Transcriptome analysis reveals the mechanism of anthocyanidins biosynthesis during grains development in purple corn (Zea mays L.)

De novo transcriptome analysis identifies RpMYB1 as an activator of anthocyanin biosynthesis in Rehmannia piasezkii

Rehmannia piasezkii is a kind of medicinal plants, of the Orobanchaceae family, and well known for its large pink or purple corolla. However, no research on the molecular mechanism of flower color formation in R. piasezkii has been conducted so far. In this study, we investigated the transcriptome of root, stem, leaf and corollas of R. piasezkii using transcriptome sequencing technology and assembled 144,582 unigenes. A total of 58 anthocyanin biosynthetic genes were identified in the R. piasezkii transcriptome, fourteen of which were highly correlated with anthocyanin content, especially RpF3H2, RpDFR2, RpANS1, RpANS2 and RpUFGT. Totally, 35 MYB genes with FPKM values greater than 5 were identified in the R. piasezkii transcriptome, including an R2R3 MYB transcriptional factor RpMYB1, which belongs to subgroup 6 of the R2R3 MYB family. Agrobacterium-mediated transient expression of Nicotiana benthamiana revealed that overexpression of RpMYB1 could activate the expression of structural genes in anthocyanin synthesis pathway and promote the accumulation of anthocyanins in N. benthamiana leaves, indicating that RpMYB1 is a positive regulator of anthocyanin synthesis. Furthermore, combined transient overexpression of RpMYB1 with RpANS1, RpMYB1+RpANS1 with other structural genes all could further enhance the accumulation of anthocyanins in N. benthamiana leaves. Permanent overexpression of RpMYB1 in R. glutinosa promoted anthocyanin accumulation and expression levels of RgCHS, RgF3H, RgDFR and RgANS. Further evidence from dual-luciferase assay suggested that RpMYB1 could bind to the promoter of RpDFR2 and hence activating its expression. These findings provide insight into the molecular regulation in anthocyanin biosynthesis in R. piasezkii and provide valuable genetic resources for the genetic improvement of flower color.

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

Identification of crucial metabolites in colored grain wheat (Triticum aestivum L.) regulated by nitrogen application

Colored wheats have drawn attention due to their nutritional compounds. However, limited information is obtained on the effects of nitrogen fertilizer on crucial metabolites and grain quality of wheats with different color grain. In the study, the pot experiment was conducted with white (W), blue (B), and purple (P) grain wheats treated with three levels of N (LN, 0 g kg-1; MN, 0.05 g kg-1; HN, 0.1 g kg-1). Higher N level could promote wheat growth, improve grain indexes, and nutrient uptake. SPAD values of flag leaves remained in the order HN > MN > LN across all wheat varieties, and maintained increasing during tested stages under purple wheat. Metabolomics analysis showed that the annotated 358 metabolites mainly belonged to 29 classes, including carboxylic acids and their derivatives, fatty acids, flavonoids, and phenols. 35, 39, and 70 differential accumulated metabolites were respectively found between the WLN vs. WHN, the BHN vs. BLN, and the PHN vs. PLN, which were mainly enriched in "biosynthesis of plant secondary metabolites", "cGMP-PKG signaling pathway", "sphingolipid signaling pathway", "biosynthesis of alkaloids derived from histidine and purine", and "biosynthesis of plant hormones". Additionally, erucic acid was dominated in the three wheat cultivars, and was decreased after treated with high N levels. Our study preliminarily revealed the different response mechanisms to different N levels in the white, blue, and purple grain wheats, and lay a theoretical foundation for further breeding of excellent colored grain varieties.

