Physiological aspects of raffinose family oligosaccharides in plants: protection against abiotic stress

Glutathione metabolism contributes to citric acid tolerance and antioxidant capacity in Acetobacter tropicalis

Acetobacter is one of the main species producing fruit vinegar and its tolerance mechanism to citric acid has not been fully studied. This limits fruit vinegar production from high-citric-acid fruits, which are excellent materials for fruit vinegar production. This study analyzed the metabolic differences between two strains of A. tropicalis with different citric acid tolerances using non-targeted metabolomics. Differential metabolites and metabolic pathways analysis showed that the enhanced amino acid metabolism significantly improved the citric acid tolerance of A. tropicalis and the deamination of amino acids may also play a role. In addition, the up-regulated phosphatidylcholine (PC) and N-heptanoylhonoserine lactone indicated decreased membrane permeability and enhanced quorum sensing (QS), respectively. The analysis of the interaction between pathways and metabolites indicated that Gln, Cys, and Tyr contribute to improving citric acid tolerance, which was also confirmed by the exogenous addition. After adding the amino acids, the down-regulated qdh, up-regulated ggt, and improved glutathione reductase (GR) activity in J-2736 indicated that glutathione metabolism played an important role in resisting citric acid, and cellular antioxidant capacity was increased. This study provides a theoretical basis for efficient fruit vinegar production from citric-acid-type fruits.

Distribution of Non-Structural Carbohydrates and Root Structure of Plantago lanceolata L. under Different Defoliation Frequencies and Intensities

Plantago lanceolata L. (plantain) increases herbage dry matter (DM) production and quality during warm and dry conditions due to its deep roots and drought tolerance and reduces nitrogen losses in grazing systems compared to traditional pastures. However, plantain density usually declines after the third growing season, mainly due to defoliation management. The effects of defoliation frequency and intensity on water-soluble carbohydrate (WSC) reserves and below-ground plant responses need further research to optimize grazing strategies for improved productivity and sustainability of grazing systems. Our study investigated the effects of defoliation frequencies (15, 25, and 35 cm of extended leaf length, ELL) and intensities (5 and 8 cm of residual heights) on morphological traits and WSC concentrations in plantain biomass under controlled environmental conditions. Defoliation frequency significantly influenced morphological and chemical characteristics and biomass distribution more than residual height. Less frequent defoliations promoted above-ground herbage DM production, reproductive stems, and root biomass. Root architecture showed adaptations in response to defoliation frequency, optimizing resource acquisition efficiency. Frequent defoliation reduced high molecular weight WSC concentrations in leaves, affecting regrowth capacity and DM mass. A defoliation frequency of 25 cm ELL (~15 days) balances herbage production and root development, promoting long-term pasture sustainability.

Cold tolerance of woodland strawberry (Fragaria vesca) is linked to Cold Box Factor 4 and the dehydrin Xero2

Domesticated strawberry is susceptible to sudden frost episodes, limiting the productivity of this cash crop in regions where they are grown during early spring. In contrast, the ancestral woodland strawberry (Fragaria vesca) has successfully colonized many habitats of the Northern Hemisphere. Thus, this species seems to harbour genetic factors promoting cold tolerance. Screening a germplasm established in the frame of the German Gene Bank for Crop Wild Relatives, we identified, among 70 wild accessions, a pair with contrasting cold tolerance. By following the physiological, biochemical, molecular, and metabolic responses of this contrasting pair, we identified the transcription factor Cold Box Factor 4 and the dehydrin Xero2 as molecular markers associated with superior tolerance to cold stress. Overexpression of green fluorescent protein fusions with Xero2 in tobacco BY-2 cells conferred cold tolerance to these recipient cells. A detailed analysis of the metabolome for the two contrasting genotypes allows the definition of metabolic signatures correlated with cold tolerance versus cold stress. This work provides a proof-of-concept for the value of crop wild relatives as genetic resources to identify genetic factors suitable to increase the stress resilience of crop plants.

Mitigating gadolinium toxicity in guar (Cyamopsis tetragonoloba L.) through the symbiotic associations with arbuscular mycorrhizal fungi: physiological and biochemical insights

BACKGROUND

Gadolinium (Gd) is an increasingly found lanthanide element in soil; thus, understanding its impact on plant physiology, biochemistry, and molecular responses is crucial. Here, we aimed to provide a comprehensive understanding of Gd (150 mg kg- 1) impacts on guar (Cyamopsis tetragonoloba L.) plant yield and metabolism and whether the symbiotic relationship with arbuscular mycorrhizal fungi (AMF) can mitigate Gd toxicity of soil contamination.

RESULTS

AMF treatment improved mineral nutrient uptake and seed yield by 38-41% under Gd stress compared to non-inoculated stressed plants. Metabolic analysis unveiled the defense mechanisms adopted by AMF-treated plants, revealing carbon and nitrogen metabolism adaptations to withstand Gd contamination. This included an increase in the synthesis of primary metabolites, such as total sugar (+ 39% compared to control), soluble sugars (+ 29%), starch (+ 30%), and some main amino acids like proline (+ 57%) and phenylalanine (+ 87%) in the seeds of AMF-treated plants grown under Gd contamination. Furthermore, fatty acid and organic acid profile changes were accompanied by the production of secondary metabolites, including tocopherols, polyamines, phenolic acids, flavones, and anthocyanins.

CONCLUSIONS

Overall, the coordinated synthesis of these compounds underscores the intricate regulatory mechanisms underlying plant-AMF interactions and highlights the potential of AMF to modulate plant secondary metabolism for enhanced Gd stress tolerance.

GC-MS metabolomics of French lettuce (Lactuca Sativa L. var capitata) leaves exposed to bisphenol A via the hydroponic media

INTRODUCTION

Bisphenol A (BPA), an organic compound used to produce polycarbonate plastics and epoxy resins, has become a ubiquitous contaminant due to its high-volume production and constant release to the environment. Plant metabolomics can trace the stress effects induced by environmental contaminants to the variation of specific metabolites, making it an alternative way to study pollutants toxicity to plants. Nevertheless, there is an important knowledge gap in metabolomics applications in this area.

OBJECTIVE

Evaluate the influence of BPA in French lettuce (Lactuca Sativa L. var capitata) leaves metabolic profile by gas chromatography coupled to mass spectrometry (GC-MS) using a hydroponic system.

METHODS

Lettuces were cultivated in the laboratory to minimize biological variation and were analyzed 55 days after sowing (considered the plant's adult stage). Hexanoic and methanolic extracts with and without derivatization were prepared for each sample and analyzed by GC-MS.

RESULTS

The highest number of metabolites was obtained from the hexanoic extract, followed by the derivatized methanolic extract. Although no physical differences were observed between control and contaminated lettuce leaves, the multivariate analysis determined a statistically significant difference between their metabolic profiles. Pathway analysis of the most affected metabolites showed that galactose metabolism, starch and fructose metabolism and steroid biosynthesis were significantly affected by BPA exposure.

CONCLUSIONS

The preparation of different extracts from the same sample permitted the determination of metabolites with different physicochemical properties. BPA alters the leaves energy and membrane metabolism, plant growth could be affected at higher concentrations and exposition times.

Carbohydrate accumulation patterns in mangrove and halophytic plant species under seasonal variation

This study investigates the impact of carbohydrate accumulation in mangrove and halophytic plants on their response to abiotic stress. Using soil analysis and FT-IR spectroscopy, key species (Sueda nudiflora, Aeluropus lagopoides, Avicennia marina) were examined for seasonal changes in sugar content (reducing sugars, total soluble sugars, starch). The elevated carbohydrate levels may serve as an indication of the plant's ability to adapt to different environmental conditions throughout the year. This accumulation enables plants to adapt to variations in their environment, assuring their survival and functionality during periods of environmental fluctuation. Halophytic plants' sugar content peaked during the monsoon, suggesting biotic adaptations. The mangrove Avicennia marina had year-round sugar levels. PCA and Hierarchical Cluster Analysis revealed sugar accumulation trends across species and seasons. Partial Least Squares (PLS) analysis revealed correlations between soil characteristics and sugar content, suggesting plant-microbe interactions. K-means clustering and correlation analysis of FT-IR data revealed sugar composition and resource allocation trade-offs. These findings shed light on the role of carbohydrate metabolism in enabling coastal plants to endure stress. Gaining insight into these mechanisms can enhance sustainable agriculture in challenging environments and shed light on plant adaptations to evolving environmental conditions, especially biotic interactions.

Comprehensive metabolome characterization of leaves, internodes, and aerial roots of Vanilla planifolia by untargeted LC-MS and GC × GC-MS

INTRODUCTION

Untargeted metabolomics is a powerful tool that provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites, especially when combining different metabolomic platforms. Vanilla is one of the world's most popular flavors originating from cured pods of the orchid Vanilla planifolia. However, only a few studies have investigated the metabolome of V. planifolia, and no LC-MS or GC-MS metabolomics studies with respect to leaves have been performed.

