significantly higher than that in 'Italia'; in addition, the TPM values (expression levels) of VvMYBPA1 and miR828a also showed an evident negative correlation. The determination of the proanthocyanidin (PA) content in 'Italia' and 'Benitaka' peels at 11 wpf demonstrated that the PA content of 'Benitaka' was significantly higher than that of 'Italia'. The outcomes of RT-qRCR analysis exhibited that the expression levels of the VdPAL, VdCHS, VdCHI, VdDFR, VdMYB5b, VdANR, and VdMYBPA1 genes related anthocyanin and proanthocyanidin pathways were reduced, while the expression levels of all of the above genes were increased after the transient expression of the VvMYBPA1 vector into grape leaves. The results of the transient overexpression experiment of vvi-miR828a before the veraison period of strawberry fruits showed that vvi-miR828a can significantly slow down the coloration of strawberries. The vvi-miR828a negatively regulates the accumulation of proanthocyanidins in grape fruits by inhibiting the expression of VvMYBPA1.

Unraveling the Molecular Basis of Color Variation in Dioscorea alata Tubers: Integrated Transcriptome and Metabolomics Analysis

Dioscorea alata L. (Dioscoreaceae) is a widely cultivated tuber crop with variations in tuber color, offering potential value as health-promoting foods. This study focused on the comparison of D. alata tubers possessing two distinct colors, white and purple, to explore the underlying mechanisms of color variation. Flavonoids, a group of polyphenols known to influence plant color and exhibit antioxidant properties, were of particular interest. The total phenol and total flavonoid analyses revealed that purple tubers (PTs) have a significantly higher content of these metabolites than white tubers (WTs) and a higher antioxidant activity than WTs, suggesting potential health benefits of PT D. alata. The transcriptome analysis identified 108 differentially expressed genes associated with the flavonoid synthesis pathway, with 57 genes up-regulated in PTs, including CHS, CHI, DFR, FLS, F3H, F3'5'H, LAR, ANS, and ANR. The metabolomics analysis demonstrated that 424 metabolites, including 104 flavonoids and 8 tannins, accumulated differentially in PTs and WTs. Notably, five of the top ten up-regulated metabolites were flavonoids, including 6-hydroxykaempferol-7-O-glucoside, pinocembrin-7-O-(6″-O-malonyl)glucoside, 6-hydroxykaempferol-3,7,6-O-triglycoside, 6-hydroxykaempferol-7-O-triglycoside, and cyanidin-3-O-(6″-O-feruloyl)sophoroside-5-O-glucoside, with the latter being a precursor to anthocyanin synthesis. Integrating transcriptome and metabolomics data revealed that the 57 genes regulated 20 metabolites within the flavonoid synthesis pathway, potentially influencing the tubers' color variation. The high polyphenol content and antioxidant activity of PTs indicate their suitability as nutritious and health-promoting food sources. Taken together, the findings of this study provide insights into the molecular basis of tuber color variation in D. alata and underscore the potential applications of purple tubers in the food industry and human health promotion. The findings contribute to the understanding of flavonoid biosynthesis and pigment accumulation in D. alata tubers, opening avenues for future research on enhancing the nutritional quality of D. alata cultivars.

Integrated metabolic profiling and transcriptome analysis of Lonicera japonica flowers for chlorogenic acid, luteolin and endogenous hormone syntheses

The active ingredients of many medicinal plants are the secondary metabolites associated with the growth period. Lonicera japonica Thunb. is an important traditional Chinese medicine, and the flower development stage is an important factor that influences the quality of medicinal ingredients. In this study, transcriptomics and metabolomics were performed to reveal the regulatory mechanism of secondary metabolites during flowering of L. japonica. The results showed that the content of chlorogenic acid (CGA) and luteolin gradually decreased from green bud stage (Sa) to white flower stage (Sc), especially from white flower bud stage (Sb) to Sc. Most of the genes encoding the crucial rate-limiting enzymes, including PAL, C4H, HCT, C3'H, F3'H and FNSII, were down-regulated in three comparisons. Correlation analysis identified some members of the MYB, AP2/ERF, bHLH and NAC transcription factor families that are closely related to CGA and luteolin biosynthesis. Furthermore, differentially expressed genes (DEGs) involved in hormone biosynthesis, signalling pathways and flowering process were analysed in three flower developmental stage.

Advancing understanding of Ficus carica: a comprehensive genomic analysis reveals evolutionary patterns and metabolic pathway insights

Ficus carica L. (dioecious), the most significant commercial species in the genus Ficus, which has been cultivated for more than 11,000 years and was one of the first species to be domesticated. Herein, we reported the most comprehensive F. carica genome currently. The contig N50 of the Orphan fig was 9.78 Mb, and genome size was 366.34 Mb with 13 chromosomes. Based on the high-quality genome, we discovered that F. carica diverged from Ficus microcarpa ~34 MYA, and a WGD event took place about 2─3 MYA. Throughout the evolutionary history of F. carica, chromosomes 2, 8, and 10 had experienced chromosome recombination, while chromosome 3 saw a fusion and fission. It is worth proposing that the chromosome 9 experienced both inversion and translocation, which facilitated the emergence of the F. carica as a new species. And the selections of F. carica for the genes of recombination chromosomal fragment are compatible with their goal of domestication. In addition, we found that the F. carica has the FhAG2 gene, but there are structural deletions and positional jumps. This gene is thought to replace the one needed for female common type F. carica to be pollinated. Subsequently, we conducted genomic, transcriptomic, and metabolomic analysis to demonstrate significant differences in the expression of CHS among different varieties of F. carica. The CHS playing an important role in the anthocyanin metabolism pathway of F. carica. Moreover, the CHS gene of F. carica has a different evolutionary trend compared to other Ficus species. These high-quality genome assembly, transcriptomic, and metabolomic resources further enrich F. carica genomics and provide insights for studying the chromosomes evolution, sexual system, and color characteristics of Ficus.

The Classification, Molecular Structure and Biological Biosynthesis of Flavonoids, and Their Roles in Biotic and Abiotic Stresses

With the climate constantly changing, plants suffer more frequently from various abiotic and biotic stresses. However, they have evolved biosynthetic machinery to survive in stressful environmental conditions. Flavonoids are involved in a variety of biological activities in plants, which can protect plants from different biotic (plant-parasitic nematodes, fungi and bacteria) and abiotic stresses (salt stress, drought stress, UV, higher and lower temperatures). Flavonoids contain several subgroups, including anthocyanidins, flavonols, flavones, flavanols, flavanones, chalcones, dihydrochalcones and dihydroflavonols, which are widely distributed in various plants. As the pathway of flavonoid biosynthesis has been well studied, many researchers have applied transgenic technologies in order to explore the molecular mechanism of genes associated with flavonoid biosynthesis; as such, many transgenic plants have shown a higher stress tolerance through the regulation of flavonoid content. In the present review, the classification, molecular structure and biological biosynthesis of flavonoids were summarized, and the roles of flavonoids under various forms of biotic and abiotic stress in plants were also included. In addition, the effect of applying genes associated with flavonoid biosynthesis on the enhancement of plant tolerance under various biotic and abiotic stresses was also discussed.

