Metabolomic analysis of tomato seed germination

Foliar infections by Botrytis cinerea modulate the tomato root volatilome and microbiome

The fungal pathogen Botrytis cinerea causes significant damage to aboveground plant parts, but its impact on root chemistry and microbiome composition is less understood. This study investigated how B. cinerea foliar infection influences the root volatilome and microbiome of two tomato genotypes: wild Solanum pimpinellifolium and domesticated Solanum lycopersicum var. Moneymaker. In the absence of infection, wild tomato roots emitted higher levels of monoterpenes such as α-pinene and terpinene compared to domesticated tomato roots. The fungal infection induced elevated levels of benzyl alcohol and benzofuran in the root headspace and/or rhizosphere of both genotypes, alongside genotype-specific changes. Multivariate analyses revealed that B. cinerea significantly altered bacterial and fungal community compositions in the rhizosphere and rhizoplane, with stronger bacterial community shifts in the rhizoplane. Taxa depletion and enrichment were observed, particularly among Proteobacteria and Ascomycota. Mantel tests showed significant correlations between rhizoplane bacterial community compositions and root-associated volatilome. Notably, enriched bacterial taxa such as Pelomonas and Comamonadaceae positively correlated with benzyl alcohol and benzofuran levels in the root volatilome. These findings demonstrate that B. cinerea foliar infection might induce profound changes in root-associated volatilome and microbiome composition, highlighting its systemic effects on plant root chemistry and microbiome composition.

Functions of Tomato (Solanum lycopersicum L.) Signal Transducer and Activator of Transcription (STAT) in Seed Germination and Low-Temperature Stress Response

Tomato (Solanum lycopersicum L.) is one of the major vegetable crops worldwide. Research on the Janus kinase-signal transducer and activator of transcription (JAK-STAT) signaling pathway in tomatoes and other plant systems is extremely limited. In this study, the roles of STAT, a crucial element of the JAK-STAT signaling pathway in tomato seed germination and low-temperature stress responses are examined, employing gene family analysis and genetic transformation. The results indicate that the S. lycopersicum genome contains only one member of the STAT gene family, SlSTAT. Subcellular localization experiments reveal that SlSTAT is found in both the cytoplasm and nucleus, suggesting its potential involvement in biological functions within these cellular compartments. Among the 26 different tomato tissue/organs tested, SlSTAT exhibited higher expression levels in hypocotyl (8 days past germination; 8 DPG), and low expression of SlSTAT significantly reduced the germination rate and impacted biomass at 8 DPG. In addition, the SlSTAT gene was significantly downregulated during low-temperature treatment. Compared with the wild-type (WT) tomatoes, the SlSTAT-overexpressing plants showed more resistance to low-temperature conditions, whereas the downexpressing tomatoes exhibited increased sensitivity. The expressions of low-temperature marker genes (SlCBF1-3) and N6-methyladenosine (m6A)-modification-related genes (m6A writer, reader, and eraser genes) were detected to explore possible molecular mechanisms by which SlSTAT causes changes in tomato low-temperature stress resistance. The expression changes of SlCBF1-3 in transgenic plants do not merely follow a straightforward linear relationship with the changes in SlSTAT expression, suggesting a more complex molecular mechanism and a non-direct interaction between SlSTAT and the promoters of SlCBFs. On the other hand, SlSTAT also changes the expression levels of RNA m6A-modification-related genes, especially SlFIP37 (writer gene), SlYTP8/9 (reader genes), and SlALKBH8 (eraser gene), ultimately leading to changes in the levels of m6A modification. These research findings lay the groundwork for exploring functions of JAK-STAT pathway in tomato development and stress responses, expanding the scope of JAK-STAT signaling studies in plant systems.

Metabolomic Insights into the Allelopathic Effects of Ailanthus altissima (Mill.) Swingle Volatile Organic Compounds on the Germination Process of Bidens pilosa (L.)

