Glucosinolate Biosynthesis Research Articles

Structural variation reshapes population gene expression and trait variation in 2,105 Brassica napus accessions

Although individual genomic structural variants (SVs) are known to influence gene expression and trait variation, the extent and scale of SV impact across a species remain unknown. In the present study, we constructed a reference library of 334,461 SVs from genome assemblies of 16 representative morphotypes of neopolyploid Brassica napus accessions and detected 258,865 SVs in 2,105 resequenced genomes. Coupling with 5 tissue population transcriptomes, we uncovered 285,976 SV-expression quantitative trait loci (eQTLs) that associate with altered expression of 73,580 genes. We developed a pipeline for the high-throughput joint analyses of SV-genome-wide association studies (SV-GWASs) and transcriptome-wide association studies of phenomic data, eQTLs and eQTL-GWAS colocalization, and identified 726 SV–gene expression–trait variation associations, some of which were verified by transgenics. The pervasive SV impact on how SV reshapes trait variation was demonstrated with the glucosinolate biosynthesis and transport pathway. The study highlighting the impact of genome-wide and species-scale SVs provides a powerful methodological strategy and valuable resources for studying evolution, gene discovery and breeding.

Physiological Effects and Mechanisms of Chlorella vulgaris as a Biostimulant on the Growth and Drought Tolerance of Arabidopsis thaliana.

Microalgae have demonstrated biostimulant potential owing to their ability to produce various plant growth-promoting substances, such as amino acids, phytohormones, polysaccharides, and vitamins. Most previous studies have primarily focused on the effects of microalgal biostimulants on plant growth. While biomass extracts are commonly used as biostimulants, research on the use of culture supernatant, a byproduct of microalgal culture, is scarce. In this study, we aimed to evaluate the potential of Chlorella vulgaris culture as a biostimulant and assess its effects on the growth and drought tolerance of Arabidopsis thaliana, addressing the gap in current knowledge. Our results demonstrated that the Chlorella cell-free supernatant (CFS) significantly enhanced root growth and shoot development in both seedlings and mature Arabidopsis plants, suggesting the presence of specific growth-promoting compounds in CFS. Notably, CFS appeared to improve drought tolerance in Arabidopsis plants by increasing glucosinolate biosynthesis, inducing stomatal closure, and reducing water loss. Gene expression analysis revealed considerable changes in the expression of drought-responsive genes, such as IAA5, which is involved in auxin signaling, as well as glucosinolate biosynthetic genes, including WRKY63, MYB28, and MYB29. Overall, C. vulgaris culture-derived CFS could serve as a biostimulant alternative to chemical products, enhancing plant growth and drought tolerance.

Integrated Analysis of Metabolome and Transcriptome Reveals the Effect of Burdock Fructooligosaccharide on the Quality of Chinese Cabbage (Brassica rapa L. ssp. Pekinensis).

Burdock fructooligosaccharide (BFO) is fructose with a low polymerization degree, which could improve the immunity to pathogens, quality, and stress resistance of vegetables. Still, there are no studies on applying BFO in Chinese cabbage. In this study, the effects of exogenous BFO sprayed with different concentrations (0, 5, 10, 20, 30 g·L-1) on the growth and soluble sugar content of Chinese cabbage seedlings were determined. The result showed that 10 g·L-1 was the appropriate spraying concentration. Based on metabolome analysis, a total of 220 differentially accumulated metabolites (DAMs) were found, among which flavonoid metabolites, glucosinolate metabolites, and soluble sugar-related metabolites were the key metabolites involved in improving the quality of Chinese cabbage caused by BFO. Further combination analysis with transcriptome, trans-cinnamate 4-monooxygenase (CYP73A5), and chalcone synthase 1 (CHS1) were more closely associated with the DAMs of flavonoid biosynthesis. Sulfotransferases 18 (SOT18), Branched-chain amino acid amino transferases 6 (BCAT6), and cytochrome P450 monooxygenase (CYP83A1) were the key genes in glucosinolate biosynthesis. Hexokinase (HxK1), beta-glucosidase 8 (BGL08), invertase 3 (INV3), beta-glucosidase 3B (BGL3B), and sucrose phosphate synthase 1 (SPS1) were significantly upregulated, potentially playing crucial roles in the soluble sugar metabolism. In conclusion, these results provided an understanding of the effects of BFO on the expression of genes and the accumulation of metabolites related to quality formation in Chinese cabbage.