Comparative analysis of the MYB gene family in seven Ipomoea species

The MYB transcription factors regulate plant growth, development, and defense responses. However, information about the MYB gene family in Ipomoea species is rare. Herein, we performed a comprehensive genome-wide comparative analysis of this gene family among seven Ipomoea species, sweet potato (I. batatas), I. trifida, I. triloba, I. nil, I. purpurea, I. cairica, and I. aquatic, and identified 296, 430, 411, 291, 226, 281, and 277 MYB genes, respectively. The identified MYB genes were classified into five types: 1R-MYB (MYB-related), 2R-MYB (R2R3-MYB), 3R-MYB (R1R2R3-MYB), 4R-MYB, and 5R-MYB, and the MYB-related or R2R3-MYB type was the most abundant MYB genes in the seven species. The Ipomoea MYB genes were classed into distinct subgroups based on the phylogenetic topology and the classification of the MYB superfamily in Arabidopsis. Analysis of gene structure and protein motifs revealed that members within the same phylogenetic group presented similar exon/intron and motif organization. The identified MYB genes were unevenly mapped on the chromosomes of each Ipomoea species. Duplication analysis indicated that segmental and tandem duplications contribute to expanding the Ipomoea MYB genes. Non-synonymous substitution (Ka) to synonymous substitution (Ks) [Ka/Ks] analysis showed that the duplicated Ipomoea MYB genes are mainly under purifying selection. Numerous cis-regulatory elements related to stress responses were detected in the MYB promoters. Six sweet potato transcriptome datasets referring to abiotic and biotic stresses were analyzed, and MYB different expression genes' (DEGs') responses to stress treatments were detected. Moreover, 10 sweet potato MYB DEGs were selected for qRT-PCR analysis. The results revealed that four responded to biotic stress (stem nematodes and Ceratocystis fimbriata pathogen infection) and six responded to the biotic stress (cold, drought, and salt). The results may provide new insights into the evolution of MYB genes in the Ipomoea genome and contribute to the future molecular breeding of sweet potatoes.

Phylogenetic Analysis of R2R3-MYB Family Genes in Tetrastigma hemsleyanum Diels et Gilg and Roles of ThMYB4 and ThMYB7 in Flavonoid Biosynthesis

Tetrastigma hemsleyanum Diels et Gilg (T. hemsleyanum) is an extensively used Chinese folk herb with multiple bioactivities. Among these bioactivities, flavonoids are recognized as the representative active ingredients. We previously found an elevated accumulation of flavonoids in T. hemsleyanum under water stress; however, the mechanism remains unclear. R2R3-MYB transcription factors play vital roles in the plant response to environmental stress and the regulation of secondary metabolites. Herein, a systematic transcriptome identification of R2R3-MYB family genes under water stress in T. hemsleyanum was performed to explore their potential function in the biosynthesis of flavonoids. A total of 26 R2R3-MYB genes were identified, most of which were clustered into functional branches of abiotic stress. ThMYB4 and ThMYB7 were then screened out to be associated with the biosynthesis of flavonoids through a protein-protein interaction prediction. An expression correlation analysis based on RNA-seq further confirmed that ThMYB4 and ThMYB7 were positively related to the flavonoid biosynthetic pathway genes of T. hemsleyanum. In ThMYB4- and ThMYB7-overexpression hairy roots, it was found that the expression of ThCHS and ThCHI was significantly increased, suggesting that ThMYB4 and ThMYB7 may act as regulators in flavonoid biosynthesis. This will shed new light on the promotion of flavonoid production and the medicinal value of T. hemsleyanum by manipulating transcription factors.

Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit

Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared 'JF308' (a normal tomato cultivar) and 'YS006' (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in 'YS006' compared to 'JF308' on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in 'YS006'. 'YS006' had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than 'JF308'. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in 'YS006' compared to 'JF308' on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.

VvMYB14 participates in melatonin-induced proanthocyanidin biosynthesis by upregulating expression of VvMYBPA1 and VvMYBPA2 in grape seeds

This work demonstrated that melatonin increases continuously in seeds, particularly seed coats, during berry ripening. Exogenous melatonin treatments significantly increased the proanthocyanidin (PA) content, partially through ethylene signaling, in seed coats. VvMYB14 expression exhibited patterns similar to melatonin accumulation over time, which was largely induced by melatonin treatment in seed coats during berry ripening. Additionally, VvMYB14 bound to the MBS element of the VvMYBPA1 promoter to activate expression. VvMYB14 overexpression largely upregulated expression of VvMYBPA1, VvMYBPA2 and VvLAR1 and increased the PA content in grape seed-derived calli. Similar increases in AtTT2 and AtBAN expression and PA content were found in VvMYB14-overexpressing Arabidopsis seeds. It was also observed that VvMYB14 overexpression increased ethylene production and thereby induced expression of VvERF104, which bound to the ERF element of the VvMYBPA2 promoter and activated its expression. Additionally, VvERF104 suppression reduced the VvMYB14 overexpression-induced increases in expression of VvMYBPA2 and VvLAR1 and PA content. Further experiments revealed that melatonin-induced increases in the expression of VvMYBPA1, VvMYBPA2, VvERF104 and VvLAR1 and PA accumulation were significantly reduced in VvMYB14-suppressing grape calli and leaves. Collectively, VvMYB14 mediates melatonin-induced PA biosynthesis by directly transactivating VvMYBPA1 expression and indirectly upregulating VvMYBPA2 expression via VvERF104.

A Genome-Wide View of the Transcriptome Dynamics of Fresh-Cut Potato Tubers

Fresh fruits and vegetable products are easily perishable during postharvest handling due to enzymatic browning reactions. This phenomenon has contributed to a significant loss of food. To reveal the physiological changes in fresh-cut potato tubers at the molecular level, a transcriptome analysis of potato tubers after cutting was carried out. A total of 10,872, 10,449, and 11,880 differentially expressed genes (DEGs) were identified at 4 h, 12 h and 24 h after cutting, respectively. More than 87.5% of these DEGs were classified into the categories of biological process (BP) and molecular function (MF) based on Gene Ontology (GO) analysis. There was a difference in the response to cutting at different stages after the cutting of potato tubers. The genes related to the phenol and fatty biosynthesis pathways, which are responsible for enzymatic browning and wound healing in potato tubers, were significantly enriched at 0-24 h after cutting. Most genes related to the enzymatic browning of potato tubers were up-regulated in response to cut-wounding. Plant hormone biosynthesis, signal molecular biosynthesis and transduction-related genes, such as gibberelin (GA), cytokinin (CK), ethylene (ET), auxin (IAA), jasmonic acid (JA), salicylic (SA), and Respiratory burst oxidase (Rboh) significantly changed at the early stage after cutting. In addition, the transcription factors involved in the wound response were the most abundant at the early stage after cutting. The transcription factor with the greatest response to injury was MYB, followed by AP2-EREBP, C3H and WRKY. This study revealed the physiological changes at the molecular level of fresh-cut potato tubers after cutting. This information is needed for developing a better approach to enhancing the postharvest shelf life of fresh processed potato and the breeding of potato plants that are resistant to enzymatic browning.

