The role of photosynthesis and amino acid metabolism in the energy status during seed development

Transcriptomics and starch biosynthesis analysis in leaves and developing seeds of mung bean provide a basis for genetic engineering of starch composition and seed quality

Mung bean starch is distinguished by its exceptional high amylose content and regulation of starch biosynthesis in leaves and storage tissues, such as seeds, share considerable similarities. Genetic engineering of starch composition and content, requires detailed knowledge of starch biosynthetic gene expression and enzymatic regulation. In this study we applied detailed transcriptomic analyses to unravel the global differential gene expression patterns in mung bean leaves and in seeds during various stages of development. The objective was to identify candidate genes and regulatory mechanisms that may enable generation of desirable seed qualities through the use of genetic engineering. Notable differences in gene expression, in particular low expression of the Protein Targeting to Starch (PTST), starch synthase (SS) 3, and starch branching enzyme1 (SBE1) encoding genes in developing seeds as compared to leaves were evident. These differences were related to starch molecular structures and granule morphologies. Specifically, the starch molecular size distribution at different stages of seed development correlated with the starch biosynthesis gene expression of the SBE1, SS1, granule-bound starch synthases (GBSS) and isoamylase 1 (ISA1) encoding genes. Furthermore, putative hormonal and redox controlled regulation were observed, which may be explained by abscisic acid (ABA) and indole-3-acetic acid (IAA) induced signal transduction, and redox regulation of ferredoxins and thioredoxins, respectively. The morphology of starch granules in leaves and developing seeds were clearly distinguishable and could be correlated to differential expression of SS1. Here, we present a first comprehensive transcriptomic dataset of developing mung bean seeds, and combined these findings may enable generation of genetic engineering strategies of for example starch biosynthetic genes for increasing starch levels in seeds and constitute a valuable toolkit for improving mung bean seed quality.

A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways

D-2-hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D-2HG to 2-oxoglutarate (2-OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome-wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT-PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early-maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed-maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus-induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early- and delayed-maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two-hybrid, luciferase complementation (LUC), and GST pull-down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.

GWAS Combined with WGCNA of Transcriptome and Metabolome to Excavate Key Candidate Genes for Rice Anaerobic Germination

Direct seeding of rice is a lightweight and simple cultivation method, which can effectively promote rice production. Anaerobic germination tolerance is one of the main traits of rice adaptability to direct seeding. The mining of related genetic loci, analysis of anaerobic traits and screening of tolerance genes provided valuable genetic resources for improving the anaerobic germination ability of direct seeding rice. This study conducted a dynamic genome-wide association study (GWAS) based on coleoptile-related traits of 591 rice natural populations, and a total of 317 SNP sites were detected. Integrated dynamic widely targeted metabolomics analysis, we found that xanthine, L-alanine and GABA may be key biomarkers that are sensitive and respond strongly to hypoxic stress perception. By WGCNA analysis of targeted metabolomics and transcriptomics, a total of 3 modules were obtained that were significantly correlated with the above three marker metabolites, namely dark green, dark gray and light green modules, respectively, and several key structural genes of OsAlaAT1, OsGAD4, OsAAH and Os09g0424600 that may affect hypoxic germination were screened from the 3 modules. Among them, OsAlaAT1 (Os10g0390500), located in Chr10-12877840, which is within the GWAS location range of CVAN3d, is considered to be a more reliable candidate gene. Overall, in addition to providing new insight into the metabolic regulation of L-alanine, GABA and xanthine during hypoxic germination of rice. This study also provided a reference for the basic theoretical research and breeding application research on the related traits of anaerobic germination in direct-seeding rice.

Mapping the castor bean endosperm proteome revealed a metabolic interaction between plastid, mitochondria, and peroxisomes to optimize seedling growth

In this work, we studied castor-oil plant Ricinus communis as a classical system for endosperm reserve breakdown. The seeds of castor beans consist of a centrally located embryo with the two thin cotyledons surrounded by the endosperm. The endosperm functions as major storage tissue and is packed with nutritional reserves, such as oil, proteins, and starch. Upon germination, mobilization of the storage reserves requires inter-organellar interplay of plastids, mitochondria, and peroxisomes to optimize growth for the developing seedling. To understand their metabolic interactions, we performed a large-scale organellar proteomic study on castor bean endosperm. Organelles from endosperm of etiolated seedlings were isolated and subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS). Computer-assisted deconvolution algorithms were applied to reliably assign the identified proteins to their correct subcellular localization and to determine the abundance of the different organelles in the heterogeneous protein samples. The data obtained were used to build a comprehensive metabolic model for plastids, mitochondria, and peroxisomes during storage reserve mobilization in castor bean endosperm.