Transcriptomic and metabolic analysis unveils the mechanism behind leaf color development in Disanthus cercidifolius var. longipes

Introduction: Leaf coloration in Disanthus cercidifolius var. longipes results from the interplay of various pigments undergoing complex catalytic reactions. Methods: We aimed to elucidate the mechanisms of pigment biosynthesis affecting leaf color transition in D. cercidifolius var. longipes by analyzing variations in pigment accumulation and levels of gene expression. Results: We identified 468, 577, and 215 differential metabolites in green leaves (GL), gradual-color-changing leaves (GCCL), and red leaves (RL), respectively, with 94 metabolites shared across all comparisons. Metabolite accumulation patterns were similar among GL, GCCL, and RL, with flavonoids being the main differential metabolites. Delphinidin, malvidin, and petunidin derivatives were mostly accumulated in GCCL, whereas cyanidin, pelargonidin, and peonidin derivatives accumulated in RL. Transcriptome sequencing was used to identify differentially expressed genes. The expression of anthocyanin biosynthetic pathway genes was associated with anthocyanin accumulation patterns. Discussion: Our findings reveal that the content of delphinidin, malvidin, petunidin, and carotenoids collectively determines the gradual transition of leaf color from green in spring and summer to green, purple, and orange-yellow in early autumn, whereas the content of cyanidin, peonidin, pelargonidin, and carotenoids together causes the autumnal transition to red or orange-red colors as leaves of D. cercidifolius var. longipes age.

Association Analysis of Transcriptome and Targeted Metabolites Identifies Key Genes Involved in Iris germanica Anthocyanin Biosynthesis

The anthocyanin biosynthetic pathway is the main pathway regulating floral coloration in Iris germanica, a well-known ornamental plant. We investigated the transcriptome profiles and targeted metabolites to elucidate the relationship between genes and metabolites in anthocyanin biosynthesis in the bitone flower cultivar 'Clarence', which has a deep blue outer perianth and nearly white inner perianth. In this study, delphinidin-, pelargonidin-, and cyanidin-based anthocyanins were detected in the flowers. The content of delphinidin-based anthocyanins increased with the development of the flower. At full bloom (stage 3), delphinidin-based anthocyanins accounted for most of the total anthocyanin metabolites, whereas the content of pelargonidin- and cyanidin-based anthocyanins was relatively low. Based on functional annotations, a number of novel genes in the anthocyanin pathway were identified, which included early biosynthetic genes IgCHS, IgCHI, and IgF3H and late biosynthetic genes Ig F3'5'H, IgANS, and IgDFR. The expression of key structural genes encoding enzymes, such as IgF3H, Ig F3'5'H, IgANS, and IgDFR, was significantly upregulated in the outer perianth compared to the inner perianth. In addition, most structural genes exhibited their highest expression at the half-color stage rather than at the full-bloom stage, which indicates that these genes function ahead of anthocyanins synthesis. Moreover, transcription factors (TFs) of plant R2R3-myeloblastosis (R2R3-MYB) related to the regulation of anthocyanin biosynthesis were identified. Among 56 R2R3-MYB genes, 2 members belonged to subgroup 4, with them regulating the expression of late biosynthetic genes in the anthocyanin biosynthetic pathway, and 4 members belonged to subgroup 7, with them regulating the expression of early biosynthetic genes in the anthocyanin biosynthetic pathway. Quantitative real-time PCR (qRT-PCR) analysis was used to validate the data of RNA sequencing (RNA-Seq). The relative expression profiles of most candidate genes were consistent with the FPKM of RNA-seq. This study identified the key structural genes encoding enzymes and TFs that affect anthocyanin biosynthesis, which provides a basis and reference for the regulation of plant anthocyanin biosynthesis in I. germanica.

Integrative transcriptome and metabolome analysis reveals the mechanisms of light-induced pigmentation in purple waxy maize

Introduction

Waxy maize, mainly consumed at the immature stage, is a staple and vegetable food in Asia. The pigmentation in the kernel of purple waxy maize enhances its nutritional and market values. Light, a critical environmental factor, affects anthocyanin biosynthesis and results in pigmentation in different parts of plants, including in the kernel. SWL502 is a light-sensitive waxy maize inbred line with purple kernel color, but the regulatory mechanism of pigmentation in the kernel resulting in purple color is still unknown.

