Integrated metabolomic and transcriptomic analysis reveals the mechanism underlying the accumulation of anthocyanins and other flavonoids in the flesh and skin of teinturier grapes

Effects of negative air ion treatment on postharvest storage quality and anthocyanin metabolism of grape

Grapes are rich in anthocyanin but are prone to postharvest quality deterioration. Many studies proved that negative air ion (NAI) preserved horticultural products. We hypothesized that NAI kept postharvest quality and repressed anthocyanin degradation of grape. In this study, NAI delayed grape firmness loss, mitigated rot and shattering gloss. It also preserved quality attributes like total soluble solids, acidity, vitamin C (Vc), phenols, and anthocyanins. Among treatments, NAI3 (treat with NAI every 3 days for 1 h) was most effective. Ultra-high performance liquid chromatography analysis showed NAI3 increased delphinidin, malvidin, paeonidin, petunidin, and pelargonidin levels while reducing cyanidin. NAI3 maintained activities of anthocyanin synthesis-related enzymes and inhibited degradation-related ones. Gene expression analysis showed NAI3 induced synthesis-related genes and inhibited degradation-related genes. Thus, NAI maintained anthocyanin content and composition by regulating activities and gene expressions of enzymes involved in anthocyanin metabolism, playing a crucial role in grape storage.

Integrative Metabolomic and Transcriptomic Analysis Provides Novel Insights into the Effects of SO2 on the Postharvest Quality of 'Munage' Table Grapes

Postharvest grapes exhibit a limited shelf life due to susceptibility to rot and deterioration, significantly reducing their nutritional and economic value. Sulfur dioxide (SO2) is a widely recognized preservative for extending grape storage life. This study performed a detailed analysis of 'Munage' table grapes treated with SO2 fumigation, employing transcriptomic and metabolomic approaches. Results indicate that SO2 fumigation significantly extends the shelf life of grapes, as demonstrated by improved visual quality, reduced decay rates, and increased fruit firmness. We identified 309 differentially accumulated metabolites (DAMs) and 1906 differentially expressed genes (DEGs), including 135 transcription factors (TFs). Both DEGs and DAMs showed significant enrichment of flavonoid-related metabolism compared with the control, and the relative content of four flavonoid metabolites (Wogonin-7-O-glucuronide, Acacetin-7-O-glucuronide, Apigenin-7-O-glucuronide, and Baicalein 7-O-glucuronide) were significantly increased in grapes upon SO2 treatment, suggesting that SO2 treatment had a substantial regulatory effect on grape flavonoid metabolism. Importantly, we constructed complex regulatory networks by screening key enzyme genes (e.g., PAL, 4CLs, CHS, CHI2, and UGT88F3) related to the metabolism of target flavonoid, as well as potential regulatory transcription factors (TFs). Overall, our findings offer new insights into the regulatory mechanisms by which SO2 maintains the postharvest quality of table grapes.

Uncovering fruit flavor and genetic diversity across diploid wild Fragaria species via comparative metabolomics profiling

Wild Fragaria resources exhibit extensive genetic diversity and desirable edible traits, such as high soluble solid content and flavor compounds. However, specific metabolites in different wild strawberry fruits remain unknown. In this study, we characterized 1008 metabolites covering 11 subclasses among 13 wild diploid resources representing eight species, including F. vesca, F. nilgerrensis, F. viridis, F. nubicola, F. pentaphylla, F. mandschurica, F. chinensis, and F. emeiensis. Fifteen potential metabolite biomarkers were identified to distinguish fruit flavors among the 13 diploid wild Fragaria accessions. A total of nine distinct modules were employed to explore key metabolites related to fruit quality through weighted gene co-expression module analysis, with significant enrichment in amino acid biosynthesis pathway. Notably, the identified significantly different key metabolites highlighted the close association of amino acids, sugars, and anthocyanins with flavor formation. These findings offer valuable resources for improving fruit quality through metabolome-assisted breeding.

Comparative transcriptomic and metabolomic analysis reveals mechanisms of selenium-regulated anthocyanin synthesis in waxy maize (Zea mays L.)