Background/Objectives: This study explores the allelopathic effects of volatile organic compounds (VOCs) emitted by the invasive species Ailanthus altissima (Mill.) Swingle on the seed germination of Bidens pilosa. A. altissima is known for releasing allelopathic VOCs that suppress the growth of neighbouring plants, contributing to its invasive potential. Methods: To examine these effects, we exposed B. pilosa seeds to varying concentrations of A. altissima VOCs, assessing germination rates and metabolic changes through untargeted metabolomics. Results: Our findings revealed that VOCs from A. altissima significantly inhibited the germination speed and overall germination rates of B. pilosa in a dose-dependent manner. Metabolomic profiling showed disruptions in energy and amino acid metabolism pathways, specifically involving delayed breakdown of starch and key metabolites, indicating inhibition of critical metabolic processes during early germination stages. This metabolic delay likely impairs B. pilosa's establishment and competitiveness, enhancing A. altissima's ecological dominance. Conclusions: The results underscore the potential of VOC-based allelopathy as a mechanism of plant invasion, offering insights into the role of VOCs in interspecies plant competition and ecosystem dynamics.

Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato fruits and seeds

Steryl esters (SE) are a storage pool of sterols that accumulates in cytoplasmic lipid droplets and helps to maintain plasma membrane sterol homeostasis throughout plant growth and development. Ester formation in plant SE is catalyzed by phospholipid:sterol acyltransferase (PSAT) and acyl-CoA:sterol acyltransferase (ASAT), which transfer long-chain fatty acid groups to free sterols from phospholipids and acyl-CoA, respectively. Comparative mass spectrometry-based metabolomic analysis between ripe fruits and seeds of a tomato (Solanum lycopersicum cv Micro-Tom) mutant lacking functional PSAT and ASAT enzymes (slasat1xslpsat1) shows that disruption of SE biosynthesis has a differential impact on the metabolome of these organs, including changes in the composition of free and glycosylated sterols. Significant perturbations were observed in the fruit lipidome in contrast to the mild effect detected in the lipidome of seeds. A contrasting response was also observed in phenylpropanoid metabolism, which is down-regulated in fruits and appears to be stimulated in seeds. Comparison of global metabolic changes using volcano plot analysis suggests that disruption of SE biosynthesis favours a general state of metabolic activation that is more evident in seeds than fruits. Interestingly, there is an induction of autophagy in both tissues, which may contribute along with other metabolic changes to the phenotypes of early seed germination and enhanced fruit tolerance to Botrytis cinerea displayed by the slasat1xslpsat1 mutant. The results of this study reveal unreported connections between SE metabolism and the metabolic status of plant cells and lay the basis for further studies aimed at elucidating the mechanisms underlying the observed effects.

Hints of Biological Activity of Xerosydryle: Preliminary Evidence on the Early Stages of Seedling Development

Xerosydryle belongs to a new category of materials resulting from the interaction of water with various hydrophilic polymers. These materials can exhibit different properties depending on the kind of polymer-water interaction. Previous research confirmed the existence of a solid manifestation of water at room temperature. The thermal properties of dissolved xerosydryle in water are similar to those of biological macromolecules during denaturation but with greater stability. This study investigated the biological effect of xerosydryle on a living system for the first time, using a seed germination model. The interaction was evaluated using physiological assays such as chlorophyll shifts, potassium (re)uptake during the onset of germination and a transcriptome approach. Seeds were treated with samples of xerosydryle and distilled water. Transcriptome analysis of germinating seeds highlighted differences (up- and down-regulated genes) between seeds treated with xerosydryle and those treated with distilled water. Overall, the experiments performed indicate that xerosydryle, even at low concentrations, interferes with seedling growth in a manner similar to an osmotic modulator. This work paves the way for a more comprehensive exploration of the active biological role of xerosydryle and similar compounds on living matter and opens up speculation on the interactions at the boundaries between physics, chemistry, and biology.