Methods

In this study, cyanidin, peonidin, and pelargonidin were identified as the main anthocyanin components in SWL502, evaluated by the ultra-performance liquid chromatography (UPLC) method. Investigation of pigment accumulation in the kernel of SWL502 was performed at 12, 17, and 22 days after pollination (DAP) under both dark and light treatment conditions via transcriptome and metabolome analyses.

Results

Dark treatment affected genes and metabolites associated with metabolic pathways of amino acid, carbohydrate, lipid, and galactose, biosynthesis of phenylpropanoid and terpenoid backbone, and ABC transporters. The expression of anthocyanin biosynthesis genes, such as 4CL2, CHS, F3H, and UGT, was reduced under dark treatment. Dynamic changes were identified in genes and metabolites by time-series analysis. The genes and metabolites involved in photosynthesis and purine metabolism were altered in light treatment, and the expression of genes and metabolites associated with carotenoid biosynthesis, sphingolipid metabolism, MAPK signaling pathway, and plant hormone signal transduction pathway were induced by dark treatment. Light treatment increased the expression level of major transcription factors such as LRL1, myc7, bHLH125, PIF1, BH093, PIL5, MYBS1, and BH074 in purple waxy maize kernels, while dark treatment greatly promoted the expression level of transcription factors RVE6, MYB4, MY1R1, and MYB145.

Discussion

This study is the first report to investigate the effects of light on waxy maize kernel pigmentation and the underlying mechanism at both transcriptome and metabolome levels, and the results from this study are valuable for future research to better understand the effects of light on the regulation of plant growth.

Transcriptome Analysis Revealed the Potential Molecular Mechanism of Anthocyanidins' Improved Salt Tolerance in Maize Seedlings

Anthocyanin, a kind of flavonoid, plays a crucial role in plant resistance to abiotic stress. Salt stress is a kind of abiotic stress that can damage the growth and development of plant seedlings. However, limited research has been conducted on the involvement of maize seedlings in salt stress resistance via anthocyanin accumulation, and its potential molecular mechanism is still unclear. Therefore, it is of great significance for the normal growth and development of maize seedlings to explore the potential molecular mechanism of anthocyanin improving salt tolerance of seedlings via transcriptome analysis. In this study, we identified two W22 inbred lines (tolerant line pur-W22 and sensitive line bro-W22) exhibiting differential tolerance to salt stress during seedling growth and development but showing no significant differences in seedling characteristics under non-treatment conditions. In order to identify the specific genes involved in seedlings' salt stress response, we generated two recombinant inbred lines (RILpur-W22 and RILbro-W22) by crossing pur-W22 and bro-W22, and then performed transcriptome analysis on seedlings grown under both non-treatment and salt treatment conditions. A total of 6100 and 5710 differentially expressed genes (DEGs) were identified in RILpur-W22 and RILbro-W22 seedlings, respectively, under salt-stressed conditions when compared to the non-treated groups. Among these DEGs, 3160 were identified as being present in both RILpur-W22 and RILbro-W22, and these served as commonly stressed EDGs that were mainly enriched in the redox process, the monomer metabolic process, catalytic activity, the plasma membrane, and metabolic process regulation. Furthermore, we detected 1728 specific DEGs in the salt-tolerant RILpur-W22 line that were not detected in the salt-sensitive RILbro-W22 line, of which 887 were upregulated and 841 were downregulated. These DEGs are primarily associated with redox processes, biological regulation, and the plasma membrane. Notably, the anthocyanin synthesis related genes in RILpur-W22 were strongly induced under salt treatment conditions, which was consistented with the salt tolerance phenotype of its seedlings. In summary, the results of the transcriptome analysis not only expanded our understanding of the complex molecular mechanism of anthocyanin in improving the salt tolerance of maize seedlings, but also, the DEGs specifically expressed in the salt-tolerant line (RILpur-W22) provided candidate genes for further genetic analysis.

