Search Results (62)

Pea (Pisum sativum L.) is a significant source of dietary protein, starch, fiber, and minerals, offering health benefits and serving as both a green vegetable and dry grain. The pigment contents in pea pods with different colors and related genes are still unclear. We conducted an integrated transcriptome and metabolome analysis on three cultivars, including QiZhen (QZ) with green immature pods, FengMi (FM) with yellow immature pods, and ZiYu (ZY) with purple immature pods, to identify the key genes and metabolites involved in anthocyanin accumulation. ZY showed the highest total anthocyanin content compared with FM and QZ. Subsequent quantification revealed that four metabolites, including Delphinidin-3-O-galactoside, Delphinidin-3-O-(6″-O-xylosyl)glucoside, Cyanidin-3-O-galactoside, and Pelargonidin-3-O-(xylosyl)glucoside, were the most highly accumulated in the ZY cultivar, suggesting their role in the purple pigmentation of ZY pea pods. There were 49 differentially accumulated anthocyanidins in ZY vs. FM, 43 differentially accumulated anthocyanidins in ZY vs. QZ, and 21 differentially accumulated anthocyanidins in FM vs. QZ. These findings highlight the importance of the type and concentration of anthocyanin compounds, especially those based on delphinidin, cyanidin, and pelargonidin, in the development of purple pea pods. The transcriptomic analysis revealed that certain anthocyanin biosynthetic genes were expressed at higher levels in ZY than in FM and QZ. In ZY, the higher expression levels of five key genes (PAL, 4CL, CHS, F3H, and UFGT) resulted in elevated anthocyanin content compared to FM and QZ. Furthermore, the BSA-seq analysis identified a candidate region associated with purple color in pea pods, which is located on chromosome 6 and contains 21 DEGs. Sequence variation in KIW84_061698, which encodes a bHLH transcription factor, was identified as the key candidate gene controlling anthocyanin content. This study clarifies the molecular mechanisms behind pea pod coloration and identifies potential genetic engineering targets for breeding anthocyanin-rich sugar snap peas. Full article

This research examines a detailed metabolomic and comparative analysis of bioactive substances of soybean varieties: “Primorskaya-4”, “Primorskaya-86”, “Primorskaya-96”, “Locus”, “Sphere”, “Breeze”, “Namul”, and “Musson” by the laser confocal microscope CLSM 800 and the mass spectrometry of bioactive compounds by tandem mass spectrometry. The laser microscopy allowed us to clarify in detail the spatial arrangement of phenolic acids, flavonols, and anthocyanin contents in soybeans. Research has convincingly shown that the polyphenolic content of soybeans, and, in particular, the anthocyanins, are spatially localized mainly in the seed coat of soybeans. Tandem mass spectrometry was used to identify chemical constituents in soybean extracts. The results of initial studies revealed the presence of one hundred and fourteen compounds; sixty-nine of the target analytes were tentatively identified as compounds from polyphenol groups. Full article

Pomegranates are rich in nutrients and classified among ready-to-eat fruits and vegetables. Although this ready-to-eat produce offers convenience, it presents risks associated with pathogenic microorganisms, highlighting the need for pre-sale disinfection. Ultraviolet light-emitting diodes (UV-LEDs) constitute an innovative non-thermal processing technology for food products, offering reduced heat generation and lower energy consumption compared to traditional ultraviolet (UV) irradiation methods. This study analyzed the effects of UV-LED technology on pomegranate seed quality over 0 to 5 days of storage. The results demonstrated significant increases in anthocyanins, polyphenols, ascorbic acid, and the antioxidant capacity in pomegranate following treatment, peaking on day 3. In contrast, the control group showed declining trends. After treatment, the aerobic mesophilic counts and counts of mold and yeast levels during storage measured between 2.73–3.23 log CFU/g and 2.56–3.29 log CFU/g, respectively, significantly lower than the control group. Non-targeted metabolomic analysis showed that UV-LED treatment prompted modifications in the biosynthetic pathways of flavonoids, flavonols, and anthocyanins. The expression of peonidin-3-O-rutinoside chloride increased by 46.46-fold within the anthocyanin biosynthesis pathway. In conclusion, UV-LED treatment represents a potential approach to the disinfection of ready-to-eat fruits and vegetables. Full article