Effect of sodium selenite on the synthesis of glucosinolates and antioxidant capacity in Chinese cabbage (Brassica rapa L.ssp.pekinensis).

Chinese cabbage (Brassica rapa ssp. pekinensis) is a globally cultivated and consumed leafy vegetable due to its abundant plant secondary metabolites and antioxidant compounds, including flavonoids, ascorbic acids, glucosinolates, and vitamins, which have been reported to confer health-promoting effects. Glucosinolates components in leaves of Chinese cabbage plantlets under different concentrations of sodium selenite (0, 30, and 50μmol/L) were analyzed. Seven glucosinolates were identified and quantified using UHPLC-QTOF-MS. Finally, treatments with 30 and 50μmol/L Na2SeO3 solution significantly increased the levels of total selenium content as well as total phenols, flavonoids, anthocyanins, and DPPH free radical scavenging ability in Chinese cabbage seedlings. Our results revealed that 30μmol/L Na2SeO3 effectively enhanced aliphatic glucosinolate levels and total glucosinolate content while causing a significant reduction in indole glucosinolates. Furthermore, downregulation was observed for BrCYP79F1, BrBCAT4, and BrMAM1 genes associated with aliphatic glucosinolate synthesis. Conversely, BrMYB28 and BrCYP83A1 genes exhibited significant upregulation. Thus, the positive influence of Na2SeO3 on glucosinolate biosynthesis in Chinese cabbage can be attributed to the upregulation of key genes related to this process.

Kinetic and catalytic mechanism of the methionine-derived glucosinolate biosynthesis enzyme methylthioalkylmalate synthase

In Brassica plants, methionine-derived aliphatic glucosinolates are chemically diverse natural products that serve as plant defense compounds, as well as molecules with dietary health-promoting effects. During their biosynthesis, methylthioalkylmalate synthase (MAMS) catalyzes the elongation reaction of the aliphatic chain. The MAMS catalyzed condensation of 4-methylthio-2-oxobutanoic acid (4-MTOB) and acetyl-CoA generates a 2-malate derivative that either enters the pathway for synthesis of C3-glucosinolates or undergoes additional extension reactions, which lead to C4- to C9-glucosinolates. Recent determination of the x-ray crystal structure of MAMS from Brassica juncea (Indian mustard) provided insight on the molecular evolution of MAMS, especially substrate specificity changes, from the leucine biosynthesis enzyme α-isopropylmalate synthase (IPMS) but left details of the reaction mechanism unanswered. Here we use the B. juncea MAMS2A (BjMAMS2A) isoform to analyze the kinetic and catalytic mechanism of this enzyme. Initial velocity studies indicate that MAMS follows an ordered bi bi kinetic mechanism, which based on the x-ray crystal structure, involves binding of 4-MTOB followed by acetyl-CoA. Examination of the pH-dependence of kcat and kcat/Km are consistent with acid/base catalysis. Site-directed mutagenesis of three residues originally proposed to function in the reaction mechanism - Arg89 (R89A, R89K, R89Q), Glu227 (E227A, E227D, E227Q), and His388 (H388A, H388N, H388Q, H388D, and H388E) - showed that only two mutants (E227Q and H388N) retained activity. Based on available structural and biochemical data, a revised reaction mechanism for MAMS-catalyzed elongation of methionine-derived aliphatic glucosinolates is proposed, which is likely also conserved in IPMS from leucine biosynthesis in plants and microbes.