OBJECTIVE

The aim of the study was to comprehensively characterize the metabolome of different organs (leaves, internodes, and aerial roots) of V. planifolia.

MATERIAL AND METHODS

Characterization of the metabolome was achieved using two complementary platforms (GC × GC-MS, LC-QToF-MS), and metabolite identification was based on a comparison with in-house databases or curated external spectral libraries.

RESULTS

In total, 127 metabolites could be identified with high certainty (confidence level 1 or 2) including sugars, amino acids, fatty acids, organic acids, and amines/amides but also secondary metabolites such as vanillin-related metabolites, flavonoids, and terpenoids. Ninty-eight metabolites showed significantly different intensities between the plant organs. Most strikingly, aglycons of flavonoids and vanillin-related metabolites were elevated in aerial roots, whereas its O-glycoside forms tended to be higher in leaves and/or internodes. This suggests that the more bioactive aglycones may accumulate where preferably needed, e.g. for defense against pathogens.

CONCLUSION

The results derived from the study substantially expand the knowledge regarding the vanilla metabolome forming a valuable basis for more targeted investigations in future studies, e.g. towards an optimization of vanilla plant cultivation.

Insights into the effects of saline forage on the meat quality of Tibetan sheep by metabolome and multivariate analysis

This work aimed to investigate how two different types of forage (saline and alkaline) impact the meat quality and muscle metabolism of Tibetan sheep. An integrative multi-omics analysis of meat quality and different metabolites was performed using untargeted and targeted metabolomics approaches. The research results indicated that GG grass (saline and alkaline forage) possessed superior characteristics in terms of apparent quality and secondary metabolite content compared with HG grass (Non saline alkali forage), regardless of the targeted metabolites or non-targeted ones. Simultaneously, under stress conditions, the carbohydrates-rich salt-alkali grass play a significant role in slowing down the decline in pH, increasing the unsaturated fatty acid content and reducing the thawing loss in Tibetan sheep. This study provides an understanding of the impact of different salt-alkali grass on the quality of Tibetan sheep meat, while providing a scientific basis for the future development of salt-alkali livestock industry.

Harnessing cold adaptation for postglacial colonisation: Galactinol synthase expression and raffinose accumulation in a polyploid and its progenitors

Allotetraploid white clover (Trifolium repens) formed during the last glaciation through hybridisation of two European diploid progenitors from restricted niches: one coastal, the other alpine. Here, we examine which hybridisation-derived molecular events may have underpinned white clover's postglacial niche expansion. We compared the transcriptomic frost responses of white clovers (an inbred line and an alpine-adapted ecotype), extant descendants of its progenitor species and a resynthesised white clover neopolyploid to identify genes that were exclusively frost-induced in the alpine progenitor and its derived subgenomes. From these analyses we identified galactinol synthase, the rate-limiting enzyme in biosynthesis of the cryoprotectant raffinose, and found that the extant descendants of the alpine progenitor as well as the neopolyploid white clover rapidly accumulated significantly more galactinol and raffinose than the coastal progenitor under cold stress. The frost-induced galactinol synthase expression and rapid raffinose accumulation derived from the alpine progenitor likely provided an advantage during early postglacial colonisation for white clover compared to its coastal progenitor.

Transcriptome Analysis of the Regulatory Mechanisms of Holly (Ilex dabieshanensis) under Salt Stress Conditions

The holly Ilex dabieshanensis K. Yao & M. B. Deng, a tree endemic to the Dabieshan Mountains region in China, is a commonly used landscaping plant. Like other crops, its growth is affected by salt stress. The molecular mechanism underlying salt tolerance in holly is still unclear. In this study, we used NaCl treatment and RNA sequencing (RNA-seq) at different times to identify the salt stress response genes of holly. A total of 4775 differentially expressed genes (DEGs) were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the DEGs obtained at different salt treatment times (3, 6, 9, 12, and 24 h), as compared to control (ck, 0 h), showed that plant hormone signal transduction and carotenoid biosynthesis were highly enriched. The mechanism by which holly responds to salt stress involves many plant hormones, among which the accumulation of abscisic acid (ABA) and its signal transduction may play an important role. In addition, ion homeostasis, osmotic metabolism, accumulation of antioxidant enzymes and nonenzymatic antioxidant compounds, and transcription factors jointly regulate the physiological balance in holly, providing important guarantees for its growth and development under conditions of salt stress. These results lay the foundation for studying the molecular mechanisms of salt tolerance in holly and for the selection of salt-tolerant varieties.

Metabolome profiling of cacao (Theobroma cacao L.) callus under drought stress conditions induced by polyethylene glycol (PEG) as osmoticant

INTRODUCTION

The cacao tree (Theobroma cacao), a perennial crop that serves as a source of cacao beans, can suffer from drastic climate changes such as irregular rainfall and shorter rainy seasons. The search for hybrids which are capable of producing specific metabolites favoring adaptation in new climatic conditions is a challenge in cacao farming.

OBJECTIVES

We aimed to (1) analyze the metabolic changes in calli of three cacao genotypes during water deficit induced by incubation with polyethylene glycol and (2) assess their response to water deficit stress with regard to somatic embryo differentiation.

METHODS

Metabolic profiling was carried out using 1H-NMR spectroscopy and multivariate data analysis was applied to crude extracts of calli grown in non-stress or water deficit stress conditions.

RESULTS

Water deficit stress influences the capacity of calli to produce embryos. The SCA12 genotype exhibited the best conversion capacity under severe conditions and was considered as tolerant to drought, followed by the SCA6 genotype (mid-tolerant) and the MA12 genotype (sensitive). Fifty-four metabolites were identified in the three cacao genotypes and discriminant metabolites were identified. Metabolites involved in water stress tolerance such as fructose, trans-aconitic acid, leucine, and hydroxybenzene derivatives were observed in SCA12, the tolerant genotype.

CONCLUSION

These results demonstrate the utility of 1H-NMR metabolomics as an essential tool for the analysis of the drought tolerance characteristics of T. cacao.

Water deprivation modifies the metabolic profile of lavender (Lavandula angustifolia Mill.) leaves

Lavender plantation is globally expanded due to the increasing demand of its essential oil and its popularity as an ornamental species. However, lavender plantations, and consequently essential oil industries, are threatened by more frequent and severe drought episodes in a globally changing climate. Still little is known about the changes in the general metabolome, which provides the precursors of essential oil production, by extended drought events. Prolonged drought fundamentally results in yield losses and changing essential oil composition. In the present study, the general metabolome of a main cultivated lavender species (Lavandula angustifolia Mill.) in response to water deprivation (WD) and re-watering was analyzed to identify the metabolomics responses. We found prolonged WD resulted in significant accumulations of glucose, 1,6-anhydro-β-D-glucose, sucrose, melezitose and raffinose, but declines of allulose, β-D-allose, altrose, fructose and D-cellobiose accompanied by decreased organic acids abundances. Amino acids and aromatic compounds of p-coumaric acid, hydrocaffeic acid and caffeic acid significantly accumulated at prolonged WD, whereas aromatics of cis-ferulic acid, taxifolin and two fatty acids (i.e., palmitic acid and stearic acid) significantly decreased. Prolonged WD also resulted in decreased abundances of polyols, particularly myo-inositol, galactinol and arabitol. The altered metabolite profiles by prolonged WD were mostly not recovered after re-watering, except for branched-chain amino acids, proline, serine and threonine. Our study illustrates the complex changes of leaf primary and secondary metabolic processes of L. angustifolia by drought events and highlights the potential impact of these precursors of essential oil production on the lavender industry.

A pattern for the early, middle, and late phase of tea chrysanthemum response to Fusarium oxysporum

Chrysanthemum morifolium is cultivated worldwide and has high ornamental, tea, and medicinal value. With the increasing area of chrysanthemum cultivation and years of continuous cropping, Fusarium wilt disease frequently occurs in various production areas, seriously affecting the quality and yield and causing huge economic losses. However, the molecular response mechanism of Fusarium wilt infection remains unclear, which limits the molecular breeding process for disease resistance in chrysanthemums. In the present study, we analyzed the molecular response mechanisms of 'Huangju,' one of the tea chrysanthemum cultivars severely infested with Fusarium wilt in the field at the early, middle, and late phases of F. oxysporum infestation. 'Huangju' responded to the infestation mainly through galactose metabolism, plant-pathogen interaction, auxin, abscisic acid, and ethylene signalling in the early phase; galactose metabolism, plant-pathogen interaction, auxin, salicylic acid signal, and certain transcription factors (e.g., CmWRKY48) in the middle phase; and galactose metabolism in the late phase. Notably, the galactose metabolism was important in the early, middle, and late phases of 'Huangju' response to F. oxysporum. Meanwhile, the phytohormone auxin was involved in the early and middle responses. Furthermore, silencing of CmWRKY48 in 'Huangju' resulted in resistance to F. oxysporum. Our results revealed a new molecular pattern for chrysanthemum in response to Fusarium wilt in the early, middle, and late phases, providing a foundation for the molecular breeding of chrysanthemum for disease resistance.