Spatial specificity of metabolism regulation of abscisic acid-imposed seed germination inhibition in Korean pine (Pinus koraiensis sieb et zucc)

Introduction

Abscisic acid (ABA) can negatively regulate seed germination, but the mechanisms of ABA-mediated metabolism modulation are not well understood. Moreover, it remains unclear whether metabolic pathways vary with the different tissue parts of the embryo, such as the radicle, hypocotyl and cotyledon.

Methods

In this report, we performed the first comprehensive metabolome analysis of the radicle and hypocotyl + cotyledon in Pinus koraiensis seeds in response to ABA treatment during germination.

Results and discussion

Metabolome profiling showed that following ABA treatment, 67 significantly differentially accumulated metabolites in the embryo were closely associated with pyrimidine metabolism, phenylalanine metabolism, cysteine and methionine metabolism, galactose metabolism, terpenoid backbone biosynthesis, and glutathione metabolism. Meanwhile, 62 metabolites in the hypocotyl + cotyledon were primarily involved in glycerophospholipid metabolism and glycolysis/gluconeogenesis. We can conclude that ABA may inhibit Korean pine seed germination primarily by disrupting the biosynthesis of certain plant hormones mediated by cysteine and methionine metabolism and terpenoid backbone biosynthesis, as well as reducing the reactive oxygen species scavenging ability regulated by glutathione metabolism and shikimate pathway in radicle. ABA may strongly disrupt the structure and function of cellular membranes due to alterations in glycerophospholipid metabolism, and weaken glycolysis/gluconeogenesis in the hypocotyl + cotyledon, both of which are major contributors to ABA-mediated inhibition of seed germination. These results highlight that the spatial modulation of metabolic pathways in Pinus koraiensis seeds underlies the germination response to ABA.

Plant Life with and without Oxygen: A Metabolomics Approach

Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.

Plant Metabolomics: Current Initiatives and Future Prospects

Plant metabolomics is a rapidly advancing field of plant sciences and systems biology. It involves comprehensive analyses of small molecules (metabolites) in plant tissues and cells. These metabolites include a wide range of compounds, such as sugars, amino acids, organic acids, secondary metabolites (e.g., alkaloids and flavonoids), lipids, and more. Metabolomics allows an understanding of the functional roles of specific metabolites in plants' physiology, development, and responses to biotic and abiotic stresses. It can lead to the identification of metabolites linked with specific traits or functions. Plant metabolic networks and pathways can be better understood with the help of metabolomics. Researchers can determine how plants react to environmental cues or genetic modifications by examining how metabolite profiles change under various crop stages. Metabolomics plays a major role in crop improvement and biotechnology. Integrating metabolomics data with other omics data (genomics, transcriptomics, and proteomics) provides a more comprehensive perspective of plant biology. This systems biology approach enables researchers to understand the complex interactions within organisms.

Longitudinal Plant Health Monitoring via High-Resolution Mass Spectrometry Screening Workflows: Application to a Fertilizer Mediated Tomato Growth Experiment

Significant efforts have been spent in the modern era towards implementing environmentally friendly procedures like composting to mitigate the negative effects of intensive agricultural practices. In this context, a novel fertilizer was produced via the hydrolysis of an onion-derived compost, and has been previously comprehensively chemically characterized. In order to characterize its efficacy, the product was applied to tomato plants at five time points to monitor plant health and growth. Control samples were also used at each time point to eliminate confounding parameters due to the plant's normal growth process. After harvesting, the plant leaves were extracted using aq. MeOH (70:30, v/v) and analyzed via UPLC-QToF-MS, using a C18 column in both ionization modes (±ESI). The data-independent (DIA/bbCID) acquisition mode was employed, and the data were analyzed by MS-DIAL. Statistical analysis, including multivariate and trend analysis for longitudinal monitoring, were employed to highlight the differentiated features among the controls and treated plants as well as the time-point sequence. Metabolites related to plant growth belonging to several chemical classes were identified, proving the efficacy of the fertilizer product. Furthermore, the efficiency of the analytical and statistical workflows utilized was demonstrated.