Anthocyanins in metabolites of purple corn

Purple corn (Zea mays L.) is a special variety of corn, rich in a large amount of anthocyanins and other functional phytochemicals, and has always ranked high in the economic benefits of the corn industry. However, most studies on the stability of agronomic traits and the interaction between genotype and environment in cereal crops focus on yield. In order to further study the accumulation and stability of special anthocyanins in the growth process of purple corn, this review starts with the elucidation of anthocyanins in purple corn, the biosynthesis process and the gene regulation mechanism behind them, points out the influence of anthocyanin metabolism on anthocyanin metabolism, and introduces the influence of environmental factors on anthocyanin accumulation in detail, so as to promote the multi-field production of purple corn, encourage the development of color corn industry and provide new opportunities for corn breeders and growers.

Metabolic profiling and transcriptome analysis provide insights into the accumulation of flavonoids in chayote fruit during storage

Chayote (Sechium edulel) fruits are rich in flavonoids, folate, and low-calorie food. However, studies about the flavonoids and the corresponding regulatory mechanism of flavonoid synthesis in chayote fruits was still unclear. In present study, an integrated transcriptome and metabolite analysis of chayote fruits at three different storage stages were conducted to explore the flavonoid compositions and gene expression associated with flavonoid synthesis. Through the UPLC-MS/MS analysis, a total of 57 flavonoid compounds were detected. Of these, 42 flavonoid glycosides were significantly differential accumulation in chayote fruits at three different storage stages. Many genes associated with flavonoid synthesis were differentially expressed in chayote fruits at three different storage stages through RNA-seq analysis, including structural genes and some TFs. There was a high correlation between RNA-seq analysis and metabolite profiling, and the expression level of candidate genes in the flavonoid synthesis pathway were consistent with the dynamic changes of flavonoids. In addition, one R2R3-MYB transcription factor, FSG0057100, was defined as the critical regulatory gene of flavonoid synthesis. Furthermore, exogenous application of phenylalanine increased the total content of flavonoids and promoted some flavonoid biosynthesis-related gene expression in chayote fruits. The above results not only make us better understand the molecular mechanism of flavonoid synthesis in chayote fruits, but also contribute to the promotion and application of chayote products.

The Anthocyanin Accumulation Related ZmBZ1, Facilitates Seedling Salinity Stress Tolerance via ROS Scavenging

Anthocyanins are a class of antioxidants that scavenge free radicals in cells and play an important role in promoting human health and preventing many diseases. Here, we characterized a maize Bronze gene (BZ1) from the purple colored W22 introgression line, which encodes an anthocyanin 3-O-glucosyltransferase, a key enzyme in the anthocyanin synthesis pathway. Mutation of ZmBZ1 showed bronze-colored seeds and reduced anthocyanins in seeds aleurone layer, seedlings coleoptile, and stem of mature plants by comparison with purple colored W22 (WT). Furthermore, we proved that maize BZ1 is an aleurone layer-specific expressed protein and sub-located in cell nucleus. Real-time tracing of the anthocyanins in developing seeds demonstrated that the pigment was visible from 16 DAP (day after pollination) in field condition, and first deposited in the crown part then spread all over the seed. Additionally, it was transferred along with the embryo cell activity during seed germination, from aleurone layer to cotyledon and coleoptile, as confirmed by microscopy and real-time qRT-PCR. Finally, we demonstrated that the ZmBZ1 contributes to stress tolerance, especially salinity. Further study proved that ZmBZ1 participates in reactive oxygen scavenging (ROS) by accumulating anthocyanins, thereby enhancing the tolerance to abiotic stress.