Multi-omics analysis provides insights intro lysine accumulation in quinoa (Chenopodium quinoa Willd.) sprouts

Lysine, the first limiting essential amino acid, the deficiency of which seriously affects the health of human and animals. In this study, quinoa germination significantly increased the nutrients, especially lysine content. To better understanding the underlying molecular mechanism of lysine biosynthesis, isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics, RNA-sequencing (RNA-Seq) technology and liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) platform-based phytohormones analyses were conducted. Through proteome analyses, a total of 11,406 differentially expressed proteins were identified, which were mainly related to secondary metabolites. The lysine-rich storage globulins and endogenous phytohormones probably contributed the increased lysine content in quinoa during germination. Furthermore, aspartic acid semialdehyde dehydrogenase is essential for lysine synthesis in addition to aspartate kinase and dihydropyridine dicarboxylic acid synthase. Protein-protein interaction analysis indicated lysine biosynthesis is associated with "amino metabolism" and "starch and sucrose metabolism". Above all, our study screens the candidate genes participated in lysine accumulation and explores the factors affected lysine biosynthesis by multi-omics analysis. These information not only paves a foundation for breeding lysine-rich quinoa sprouts but also provides valuable multi-omics resource to explore the characteristic of nutrients during quinoa germination.

WEAK SEED DORMANCY 1, an aminotransferase protein, regulates seed dormancy in rice through the GA and ABA pathways

Seed dormancy is a critical trait that enhances plant survival by preventing seed germination at the wrong time or under unsuitable conditions. Lack of seed dormancy in rice can lead to pre-harvest sprouting on mother plants leading to reduced yield and seed quality. Although some genes have been identified, knowledge of regulation of seed dormancy is limited. Here, we characterized a weak seed dormancy mutant named weak seed dormancy 1 (wsd1) that showed a higher seed germination percentage than the wild-type following the harvest ripeness. We cloned the WSD1 encoding an aminotransferase protein using a MutMap approach. WSD1 was stably expressed after imbibition and its protein was localized in the endoplasm reticulum. A widely targeted metabolomics assay and amino acid analysis showed that WSD1 had a role in regulating homeostasis of amino acids. PAC treatment and RNA-seq analysis showed that WSD1 regulates seed dormancy by involvement in the GA biosynthesis pathway. GA1 content and expression of GA biosynthesis-related genes were increased in the wsd1 mutant compared with the wild-type. The wsd1 mutant had reduced sensitivity to ABA. Our overall results indicated that WSD1 regulates seed dormancy by balancing the ABA and GA pathways.

The Role of TCA Cycle Enzymes in Plants

As one of the iconic pathways in plant metabolism, the tricarboxylic acid (TCA) cycle is commonly thought to not only be responsible for the oxidization of respiratory substrate to drive ATP synthesis but also provide carbon skeletons to anabolic processes and contribute to carbon-nitrogen interaction and biotic stress responses. The functions of the TCA cycle enzymes are characterized by a saturation transgenesis approach, whereby the constituent expression of proteins is knocked out or reduced in order to investigate their function in vivo. The alteration of TCA cycle enzyme expression results in changed plant growth and photosynthesis under controlled conditions. Moreover, improvements in plant performance and postharvest properties are reported by overexpression of either endogenous forms or heterologous genes of a number of the enzymes. Given the importance of the TCA cycle in plant metabolism regulation, here, the function of each enzyme and its roles in different tissues are discussed. This article additionally highlights the recent finding that the plant TCA cycle, like that of mammals and microbes, dynamically assembles functional substrate channels or metabolons and discusses the implications of this finding to the current understanding of the metabolic regulation of the plant TCA cycle.

Comparative transcriptomics reveals the role of altered energy metabolism in the establishment of single-cell C4 photosynthesis in Bienertia sinuspersici

Single-cell C₄ photosynthesis (SCC₄) in terrestrial plants without Kranz anatomy involves three steps: initial CO₂ fixation in the cytosol, CO₂ release in mitochondria, and a second CO₂ fixation in central chloroplasts. Here, we investigated how the large number of mechanisms underlying these processes, which occur in three different compartments, are orchestrated in a coordinated manner to establish the C₄ pathway in Bienertia sinuspersici, a SCC₄ plant. Leaves were subjected to transcriptome analysis at three different developmental stages. Functional enrichment analysis revealed that SCC₄ cycle genes are coexpressed with genes regulating cyclic electron flow and amino/organic acid metabolism, two key processes required for the production of energy molecules in C₃ plants. Comparative gene expression profiling of B. sinuspersici and three other species (Suaeda aralocaspica, Amaranthus hypochondriacus, and Arabidopsis thaliana) showed that the direction of metabolic flux was determined via an alteration in energy supply in peripheral chloroplasts and mitochondria via regulation of gene expression in the direction of the C₄ cycle. Based on these results, we propose that the redox homeostasis of energy molecules via energy metabolism regulation is key to the establishment of the SCC₄ pathway in B. sinuspersici.

