Metabolic profile analysis and identification of key metabolites during rice seed germination under low-temperature stress

The Vacuolar Inositol Transporter BvINT1;1 Contributes to Raffinose Biosynthesis and Reactive Oxygen Species Scavenging During Cold Stress in Sugar Beet

Despite a high sucrose accumulation in its taproot vacuoles, sugar beet (Beta vulgaris subsp. vulgaris) is sensitive to freezing. Earlier, a taproot-specific accumulation of raffinose was shown to have beneficial effects on the freezing tolerance of the plant. However, synthesis of raffinose and other oligosaccharides of the raffinose family depends on the availability of myo-inositol. Since inositol and inositol-metabolising enzymes reside in different organelles, functional inositol metabolism and raffinose synthesis depend on inositol transporters. We identified five homologues of putative inositol transporters in the sugar beet genome, two of which, BvINT1;1 and BvINT1;2, are localised at the tonoplast. Among these, only the transcript of BvINT1;1 is highly upregulated in sugar beet taproots under cold. BvINT1;1 exhibits a high transport specificity for inositol and sugar beet mutants lacking functional BvINT1;1 contain increased inositol levels, likely accumulating in the vacuole, and decreased raffinose contents under cold treatment. Due to the quenching capacity of raffinose for Reactive Oxygen Species (ROS), which accumulate under cold stress, bvint1;1 sugar beet plants show increased expression of both, ROS marker genes and detoxifying enzymes. Based on these findings, we conclude that the vacuolar inositol transporter BvINT1;1 is contributing to ROS-homoeostasis in the cold metabolism of sugar beet.

Different responses of canopy and shrub leaves to canopy nitrogen and water addition in warm temperate forest

Introduction

Understanding the effects of nitrogen deposition and increased rainfall on plants is critical for maintaining forest ecosystem services. Although previous studies primarily examined the effects of environmental changes on leaf functional traits, the underlying physiological and metabolic processes associated with these traits remain poorly understood and warrant further investigation.

Methods

To address this knowledge gap, we evaluated the influence of canopy nitrogen (25 kg ha-1 yr-1) and water (30% of the local precipitation) addition on leaf functional traits, diversity, and associated physiological and metabolic processes in the dominant species of tree and shrub layers.

Results

Only the interaction between nitrogen and water significantly reduced the functional richness (FRic) of the community. The other treatments had no notable effects on functional diversity. Importantly, the physiological processes of trees and shrubs showed different regulatory strategies. In addition, there were significant changes in 29 metabolic pathways of the tree, whereas only 18 metabolic pathways were significantly altered in shrub. Among the identified metabolic pathways, four were annotated multiple times, with amino acid metabolism being the most active.

Discussion

These regulatory processes enable the leaves to withstand external disturbances and maintain their relative stability under changing environmental conditions. The study findings underscore the limitations of previous research, which often relied on the direct application of treatments to the understory and so failed to accurately assess the effects of nitrogen and water on leaf functional traits. Future studies should adopt canopy-level nitrogen and water addition to better simulate the impacts of global environmental change.

Unraveling the response of secondary metabolites to cold tolerance in oil palm by integration of physiology and metabolomic analyses

BACKGROUND

Oil palm (Elaeis guineensis), a tropical crop, is highly sensitive to temperature fluctuations, with low temperatures significantly limiting its growth, development, and geographical distribution. Understanding the adaptive mechanisms of oil palm under low-temperature stress is essential for developing cold-tolerant varieties. This study focused on analyzing the physiological and metabolomic responses of annual thin-shell oil palm seedlings to low-temperature exposure (8 °C) for different time periods: 0 h (CK), 0.5 h (CD05), 1 h (CD1), 2 h (CD2), 4 h (CD4), and 8 h (CD8).

RESULTS

Physiological analysis showed a significant increase in the activity of antioxidant enzymes, such as superoxide dismutase (SOD) and peroxidase (POD), highlighting the activation of oxidative stress defense mechanisms. Concurrently, elevated relative conductivity, indicated cell membrane damage, a common consequence of cold-induced oxidative stress. Metabolomic profiling using LC-MS/MS revealed significant changes in metabolite composition, with differential metabolites predominately enriched in key metabolic pathways such as arginine and proline metabolism, glycine, serine, and threonine metabolism, plant hormone biosynthesis, and flavonoid biosynthesis pathways. Notable metabolites such as citric acid, L-aspartic acid, L-tryptophan, and vitexin showed significant accumulation, indicating their roles in enhancing cold tolerance through improved antioxidant defenses, promoting osmoregulation, and stabilizing cellular structures. Correlation analysis further emphasized the importance of flavonoids and plant hormones in the cold stress response. In particular, vitexin, isovitexin, and apigenin 6-C-glucoside were significantly enriched, suggesting their contribution to antioxidant and stress signaling networks. Furthermore, metabolites involved in amino acid metabolism, including L-glutamic acid, sarcosine, and proline, were upregulated, supporting enhanced protein synthesis and cellular repair under stress. This metabolic reprogramming correlated with physiological improvements, as evidenced by increased relative conductivity and post cold exposure growth recovery.

CONCLUSION

This study provides critical insights into the physiological and metabolic adaptations of oil palm to cold stress, emphasizing the significant role of secondary metabolites-such as flavonoids, amino acids, and plant hormones-in enhancing cold tolerance. Theses metabolites contribute to oxidative stress protection, osmotic regulation, and cell wall stabilization enabling the plant to better withstand with low temperature condition. The findings provide a strong foundation for molecular research and breeding initiatives aimed at developing cold tolerant oil palm varieties, a crop of siginificant economic value. By combining metabolomic profiling with physiological analyses, provides a holistic understanding of the adaptive mechanisms in oil palm under cold stress.This integrated approach identifies key metabolic pathways that can be targeted in breeding programs to enhance cold resilience, paving the way for improved crop performance in challenging environments.

Proteomics- and metabolomics-based analysis of the regulation of germination in Norway maple and sycamore embryonic axes

Norway maple and sycamore belong to the Acer genus and produce desiccation-tolerant and desiccation-sensitive seeds, respectively. We investigated the seed germination process at the imbibed and germinated stages using metabolomic and proteomic approaches to determine why sycamore seeds germinate earlier and are more successful at establishing seedlings than Norway maple seeds under controlled conditions. Embryonic axes and embryonic axes with protruded radicles were analyzed at the imbibed and germinated stages, respectively. Among the 212 identified metabolites, 44 and 67 differentially abundant metabolites were found at the imbibed and germinated stages, respectively, in both Acer species. Higher levels of amines, growth and defense stimulants, including B vitamins, were found in sycamore. We identified 611 and 447 proteins specific to the imbibed and germinated stages, respectively, in addition to groups of proteins expressed at different levels. Functional analysis of significantly regulated proteins revealed that proteins with catalytic and binding activity were enriched during germination, and proteins possibly implicated in nitrogen metabolism and metabolite interconversion enzymes were the predominant classes. Proteins associated with the control of plant growth regulation and seed defense were observed in both species at both germination stages. Sycamore proteins possibly involved in abscisic acid signal transduction pathway, stress tolerance and alleviation, ion binding and oxygenase activities appeared to accompany germination in sycamore. We identified peptides containing methionine (Met) oxidized to methionine sulfoxide (MetO), and functional analyses of proteins with significantly regulated MetO sites revealed that translation, plant growth and development and metabolism of nitrogen compounds were the main processes under Met/MetO redox control. We propose that higher levels of storage proteins and amines, together with higher levels of B vitamins, supported more efficient nitrogen utilization in sycamore, resulting in faster seedling growth. In conclusion, omic signatures identified in sycamore seem to predispose germinated sycamore seeds to better postgerminative growth.

Impact of magnetic field-assisted freezing on the physicochemical properties and starch structure of cooked rice: Effects of magnetic types, intensities, and cryostasis time

A magnetic field-assisted freezing system was developed to mitigate the degradation of taste quality in frozen cooked rice (FCR). The physicochemical properties and starch structure were analyzed under varying magnetic field types, intensities, and cryostasis time. The analysis of freezing characteristics indicated that treatments with 10 mT static magnetic fields (SMF) and 6 mT alternating magnetic fields (AMF) yielded optimal results, significantly reducing the duration of the maximum ice crystal generation zone by approximately 18 min. Compared to no magnetic field (NMF) treatment, a 16-day frozen storage experiment showed significant improvements in the texture characteristics of cooked rice treated with magnetic fields. However, the moisture content of rice treated with AMF closely resembled those of freshly cooked rice, with a slight increase in yellowness compared to SMF treatment. Throughout the storage period, the crystallinity for the AMF treatment exceeded that of the SMF treatment by 2.99 %. Furthermore, compared to SMF treatment, water molecules in FCR treated with AMF are more tightly bound. Given the superior sensory scores in the AMF treatment, it can be concluded that while SMF reduces color degradation, AMF is more effective in preserving moisture, and structural density. Hence, magnetic fields, especially AMF, emerge as a promising auxiliary technology for FCR, offering a theoretical basis for advancing cold chain logistics technology for cooked rice.

