Discovery of a DFR gene that controls anthocyanin accumulation in the spiny Solanum group: roles of a natural promoter variant and alternative splicing

In pursuit of purple: anthocyanin biosynthesis in fruits of the tomato clade

Over the past decade, progress has been made in the characterization of anthocyanin synthesis in fruits of plants belonging to the tomato clade. The genomic elements underlying the activation of the process were identified, providing the basis for understanding how the pathway works in these species. In this review we explore the genetic mechanisms that have been characterized to date, and detail the various wild relatives of the tomato, which have been crucial for recovering ancestral traits that were probably lost during evolution from green-purple to yellow and red tomatoes. This knowledge should help developing strategies to further enhance the status of the commercial tomato lines on sale, based on both genome editing and breeding techniques.

A 224-bp Indel in the Promoter of PeMYB114 Accounts for Anthocyanin Accumulation of Skin in Passion Fruit (Passiflora spp.)

Passion fruit (Passiflora spp.) is an important fruit tree in the family Passifloraceae. The color of the fruit skin, a significant agricultural trait, is determined by the content of anthocyanin in passion fruit. However, the regulatory mechanisms behind the accumulation of anthocyanin in different passion fruit skin colors remain unclear. In the study, we identified and characterized a R2R3-MYB transcription factor, PeMYB114, which functions as a transcriptional activator in anthocyanin biosynthesis. Yeast one-hybrid system and dual-luciferase analysis showed that PeMYB114 could directly activate the expression of anthocyanin structural genes (PeCHS and PeDFR). Furthermore, a natural variation in the promoter region of PeMYB114 alters its expression. PeMYB114purple accessions with the 224-bp insertion have a higher anthocyanin level than PeMYB114yellow accessions with the 224-bp deletion. The findings enhance our understanding of anthocyanin accumulation in fruits and provide genetic resources for genome design for improving passion fruit quality.

The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation

Visual cues are of critical importance for the attraction of animal pollinators, however, little is known about the molecular mechanisms underpinning intraspecific floral colour variation. Here, we combined comparative spectral analysis, targeted metabolite profiling, multi-tissue transcriptomics, differential gene expression, sequence analysis and functional analysis to investigate a bee-pollinated orchid species, Glossodia major with common purple- and infrequent white-flowered morphs. We found uncommon and previously unreported delphinidin-based anthocyanins responsible for the conspicuous and pollinator-perceivable colour of the purple morph and three genetic changes underpinning the loss of colour in the white morph - (1) a loss-of-function (LOF; frameshift) mutation affecting dihydroflavonol 4-reductase (DFR1) coding sequence due to a unique 4-bp insertion, (2) specific downregulation of functional DFR1 expression and (3) the unexpected discovery of chimeric Gypsy transposable element (TE)-gene (DFR) transcripts with potential consequences to the genomic stability and post-transcriptional or epigenetic regulation of DFR. This is one of few known cases where regulatory changes and LOF mutation in an anthocyanin structural gene, rather than transcription factors, are important. Furthermore, if TEs prove to be a frequent source of mutation, the interplay between environmental stress-induced TE evolution and pollinator-mediated selection for adaptive colour variation may be an overlooked mechanism maintaining floral colour polymorphism in nature.

FvDFR2 rather than FvDFR1 play key roles for anthocyanin synthesis in strawberry petioles

The accumulation of anthocyanins can be found in both the fruit and petioles of strawberries, but the fruit appears red while the petioles appear purple-red. Additionally, in the white-fruited diploid strawberries, the petioles can accumulate anthocyanins normally, suggesting a different synthesis pattern between the petioles and fruits. We screened the EMS mutagenized population of a red-fruited diploid strawberry 'Ruegen' and discovered a mutant which showed no anthocyanin accumulation in the petioles but normal accumulation in the fruit. Through BSA sequencing and allelic test, it was found that a mutation in FvDFR2 was responsible for this phenotype. Furthermore, the complex formed by the interaction between the petiole-specific FvMYB10L and FvTT8 only binds the promoter of FvDFR2 but not FvDFR1, resulting in the expression of only FvDFR2 in the petiole. FvDFR2 can catalyze the conversion of DHQ and eventually the formation of cyanidin and peonidin, giving the petiole a purplish-red color. In the fruit, however, both FvDFR1 and FvDFR2 can be expressed, which can mediate the synthesis of cyanidin and pelargonidin. Our study clearly reveals different regulation of FvDFR1 and FvDFR2 in mediating anthocyanin synthesis in petioles and fruits.