Fruit Photosynthesis: More to Know about Where, How and Why

Not only leaves but also other plant organs and structures typically considered as carbon sinks, including stems, roots, flowers, fruits and seeds, may exhibit photosynthetic activity. There is still a lack of a coherent and systematized body of knowledge and consensus on the role(s) of photosynthesis in these "sink" organs. With regard to fruits, their actual photosynthetic activity is influenced by a range of properties, including fruit anatomy, histology, physiology, development and the surrounding microclimate. At early stages of development fruits generally contain high levels of chlorophylls, a high density of functional stomata and thin cuticles. While some plant species retain functional chloroplasts in their fruits upon subsequent development or ripening, most species undergo a disintegration of the fruit chloroplast grana and reduction in stomata functionality, thus limiting gas exchange. In addition, the increase in fruit volume hinders light penetration and access to CO₂, also reducing photosynthetic activity. This review aimed to compile information on aspects related to fruit photosynthesis, from fruit characteristics to ecological drivers, and to address the following challenging biological questions: why does a fruit show photosynthetic activity and what could be its functions? Overall, there is a body of evidence to support the hypothesis that photosynthesis in fruits is key to locally providing: ATP and NADPH, which are both fundamental for several demanding biosynthetic pathways (e.g., synthesis of fatty acids); O₂, to prevent hypoxia in its inner tissues including seeds; and carbon skeletons, which can fuel the biosynthesis of primary and secondary metabolites important for the growth of fruits and for spreading, survival and germination of their seed (e.g., sugars, flavonoids, tannins, lipids). At the same time, both primary and secondary metabolites present in fruits and seeds are key to human life, for instance as sources for nutrition, bioactives, oils and other economically important compounds or components. Understanding the functions of photosynthesis in fruits is pivotal to crop management, providing a rationale for manipulating microenvironmental conditions and the expression of key photosynthetic genes, which may help growers or breeders to optimize development, composition, yield or other economically important fruit quality aspects.

Elucidating the importance of the catabolic enzyme, methionine-gamma-lyase, in stresses during Arabidopsis seed development and germination

The sulfur-containing essential amino acid, methionine, is a key metabolite in plant cells since it is used as a precursor for the synthesis of vital metabolites. The transcript level of methionine's catabolic enzyme, methionine γ-lyase (MGL), accumulates in the seeds to a high level compared to other organs. The aim of this study was to reveal the role of MGL during seed development and germination. Using [¹³C]S-methylmethionine (SMM), the mobile form of methionine that is used to feed flower stalks of wild-type (WT) plants, revealed that the contents of [¹³C]methionine in seeds were significantly reduced when the plants underwent heat and osmotic stresses. Moreover, the levels of [¹³C]isoleucine, a product of MGL, significantly increased. Also, using the MGL promoter and gene fused to the GUS reporter gene, it was demonstrated that the heat stress significantly increased the protein level in the seeds. Therefore, we can conclude that MGL became active under stresses apparently to produce isoleucine, which is used as an osmoprotectant and an energy source. Transgenic Arabidopsis thaliana RNAi seeds with targeted repression of AtMGL during the late developmental stages of seeds show that the seeds did not accumulate methionine when they were grown under standard growth conditions, unlike the mgl-2, a knockout mutant, which showed a three-fold higher level of methionine. Also, when the RNAi plants developed under mid-heat stress, the level of methionine significantly increased while the content of isoleucine decreased compared to the control seeds, which strengthened the assumption that MGL is active under stress. The germination efficiency of the RNAi lines and mgl seeds were similar to their controls. However, the seeds that developed during heat or salt stress showed significantly lower germination efficiency compared to the control seeds. This implies that MGL is important to maintain the ability of the seeds to germinate. The RNAi lines and mgl seeds that developed under regular conditions, but germinated during salt or osmotic stress, exhibited a lower germination rate, suggesting an essential role of MGL also during this process. The results of this study show the important role of AtMGL in seeds under stresses.