Unveiling the mechanism of source-sink rebalancing in cucumber-pumpkin heterografts: the buffering roles of rootstock cotyledon

Grafting onto pumpkin rootstock is widely applied in cucumber production to improve growth and yield, as well as to overcome soil-borne diseases and enhance resistance to abiotic stresses. In this study, we constructed the cucumber-pumpkin heterografts with the one-cotyledon grafting method, and examined the effects of heterografting on biomass allocation and sugar partitioning, with cucumber and pumpkin self-grafts used as control. Compared with cucumber self-grafts, heterografting onto pumpkin rootstock promoted photosynthesis in cucumber scion, and led to higher sucrose contents in the 1st true leaf (source) and newly emerged leaf (sink). Thereby, the scion part of heterografts accumulated more biomass than cucumber self-grafts. In contrast, when compared to pumpkin self-grafts, grafting with cucumber scion reduced root vigor and biomass but promoted cotyledon growth in pumpkin rootstock. The roots (sink) of heterografts contained less sucrose and hexoses, and showed reduced sucrose synthase (SuSy) and hexokinase (HXK) activities. However, the rootstock cotyledon (source) contained more sucrose and starch, and showed higher activities of HXK, cell-wall invertase (CWIN), and enzymes for starch synthesis and degradation. Furthermore, removal or shade of rootstock cotyledon led to reduced growth of root and scion. Silencing of CmoMEX1a gene in rootstock cotyledon inhibited maltose export and reduced root growth of heterografts. These results indicated that rootstock cotyledon, especially its starch content, played a buffering role in the growth regulation of cucumber-pumpkin heterografts. Taken together, our results provided a major contribution to our understanding of source-sink sugar partitioning and scion-rootstock growth balancing in cucumber-pumpkin heterografts.

Plant Heterotrophic Cultures: No Food, No Growth

Plant cells are capable of uptaking exogenous organic substances. This inherited trait allows the development of heterotrophic cell cultures in various plants. The most common of them are Nicotiana tabacum and Arabidopsis thaliana. Plant cells are widely used in academic studies and as factories for valuable substance production. The repertoire of compounds supporting the heterotrophic growth of plant cells is limited. The best growth of cultures is ensured by oligosaccharides and their cleavage products. Primarily, these are sucrose, raffinose, glucose and fructose. Other molecules such as glycerol, carbonic acids, starch, and mannitol have the ability to support growth occasionally, or in combination with another substrate. Culture growth is accompanied by processes of specialization, such as elongation growth. This determines the pattern of the carbon budget. Culture ageing is closely linked to substrate depletion, changes in medium composition, and cell physiological rearrangements. A lack of substrate leads to starvation, which results in a decrease in physiological activity and the mobilization of resources, and finally in the loss of viability. The cause of the instability of cultivated cells may be the non-optimal metabolism under cultural conditions or the insufficiency of internal regulation.

Novel Soybean Variety Lacking Raffinose Synthase 2 Activity

Variation in the raffinose family oligosaccharide (RFO) content in soybean is advantageous for livestock farming and health science. In this study, a soybean variety (GmJMC172) with a significantly low stachyose content in its seeds was identified in the NARO Genebank core collection. The results of the single-nucleotide polymorphism (SNP) analysis suggested that this phenomenon was related to a single-base deletion, inducing a frameshift mutation in raffinose synthase 2 (RS2), rather than the polymorphisms in the RS3, RS4, and stachyose synthase (STS) sequences. Differences in the enzymatic properties between the native RS2 and truncated RS2 were examined by using a three-dimensional model predicted using Alphafold2. In addition to revealing the missing active pocket in truncated RS2, the modeled structure explained the catalytic role of W331* and suggested a sufficient space to bind both sucrose and raffinose in the ligand-binding pocket. The soybean line, with seeds available from the NARO Genebank, could serve as breeding materials for manipulating the RFO content.

Metabolomics Reveals Rubiadin Accumulation and the Effects of Methyl Jasmonate Elicitation in Damnacanthus major Calli

Callus suspension techniques have been considered attractive for improving bioactive metabolite productivity; methyl jasmonate (MeJA) is a widely used elicitor for stimulating synthetic pathways. In this study, a multivariate analysis-based metabolomics approach was employed to investigate the primary and specialized metabolites in the leaves, unelicited calli, and 100 or 200 μM MeJA elicited calli of Damnacanthus major. Rubiadin, a powerful anthraquinone with various therapeutic properties, was only identified in D. major calli, accumulating in a MeJA elicitation concentration-dependent manner. Callus cultures also contained high levels of amino acids, sugars, and phenolic compounds, indicating energy metabolism and metabolic adaptation responses for proliferation and stabilization. Regarding MeJA application, elicited calli contained higher amounts of quinic acid, kaempferol, and glucose with lower amounts of sucrose and raffinose than those in the unelicited control, which were closely related to protective mechanisms against MeJA. Moreover, excessive elicitation increased the asparagine, fructose, and raffinose levels and decreased the glucose and sucrose levels, which was ascribed to increased activation of the aminoacyl-tRNA biosynthesis pathway and wider utilization of glucose than of fructose after sucrose degradation. These results will be useful for optimizing plant cell culture techniques to achieve high production rates for valuable specialized metabolites.

Metabolomic Analysis of the Desert Moss Syntrichia caninervis Provides Insights into Plant Dehydration and Rehydration Response

Desiccation-tolerant (DT) plants can survive extreme dehydration and tolerate the loss of up to 95% of their water content, making them ideal systems to determine the mechanism behind extreme drought stress and identify potential approaches for developing drought-tolerant crops. The desert moss Syntrichia caninervis is an emerging model for extreme desiccation tolerance that has benefited from high-throughput sequencing analyses, allowing identification of stress-tolerant genes; however, its metabolic response to desiccation is unknown. A liquid chromatography-mass spectrometry analysis of S. caninervis at six dehydration-rehydration stages revealed 912 differentially abundant compounds, belonging to 93 metabolic classes. Many (256) metabolites accumulated during rehydration in S. caninervis, whereas only 71 accumulated during the dehydration period, in contrast to the pattern observed in vascular DT plants. During dehydration, nitrogenous amino acids (l-glutamic acid and cysteinylglycine), alkaloids (vinleurosine) and steroids (physalin D) accumulated, whereas glucose 6-phosphate decreased. During rehydration, γ-aminobutyric acid, glucose 6-phosphate and flavonoids (karanjin and aromadendrin) accumulated, as did the plant hormones 12-oxo phytodienoic acid (12-OPDA) and trans-zeatin riboside. The contents ofl-arginine, maltose, turanose, lactulose and sucrose remained high throughout dehydration-rehydration. Syntrichia caninervis thus accumulates antioxidants to scavenge reactive oxygen species, accumulating nitrogenous amino acids and cytoprotective metabolites and decreasing energy metabolism to enter a protective state from dehydration-induced damage. During subsequent rehydration, many metabolites rapidly accumulated to prevent oxidative stress and restore physiological activities while repairing cells, representing a more elaborate rehydration repair mechanism than vascular DT plants, with a faster and greater accumulation of metabolites. This metabolic kinetics analysis in S. caninervis deepens our understanding of its dehydration mechanisms and provides new insights into the different strategies of plant responses to dehydration and rehydration.

Solid-state fermentation production of L-lysine by Corynebacterium glutamicum (ATCC 13032) using agricultural by-products as substrate

To meet the growing demand for L-lysine, an essential amino acid with various applications, it is crucial to produce it on a large scale locally instead of relying solely on imports. This study aimed to evaluate the potential of using Corynebacterium glutamicum ATCC 13032 for L-lysine production from agricultural by-products such as palm kernel cake, soybean cake, groundnut cake, and rice bran. Solid-state fermentation was conducted at room temperature for 72 h, with the addition of elephant grass extract as a supplement. The results revealed that these agricultural by-products contain residual amounts of L-lysine. By employing solid-state fermentation with C. glutamicum (106 CFU/ml) in 100 g of various agricultural by-products, L-lysine production was achieved. Interestingly, the addition of elephant grass extract (1 g of elephant grass: 10 ml of water) further enhanced L-lysine production. Among the tested substrates, 100 g of groundnut cake moistened with 500 ml of elephant grass extract yielded the highest L-lysine concentration of 3.27 ± 0.02 (mg/gds). Furthermore, fermentation led to a substantial rise (p < 0.05) in soluble protein, with solid-state fermented soybean cake moistened with 500 ml of elephant grass extract exhibiting the highest amount of 7.941 ± 0.05 mg/gds. The activities of xylanase, amylase and protease were also significantly enhanced. This study demonstrates a viable biotechnological approach for locally producing L-lysine from agricultural by-products using solid-state fermentation with C. glutamicum. The findings hold potential for both health and industrial applications, providing a sustainable and economically feasible method for L-lysine production.

Novel genetic resources associated with sucrose and stachyose content through genome-wide association study in soybean (Glycine max (L.) Merr.)