Transcriptomic Analyses of Grapevine Leafroll-Associated Virus 3 Infection in Leaves and Berries of 'Cabernet Franc'

Grapevine leafroll-associated virus 3 (GLRaV-3) is one of the most important viruses affecting global grape and wine production. GLRaV-3 is the chief agent associated with grapevine leafroll disease (GLRD), the most prevalent and economically destructive grapevine viral disease complex. Response of grapevine to GLRaV-3 infection at the gene expression level is poorly characterized, limiting the understanding of GLRaV-3 pathogenesis and viral-associated symptom development. In this research, we used RNA-Seq to profile the changes in global gene expression of Cabernet franc, a premium red wine grape, analyzing leaf and berry tissues at three key different developmental stages. We have identified 1457 differentially expressed genes (DEGs) in leaves and 1181 DEGs in berries. The expression profiles of a subset of DEGs were validated through RT-qPCR, including those involved in photosynthesis (VvPSBP1), carbohydrate partitioning (VvSUT2, VvHT5, VvGBSS1, and VvSUS), flavonoid biosynthesis (VvUFGT, VvLAR1, and VvFLS), defense response (VvPR-10.3, and VvPR-10.7), and mitochondrial activities (ETFB, TIM13, and NDUFA1). GLRaV-3 infection altered source-sink relationship between leaves and berries. Photosynthesis and photosynthate assimilation were inhibited in mature leaves while increased in young berries. The expression of genes involved in anthocyanin biosynthesis increased in GLRaV-3-infected leaves, correlating with interveinal tissue reddening, a hallmark of GLRD symptoms. Notably, we identified changes in gene expression that suggest a compromised sugar export and increased sugar retrieval in GLRaV-3-infected leaves. Genes associated with mitochondria were down-regulated in both leaves and berries of Cabernet franc infected with GLRaV-3. Results of the present study suggest that GLRaV-3 infection may disrupt mitochondrial function in grapevine leaves, leading to repressed sugar export and accumulation of sugar in mature leaf tissues. The excessive sugar accumulation in GLRaV-3-infected leaves may trigger downstream GLRD symptom development and negatively impact berry quality. We propose a working model to account for the molecular events underlying the pathogenesis of GLRaV-3 and symptom development.

De novo transcriptome revealed genes involved in anthocyanin biosynthesis, transport, and regulation in a mutant of Acer pseudosieboldianum

BACKGROUND

Acer pseudosieboldianum is a kind of excellent color-leafed plants, and well known for its red leaves in autumn. At the same time, A. pseudosieboldianum is one of the native tree species in the northeast of China, and it plays an important role in improving the lack of color-leafed plants in the north. In previous study, we found a mutant of the A. pseudosieboldianum that leaves intersect red and green in spring and summer. However, it is unclear which genes cause the color change of mutant leaves.

RESULTS

In order to study the molecular mechanism of leaf color formation, we analyzed the leaves of the mutant group and the control group from A. pseudosieboldianum by RNA deep sequencing in this study. Using an Illumina sequencing platform, we obtained approximately 276,071,634 clean reads. After the sequences were filtered and assembled, the transcriptome data generated a total of 70,014 transcripts and 54,776 unigenes, of which 34,486 (62.96%) were successfully annotated in seven public databases. There were 8,609 significant DEGs identified between the control and mutant groups, including 4,897 upregulated and 3,712 downregulated genes. We identified 13 genes of DEGs for leaf color synthesis that was involved in the flavonoid pathway, 26 genes that encoded transcription factors, and eight genes associated with flavonoid transport.

CONCLUSION

Our results provided comprehensive gene expression information about A. pseudosieboldianum transcriptome, and directed the further study of accumulation of anthocyanin in A. pseudosieboldianum, aiming to provide insights into leaf coloring of it through transcriptome sequencing and analysis.

Constitutive expression of VviNAC17 transcription factor significantly induces the synthesis of flavonoids and other phenolics in transgenic grape berry cells

VviNAC17 is a grapevine transcription factor activated by ABA. Because ABA has been proposed as the main signal modulating the secondary metabolism in grape berry skins, here we postulated VviNAC17 as a positive regulator of secondary metabolism in grape cells. To validate the hypothesis, VviNAC17 was constitutively and stably overexpressed in grape berry suspension-cultured cells of Gamay Fréaux cv. by Agrobacterium-mediated transformation. Targeted transcriptional analyses by qPCR showed that several genes involved the phenylpropanoid (VviPAL1), stilbenoid (VviSTS1) and flavonoid pathways (VviDFR, VviLAR1, VviANR, VviLDOX, and VviUFGT1), as well as anthocyanin vacuolar transport and accumulation (VviGST4 and VvMATE1) were significantly upregulated in VviNAC17-overexpressing transgenic cells, which translated in the stimulation of a number of enzymatic activities in those pathways. This was the case of phenylalanine ammonia lyase (PAL) and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT) that were about 2-fold and 3.5-fold higher in VviNAC17-overexpressing cells than in control cells. VviNAC17-overexpressing cells accumulated significantly higher amounts of anthocyanins, proanthocyanidins, total flavonoids and total phenolics. These findings confirmed that VviNAC17 is an important positive regulator of secondary metabolism in grapevine contributing to the accumulation of important berry quality-related secondary metabolites.

Effect of VaMyb40 and VaMyb60 Overexpression on Stilbene Biosynthesis in Cell Cultures of Grapevine Vitis amurensis Rupr

Stilbenes are plant defense compounds known to rapidly accumulate in grapevine and some other plant species in response to microbial infection and several abiotic stresses. Stilbenes have attracted considerable attention due to valuable biological effects with multi-spectrum therapeutic application. However, there is a lack of information on natural signaling pathways and transcription factors regulating stilbene biosynthesis. It has been previously shown that MYB R2R3 transcription factor genes VaMyb40 and VaMyb60 were up-regulated in cell cultures of wild-growing grapevine Vitis amurensis Rupr. in response to UV irradiation. In this study, the effects of VaMyb40 or VaMyb60 overexpression in cell cultures of V. amurensis on their capability to produce stilbenes were investigated. Overexpression of the VaMyb60 gene led to a considerable increase in the content of stilbenes in three independently transformed transgenic lines in 5.9–13.9 times, while overexpression of the VaMyb40 gene also increased the content of stilbenes, although to a lesser extent (in 3.4–4.0 times) in comparison with stilbene levels in the empty vector-transformed calli. Stilbene content and stilbene production in the VaMyb60-transgenic calli reached 18.8 mg/g of dry weight (DW) and 150.8 mg/L, respectively. Using HPLC analysis, we detected eight individual stilbenes: t-resveratrol diglucoside, t-piceid, t-resveratrol, ε-viniferin, δ-viniferin, cis-resveratrol, cis-piceid, t-piceatannol. T-resveratrol prevailed over other stilbenoid compounds (53.1–89.5% of all stilbenes) in the VaMyb-overexpressing cell cultures. Moreover, the VaMyb40- and VaMyb60-transformed calli were capable of producing anthocyanins up to 0.035 mg/g DW, while the control calli did not produce anthocyanins. These findings show that the VaMyb40 and VaMyb60 genes positively regulate the stilbene biosynthesis as strong positive transcription regulators and can be used in biotechnological applications for stilbene production or high-quality viticulture and winemaking.