Insights into the regulation of energy metabolism during the seed-to-seedling transition in marine angiosperm Zostera marina L.: Integrated metabolomic and transcriptomic analysis

Seed development is a crucial phase in the life cycle of seed-propagated plants. As the only group of angiosperms that evolved from terrestrial plants to complete their life cycle submerged in marine environments, the mechanisms underlying seed development in seagrasses are still largely unknown. In the present study, we attempted to combine transcriptomic, metabolomic, and physiological data to comprehensively analyze the molecular mechanism that regulates energy metabolism in Zostera marina seeds at the four major developmental stages. Our results demonstrated that seed metabolism was reprogrammed with significant alteration of starch and sucrose metabolism, glycolysis, the tricarboxylic acid cycle (TCA cycle), and the pentose phosphate pathway during the transition from seed formation to seedling establishment. The interconversion of starch and sugar provided energy storage substances in mature seeds and further acted as energy sources to support seed germination and seedling growth. The glycolysis pathway was active during Z. marina germination and seedling establishment, which provided pyruvate for TCA cycle by decomposing soluble sugar. Notably, the biological processes of glycolysis were severely inhibited during Z. marina seed maturation may have a positive effect on seed germination, maintaining a low level of metabolic activity during seed maturation to preserve seed viability. Increased acetyl-CoA and ATP contents were accompanied with the higher TCA cycle activity during seed germination and seedling establishment, indicating that the accumulations of precursor and intermediates metabolite that can strengthen the TCA cycle and facilitate energy supply for Z. marina seed germination and seedling growth. The large amount of oxidatively generated sugar phosphate promotes fructose 1,6-bisphosphate synthesis to feed back to glycolysis during seed germination, indicating that the pentose phosphate pathway not only provides energy for germination, but also complements the glycolytic pathway. Collectively, our findings suggest these energy metabolism pathways cooperate with each other in the process of seed transformation from maturity to seedling establishment, transforming seed from storage tissue to highly active metabolic tissue to meet the energy requirement seed development. These findings provide insights into the roles of the energy metabolism pathway in the complete developmental process of Z. marina seeds from different perspectives, which could facilitate habitat restoration of Z. marina meadows via seeds.

Turning Food Protein Waste into Sustainable Technologies

For each kilogram of food protein wasted, between 15 and 750 kg of CO₂ end up in the atmosphere. With this alarming carbon footprint, food protein waste not only contributes to climate change but also significantly impacts other environmental boundaries, such as nitrogen and phosphorus cycles, global freshwater use, change in land composition, chemical pollution, and biodiversity loss. This contrasts sharply with both the high nutritional value of proteins, as well as their unique chemical and physical versatility, which enable their use in new materials and innovative technologies. In this review, we discuss how food protein waste can be efficiently valorized not only by reintroduction into the food chain supply but also as a template for the development of sustainable technologies by allowing it to exit the food-value chain, thus alleviating some of the most urgent global challenges. We showcase three technologies of immediate significance and environmental impact: biodegradable plastics, water purification, and renewable energy. We discuss, by carefully reviewing the current state of the art, how proteins extracted from food waste can be valorized into key players to facilitate these technologies. We furthermore support analysis of the extant literature by original life cycle assessment (LCA) examples run ad hoc on both plant and animal waste proteins in the context of the technologies considered, and against realistic benchmarks, to quantitatively demonstrate their efficacy and potential. We finally conclude the review with an outlook on how such a comprehensive management of food protein waste is anticipated to transform its carbon footprint from positive to negative and, more generally, have a favorable impact on several other important planetary boundaries.

Integrated metabolic and transcriptomic profiles reveal the germination-associated dynamic changes for the seeds of Cassia obtusifolia L

INTRODUCTION

The seeds of Cassia obtusifolia L. (Cassiae [C.] semen) have been widely used as both food and traditional Chinese medicine in China.

OBJECTIVES

We aimed to analyze the metabolic mechanisms underlying C. semen germination.

MATERIALS AND METHODS

Different samples of C. semen at various germination stages were collected. These samples were subjected to ¹ H-NMR and UHPLC/Q-Orbitrap-MS-based untargeted metabolomics analysis together with transcriptomics analysis.

RESULTS

A total of 50 differential metabolites (mainly amino acids and sugars) and 20 key genes involved in multiple pathways were identified in two comparisons of different groups (36 h vs 12 h and 84 h vs 36 h). The metabolite-gene network for seed germination was depicted. In the germination of C. semen, fructose and mannose metabolism was activated in the testa rupture period, indicating more energy was needed (36 h). In the embryonic axis elongation period (84 h), the pentose and glucuronate interconversions pathway and the phenylpropanoid biosynthesis pathway were activated, which suggested some nutrient sources (nitrogen and sugar) were in demand. Furthermore, oxygen, energy, and nutrition should be supplied throughout the whole germination process. These global views open up an integrated perspective for understanding the complex biological regulatory mechanisms during the germination process of C. semen.