The nutritional value of soybean [Glycine max (L.) Merr.] for animals is influenced by soluble carbohydrates, such as sucrose and stachyose. Although sucrose is nutritionally desirable, stachyose is an antinutrient causing diarrhea and flatulence in non-ruminant animals. We conducted a genome-wide association study of 220 soybean accessions using 21,317 single nucleotide polymorphisms (SNPs) from the SoySNP50K iSelect Beadchip data to identify significant SNPs associated with sucrose and stachyose content. Seven significant SNPs were identified for sucrose content across chromosomes (Chrs.) 2, 8, 12, 17, and 20, while thirteen significant SNPs were identified for stachyose content across Chrs. 2, 5, 8, 9, 10, 13, 14, and 15. Among those significant SNPs, three sucrose-related SNPs on Chrs. 8 and 17 were novel, while twelve stachyose-related SNPs on Chrs. 2, 5, 8, 9, 10, 13, 14, and 15 were novel. Based on Phytozome, STRING, and GO annotation, 17 and 24 candidate genes for sucrose and stachyose content, respectively, were highly associated with the carbohydrate metabolic pathway. Among these, the publicly available RNA-seq Atlas database highlighted four candidate genes associated with sucrose (Glyma.08g361200 and Glyma.17g258100) and stachyose (Glyma.05g025300 and Glyma.13g077900) content, which had higher gene expression levels in developing seed and multiple parts of the soybean plant. The results of this study will extend knowledge of the molecular mechanism and genetic basis underlying sucrose and stachyose content in soybean seed. Furthermore, the novel candidate genes and SNPs can be valuable genetic resources that soybean breeders may utilize to modify carbohydrate profiles for animal and human usage.

A horizontal view of primary metabolomes in vegetative desiccation tolerance

Vegetative desiccation tolerance (VDT), the ability of such tissues to survive the near complete loss of cellular water, is a rare but polyphyletic phenotype. It is a complex multifactorial trait, typified by universal (core) factors but with many and varied adaptations due to plant architecture, biochemistry and biotic/abiotic dynamics of particular ecological niches. The ability to enter into a quiescent biophysically stable state is what ultimately determines desiccation tolerance. Thus, understanding the metabolomic complement of plants with VDT gives insight into the nature of survival as well as evolutionary aspects of VDT. In this study, we measured the soluble carbohydrate profiles and the polar, TMS-derivatisable metabolomes of 7 phylogenetically diverse species with VDT, in contrast with two desiccation sensitive (DS) species, under conditions of full hydration, severe water deficit stress, and desiccation. Our study confirmed the existence of core mechanisms of VDT systems associated with either constitutively abundant trehalose or the accumulation of raffinose family oligosaccharides and sucrose, with threshold ratios conditioned by other features of the metabolome. DS systems did not meet these ratios. Considerable chemical variations among VDT species suggest that co-occurring but distinct stresses (e.g., photooxidative stress) are dealt with using different chemical regimes. Furthermore, differences in the timing of metabolic shifts suggest there is not a single "desiccation programme" but that subprocesses are coordinated differently at different drying phases. There are likely to be constraints on the composition of a viable dry state and how different adaptive strategies interact with the biophysical constraints of VDT.

Comparison of the metabolic profile of pecan nuts cultivars [Carya illinoinensis (Wangenh.) K. Koch] by NMR spectroscopy

Pecan nuts (Carya illinoinensis (Wangenh.) K. Koch) contain the highest number of phytochemicals of all nuts, are a natural source of unsaturated fatty acids and other nutrients and can be considered an important addition to the Mediterranean diet al.though several studies have been carried out on pecans, employing several analytical techniques, no systematic study of the metabolic profile is available in literature. In this study, the metabolic profile of pecan nuts of three different cultivars was analysed by Nuclear Magnetic Resonance Spectroscopy. The cultivars compared were Wichita, Stuart, and Sioux, all grown in Italy in the same pedoclimatic conditions. 31 metabolites were identified and 28 were quantified and the three species were differentiated based on multivariate PCA analysis. The differences among them, and the levels of scutellarein and GABA, in particular, were attributed to the adaptation of the plants to the climate in their original areas.

Genome-Wide Identification of HSF Gene Family in Kiwifruit and the Function of AeHSFA2b in Salt Tolerance

Heat shock transcription factors (HSFs) play a crucial role in regulating plant growth and response to various abiotic stresses. In this study, we conducted a comprehensive analysis of the AeHSF gene family at genome-wide level in kiwifruit (Actinidia eriantha), focusing on their functions in the response to abiotic stresses. A total of 41 AeHSF genes were identified and categorized into three primary groups, namely, HSFA, HSFB, and HSFC. Further transcriptome analysis revealed that the expression of AeHSFA2b/2c and AeHSFB1c/1d/2c/3b was strongly induced by salt, which was confirmed by qRT-PCR assays. The overexpression of AeHSFA2b in Arabidopsis significantly improved the tolerance to salt stress by increasing AtRS5, AtGolS1 and AtGolS2 expression. Furthermore, yeast one-hybrid, dual-luciferase, and electrophoretic mobility shift assays demonstrated that AeHSFA2b could bind to the AeRFS4 promoter directly. Therefore, we speculated that AeHSFA2b may activate AeRFS4 expression by directly binding its promoter to enhance the kiwifruit's tolerance to salt stress. These results will provide a new insight into the evolutionary and functional mechanisms of AeHSF genes in kiwifruit.

The Root-Colonizing Endophyte Piriformospora indica Supports Nitrogen-Starved Arabidopsis thaliana Seedlings with Nitrogen Metabolites

The root-colonizing endophytic fungus Piriformospora indica promotes the root and shoot growth of its host plants. We show that the growth promotion of Arabidopsis thaliana leaves is abolished when the seedlings are grown on media with nitrogen (N) limitation. The fungus neither stimulated the total N content nor did it promote 15NO3- uptake from agar plates to the leaves of the host under N-sufficient or N-limiting conditions. However, when the roots were co-cultivated with 15N-labelled P. indica, more labels were detected in the leaves of N-starved host plants but not in plants supplied with sufficient N. Amino acid and primary metabolite profiles, as well as the expression analyses of N metabolite transporter genes suggest that the fungus alleviates the adaptation of its host from the N limitation condition. P. indica alters the expression of transporter genes, which participate in the relocation of NO3-, NH4+ and N metabolites from the roots to the leaves under N limitation. We propose that P. indica participates in the plant's metabolomic adaptation against N limitation by delivering reduced N metabolites to the host, thus alleviating metabolic N starvation responses and reprogramming the expression of N metabolism-related genes.

Reduced glutathione and raffinose lengthens postharvest storage of cassava root tubers by improving antioxidant capacity and antibiosis

Cassava is an ideal food security crop in marginal and drought environment. However, the post-harvest storage of cassava is urgent problem to be resolved. In this study, the storage tolerant and non-tolerant cassava were screened by measuring the change of Peroxidase (POD), Superoxide dismutase (SOD), Catalase (CAT) and Malondialdehyde (MDA) in seven cultivars of cassava. Compared with other cultivars, the cultivar of SC14 showed the highest level of SOD, MDA and POD respectively at 0 day, 12 day and 9 day postharvest while exhibited lowest level of CAT at 0 day postharvest, indicating the strongest antioxidant capability and storage tolerance. In contrast, GR15231, termed as storage non-tolerance cultivars, showed lowest SOD and POD at 12 day and kept a relative high level of CAT at 12 day post-harvest. In addition, SC14 has higher level of starch and dry substance than GR15231. Mass spectrum was performed for SC14 and GR15231 to explore the key metabolites regulating the storage tolerance of cassava. The results showed that the expression of glutathione (reduced) and raffinose was significantly decreased at 12 day post-harvest both in tolerant SC14 and non-tolerant GR15231. Compared with GR15231, SC14 showed higher level of raffinose both at 0 and 12 day post-harvest, indicating that raffinose may be the potential metabolites protecting SC14 cultivar from deterioration post-harvest. Additionally, raffinose ratio of SC14a/SC14b was five times less than that of GR15231a/GR15231b, reflecting the slower degradation of raffinose in SC14 cultivar compared with GR15231 cultivar. In conclusion, the antioxidant microenvironment induced by reduced glutathione and higher level of raffinose in SC14 cultivar might be the promising metabolites to improve its antioxidant capacity and antibiosis and thus maintained the quality of Cassava root tubers.