The RAD6-like Ubiquitin Conjugase Gene OsUBC7 Has a Positive Role in the Early Cold Stress Tolerance Response of Rice

BACKGROUND/OBJECTIVES

Cold stress poses a significant threat to Asian rice cultivation, disrupting important physiological processes crucial for seedling establishment and overall plant growth. It is, thus, crucial to elucidate genetic pathways involved in cold stress tolerance response mechanisms.

METHODS

We mapped OsUBC7, a Radiation-sensitive 6 (RAD6)-type homolog of rice, to a low-temperature seedling survivability (LTSS) QTL and used genomics, molecular genetics, and physiological assays to assess its role in plant resilience against low-temperature stress.

RESULTS

OsUBC7 is cold responsive and has higher expression levels in cold-tolerant japonica than cold-sensitive indica. Overexpression of OsUBC7 enhances LTSS of indica and freezing tolerance of Arabidopsis, increases levels of soluble sugars and chlorophyll A, boosts leaf development after cold exposure, and increases leaf cell numbers and plants size, but it does not affect membrane stability after cold stress exposure. Additionally, OsUBC7 has a positive role for germinability in the presence of salt and for flowering and yield-related traits. The OsUBC7 protein physically interacts with the developmental stage-specific and histone-modifying E3 ligases OsRFPH2-12 and OsHUB1/2, respectively, and potential target genes such as cell cycle dependent kinases were identified.

CONCLUSIONS

OsUBC7 might contribute to cold resilience by regulating sugar metabolism to provide energy for promoting cellular homeostasis restoration after cold stress exposure via new cell growth, particularly in leaf cells crucial for photosynthesis and metabolic activity, possibly by interacting with cell cycle regulating proteins. Overall, the present study suggests that OsUBC7 may be involved in plant development, reproduction, and stress adaptation, and contributes to a deeper understanding of rice plant cold stress tolerance response mechanisms. OsUBC7 may be a promising candidate for improving crop productivity and resilience to stressful environments.

OsNAL11 and OsGASR9 Regulate the Low-Temperature Germination of Rice Seeds by Affecting GA Content

Low temperatures cause serious threat to rice seed emergence, which has become one of the main limiting factors in the production of direct seeding rice. It is of great importance to study the genes controlling low-temperature tolerance during seed germination and to mine the possible regulatory mechanism for developing new rice varieties with immense low-temperature germination ability. In the current research study, two types of mutants of nal11 and gasr9, derived from the WT (wild type) ZH11, were used for the analysis of low-temperature germinability. The results showed that the nal11 and gasr9 mutants displayed no significant difference in germination rate with ZH11 at room temperature, but the mutants showed significantly lower germination rates, germination potential and germination index, and slowed seedling growth in the simulated direct seeding experiments at low temperatures compared to ZH11. Additionally, the activity of POD, SOD, CAT, and anti-superoxide anion radial activity were significantly reduced, but the levels of MDA and H2O2 were significantly higher in the nal11 and gasr9 mutant seeds that were germinated at low temperatures compared to ZH11. Further analysis revealed that the levels of total active GA, especially GA4 and GA7, were significantly lower in the nal11 and gasr9 mutants than that in ZH11 during low-temperature germination. Based on qRT-PCR analysis, the expression levels of some GA synthesis-related genes were higher, whereas some were lower in the nal11 and gasr9 mutants than those in ZH11, however, the GA metabolism-related genes OsGA2ox8 and OsGA2ox10 and the GA signaling negative regulator gene SLR1 were significantly up-regulated in both nal11 and gasr9 mutants at several time points during low-temperature germination. This may explain the lower GA levels in the nal11 and gasr9 mutants. Furthermore, the interaction between the OsNAL11 and OsGASR9 proteins was confirmed by Y2H, LUC, and Co-IP assays. This study provides preliminary insights into the regulatory mechanism of the OsNAL11 and OsGASR9 genes, which control the low-temperature germination of rice seeds by affecting the GA pathway. Our study will provide the basis for further mining the molecular mechanisms of low-temperature germination in rice and valuable theoretical reference for breeding varieties with strong low-temperature germinability.

OsRAV1 Regulates Seed Vigor and Salt Tolerance During Germination in Rice

Seed vigor is a complex trait encompassing seed germination, seedling emergence, growth, seed longevity, and stress tolerance, all are crucial for direct seeding in rice. Here, we report that the AP2/ERF transcription factor OsRAV1 (RELATED TO ABI3 AND VP1) positively regulates seed germination, vigor, and salt tolerance. Additionally, OsRAV1 was differently expressed in embryo and endosperm, with the OsRAV1 localized in the nucleus. Transcriptomic analysis revealed that OsRAV1 modulates seed vigor through plant hormone signal transduction and phenylpropanoid biosynthesis during germination. Haplotype analysis showed that rice varieties carrying Hap3 displayed enhanced salt tolerance during seed germination. These findings suggest that OsRAV1 is a potential target in breeding rice varieties with high seed vigor suitable for direct seeding cultivation.

Deciphering the alleviation potential of nitric oxide, for low temperature and chromium stress via maintaining photosynthetic capacity, antioxidant defence, and redox homeostasis in rice (Oryza sativa)

Sodium nitroprusside (SNP) is a potent nitric oxide (NO) donor that enhances plant tolerance to various abiotic stresses. This research aims to assess the effect of SNP application on rice seedlings subjected to individual and combined exposure to two abiotic stresses viz., low-temperature (LT) and chromium (Cr). Exposure to LT, Cr, and LT+Cr caused severe oxidative damage by stimulating greater production and accumulation of reactive oxygen species (ROS) leading to lipid peroxidation and cell membrane instability. The combined LT+CR stress more intensly increased the cellular oxidative stress and excessive Cr uptake that in turn deteriorated the chlorophyll pigments and photosynthesis, as well as effected the level of tetrapyrrole biosynthesis in rice plants. The reduction in rice seedling growth was more obvious under LT+Cr treatment than their individual effects. The exogenous application of SNP diminished the toxic impact of LT and Cr stress. This was attributed to the positive role of SNP in regulating the endogenous NO levels, free amino acids (FAAs) contents, tetrapyrrole biosynthesis and antioxidants. Consequently, SNP-induced NO decreased photorespiration, ROS generation, lipid peroxidation, and electrolyte leakage. Moreover, exogenous SNP diminished the Cr uptake and accumulation by modulating the ionic homeostasis and strengthening the heavy metals detoxification mechanism, thus improving plant height, biomass and photosynthetic indexes. Essentially, SNP boosts plant tolerance to LT and Cr stress by regulating antioxidants, detoxification mechanism, and the plant's physio-biochemical. Hence, applying SNP is an effective method for boosting rice plant resilience and productivity in the face of escalating environmental stresses and pollutants.

Transcription factor DcbZIPs regulate secondary metabolism in Dendrobium catenatum during cold stress

Cold stress seriously affects plant development and secondary metabolism. The basic region/leucine zipper (bZIP) is one of the largest transcription factor (TFs) family and widely involved in plant cold stress response. However, the function of bZIP in Dendrobium catenatum has not been well-documented. Cold inhibited the growth of D. catenatum and increased total polysaccharide and alkaloid contents in stems. Here, 62 DcbZIP genes were identified in D. catenatum, which were divided into 13 subfamilies. Among them, 58 DcbZIPs responded to cold stress, which were selected based on the transcriptome database produced from cold-treated D. catenatum seedlings. Specifically, the expression of DcbZIP3/6/28 was highly induced by cold treatment in leaves or stems. Gene sequence analysis indicated that DcbZIP3/6/28 contains the bZIP conserved domain and is localized to the cell nucleus. Co-expression networks showed that DcbZIP6 was significantly negatively correlated with PAL2 (palmitoyl-CoA), which is involved in flavonoid metabolism. Moreover, DcbZIP28 has significant negative correlations with various metabolism-related genes in the polysaccharide metabolic pathway, including PFKA1 (6-phosphofructokinase), ALDO2 (aldose-6-phosphate reductase) and SCRK5 (fructokinase). These results implied that DcbZIP6 or DcbZIP28 are mainly involved in flavonoid or polysaccharide metabolism. Overall, these findings provide new insights into the roles of the DcbZIP gene family in secondary metabolism in D. catenatum under cold stress.