Fruit color serves as a crucial visual indicator in chili peppers and is closely linked to the bioactive components that determine their economic and nutritional value. However, the specific components and potential molecular mechanisms that impact fruits’ development and color changes are less thoroughly understood. Here, we utilized three chili pepper varieties (CS03, CS29, and L816) at different developmental stages (young fruit stage, turning color stage, and mature stage) as research materials and integrated transcriptome and non-targeted metabolome analyses to explore the variation in bioactive components and color to explain the molecular regulatory mechanisms underlying different colors of chili peppers during the young fruit stage. Our results showed that flavonoids were the most enriched differential metabolites; aromadendrin 4′-glucoside, diospyrin, precarthamin, kaempferol-3-O-rutinoside, and kaempferol-3-O-Glucoside were significantly enriched in the young fruit stage of pepper CS03; and cyanidin, delphinidin, and cyanidin 3-glucoside were major contributors to the color formation. The upregulation of anthocyanin was related to the structural genes CaC4H, Ca4CL, CaCHS, CaF3H, CaANS, and CaUFGT, and key transcription factors such as CaMYBs and CabHLHs may have contributed to the differential accumulation of anthocyanins in CS03; in addition, RT-qPCR validation was correlated with anthocyanins, but also with flavonoids. This article mainly focuses on the changes in chili pigments, particularly anthocyanins, and explores the molecular mechanisms involved. This provides a reference for research on color in solanaceae vegetables and lays a theoretical foundation for further research on the bioactive components of chili peppers, as well as for optimizing harvesting practices and dietary recommendations. Full article

Grafting is a prevalent horticultural technique that enhances crop yields and stress resilience; nevertheless, compatibility issues frequently constrain its efficacy. This research examined the physiological, hormonal, and transcriptional factors regulating compatibility between the litchi (Litchi chinensis Sonn.) cultivars Feizixiao (FZX) and Ziniangxi (ZNX). The anatomical and growth investigations demonstrated significant disparities between compatible (FZX as scion and ZNX as rootstock) and incompatible (ZNX as scion and FZX as rootstock) grafts, with the latter showing reduced levels of indole acetic acid (IAA). Exogenous 1-naphthalene acetic acid (NAA) application markedly improved the graft survival, shoot development, and hormonal synergy, whereas the auxin inhibitor tri-iodobenzoic acid (TIBA) diminished these parameters. The incompatible grafts showed downregulation of auxin transporter genes, including ATP-binding cassette (ABC) transporter, AUXIN1/LIKE AUX1 (AUX/LAX), and PIN-FORMED (PIN) genes, suggesting impaired vascular tissue growth. Metabolomic profiling revealed dynamic interactions between auxin, salicylic acid, and jasmonic acid, with NAA-treated grafts exhibiting enhanced levels of stress-responsive metabolites. Transcriptome sequencing identified differentially expressed genes (DEGs) linked to auxin signaling (ARF, GH3), seven additional phytohormones, secondary metabolism (terpenoids, anthocyanins, and phenylpropanoids), and ABC transporters. Gene ontology and KEGG analyses highlighted the significance of hormone interactions and the biosynthesis of secondary metabolites in successful grafting. qRT-PCR validation substantiated the veracity of the transcriptome data, emphasizing the significance of auxin transport and signaling in effective graft development. This study provides an in-depth review of the molecular and physiological factors influencing litchi grafting. These findings provide critical insights for enhancing graft success rates in agricultural operations via targeted hormonal and genetic approaches. Full article