Variation in the Main Health-Promoting Compounds and Antioxidant Activity of Different Edible Parts of Purple Flowering Stalks (Brassica campestris var. purpuraria) and Green Flowering Stalks (Brassica campestris var. campestris)

Purple flowering stalks and green flowering stalks of Brassica campestris are widely cultivated in the middle and upper reaches of the Yangtze River. Here, concentrations of the main health-promoting compounds and antioxidant capacity levels were characterized in different parts (leaves, peel, flesh, and inflorescences) of purple and green flowering stalks. There were significant differences in the concentrations of health-promoting compounds between the two variants; the concentrations of pigments, especially anthocyanidins, and gluconapin, were significantly higher in purple flowering stalks than in green flowering stalks, and the progoitrin content was significantly higher in green flowering stalks than in purple flowering stalks. The leaves were judged to be the most nutritional edible part because they had the highest concentrations of pigments, ascorbic acid, proanthocyanidins, flavonoids, and total phenolics. Antioxidant capacity was also highest in the leaves, and it was positively correlated with the concentration of health-promoting compounds. Purple flowering stalks and green flowering stalks were found to be rich in health-promoting compounds, especially glucosinolates. Overall, our findings indicate that consumption of the leaves and peel would provide the most health benefits. Some suggestions are provided regarding the processing and utilization of these edible components.

Comprehensive Transcriptome–Metabolome Analysis and Evaluation of the Dark_Pur Gene from Brassica juncea That Controls the Differential Regulation of Anthocyanins in Brassica rapa

Chinese cabbage (Brassica rapa) is a major vegetable crop in China. The accumulation of anthocyanins improves the quality and flavor of Brassica crops and is beneficial for human health. There has been great research interest in breeding purple Chinese cabbage, for which it is necessary to study the key genes and mechanisms of anthocyanin accumulation. Through distant hybridization between purple mustard (Brassica. juncea) and green Chinese cabbage (B. rapa), purple Chinese cabbage plants were obtained. Furthermore, the Dark_Pur gene was cloned in the purple Chinese cabbage plants, which came from purple mustard and may be responsible for the purple phenotype in purple Chinese cabbage plants. Through particle bombardment of isolated microspores from Chinese cabbage to transform the Dark_Pur gene, the transformed purple Chinese cabbage plant was obtained, thus verifying the function of the Dark_Pur gene. To further study the Dark_Pur gene regulatory mechanism of anthocyanin accumulation in Chinese cabbage, the purple/green Chinese cabbage lines and purple/green mustard lines were subjected to transcriptome–metabolome analysis. Three stages (cotyledon, seedling, and large-leaf stages) of the purple/green Chinese cabbage lines and purple/green mustard lines were selected for analysis. The results indicated that the expression level of the transcription factor genes BraA09g028560.3C, BraA03g019460.3C, and BraA07g035710.3C may be induced by the Dark_Pur gene and they play an important role in purple Chinese cabbage, and BjuB010898 and BjuO006089 may be responsible for anthocyanin accumulation in mustard. Studying the structural genes of the purple Chinese cabbage showed that PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, FLS, DFR, ANS, and UGT were up-regulated in three growth periods. There were 22 and 10 differentially expressed metabolites (DEMs) in seedling and large-leaf stages between purple/green Chinese cabbage, respectively, and 12 and 14 differentially expressed metabolites (DEMs) in seedling and large-leaf stages between purple/green mustard, respectively, which may indicate that the Dark_Pur gene from purple mustard greatly regulates anthocyanin accumulation in purple Chinese cabbage. This study provides a foundation for further elucidating anthocyanin regulation.

Colored Corn: An Up-Date on Metabolites Extraction, Health Implication, and Potential Use

Colored (orange, pink, red, purple, and blue) corn strongly attracted attention on its healthy properties mainly due to its anthocyanin and carotenoid composition which is also responsible for its pigmentation. The present review summarized the recent updates on the extraction and chemical characterization of the main plant secondary metabolites present in colored seeds, kernel, cob, husk, and silk. The main approaches used to stabilize the extracts have been discussed as well as their food and non-food uses. Both in vitro and in vivo (animal models) studies on the different effects (antibacterial, antimutagenic, antioxidant, and anti-inflammatory activities, effects on metabolic syndrome, diabetes, glucose and lipidic metabolism, and neuroprotection) of pigmented extracts on animal and human health have been summarized.