The secreted feruloyl esterase of Verticillium dahliae modulates host immunity via degradation of GhDFR

Feruloyl esterase (ferulic acid esterase, FAE) is an essential component of many biological processes in both eukaryotes and prokaryotes. This research aimed to investigate the role of FAE and its regulation mechanism in plant immunity. We identified a secreted feruloyl esterase VdFAE from the hemibiotrophic plant pathogen Verticillium dahliae. VdFAE acted as an important virulence factor during V. dahliae infection, and triggered plant defence responses, including cell death in Nicotiana benthamiana. Deletion of VdFAE led to a decrease in the degradation of ethyl ferulate. VdFAE interacted with Gossypium hirsutum protein dihydroflavanol 4-reductase (GhDFR), a positive regulator in plant innate immunity, and promoted the degradation of GhDFR. Furthermore, silencing of GhDFR led to reduced resistance of cotton plants against V. dahliae. The results suggested a fungal virulence strategy in which a fungal pathogen secretes FAE to interact with host DFR and interfere with plant immunity, thereby promoting infection.

Transcription factor NnMYB5 controls petal color by regulating GLUTATHIONE S-TRANSFERASE2 in Nelumbo nucifera

Lotus (Nelumbo spp.) is an important aquatic ornamental genus in the family Nelumbonaceae comprising only 2 species: Nelumbo lutea with yellow flowers and Nelumbo nucifera with red or white flowers. The petal color variations between these 2 species have previously been associated with the potential activities of FLAVONOL SYNTHASE (FLS) and MYB5. However, the underlying genetic mechanisms of flower color divergence within the N. nucifera species remain unclear. Here, quantitative trait locus mapping led to the identification of MYB5, a candidate gene controlling petal color in N. nucifera. Genotyping of 213 natural lotus accessions revealed an 80 kb presence/absence variant (PAV) of the NnMYB5 gene that is associated with petal color variation. Transcriptome analysis, dual-luciferase, and yeast 1-hybrid assays showed that NnMYB5 could directly activate the anthocyanin transporter gene GLUTATHIONE S-TRANSFERASE2 (NnGST2). Heterologous expression of NnGST2 in Arabidopsis (Arabidopsis thaliana) and its overexpression in lotus petals induced anthocyanin accumulation. Deletion of the 80 kb PAV within NnMYB5 inactivated NnGST2 expression and blocked anthocyanin accumulation in white N. nucifera petals. In contrast, the anthocyanin deficiency of N. lutea occurred due to pseudogenized NlMYB5 alleles. Our results establish a regulatory link between NnMYB5 and NnGST2 in petal anthocyanin accumulation and demonstrate the independent mechanisms controlling flower coloration in Nelumbo.

Transcriptomics integrated with metabolomics to characterize key pigment compounds and genes related to anthocyanin biosynthesis in Zanthoxylum bungeanum peel

Zanthoxylum bungeanum is an important condiment with high economic value and its peel color is one of the main quality indexes. However, the key pigment compounds and related genes are still unclear affecting the quality control of the plants. In this study, the contents of four types of pigments were measured in Z. bungeanum and flavonoids were identified as the most important pigments. Based on the targeted flavonoid metabolomics of Z. bungeanum peels, 14 key pigment compounds were screened out from 152 flavonoids, among which cyanidin-3-O-rutinoside and cyanidin-3-O-glucoside were the most critical compounds for peel color. They were further verified to be present in nine varieties of Z. bungeanum by HPLC fingerprints. The 14 compounds were all associated with flavonoid and anthocyanin biosynthesis pathways and the 39 differentially expressed genes related to these pathways were annotated and screened based on transcriptomics. The genes ZbDFR, ZbANS, and ZbUFGT were identified as three key genes for anthocyanin synthesis in Z. bungeanum peels. Further qRT-PCR results confirmed the reliability of transcriptomics and the accuracy of gene screening. Subsequent protein induced expression demonstrated that ZbANS and ZbUFGT were expressed after 12 h induced by IPTG while ZbDFR was expressed after 15 h. Further transient and stable transformation analysis confirmed that both anthocyanin content and the expression of ZbDFR were significantly increased in overexpression Z. bungeanum leaves and Nicotiana benthamiana. The functional effect of stable transformation of ZbDFR was more significant than that of transient transformation with a 7.67-fold/1.49-fold difference in total anthocyanin content and a 42.37-fold/12.32-fold difference in the expression of ZbDFR. This study provides new insights into the chemical composition and the molecular mechanisms of Z. bungeanum peel color and lays an effective foundation for the color quality control, multi-purpose utilization of Z. bungeanum and the creation of new germplasm.

