Forward genetics has been instrumental in identifying genes underlying desirable traits, yet its application to polyploid plants, many of which are key agricultural crops, remains challenging due to their genomic complexity. Therefore, we developed BenthMap, a bulk segregant analysis platform for high-throughput trait mapping and gene discovery, in the allotetraploid model plant Nicotiana benthamiana. BenthMap leverages high-quality genome assemblies of two genetically and phenotypically distinct strains, LAB and QLD. To validate the pipeline, we investigated their contrasting anthocyanin responses. Transient overexpression of AcMYB110, an activation regulator of anthocyanin biosynthesis, induces robust anthocyanin production in QLD leaves but gives a detrimental, often necrotic, response in LAB. Using BenthMap and a population derived from selfing the F1 hybrid of a LAB × QLD cross (F1S1 population), with genome coverage as low as 10×, we mapped the necrotic LAB response to a 3.5 Mb homozygous region on chromosome 10. This region contains a leucoanthocyanidin dioxygenase gene. Transiently expressing the QLD version of this gene, along with AcMYB110, restored robust anthocyanin accumulation in LAB, validating the causal gene. These findings demonstrate BenthMap's utility for rapid trait-gene identification in N. benthamiana and have potential for application to other allopolyploid plants.

Ultraviolet-B (UV-B) light, a natural component of sunlight, plays a crucial role in the regulation of plant growth and development. B-box (BBX) proteins are zinc-finger transcription factors essential for plant growth, development, and responses to abiotic stress. The role of BBX5 in UV-B stress responses has not been previously identified. Here, we identify BBX5 as a novel regulator of UV-B stress tolerance in Arabidopsis. Firstly, UV-B treatment significantly induced the expression of BBX5. Transcriptome analyses revealed that BBX5 was associated with the anthocyanin biosynthesis pathway. Phenotypic analysis showed that bbx5 mutant exhibited heightened UV-B sensitivity and reduced anthocyanin levels under UV-B exposure, whereas BBX5-overexpressing lines displayed increased anthocyanin content and enhanced UV-B resilience. Mechanistically, BBX5 directly interacts with the promoter of anthocyanidin synthase (ANS), thereby stimulating its expression. HY5, a key regulator in UV-B signaling, enhances the expression of BBX5 by binding to its promoter region. Genetic analysis showed that BBX5 overexpression partially restored anthocyanin levels and improved UV-B resistance in hy5-215 mutant. Our study highlights the crucial role of the HY5-BBX5-ANS regulatory axis in modulating anthocyanin biosynthesis and UV-B acclimation in Arabidopsis.

Although the ripening process of climacteric fruits is well-characterized, the regulatory mechanisms underlying ripening in non-climacteric fruits, such as sweet cherry, remain poorly understood. In this study, we present an extensive physiological, biochemical and transcriptomic analysis of pedicel and fruit tissues across eight developmental stages in the late-maturing sweet cherry cultivar 'Regina', providing a comprehensive map of tissue-specific gene expression dynamics during fruit ripening. Our data reveal widespread transcriptomic and metabolomic reprogramming, particularly in sugar metabolism within the pedicel, suggesting that cherry ripening may be partially regulated by pedicel-derived signals. Through integrative analysis, we identified key transcription factors, most notably PaWRKY57 and PaNAC29, as putative regulators of fruit development. Silencing the genes encoding these transcription factors at the color breaking stage in both the 'Regina' and early-maturing 'Carmen' cultivars resulted in delayed pigmentation and reduced fruit size. Subsequent transcriptomic and proteomic analysis of silenced fruit revealed several candidate downstream targets and regulatory networks specifically linked to anthocyanin biosynthesis. Levels of central metabolic components and major anthocyanins, particularly cyanidin glucoside and cyanidin rutinoside, were reduced alongside altered abscisic acid levels following PaWRKY57 and PaNAC29 silencing. Furthermore, we demonstrate that PaWRKY57 and PaNAC29 interact with the promoter regions of dihydroflavonol4-reductase (PaDFR) and leucoanthocyanidin dioxygenase (PaLDOX), regulating flavonoid biosynthesis. Notably, PaNAC29 also binds to the promoters of PACLOBUTRAZOL RESISTANCE 6 (PaPRE6) and linoleate 9S-lipoxygenase 5 (PaLOX5), influencing the biosynthesis of abscisic acid and aroma-related volatile compounds. This work provides insights into tissue-specific regulatory dynamics in sweet cherry, establishes a framework for non-climacteric fruit ripening, and identifies promising targets for improving cherry yield and fruit quality.