Integrated transcriptomic and miRNA-seq analysis of Pak-choi provides insight into the molecular mechanisms involved in the preservation of postharvest quality by white LED light irradiation

Low-intensity white light-emitting diode (LED) irradiation effectively delays postharvest senescence in pak-choi at 20 °C and 90 % relative humidity. In this study, RNA-seq and miRNA-seq analyses were conducted on samples collected at 0 d (initial sample) and 5 d (CK and LED-treated samples) to evaluate the regulatory effects of white LED irradiation on miRNA. The resulting data revealed a total of 23 differentially expressed miRNAs (DEmiRNAs) in the CK/LED group on 5 d of storage. LED irradiation induced the expression of AP2 family genes and the biosynthesis of aliphatic glucosinolates by modulating the level of bra-miR172 family miRNAs. LED irradiation also stimulated the expression of genes associated with the photosynthetic pathway in pak-choi and regulated biosynthesis of ascorbic acid and resistance-associated transcription factors by modulating the level of novel miRNAs. Furthermore, LED irradiation suppressed cellulase and polygalacturonase activity, and maintained the pectin content. These findings demonstrate the ability of white LED light irradiation to significantly delay the postharvest senescence process in pak-choi by modulating miRNA expression.

Constitutive BoHAK5 expression and early robust induction of salicylic acid biosynthesis genes as candidates to explain the tolerance of broccoli to limiting potassium

Potassium (K+) is vital for optimum plant growth and crop yield, and it is an important component of fertilizers. However, our knowledge of the physiological and molecular response to limiting K+ conditions is incomplete. Despite their close phylogenetic relationship, we observed that broccoli is more tolerant to limiting K+ conditions than Arabidopsis. For this reason, we performed a detailed physiological and transcriptomic analysis to compare and contrast their response to this abiotic stress. Our results show that the K+ content of broccoli roots decreases at a slower rate than Arabidopsis. Both species exhibited characteristic responses observed in other plants, such as those related to oxidative stress, hypoxia and jasmonic and abscisic acid signaling. However, we observed notable differences in their responses, especially in the expression of BoHAK5 and the early and strong induction of isoforms of salicylic acid (SA) biosynthesis genes in broccoli, which was reflected in the increased SA accumulation in broccoli leaves. We also observed alterations in the gene expression patterns of enzymes and in the levels of intermediates involved in the biosynthesis of glucosinolates, which are important molecules contributing to the added nutritional value of broccoli. Lastly, we provide evidence for concomitant alterations in the expression patterns of genes encoding transporters of several other ions, such as Fe2+, PO43− and NO3−. Our data provide insight into the possible mechanisms of broccoli’s tolerance to limiting K+ conditions and identify specific targets for the development of crop plants with reduced fertilization requirements.

Integrative Analyses of Metabolites and Transcriptome Reveal the Metabolic Pattern of Glucosinolates in Potherb Mustard (Brassica juncea var. multiceps).

Potherb mustard (Brassica juncea var. multiceps) is one of the most commonly consumed leafy vegetable mustards, either fresh or in pickled form. It is rich in glucosinolates, whose hydrolyzed products confer potherb mustard's distinctive flavor and chemopreventive properties. In this study, the composition and content of glucosinolates, as well as the hydrolysis pattern of sinigrin were investigated in potherb mustard leaves of different varieties. Variations in the glucosinolate profile and accumulation were observed among the potherb mustard varieties studied, with sinigrin being the predominant one in all varieties, accounting for 81.55% to 97.27%. Sinigrin tended to be hydrolyzed to isothiocyanate (ITC) rather than epithionitrile (EPN) in potherb mustard, while 3-butenyl nitrile (SIN-NIT) could be hardly detected. Transcriptome analysis revealed a higher expression level of numerous genes involved in aliphatic glucosinolate biosynthesis in X11 compared to X57, corresponding to the higher aliphatic glucosinolate accumulation in X11 (91.07 µmol/g) and lower level in X57 (25.38 µmol/g). ESM1 is known to repress nitrile formation and favor isothiocyanate production during glucosinolate hydrolysis. In this study, all four ESM1s showed a higher expression level in X11 compared to X57, which may determine the hydrolysis pattern of sinigrin in potherb mustard. Altogether, our findings shed light on the glucosinolate metabolic pattern in potherb mustard, which will also facilitate the engineering of metabolic pathways at key checkpoints to enhance bioactive compounds for tailored flavor or pharmaceutical needs.

Epigenetic regulation of glucosinolate biosynthesis sees the light of day.