Flavonoid synthesis in Lamiophlomis rotata from Qinghai-Tibet Plateau is influenced by soil properties, microbial community, and gene expression

Lamiophlomis rotata is a medicinal plant in Qinghai-Tibet Plateau, in which flavonoid compounds are the major medicinal components. However, it remains unclear how flavonoid metabolism of L. rotata is influenced by soil properties and microbial community. In this study, we collected L. rotata seedlings and rhizosphere soils from five habitats ranging from 3750 to 4270 m of altitude and analyzed the effects of habitat conditions on flavonoid metabolism. The activities of peroxidase, cellulase, and urease were increased with altitude, while those of alkaline phosphatase, alkaline protease, and sucrase were decreased with altitude. Analysis of OTUs showed that the total number of bacterial genera was higher than that of fungal genera. The highest number of fungal genera was 132, and that of bacterial genera was 33 in Batang (BT) town in Yushu County at an altitude of 3880 m, suggesting that the fungal communities may play a critical role in L. rotata rhizosphere soils. Flavonoids in leaves and roots of L. rotata shared a similar pattern, with a trend of increasing levels with altitude. The highest flavonoid content measured, 12.94 mg/g in leaves and 11.43 mg/g in roots, was from Zaduo (ZD) County at an altitude of 4208 m. Soil peroxidases affected quercetin content in leaves of L. rotata, while the fungus Sebacina affected flavonoid content in leaves and roots of L. rotata. The expression of PAL, F3'H, FLS, and FNS genes showed a declining trend in leaves with altitude, while F3H showed an increasing trend in both leaves and roots. Overall, soil physicochemical properties and microbial community affect flavonoid metabolism in L. rotata in Qinghai-Tibet Plateau. The variations in flavonoid content and gene expression as well as their associations with soil factors revealed the complexity of the growth conditions and genetic makeup in L. rotata habitats of Qinghai-Tibet Plateau.

A Compendium for Novel Marker-Based Breeding Strategies in Eggplant

The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.

DNA methylation-mediated phenylpropane and starch metabolism causes male poplars to be more tolerant to nitrogen deficiency than females

Nitrogen (N) is an essential nutrient for plant growth and development. Dioecious plants, especially perennial plants, are often faced with a shortage of N supply in nature. Poplar is one of the most important dioecious and perennials species. Due to the different ecological functions, female and male poplars adopt different adaptation strategies to N limitation. However, the regulation in epigenetic mechanism is poorly understood on sexes. Here, the integrative analysis of whole-genome bisulfite sequencing (WGBS), RNA sequencing, and plant physiological analysis on female and male Populus cathayana were performed. We found that N deficiency reprograms methylation in both sexes, and the CG and CHH methylation types played critical roles in female and male poplars, respectively. Induced by DNA methylation, N-deficient males had a stronger phenylpropanoid synthesis pathway and less anthocyanin accumulation than females, which not only strengthened the N cycle but also reduced the defense cost of males. In addition, compared with male poplars, females accumulated more starch to expend excess energy under N limited condition. Additionally, DNA methylation also mediated hormone signalling involved in anthocyanin synthesis and starch metabolism. Therefore, our study reveals new molecular evidences that male poplars are more tolerant to N deficiency than females, which provides a reference for ecological adaptability of forest trees.

Alternative splicing: transcriptional regulatory network in agroforestry

Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNA^ir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.