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

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

Transcriptomic and Non-Targeted Metabolomic Analyses Reveal the Flavonoid Biosynthesis Pathway in Auricularia cornea

Flavonoids, which are abundant in plants, are recognized for their antioxidant and anticancer roles in clinical applications. However, little is known about the molecular basis of flavonoid biosynthesis in fungi. In this study, we found that inclusion of leachate of Korshinsk peashrub (Caragana korshinskii) in the fermentation medium increased the total flavonoid content of the edible fungus Auricularia cornea by 23.6% relative to that grown in a control medium. Combined transcriptomic and non-targeted metabolomic analysis of the flavonoid biosynthesis pathway in A. cornea illustrated that there are important metabolites in the phenylpropanoid, coumarin and isoflavonoid biosynthesis pathways. In addition, we found that certain homologous genes encode phenylalanine ammonia lyase (PAL), polyphenol oxidase (PPO) and chalcone isomerase (CHI) in these biosynthesis pathways. These results, in this study, provide a new line for studying the regulation of flavonoid production in edible fungi.

A 69 kbp Deletion at the Berry Color Locus Is Responsible for Berry Color Recovery in Vitis vinifera L. Cultivar 'Riesling Rot'

‘Riesling Weiss’ is a white grapevine variety famous worldwide for fruity wines with higher acidity. Hardly known is ‘Riesling Rot’, a red-berried variant of ‘Riesling Weiss’ that disappeared from commercial cultivation but has increased in awareness in the last decades. The question arises of which variant, white or red, is the original and, consequently, which cultivar is the true ancestor. Sequencing the berry color locus of ‘Riesling Rot’ revealed a new VvmybA gene variant in one of the two haplophases called VvmybA3/1RR. The allele displays homologous recombination of VvmybA3 and VvmybA1 with a deletion of about 69 kbp between both genes that restores VvmybA1 transcripts. Furthermore, analysis of ‘Riesling Weiss’, ‘Riesling Rot’, and the ancestor ‘Heunisch Weiss’ along chromosome 2 using SSR (simple sequence repeat) markers elucidated that the haplophase of ‘Riesling Weiss’ was inherited from the white-berried parent variety ‘Heunisch Weiss’. Since no color mutants of ‘Heunisch Weiss’ are described that could have served as allele donors, we concluded that, in contrast to the public opinion, ‘Riesling Rot’ resulted from a mutational event in ‘Riesling Weiss’ and not vice versa.

Grafting with rootstocks promotes phenolic compound accumulation in grape berry skin during development based on integrative multi-omics analysis

In viticulture, grafting has been practiced widely and influences grape development as well as berry and wine quality. However, there is limited understanding of the effects of rootstocks on grape phenolic compounds, which are located primarily in the berry skin and contribute to certain sensory attributes of wine. In this study, scion-rootstock interactions were investigated at the green-berry stage and the veraison stage when grapevines were hetero-grafted with three commonly used rootstock genotypes (5BB, 101-14MG, and SO4). Physiological investigations showed that hetero-grafts, especially CS/5BB, contained higher concentrations of total proanthocyanidins (PAs) and various PA components in berry skins compared with the auto-grafted grapevines. Further metabolomics analysis identified 105 differentially accumulated flavonoid compounds, the majority of which, including anthocyanins, PAs, and flavonols, were significantly increased in the berry skins of hetero-grafted grapevines compared with auto-grafted controls. In addition, transcriptomic analysis of the same samples identified several thousand differentially expressed genes between hetero-grafted and auto-grafted vines. The three rootstocks not only increased the transcript levels of stilbene, anthocyanin, PA, and flavonol synthesis genes but also affected the expression of numerous transcription factor genes. Taken together, our results suggest that hetero-grafting can promote phenolic compound accumulation in grape berry skin during development. These findings provide new insights for improving the application value of grafting by enhancing the accumulation of nutritious phenolic components in grape.

Effect of Early Basal Leaf Removal on Phenolic and Volatile Composition and Sensory Properties of Aglianico Red Wines

The aim of this work was to study the influence of early basal leaf removal on Aglianico wines produced in the Apulia region (Italy). Three treatments were carried out, where 100% of fruit-zone leaves on the north (DN), south (DS) and on both sides of the canopy (DNS) were removed. A control (CT), where all basal leaves were retained, was also performed. Instrumental (HPLC-DAD-MS and GC-MS) and sensory analysis (QDA) were used to evaluate the treatment effect on the phenolic and volatile compositions and on the sensory descriptors of wines. DNS reached the highest amounts of phenolic compounds, showing a change in the phenolic pattern from flavonols and anthocyanins. Moreover, leaf removal influenced the levels of 37.8% of volatile compounds, quantified by increasing the concentration when early leaf removal was applied on the north side of the canopy (DN), with respect to the south (DS) and both sides (DNS). In the sensory analysis, Aglianico wines were defined by 16 sensory attributes with GM > 30%, where the highest values were reached for defoliation treatments vs. control. In conclusion, early leaf removal treatments allowed us to modulate the phenolic and volatile concentrations of Aglianico wines.

CRISPR/Cas9-mediated mutagenesis of VvbZIP36 promotes anthocyanin accumulation in grapevine (Vitis vinifera)

Anthocyanins are plant secondary metabolites that have a variety of biological functions, including pigmentation. The accumulation of anthocyanins is regulated by both transcriptional activators and repressors. Studies have shown that the bZIP family act primarily as positive regulators of anthocyanin biosynthesis, but there are few reports of negative regulation. Here, we report that a grapevine (Vitis vinifera) bZIP gene from group K, VvbZIP36, acts as a negative regulator of anthocyanin biosynthesis. Knocking-out one allele of VvbZIP36 in grapevine utilizing the CRISPR/Cas9 technology promoted anthocyanin accumulation. Correlation analysis of transcriptome and metabolome data showed that, compared with wild type, a range of anthocyanin biosynthesis genes were activated in VvbZIP36 mutant plants, resulting in the accumulation of related metabolites, including naringenin chalcone, naringenin, dihydroflavonols and cyanidin-3-O-glucoside. Furthermore, the synthesis of stilbenes (α-viniferin), lignans and some flavonols (including quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside and kaempferol-7-O-rhamnoside) was significantly inhibited and several genes linked to these metabolism, were down-regulated in the mutant plants. In summary, our results demonstrate that VvbZIP36, as a negative regulator of anthocyanin biosynthesis, plays a role in balancing the synthesis of stilbenes (α-viniferin), lignans, flavonols and anthocyanins.