Quantitative Trait Loci and Candidate Genes That Control Seed Sugars Contents in the Soybean 'Forrest' by 'Williams 82' Recombinant Inbred Line Population

Soybean seed sugars are among the most abundant beneficial compounds for human and animal consumption in soybean seeds. Higher seed sugars such as sucrose are desirable as they contribute to taste and flavor in soy-based food. Therefore, the objectives of this study were to use the 'Forrest' by 'Williams 82' (F × W82) recombinant inbred line (RIL) soybean population (n = 309) to identify quantitative trait loci (QTLs) and candidate genes that control seed sugar (sucrose, stachyose, and raffinose) contents in two environments (North Carolina and Illinois) over two years (2018 and 2020). A total of 26 QTLs that control seed sugar contents were identified and mapped on 16 soybean chromosomes (chrs.). Interestingly, five QTL regions were identified in both locations, Illinois and North Carolina, in this study on chrs. 2, 5, 13, 17, and 20. Amongst 57 candidate genes identified in this study, 16 were located within 10 Megabase (MB) of the identified QTLs. Amongst them, a cluster of four genes involved in the sugars' pathway was collocated within 6 MB of two QTLs that were detected in this study on chr. 17. Further functional validation of the identified genes could be beneficial in breeding programs to produce soybean lines with high beneficial sucrose and low raffinose family oligosaccharides.

Structure-function analysis of bacterial GH31 α-galactosidases specific for α-(1→4)-galactobiose

Glycoside hydrolase family 31 (GH31) contains α-glycoside hydrolases with different substrate specificities involved in various physiological functions. This family has recently been classified into 20 subfamilies using sequence similarity networks. An α-galactosidase from the gut bacterium Bacteroides salyersiae (BsGH31_19, which belongs to GH31 subfamily 19) was reported to have hydrolytic activity against the synthetic substrate p- nitrophenyl α-galactopyranoside, but its natural substrate remained unknown. BsGH31_19 shares low sequence identity (around 20%) with other reported GH31 α-galactosidases, PsGal31A from Pseudopedobacter saltans and human myogenesis-regulating glycosidase (MYORG), and was expected to have distinct specificity. Here, we characterized BsGH31_19 and its ortholog from a soil Bacteroidota bacterium, Flavihumibacter petaseus (FpGH31_19), and demonstrated that they showed high substrate specificity against α-(1→4)-linkages in α-(1→4)-galactobiose and globotriose [α-Gal-(1→4)-β-Gal-(1→4)-Glc], unlike PsGal31A and MYORG. The crystallographic analyses of BsGH31_19 and FpGH31_19 showed that their overall structures resemble those of MYORG and form a dimer with an interface different from that of PsGal31A and MYORG dimers. The structures of FpGH31_19 complexed with d-galactose and α-(1→4)-galactobiose revealed that amino acid residues that recognize a galactose residue at subsite +1 are not conserved between FpGH31_19 and BsGH31_19. The tryptophan (Trp153) that recognizes galactose at subsite -1 is homologous to the tryptophan residues in MYORG and α-galactosidases belonging to GH27, GH36, and GH97, but not in the bacterial GH31 member PsGal31A. Our results provide structural insights into molecular diversity and evolutionary relationships in the GH31 α-galactosidase subfamilies and the other α-galactosidase families.

Two galactinol synthases contribute to the drought response of Camellia sinensis

MAIN CONCLUSION

CsGolS2-1 and CsGolS2-2 are involved in the transcriptional mechanism and play an important role in the drought response of tea plants. GolS is critical for the biosynthesis of galactinol and has been suggested to contribute to drought tolerance in various plants. However, whether GolS plays a role in drought response and the underlying transcriptional mechanism of GolS genes in response to drought stress in tea plants is still unclear. In this study, we found that drought stress promotes the accumulation of galactinol in tea leaves and that the expression of CsGolS2-1 and CsGolS2-2, which encode proteins capable of catalyzing galactinol biosynthesis, is continuously and dramatically induced by drought stress. Moreover, transgenic Arabidopsis plants expressing CsGolS2-1 and CsGolS2-2 were more drought-tolerant than WT plants, as evidenced by increased cell membrane stability. In addition, the drought-responsive transcription factor CsWRKY2 has been shown to positively regulate the expression of CsGolS2-1 and CsGolS2-2 by directly binding to their promoters. Furthermore, CsVQ9 was found to interact with CsWRKY2 and promote its transcriptional function to activate CsGolS2-1 and CsGolS2-2 expression. Taken together, our findings provide insights not only into the positive role played by CsGolS2-1 and CsGolS2-2 in the drought response of tea plants but also into the transcriptional mechanisms involved.

Rhizobacteria-enhanced drought tolerance and post-drought recovery of creeping bentgrass involving differential modulation of leaf and root metabolism

Rhizobacteria that produce 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase (ACCd) that inhibits ethylene production may mitigate stress damages. The objectives of this study were to examine whether a novel strain of ACCd-producing bacteria, Paraburkholderia aspalathi "WSF23," promotes plant tolerance to drought stress and post-stress recovery and determine changes in metabolic profiles in leaves and roots associated with the positive ACCd-bacteria effects in cool-season perennial grass species. Creeping bentgrass (Agrostis Stolonifera L. cv. "Penncross") plants were inoculated with P. aspalathi "WSF23" and exposed to drought by withholding irrigation for 35 days, followed by re-watering for 15 days in growth chambers. Inoculated plants demonstrated increased turf quality, canopy density, and root growth during drought stress and more rapid re-growth upon re-watering. Metabolomic analysis demonstrated that inoculation with P. aspalathi "WSF 23" increased the content of metabolites in the metabolic pathways related to stress defense, including osmoregulation, cell wall stability, and antioxidant protection in both leaves and roots, as well as nitrogen metabolism in roots of creeping bentgrass exposed to drought stress. The promotion of post-stress recovery by P. aspalathi "WSF 23" was mainly associated with enhanced carbohydrate and pyrimidine metabolism and zeatin biosynthesis pathways in leaves and increased carbohydrates, biosynthesis of DNA and proteins, cellular metabolism, and TCA cycle activity in roots. These results provide insights into the metabolic pathways regulated by "WSF23," with the PGPR conferring improvements in drought stress tolerance and post-drought recovery in a perennial grass species.

Carbon allocation of Spirodela polyrhiza under boron toxicity

Pectic polysaccharides containing apiose, xylose, and uronic acids are excellent candidates for boron fixation. Duckweeds are the fastest-growing angiosperms that can absorb diverse metals and contaminants from water and have high pectin content in their cell walls. Therefore, these plants can be considered excellent boron (B) accumulators. This work aimed to investigate the relationship between B assimilation capacity with apiose content in the cell wall of Spirodela polyrhiza subjected to different boric acid concentrations. Plants were grown for 7 and 10 days in ½ Schenck-Hildebrandt media supplemented with 0 to 56 mg B.L^-1, the non-structural and structural carbohydrates, and related genes were evaluated. The results showed that B altered the morphology and carbohydrate composition of this species during plant development. The optimum B concentration (1.8 mg B.L^-1) led to the highest relative growth and biomass accumulation, reduced starch, and high pectin and apiose contents, together with increased expression of UDP-apiose/UDP-xylose synthase (AXS) and 1,4-α-galacturonosyltransferase (GAUT). The toxic state (28 and 56 mg B.L^-1) increased the hexose contents in the cell wall with a concomitant reduction of pectins, apiose, and growth. The pectin content of S. polyrhiza was strongly associated with its growth capacity and regulation of B content within the cells, which have AXS as an important regulator. These findings suggest that duckweeds are suitable for B remediation, and their biomass can be used for bioenergy production.

Analysis of Raffinose Synthase Gene Family in Bread Wheat and Identification of Drought Resistance and Salt Tolerance Function of TaRS15-3B

Raffinose synthase (RS) plays a crucial role in plant growth and development, as well as in responses to biotic stresses and abiotic stresses, yet few studies have been conducted on its role in bread wheat. Therefore, in this study we screened and identified a family of bread wheat raffinose synthase genes based on bread wheat genome information and analyzed their physicochemical properties, phylogenetic evolutionary relationships, conserved structural domains, promoter cis-acting elements, and expression patterns. The BSMV-induced silencing of TaRS15-3B resulted in the bread wheat seedlings being susceptible to drought and salt stress and reduced the expression levels of stress-related and ROS-scavenging genes in bread wheat plants. This further affected the ability of bread wheat to cope with drought and salt stress. In conclusion, this study revealed that the RS gene family in bread wheat plays an important role in plant response to abiotic stresses and that the TaRS15-3B gene can improve the tolerance of transgenic bread wheat to drought and salt stresses, provide directions for the study of other RS gene families in bread wheat, and supply candidate genes for use in molecular breeding of bread wheat for stress resistance.