Stage-specific metabolomics suggests a trade-off between primary and secondary metabolites for nutritional advantage in Lepidium latifolium L

Lepidium latifolium L. is an established phytofood of the Ladakh Himalayas that contains differential content of important glucosinolates (GLS) in specific stages of sprouts. Therefore, in order to harness its nutraceutical potential, a comprehensive mass spectrometry-based stage-specific untargeted metabolomic analysis was performed. A total of 318 metabolites were detected, out of which 229 were significantly (p ≤ 0.05) changed during different stages. The Principal Component Analysis plot clearly differentiated different growth stages into three clusters. The nutritionally important metabolites, including amino acids, sugars, organic acids, and fatty acids, were found significantly (p ≤ 0.05) higher in the first cluster consisting of 1st, 2nd and 3rd week sprouts. The higher energy requirements during the early growth stages were observed with the higher metabolites of glycolysis and the TCA cycle. Further, the trade-off between primary and secondary sulfur-containing metabolites was observed, which may explain the differential GLS content in different growth stages.

Transcriptome and metabolome analyses reveal novel insights into the seed germination of Michelia chapensis, an endangered species in China

Michelia chapensis Dandy, a well-known medicinal woody plant endemic to China, is endangered and seriously constricted by seed dormancy-induced low-regeneration in natural conditions. Cold stratification can effectively reduce seed dormancy and promote the seed germination of M. chapensis. However, the molecular events and systematic changes that occurred during seed germination in M. chapensis remain largely unknown. In this study, we carried out transcriptomic and metabolomic analyses to elucidate the potential molecular mechanisms underlying seed germination in M. chapensis under cold stratification. The results showed that the embryo cells became bigger and looser with increasing stratification time. Moreover, the endosperm appeared reduced due to the consumption of nutrients. Seventeen phytohormones were examined by the metabolome targeted for hormones. Compared with the ES (no stratification), the levels of indole-3-acetic acid (IAA) and gibberellin A₃ (GA₃) were increased in the MS (stratification for 45 days), while the abscisic acid (ABA) was downregulated in both MS and LS (stratification for 90 days). The transcriptome profiling identified 24975 differentially expressed genes (DEGs) in the seeds during germination. The seed germination of M. chapensis was mainly regulated by the biological pathways of plant hormone signal transduction, energy supply, secondary metabolite biosynthesis, photosynthesis-related metabolism, and transcriptional regulation. This study reveals the biological evidence of seed germination at the transcriptional level and provides a foundation for unraveling molecular mechanisms regulating the seed germination of M. chapensis.

Progress in understanding and improving oil content and quality in seeds

The world's population is projected to increase by two billion by 2050, resulting in food and energy insecurity. Oilseed crops have been identified as key to address these challenges: they produce and store lipids in the seeds as triacylglycerols that can serve as a source of food/feed, renewable fuels, and other industrially-relevant chemicals. Therefore, improving seed oil content and composition has generated immense interest. Research efforts aiming to unravel the regulatory pathways involved in fatty acid synthesis and to identify targets for metabolic engineering have made tremendous progress. This review provides a summary of the current knowledge of oil metabolism and discusses how photochemical activity and unconventional pathways can contribute to high carbon conversion efficiency in seeds. It also highlights the importance of ¹³C-metabolic flux analysis as a tool to gain insights on the pathways that regulate oil biosynthesis in seeds. Finally, a list of key genes and regulators that have been recently targeted to enhance seed oil production are reviewed and additional possible targets in the metabolic pathways are proposed to achieve desirable oil content and quality.

Designing synthetic consortia of Trichoderma strains that improve antagonistic activities against pathogens and cucumber seedling growth

Background

Trichoderma spp. are important agricultural biocontrol microorganisms that are often used as effective components of microbial fungicides and microbial biofertilizers. However, most of these products are prepared by a single strain in monoculture, which significantly limits the biocontrol efficiency and stability of Trichoderma products. Therefore, the establishment of a design and screening approach for consortia with multi-Trichoderma strains for co-culture is of great importance to overcome the shortage of traditional Trichoderma biocontrol products.