Plasticity of maternal environment-dependent expression-QTLs of tomato seeds

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depend on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to construct a linkage map and measure gene expression of seeds of a tomato recombinant inbred line (RIL) population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments, i.e., on high phosphorus or low nitrogen. The obtained single-nucleotide polymorphisms (SNPs) were subsequently used to construct a genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants.

Mass Spectrometry-Based Nontargeted and Targeted Analytical Approaches in Fingerprinting and Metabolomics of Food and Agricultural Research

Mass spectrometry (MS)-based techniques have been extensively applied in food and agricultural research. This review aims to address the advances and applications of MS-based analytical strategies in nontargeted and targeted analysis and summarizes the recent publications of MS-based techniques, including flow injection MS fingerprinting, chromatography-tandem MS metabolomics, direct analysis using ambient mass spectrometry, as well as development in MS data deconvolution software packages and databases for metabolomic studies. Various nontargeted and targeted approaches are employed in marker compounds identification, material adulteration detection, and the analysis of specific classes of secondary metabolites. In the newly emerged applications, the recent advances in computer tools for the fast deconvolution of MS data in targeted secondary metabolite analysis are highlighted.

Transcriptome and Metabolome Analyses Reveal Differences in Terpenoid and Flavonoid Biosynthesis in Cryptomeria fortunei Needles Across Different Seasons

Cryptomeria fortunei (Chinese cedar) has outstanding medicinal value due to its abundant flavonoid and terpenoid contents. The metabolite contents of C. fortunei needles differ across different seasons. However, the biosynthetic mechanism of these differentially synthesized metabolites (DSMs) is poorly understood. To improve our understanding of this process, we performed integrated non-targeted metabolomic liquid chromatography and gas chromatography mass spectrometry (LC-MS and GC-MS), and transcriptomic analyses of summer and winter needles. In winter, the C. fortunei needle ultrastructure was damaged, and the chlorophyll content and F _v/F _m were significantly (p < 0.05) reduced. Based on GC-MS and LC-MS, we obtained 106 and 413 DSMs, respectively; based on transcriptome analysis, we obtained a total of 41.17 Gb of clean data and assembled 33,063 unigenes, including 14,057 differentially expressed unigenes (DEGs). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these DSMs/DEGs were significantly (p < 0.05) enriched in many biosynthesis pathways, such as terpenoids, photosynthates, and flavonoids. Integrated transcriptomic and metabonomic analyses showed that seasonal changes have the greatest impact on photosynthesis pathways, followed by terpenoid and flavonoid biosynthesis pathways. In summer Chinese cedar (SCC) needles, DXS, DXR, and ispH in the 2-methyl-pentaerythritol 4-phosphate (MEP) pathway and GGPS were highly expressed and promoted the accumulation of terpenoids, especially diterpenoids. In winter Chinese cedar (WCC) needles, 9 genes (HCT, CHS, CHI, F3H, F3'H, F3'5'H, FLS, DFR, and LAR) involved in flavonoid biosynthesis were highly expressed and promoted flavonoid accumulation. This study broadens our understanding of the metabolic and transcriptomic changes in C. fortunei needles caused by seasonal changes and provides a reference regarding the adaptive mechanisms of C. fortunei and the extraction of its metabolites.

ZnO Nanoparticles Obtained by Green Synthesis as an Alternative to Improve the Germination Characteristics of L. esculentum