Recent anthropogenic activities have spurred unparalleled abiotic environmental pressures, including drought, heat, cold, salinity, alkalinity, heavy metal stress. Among these stresses, salinity and alkalinity present substantial threats to agriculture, leading to poor crop yields, reduced food quality, economic losses, and challenges to food security and long-term agricultural sustainability. Elevated salt levels increase the production of reactive oxygen species (ROS) like superoxide anions (O2•-, hydrogen peroxide (H2O2), and hydroxyl radicals (•OH), which can severely damage cell components like lipids, carbohydrates, proteins, and DNA. The study aimed to investigate the biochemical parameters of three red landraces of rice (Oryza sativa L.)‒ Karad, Jattoo, and Jhinjhan‒ to alkalinity-induced oxidative stress. Coloured crop landraces contain a plethora of antioxidants, have high nutritional value, and exhibit tolerance to a variety of stresses; hence, their utilization in agriculture can improve crop yields. The 4-day germinated rice seedlings were raised hydroponically and exposed to two different intensities of alkaline stress (25 and 50 mM NaHCO3). After 4 days, roots and coleoptiles were evaluated for various parameters, including ROS (O2•-, H2O2), antioxidant assays (enzymatic and non-enzymatic antioxidants), and gene expression analysis to study the response to alkaline stress. Alkaline stress enhanced ROS production and lipid peroxidation, to a greater extent in the least alkaline-resistant landrace (Jhinjhan). Enzymatic antioxidants such as catalase, guaiacol peroxidase, ascorbate peroxidase, superoxide dismutase, monodehydroascorbate reductase, and dehydroascorbate reductase displayed higher activity in the stress-tolerant Karad landrace. The antioxidant enzyme activity increased with the highest stress dose, indicating that these enzymes play a crucial role in cellular defense against ROS and metabolites. In Karad, a significantly higher expression of anthocyanin biosynthetic pathway genes (chalcone synthase, phenylalanine ammonia-lyase, anthocyanidin synthase, and dihydroflavanol reductase) occurred, with over-representation of non-enzymatic antioxidants (proline, phenolics, ascorbate, non-protein thiols, and anthocyanins). Anthocyanin gene expression correlated well with the tissue anthocyanin concentration. Conversely, Jattoo and Jhinjhan showed less tolerance to alkaline stress in terms of biochemical parameters, together with the comparatively reduced expression of anthocyanin genes. Thus, the present study aims to offer valuable insights into the alkaline stress tolerance of red rice landraces, which could be related to the augmented responsiveness of antioxidant machinery and constitutive/induced anthocyanin genes, resulting in more efficient anthocyanin accumulation. As research advances, understanding the full potential of modern techniques, such as developing gene-specific molecular markers from coloured rice, genetic engineering, and genomic approaches, is crucial to increasing the frequency of desired traits in breeding populations, especially those designed for deployment in target environments.

Nonheme iron enzymes are among nature's most versatile catalysts for molecular functionalization. Engineering nonheme enzymes for abiological reactions unlocks new catalytic possibilities beyond the limits of natural evolution. In this work, we engineered a nonheme enzyme, leucoanthocyanidin dioxygenase from Arabidopsis thaliana (AtLDOX), to catalyze an asymmetric 1,3-migratory nitrene C(sp3)─H insertion reaction. Through directed evolution, the final optimized AtLDOX_LS variant efficiently delivers a range of chiral α-amino acids derivatives with exceptional activity and enantioselectivity (up to 81% yield, 850 total turnover number, and 98:2 enantiomeric ratio). Preliminary mechanistic studies suggest the involvement of radical intermediates for this transformation. This work advances the biocatalytic toolbox for radical involved transformations and broadens the scope of enzymatic migration chemistry.