Analysis of genome-wide association studies of low-temperature germination in Xian and Geng rice

Rice is the leading global staple crop. Low temperatures pose negative impacts on rice's optimal growth and development. Rice cultivars acclimating to low temperatures exhibited improved seedling emergence under direct-seeded sowing conditions, yet little is known about the genes that regulate germination at low temperatures (LTG). In this research investigation, we've performed whole genome sequencing for the 273 rice plant materials. Using the best linear unbiased prediction (BLUP) values for each rice material, we identified 7 LTG-related traits and performed the efficient genetic analysis and genome-wide association study (GWAS). As a result of this, 95 quantitative trait loci (QTLs) and 1001 candidate genes associated with LTG in rice were identified. Haplotype analysis and functional annotation of the candidate genes resulted in the identification of three promising candidate genes (LOC_Os08g30520 for regulating LTG4 and LTG5, LOC_Os10g02625 for regulating LTG6, LTg7 and LTG8, and LOC_Os12g31460 for regulating LTG7, LTg8 and LTG9) involving in the regulation of LTG in rice. This research provides a solid foundation for addressing the LTG issue in rice and will be valuable in future direct-seeded rice breeding programs.

Integration of widely targeted metabolomics and the e-tongue reveals the chemical variation and taste quality of Yunnan Arabica coffee prepared using different primary processing methods

UPLC-Q-TOF-MS and electronic tongue analysis were applied to analyse the metabolic profile and taste quality of Yunnan Arabica coffee under seven primary processing methods. The total phenolic content ranged from 34.44 to 44.42 mg/g DW, the e-tongue results revealed the strongest umami sensor response value in the sample prepared with traditional dry processing, while the samples prepared via honey processing II had the strongest astringency sensor response value. Metabolomics analysis identified 221 differential metabolites, with higher contents of amino acids and derivatives within dry processing II sample, and increased contents of lipids and phenolic acids in the honey processing III sample. The astringency and aftertaste-astringency of the coffee samples positively correlated with the trigonelline, 3,5-di-caffeoylquinic acid and 4-caffeoylquinic acid content. The results contributed to a better understanding of how the primary processing process affects coffee quality, and supply useful information for the enrichment of coffee biochemistry theory.

The GA and ABA signaling is required for hydrogen-mediated seed germination in wax gourd

BACKGROUND

Hydrogen gas (H2), a novel and beneficial gaseous molecule, plays a significant role in plant growth and development processes. Hydrogen-rich water (HRW) is regarded as a safe and easily available way to study the physiological effects of H2 on plants. Several recent research has shown that HRW attenuates stress-induced seed germination inhibition; however, the underlying modes of HRW on seed germination remain obscure under non-stress condition.

RESULTS

In this current study, we investigated the possible roles of gibberellin (GA) and abscisic acid (ABA) in HRW-regulated seed germination in wax gourd (Benincasa hispida) through pharmacological, physiological, and transcriptome approaches. The results showed that HRW application at an optimal dose (50% HRW) significantly promoted seed germination and shortened the average germination time (AGT). Subsequent results suggested that 50% HRW treatment stimulated GA production by regulating GA biosynthesis genes (BhiGA3ox, BhiGA2ox, and BhiKAO), whereas it had no effect on the content of ABA and the expression of its biosynthesis (BhiNCED6) and catabolism genes (BhiCYP707A2) but decreased the expression of ABA receptor gene (BhiPYL). In addition, inhibition of GA production by paclobutrazol (PAC) could block the HRW-mediated germination. Treatment with ABA could hinder HRW-mediated seed germination and the ABA biosynthesis inhibitor sodium tungstate (ST) could recover the function of HRW. Furthermore, RNA-seq analysis revealed that, in the presence of GA or ABA, an abundance of genes involved in GA, ABA, and ethylene signal sensing and transduction might involve in HRW-regulated germination.

CONCLUSIONS

This study portrays insights into the mechanism of HRW-mediated seed germination, suggesting that HRW can regulate the balance between GA and ABA to mediate seed germination through ethylene signals in wax gourd.

Transcriptome Analysis Reveals POD as an Important Indicator for Assessing Low-Temperature Tolerance in Maize Radicles during Germination

Low-temperature stress (TS) limits maize (Zea mays L.) seed germination and agricultural production. Exposure to TS during germination inhibits radicle growth, triggering seedling emergence disorders. Here, we aimed to analyse the changes in gene expression in the radicles of maize seeds under TS by comparing Demeiya1 (DMY1) and Zhengdan958 (ZD958) (the main Northeast China cultivars) and exposing them to two temperatures: 15 °C (control) and 5 °C (TS). TS markedly decreased radicle growth as well as fresh and dry weights while increasing proline and malondialdehyde contents in both test varieties. Under TS treatment, the expression levels of 5301 and 4894 genes were significantly different in the radicles of DMY1 and ZD958, respectively, and 3005 differentially expressed genes coexisted in the radicles of both varieties. The phenylpropanoid biosynthesis pathway was implicated within the response to TS in maize radicles, and peroxidase may be an important indicator for assessing low-temperature tolerance during maize germination. Peroxidase-encoding genes could be important candidate genes for promoting low-temperature resistance in maize germinating radicles. We believe that this study enhances the knowledge of mechanisms of response and adaptation of the maize seed germination process to TS and provides a theoretical basis for efficiently assessing maize seed low-temperature tolerance and improving maize adversity germination performance.

Widely-targeted metabolomics and transcriptomics identify metabolites associated with flowering regulation of Choy Sum

Choy Sum, a stalk vegetable highly valued in East and Southeast Asia, is characterized by its rich flavor and nutritional profile. Metabolite accumulation is a key factor in Choy Sum stalk development; however, no research has focused on metabolic changes during the development of Choy Sum, especially in shoot tip metabolites, and their effects on growth and flowering. Therefore, in the present study, we used a widely targeted metabolomic approach to analyze metabolites in Choy Sum stalks at the seedling (S1), bolting (S3), and flowering (S5) stages. In total, we identified 493 metabolites in 31 chemical categories across all three developmental stages. We found that the levels of most carbohydrates and amino acids increased during stalk development and peaked at S5. Moreover, the accumulation of amino acids and their metabolites was closely related to G6P, whereas the expression of flowering genes was closely related to the content of T6P, which may promote flowering by upregulating the expressions of BcSOC1, BcAP1, and BcSPL5. The results of this study contribute to our understanding of the relationship between the accumulation of stem tip substances during development and flowering and of the regulatory mechanisms of stalk development in Choy Sum and other related species.

Metabolic profiling of Oryza sativa seedlings under chilling stress using nanoliter electrospray ionization mass spectrometry

Low temperatures significantly impact on rice (Oryza sativa) yield and quality. Traditional metabolomic techniques, often involving time-consuming chromatography-mass spectrometry procedures, are currently in use. This study investigated metabolomic responses of rice seedlings under low-temperature stress using nanoliter electrospray ionization mass spectrometry (nanoESI-MS) in combination with multivariate analysis. Results revealed distinct metabolic profiles in 'Qiutianxiaoting' (japonica) and '93-11' (indica) rice seedlings. Among the 36 identified compounds in rice, seven key metabolites, comprising l-glutamic acid, asparagine, tryptophan, citric acid, α-linolenic acid, malic acid, and inositol, were identified as responsive to cold stress. Notably, malic acid content reached 1332.40 μg/g dry weight in Qiutianxiaoting and 1444.13 μg/g in 93-11. Both the qualitative and quantitative results of nanoESI-MS were further confirmed through gas chromatography-mass spectrometry validation. The findings highlight the potential of nanoESI-MS for rapidly characterizing crucial metabolites across diverse plant species under exposure to stress.

Effect of Porphyra haitanensis polyphenols from different harvest periods on hypoglycaemic activity based on in vitro digestion and widely targeted metabolomic analysis

The hypoglycemic effect of Porphyra is well known. Based on in vitro digestion and metabolomics, the bioaccessibility, antidiabetic activity and phenolic conversion of P. haitanensis were investigated at different harvests. Total polyphenol content (TPC), α-glucosidase inhibition and oxygen radical absorbance capacity (ORAC) increased with harvesting and digestion stages, reaching maximum at the fourth harvest. TPC and α-glucosidase inhibition after digestion reached 130-150 mg/g and 50-90 %, ORAC was 8.7-13.5 times higher than the undigestion. However, bioaccessibility in the first and second harvests was 10-80 % higher than other harvests. The phenolic content in the fourth harvest was up-regulated to 2-30 times than the first and mostly were citrus flavonoids. Redundancy analysis indicated significant correlation between phenolic metabolites and bioactivities in different harvests of P. haitanensis during digestion, with the strongest correlation coefficients were apigenin and genistein. This study provides reference for the application of P. haitanensis in treating type 2 diabetes.

Integrative physiological, metabolomic, and transcriptomic analysis reveals the drought responses of two apple rootstock cultivars

BACKGROUND

Drought is considered the main environmental factor restricting apple production and thus the development of the apple industry. Rootstocks play an important role in enhancing the drought tolerance of apple plants. Studies of the physiology have demonstrated that 'ZC9-3' is a strong drought-resistant rootstock, whereas 'Jizhen-2' is a weak drought-resistant rootstock. However, the metabolites in these two apple rootstock varieties that respond to drought stress have not yet been characterized, and the molecular mechanisms underlying their responses to drought stress remain unclear.