Results

First, 15 Trichoderma strains were screened in terms of mycelium growth rate, antagonistic activity to a variety of pathogens, stress tolerance to high temperature and salt stress, and cucumber seedling growth promotion level. Then, the combinations of Trichoderma asperellum GDSF1009 (CGMCC NO. 9512), Trichoderma asperelloides Z4-1 (CGMCC NO. 40245), Trichoderma harzianum 10569 (CGMCC NO. 40246), and T. asperellum 10264 (CGMCC NO. 22404) were finally screened as an optimal consortium for co-culture underlying the levels of plant growth-promoting and antagonistic activity to Fusarium oxysporum and seed germination promotion relative to the monoculture of a single strain. Consortia with multiple co-cultured strains were found to generate larger amounts of free amino acids than those from the monoculture of a single strain, and a pot assay also indicated that metabolites of co-cultures were able to promote cucumber seedling growth superior to that with monoculture of a single strain, even though the promotion was better than from simply mixed cultures from each of the four Trichoderma strains. Taken together, the co-culture consortia composed of the four compatible interactive Trichoderma strains was a potential novel multiple strain biocontrol agent based on the combination of synthetic consortia design and co-culture. In the field experiment, we found that the growth-promoting effect of the co-culture fermentation filtrate was better than that of the single culture fermentation filtrate. Compared with T-Z4-1, T-1009, T-10264 and T-10569, the plant height of cucumber was increased by 22.99%, 42.06%, 24.18% and 30.09%, respectively, and the stem diameter was increased by 16.59%, 18.83%, 13.65% and 14.70%, respectively.

Conclusion

An approach to designing and screening Trichoderma consortia for co-culture was established. The consortia co-culture presented a better performance in antagonistic activity and cucumber growth compared with a monoculture of a single strain. Thus, it is of great significance to lay the foundation for the creation of a novel Trichoderma biofungicide or biomanure to resist cucumber Fusarium wilt and promote cucumber growth.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-022-01959-2.

Genome-wide association studies of five free amino acid levels in rice

Rice (Oryza sativa L.) is one of the important staple foods for human consumption and livestock use. As a complex quality trait, free amino acid (FAA) content in rice is of nutritional importance. To dissect the genetic mechanism of FAA level, five amino acids' (Val, Leu, Ile, Arg, and Trp) content and 4,325,832 high-quality SNPs of 448 rice accessions were used to conduct genome-wide association studies (GWAS) with nine different methods. Of these methods, one single-locus method (GEMMA), seven multi-locus methods (mrMLM, pLARmEB, FASTmrEMMA, pKWmEB, FASTmrMLM, ISIS EM-BLASSO, and FarmCPU), and the recent released 3VmrMLM were adopted for methodological comparison of quantitative trait nucleotide (QTN) detection and identification of stable quantitative trait nucleotide loci (QTLs). As a result, 987 QTNs were identified by eight multi-locus GWAS methods; FASTmrEMMA detected the most QTNs (245), followed by 3VmrMLM (160), and GEMMA detected the least QTNs (0). Among 88 stable QTLs identified by the above methods, 3VmrMLM has some advantages, such as the most common QTNs, the highest LOD score, and the highest proportion of all detected stable QTLs. Around these stable QTLs, candidate genes were found in the GO classification to be involved in the primary metabolic process, biosynthetic process, and catalytic activity, and shown in KEGG analysis to have participated in metabolic pathways, biosynthesis of amino acids, and tryptophan metabolism. Natural variations of candidate genes resulting in the content alteration of five FAAs were identified in this association panel. In addition, 95 QTN-by-environment interactions (QEIs) of five FAA levels were detected by 3VmrMLM only. GO classification showed that the candidate genes got involved in the primary metabolic process, transport, and catalytic activity. Candidate genes of QEIs played important roles in valine, leucine, and isoleucine degradation (QEI_09_03978551 and candidate gene LOC_Os09g07830 in the Leu dataset), tryptophan metabolism (QEI_01_00617184 and candidate gene LOC_Os01g02020 in the Trp dataset), and glutathione metabolism (QEI_12_09153839 and candidate gene LOC_Os12g16200 in the Arg dataset) pathways through KEGG analysis. As an alternative of the multi-locus GWAS method, these findings suggested that the application of 3VmrMLM may provide new insights into better understanding FAA accumulation and facilitate the molecular breeding of rice with high FAA level.

Integrated metabolomic and transcriptomic analyses of two peanut (Arachis hypogaea L.) cultivars differing in amino acid metabolism of the seeds

Peanut is an important economic crop worldwide. The content of amino acids, especially essential amino acids, is an important nutritional quality trait of peanut seeds. However, the regulation of amino acid metabolism in peanut seeds is poorly understood. Here, two peanut cultivars, Zhonghuahei 1 and Zhongkaihua 151, with high and low free amino acids in mature seeds, respectively, were selected to investigate the regulatory mechanisms of amino acids during seed development. Zhonghuahei 1 is composed of significantly higher arginine (Arg), asparagine (Asn), and glutamate (Glu) contents than Zhongkaihua 151. However, the metabolomic analyses indicated that the contents of most amino acids were significantly lower in Zhonghuahei 1 at the early developmental stage, while they were reverse at the middle and late stages. Transcriptomic analyses also revealed that the differentially expressed genes between the two cultivars during different stages were enriched in multiple pathways associated with amino acid metabolism. Among them, the Arg biosynthesis pathway showed different regulatory profiles between the two cultivars according to the temporal analysis of gene expression patterns. Subsequent gene co-expression network analysis showed that the gene module darkorange was significantly correlated with Arg content, with an enriched Arg biosynthesis pathway. Accordingly, a gene regulatory network for Arg biosynthesis and metabolism, including key genes (ALDH, ASS1, OTC, and GAD) and transcription factors (GATA, HEX, and ATF), was constructed. These findings provide insights into the regulatory network of amino acid metabolism in peanuts and provide candidate genes that can be applied to facilitate peanut breeding with desirable seeds.