Abstract Nonheme iron enzymes are among nature's most versatile catalysts for molecular functionalization. Engineering nonheme enzymes for abiological reactions unlocks new catalytic possibilities beyond the limits of natural evolution. In this work, we engineered a nonheme enzyme, leucoanthocyanidin dioxygenase from Arabidopsis thaliana ( At LDOX), to catalyze an asymmetric 1,3‐migratory nitrene C(sp 3 )─H insertion reaction. Through directed evolution, the final optimized At LDOX_LS variant efficiently delivers a range of chiral α ‐amino acids derivatives with exceptional activity and enantioselectivity (up to 81% yield, 850 total turnover number, and 98:2 enantiomeric ratio). Preliminary mechanistic studies suggest the involvement of radical intermediates for this transformation. This work advances the biocatalytic toolbox for radical involved transformations and broadens the scope of enzymatic migration chemistry.

Physical dormancy, or hardseededness, refers to a type of dormancy in which seeds cannot germinate due to seed coat impermeability. Physical dormancy broadly exists in seed plants, especially in leguminous species, and plays an essential role in maintaining the durability of natural seed banks. However, physical dormancy restricts the utilization of leguminous seeds in agricultural production. Seeds of the leguminous model plant Medicago truncatula show typical physical dormancy. In this study, we report a function of anthocyanidin reductase (ANR) in controlling M. truncatula seed physical dormancy. The ANR gene was mostly highly expressed in the M. truncatula seed coat. Loss-of-function mutations in ANR resulted in the absence of hardseededness, allowing the seed to absorb water quickly without scarification. The content of glycolipids, especially MDGD, was significantly decreased in the seed coat of the anr mutant. A large increase in the levels of the most abundant flavonoids (flavonoid-3-O-glucosides) was also observed in the anr mutant seed coat. Knockout of the upstream genes transparent testa 8 (TT8), flavonoid 3',5'-hydroxylase 1 (F3'5'H1), or anthocyanidin synthase (ANS) hindered flavonoid-3-O-glucoside accumulation. Accordingly, mutating these genes in the anr background (anr tt8, anr f3'5'h1, and anr ans) restored seed physical dormancy. These results indicate that proanthocyanidins are not directly associated with hardseededness. Rather, an excessive accumulation of flavonoid-3-O-glycosides and a reduction in lipids are associated with seed physical dormancy. This study provides information regarding the molecular and biochemical mechanisms underlying physical dormancy.

Melatonin (MT) is a growth regulator that influences anthocyanin synthesis during plant growth. However, the regulation mechanism of MT on the coloration of plum peels remains unclear. Here, the effects of MT on the anthocyanin accumulation and coloration in Chinese plum peels were examined after MT (100 μmol/L) or water (control) treatment. The results showed that MT treatment accelerated the changes in plum peels from green to red by increasing the anthocyanin and phenolic contents. MT treatment also increased the antioxidant capacity, including the scavenging capacity of 2,2-diphenyl-1-picrylhydrazyl (DPPH) and ferric reducing antioxidant power (FRAP); and promoted the enzyme activities of anthocyanin synthesis, such as chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), chalcone isomerase (CHI), and UDP-glucose 3-O-glucosyltransferase (UFGT). Moreover, transcriptome analysis indicated that MT treatment up-regulated the expression of several key anthocyanin-related genes, including CHS, F3H, dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and UFGT, revealing the regulatory role of MT in anthocyanin metabolism. In conclusion, MT treatment can promote the anthocyanin accumulation and coloration in plum peels.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12870-025-07236-9.