RESULTS

In this study, the physiological and molecular mechanisms underlying differences in the drought resistance of 'Jizhen-2' (drought-sensitive) and 'ZC9-3' (drought-resistant) apple rootstocks were explored. Under drought stress, the relative water content of the leaves was maintained at higher levels in 'ZC9-3' than in 'Jizhen-2', and the photosynthetic, antioxidant, and osmoregulatory capacities of 'ZC9-3' were stronger than those of 'Jizhen-2'. Metabolome analysis revealed a total of 95 and 156 differentially accumulated metabolites in 'Jizhen-2' and 'ZC9-3' under drought stress, respectively. The up-regulated metabolites in the two cultivars were mainly amino acids and derivatives. Transcriptome analysis revealed that there were more differentially expressed genes and transcription factors in 'ZC9-3' than in 'Jizhen-2' throughout the drought treatment. Metabolomic and transcriptomic analysis revealed that amino acid biosynthesis pathways play key roles in mediating drought resistance in apple rootstocks. A total of 13 metabolites, including L-α-aminoadipate, L-homoserine, L-threonine, L-isoleucine, L-valine, L-leucine, (2S)-2-isopropylmalate, anthranilate, L-tryptophan, L-phenylalanine, L-tyrosine, L-glutamate, and L-proline, play an important role in the difference in drought resistance between 'ZC9-3' and 'Jizhen-2'. In addition, 13 genes encoding O-acetylserine-(thiol)-lyase, S-adenosylmethionine synthetase, ketol-acid isomeroreductase, dihydroxyacid dehydratase, isopropylmalate isomerase, branched-chain aminotransferase, pyruvate kinase, 3-dehydroquinate dehydratase/shikimate 5-dehydrogenase, N-acetylglutamate-5-P-reductase, and pyrroline-5-carboxylate synthetase positively regulate the response of 'ZC9-3' to drought stress.

CONCLUSIONS

This study enhances our understanding of the response of apple rootstocks to drought stress at the physiological, metabolic, and transcriptional levels and provides key insights that will aid the cultivation of drought-resistant apple rootstock cultivars. Especially, it identifies key metabolites and genes underlying the drought resistance of apple rootstocks.

Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops

Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop productivity. Perception of cold stress by plant cells leads to the activation of cold-responsive transcription factors and downstream genes, which ultimately impart cold tolerance. The response triggered in crops to cold stress includes gene expression/suppression, the accumulation of sugars upon chilling, and signaling molecules, among others. Much of the information on the effects of cold stress on perception, signal transduction, gene expression, and plant metabolism are available in the model plant Arabidopsis but somewhat lacking in major crops. Hence, a complete understanding of the molecular mechanisms by which staple crops respond to cold stress remain largely unknown. Here, we make an effort to elaborate on the molecular mechanisms employed in response to low-temperature stress. We summarize the effects of cold stress on the growth and development of these crops, the mechanism of cold perception, and the role of various sensors and transducers in cold signaling. We discuss the progress in cold tolerance research at the genome, transcriptome, proteome, and metabolome levels and highlight how these findings provide opportunities for designing cold-tolerant crops for the future.

Transcription factor OsMYB30 increases trehalose content to inhibit α-amylase and seed germination at low temperature

Low-temperature germination (LTG) is an important agronomic trait for direct-seeding cultivation of rice (Oryza sativa). Both OsMYB30 and OsTPP1 regulate the cold stress response in rice, but the function of OsMYB30 and OsTPP1 in regulating LTG and the underlying molecular mechanism remains unknown. Employing transcriptomics and functional studies revealed a sugar signaling pathway that regulates seed germination in response to low temperature (LT). Expression of OsMYB30 and OsTPP1 was induced by LT during seed germination, and overexpressing either OsMYB30 or OsTPP1 delayed seed germination and increased sensitivity to LT during seed germination. Transcriptomics and qPCR revealed that expression of OsTPP1 was upregulated in OsMYB30-overexpressing lines but downregulated in OsMYB30-knockout lines. In vitro and in vivo experiments revealed that OsMYB30 bound to the promoter of OsTPP1 and regulated the abundance of OsTPP1 transcripts. Overaccumulation of trehalose (Tre) was found in both OsMYB30- and OsTPP1-overexpressing lines, resulting in inhibition of α-amylase 1a (OsAMY1a) gene during seed germination. Both LT and exogenous Tre treatments suppressed the expression of OsAMY1a, and the osamy1a mutant was not sensitive to exogenous Tre during seed germination. Overall, we concluded that OsMYB30 expression was induced by LT to activate the expression of OsTPP1 and increase Tre content, which thus inhibited α-amylase activity and seed germination. This study identified a phytohormone-independent pathway that integrates environmental cues with internal factors to control seed germination.

Metabolomics reveal root differential metabolites of different root-type alfalfa under drought stress

Introduction

Alfalfa (Medicago sativa L.) is the favored premium feed ingredient in animal husbandry production which is in serious jeopardy due to soil moisture shortages. It is largely unknown how different root types of alfalfa respond to arid-induced stress in terms of metabolites and phytohormones.

Methods

Therefore, rhizomatous rooted M. sativa 'Qingshui' (or QS), tap-rooted M. sativa 'Longdong' (or LD), and creeping rooted M. varia 'Gannong No. 4' (or GN) were investigated to identify metabolites and phytohormones responses to drought conditions.

Results

We found 164, 270, and 68 significantly upregulated differential metabolites were categorized into 35, 38, and 34 metabolic pathways in QS, LD, and GN within aridity stress, respectively. Amino acids, organic acids, sugars, and alkaloids were the four categories of primary differential metabolites detected, which include 6-gingerol, salicylic acid (SA), indole-3-acetic acid (IAA), gibberellin A4 (GA4), abscisic acid (ABA), trans-cinnamic acid, sucrose, L-phenylalanine, L-tyrosine, succinic acid, and nicotinic acid and so on, turns out these metabolites are essential for the resistance of three root-type alfalfa to aridity coercing.

Discussion

The plant hormone signal transduction (PST) pathway was dramatically enriched after drought stress. IAA and ABA were significantly accumulated in the metabolites, indicating that they play vital roles in the response of three root types of alfalfa to water stress, and QS and LD exhibit stronger tolerance than GN under drought stress.

Metabolomic profiling reveals key factors and associated pathways regulating the differential behavior of rice (Oryza sativa L.) genotypes exposed to geogenic arsenic

Arsenic (As) toxicity is an escalating problem; however, information about the metabolic events controlling the varied pattern of As accumulation in rice genotypes within their natural environment is still lacking. The present study is thus an advancement in unravelling the response of such rice genotypes. Soil-water-rice samples were analyzed for As accumulation using ICP-MS. Furthermore, we implemented metabolomics through LC-MS/MS and UHPLC to identify metabolic signatures regulating As content by observing the metalloid's composition in rice agrosystem. Results showed that rice genotypes differed significantly in their levels of metabolites, with Mini mansoori and Pioneer having the highest levels. Mini mansoori contained least As which might have been regulated by Ala, Ser, Glu, Phe, Asn, His, Ile, Lys, Gln, Trp, Tyr, chlorogenic, p-coumaric, trans-ferulic, rutin, morin, naringenin, kampferol, and myricetin, while Asp, Arg, Met, syringic, epigalocatechin, and apigenin contributed to the greater As acclimatization ability of Pioneer. Multivariate tools separated the rice genotypes into two major clusters: Pioneer-Mini mansoori and Damini-Sampoorna-Chintu. KEGG identified three major metabolic pathways (aminoacyl-tRNA, phenylpropanoid, and secondary metabolites biosynthesis route) linked with As tolerance and adaptation mechanisms in rice. Overall, these two genotypes symbolize their As hostile and accommodating attitudes probably due to the accumulated metabolites and the physicochemical attributes of the soil-water. Thus, thorough understanding of the metabolic reactions to As may facilitate the emergence of As tolerant/resilient genotypes. This will aid in the selection of molecular markers to cultivate healthier rice genotypes in As-contaminated areas.

Elucidation of the Mechanism of Rapid Growth Recovery in Rice Seedlings after Exposure to Low-Temperature Low-Light Stress: Analysis of Rice Root Transcriptome, Metabolome, and Physiology

Late spring cold is a disastrous weather condition that often affects early rice seedlings in southern China, limiting the promotion of direct seeding cultivation. However, there are few reports on the effect of these events and on the growth recovery mechanism of rice root systems after rice seedlings are exposed to this stress. This study selected the strong-growth-recovery variety B116 (R310/R974, F17) and the slow-recovery variety B811 (Zhonghui 286) for direct seeding cultivation and exposed them to low temperature and low-light stress to simulate a late spring cold event in an artificial climate chamber. The treatment consisted of 4 days of exposure to a day/night temperature of 14/10 °C and a light intensity of 266 µmol m-2s-1 while the control group was kept at a day/night temperature of 27/25 °C and light intensity of 533 µmol m-2s-1. The results showed that 6 days after stress, the total length, surface area, and volume of B116 roots increased by 335.5%, 290.1%, and 298.5%, respectively, while those of B811 increased by 228.8%, 262.0%, and 289.1%, respectively. In B116, the increase in root fresh weight was 223.1%, and that in B811 was 165.6%, demonstrating rapid root recovery after stress and significant differences among genotypes. The content of H2O2 and MDA in the B116 roots decreased faster than that in the B811 roots after normal light intensity and temperature conditions were restored, and the activity of ROS metabolism enzymes was stronger in B116 roots than in B811 roots. The correlation analysis between the transcriptome and metabolome showed that endogenous signal transduction and starch and sucrose metabolism were the main metabolic pathways affecting the rapid growth of rice seedling roots after exposure to combined stress from low temperature and low light intensities. The levels of auxin and sucrose in the roots of the strong-recovery variety B116 were higher, and this variety's metabolism was downregulated significantly faster than that of B811. The auxin response factor and sucrose synthesis-related genes SPS1 and SUS4 were significantly upregulated. This study contributes to an understanding of the rapid growth recovery mechanism in rice after exposure to combined stress from low-temperature and low-light conditions.