Systematic analysis reveals O-methyltransferase gene family members involved in flavonoid biosynthesis in grape

O-methyltransferases (OMTs) are an important group of enzymes involved in the methylation of various secondary metabolites, including flavonoids. However, the features and functions of OMTs have not been comprehensively studied in grape (Vitis vinifera), a rich source of methylated flavonoids. Here, 47 OMT members were identified in grape genome. They were unevenly distributed on grape chromosomes and some genes were tandem duplicated, indicating the role of duplication processes in the expansion of this gene family. Based on the phylogenetic relationship, these OMTs were clustered into CCoAOMT and COMT subclades, which were further supported by the results of conserved motif and gene structure analysis. Correlation analysis revealed that three members (VvCCoAOMT1, VvCCoAOMT4, and VvCOMT1) were potentially involved in the synthesis of most methylated flavonoids in the berry skins. Expression profiling based on RNA-seq data and qRT-PCR experiments indicated that VvCCoAOMT1 and VvCCoAOMT4 had specific and high expression in berry skins, and responded to abscisic acid and high temperature treatments; and that VvCOMT1 expression was significantly induced during berry development and UVC treatment. Cis-regulatory element analysis suggested important roles of OMTs in growth, development, and defense against stresses. We further demonstrated the transcriptional regulation of VvCCoAOMT4 by VvMYBA1, a master regulator of grape berry anthocyanin, and verified the protein localization of VvCCoAOMT4 in membrane and nucleus. These findings facilitate a better understanding of the characteristics of OMT gene family, especially of the potential members involved in the formation of O-methylated flavonoids in grape.

Genome-Wide Association Study of Pericarp Color in Rice Using Different Germplasm and Phenotyping Methods Reveals Different Genetic Architectures

Pericarp colors (PC) in rice are determined by the types and content of flavonoids in the pericarp. The flavonoid compounds have strong antioxidant activities and are beneficial to human health. However, the genetic basis of PC in rice is still not well-understood. In this study, a genome-wide association study (GWAS) of PC was performed in a diverse rice collection consisting of 442 accessions using different phenotyping methods in two locations over 2 years. In the whole population consisting of white and colored pericarp rice, a total of 11 quantitative trait loci (QTLs) were identified using two phenotyping methods. Among these QTLs, nine were identified using the phenotypes represented by the presence and absence of pigmentation in pericarp, while 10 were identified using phenotypes of the degree of PC (DPC), in which eight are common QTLs identified using the two phenotyping methods. Using colored rice accessions and phenotypes based on DPC, four QTLs were identified, and they were totally different from the QTLs identified using the whole population, suggesting the masking effects of major genes on minor genes. Compared with the previous studies, 10 out of the 15 QTLs are first reported in this study. Based on the differential expression analysis of the predicted genes within the QTL region by both RNA-seq and real-time PCR (RT-PCR) and the gene functions in previous studies, LOC_Os01g49830, encoding a RAV transcription factor was considered as the candidate gene underlying qPC-1, a novel QTL with a large effect in this study. Our results provide a new insight into the genetic basis of PC in rice and contribute to developing the value-added rice with optimized flavonoid content through molecular breeding.

Methylation of MYBA1 is Associated with the Coloration in "Manicure Finger" Grape Skin

The "Manicure Finger" grape is notable for its fingerlike berries with a bright red top and yellow base; however, the mechanism underlying this color difference remains unknown. This study showed that the anthocyanin concentration and the expression levels of anthocyanin-related genes in the top skin were notably higher than those in the basal skin. The expression levels of DFR, UFGT, and GST were significantly correlated with the anthocyanin content. The promoters of the two VvUFGT alleles can be activated by VvMYBA1, which was verified by the yeast one-hybrid assay, the dual-luciferase reporter gene assay, and the electrophoretic mobility shift assay. Moreover, the methylation level of the VvMYBA1 promoter (-1488 to -1083 bp) in the top skin was significantly lower than that in the basal skin and was positively correlated with the anthocyanin content. Our data suggest that methylation levels of the VvMYBA1 promoter play a crucial role in regulating grape skin coloration.

Transcriptome Analysis Reveals Differentially Expressed Genes That Regulate Biosynthesis of the Active Compounds with Methyl Jasmonate in Rosemary Suspension Cells

To study the effects of Methyl jasmonates (MeJA) on rosemary suspension cells, the antioxidant enzymes’ change of activities under different concentrations of MeJA, including 0 (CK), 10 (M10), 50 (M50) and 100 μM MeJA (M100). The results demonstrated that MeJA treatments increased the activities of phenylalanine ammonla-lyase (PAL), superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) and polyphenol oxidase (PPO) and reduced the contents of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), thus accelerating the ROS scavenging. Comparative transcriptome analysis of different concentrations of MeJA showed that a total of 7836, 6797 and 8310 genes were differentially expressed in the comparisons of CKvsM10, CKvsM50, CKvsM100, respectively. The analysis of differentially expressed genes (DEGs) showed phenylpropanoid biosynthesis, vitamin B6, ascorbate and aldarate metabolism-related genes were significantly enriched. The transcripts of flavonoid and terpenoid metabolism pathways and plant hormone signal transduction, especially the jasmonic acid (JA) signal-related genes, were differentially expressed in CKvsM50 and CKvsM100 comparisons. In addition, the transcription factors (TFs), e.g., MYC2, DELLA, MYB111 played a key role in rosemary suspension cells under MeJA treatments. qRT-PCR of eleven DEGs showed a high correlation between the RNA-seq and the qRT-PCR result. Taken together, MeJA alleviated peroxidative damage of the rosemary suspension cells in a wide concentration range via concentration-dependent differential expression patterns. This study provided a transcriptome sequence resource responding to MeJA and a valuable resource for the genetic and genomic studies of the active compounds engineering in rosemary.

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

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

Integrative Analyses of Metabolomes and Transcriptomes Provide Insights into Flavonoid Variation in Grape Berries

Flavonoids in grapes contribute the quality of the berry, but the flavonoid diversity and the regulatory networks underlying the variation require a further investigation. In this study, we integrated multi-omics data to systematically explore the global metabolic and transcriptional profiles in the skins and pulps of three grape cultivars. The results revealed large-scale differences involved in the flavonoid metabolic pathway. A total of 133 flavonoids, including flavone and flavone C-glycosides, were identified. Beyond the visible differences of anthocyanins, there was large variation in other sub-branched flavonoids, most of which were positively correlated with anthocyanins in grapes. The expressions of most flavonoid biosynthetic genes and the major regulators MYBA1 were strongly consistent with the changes in flavonoids. Integrative analysis identified two novel transcription factors (MYB24 and MADS5) and two ubiquitin proteins (RHA2) as promising regulatory candidates for flavonoid biosynthesis in grapes. Further verification in various grape accessions indicated that five major genes including flavonol 3'5'-hydroxylase (F3'5'H), UDP-glucose:flavonoid 3-O-glycosyl-transferase, anthocyanin O-methyltransferase, acyltransferase (3AT), and glutathione S-transferase (GST4) controlled flavonoid variation in grape berries. These findings provide valuable information for understanding the mechanism of flavonoid biosynthesis in grape berries and the further development of grape health products.