Peach is a typical ethylene-sensitive fruit, and low levels of ethylene can accelerate softening during storage. In this study, we used an ethylene absorbent (EA) and 1-methylcyclopropene (1-MCP) to minimize the detrimental impact of ethylene on the quality of peaches in modified atmosphere packaging (MAP), and analyzed fruit firmness, color change, anthocyanin content, and the expression patterns of cell wall metabolism-related genes and anthocyanin synthesis-related genes during storage. The results showed that ethylene in the MAP package decreased the firmness and total anthocyanin content of the peaches, while MAP combined with EA (MAP+EA) treatment effectively maintained the firmness of the peaches and counteracted the inhibition of anthocyanin accumulation in the peach skin by ethylene. In addition, the peaches treated with MAP+EA exhibited higher a* values, lower weight loss, and lower activities of cell-wall-modifying enzymes. Meanwhile, MAP+EA treatment also significantly increased the expression of color-related genes such as flavonoid 3'-hydroxylase gene (F3'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and UDP-flavonoid 3-O-glucosyltransferase (UFGT). Furthermore, a good synergistic effect was observed between 1-MCP and EA in delaying softening and promoting coloring of peach fruit in the MAP package. The combination of 1-MCP and EA treatment may have the potential to alleviate softening and improve the color and quality of post-harvest fruit during storage.

Flavonoids play a crucial role in plant development, resistance, and the pigmentation of fruits and flowers. This study aimed to uncover the mechanism of flavonoid biosynthesis and fruit coloring in muscadine grapes. Two muscadine genotypes (Paulk and Supreme) were investigated via metabolomic and transcriptomic analysis during three developmental stages (bunch closure, veraison stage, and ripening stage). A total of 314 flavonoids were identified, with flavones and flavonols being the primary constituents. The contents of many differentially accumulated metabolites (DAMs) were higher at the veraison stage. The total anthocyanin content was upregulated during berry development, with the dominant type of anthocyanidin-3,5-O-diglucoside. Proanthocyanins accumulated higher levels in the ripening stage of Paulk than Supreme. Transcriptomic analyses revealed that over 46% of the DEGs exhibited higher expression levels in the bunch closure stage. Moreover, phenylalanine ammonia-lyase (PAL), cinnamyl 4-hydroxylase (C4H), and coumaryl CoA ligase (4CL) genes were upregulated during berry development, suggesting they promote second metabolites biosynthesis. The upregulation of dihydroflavonol 4-reductase (DFR) and leucoanthocyanin reductase (LAR) may related to the higher levels of PA in Paulk. Anthocyanidin synthase (ANS) and UDP-glucose:flavonoid-3-O-glucosyltransferase (UFGT) showed higher expression levels in the ripening stage, which may relate to the accumulation of anthocyanidins. This study provides comprehensive insights into flavonoid metabolism and berry coloration in Vitis rotundifolia.

BackgroundAnthocyanin and chlorophyll are two compounds responsible for coloration in plants. Plant hormones can influence the accumulation of anthocyanins and chlorophyll. In this study, Paeonia ostii and Paeonia qiui, which exhibit red leaves during their juvenile stage, were selected to explore the effects of different hormones on leaf coloration.ResultsTree peony leaves predominantly contained cyanidin-3,5-O-diglucoside (Cy3G5G) and peonidin-3,5-O-diglucoside (Pn3G5G), with minimal peonidin-3-O-glucoside (Pn3G). Among eight phytohormone treatments, gibberellins (GA3), group maximized anthocyanin accumulation while methyl jasmonate (MeJA) group showed opposite effects. Anthocyanin accumulation was influenced by eight plant hormones, but only MeJA group had a notable effect on chlorophyll production. GA3 group significantly upregulated gibberellin 2-oxidase (GA2ox) expression in two tree peony species, enhancing endogenous GA biosynthesis. Concurrently, GA3 group significantly upregulated the expression of multiple key genes in the anthocyanin biosynthetic pathway in tree peony leaves. Specifically, dihydro flavonol 4-reductase (PoDFR) exhibited the most pronounced upregulation (1.325-fold) in Paeonia ostii leaves, while anthocyanidin synthase (PqANS) showed a remarkable (5.72-fold) increase in expression in Paeonia qiui leaves. MeJA group significantly upregulated the expression of allene oxide synthase (AOS) and allene oxide cyclase (AOC) genes in the jasmonic acid (JA) biosynthesis pathway, consequently enhancing endogenous JA levels in the leaves. High levels of JA stimulated the activation of genes involved in chlorophyll synthesis in plants. However, the expression of most anthocyanin biosynthetic genes in MeJA group was significantly suppressed, with particularly marked downregulation observed in chalcone synthase (CHS) and glucose-flavonoid-3-glucosyltransferase (UFGT). Furthermore, MeJA and GA3 may engage in complex crosstalk with other hormones, potentially exhibiting either synergistic or antagonistic interactions that modulate plant physiological responses.ConclusionsThe tree peony leaves treated with GA3, strigolactone analog (rac-GR24), brassinosteroids (BR), and 6-benzyladenine (6-BA) were redder in color, but leaves treated with indole-3-acetic acid (IAA), salicylic acid (SA), abscisic acid (ABA), and MeJA were greener than control (CK) group. This study provides a basis for further research on the mechanism of hormone regulation of leaf color in tree peony.