A comparative metabolomics study of polyphenols in highland barley (Hordeum vulgare L.) grains with different colors

Highland barley (HB) grains are gaining increasing popularity owing to their high nutritional merits. However, only limited information is available on the metabolic profiles of HB grains polyphenols, especially the difference of polyphenols in different colors of HB. In this study, we determined the metabolic profiles of black, blue, and white HB grains via an ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS)-based metabolomics. A total of 402 metabolites were identified, among which 198, 62, and 189 metabolites displayed different accumulation patterns in the three comparison groups (WHB vs. BKHB, WHB vs. BEHB, BEHB vs. BKHB), respectively. In particular, flavonoids and phenolic acids contents displayed considerable differences among the three HB cultivars. The phenolics content of black HB was relatively high. Additionally, "Flavonoid biosynthesis" and "flavone and flavonol biosynthesis" were the significantly enriched pathways. In conclusion, this study provides comprehensive insights into the adequate utilization and development of novel HB-based functional foods.

Lipid and Amino Acid Pathway Metabolites Contribute to Cold Tolerance in Quercus wutaishanica

Cold is an important environmental stress affecting the growth, productivity, and geographic distribution of tree species. Oaks are important for environmental conservation and wood supplies. Oak metabolites respond to low temperatures (LTs). In this study, the physiological and metabolic responses of two oak species to cold stress were investigated and compared. The field observations and physiological responses showed that Quercus wutaishanica was more cold-tolerant than Q. acutissima. After frost, the one-year-old twigs of Q. wutaishanica had higher survival rates, accumulated more soluble sugar and protein, and exhibited higher superoxide dismutase (SOD) activity than those of Q. acutissima. Untargeted metabolomics identified 102 and 78 differentially accumulated metabolites in Q. acutissima and Q. wutaishanica, respectively, when the leaves were subjected to LTs (4 °C for 24 h). The carbohydrate and flavonoid metabolites contributed to the cold tolerance of both oak species. Succinate, an intermediate in the citric acid cycle, was significantly inhibited by LTs, a potential energy conservation strategy. Unlike Q. acutissima, Q. wutaishanica underwent metabolic reprogramming that significantly increased the contents of phosphatidylcholine, gallic acid, oxidized glutathione, shikimate, and phenylpyruvate under LTs. Our data provide a reference for characterizing the mechanisms involved in the response of oak species to cold temperatures and enhancing the cold tolerance of forest trees.

Raman Multi-Omic Snapshots of Koshihikari Rice Kernels Reveal Important Molecular Diversities with Potential Benefits in Healthcare

This study exploits quantitative algorithms of Raman spectroscopy to assess, at the molecular scale, the nutritional quality of individual kernels of the Japanese short-grain rice cultivar Koshihikari in terms of amylose-to-amylopectin ratio, fractions of phenylalanine and tryptophan aromatic amino acid residues, protein-to-carbohydrate ratio, and fractions of protein secondary structures. Statistical assessments on a large number of rice kernels reveal wide distributions of the above nutritional parameters over nominally homogeneous kernel batches. This demonstrates that genetic classifications cannot catch omic fluctuations, which are strongly influenced by a number of extrinsic factors, including the location of individual grass plants within the same rice field and the level of kernel maturation. The possibility of collecting nearly real-time Raman "multi-omic snapshots" of individual rice kernels allows for the automatic (low-cost) differentiation of groups of kernels with restricted nutritional characteristics that could be used in the formulation of functional foods for specific diseases and in positively modulating the intestinal microbiota for protection against bacterial infection and cancer prevention.

Study on the metabolic process of phthalic acid driven proliferation of Rhizoctonia solani

Introduction

Continuous cropping obstacle seriously affects the quality and yield of Salvia miltiorrhiza, and the synergistic effect of root exudates and rhizosphere pathogenic microorganisms may be an important cause of continuous cropping obstacle. This study aimed to explore the effects of representative organic acids on the growth and metabolism of specific microorganisms in the S. miltiorrhiza rhizosphere soil under continuous cropping, and clarify its mechanism.

Methods

The effect of phthalic acid (PA) on the growth and metabolism of Rhizoctonia solani was evaluated by mycelial growth inhibition method. Ultra-high performance liquid chromatography and tandem mass spectrometry were used to identify the differential metabolites of R. solani induced by exogenous PA.

Results

PA exerted a concentration-dependent effect on mycelial growth, biomass, intracellular polysaccharides con-tent, and total protein content in R. solani. A total of 1773 metabolites and 1040 differential metabolites were identified in the blank medium (CK), Fungi (CK + fungi), and PA-Fungi (CK + fungi + acid) groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the differential metabolites were mainly involved in the sugar, lipid, and protein metabolic pathways related to stable membrane structure and cell growth.

Discussion

The proliferation and metabolism network of R. solani induced by PA was proposed, and the enhancement of sugar, lipid, and amino acid metabolism was presumed to be related to the active resistance of cells to organic acid stress. These results offer new in-sights into the effects of PA metabolism on promoting R. solani proliferation, and provide theoretical support for further optimizing the rhizosphere microecological environment of Salvia miltiorrhiza continuous cropping soil and reducing continuous cropping obstacle.

Revealing the Mechanistic Basis of Regulation of Phosphorus Uptake in Soybean (Glycine max) Roots by Molybdenum: An Integrated Omics Approach

While molybdenum (Mo) application can improve phosphorus (P) availability to plants by changing P speciation in the rhizosphere, the mechanistic basis of this process remains unclear. This work investigated the impact of various combinations of Mo and P treatments on root morphology, P and Mo uptake, and root transcriptome and metabolome. Mo application significantly increased soybean biomass and the number of lateral roots at both low (5 μmol) or normal (500 μmol) P levels and significantly improved P concentration and accumulation in Normal P treatment. Compared with the Normal P treatment, Low P significantly increased the number of roots, root surface area, and root acid phosphatase secretion. A total of 6811 Mo-responsive differentially expressed genes and 135 differential metabolites were identified at two P levels. At Low P, transcriptional changes significantly increased root synthesis and secretion of succinic acid, methylmalonic acid, and other organic acids as well as acid phosphatase, thereby increasing the conversion of soil aluminum-bound P and organic P into available P. At Normal P, Mo application increased P uptake mainly by increasing the number of lateral roots. Thus, Mo helps crops adapt to different P levels by regulating root anatomy and transcriptional and metabolic profiles of their roots.

Natural Algaecide Sphingosines Identified in Hybrid Straw Decomposition Driven by White-Rot Fungi

Harmful algal blooms (HABs), which are promoted by eutrophication and intensified by global warming, occur worldwide. Allelochemicals, which are natural chemicals derived from plants or microbes, are emerging weapons to eliminate these blooms. However, the cost and technical challenges have limited the discovery of novel antialgal allelochemicals. Herein, the decomposition of agricultural straws is manipulated by white-rot fungi and achieved elevated antialgal efficiency. The transcriptomic analysis reveals that nutrient limitation activated fungal decomposition. By using a comparative nontarget metabolomics approach, a new type of allelochemical sphingosines (including sphinganine, phytosphingosine, sphingosine, and N-acetylsphingosine) is identified. These novel natural algaecides exhibit superior antialgal capability, with as high as an order of magnitude lower effective concentration on blooming species than other prevalent allelochemicals. The co-expression relationship between transcriptomic and metabolomic results indicate that sphinganine is strongly correlated with the differentially expressed lignocellulose degradation unigenes. The algal growth suppression is triggered by the activation of programmed cell death, malfunction of algal photosystem and antioxidant system, the disruption on CO2 assimilation and light absorption. The sphingosines reported here are a new category of allelochemicals in addition to the well-known antialgal natural chemicals, which are potential species-specific agents for HABs control identified by multi-omics methodology.