Sdr4 dominates pre-harvest sprouting and facilitates adaptation to local climatic condition in Asian cultivated rice

Pre-harvest sprouting (PHS), which reduces grain yield and quality, is controlled by seed dormancy genes. Because few dormancy-related genes have been cloned, the genetic basis of seed dormancy in rice (Oryza sativa L.) remains unclear. Here, we performed a genome-wide association study and linkage mapping to dissect the genetic basis of seed dormancy in rice. Our findings suggest that Seed Dormancy4 (Sdr4), a central modulator of seed dormancy, integrates the abscisic acid and gibberellic acid signaling pathways at the transcriptional level. Haplotype analysis revealed that three Sdr4 alleles in rice cultivars already existed in ancestral Oryza rufipogon accessions. Furthermore, like the semi-dwarf 1 (SD1) and Rc loci, Sdr4 underwent selection during the domestication and improvement of Asian cultivated rice. The distribution frequency of the Sdr4-n allele in different locations in Asia is negatively associated with local annual temperature and precipitation. Finally, we developed functional molecular markers for Sdr4, SD1, and Rc for use in molecular breeding. Our results provide clues about the molecular basis of Sdr4-regulated seed dormancy. Moreover, these findings provide guidance for utilizing the favorable alleles of Sdr4 and Rc to synergistically boost PHS resistance, yield, and quality in modern rice varieties.

Transcriptomic and metabolomic landscape of quinoa during seed germination

BACKGROUND

Quinoa (Chenopodium quinoa), a dicotyledonous species native to Andean region, is an emerging crop worldwide nowadays due to its high nutritional value and resistance to extreme abiotic stresses. Although it is well known that seed germination is an important and multiple physiological process, the network regulation of quinoa seed germination is largely unknown.

RESULTS

Here, we performed transcriptomic study in five stages during transition from quinoa dry seed to seedling. Together with the GC-MS based metabolome analysis, we found that seed metabolism is reprogrammed with significant alteration of multiple phytohormones (especially abscisic acid) and other nutrients during the elongation of radicels. Cell-wall remodeling is another main active process happening in the early period of quinoa seed germination. Photosynthesis was fully activated at the final stage, promoting the biosynthesis of amino acids and protein to allow seedling growth. The multi-omics analysis revealed global changes in metabolic pathways and phenotype during quinoa seed germination.

CONCLUSION

The transcriptomic and metabolomic landscape depicted here pave ways for further gene function elucidation and quinoa development in the future.

Effect of ACGT motif in spatiotemporal regulation of AtAVT6D, which improves tolerance to osmotic stress and nitrogen-starvation

Plasma membrane-localized AtAVT6D importing aspartic acid can be targeted to develop plants with enhanced osmotic and nitrogen-starvation tolerance. AtAVT6D promoter can be exploited as a stress-inducible promoter for genetic improvements to raise stress-resilient crops. The AtAVT6 family of amino acid transporters in Arabidopsis thaliana has been predicted to export amino acids like aspartate and glutamate. However, the functional characterization of these amino acid transporters in plants remains unexplored. The present study investigates the expression patterns of AtAVT6 genes in different tissues and under various abiotic stress conditions using quantitative Real-time PCR. The expression analysis demonstrated that the member AtAVT6D was significantly induced in response to phytohormone ABA and stresses like osmotic and drought. The tissue-specific expression analysis showed that AtAVT6D was strongly expressed in the siliques. Taking together these results, we can speculate that AtAVT6D might play a vital role in silique development and abiotic stress tolerance. Further, subcellular localization study showed AtAVT6D was localized to the plasma membrane. The heterologous expression of AtAVT6D in yeast cells conferred significant tolerance to nitrogen-deficient and osmotic stress conditions. The Xenopus oocyte studies revealed that AtAVT6D is involved in the uptake of Aspartic acid. While overexpression of AtAVT6D resulted in smaller siliques in Arabidopsis thaliana. Additionally, transient expression studies were performed with the full-length AtAVT6D promoter and its deletion constructs to study the effect of ACGT-N₂₄-ACGT motifs on the reporter gene expression in response to abiotic stresses and ABA treatment. The fluorometric GUS analyses revealed that the promoter deletion construct-2 (Pro.C2) possessing a single copy of ACGT-N₂₄-ACGT motif directed the strongest GUS expression under all the abiotic conditions tested. These results suggest that Pro.C2 can be used as a stress-inducible promoter to drive a significant transgene expression.