Light Microclimate-Driven Changes at Transcriptional Level in Photosynthetic Grape Berry Tissues

Viticulture practices that change the light distribution in the grapevine canopy can interfere with several physiological mechanisms, such as grape berry photosynthesis and other metabolic pathways, and consequently impact the berry biochemical composition, which is key to the final wine quality. We previously showed that the photosynthetic activity of exocarp and seed tissues from a white cultivar (Alvarinho) was in fact responsive to the light microclimate in the canopy (low and high light, LL and HL, respectively), and that these different light microclimates also led to distinct metabolite profiles, suggesting a berry tissue-specific interlink between photosynthesis and metabolism. In the present work, we analyzed the transcript levels of key genes in exocarps and seed integuments of berries from the same cultivar collected from HL and LL microclimates at three developmental stages, using real-time qPCR. In exocarp, the expression levels of genes involved in carbohydrate metabolism (VvSuSy1), phenylpropanoid (VvPAL1), stilbenoid (VvSTS1), and flavan-3-ol synthesis (VvDFR, VvLAR2, and VvANR) were highest at the green stage. In seeds, the expression of several genes associated with both phenylpropanoid (VvCHS1 and VvCHS3) and flavan-3-ol synthesis (VvDFR and VvLAR2) showed a peak at the véraison stage, whereas that of RuBisCO was maintained up to the mature stage. Overall, the HL microclimate, compared to that of LL, resulted in a higher expression of genes encoding elements associated with both photosynthesis (VvChlSyn and VvRuBisCO), carbohydrate metabolism (VvSPS1), and photoprotection (carotenoid pathways genes) in both tissues. HL also induced the expression of the VvFLS1 gene, which was translated into a higher activity of the FLS enzyme producing flavonol-type flavonoids, whereas the expression of several other flavonoid pathway genes (e.g., VvCHS3, VvSTS1, VvDFR, and VvLDOX) was reduced, suggesting a specific role of flavonols in photoprotection of berries growing in the HL microclimate. This work suggests a possible link at the transcriptional level between berry photosynthesis and pathways of primary and secondary metabolism, and provides relevant information for improving the management of the light microenvironment at canopy level of the grapes.

A Synchronized Increase of Stilbenes and Flavonoids in Metabolically Engineered Vitis vinifera cv. Gamay Red Cell Culture

Stilbenes and flavonoids are two major health-promoting phenylpropanoid groups in grapes. Attempts to promote the accumulation of one group usually resulted in a decrease in the other. This study presents a unique strategy for simultaneously increasing metabolites in both groups in V. vinifera cv. Gamay Red grape cell culture, by overexpression of flavonol synthase (FLS) and increasing Phe availability. Increased Phe availability was achieved by transforming the cell culture with a second gene, the feedback-insensitive E. coli DAHP synthase (AroG*), and feeding them with Phe. A combined metabolomic and transcriptomic analysis reveals that the increase in both phenylpropanoid groups is accompanied by an induction of many of the flavonoid biosynthetic genes and no change in the expression levels of stilbene synthase. Furthermore, FLS overexpression with increased Phe availability resulted in higher anthocyanin levels, mainly those derived from delphinidin, due to the induction of F3'5'H. These insights may contribute to the development of grape berries with increased health benefits.

Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

BACKGROUND

Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide.

RESULTS

Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for 'response to stress', 'response to biotic stimulus', 'immune system process', etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism.

CONCLUSIONS

Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.

Genome-Wide Identification and Expression Analysis of MYB Transcription Factors and Their Responses to Abiotic Stresses in Woodland Strawberry (Fragaria vesca)

Woodland strawberry (Fragaria vesca) is a diploid strawberry that is widely used as a model of cultivated octoploid strawberry (Fragaria × ananassa). It has also been used as a model for Rosaceae fruits, non-climacteric fruits, and stolons. The MYB superfamily is the largest transcription factor family in plants, and its members play important roles in plant growth and development. However, the complete MYB superfamily in woodland strawberry has not been studied. In this study, a total of 217 MYB genes were identified in woodland strawberry and classified into four groups: one 4R-MYB protein, five 3R-MYB proteins, 113 2R-MYB proteins, and 98 1R-MYB proteins. The phylogenetic relationship of each MYB subgroup was consistent in terms of intron/exon structure and conserved motif composition. The MYB genes in woodland strawberry underwent loss and expansion events during evolution. The transcriptome data revealed that most FveMYB genes are expressed in several organs, whereas 15 FveMYB genes exhibit organ-specific expression, including five genes (FveMYB101, -112, -44, and -8; FveMYB1R81) in roots, two genes (FveMYB62 and -77) in stolon tips, three genes (FveMYB99 and -35; FveMYB1R96) in open flowers, and five genes (FveMYB76 and -100; FveMYB1R4, -5, and -86) in immature fruits. During fruit ripening of woodland strawberry, the expression levels of 84 FveMYB genes were decreased, of which five genes (FveMYB4, -22, -50, and -66; FveMYB1R57) decreased more than 10-fold, whereas those 18 FveMYB genes were increased, especially FveMYB10 and FveMYB74 increased more than 30-fold. In addition, the expression levels of 36, 68, 52, and 62 FveMYB genes were altered by gibberellic acid, abscisic acid, cold, and heat treatments, respectively, and among them, several genes exhibited similar expression patterns for multiple treatments, suggesting possible roles in the crosstalk of multiple signaling pathways. This study provides candidate genes for the study of stolon formation, fruit development and ripening, and abiotic stress responses.

DcTT8, a bHLH transcription factor, regulates anthocyanin biosynthesis in Dendrobium candidum

Dendrobium candidum stems are used as Chinese medicine and functional food. Red stems of D. candidum are rich in anthocyanins, which attract pollinator insects, protect the plants against environmental stress, and improve human health. The regulatory mechanisms of anthocyanin biosynthesis and stem color differentiation in D. candidum are not fully understood. Using transcriptome profiling, we identified a basic helix-loop-helix transcription factor (DcTT8) involved in anthocyanin biosynthesis in D. candidum stems. Ultraperformance liquid chromatography-tandem mass spectrometry was used to determine pigment contents and compositions in red and green stems, revealing that cyanidin is responsible for the red color. DcTT8 could bind the DcF3'H and DcUFGT promoters and finely regulate DcF3'H and DcUFGT expression. Our data indicate that DcTT8 participates in anthocyanin biosynthesis and offers novel insights into the transcriptional regulation of anthocyanin biosynthesis in D. candidum.