Tomato is an important crop due to its nutritional contributions and organoleptic properties, which make it an appetizing vegetable around the world. In its sowing, the use of seed is the most accessible propagation mechanism for farmers. However, the induction to germination and emergence is often limited in the absence of stimulants that promote the development and growth of the seedling, added to the interference of infectious agents that notoriously reduce the vitality and viability of the seed. Given this, it was proposed as a research objective to determine the effect of zinc oxide nanoparticles (ZnO NPs) mediated by a green route on the germinative characteristics of Lycopersicon esculentum Mill. 1768 "tomato". The experimental phase consisted of the synthesis of ZnO NPs and its subsequent characterization. After its synthesis, its inoculation was conducted during the germination of seeds of L. esculentum, considering six sample groups for the treatment with zinc nanoparticles (T1: Control; T2: 21.31 ppm; T3: 33.58 ppm; T4: 49.15 ppm; T5: 63.59 and T6: 99.076 ppm). The results indicate that concentrations close to 100 ppm of ZnO NPs are ideal in the treatment of L. esculentum seeds, due to the promotion of enzymatic and metabolic activity to achieve cell elongation; likewise, the biosynthesized nanoparticles showed no phytotoxicity, due to the fact that, in all the treatments, there were processes of germination and emergence. This was linked to the generation of a Zn0-phenolate complex through a chelating effect, which generates compatibility with the seed and, compared to classic inorganic synthesis, usually shows phytotoxicity. In this sense, green synthesis is presented as a great alternative in this type of application.

Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.

Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins

During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.

Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China

BACKGROUND

Cinnamomum migao is an endangered evergreen woody plant species endemic to China. Its fruit is used as a traditional medicine by the Miao nationality of China and has a high commercial value. However, its seed germination rate is extremely low under natural and artificial conditions. As the foundation of plant propagation, seed germination involves a series of physiological, cellular, and molecular changes; however, the molecular events and systematic changes occurring during C. migao seed germination remain unclear.

RESULTS

In this study, combined with the changes in physiological indexes and transcription levels, we revealed the regulation characteristics of cell structures, storage substances, and antioxidant capacity during seed germination. Electron microscopy analysis revealed that abundant smooth and full oil bodies were present in the cotyledons of the seeds. With seed germination, oil bodies and other substances gradually degraded to supply energy; this was consistent with the content of storage substances. In parallel to electron microscopy and physiological analyses, transcriptome analysis showed that 80-90 % of differentially expressed genes (DEGs) appeared after seed imbibition, reflecting important development and physiological changes. The unigenes involved in material metabolism (glycerolipid metabolism, fatty acid degradation, and starch and sucrose metabolism) and energy supply pathways (pentose phosphate pathway, glycolysis pathway, pyruvate metabolism, tricarboxylic acid cycle, and oxidative phosphorylation) were differentially expressed in the four germination stages. Among these DEGs, a small number of genes in the energy supply pathway at the initial stage of germination maintained high level of expression to maintain seed vigor and germination ability. Genes involved in lipid metabolism were firstly activated at a large scale in the LK (seed coat fissure) stage, and then genes involved in carbohydrates (CHO) metabolism were activated, which had their own species specificity.

CONCLUSIONS

Our study revealed the transcriptional levels of genes and the sequence of their corresponding metabolic pathways during seed germination. The changes in cell structure and physiological indexes also confirmed these events. Our findings provide a foundation for determining the molecular mechanisms underlying seed germination.

Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome

Plant microbiome assembly is a spatial and dynamic process driven by root exudates and influenced by soil type, plant developmental stage and genotype. Genotype-dependent microbiome assembly has been reported for different crop plant species. Despite the effect of plant genetics on microbiome assembly, the magnitude of host control over its root microbiome is relatively small or, for many plant species, still largely unknown. Here we cultivated modern and wild tomato genotypes for four successive cycles and showed that divergence in microbiome assembly between the two genotypes was significantly amplified over time. Also, we show that the composition of the rhizosphere microbiome of modern and wild plants became more dissimilar from the initial bulk soil and from each other. Co-occurrence analyses further identified amplicon sequence variants (ASVs) associated with early and late successions of the tomato rhizosphere microbiome. Among the members of the Late Successional Rhizosphere microbiome, we observed an enrichment of ASVs belonging to the genera Acidovorax, Massilia and Rhizobium in the wild tomato rhizosphere, whereas the modern tomato rhizosphere was enriched for an ASV belonging to the genus Pseudomonas. Collectively, our approach allowed us to study the dynamics of rhizosphere microbiome over successional cultivation as well as to categorize rhizobacterial taxa for their ability to form transient or long-term associations with their host plants.