Epigenetic regulation of glucosinolate biosynthesis sees the light of day.

Natural variation in BnaA07.MKK9 confers resistance to Sclerotinia stem rot in oilseed rape

Sclerotinia stem rot (SSR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating diseases for several major oil-producing crops. Despite its impact, the genetic basis of SSR resistance in plants remains poorly understood. Here, through a genome-wide association study, we identify a key gene, BnaA07. MKK9, that encodes a mitogen-activated protein kinase kinase that confers SSR resistance in oilseed rape. Our functional analyses reveal that BnaA07.MKK9 interacts with BnaC03.MPK3 and BnaC03.MPK6 and phosphorylates them at the TEY activation motif, triggering a signaling cascade that initiates biosynthesis of ethylene, camalexin, and indole glucosinolates, and promotes accumulation of H2O2 and the hypersensitive response, ultimately conferring resistance. Furthermore, variations in the coding sequence of BnaA07.MKK9 alter its kinase activity and improve SSR resistance by ~30% in cultivars carrying the advantageous haplotype. These findings enhance our understanding of SSR resistance and may help engineer novel diversity for future breeding of oilseed rape.

Disease resistance of Brassica juncea to Sclerotinia sclerotiorum is established through the induction of indole glucosinolate biosynthesis

Sclerotinia stem rot (SSR), caused by Sclerotinia sclerotiorum, is the main disease threat to oilseeds in Brassiceae, causing significant yield losses and reduction in oil content and quality. While the genetic mechanism underlying its lethal phenotype, particularly in B. juncea, remains largely unexplored. Transcriptome analysis revealed a large number of defense-related genes and response processes in B. napus and B. oleracea. However, similarities and differences in the defense responses to S. sclerotiorum on B. juncea are rarely reported. In the present study, we reported a B. juncea breeding line of H83 with high S. sclerotiorum resistance, which was used for transcriptome analysis compared to L36 with low resistance. A novel regulatory network was proposed to defend against S. sclerotiorum invasion in B. juncea. Upon infection of S. sclerotiorum, a series of were initiated within 12 h, and then defenses were activated to restrict the development and spread of S. sclerotiorum by inducing the massive synthesis of indole glucosinolates after 24 h. Twelve hub genes involved in the network were identified by the weighted gene co-expression network (WGCNA), which are involved in plant-pathogen interaction, signaling pathway genes, indole glucosinolate biosynthesis and cell wall formation. The hub genes were further validated by qRT-PCR. The research revealed a new resistant line of H83 against S. sclerotiorum and a different regulatory network in B. juncea, which would be beneficial for the future effective breeding of Sclerotinia-resistant varieties.

UV-B irradiation enhances the accumulation of beneficial glucosinolates induced by melatonin in Chinese kale sprout

Cruciferous sprout is a new form of vegetable product rich in bioactive compounds, especially glucosinolates. Previous studies have focused on increasing the accumulation of glucosinolates in cruciferous sprouts by applying different chemical regulators, with a particular focus on their contribution to nutritional quality and health benefits. Nevertheless, the effects of melatonin and UV-B irradiation on glucosinolate biosynthesis remain unclear. In this study, it was found that changes in melatonin concentrations significantly affected the contents of individual as well as total aliphatic and indolic glucosinolates. The 5 μmol · L−1 melatonin was decided as the optimum concentration that could increase the content of beneficial glucosinolates including glucoraphanin and 4-methoxy glucobrassicin in Chinese kale sprouts. Notably, the enhancement of glucosinolate accumulation by melatonin treatment could be further amplified by UV-B irradiation. Furthermore, our results showed that R2R3-MYB transcription factor BoaMYB28 and BoaMYB51, which are central regulators of aliphatic and indolic glucosinolate biosynthesis respectively, were both involved in the regulation of glucosinolate biosynthesis by melatonin and UV-B irradiation. Additionally, the expression of glucosinolate biosynthetic genes, including BoaCYP79F1, BoaCYP83A1, BoaSUR1, BoaUGT74B1, BoaCYP79B2, BoaCYP79B3, and BoaCYP83B1 participated in the formation of core structures and BoaFMOGS-OX5, BoaAOP2, BoaCYP81F2, and BoaIGMT1 involved in the side-chain modification of aliphatic and indolic glucosinolate, was regulated by melatonin or UV-B irradiation. Taken together, these findings provide a potential strategy for improving the nutritional quality and resistance of Chinese kale sprouts.