Anthocyanins in maize (Zea mays L.) kernels determine the plant's color and can enhance its resistance. Selenium (Se) significantly impacts plant growth, development, and secondary metabolic regulation. However, the molecular mechanisms by which Se regulates anthocyanin synthesis in waxy corn remain unclear. This study employed integrated transcriptomic and metabolomic analyses to investigate the mechanisms through which selenium influences anthocyanin synthesis in yellow and purple waxy corn. The results showed that maize varieties with higher anthocyanin content had higher selenium enrichment capacity in their kernels. Under selenium stress, HN2025 exhibited 1,904 more differentially expressed genes (DEGs) and 140 more differential metabolites compared to HN5. The expression levels of anthocyanin synthesis-related genes and transcription factors such as phenylalanine ammonia-lyase, flavonoid 3-hydroxylase (F3H), dihydroflavonol reductase (DFR), chalcone synthase (CHS), cinnamate-4-hydroxylase (C4H), anthocyanin 5,3-O-glucosyltransferases, and anthocyanidin reductase, MYB, and bHLH were strongly induced in HN2025. Metabolomic analysis revealed significant enrichment in anthocyanin biosynthesis, flavonoid and flavonol biosynthesis, glutathione metabolism, phenylalanine biosynthesis, and phenylalanine metabolism under selenium treatment. Three up-regulated PAL genes and one C4H gene were significantly enriched with DAMs in phenylalanine metabolism, phenylpropanoid biosynthesis, flavonoid biosynthesis, and anthocyanin biosynthesis, resulting in significant differences between HN5 and HN2025 in selenium-induced anthocyanin metabolism-related pathways. These findings provide a theoretical basis for understanding the effects of selenium on the molecular regulatory mechanisms of anthocyanin biosynthesis in maize kernels.

Combined Metabolome and Transcriptome Analysis Revealed the Accumulation of Anthocyanins in Grape Berry (Vitis vinifera L.) under High-Temperature Stress

In grape (Vitis vinifera L.) cultivation, high temperatures (HTs) usually reduce the accumulation of anthocyanins. In order to elucidate the regulatory mechanism of anthocyanin biosynthesis under high-temperature environments, we investigated the effects of HT stress at veraison (5% coloring of grape ears) on fruit coloration and anthocyanin biosynthesis in 'Summer Black' (XH) and 'Flame seedless' (FL) grapevines. Compared to the control group (35 °C), the total anthocyanin content of XH and FL grapes subjected to a high-temperature (HT) treatment group (40 °C) decreased significantly as the HT treatment continued, but showed an upward trend with fruit development. However, the concentration of procyanidins increased significantly following HT treatment but decreased with fruit development. Nonetheless, FL grapes showed some resistance to the HT condition, producing anthocyanin content at ripeness comparable to the control group, demonstrating a greater adaptability to HT conditions than XH grapes. Based on the CIRG index, at stage S4, the fruit of FL was classified as dark red, while XH was classified as blue-black in the control group. Anthocyanin-targeted metabonomics identified eight different types of anthocyanins accumulating in the peels of XH and FL grapes during ripening, including cyanidins, delphinidins, malvidins, pelargonidins, peonidins, petunidins, procyanidins, and flavonoids. Malvidins were the most abundant in the two grape varieties, with malvidin-3-O-glucoside being more sensitive to high temperatures. HT treatment also down-regulated the expression of structural genes and regulators involved in the anthocyanin synthesis pathways. We used the WGCNA method to identify two modules that were significantly correlated with total anthocyanin and procyanidin contents. Among them, MYBCS1, bHLH137, WRKY65, WRKY75, MYB113-like, bZIP44, and GST3 were predicted to be involved in grape anthocyanin biosynthesis. In conclusion, this study conducted in-depth research on the HT inhibition of the biosynthesis of anthocyanins in XH and FL grapes, for reference.

Integrated Untargeted Metabolome, Full-Length Sequencing and Transcriptome Analyses Reveal the Mechanism of Flavonoid Biosynthesis in Blueberry (Vaccinium spp.) Fruit