Floret color is a crucial phenotypic trait in broccoli, serving as an indicator of maturity and determining its market value. However, the mechanisms underlying color variation remain unclear. In this study, six broccoli varieties with different floret colors at harvest were chosen as materials. The color difference and pigment content of florets were measured, and a combined analysis of anthocyanin-targeted metabolome and transcriptome was conducted. Our findings revealed that chlorophyll a primarily influences green, yellow-green, and light green coloration, while the wax content may contribute to gray-green coloration. The blue-green and dark blue-green coloration are regulated by both chlorophyll a and anthocyanins. Targeted metabolomics identified five anthocyanin compounds, with peonidin-3-O-glucoside as a key metabolite for blue-green coloration and delphinidin-3-O-glucoside-5-O-galactoside and peonidin-3,5-O-diglucoside for dark blue-green coloration. Transcriptomic analysis identified CHLG as a potential key regulator for yellow-green and light-green floret coloration. The blue-green coloration appears to be coregulated by a combination of genes, including the chlorophyll biosynthesis gene HEMF; anthocyanin biosynthesis genes (PAL, FLS, and UGT); and chlorophyll degradation genes (SGR, PPD, and NYC). Furthermore, upstream genes involved in both chlorophyll metabolism (CHLI, CHLD, CHLM, DVR, and CLH) and anthocyanin biosynthesis (PAL, 4CL, CHS, F3′H, and FLS) play crucial roles in determining the dark blue-green coloration of florets. Meanwhile, transcription factors of the WRKY, NAC, and TCP families are involved in chlorophyll metabolism, while those of the bHLH and MYB families participate in anthocyanin synthesis. The WGCNA identified one Hub gene for chlorophyll metabolism and two for anthocyanin synthesis. In conclusion, 35 candidate genes were identified, including 21 involved in chlorophyll metabolism and 14 in anthocyanin biosynthesis. This study provides novel insights into the molecular mechanisms of floret coloration and establishes a foundation for molecular breeding in broccoli. Full article

Hypericum monogynum is a valuable perennial species with multiple uses, one of which is its ornamental value. In this study, we found that cytokinin treatment not only efficiently induced anthocyanin biosynthesis but also promoted leaf expansion in H. monogynum, both of which could potentially enhance its ornamental qualities. To investigate the molecular regulatory network underlying these processes, time-resolved transcriptomic sequencing and widely targeted metabolomic analysis were conducted. The results revealed 752, 385, and 1009 differentially expressed genes (DEGs) at 6, 12, and 24 h after 6-BA (6-benzylaminopurine) treatment, respectively. A total of 101 DEGs were co-regulated at all three time points, including key components of cytokinin metabolism and signaling. KEGG analysis identified metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction as the most significantly enriched pathways. Key DEGs associated with the MYB and bHLH families, involved in flavonoid biosynthesis and cell proliferation, were also identified. Specifically, four MYB113 genes were found to be cytokinin-responsive and upregulated by 6-BA treatment at various time points. Several genes in the anthocyanin biosynthesis pathway, such as CHS, F3H, and F3′H, were upregulated by 6-BA treatment. Additionally, many DEGs related to nutrient transport, sugar metabolism, cell cycle, and cell expansion were identified, most of which were upregulated by 6-BA treatment, supporting cytokinin’s role in promoting leaf growth and expansion. Furthermore, metabolomic analysis revealed key differentially accumulated metabolites in the flavonoid biosynthesis pathway, with major anthocyanins being identified. In conclusion, this study suggests that cytokinin application is an effective strategy for enhancing the ornamental value of H. monogynum and provides new insights into its role in regulating anthocyanin biosynthesis and leaf expansion in tree species. Full article