Transcriptome and metabolome analysis reveal key genes and metabolic pathway responses in Leersia hexandra Swartz under Cr and Ni co-stress

Phytoremediation, an eco-friendly approach for mitigating heavy metal contamination, is reliant on hyperaccumulators. This study focused on Leersia hexandra Swart, a known chromium (Cr) hyperaccumulator with demonstrated tolerance to multiple heavy metals. Our objective was to investigate its response to simultaneous Cr and nickel (Ni) stress over 12 days. Results from physiological experiments demonstrated a significant increase in the activities of antioxidant enzymes (APX, SOD, CAT) and glutathione (GSH) content under Cr and Ni stress, indicating enhanced antioxidant mechanisms. Transcriptome analysis revealed that stress resulted in the differential expression of 27 genes associated with antioxidant activity and metal binding, including APX, SOD, CAT, GSH, metallothionein (MT), and nicotinamide (NA). Among them, twenty differentially expressed genes (DEGs) related to GSH metabolic cycle were identified. Notably, GSTU6, GND1, and PGD were the top three related genes, showing upregulation with fold changes of 4.57, 6.07, and 3.76, respectively, indicating their crucial role in metal tolerance. The expression of selected DEGs was validated by quantitative real-time PCR, confirming the reliability of RNA-Seq data. Metabolomic analysis revealed changes in 1121 metabolites, with amino acids, flavonoids, and carbohydrates being the most affected. Furthermore, glucosinolate biosynthesis and amino acid biosynthesis pathways were represented in the KEGG pathway of differentially expressed metabolites (DEMs). This study provides insights into the tolerance mechanisms of L. hexandra under the co-stress of Cr and Ni, offering a new perspective for enhancing its remediation performance.

The RNA-Binding Protein BoRHON1 Positively Regulates the Accumulation of Aliphatic Glucosinolates in Cabbage.

Aliphatic glucosinolates are an abundant group of plant secondary metabolites in Brassica vegetables, with some of their degradation products demonstrating significant anti-cancer effects. The transcription factors MYB28 and MYB29 play key roles in the transcriptional regulation of aliphatic glucosinolates biosynthesis, but little is known about whether BoMYB28 and BoMYB29 are also modulated by upstream regulators or how, nor their gene regulatory networks. In this study, we first explored the hierarchical transcriptional regulatory networks of MYB28 and MYB29 in a model plant, then systemically screened the regulators of the three BoMYB28 homologs in cabbage using a yeast one-hybrid. Furthermore, we selected a novel RNA binding protein, BoRHON1, to functionally validate its roles in modulating aliphatic glucosinolates biosynthesis. Importantly, BoRHON1 induced the accumulation of all detectable aliphatic and indolic glucosinolates, and the net photosynthetic rates of BoRHON1 overexpression lines were significantly increased. Interestingly, the growth and biomass of these overexpression lines of BoRHON1 remained the same as those of the control plants. BoRHON1 was shown to be a novel, potent, positive regulator of glucosinolates biosynthesis, as well as a novel regulator of normal plant growth and development, while significantly increasing plants' defense costs.

Effects of combined treatment of light quality and melatonin on health-promoting compounds in Chinese kale sprouts

Chinese kale sprouts have garnered attention owing to its rich health-promoting compounds. This study aimed to investigate the effects of different light qualities (white, blue, and red light) and melatonin (100 μmol L−1), both individually and in combination, on the growth and accumulation of health-promoting compounds in Chinese kale sprouts. Red light positively influenced sprout growth (compared with white light, plant height and fresh weight increased by 16.67 % and 4.87 %, respectively), and the red light + melatonin treatment further enhanced growth (compared with single red light, the plant height and fresh weight increased by 14.97 % and 12.29 %, respectively), while increasing glucosinolate accumulation through the up-regulation of glucosinolate biosynthetic genes (UGT74B1, CYP83B1, SOT18 and IGMT1). Conversely, blue light inhibited sprout growth, elevated the expression levels of PAL, CHS, CHI, GGP, and PAX, improved antioxidant levels, and accelerated the accumulation of aliphatic glucosinolates, reducing indolic glucosinolates. The blue light + melatonin treatment promoted the accumulation of sprout biomass and anthocyanins (11.91 % and 13.33 % higher than that of single blue light). The study unveiled various pathways influencing plant growth, development, and secondary metabolite accumulation, including plant circadian rhythms, ascorbate and aldarate metabolism, phenylpropanoid biosynthesis, and glucosinolate biosynthesis.