Metabolomics and transcriptomics analyses provide new insights into the nutritional quality during the endosperm development of different ploidy rice

Autotetraploid rice is developed from diploid rice by doubling the chromosomes, leading to higher nutritional quality. Nevertheless, there is little information about the abundances of different metabolites and their changes during endosperm development in autotetraploid rice. In this research, two different kinds of rice, autotetraploid rice (AJNT-4x) and diploid rice (AJNT-2x), were subjected to experiments at various time points during endosperm development. A total of 422 differential metabolites, were identified by applying a widely used metabolomics technique based on LC-MS/MS. KEGG classification and enrichment analysis showed the differences in metabolites were primarily related to biosynthesis of secondary metabolites, microbial metabolism in diverse environments, biosynthesis of cofactors, and so on. Twenty common differential metabolites were found at three developmental stages of 10, 15 and 20 DAFs, which were considered the key metabolites. To identify the regulatory genes of metabolites, the experimental material was subjected to transcriptome sequencing. The DEGs were mainly enriched in starch and sucrose metabolism at 10 DAF, and in ribosome and biosynthesis of amino acids at 15 DAF, and in biosynthesis of secondary metabolites at 20 DAF. The numbers of enriched pathways and the DEGs gradually increased with endosperm development of rice. The related metabolic pathways of rice nutritional quality are cysteine and methionine metabolism, tryptophan metabolism, lysine biosynthesis and histidine metabolism, and so on. The expression level of the genes regulating lysine content was higher in AJNT-4x than in AJNT-2x. By applying CRISPR/Cas9 gene-editing technology, we identified two novel genes, OsLC4 and OsLC3, negatively regulated lysine content. These findings offer novel insight into dynamic metabolites and genes expression variations during endosperm development of different ploidy rice, which will aid in the creation of rice varieties with better grain nutritional quality.

Comparative Metabolomic Analysis Reveals the Role of OsHPL1 in the Cold-Induced Metabolic Changes in Rice

Cytochrome P450 (CYP74) family members participate in the generation of oxylipins and play essential roles in plant adaptation. However, the metabolic reprogramming mediated by CYP74s under cold stress remains largely unexplored. Herein, we report how cold-triggered OsHPL1, a member of the CYP74 family, modulates rice metabolism. Cold stress significantly induced the expression of OsHPL1 and the accumulation of OPDA (12-oxo-phytodienoic acid) and jasmonates in the wild-type (WT) plants. The absence of OsHPL1 attenuates OPDA accumulation to a low temperature. Then, we performed a widely targeted metabolomics study covering 597 structurally annotated compounds. In the WT and hpl1 plants, cold stress remodeled the metabolism of lipids and amino acids. Although the WT and hpl1 mutants shared over one hundred cold-affected differentially accumulated metabolites (DAMs), some displayed distinct cold-responding patterns. Furthermore, we identified 114 and 56 cold-responding DAMs, specifically in the WT and hpl1 mutants. In conclusion, our work characterized cold-triggered metabolic rewiring and the metabolic role of OsHPL1 in rice.

Combined QTL-sequencing, linkage mapping, and RNA-sequencing identify candidate genes and KASP markers for low-temperature germination in Oryza sativa L. ssp. Japonica

MAIN CONCLUSION

Through QTL-seq, QTL mapping and RNA-seq, six candidate genes of qLTG9 can be used as targets for cold tolerance functional characterization, and six KASP markers can be used for marker-assisted breeding to improve the germination ability of japonica rice at low temperature. The development of direct-seeded rice at high latitudes and altitudes depends on the seed germination ability of rice under a low-temperature environment. However, the lack of regulatory genes for low-temperature germination has severely limited the application of genetics in improving the breeds. Here, we used cultivars DN430 and DF104 with significantly different low-temperature germination (LTG) and 460 F_2:3 progeny derived from them to identify LTG regulators by combining QTL-sequencing, linkage mapping, and RNA-sequencing. The QTL-sequencing mapped qLTG9 within a physical interval of 3.4 Mb. In addition, we used 10 Kompetitive allele-specific PCR (KASP) markers provided by the two parents, and qLTG9 was optimized from 3.4 Mb to a physical interval of 397.9 kb and accounted for 20.4% of the phenotypic variation. RNA-sequencing identified qLTG9 as eight candidate genes with significantly different expression within the 397.9 kb interval, six of which possessed SNPs on the promoter and coding regions. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) completely validated the results of these six genes in RNA-sequencing. Subsequently, six non-synonymous SNPs were designed using variants in the coding region of these six candidates. Genotypic analysis of these SNPs in 60 individuals with extreme phenotypes indicated these SNPs determined the differences in cold tolerance between parents. The six candidate genes of qLTG9 and the six KASP markers could be used together for marker-assisted breeding to improve LTG.

Comparative Metabolomics Profiling Reveals Key Metabolites and Associated Pathways Regulating Tuber Dormancy in White Yam (Dioscorea rotundata Poir.)

Yams are economic and medicinal crops with a long growth cycle, spanning between 9-11 months due to their prolonged tuber dormancy. Tuber dormancy has constituted a major constraint in yam production and genetic improvement. In this study, we performed non-targeted comparative metabolomic profiling of tubers of two white yam genotypes, (Obiaoturugo and TDr1100873), to identify metabolites and associated pathways that regulate yam tuber dormancy using gas chromatography-mass spectrometry (GC-MS). Yam tubers were sampled between 42 days after physiological maturity (DAPM) till tuber sprouting. The sampling points include 42-DAPM, 56-DAPM, 87DAPM, 101-DAPM, 115-DAPM, and 143-DAPM. A total of 949 metabolites were annotated, 559 in TDr1100873 and 390 in Obiaoturugo. A total of 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. A total of 27 DAMs were conserved between the two genotypes, whereas 5 DAMs were unique in the tubers of TDr1100873 and 7 DAMs were in the tubers of Obiaoturugo. The differentially accumulated metabolites (DAMs) spread across 14 major functional chemical groups. Amines and biogenic polyamines, amino acids and derivatives, alcohols, flavonoids, alkaloids, phenols, esters, coumarins, and phytohormone positively regulated yam tuber dormancy induction and maintenance, whereas fatty acids, lipids, nucleotides, carboxylic acids, sugars, terpenoids, benzoquinones, and benzene derivatives positively regulated dormancy breaking and sprouting in tubers of both yam genotypes. Metabolite set enrichment analysis (MSEA) revealed that 12 metabolisms were significantly enriched during yam tuber dormancy stages. Metabolic pathway topology analysis further revealed that six metabolic pathways (linoleic acid metabolic pathway, phenylalanine metabolic pathway, galactose metabolic pathway, starch and sucrose metabolic pathway, alanine-aspartate-glutamine metabolic pathways, and purine metabolic pathway) exerted significant impact on yam tuber dormancy regulation. This result provides vital insights into molecular mechanisms regulating yam tuber dormancy.

Regulatory network characterization of anthocyanin metabolites in purple sweetpotato via joint transcriptomics and metabolomics

INTRODUCTION

Sweet potato is an important staple food crop in the world and contains abundant secondary metabolites in its underground tuberous roots. The large accumulation of several categories of secondary metabolites result in colorful pigmentation of the roots. Anthocyanin, is a typical flavonoid compound present in purple sweet potatoes and it contributes to the antioxidant activity.

METHODS

In this study, we developed joint omics research via by combing the transcriptomic and metabolomic analysis to explore the molecular mechanisms underlying the anthocyanin biosynthesis in purple sweet potato. Four experimental materials with different pigmentation phenotypes, 1143-1 (white root flesh), HS (orange root flesh), Dianziganshu No.88 (DZ88, purple root flesh), and Dianziganshu No.54 (DZ54, dark purple root flesh) were comparably studied.

RESULTS AND DISCUSSION

We identified 38 differentially accumulated pigment metabolites and 1214 differentially expressed genes from a total of 418 metabolites and 50893 genes detected. There were 14 kinds of anthocyanin detected in DZ88 and DZ54, with glycosylated cyanidin and peonidin as the major components. The significantly enhanced expression levels of multiple structural genes involved in the central anthocyanin metabolic network, such as chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase/leucocyanidin oxygenase (ANS), and glutathione S-transferase (GST) were manifested to be the primary reason why the purple sweet potatoes had a much higher accumulation of anthocyanin. Moreover, the competition or redistribution of the intermediate substrates (i.e. dihydrokaempferol and dihydroquercetin) between the downstream production of anthocyanin products and the flavonoid derivatization (i.e. quercetin and kaempferol) under the regulation of the flavonol synthesis (FLS) gene, might play a crucial role in the metabolite flux repartitioning, which further led to the discrepant pigmentary performances in the purple and non-purple materials. Furthermore, the substantial production of chlorogenic acid, another prominent high-value antioxidant, in DZ88 and DZ54 seemed to be an interrelated but independent pathway differentiated from the anthocyanin biosynthesis. Collectively, these data from the transcriptomic and metabolomic analysis of four kinds of sweet potatoes provide insight to understand the molecular mechanisms of the coloring mechanism in purple sweet potatoes.