Sunburn in Grapes: A Review

Sunburn is a physiological disorder that affects the visual and organoleptic properties of grapes. The appearance of brown and necrotic spots severely affects the commercial value of the fruit, and in extreme cases, significantly decreases yield. Depending on the severity of the damage and the driving factors, sunburn on grapes can be classified as sunburn browning (SB) or as sunburn necrosis (SN). Sunburn results from a combination of excessive photosynthetically active radiation (PAR) and UV radiation and temperature that can be exacerbated by other stress factors such as water deficit. Fruit respond to these by activating antioxidant defense mechanisms, de novo synthesis of optical screening compounds and heat-shock proteins as well as through morphological adaptation. This review summarizes the current knowledge on sunburn in grapes and compares it with relevant literature on other fruits. It also discusses the different factors affecting the appearance and degree of sunburn, as well as the biochemical response of grapes to this phenomenon and different potential mitigation strategies. This review proposes further directions for research into sunburn in grapes.

Transcriptome Profiling During Muscadine Berry Development Reveals the Dynamic of Polyphenols Metabolism

Muscadine grapes accumulate higher amounts of bioactive phenolics compared with other grape species. To identify the molecular events associated with polyphenolic accumulation that influence antioxidant capacity, two contrasting muscadine genotypes (C5 and C6) with varied phenolic/flavonoid content and antioxidant activity were investigated via RNA-sequencing during berry development. The results showed that berry development is concomitant with transcriptome profile changes, which was more pronounced at the véraison (V) stage. Despite that the downregulation pattern of gene expression dominated the upregulation through berry development, the C5 genotype maintained higher expression levels. Comparative transcript profiling allowed the identification of 94 differentially expressed genes with potential relevance in regulating fruit secondary metabolism, including 18 transcription factors and 76 structural genes. The genes underlying the critical enzymes in the modification reactions of polyphenolics biosynthetic pathway, including hydroxylation, methylation, and glycosylation were more pronounced during the immature stages of prevéraison (PrV), V, and postvéraison (PoV) in the C5 genotype, resulting in more accumulation of biologically active phenolic/flavonoid derivatives. The results suggested that muscadine grapes, as in bunch grapes (Vitis sp.); possess a similar mechanism that organizes polyphenolics accumulation; however, the set of total flavonoids (TFs) and structural genes coordinating the pathway varies between the two species.

Genome-wide identification of R2R3-MYB family in wheat and functional characteristics of the abiotic stress responsive gene TaMYB344

Background

MYB superfamily is one of the most abundant families in plants, which plays important roles in plant growth, development, and productivity. However, to date, researches on MYBs in wheat (Triticum aestivum L.) are scattered mostly, not comprehensive.

Results

In this study, a total of 393 R2R3-MYBs and 12 R1R2R3-MYBs were identified and analyzed including gene structure, chromosomal distribution, synteny relationship, and evolutionary relationship. Then, 29 clusters tandem duplication and 8 clusters segmental duplication genes were discovered. The expression profile of the identified genes under abiotic and biotic stress was analyzed using RNA-seq data. Based on expression patterns analysis, we screened many candidate genes involved in plant response to abiotic and biotic stress. Among them, the functional characteristics of TaMYB344 were further studied. TaMYB344 was localized in the nucleus and functioned as a weak transcriptional activator. We demonstrated that TaMYB344-overexpressing transgenic tobacco plants had enhanced tolerance to drought, heat, and high salt stress.

Conclusions

In this study, 393 R2R3-MYBs and 12 R1R2R3-MYBs in wheat were systemically identified and analyzed. Differential expression analysis indicated that many R2R3-MYBs were involved in abiotic and biotic stress response. We identified a potential candidate gene TaMYB344, overexpression of which in tobacco plants enhanced drought, heat, and salt stress tolerance. These results will provide abundant molecular data for breeding new varieties of wheat in the future.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s12864-020-07175-9.

SmMYB2 promotes salvianolic acid biosynthesis in the medicinal herb Salvia miltiorrhiza

MYB transcription factors play vital roles in plant growth and metabolism. The phytohormone methyl jasmonate (MeJA) promotes phenolic acid accumulation in the medicinal herb Salvia miltiorrhiza, but the regulatory mechanism is poorly understood. Here, we identified the MeJA-responsive R2R3-MYB transcription factor gene SmMYB2 from a transcriptome library produced from MeJA-treated S. miltiorrhiza hairy roots. SmMYB2 expression was tightly correlated with the expression of key salvianolic acid biosynthetic genes including CYP98A14. SmMYB2 was highly expressed in the periderm of S. miltiorrhiza and SmMYB2 localized to the nucleus. Overexpressing SmMYB2 in S. miltiorrhiza hairy roots significantly increased the levels of salvianolic acids (including rosmarinic acid and salvianolic acid B) by upregulating salvianolic acid biosynthetic genes such as CYP98A14. SmMYB2 binds to the MYB-binding motifs in the promoter of CYP98A14, as confirmed by a dual-luciferase assay and electrophoretic mobility shift assays. Anthocyanin contents were significantly higher in SmMYB2-overexpressing hairy root lines than the control, primarily due to the increased expression of CHI, DFR, and ANS. These findings reveal the novel regulatory role of SmMYB2 in MeJA-mediated phenolic acid biosynthesis, providing a useful target gene for metabolic engineering and shedding light on the salvianolic acid regulatory network.

Combined Transcriptome and Metabolome analysis of Pitaya fruit unveiled the mechanisms underlying Peel and pulp color formation

BACKGROUND

Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transcriptome (RNA-Seq) and metabolome analysis (UPLC-MS/MS) to identify structural and regulatory genes and key metabolites associated with peel and pulp colors in three pitaya fruit types belonging to two different Hylocereus species.

RESULT

Our combined transcriptome and metabolome analyses suggest that the main strategy for obtaining red color is to increase tyrosine content for downstream steps in the betalain pathway. The upregulation of CYP76ADs is proposed as the color-breaking step leading to red or colorless pulp under the regulation by WRKY44 transcription factor. Supported by the differential accumulation of anthocyanin metabolites in red pulped pitaya fruit, our results showed the regulation of anthocyanin biosynthesis pathway in addition to betalain biosynthesis. However, no color-breaking step for the development of anthocyanins in red pulp was observed and no biosynthesis of anthocyanins in white pulp was found. Together, we propose that red pitaya pulp color is under the strict regulation of CYP76ADs by WRKYs and the anthocyanin coexistence with betalains is unneglectable. We ruled out the possibility of yellow peel color formation due to anthocyanins because of no differential regulation of chalcone synthase genes between yellow and green and no detection of naringenin chalcone in the metabolome. Similarly, the no differential regulation of key genes in the carotenoid pathway controlling yellow pigments proposed that the carotenoid pathway is not involved in yellow peel color formation.

CONCLUSIONS

Together, our results propose several candidate genes and metabolites controlling a single horticultural attribute i.e. color formation for further functional characterization. This study presents useful genomic resources and information for breeding pitaya fruit with commercially attractive peel and pulp colors. These findings will greatly complement the existing knowledge on the biosynthesis of natural pigments for their applications in food and health industry.