Allotetraploidization in Brachypodium May Have Led to the Dominance of One Parent's Metabolome in Germinating Seeds

Seed germination is a complex process during which a mature seed resumes metabolic activity to prepare for seedling growth. In this study, we performed a comparative metabolomic analysis of the embryo and endosperm using the community standard lines of three annual Brachypodium species, i.e., B. distachyon (Bd) and B. stacei (Bs) and their natural allotetraploid B. hybridum (BdBs) that has wider ecological range than the other two species. We explored how far the metabolomic impact of allotetraploidization would be observable as over-lapping changes at 4, 12, and 24 h after imbibition (HAI) with water when germination was initiated. Metabolic changes during germination were more prominent in Brachypodium embryos than in the endosperm. The embryo and endosperm metabolomes of Bs and BdBs were similar, and those of Bd were distinctive. The Bs and BdBs embryos showed increased levels of sugars and the tricarboxylic acid cycle compared to Bd, which could have been indicative of better nutrient mobilization from the endosperm. Bs and BdBs also showed higher oxalate levels that could aid nutrient transfer through altered cellular events. In Brachypodium endosperm, the thick cell wall, in addition to starch, has been suggested to be a source of nutrients to the embryo. Metabolites indicative of sugar metabolism in the endosperm of all three species were not prominent, suggesting that mobilization mostly occurred prior to 4 HAI. Hydroxycinnamic and monolignol changes in Bs and BdBs were consistent with cell wall remodeling that arose following the release of nutrients to the respective embryos. Amino acid changes in both the embryo and endosperm were broadly consistent across the species. Taking our data together, the formation of BdBs may have maintained much of the Bs metabolome in both the embryo and endosperm during the early stages of germination. In the embryo, this conserved Bs metabolome appeared to include an elevated sugar metabolism that played a vital role in germination. If these observations are confirmed in the future with more Brachypodium accessions, it would substantiate the dominance of the Bs metabolome in BdBs allotetraploidization and the use of metabolomics to suggest important adaptive changes.

Metabolomics Intervention Towards Better Understanding of Plant Traits

The majority of the most economically important plant and crop species are enriched with the availability of high-quality reference genome sequences forming the basis of gene discovery which control the important biochemical pathways. The transcriptomics and proteomics resources have also been made available for many of these plant species that intensify the understanding at expression levels. However, still we lack integrated studies spanning genomics–transcriptomics–proteomics, connected to metabolomics, the most complicated phase in phenotype expression. Nevertheless, for the past few decades, emphasis has been more on metabolome which plays a crucial role in defining the phenotype (trait) during crop improvement. The emergence of modern high throughput metabolome analyzing platforms have accelerated the discovery of a wide variety of biochemical types of metabolites and new pathways, also helped in improving the understanding of known existing pathways. Pinpointing the causal gene(s) and elucidation of metabolic pathways are very important for development of improved lines with high precision in crop breeding. Along with other-omics sciences, metabolomics studies have helped in characterization and annotation of a new gene(s) function. Hereby, we summarize several areas in the field of crop development where metabolomics studies have made its remarkable impact. We also assess the recent research on metabolomics, together with other omics, contributing toward genetic engineering to target traits and key pathway(s).

GC-MS based metabolomic approach to understand nutraceutical potential of Cannabis seeds from two different environments

Cannabis sativa L. is a valuable plant that has regained its importance for medicinal use. Gas chromatography-mass spectrometry based untargeted metabolomic study was conducted in seeds of two accessions from different environments. A total of 236 metabolites were observed, and 43 metabolites were found differentially significant (p ≤ 0.05) in both the accessions. Based on the qualitative and quantitative accumulation of the nutraceutically important amino acids, cannabinoids, alkaloids, and fatty acids, the high altitude temperate Himalayan accession (CAN2) was found to have an advantage over the low altitude subtropical accession (CAN1). Seed oil from CAN2 showed the exclusive presence of linoleic acid and α- linolenic acid. The reducing power and DNA nicking assay on the methanolic extracts suggested higher antioxidant and nutraceutical potential in CAN2 and corroborated with the metabolic content of phenols and flavonoids. The environmental effect on the antioxidant and nutraceutical value in seeds is further discussed.