In nature, plants have rich and vivid colors. Flower color can confer economic and ornamental value to ornamental plants, and is one of the target traits for current directed breeding. Therefore, it is essential to understand the molecular regulatory mechanisms behind flower color formation in ornamental plants. However, in Cosmos bipinnata Cav., one of the most important ornamental plants, the metabolic pathways and molecular regulatory mechanisms underlying the formation of different flower colors are not yet clear, which greatly restricts the molecular breeding of flower color varieties. We selected three varieties of Cosmos bipinnata Cav. with white, pink, and red flowers as research materials, and identified significantly different metabolites among them through ultra performance liquid chromatography mass spectrometry (UPLC-MS/MS) analysis and principal component analysis (PCA). Then, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and transcriptome sequencing analysis in different colors flowers were used to reveal that the differential metabolites were enriched in flavonoid metabolic pathways and related structural genes were differentially expressed. Furthermore, we identified differentially expressed members of the MYB and bHLH transcription factor families, which play key roles in regulating the anthocyanin biosynthesis. By constructing a phylogenetic tree and performing a joint analysis of transcriptome and metabolome data, we further elucidated the molecular regulatory network underlying the formation of flower colors in Cosmos bipinnata Cav. This study not only provides a theoretical basis and gene resources for color-oriented breeding and the creation of new color varieties, but also offers new insights into the molecular mechanisms of flower color formation in plants. Full article

Capsicum frutescens is a valuable economic crop that is widely cultivated for its unique flavor and rich nutritional content. While some studies have shown differences in flavonoid content among different chili species, the mechanism by which changes in flavonoid composition lead to fruit color variations in C. frutescens remains underreported. We performed transcriptomics and widely targeted metabolome sequencing on three different growth stages of the C. frutescens fruit and analyzed the data to better understand the mechanism of color change. Based on previous research on the genes that regulate flavonoid compounds and the MBW complex, we have identified a total of 28 core genes related to flavonoid biosynthesis and 8 genes that may be related to flavonoid synthesis. Through extensive targeted metabolomic analysis, 581 differential metabolites were identified, including 43 flavonoids. Most anthocyanins, flavonols, and flavonoids were found to be more abundant during the immature fruit stage, which we presume is associated with the differential expression of genes involved in flavonoid biosynthesis and regulation. These findings provide a useful reference for understanding flavonoid synthesis and the accumulation of fruits in C. frutescens. Full article

Djulis (Chenopodium formosanum Koidz.), a member of the Amaranthaceae family plant, is noted for its vibrant appearance and significant ornamental value. However, the mechanisms underlying color variation in its spikes remain unexplored. This research initially detected the anthocyanin content at different developmental stages of the spike and subsequently utilized an integrative approach, combining targeted metabolomics, transcriptomics, and untargeted metabolomics analyses, to elucidate the mechanisms of anthocyanin biosynthesis in the spikes of djulis. The results of the combined multi-omics analysis showed that the metabolites associated with anthocyanin synthesis were mainly enriched in the flavonoid biosynthesis pathway (ko00941) and the anthocyanin biosynthesis pathway (ko00942). With the maturation of djulis spikes, a total of 28 differentially expressed genes and 17 differentially expressed metabolites were screened during the transition of spike color from green (G) to red (R) or orange (O). Twenty differentially expressed genes were selected for qRT-PCR validation, and the results are consistent with transcriptome sequencing. The upregulation of seven genes, including chalcone synthase (CfCHS3_1, CfCHS3_2, CfCHS3_3), flavanone 3-hydroxylase (CfF3H_3), flavonoid 3′5′-hydroxylase (CfCYP75A6_1), dihydroflavonol reductase (CfDFRA), and glucosyltransferase (Cf3GGT), promotes the formation and accumulation of delphinidin 3-sambubioside and peonidin 3-galactoside. The research results also showed that anthocyanins and betalains can coexist in the spike of djulis, and the reason for the change in spike color during development may be the result of the combined action of the two pigments. A possible regulatory pathway for anthocyanin biosynthesis during the spike maturation was constructed based on the analysis results. The results provide a reference and theoretical basis for further studying the molecular mechanism of anthocyanin regulation of color changes in Amaranthaceae plants. Full article