Epichloë bromicola from wild barley improves salt-tolerance of cultivated barley by altering physiological responses to salt stress

Introduction

Epichloë bromicola is a cultivable fungal endophyte that lives in symbiosis with wild barley (Hordeum brevisubulatum) to which it confers salt tolerance. This study tested the hypothesis that E. bromicola derived from wild barley has the potential to increase salt tolerance in cultivated barley under salt stress.

Methods

To test this hypothesis, the growth response, physiological parameters, and metabolic profiles of barley plants inoculated with E. bromicola (E+) and those not inoculated with E. bromicola (E-) were compared under salt stress.

Results

Compared with E- barley plants, E+ barley plants had significantly increased plant height, shoot biomass, total biomass, chlorophyll content, osmotic synthesis, and accumulation of stress adaptation metabolites. E. bromicola increased the salt stress tolerance of cultivated barley, and the positive effects correlated with different salt stress conditions.

Discussion

These results suggest that E. bromicola has promising potential for enhancing the salt tolerance of barley. New insights into the mechanisms underlying this barley-fungal endophyte association are provided, and interesting questions regarding the role of E. bromicola in fungus-enhanced tolerance to salt stress in this symbiosis are raised.

Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

RNA-seq analysis reveals key genes associated with seed germination of Fritillaria taipaiensis P.Y.Li by cold stratification

Seed dormancy is an adaptive strategy for environmental evolution. However, the molecular mechanism of the breaking of seed dormancy at cold temperatures is still unclear, and the genetic regulation of germination initiated by exposure to cold temperature requires further investigation. In the initial phase of the current study, the seed coat characteristics and embryo development of Fritillaria taipaiensis P.Y.Li at different temperatures (0°C, 4°C, 10°C & 25°C) was recorded. The results obtained demonstrated that embryo elongation and the dormancy-breaking was most significantly affected at 4°C. Subsequently, transcriptome analyses of seeds in different states of dormancy, at two stratification temperatures (4°C and 25°C) was performed, combined with weighted gene coexpression network analysis (WGCNA) and metabolomics, to explore the transcriptional regulation of seed germination in F. taipaiensis at the two selected stratification temperatures. The results showed that stratification at the colder temperature (4°C) induced an up-regulation of gene expression involved in gibberellic acid (GA) and auxin biosynthesis and the down-regulation of genes related to the abscisic acid (ABA) biosynthetic pathway. Thereby promoting embryo development and the stimulation of seed germination. Collectively, these data constitute a significant advance in our understanding of the role of cold temperatures in the regulation of seed germination in F. taipaiensis and also provide valuable transcriptomic data for seed dormancy for other non-model plant species.

Bruceine D may affect the phenylpropanoid biosynthesis by acting on ADTs thus inhibiting Bidens pilosa L. seed germination

Bruceine D is a natural quassinoid, which was successfully isolated in our research group from the residue of Brucea javanica (L.) seeds. Our previous research showed that Bruceine D prevented Bidens pilosa L. seed germination by suppressing the activity of key enzymes and the expression levels of key genes involved in the phenylpropanoid biosynthesis pathway. In this study, integrated analyses of non-targeted metabolomic and transcriptomic were performed. A total of 356 different accumulated metabolites (DAMs) were identified, and KEGG pathway analyses revealed that most of these DAMs were involved in phenylpropanoid biosynthesis. The decreased expression of ADTs and content of L-phenylalanine implicates that Bruceine D may suppress the downstream phenylpropanoid biosynthesis pathway by disrupting primary metabolism, that is, the phenylalanine biosynthesis pathway, thus inhibiting the final products, resulting in the interruption of B. pilosa seed germination. These results suggest that Bruceine D may inhibit the B. pilosa seed germination by suppressing phenylpropanoid biosynthesis through acting on ADTs.

Effects of exogenous selenium application on nutritional quality and metabolomic characteristics of mung bean (Vigna radiata L.)

Selenium (Se) biofortification is an important strategy for reducing hidden hunger by increasing the nutritional quality of crops. However, there is limited metabolomic information on the nutritional quality of Se-enriched mung beans. In this study, physiological assays and LC-MS/MS based widely targeted metabolomics approach was employed to reveal the Se biofortification potential of mung bean by evaluating the effect of Se on mung bean nutraceutical compounds and their qualitative parameters. Physiological data showed that foliar application of 30 g ha^-1 Se at key growth stages significantly increased the content of Se, protein, fat, total phenols, and total flavonoids content in two mung bean varieties. Widely targeted metabolomics identified 1,080 metabolites, among which L-Alanyl-L-leucine, 9,10-Dihydroxy-12,13-epoxyoctadecanoic acid, and 1-caffeoylquinic acid could serve as biomarkers for identifying highly nutritious mung bean varieties. Pathway enrichment analysis revealed that the metabolic pathways of different metabolites were different in the Se-enriched mung bean. Specifically, P1 was mainly enriched in the linoleic acid metabolic pathway, while P2 was mainly enriched in the phosphonate and phosphinate metabolic pathways. Overall, these results revealed the specific Se enrichment mechanism of different mung bean varieties. This study provides new insights into the comprehensive improvement of the nutritional quality of mung beans.

Metabolomic Analysis Revealed Distinct Physiological Responses of Leaves and Roots to Huanglongbing in a Citrus Rootstock

Huanglongbing (HLB) is an obstinate disease in the citrus industry. No resistant citrus resources were currently available, but various degrees of Huanglongbing tolerance exist in different germplasm. Citrus junos is emerging as one of the popular rootstocks widely used in the citrus production. However, its responses to the HLB causal agent, Candidatus Liberibacter asiaticus (CLas), were still elusive. In the current study, we investigated the physiological, anatomical, and metabolomic responses of a C. junos rootstock ‘Pujiang Xiangcheng’ by a controlled CLas grafting inoculation. The summer flushes and roots were impaired at 15 weeks after inoculation, although typical leaf symptomatic phenotypes were not obvious. The chlorophyll pigments and the photosynthetic rate were compromised. The phloem sieve tubes were still working, despite the fact that the callose was deposited and the starch granules were accumulated in the phloem cells. A wide, targeted metabolomic analysis was carried out to explore the systematic alterations of the metabolites at this early stage of infection in the leaves and root system. The differentially accumulated metabolites in the CLas-affected leaves and roots compared with the mock-inoculation control tissues revealed that distinct responses were obvious. Besides the commonly observed alteration of sugar and amino acids, the active break down of starch in the roots was discovered. The different types of fatty acids were altered in the two tissues, with a more pronounced content decline in the roots. Our results not only provided fundamental knowledge about the response of the C. junos rootstock to the HLB disease, but also presented new insights into the host–pathogen interaction in the early stages.

Light and Potassium Improve the Quality of Dendrobium officinale through Optimizing Transcriptomic and Metabolomic Alteration

Background: Dendrobium officinale is a perennial epiphytic herb in Orchidaceae. Cultivated products are the main alternative for clinical application due to the shortage of wild resources. However, the phenotype and quality of D. officinale have changed post-artificial cultivation, and environmental cues such as light, temperature, water, and nutrition supply are the major influencing factors. This study aims to unveil the mechanisms beneath the cultivation-induced variation by analyzing the changes of the metabolome and transcriptome of D. officinale seedlings treated with red- blue LED light and potassium fertilizer. Results: After light- and K-treatment, the D. officinale pseudobulbs turned purple and the anthocyanin content increased significantly. Through wide-target metabolome analysis, compared with pseudobulbs in the control group (P), the proportion of flavonoids in differentially-accumulated metabolites (DAMs) was 22.4% and 33.5% post light- and K-treatment, respectively. The gene modules coupled to flavonoids were obtained through the coexpression analysis of the light- and K-treated D. officinale transcriptome by WGCNA. The KEGG enrichment results of the key modules showed that the DEGs of the D. officinale pseudobulb were enriched in phenylpropane biosynthesis, flavonoid biosynthesis, and jasmonic acid (JA) synthesis post-light- and K-treatment. In addition, anthocyanin accumulation was the main contribution to the purple color of pseudobulbs, and the plant hormone JA induced the accumulation of anthocyanins in D. officinale. Conclusions: These results suggested that light and potassium affected the accumulation of active compounds in D. officinale, and the gene-flavone network analysis emphasizes the key functional genes and regulatory factors for quality improvement in the cultivation of this medicinal plant.