Impact of drought and salt stress on galactinol and raffinose family oligosaccharides in common bean (Phaseolus vulgaris)

Due to climate change, farmers will face more extreme weather conditions and hence will need crops that are better adapted to these challenges. The raffinose family oligosaccharides (RFOs) could play a role in the tolerance of crops towards abiotic stress. To investigate this, we determined for the first time the importance of galactinol and RFOs in the roots and leaves of common bean under drought and salt stress conditions. Initially, the physiological characteristics of common bean under agronomically relevant abiotic stress conditions were investigated by measuring the growth rate, transpiration rate, chlorophyll concentration and membrane stability, allowing to establish relevant sampling points. Subsequently, the differential gene expression profiles of the galactinol and RFO biosynthetic genes and the amount of galactinol and RFO molecules were measured in the primary leaves and roots of Phaseolus vulgaris cv. CIAP7247F at these sampling points, using RT-qPCR and HPAEC-PAD, respectively. Under drought stress, the genes galactinol synthase 1, galactinol synthase 3 and stachyose synthase were significantly upregulated in the leaves and had a high transcript level in comparison with the other galactinol and RFO biosynthetic genes. This was in accordance with the significantly higher amount of galactinol and raffinose detected in the leaves. Under salt stress, raffinose was also present in a significantly higher quantity in the leaves. In the roots, transcript levels of the RFO biosynthetic genes were generally low and no galactinol, raffinose or stachyose could be detected. These results suggest that in the leaves, both galactinol and raffinose could play a role in the protection of common bean against abiotic stresses. Especially, the isoform galactinol synthase 3 could have a specific role during drought stress and forms an interesting candidate to improve the abiotic stress resistance of common bean or other plant species.

Systematic Analysis of Galactinol Synthase and Raffinose Synthase Gene Families in Potato and Their Expression Patterns in Development and Abiotic Stress Responses

Raffinose family oligosaccharides (RFOs) are very important for plant growth, development, and abiotic stress tolerance. Galactinol synthase (GolS) and raffinose synthase (RFS) are critical enzymes involved in RFO biosynthesis. However, the whole-genome identification and stress responses of their coding genes in potato remain unexplored. In this study, four StGolS and nine StRFS genes were identified and classified into three and five subgroups, respectively. Remarkably, a total of two StGolS and four StRFS genes in potato were identified to form collinear pairs with those in both Arabidopsis and tomato, respectively. Subsequent analysis revealed that StGolS4 exhibited significantly high expression levels in transport-related tissues, PEG-6000, and ABA treatments, with remarkable upregulation under salt stress. Additionally, StRFS5 showed similar responses to StGolS4, but StRFS4 and StRFS8 gene expression increased significantly under salt treatment and decreased in PEG-6000 and ABA treatments. Overall, these results lay a foundation for further research on the functional characteristics and molecular mechanisms of these two gene families in response to ABA, salt, and drought stresses, and provide a theoretical foundation and new gene resources for the abiotic-stress-tolerant breeding of potato.

Integrating Transcriptional, Metabolic, and Physiological Responses to Drought Stress in Ilex paraguariensis Roots

The appearance of water stress episodes triggers leaf abscission and decreases Ilex paraguariensis yield. To explore the mechanisms that allow it to overcome dehydration, we investigated how the root gene expression varied between water-stressed and non-stressed plants and how the modulation of gene expression was linked to metabolite composition and physiological status. After water deprivation, 5160 differentially expressed transcripts were obtained through RNA-seq. The functional enrichment of induced transcripts revealed significant transcriptional remodelling of stress-related perception, signalling, transcription, and metabolism. Simultaneously, the induction of the enzyme 9-cis-expoxycarotenoid dioxygenase (NCED) transcripts reflected the central role of the hormone abscisic acid in this response. Consequently, the total content of amino acids and soluble sugars increased, and that of starch decreased. Likewise, osmotic adjustment and radical growth were significantly promoted to preserve cell membranes and water uptake. This study provides a valuable resource for future research to understand the molecular adaptation of I. paraguariensis plants under drought conditions and facilitates the exploration of drought-tolerant candidate genes.

Prevention of Chilling Injury in Pomegranates Revisited: Pre- and Post-Harvest Factors, Mode of Actions, and Technologies Involved

The storage life of pomegranate fruit (Punica granatum L.) is limited by decay, chilling injury, weight loss, and husk scald. In particular, chilling injury (CI) limits pomegranate long-term storage at chilling temperatures. CI manifests as skin browning that expands randomly with surface spots, albedo brown discoloration, and changes in aril colors from red to brown discoloration during handling or storage (6-8 weeks) at <5-7 °C. Since CI symptoms affect external and internal appearance, it significantly reduces pomegranate fruit marketability. Several postharvest treatments have been proposed to prevent CI, including atmospheric modifications (MA), heat treatments (HT), coatings, use of polyamines (PAs), salicylic acid (SA), jasmonates (JA), melatonin and glycine betaine (GB), among others. There is no complete understanding of the etiology and biochemistry of CI, however, a hypothetical model proposed herein indicates that oxidative stress plays a key role, which alters cell membrane functionality and integrity and alters protein/enzyme biosynthesis associated with chilling injury symptoms. This review discusses the hypothesized mechanism of CI based on recent research, its association to postharvest treatments, and their possible targets. It also indicates that the proposed mode of action model can be used to combine treatments in a hurdle synergistic or additive approach or as the basis for novel technological developments.

Optimizing raffinose family oligosaccharides content in plants: A tightrope walk

Plants synthesize various compounds for their growth, metabolism, and stress mitigation, and one such group of compounds is the raffinose family of oligosaccharides (RFOs). RFOs are non-reducing oligosaccharides having galactose residues attached to a sucrose moiety. They act as carbohydrate reserves in plants, assisting in seed germination, desiccation tolerance, and biotic/abiotic stress tolerance. Although legumes are among the richest sources of dietary proteins, the direct consumption of legumes is hindered by an excess of RFOs in the edible parts of the plant, which causes flatulence in humans and monogastric animals. These opposing characteristics make RFOs manipulation a complicated tradeoff. An in-depth knowledge of the chemical composition, distribution pattern, tissue mobilization, and metabolism is required to optimize the levels of RFOs. The most recent developments in our understanding of RFOs distribution, physiological function, genetic regulation of their biosynthesis, transport, and degradation in food crops have been covered in this review. Additionally, we have suggested a few strategies that can sustainably reduce RFOs in order to solve the flatulence issue in animals. The comprehensive information in this review can be a tool for researchers to precisely control the level of RFOs in crops and create low antinutrient, nutritious food with wider consumer acceptability.

Review: Status and prospects of association mapping in grapevine

Thanks to current advances in sequencing technologies, novel bioinformatics tools, and efficient modeling solutions, association mapping has become a widely accepted approach to unravel the link between genotype and phenotype diversity in numerous crops. In grapevine, this strategy has been used in the last decades to understand the genetic basis of traits of agronomic interest (fruit quality, crop yield, biotic and abiotic resistance), of special relevance nowadays to improve crop resilience to cope with future climate scenarios. Genome-wide association studies have identified many putative causative loci for different traits, some of them overlapping well-known causal genes identified by conventional quantitative trait loci studies in biparental progenies, and/or validated by functional approaches. In addition, candidate-gene association studies have been useful to pinpoint the causal mutation underlying phenotypic variation for several traits of high interest in breeding programs (like berry color, seedlessness, and muscat flavor), information that has been used to develop highly informative and useful markers already in use in marker-assisted selection processes. Thus, association mapping has proved to represent a valuable step towards high quality and sustainable grape production. This review summarizes current applications of association mapping in grapevine research and discusses future prospects in view of current viticulture challenges.

Targeted and untargeted metabolomics reveals deep analysis of drought stress responses in needles and roots of Pinus taeda seedlings

Drought stress is one of major environmental stresses affecting plant growth and yield. Although Pinus taeda trees are planted in rainy southern China, local drought sometime occurs and can last several months, further affecting their growth and resin production. In this study, P. taeda seedlings were treated with long-term drought (42 d), and then targeted and untargeted metabolomics analysis were carried out to evaluate drought tolerance of P. taeda. Targeted metabolomics analysis showed that levels of some sugars, phytohormones, and amino acids significantly increased in the roots and needles of water-stressed (WS) P. taeda seedlings, compared with well-watered (WW) pine seedlings. These metabolites included sucrose in pine roots, the phytohormones abscisic acid and sacylic acid in pine needles, the phytohormone gibberellin (GA4) and the two amino acids, glycine and asparagine, in WS pine roots. Compared with WW pine seedlings, the neurotransmitter acetylcholine significantly increased in needles of WS pine seedlings, but significantly reduced in their roots. The neurotransmitters L-glutamine and hydroxytyramine significantly increased in roots and needles of WS pine seedlings, respectively, compared with WW pine seedlings, but the neurotransmitter noradrenaline significantly reduced in needles of WS pine seedlings. Levels of some unsaturated fatty acids significantly reduced in roots or needles of WS pine seedlings, compared with WW pine seedlings, such as linoleic acid, oleic acid, myristelaidic acid, myristoleic acid in WS pine roots, and palmitelaidic acid, erucic acid, and alpha-linolenic acid in WS pine needles. However, three saturated fatty acids significantly increased in WS pine seedlings, i.e., dodecanoic acid in WS pine needles, tricosanoic acid and heptadecanoic acid in WS pine roots. Untargeted metabolomics analysis showed that levels of some metabolites increased in WS pine seedlings, especially sugars, long-chain lipids, flavonoids, and terpenoids. A few of specific metabolites increased greatly, such as androsin, piceatanol, and panaxatriol in roots and needles of WS pine seedlings. Comparing with WW pine seedlings, it was found that the most enriched pathways in WS pine needles included flavone and flavonol biosynthesis, ABC transporters, diterpenoid biosynthesis, plant hormone signal transduction, and flavonoid biosynthesis; in WS pine roots, the most enriched pathways included tryptophan metabolism, caffeine metabolism, sesquiterpenoid and triterpenoid biosynthesis, plant hormone signal transduction, biosynthesis of phenylalanine, tyrosine, and tryptophan. Under long-term drought stress, P. taeda seedlings showed their own metabolomics characteristics, and some new metabolites and biosynthesis pathways were found, providing a guideline for breeding drought-tolerant cultivars of P. taeda.