Integrated Analysis of Transcriptome and Metabolome Reveals Differential Responses to Alternaria brassicicola Infection in Cabbage (Brassica oleracea var. capitata).

Black spot, caused by Alternaria brassicicola (Ab), poses a serious threat to crucifer production, and knowledge of how plants respond to Ab infection is essential for black spot management. In the current study, combined transcriptomic and metabolic analysis was employed to investigate the response to Ab infection in two cabbage (Brassica oleracea var. capitata) genotypes, Bo257 (resistant to Ab) and Bo190 (susceptible to Ab). A total of 1100 and 7490 differentially expressed genes were identified in Bo257 (R_mock vs. R_Ab) and Bo190 (S_mock vs. S_Ab), respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that "metabolic pathways", "biosynthesis of secondary metabolites", and "glucosinolate biosynthesis" were the top three enriched KEGG pathways in Bo257, while "metabolic pathways", "biosynthesis of secondary metabolites", and "carbon metabolism" were the top three enriched KEGG pathways in Bo190. Further analysis showed that genes involved in extracellular reactive oxygen species (ROS) production, jasmonic acid signaling pathway, and indolic glucosinolate biosynthesis pathway were differentially expressed in response to Ab infection. Notably, when infected with Ab, genes involved in extracellular ROS production were largely unchanged in Bo257, whereas most of these genes were upregulated in Bo190. Metabolic profiling revealed 24 and 56 differentially accumulated metabolites in Bo257 and Bo190, respectively, with the majority being primary metabolites. Further analysis revealed that dramatic accumulation of succinate was observed in Bo257 and Bo190, which may provide energy for resistance responses against Ab infection via the tricarboxylic acid cycle pathway. Collectively, this study provides comprehensive insights into the Ab-cabbage interactions and helps uncover targets for breeding Ab-resistant varieties in cabbage.

Growth conditions trigger genotype-specific metabolic responses that affect the nutritional quality of kale cultivars.

Kales (Brassica oleracea convar acephala) are fast-growing, nutritious leafy vegetables ideal for year-round indoor farming. However, selection of best cultivars for growth under artificial lighting necessitates a deeper understanding of leaf metabolism in different kale types. Here we examined a curly leaved cultivar Half Tall and a lacinato type cultivar Black Magic under moderate growth light (130 µmol photons m-1s-1/22°C) and high light (800 µmol photons m-1s-1/26°C) conditions. These conditions induced genotype-dependent differences in nutritionally important metabolites, especially anthocyanins and glucosinolates (GSLs), in the kale cultivars. In the pale green Half Tall, growth under high light conditions did not induce changes in either pigmentation or total GSL content. In contrast, the purple pigmentation of Black Magic intensified due to increased anthocyanin accumulation. Black Magic showed reduced amounts of indole GSLs and increased amounts of aliphatic GSLs under high light conditions, with notable cultivar-specific adjustments in individual GSL species. Correlation analysis of metabolite profiles suggested cultivar-specific metabolic interplay between serine biosynthesis and the production of indole GSLs. RNA sequencing identified candidate genes encoding metabolic enzymes and regulatory components behind anthocyanin and GSL biosynthesis. These findings improve the understanding of leaf metabolism and its effects on the nutritional quality of kale cultivars.