As a highly economic berry fruit crop, blueberry is enjoyed by most people and has various potential health benefits, many of which are attributed to the relatively high concentrations of flavonoids. To obtain more accurate and comprehensive transcripts, the full-length transcriptome of half-highbush blueberry (Vaccinium corymbosum/angustifolium cultivar Northland) obtained using single molecule real-time and next-generation sequencing technologies was reported for the first time. Overall, 147,569 consensus transcripts (average length, 2738 bp; N50, 3176 bp) were obtained. After quality control steps, 63,425 high-quality isoforms were obtained and 5030 novel genes, 3002 long non-coding RNAs, 3946 transcription factor genes (TFs), 30,540 alternative splicing events, and 2285 fusion gene pairs were identified. To better explore the molecular mechanism of flavonoid biosynthesis in mature blueberry fruit, an integrative analysis of the metabolome and transcriptome was performed on the exocarp, sarcocarp, and seed. A relatively complete biosynthesis pathway map of phenylpropanoids, flavonoids, and proanthocyanins in blueberry was constructed. The results of the joint analysis showed that the 228 functional genes and 42 TFs regulated 78 differentially expressed metabolites within the biosynthesis pathway of phenylpropanoids/flavonoids. O2PLS analysis results showed that the key metabolites differentially accumulated in blueberry fruit tissues were albireodelphin, delphinidin 3,5-diglucoside, delphinidin 3-O-rutinoside, and delphinidin 3-O-sophoroside, and 10 structural genes (4 Vc4CLs, 3 VcBZ1s, 1 VcUGT75C1, 1 VcAT, and 1 VcUGAT), 4 transporter genes (1 VcGSTF and 3 VcMATEs), and 10 TFs (1 VcMYB, 2 VcbHLHs, 4 VcWD40s, and 3 VcNACs) exhibited strong correlations with 4 delphinidin glycosides. These findings provide insights into the molecular mechanisms of flavonoid biosynthesis and accumulation in blueberry fruit.

Integrated transcriptomic and WGCNA analyses reveal candidate genes regulating mainly flavonoid biosynthesis in Litsea coreana var. sinensis

Litsea coreana Levl. var. sinensis (Allen) Yang et P. H. Huang is a popular ethnic herb and beverage plant known for its high flavonoid content, which has been linked to a variety of pharmacological benefits and crucial health-promoting impacts in humans. The progress in understanding the molecular mechanisms of flavonoid accumulation in this plant has been hindered due to the deficiency of genomic and transcriptomic resources. We utilized a combination of Illumina and Oxford Nanopore Technology (ONT) sequencing to generate a de novo hybrid transcriptome assembly. In total, 126,977 unigenes were characterized, out of which 107,977 were successfully annotated in seven public databases. Within the annotated unigenes, 3,781 were categorized into 58 transcription factor families. Furthermore, we investigated the presence of four valuable flavonoids-quercetin-3-O-β-D-galactoside, quercetin-3-O-β-D-glucoside, kaempferol-3-O-β-D-galactoside, and kaempferol-3-O-β-D-glucoside in 98 samples, using high-performance liquid chromatography. A weighted gene co-expression network analysis identified two co-expression modules, MEpink and MEturquoise, that showed strong positive correlation with flavonoid content. Within these modules, four transcription factor genes (R2R3-MYB, NAC, WD40, and ARF) and four key enzyme-encoding genes (CHI, F3H, PAL, and C4H) emerged as potential hub genes. Among them, the R2R3-MYB (LcsMYB123) as a homologous gene to AtMYB123/TT2, was speculated to play a significant role in flavonol biosynthesis based on phylogenetic analysis. Our findings provided a theoretical foundation for further research into the molecular mechanisms of flavonoid biosynthesis. Additionally, The hybrid transcriptome sequences will serve as a valuable molecular resource for the transcriptional annotation of L. coreana var. sinensis, which will contribute to the improvement of high-flavonoid materials.

Metabolome integrated with transcriptome reveals the mechanism of three different color formations in Taxus mairei arils