The activity annotation of peach glycosyltransferase PpUGT78B based on engineering bacterial anthocyanin biosynthesis.

IntroductionNicotiana tabacum, widely cultivated for its economic and scientific value, produces a broad range of secondary metabolites that play critical roles in determining leaf quality and flavor. Despite substantial progress, the comprehensive regulatory landscape governing secondary metabolite biosynthesis during N. tabacum leaf development remains largely unclear.MethodsTo better understand the molecular regulatory mechanisms underlying the biosynthesis of secondary metabolites, particularly flavonoids, during N. tabacum leaf development, we conducted a transcriptomic and non-targeted metabolomic sequencing and analysis at three critical developmental stages: vigorous growth stage (T1), topping stage (T2), and harvest stage (T3).ResultsBased on our transcriptomic and metabolomic data, 25 unigenes exhibiting stage-specific expression patterns that were strongly associated with flavonoid accumulation were identified. We found that during early developmental stages (T1-T2), upregulated expression of chalcone synthase (CHS) and chalcone isomerase (CHI) correlated with enhanced flavonoid backbone biosynthesis. In contrast, during the later stage (T3), increased expression of dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS) was consistent with elevated anthocyanin accumulation.ConclusionThis study systematically analyzed the coordinated regulatory network of flavonoid biosynthesis during leaf development in N. tabacum, revealing dynamic metabolic shifts across developmental stages. The findings offer novel molecular insights into the mechanisms underlying leaf quality formation and establish a theoretical framework for functional studies of candidate genes, reinforcing the utility of N. tabacum as a model species for secondary metabolism research and breeding innovation.

Water stress stimulates plants to regulate flavonoid biosynthesis. Overexpression of the PgF3H gene increases flavonoid levels and drought tolerance in Arabidopsis, with stress-responsive elements in the PgF3H promoter indicating its role in drought response. Water stress significantly impairs plant growth and yield, but plants combat this through various strategies, including flavonoid biosynthesis regulation. Flavonoids, crucial secondary metabolites, aid in plant development and stress responses. Pearl millet, a drought-tolerant crop, produces high levels of secondary metabolites like flavonoids and anthocyanins via the phenylpropanoid pathway. Research indicates that flavonoid-encoding genes are prevalent in drought-tolerant pearl millet variants, hinting at their role in drought response, though their exact functions are not fully understood. This study highlights the essential role of pearl millet flavanone 3-hydroxylase (PgF3H) in flavonoid biosynthesis. To validate this function, PgF3H was expressed in flavonoid-deficient Arabidopsis mutant backgrounds: Atf3h (defective in flavanone 3-hydroxylase activity), Atans (mutated in anthocyanidin synthase, leading to impaired anthocyanin production), and Atanr (a regulatory mutant with altered anthocyanin accumulation). The PgF3H overexpression led to partial or complete restoration of flavonoid production in these mutants, reinforcing the gene's role in biosynthesis and drought resilience. In silico analysis of the PgF3H promoter revealed stress-responsive elements, and ProPgF3H::GUS expressing lines showed increased GUS expression with higher PEG concentrations. The in silico structure of PgF3H revealed a 2OG-Fe(II) oxygenase domain, crucial in the flavonoid biosynthetic pathway. In conclusion, PgF3H overexpression enhances drought tolerance in Arabidopsis, suggesting a potential strategy for improving crop drought resistance by manipulating flavonoid biosynthesis.