Dissection of complex traits of tomato in the post-genome era

We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.

Metabolomics: A Way Forward for Crop Improvement

Metabolomics is an emerging branch of "omics" and it involves identification and quantification of metabolites and chemical footprints of cellular regulatory processes in different biological species. The metabolome is the total metabolite pool in an organism, which can be measured to characterize genetic or environmental variations. Metabolomics plays a significant role in exploring environment-gene interactions, mutant characterization, phenotyping, identification of biomarkers, and drug discovery. Metabolomics is a promising approach to decipher various metabolic networks that are linked with biotic and abiotic stress tolerance in plants. In this context, metabolomics-assisted breeding enables efficient screening for yield and stress tolerance of crops at the metabolic level. Advanced metabolomics analytical tools, like non-destructive nuclear magnetic resonance spectroscopy (NMR), liquid chromatography mass-spectroscopy (LC-MS), gas chromatography-mass spectrometry (GC-MS), high performance liquid chromatography (HPLC), and direct flow injection (DFI) mass spectrometry, have sped up metabolic profiling. Presently, integrating metabolomics with post-genomics tools has enabled efficient dissection of genetic and phenotypic association in crop plants. This review provides insight into the state-of-the-art plant metabolomics tools for crop improvement. Here, we describe the workflow of plant metabolomics research focusing on the elucidation of biotic and abiotic stress tolerance mechanisms in plants. Furthermore, the potential of metabolomics-assisted breeding for crop improvement and its future applications in speed breeding are also discussed. Mention has also been made of possible bottlenecks and future prospects of plant metabolomics.

Metabolic signatures of germination triggered by kinetin in Medicago truncatula

In the present work, non-targeted metabolomics was used to investigate the seed response to kinetin, a phytohormone with potential roles in seed germination, still poorly explored. The aim of this study was to elucidate the metabolic signatures of germination triggered by kinetin and explore changes in metabolome to identify novel vigor/stress hallmarks in Medicago truncatula. Exposure to 0.5 mM kinetin accelerated seed germination but impaired seedling growth. Metabolite composition was investigated in seeds imbibed with water or with 0.5 mM kinetin collected at 2 h and 8 h of imbibition, and at the radicle protrusion stage. According to Principal Component Analysis, inositol pentakisphosphate, agmatine, digalactosylglycerol, inositol hexakisphosphate, and oleoylcholine were the metabolites that mostly contributed to the separation between 2 h, 8 h and radicle protrusion stage, irrespective of the treatment applied. Overall, only 27 metabolites showed significant changes in mean relative contents triggered by kinetin, exclusively at the radicle protrusion stage. The observed metabolite depletion might associate with faster germination or regarded as a stress signature. Results from alkaline comet assay, highlighting the occurrence of DNA damage at this stage of germination, are consistent with the hypothesis that prolonged exposure to kinetin induces stress conditions leading to genotoxic injury.

A Snapshot of the Trehalose Pathway During Seed Imbibition in Medicago truncatula Reveals Temporal- and Stress-Dependent Shifts in Gene Expression Patterns Associated With Metabolite Changes