Soybean Seed Sugars: A Role in the Mechanism of Resistance to Charcoal Rot and Potential Use as Biomarkers in Selection

Charcoal rot, caused by Macrophomina phaseolina, is a major soybean disease resulting in significant yield loss and poor seed quality. Currently, no resistant soybean cultivar is available in the market and resistance mechanisms to charcoal rot are unknown, although the disease is believed to infect plants from infected soil through the roots by unknown toxin-mediated mechanisms. The objective of this research was to investigate the association between seed sugars (sucrose, raffinose, stachyose, glucose, and fructose) and their role as biomarkers in the soybean defense mechanism in the moderately resistant (MR) and susceptible (S) genotypes to charcoal rot. Seven MR and six S genotypes were grown under irrigated (IR) and non-irrigated (NIR) conditions. A two-year field experiment was conducted in 2012 and 2013 at Jackson, TN, USA. The main findings in this research were that MR genotypes generally had the ability to maintain higher seed levels of sucrose, glucose, and fructose than did S genotypes. Conversely, susceptible genotypes showed a higher level of stachyose and lower levels of sucrose, glucose, and fructose. This was observed in 6 out of 7 MR genotypes and in 4 out of 6 S genotypes in 2012; and in 5 out of 7 MR genotypes and in 5 out of 6 S genotypes in 2013. The response of S genotypes with higher levels of stachyose and lower sucrose, glucose, and fructose, compared with those of MR genotypes, may indicate the possible role of these sugars in a defense mechanism against charcoal rot. It also indicates that nutrient pathways in MR genotypes allowed for a higher influx of nutritious sugars (sucrose, glucose, and fructose) than did S genotypes, suggesting these sugars as potential biomarkers for selecting MR soybean plants after harvest. This research provides new knowledge on seed sugars and helps in understanding the impact of charcoal rot on seed sugars in moderately resistant and susceptible genotypes.

Pristine and sulfidized zinc oxide nanoparticles alter bacterial communities and metabolite profiles in soybean rhizocompartments

A better understanding of bacterial communities and metabolomic responses to pristine zinc oxide manufacture nanoparticles (ZnO MNPs) and its sulfidized product (s-ZnO MNPs), as well as their corresponding Zn ions in rhizocompartments, critical in the plant-microbe interactions, could contribute to the sustainable development of nano-enabled agriculture. In this study, soybean (Glycine max) were cultivated in soils amended with three Zn forms, namely ZnSO₄·7H₂O, ZnO MNPs and s-ZnO MNPs at 0, 100 and 500 mg·kg^-1 for 70 days. Three Zn forms exposures profoundly decreased the bacterial alpha diversity in roots and nodules. High dose (500 mg·kg^-1) groups had a stronger impact on the bacterial beta diversity than low dose (100 mg·kg^-1) groups. In the rhizosphere soil and roots, 500 mg·kg^-1 of ZnSO₄ and s-ZnO MNPs treatments showed the largest shifts in bacterial community structure, respectively. In addition, several significant changed bacterial taxa and metabolites were found at the high dose groups, which were associated with carbon and nitrogen metabolism. PLS-DA plot showed good discrimination in metabolomic profiles of rhizosphere soil and roots between three Zn forms treatments and control. Most metabolic pathways perturbed were closely linked to oxidative stress. Overall, our study indicates either dissolved or nano-particulate Zn exposure at high dose can drastically affected bacterial communities and metabolite profiles in soybean rhizocompartments.

Metabolism of crown tissue is crucial for drought tolerance and recovery after stress cessation in Lolium/Festuca forage grasses

A process of plant recovery after drought cessation is a complex trait which has not been fully recognized. The most important organ associated with this phenomenon in monocots, including forage grasses, is the crown tissue located between shoots and roots. The crown tissue is a meristematic crossroads for metabolites and other compounds between these two plant organs. Here, for the first time, we present a metabolomic and lipidomic study focused on the crown tissue under drought and recovery in forage grasses, important for agriculture in European temperate regions. The plant materials involve high (HDT) and low drought-tolerant (LDT) genotypes of Festuca arundinacea, and Lolium multiflorum/F. arundinacea introgression forms. The obtained results clearly demonstrated that remodeling patterns of the primary metabolome and lipidome in the crown under drought and recovery were different between HDT and LDT plants. Furthermore, HDT plants accumulated higher contents of primary metabolites under drought in the crown tissue, especially carbohydrates which could function as osmoprotectants and storage materials. On the other hand, LDT plants characterized by higher membranes damage under drought, simultaneously accumulated membrane phospholipids in the crown and possessed the capacity to recover their metabolic functions after stress cessation to the levels observed in HDT plants.

An alternative pathway to plant cold tolerance in the absence of vacuolar invertase activity

To cope with cold stress, plants have developed antioxidation strategies combined with osmoprotection by sugars. In potato (Solanum tuberosum) tubers, which are swollen stems, exposure to cold stress induces starch degradation and sucrose synthesis. Vacuolar acid invertase (VInv) activity is a significant part of the cold-induced sweetening (CIS) response, by rapidly cleaving sucrose into hexoses and increasing osmoprotection. To discover alternative plant tissue pathways for coping with cold stress, we produced VInv-knockout lines in two cultivars. Genome editing of VInv in 'Désirée' and 'Brooke' was done using stable and transient expression of CRISPR/Cas9 components, respectively. After storage at 4°C, sugar analysis indicated that the knockout lines showed low levels of CIS and maintained low acid invertase activity in storage. Surprisingly, the tuber parenchyma of vinv lines exhibited significantly reduced lipid peroxidation and reduced H2 O2 levels. Furthermore, whole plants of vinv lines exposed to cold stress without irrigation showed normal vigor, in contrast to WT plants, which wilted. Transcriptome analysis of vinv lines revealed upregulation of an osmoprotectant pathway and ethylene-related genes during cold temperature exposure. Accordingly, higher expression of antioxidant-related genes was detected after exposure to short and long cold storage. Sugar measurements showed an elevation of an alternative pathway in the absence of VInv activity, raising the raffinose pathway with increasing levels of myo-inositol content as a cold tolerance response.

Cell dehydration of intergeneric hybrid induces subgenome-related specific responses

The aim was to identify subgenome-related specific responses in two types of triticale, that is, of the wheat-dominated genome (WDG) and rye-dominated genome (RDG), to water stress induced in the early phase (tillering) of plant growth. Higher activity of the primary metabolism of carbohydrates is a feature of the WDG type, while the dominance of the rye genome is associated with a higher activity of the secondary metabolism of phenolic compounds in the RDG type. The study analyzed carbohydrates and key enzymes of their synthesis, free phenolic compounds and carbohydrate-related components of the cell wall, monolignols, and shikimic acid (ShA), which is a key link between the primary and secondary metabolism of phenolic compounds. Under water stress, dominance of the wheat genome in the WDG type was manifested by an increased accumulation of the large subunit of Rubisco and sucrose phosphate synthase and a higher content of raffinose and stachyose compared with the RDG type. In dehydrated RDG plants, higher activity of L-phenylalanine ammonia lyase (PAL) and L-tyrosine ammonia lyase (TAL), as well as a higher level of ShA, free and cell wall-bound p-hydroxybenzoic acid, free homovanillic acid, free sinapic acid, and cell wall-bound syringic acid can be considered biochemical indicators of the dominance of the rye genome.

Changing winter climate and snow conditions induce various transcriptional stress responses in Scots pine seedlings

In northern boreal forests the warming winter climate leads to more frequent snowmelt, rain-on-snow events and freeze-thaw cycles. This may be harmful or even lethal for tree seedlings that spend even a half of the year under snow. We conducted a snow cover manipulation experiment in a natural forest to find out how changing snow conditions affect young Scots pine (Pinus sylvestris L.) seedlings. The ice encasement (IE), absence of snow (NoSNOW) and snow compaction (COMP) treatments affected ground level temperature, ground frost and subnivean gas concentrations compared to the ambient snow cover (AMB) and led to the increased physical damage and mortality of seedlings. The expression responses of 28 genes related to circadian clock, aerobic and anaerobic energy metabolism, carbohydrate metabolism and stress protection revealed that seedlings were exposed to different stresses in a complex way depending on the thickness and quality of the snow cover. The IE treatment caused hypoxic stress and probably affected roots which resulted in reduced water uptake in the beginning of the growing season. Without protective snowpack in NoSNOW seedlings suffered from cold and drought stresses. The combination of hypoxic and cold stresses in COMP evoked unique transcriptional responses including oxidative stress. Snow cover manipulation induced changes in the expression of several circadian clock related genes suggested that photoreceptors and the circadian clock system play an essential role in the adaptation of Scots pine seedlings to stresses under different snow conditions. Our findings show that warming winter climate alters snow conditions and consequently causes Scots pine seedlings various abiotic stresses, whose effects extend from overwintering to the following growing season.

Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation

Bioenergy sorghum hybrids are being developed with enhanced drought tolerance and high levels of stem sugars. Raffinose family oligosaccharides (RFOs) contribute to plant environmental stress tolerance, sugar storage, transport, and signaling. To better understand the role of RFOs in sorghum, genes involved in myo-inositol and RFO metabolism were identified and relative transcript abundance analyzed during development. Genes involved in RFO biosynthesis (SbMIPS1, SbInsPase, SbGolS1, SbRS) were more highly expressed in leaves compared to stems and roots, with peak expression early in the morning in leaves. SbGolS, SbRS, SbAGA1 and SbAGA2 were also expressed at high levels in the leaf collar and leaf sheath. In leaf blades, genes involved in myo-inositol biosynthesis (SbMIPS1, SbInsPase) were expressed in bundle sheath cells, whereas genes involved in galactinol and raffinose synthesis (SbGolS1, SbRS) were expressed in mesophyll cells. Furthermore, SbAGA1 and SbAGA2, genes that encode neutral-alkaline alpha-galactosidases that hydrolyze raffinose, were differentially expressed in minor vein bundle sheath cells and major vein and mid-rib vascular and xylem parenchyma. This suggests that raffinose synthesized from sucrose and galactinol in mesophyll cells diffuses into vascular bundles where hydrolysis releases sucrose for long distance phloem transport. Increased expression (>20-fold) of SbAGA1 and SbAGA2 in stem storage pith parenchyma of sweet sorghum between floral initiation and grain maturity, and higher expression in sweet sorghum compared to grain sorghum, indicates these genes may play a key role in non-structural carbohydrate accumulation in stems.

Genetic architecture of inducible and constitutive metabolic profile related to drought resistance in qingke (Tibetan hulless barley)

Qingke (Tibetan hulless barley, Hordeum vulgare L. var. nudum) is the primary food crop on the Tibet Plateau, the long-term drought and other harsh environments makes qingke an important resource for the study of abiotic resistance. Here, we evaluated the drought sensitivity of 246 qingke varieties. Genome-wide association studies (GWAS) found that root-specific expressed gene CYP84 may be involved in the regulation of drought resistance. Based on widely targeted metabolic profiling, we identified 2,769 metabolites in qingke leaves, of which 302 were significantly changed in response to drought stress, including 4-aminobutyric acid (GABA), proline, sucrose and raffinose. Unexpectedly, these drought-induced metabolites changed more violently in drought-sensitive qingkes, while the constitutive metabolites that had little response to drought stress, such as C-glycosylflavonoids and some amino acids, accumulated excessively in drought-resistant qingkes. Combined with metabolite-based genome-wide association study (mGWAS), a total of 1,006 metabolites under optimal condition and 1,031 metabolites under mild drought stress had significant associated loci. As a marker metabolite induced by drought stress, raffinose was significantly associated with two conservatively adjacent α-galactosidase genes, qRT-PCR suggests that these two genes may jointly regulate the raffinose content in qingke. Besides, as constituent metabolites with stable differences between drought-sensitive and drought-resistant qingkes, a class of C-glycosylflavonoids are simultaneously regulated by a UDP-glucosyltransferase gene. Overall, we performed GWAS for sensitivity and widely targeted metabolites during drought stress in qingke for the first time, which provides new insights into the response mechanism of plant drought stress and drought resistance breeding.

Effects of chilling on the photosynthetic performance of the CAM orchid Phalaenopsis

INTRODUCTION

Crassulacean acid metabolism (CAM) is one of the three main metabolic adaptations for CO₂ fixation found in plants. A striking feature for these plants is nocturnal carbon fixation and diurnal decarboxylation of malic acid to feed Rubisco with CO₂ behind closed stomata, thereby saving considerable amounts of water. Compared to the effects of high temperatures, drought, and light, much less information is available about the effects of chilling temperatures on CAM plants. In addition a lot of CAM ornamentals are grown in heated greenhouses, urging for a deeper understanding about the physiological responses to chilling in order to increase sustainability in the horticultural sector.

METHODS

The present study focuses on the impact of chilling temperatures (10°C) for 3 weeks on the photosynthetic performance of the obligate CAM orchid Phalaenopsis 'Edessa'. Detailed assessments of the light reactions were performed by analyzing chlorophyll a fluorescence induction (OJIP) parameters and the carbon fixation reactions by measuring diel leaf gas exchange and diel metabolite patterns.

RESULTS AND DISCUSSION

Results showed that chilling already affected the light reactions after 24h. Whilst the potential efficiency of photosystem II (PSII) (F_v/F_m) was not yet influenced, a massive decrease in the performance index (PI_abs) was noticed. This decrease did not depict an overall downregulation of PSII related energy fluxes since energy absorption and dissipation remained uninfluenced whilst the trapped energy and reduction flux were upregulated. This might point to the presence of short-term adaptation mechanisms to chilling stress. However, in the longer term the electron transport chain from PSII to PSI was affected, impacting both ATP and NADPH provision. To avoid over-excitation and photodamage plants showed a massive increase in thermal dissipation. These considerations are also in line with carbon fixation data showing initial signs of cold adaptation by achieving comparable Rubisco activity compared to unstressed plants but increasing daytime stomatal opening in order to capture a higher proportion of CO₂ during daytime. However, in accordance with the light reactions data, Rubisco activity declined and stomatal conductance and CO₂ uptake diminished to near zero levels after 3 weeks, indicating that plants were not successful in cold acclimation on the longer term.

Adaptive resilience of roadside trees to vehicular emissions via leaf enzymatic, physiological, and anatomical trait modulations

Unplanned urbanization and heavy automobile use by the rapidly growing population contribute to a variety of environmental issues. Roadside plants can mitigate air pollution by modifying their enzymatic activity, physiological and anatomical traits. Plant enzymes, physiological and anatomical traits play an important role in adaptation and mitigation mechanisms against vehicular emissions. There is a significant gap in understanding of how plant enzymes and anatomical traits respond or how they participate in modulating the effect of vehicular emissions/air pollution. Modulation of leaf anatomical traits is also useful in regulating plant physiological behavior. Hence, the present study was conducted to evaluate the effects of vehicular pollution on the enzymatic activity, physiological, and anatomical traits of plant species that grow in forests (S1) and alongside roads (S2-1 km away from the S1 site) during different seasons. The present study examines four commonly found roadside tree species i.e. Grevillea robusta, Cassia fistula, Quercus leucotrichophora and Cornus oblonga. The study found that the activities of catalase and phenylalanine ammonium enzymes were higher in G. robusta species of roadside than control site (S1). Non-enzymatic antioxidants such as flavonoid and phenol were also found in higher concentrations in roadside tree species during the summer season. However, the measured values of physiological traits were higher in Q. leucotrichophora tree species of S1 during the summer season. When compared to the other species along the roadside, Q. leucotrichophora had the highest number of stomata and epidermal cells during the summer season. Hence, we found that tree species grown along the roadside adapted towards vehicular emissions by modulating their enzymatic, physiological, and anatomical traits to mitigate the effect of air pollution.

Raffinose family oligosaccharides (RFOs): role in seed vigor and longevity

Seed vigor and longevity are important agronomic attributes, as they are essentially associated with crop yield and thus the global economy. Seed longevity is a measure of seed viability and the most essential property in gene bank management since it affects regeneration of seed recycling. Reduced seed life or storability is a serious issue in seed storage since germplasm conservation and agricultural enhancement initiatives rely on it. The irreversible and ongoing process of seed deterioration comprises a complex gene regulatory network and altered metabolism that results in membrane damage, DNA integrity loss, mitochondrial dysregulation, protein damage, and disrupted antioxidative machinery. Carbohydrates and/or sugars, primarily raffinose family oligosaccharides (RFOs), have emerged as feasible components for boosting or increasing seed vigor and longevity in recent years. RFOs are known to perform diverse functions in plants, including abiotic and biotic stress tolerance, besides being involved in regulating seed germination, desiccation tolerance, vigor, and longevity. We emphasized and analyzed the potential impact of RFOs on seed vigor and longevity in this review. Here, we comprehensively reviewed the molecular mechanisms involved in seed longevity, RFO metabolism, and how RFO content is critical and linked with seed vigor and longevity. Further molecular basis, biotechnological approaches, and CRISPR/Cas applications have been discussed briefly for the improvement of seed attributes and ultimately crop production. Likewise, we suggest advancements, challenges, and future possibilities in this area.