Cyanidin-3-O-galactoside (C3Ga), a natural pigment, has various beneficial biological activities and is widely used as a food colorant. However, traditional plant extraction methods are time-consuming and unsustainable. Rapid and sustainable synthesis of C3Ga by engineered microorganisms offers a promising alternative to traditional plant-based methods and deserves to be explored. In this study, the bioproduction of C3Ga by Escherichia coli was achieved for the first time. The biosynthetic pathway of C3Ga from (+)-catechin was constructed by introducing anthocyanidin synthase (ANS) and UDP-galactose:cyanidin galactosyltransferase. Some strategies, including enhancement of the UDP-galactose biosynthesis pathway, identification of efficient ANS, overexpression of the C3Ga transporter, and modulation of multigene expression, were subsequently used to drive the metabolic flux toward C3Ga production. Next, the two-stage process for C3Ga production was optimized to mitigate limitations for further metabolic engineering. Combined with the knockout of β-phosphoglucomutase (ycjU), a newly identified competitive pathway for UDP-galactose, the production of C3Ga finally reached 217.9 mg/L. The strategies used in this study could be applied to the biosynthesis of other anthocyanins and galactosylated natural products.

Anthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. This study compares two banana cultivars, Grand Naine (GN) and Red Banana (RB), which exhibit significant differences in anthocyanin pigmentation. Transcriptomic profiling of peel (PL) and pulp (PP) tissues revealed cytokinin-responsive type-B response regulators (RRs), MaRR_B9 and MaRR_B12, as key modulators of anthocyanin biosynthesis. Cytokinin treatment of PP tissues increased the expression of MaRR_B9 and MaRR_B12, while significantly reducing the expression of dihydroflavanol reductase (MaDFR1, MaDFR2) and anthocyanidin synthase (MaANS) genes along with anthocyanin content. Through a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, MaDFRs and MaANS. Additionally, a type B-RRs motif (AGATT) was identified in the promoter regions of MaDFR2 and MaANS, suggesting that MaRRs might directly regulate the transcription of MaDFR2 and MaANS. MaRR_B9 and MaRR_B12 interact with the promoters of MaDFR2 and MaANS, repressing these genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, notably the cyanidin derivative, accompanied by altered expression patterns of MaDFRs and MaANS. Thus, the present study identifies MaRR_B9 and MaRR_B12 as novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs, for the genetic optimization aimed at enhancing anthocyanin content, stress resilience, and nutritional value in crop plants.

Comprehensive analysis of the physiological, metabolome, and transcriptome provided insights into anthocyanin biosynthesis and degradation of Malus crabapple.

Halophytes possess inherent stress resilience and diverse adaptations, making them valuable genetic reservoirs for crop breeding. The leguminous halophyte Sesbania bispinosa is a valuable forage crop that thrives in saline soils. To explore its salt tolerance, high‐quality genome assemblies is generated for the salt‐tolerant S. bispinosa accession SbTA02 and the salt‐sensitive accession SbSA44. Genomic analysis revealed that the genomic divergence between the two accessions primarily originates from their pericentromeric and centromeric regions, which contain the two largest inversions: a >27‐Mb inversion on chromosome 5 and a ≈49‐Mb inversion on chromosome 6. Population‐level analysis revealed that the 27‐Mb inversion is widespread in S. bispinosa, dividing the tested populations into inland and coastal groups. These groups have many genetic divergence regions (GDRs), with genetically isolated haplotypes in the middle section of chromosome 5, including the large inversion and centromeric regions. Genome‐wide association studies (GWAS) identified significant salt‐tolerance signals in the GDRs, pinpointing the anthocyanidin synthase gene SbANS. Natural variation in SbANS is associated with differences in salt tolerance between salt‐tolerant and salt‐sensitive S. bispinosa accessions. These findings provide insights into the genomic evolution of the Sesbania genus and shed light on how genomic variation shapes genome architecture, genetic divergence, and phenotypic differentiation.