Modified atmosphere affects glucosinolate metabolism during postharvest storage of broccoli

Broccoli is a vegetable with a growing consumer demand worldwide due to its important nutritional properties, including high amounts of glucosinolates. However, this vegetable has a short postharvest life and quickly loses its organoleptic and nutritional quality. Modified atmosphere is one of the numerous methodologies used to delay deterioration during postharvest storage of broccoli heads. In this study, the effect of a modified atmosphere during postharvest storage of broccoli on glucosinolate metabolism was evaluated. Five glucosinolates were identified by using a UPLC system coupled to a mass spectrometer. We detected one aliphatic glucosinolate and four indolic glucosinolates, and their concentration was found to decrease during storage. The decrease in content was less marked, and in some cases, an increased level was observed in the treated samples. Moreover, the treatment made it possible to maintain higher expression (analyzed by real-time quantitative PCR) of genes linked to glucosinolate biosynthesis. We also detected an increased expression of some genes related to indolic glucosinolate biosynthesis. Overall, storage of broccoli in modified atmospheres allowed for maintaining better visual quality and higher levels of glucosinolates.

Integrated metabolomic and transcriptomic analysis of metabolic diversity and biosynthesis of glucosinolates and flavonoids in various cultivars of radish microgreens

Microgreens, with their distinctive flavor and rapid growth, have garnered significant attention as a functional and nutritious food. In this study, we performed a thorough targeted metabolomic study using ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UPLC-QqQ-MS/MS) on four distinct cultivars of radish microgreens, namely Champion Radish (CR), White Radish (WR), Hailstone Radish (HR), and China Rose Radish (CRR), in order to better understand the metabolic foundation of the nutritional value of these microgreens. A total of 1411 metabolites were found and more than a third of the total number of metabolites were accounted for by flavonoids (FL), phenolic acids, lignans, coumarins and glucosinolates (GL). Significant variations were found in the differentially accumulated metabolites (DAM) and differentially expressed genes (DEG) in each pairwise comparison of cultivars, according to further comparative analysis. The comparison of CR with the other groups identified more than 400 DAM and about 10,000 DEG, the most abundant DAM being FL, and the results showed that CR was very different from WR, HR and CRR. A total of 33 GL were newly found in radish microgreens and classified into 8 categories according to their side chains. Weighted gene co-expression network analysis and biosynthetic pathway analysis revealed the distinctive relationship between gene expression levels and characteristic GL and FL. This work aimed to provide fresh insights into the differences in metabolite profiles among radish microgreens of various cultivars in addition to establishing a theoretical framework for improving the genetic quality of radish microgreens.

Proteomic and metabolomic insights into seed germination of Ferula assa-foetida

Cold stratification is known to affect the speed of seed germination; however, its regulation at the molecular level in Ferula assa-foetida remains ambiguous. Here, we used cold stratification (4 °C in the dark) to induce germination in F. assa-foetida and adopted a proteomic and metabolomic approach to understand the molecular mechanism of germination. Compared to the control, we identified 209 non-redundant proteins and 96 metabolites in germinated F. assa-foetida seed. Results highlight the common and unique regulatory mechanisms like signaling cascade, reactivation of energy metabolism, activation of ROS scavenging system, DNA repair, gene expression cascade, cytoskeleton, and cell wall modulation in F. assa-foetida germination. A protein-protein interaction network identifies 18 hub protein species central to the interactome and could be a key player in F. assa-foetida germination. Further, the predominant metabolic pathways like glucosinolate biosynthesis, arginine and proline metabolism, cysteine and methionine metabolism, aminoacyl-tRNA biosynthesis, and carotenoid biosynthesis in germinating seed may indicate the regulation of carbon and nitrogen metabolism is prime essential to maintain the physiology of germinating seedlings. The findings of this study provide a better understanding of cold stratification-induced seed germination, which might be utilized for genetic modification and traditional breeding of Ferula assa-foetida. SignificanceSeed germination is the fundamental checkpoint for plant growth and development, which has ecological significance. Ferula assa-foetida L., commonly known as “asafoetida,” is a medicinal and food crop with huge therapeutic potential. To date, our understanding of F. assa-foetida seed germination is rudimentary. Therefore, studying the molecular mechanism that governs dormancy decay and the onset of germination in F. assa-foetida is essential for understanding the basic principle of seed germination, which could offer to improve genetic modification and traditional breeding.