Maire yew (Taxus mairei), an evergreen conifer, has high ornamental and medicinal value. The arils of this species has three different colors. However, the variation mechanisms of arils color formation remains unclear. Here, the gene expression and metabolite concentration were profiled for red (RTM), yellow (YTM), and purple (PTM) arils in different developmental stages. A total of 266 flavonoids and 35 carotenoids were identified. The predominant pigments identified in YTM were epiafzelechin, lutein, and β-Cryptoxanthin, while malvidin-3,5-di-O-glucoside and apigenin played crucial roles in PTM. And significant differential expression was observed among the HCT, DFR, LAR, ANS, crtB, NCED, and CCoAOMT genes across different color arils. During the maturation of yellow arils, the upregulation of HCT was strongly correlated with the accumulation of epiafzelechin. The diminished expression of DFR, LAR, and ANS seemed to inhibit the production of delphinidin-3-O-rutinoside. The decrease in crtB expression and concurrent increase in NCED expression potentially regulate the heightened accumulation of lutein. Meanwhile, the accumulation of β-cryptoxanthin appeared seemed to be positively influenced by NCED. As aril turning purple, the decreased expression of CCoAOMT seemed to facilitate the synthesis of apigenin. The substantial upregulation of DFR promoted the production of malvidin-3,5-di-O-glucoside. Additionally, the overexpression of MYBs may plays the important role in regulating the formation of different colored arils. In total, 14 genes were selected for qRT-PCR validation, the results indicated the reliability of the transcriptome sequences data. Our findings could provide valuable insight into the molecular breeding, development, and application of Maire yew resources.

Phytochemical profile and anti-inflammatory activity of the hull of γ-irradiated wheat mutant lines (Triticum aestivum L.)

Wheat (Triticum aestivum Linn.; Poaceae) is the second most cultivated food crop among all global cereal crop production. The high carbohydrate content of its grains provides energy, multiple nutrients, and dietary fiber. After threshing, a substantial amount of wheat hull is produced, which serves as the non-food component of wheat. For the valorization of these by-products as a new resource from which functional components can be extracted, the hull from the seeds of cultivated wheat mutant lines bred after γ-irradiation were collected. Untargeted metabolite analysis of the hull of the original cultivar (a crossbreeding cultivar., Woori-mil × D-7) and its 983 mutant lines were conducted using ultra-performance liquid chromatography-electrospray ionization quadrupole time-of-flight mass spectrometry technique. A total of 55 molecules were tentatively identified, including 21 compounds found in the Triticum species for the first time and 13 compounds not previously described. Among them, seven flavonolignans with a diastereomeric structure, isolated as a single compound from the hull of T. aestivum in our previous study, were used as the standards in the metabolite analysis. The differences in their collision cross-section values were shown to contribute to the clear distinction between tricine-lignan stereoisomers. To select functionally active agents with anti-inflammatory activity among the identified compounds, the wheat hull samples were evaluated for their inhibitory effect on nitric oxide production in lipopolysaccharide-stimulated RAW 264.7 cells. As a result of multivariate analysis based on the results of chemical and biological profiles of the wheat hull samples, 10 metabolites were identified as key markers, contributing to the distinction between active and inactive mutant lines. Considering that one of the four key markers attributed to anti-inflammatory activity has been identified to be a flavonolignan, the wheat hull could be a valuable source of diverse tricin-lignan type compounds and used as a natural health-promoting product in food supplements.

Effects of Seven Sterilization Methods on the Functional Characteristics and Color of Yan 73 (Vitis vinifera) Grape Juice

Yan 73 (Vitis vinifera) is a dyed grape variety cultivated in China. Currently, most studies have focused on the mechanism of anthocyanins or the impact of anthocyanins as auxiliary color varieties on wine color. There is little research on its direct use or direct processing of products such as juice. In order to investigate the effects of different processing methods on the juice of Yan 73 grapes, the physicochemical and functional properties, as well as the sensory indexes of the juice, were analyzed by using thermal pasteurization (TP), thermosonication (TS), TS combined with nisin (TSN), TS combined with ε-Polylysine (TSε), irradiation (IR), and high hydrostatic pressure (HHP). The physicochemical indexes, functional properties, and sensory indexes of Smoke 73 grape juice were determined and analyzed. The results of the study showed that among the seven sterilization methods, total polyphenol content (TPC) in juice was significantly increased in all treatments except HHP. TPC was the highest in TP (3773.33 mg GAE/L). Total anthocyanin content (TAC) was increased except IR5, and TSN (1202.67 mg/L) had the highest TAC. In terms of color, TP (a* = 36.57, b* = 19.70, L* = 14.81, C* = 41.55, h° = 28.30, ΔE = 5.9) promotes the dissolution of anthocyanins because of high temperatures, which basically improves all the color indicators of grape juice and makes the color of grape juice more vivid. After HHP treatment, the color (ΔE = 1.72) and aroma indicators are closer to the grape juice itself. The Entropy weight-TOPSIS, CRITIC-Topsis, and PCA integrated quality evaluation models showed that all selected TP as the best integrated quality.