In this study, red-blue light (7R3B) was used as the control (CK), while far-red (FR) and ultraviolet-A (UVA) light were supplemented to evaluate their effects on basil growth. The results showed that the FR treatment promoted plant height, stem diameter, and biomass, but reduced chlorophyll and carotenoid content, while the UVA treatment increased stem diameter and chlorophyll b content. Meanwhile, transcriptomic and metabolomic analyses were employed to examine changes in gene expression and metabolite accumulation in basil. The FR treatment reduced the levels of differentially accumulated metabolites (DAMs) in the carotenoid biosynthesis pathway, potentially contributing to the observed decrease in chlorophyll. The FR treatment upregulated the levels of five DAMs (gibberellin, cytokinin, brassinosteroid, jasmonic acid, and salicylic acid) and altered the differentially expressed genes (DEGs) such as gibberellin receptor (GID1) and jasmonate ZIM domain-containing protein (JAZ) in the plant hormone signal transduction pathway, thereby promoting plant growth and shade avoidance responses. The UVA treatment upregulated the 9-cis-epoxycarotenoid dioxygenase (NCED) expression in the carotenoid biosynthesis pathway, possibly indirectly promoting flavonoid synthesis. In the flavonoid biosynthesis pathway, the UVA treatment also promoted flavonoid accumulation by upregulating DEGs including flavonol synthase (FLS), anthocyanidin synthase (ANS), 5-O-(4-coumaroyl)-D-quinate 3'-monooxygenase (CYP98A), and flavanone 7-O-glucoside 2″-O-beta-L-rhamnosyltransferase (C12RT1), as well as increasing the levels of DAMs such as kaempferol, luteolin, apigenin, and leucopelargonidin. The accumulation of flavonoids improved antioxidant capacity and nutritional value in basil. Through a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, this study provided valuable insights into the molecular and metabolic mechanisms of the FR and UVA regulation of basil growth, providing guidance for optimizing supplementary lighting strategies in plant factories.

The seed-coat color and seed size have an impact on both the evolutionary fitness and the grain yield of crops. Soybean is a major oil crop, and the seed-coat color and seed size exhibit natural diversity among the different soybean varieties. Here, we found an R2R3-MYB transcription factor of GmMYB62, which shows a significant increase in expression as the seed-coat color changes from yellow to black in different soybean varieties. The GmMYB62 was specifically highly expressed in reproductive organs, especially in floral organs in soybeans. The GmMYB62 encodes a nuclear protein that contains two MYB domains. In the phylogenetic analysis, the GmMYB62 was relatively conserved after the divergence of the monocots and dicots, and it also grouped with transcriptional repressors of MYBs in anthocyanin synthesis. The GmMYB62 was overexpressed in Arabidopsis and the seeds displayed a pale-brown coat in GmMYB62 overexpression lines, in contrast to the dark-brown seed coat observed in wild-type of Col-0. The anthocyanin content in the GmMYB62 overexpression lines was dramatically reduced when compared to Col-0. Additionally, the seeds in overexpression lines showed shorter lengths, larger widths, and lower thousand-seed weights than those in Col-0. Furthermore, the genes related to anthocyanin synthesis and seed size regulation were investigated, and expression of eight genes that involved in anthocyanin synthesis pathway, like chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), and anthocyanidin synthase (ANS) were severely inhibited in the GmMYB62 overexpression lines when compared to Col-0. In addition, the ARGOS-LIKE (ARL), B-Type Cyclin 1 (CYCB1), and enhancer of DA1-1 (EOD3), which govern cell expansion and proliferation, were highly expressed in GmMYB62 overexpression lines when compared to Col-0. Overall, this study sheds new light on the control of seed-coat color and seed size by GmMYB62 and provides potentially valuable targets for improving crop seed quality.