The Regulation of Floral Colour Change in Pleroma raddianum (DC.) Gardner

Floral colour change is a widespread phenomenon in angiosperms, but poorly understood from the genetic and chemical point of view. This article investigates this phenomenon in Pleroma raddianum, a Brazilian endemic species whose flowers change from white to purple. To this end, flavonoid compounds and their biosynthetic gene expression were profiled. By using accurate techniques (Ultra Performance Liquid Chromatography-High-Resolution Mass Spectrometry (UPLC-HRMS)), thirty phenolic compounds were quantified. Five key genes of the flavonoid biosynthetic pathway were partially cloned, sequenced, and the mRNA levels were analysed (RT-qPCR) during flower development. Primary metabolism was also investigated by gas chromatography coupled to mass spectrometry (GC-EIMS), where carbohydrates and organic acids were identified. Collectively, the obtained results suggest that the flower colour change in P. raddianum is determined by petunidin and malvidin whose accumulation coincides with the transcriptional upregulation of early and late biosynthetic genes of the flavonoid pathway, mainly CHS and ANS, respectively. An alteration in sugars, organic acids and phenolic co-pigments is observed together with the colour change. Additionally, an increment in the content of Fe³⁺ ions in the petals, from the pink to purple stage, seemed to influence the saturation of the colour.

Color Intensity of the Red-Fleshed Berry Phenotype of Vitis vinifera Teinturier Grapes Varies Due to a 408 bp Duplication in the Promoter of VvmybA1

Grapevine (Vitis vinifera) teinturier cultivars are characterized by their typical reddish leaves and red-fleshed berries due to ectopic anthocyanin formation. Wines of these varieties have economic importance as they can be used for blending to enhance the color of red wines. The unique and heritable mutation has been known for a long time but the underlying genetic mechanism still is not yet understood. Here we describe the association of the red-fleshed berry phenotype with a 408 bp repetitive DNA element in the promoter of the VvmybA1 gene (grapevine color enhancer, GCE). Three different clones of ‘Teinturier’ were discovered with two, three and five allelic GCE repeats (MybA1t2, MybA1t3 and MybA1t5). All three clones are periclinal chimeras; these clones share the same L1 layer, but have distinct L2 layers with different quantities of GCE repeats. Quantitative real time PCR and HPLC analysis of leaf and berry samples showed that the GCE repeat number strongly correlates with an increase of the expression of VvmybA1 itself and the VvUFGT gene regulated by it and the anthocyanin content. A model is proposed based on autoregulation of VvmybA1t to explain the red phenotype which is similar to that of red-fleshed apples. This study presents results about the generation and modes of action of three MybA1t alleles responsible for the red-fleshed berry phenotype of teinturier grapevines.

Transcriptomic and biochemical investigations support the role of rootstock-scion interaction in grapevine berry quality

Background

In viticulture, rootstock genotype plays a critical role to improve scion physiology, berry quality and to adapt grapevine (Vitis vinifera L.) to different environmental conditions. This study aimed at investigating the effect of two different rootstocks (1103 Paulsen - P - and Mgt 101–14 - M) in comparison with not grafted plants - NGC - on transcriptome (RNA-seq and small RNA-seq) and chemical composition of berry skin in Pinot noir, and exploring the influence of rootstock-scion interaction on grape quality. Berry samples, collected at veraison and maturity, were investigated at transcriptional and biochemical levels to depict the impact of rootstock on berry maturation.

Results

RNA- and miRNA-seq analyses highlighted that, at veraison, the transcriptomes of the berry skin are extremely similar, while variations associated with the different rootstocks become evident at maturity, suggesting a greater diversification at transcriptional level towards the end of the ripening process. In the experimental design, resembling standard agronomic growth conditions, the vines grafted on the two different rootstocks do not show a high degree of diversity. In general, the few genes differentially expressed at veraison were linked to photosynthesis, putatively because of a ripening delay in not grafted vines, while at maturity the differentially expressed genes were mainly involved in the synthesis and transport of phenylpropanoids (e.g. flavonoids), cell wall loosening, and stress response. These results were supported by some differences in berry phenolic composition detected between grafted and not grafted plants, in particular in resveratrol derivatives accumulation.

Conclusions

Transcriptomic and biochemical data demonstrate a stronger impact of 1103 Paulsen rootstock than Mgt 101–14 or not grafted plants on ripening processes related to the secondary metabolite accumulations in berry skin tissue. Interestingly, the MYB14 gene, involved in the feedback regulation of resveratrol biosynthesis was up-regulated in 1103 Paulsen thus supporting a putative greater accumulation of stilbenes in mature berries.

New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

BACKGROUND

Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera 'Red Globe' × 'Muscat Hamburg' was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes.

RESULTS

A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs.

CONCLUSION

These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.

Transcriptome sequencing and characterization of Astragalus membranaceus var. mongholicus root reveals key genes involved in flavonoids biosynthesis

BACKGROUND

Astragalus membranaceus (Fisch.) Bge. var. mongholicus (Bge.) Hsiao is a traditional medicinal herb of Leguminosae since it contains bioactive compounds such as flavonoids, which have significant pharmacological effects on immunity and antioxidant. However, the scanty genomic and transcriptome resources of Astragalus membranaceus have hindered further exploration of its biosynthesis and accumulation mechanism.

OBJECTIVE

This project aim to further improve our understanding of the relationship between transcriptional behavior and flavonoids content of A. mongholicus.

METHODS

The accumulation of flavonoids and related gene expression in five different developmental stages (A: vegetative, B: florescence, C: fruiting, D: fruit ripening and E: defoliating stages) of A. mongholicus root were studied by combining UV spectrophotometry and transcriptomic techniques. The de novo assembly, annotation and functional evaluation of the contigs were performed with bioinformatics tools.

RESULTS

After screening and assembling the raw data, there were a total of 158,123 unigenes with an average length of 644.89 bp were finally obtained, which has 8362 unigenes could be jointly annotated by NR, SwissProt, eggNOG, GO, KEGG and Pfam databases. KEGG enrichment analysis was performed on differentially expressed genes(DEGs)in the four groups (A vs. B, B vs. C, C vs. D, D vs. E). The results showed that many DEGs in each group were significantly enriched to flavonoids biosynthesis related pathways. Among them, a number of 86 were involved in the biosynthesis of isoflavonoid (12), flavonoid (5) and phenylpropanoid (69). Further analysis of these DEGs revealed that the expression levels of key genes such as PAL, 4CL, CCR, COMT, DFR, etc. were all down-regulated at the fruiting stage, and then raised at the fruit ripening stage. This expression pattern was similar to the accumulation trend of total flavonoids content.

CONCLUSIONS

In summary, this comprehensive transcriptome dataset allowed the identification of genes associated with flavonoids metabolic pathways. The results laid a foundation for the biosynthesis and regulation of flavonoids. It also provided a scientific basis for the most suitable harvest time and resource utilization of A. mongholicus.