Analysis of Metabolomic Changes in Xylem and Phloem Sap of Cucumber under Phosphorus Stresses

Cucumber xylem and phloem sap is a key link in nutrient distribution, transportation and signal transduction of cucumber plants; however, the metabolic response mechanism of cucumber xylem and phloem sap under phosphorus stress has not been clearly revealed. In this study, gas chromatography-mass spectrometry (GC-MS) combined with principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were used to analyze the metabolites in cucumber xylem and phloem sap under different phosphorus stress. A total of 22 differential metabolites were screened from xylem and phloem sap, respectively. Through the analysis of metabolic pathways of differential metabolites, four and three key metabolic pathways were screened, respectively. The results showed that compared with the normal phosphorus level, the content of most amino acids in the key metabolic pathway increased in xylem but decreased in phloem both under low and high phosphorus stress levels. The contents of sucrose and glucose in phloem glycolysis pathway showed a positive correlation with the change of phosphorus nutrient levels. The tricarboxylic acid cycle was promoted in xylem and phloem of cucumber under low and high phosphorus nutrient levels, and the contents of malic acid and citric acid increased significantly. This study provided abundant biochemical information for the metabolic response and regulation strategies of cucumber xylem and phloem under phosphorus stress, and is committed to looking for more sensitive markers to evaluate the supply level of phosphorus nutrients in cucumber.

Integration of the metabolome and transcriptome reveals indigo biosynthesis in Phaius flavus flowers under freezing treatment

Background

Indigo-containing plant tissues change blue after a freezing treatment, which is accompanied by changes in indigo and its related compounds. Phaius flavus is one of the few monocot plants containing indigo. The change to blue after freezing was described to explore the biosynthesis of indigo in P. flavus.

Methods

In this study, we surveyed the dynamic change of P. flavus flower metabolomics and transcriptomics.

Results

The non-targeted metabolomics and targeted metabolomics results revealed a total of 98 different metabolites, the contents of indole, indican, indigo, and indirubin were significantly different after the change to blue from the freezing treatment. A transcriptome analysis screened ten different genes related to indigo upstream biosynthesis, including three anthranilate synthase genes, two phosphoribosyl-anthranilate isomerase genes, one indole-3-glycerolphosphate synthase gene, five tryptophan synthase genes. In addition, we further candidate 37 cytochrome P450 enzyme genes, one uridine diphosphate glucosyltransferase gene, and 24 β-D-glucosidase genes were screened that may have participated in the downstream biosynthesis of indigo. This study explained the changes of indigo-related compounds at the metabolic level and gene expression level during the process of P. flavus under freezing and provided new insights for increasing the production of indigo-related compounds in P. flavus. In addition, transcriptome sequencing provides the basis for functional verification of the indigo biosynthesis key genes in P. flavus.

Comparative metabolomics study of Tartary (Fagopyrum tataricum (L.) Gaertn) and common (Fagopyrum esculentum Moench) buckwheat seeds

Tartary buckwheat has higher health-promoting value than common buckwheat. However, the related metabolites information except flavonoids is largely deficient. Here, we compared the seed metabolomes of the two species using a UHPLC-QqQ-MS-based metabolomics approach. In total, 722 metabolites were obtained, of which 84 and 78 were identified as the key active ingredients of Traditional Chinese Medicines and the active pharmaceutical ingredients for six major diseases-resistance, respectively. Comparative analysis showed there were obviously difference in metabolic profiles between the two buckwheat species, and further found 61 flavonoids and 94 non-flavonoids metabolites displayed significantly higher contents (≥2 fold) in Tartary buckwheat than in common buckwheat. Our results suggest that Tartary and common buckwheat seeds are rich in metabolites beneficial to human health, and non-flavonoids metabolites also contributed to Tartary buckwheat's higher health-promoting value than common buckwheat. This study provides valuable information for the development of new functional foods of Tartary buckwheat.

Analysis of metabolites in young and mature Docynia delavayi (Franch.) Schneid leaves using UPLC-ESI-MS/MS

Docynia delavayi (Franch.) Schneid is a plant used both as food and traditional folk medicine. The leaves of D. delavayi are rich in polyphenols, plants with phenolic content are known to be extremely beneficial in terms of human nutrition. In the present study, we used metabolome technology (UPLC-ESI-MS/MS) to examine the young and mature D. delavayi leaves on metabolites changes, which were then analyzed and compared. As a result, 477 metabolites (including 111 flavonoids, 47 others (consisted of nine vitamin, 18 saccharides and alcohols, and 20 unassigned metabolites), 71 phenolic acids, 52 amino acids and derivatives, 18 alkaloids, 61 lipids, 24 terpenoids, 33 nucleotides and derivatives, 18 lignans and coumarins, 12 tannins, 30 organic acids) were identified, of which 281 differentially accumulated metabolites, including 146 up-regulated metabolites and 135 down-regulated metabolites. The result of clustering and PCA analyses showed that young and mature leaves were separated, which indicated that there was a great difference in metabolites between young and mature leaves. Meanwhile, we also found that both young and mature leaves displayed unique metabolites with important biological functions. KEGG enrichment analysis showed that 90 of the differential metabolites were mainly concentrated in 68 KEGG pathways. The result will greatly complement the existing knowledge on the D. delavayi leaves for lays a foundation for subsequent development and utilization.

Enhancement of astaxanthin accumulation in Haematococcus pluvialis by exogenous oxaloacetate combined with nitrogen deficiency

Effective inducers and stress conditions play an essential role in the regulation of astaxanthin biosynthesis. This study reports a strategy developed by combining exogenous addition of oxaloacetate (OA) with nitrogen deficiency to facilitate astaxanthin production in Haematococcus pluvialis. Significantly, addition of 10 mM-OA enhanced the cellular astaxanthin content about 7.18-fold under nitrogen deficiency on day 7, with the content of astaxanthin esters increased concomitantly. To further elucidate the role and mechanism of OA on astaxanthin synthesis, the physiological and metabolic analyses of H. pluvialis treated with exogenous OA were performed. The results showed that exogenous OA promoted respiration over photosynthesis. Concurrently, the metabolite levels in the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway and tricarboxylic acid cycle obviously increased. The enhancement of respiratory metabolic pathways led to elevated levels of substrates, thus directly promoted astaxanthin synthesis. The present findings provide a new and effective approach for optimizing astaxanthin production.

Metabolite profiles of brown planthopper-susceptible and resistant rice (Oryza sativa) varieties associated with infestation and mechanical stimuli

Understanding brown planthopper (BPH) resistance mechanism will expedite selective breeding of better BPH resistant lines of rice (Oryza sativa). Metabolic responses during BPH infestation derived from wound stress imposed by insect feeding, comparing with mechanical piercing will provide an insight into resistance mechanism in rice. Therefore, this study aimed to compare the metabolic responses of needle piercing treatment and BPH feeding treatment in BPH-susceptible (KD) and BPH-resistant (RH) varieties at four different time points (0, 6, 24 and 96 h) using liquid chromatography-high resolution mass spectrometry (LC-HRMS). Phenotypes of RH were not different among the treatments, whereas KD exhibited hopperburn symptom at 96 h post-BPH infestation. Principal component and cluster analyses revealed that metabolite profiles between KD and RH were different in response to both insect and mechanical stimuli. Metabolite profiles of RH under BPH and mechanical treatments at 24 and 96 h were different from the untreated, whereas metabolite profiles of KD after BPH infestation at 24 and 96 h were distinct from needle piercing and no treatment, suggesting that the resistant variety has an ability to adapt and defend both mechanical and insect stimuli. Metabolomics result showed that BPH infestation perturbed purine salvage biosynthesis (e.g., inosine, hypoxanthine) in both varieties, amino acid biosynthesis (e.g., phenylalanine, tryptophan) in KD, while the infestation perturbed lysine metabolism (pipecolic acid) and phenylpropanoid pathway (2-anisic acid) only in RH. BPH and mechanical stimuli perturbed phenylamide only in RH, but not in KD. These findings revealed that different rice varieties utilize different metabolites in response to insect and mechanical stimuli, resulting in different degrees of resistance.

Different Phenylalanine Pathway Responses to Cold Stress Based on Metabolomics and Transcriptomics in Tartary Buckwheat Landraces

Tartary buckwheat (Fagopyrum tataricum) is strongly adapted to growth in adverse environments. In Liangshan, the Yi people cultivate different Tartary buckwheat landraces in different habitats. In this study, we aimed to understand the molecular differences in transcriptomic and metabolomic responses underlying cold tolerance between two Tartary buckwheat landraces (TM and RG) cultivated at different altitudes. After cold treatment, TM showed normal growth in the seedling stage and had significantly higher total flavonoids (16.53 mg/g, 1.47 times), rutin (5.73 mg/g, 1.32 times), and quercetin (0.08 mg/g, 2.67 times), which were higher than those in RG. In addition, TM showed higher-level changes in carbon and nitrogen metabolism than RG. Combined transcriptome and metabolomic analyses showed that phenylpropanoid biosynthesis was upregulated after cold treatment, and in TM, rutin synthesis was upregulated with a higher-level response to cold stress. RG showed higher expression in anthocyanins in response to cold stress. In addition, 24 structural genes involved in flavonoid synthesis, including 6 PAL, 3 C4H, 2 4CL, 2 CHS, 1 CHI, 3 F3H, 3 DFR, 1 FLS, 1 F3'H, and 4 GTR genes, were identified. These results will provide sufficient information for breeding Tartary buckwheat with high cold tolerance and constructing rutin high-yield varieties based on genetic engineering.