Anthocyanins are significant secondary metabolites that are essential for plant growth and development, possessing properties such as antioxidant, anti-inflammatory, and anti-cancer activities and cardiovascular protection. They offer significant potential for applications in food, medicine, and cosmetics. However, since anthocyanins are mainly obtained through plant extraction and chemical synthesis, they encounter various challenges, including resource depletion, ecological harm, environmental pollution, and the risk of toxic residuals. To address these issues, this study proposes a plant cell factory approach as a novel alternative solution for anthocyanin acquisition. In this study, the VdCHS2 gene was successfully transformed into spine grape cells, obtaining a high-yield anthocyanin cell line designated as OE1. Investigations of the light spectrum demonstrated that white light promoted spine grape cell growth, while short-wavelength blue light significantly boosted anthocyanin production. Targeted metabolomics analysis revealed that the total anthocyanin content in the OE1 cell line reached 11 mg/g, representing a 60% increase compared to the WT. A total of 54 differentially accumulated metabolites were identified, among which 44 were upregulated. Overexpression of the CHS gene enhanced the expression of downstream genes involved in anthocyanin biosynthesis, resulting in the differential expression of CHI, F3Hb, F3′5′H, DFR4, and LDOX. This led to the differential accumulation of anthocyanin monomers, predominantly consisting of 3-O-glucosides and 3-O-galactosides, thereby causing alterations in anthocyanin levels and composition. Furthermore, the OE1 cell line increased the activity of various antioxidant enzymes, improved the clearance of reactive oxygen species, and reduced the levels of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA). The subsequent cultivation of the transformed OE1 cell line, in conjunction with cell suspension culture, established a plant cell factory for anthocyanin production, significantly increasing anthocyanin yield while shortening the culture duration. This study elucidates the molecular mechanisms through which the VdCHS2 gene influenced anthocyanin accumulation and compositional variations. Additionally, it established a model for a small-scale anthocyanin plant cell factory, thereby providing a theoretical and practical foundation for the targeted synthesis of anthocyanin components and the development and utilization of plant natural products. Full article

Betula pendula ‘Purple Rain’ is characterized by its purple leaves and has ornamental applications. A green mutant line NL, which was mutated by line NZ of B. pendula ‘Purple Rain’ during tissue culture, shows green leaves instead of the typical purple color of B. pendula ‘Purple Rain’. This study quantified the leaf color traits of NL and a normal B. pendula ‘Purple Rain’ line NZ, and uncovered differentially expressed genes involved in flavonoid biosynthesis pathway genes in NL through RNA-Seq analysis. Compared to NZ, reduced levels of six anthocyanins contained in NL were revealed via flavonoids-targeted metabolomics. Sequence mutations in transcription factors that could explain NL’s phenotype failed to be screened via whole-genome resequencing, suggesting an epigenetic basis for this variant. Therefore, a key gene, BpMYB113, was identified in NL via the combined analysis of small RNA sequencing, whole-genome methylation sequencing, and transcriptomics. In NL, this gene features a hyper CHH context methylation site and a lower transcription level compared to NZ, disrupting the expression of downstream genes in the phenylalanine metabolism pathway, and thereby reducing flavonoid biosynthesis. Our study elucidates an epigenetic mechanism underlying color variation in variegated trees, providing pivotal insights for the breeding and propagation of colored-leaf tree species. Full article