Trehalose, a non-reducing disaccharide with multiple functions, among which source of energy and carbon, stress protectant, and signaling molecule, has been mainly studied in relation to plant development and response to stress. The trehalose pathway is conserved among different organisms and is composed of three enzymes: trehalose-6-phosphate synthase (TPS), which converts uridine diphosphate (UDP)-glucose and glucose-6-phosphate to trehalose-6-phosphate (T6P), trehalose-6-phosphatase (TPP), which dephosphorylates T6P to produce trehalose, and trehalase (TRE), responsible for trehalose catabolism. In plants, the trehalose pathway has been mostly studied in resurrection plants and the model plant Arabidopsis thaliana, where 11 AtTPS, 10 AtTPP, and 1 AtTRE genes are present. Here, we aim to investigate the involvement of the trehalose pathway in the early stages of seed germination (specifically, seed imbibition) using the model legume Medicago truncatula as a working system. Since not all the genes belonging to the trehalose pathway had been identified in M. truncatula, we first conducted an in silico analysis using the orthologous gene sequences from A. thaliana. Nine MtTPSs, eight MtTPPs, and a single MtTRE gene were hereby identified. Subsequently, the expression profiles of all the genes (together with the sucrose master-regulator SnRK1) were investigated during seed imbibition with water or stress agents (polyethylene glycol and sodium chloride). The reported data show a temporal distribution and preferential expression of specific TPS and TPP isoforms during seed imbibition with water. Moreover, it was possible to distinguish a small set of genes (e.g., MtTPS1, MtTPS7, MtTPS10, MtTPPA, MtTPPI, MtTRE) having a potential impact as precocious hallmarks of the seed response to stress. When the trehalose levels were measured by high-performance liquid chromatography, a significant decrease was observed during seed imbibition, suggesting that trehalose may act as an energy source rather than osmoprotectant. This is the first report investigating the expression profiles of genes belonging to the trehalose pathway during seed imbibition, thus ascertaining their involvement in the pre-germinative metabolism and their potential as tools to improve seed germination efficiency.

Redox poise and metabolite changes in bread wheat seeds are advanced by priming with hot steam

Fast and uniform germination is key to agricultural production and can be achieved by seed 'priming' techniques. Here, we characterised the responses of bread wheat (Triticum aestivum L.) seeds to a hot steam treatment ('BioFlash'), which accelerated water uptake, resulting in faster germination and seedling growth, typical traits of primed seed. Before the completion of germination, metabolite profiling of seeds revealed advanced accumulation of several amino acids (especially cysteine and serine), sugars (ribose, glucose), and organic acids (glycerate, succinate) in hot steam-treated seeds, whereas sugar alcohols (e.g. arabitol, mannitol) and trehalose decreased in all seeds. Tocochromanols (the 'vitamin E family') rose independently of the hot steam treatment. We further assessed shifts in the half-cell reduction potentials of low-molecular-weight (LMW) thiol-disulfide redox couples [i.e. glutathione disulfide (GSSG)/glutathione (GSH) and cystine/cysteine], alongside the activities of the reactive oxygen species (ROS)-processing enzyme superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase. Upon the first 4 h of imbibition, a rapid conversion of LMW disulfides to thiols occurred. Completion of germination was associated with a re-oxidation of the LMW thiol-disulfide cellular redox environment, before more reducing conditions were re-established during seedling growth, accompanied by an increase in all ROS-processing enzyme activities. Furthermore, changes in the thiol-disulfide cellular redox state were associated to specific stages of wheat seed germination. In conclusion, the priming effect of the hot steam treatment advanced the onset of seed metabolism, including redox shifts associated with germination and seedling growth.

Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security

Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.

Salt stress inhibits germination of Stylosanthes humilis seeds through abscisic acid accumulation and associated changes in ethylene production

In Stylosanthes humilis, salt stress tolerance is associated with ethylene production by the seeds, however, how salt stress controls seed germination and ethylene production is poorly understood. Here, we studied the hormonal and metabolic changes triggered by salt stress on germination of S. humilis seeds. Salt stress led to decreased seed germination and ethylene production, concomitantly with higher abscisic acid (ABA) production by seeds. Treatment with NaCl and ABA promoted distinct changes in energy metabolism, allowing seeds to adapt to salt stress conditions. Treatment with the ABA biosynthesis inhibitor fluridone or ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) reversed the effects of salt stress on seed germination and ethylene production. Moreover, ethylene concentration was decreased by increasing the pH of the salt solution. High pH, however, did not influence concentration of ABA in seeds under salt stress. We conclude that biosynthesis of ABA and ethylene in response to salt stress constitutes a point of convergence that provides flexibility to regulate energy metabolism and embryo growth potential of S. humilis seeds within a given pH condition.