Camellia hainanica is one of the camellia plants distributed in tropical regions, and its regeneration system and genetic transformation are affected by callus browning. However, the underlying mechanism of Camellia hainanica callus browning formation remains largely unknown. To investigate the metabolic basis and molecular mechanism of the callus browning of Camellia hainanica, histological staining, high-throughput metabolomics, and transcriptomic assays were performed on calli with different browning degrees (T1, T2, and T3). The results of histological staining revealed that the brown callus cells had obvious lignification and accumulation of polyphenols. Widely targeted metabolomics revealed 1190 differentially accumulated metabolites (DAMs), with 53 DAMs annotated as phenylpropanoids and flavonoids. Comparative transcriptomics revealed differentially expressed genes (DEGs) of the T2 vs. T1 associated with the biosynthesis and regulation of flavonoids and transcription factors in Camellia hainanica. Among them, forty-four enzyme genes associated with flavonoid biosynthesis were identified, including phenylalaninase (PAL), 4-coumaroyl CoA ligase (4CL), naringenin via flavanone 3-hydroxylase (F3H), flavonol synthase (FLS), Chalcone synthase (CHS), Chalcone isomerase (CHI), hydroxycinnamoyl-CoA shikimate transferase (HCT), Dihydroflavonol reductase (DFR), anthocyanin reductase (LAR), anthocyanin synthetase (ANS), and anthocyanin reductase (ANR). Related transcription factors R2R3-MYB, basic helix-loop-helix (bHLH), and WRKY genes also presented different expression patterns in T2 vs. T1. These results indicate that the browning of calli in Camellia hainanica is regulated at both the transcriptional and metabolic levels. The oxidation of flavonoids and the regulation of related structural genes and transcription factors are crucial decisive factors. This study preliminarily revealed the molecular mechanism of the browning of the callus of Camellia hainanensis, and the results can provide a reference for the anti-browning culture of Camellia hainanica callus. Full article

This study presents the metabolomic profiles of the four Ribes species (Ribes pauciflorum Turcz., Ribes triste Pall., Ribes dicuscha Fisch., and Ribes aureum Purch.). The plant material was collected during two expeditions in the Russian Far East. Tandem mass spectrometry was used to detect target analytes. A total of 205 bioactive compounds (155 compounds from polyphenol group and 50 compounds from other chemical groups) were tentatively identified from the berries and extracts of the four Ribes species. For the first time, 29 chemical constituents from the polyphenol group were tentatively identified in the genus Ribes. The newly identified polyphenols include flavones, flavonols, flavan-3-ols, lignans, coumarins, stilbenes, and others. The other newly detected compounds in Ribes species are the naphthoquinone group (1,8-dihydroxy-anthraquinone, 1,3,6,8-tetrahydroxy-9(10H)-anthracenone, 8,8′-dihydroxy-2,2′-binaphthalene-1,1′,4,4′-tetrone, etc.), polyhydroxycarboxylic acids, omega-3 fatty acids (stearidonic acid, linolenic acid), and others. Our results imply that Ribes species are rich in polyphenols, especially flavanols, anthocyanins, flavones, and flavan-3-ols. These results indicate the utility of Ribes species for the health and pharmaceutical industry. Full article

Long non-coding RNAs (lncRNAs), a class of important regulatory factors for many biological processes in plants, have received much attention in recent years. To explore the molecular roles of lncRNAs in sweet cherry fruit ripening, we conducted widely targeted metabolome, transcriptome and lncRNA analyses of sweet cherry fruit at three ripening stages (yellow stage, pink stage, and dark red stage). The results show that the ripening of sweet cherry fruit involves substantial metabolic changes, and the rapid accumulation of anthocyanins (cyanidin 3-rutinoside, cyanidin 3-O-galactoside, and cyanidin 3-O-glucoside) is the main cause of fruit coloration. These ripening-related alterations in the metabolic profile are driven by specific enzyme genes related to the synthesis and decomposition of abscisic acid (ABA), cell wall disintegration, and anthocyanin biosynthesis, as well as transcription factor genes, such as MYBs, bHLHs, and WD40s. LncRNAs can target these ripening-related genes to form regulatory modules, incorporated into the sweet cherry fruit ripening regulatory network. Our study reveals that the lncRNA-mRNA module is an important component of the sweet cherry fruit ripening regulatory network. During sweet cherry fruit ripening, the differential expression of lncRNAs will meditate the spatio-temporal specific expression of ripening-related target genes (encoding enzymes and transcription factors related to ABA metabolism, cell wall metabolism and anthocyanin metabolism), thus driving fruit ripening. Full article