The Role of Photo-Cycles in the Modulation of Growth and Biochemical Profile of Microalgae: Part I—Food Interest Compounds

The objective of this work was to evaluate the effect of different photo-cycles on the growth and biochemical profile of Scenedesmus obliquus CPCC05, focusing on food interest compounds. The photo-cycle conditions were separated into three groups: long-term photo-cycles (24:0, 22:2, 20:4, 18:6, 12:12, and 10:14 (h:h)), frequency photo-cycles (2, 4, 8, 12, 24, and 48 times per day (t/d)), and short photo-cycles (0.91:0.09, 0.83:0.17, 0.75:0.25, and 0.50:0.50 (s:s)) of light:dark, respectively. The results showed these microalgae can store enough energy to support cell growth for continuous periods of up to 2 h in the dark, without affecting the productivity of the process. This 2 h, when divided into 2 cycles per day (2 t/d), showed the best growth condition (3700 mg L⁻¹), generation time (14.40 h), and maximum biomass productivity (21.43 mg L h⁻¹). This photo-cycle of 2 t/d was also the best condition for the production of total sterols. However, the values of polyunsaturated fatty acids, lipid content, and amino acids obtained higher yields in the short photo-cycle of 0.75:0.25. Thus, the modulation of light cycles becomes an important tool for boosting and directing the production of target molecules in phototrophic cultures of microalgae.

Cytosolic Glutamine Synthetase GS1;3 Is Involved in Rice Grain Ripening and Germination

Ammonium is combined with glutamate to form glutamine. This reaction is catalyzed by glutamine synthetase (GS or GLN). Plants harbor several isoforms of cytosolic GS (GS1). Rice GS1;3 is highly expressed in seeds during grain filling and germination, suggesting a unique role in these processes. This study aimed to investigate the role of GS1;3 for rice growth and yield. Tos17 insertion lines for GS1;3 were isolated, and the nitrogen (N), amino acid, and ammonium contents of GS1;3 mutant grains were compared to wild-type grains. The spatiotemporal expression of GS1;3 and the growth and yield of rice plants were evaluated in hydroponic culture and the paddy field. Additionally, the stable isotope of N was used to trace the foliar N flux during grain filling. Results showed that the loss of GS1;3 retarded seed germination. Seeds of GS1;3 mutants accumulated glutamate but did not show a marked change in the level of phytohormones. The expression of GS1;3 was detected at the beginning of germination, with limited promoter activity in seeds. GS1;3 mutants showed a considerably decreased ripening ratio and decreased N efflux in the 12th leaf blade under N deficient conditions. The β-glucuronidase gene expression under control of the GS1;3 promoter was detected in the vascular tissue and aleurone cell layer of developing grains. These data suggest unique physiological roles of GS1;3 in the early stage of seed germination and grain filling under N deficient conditions in rice.

Integration of Transcriptomics and Metabolomics for Understanding the Different Vegetative Growth in Morchella Sextelata

Morchella sextelata is an edible and medicinal fungus with high nutritional, medicinal, and economic value. Recently, M. sextelata has been produced through artificial cultivation in China, but its stable production remains problematic because the details of its growth and development process are limitedly understood. Herein, to investigate the dynamic process of M. sextelata development, we integrated the transcriptomics and metabolomics data of M. sextelata from three developmental stages: the young mushroom period (YMP), marketable mature period (MMP), and physiological maturity period (PMP). The results showed that the transcriptome changed dynamically at different stages and demonstrated the significant enrichment of pathways that regulate plant growth and development, such as N-glycan biosynthesis and carbon and purine metabolism. Similarly, small-molecule metabolites, such as D-fructose-1,6-biphosphate, which was upregulated during the YMP, dihydromyricetin, which was upregulated during the MMP, and L-citrulline, which was upregulated during the PMP, also showed phase-dependent characteristics. Then, combined analysis of the transcriptome data and metabolome traits revealed that the transcriptome may affect metabolic molecules during different growth stages of M. sextelata via specific enzymes, such as α-glucosidase and glucanase, which were included in two opposite transcriptome modules. In summary, this integration of transcriptomics and metabolomics data for understanding the vegetative growth of M. sextelata during different developmental stages implicated several key genes, metabolites, and pathways involved in the vegetative growth. We believe that these findings will provide comprehensive insights into the dynamic process of growth and development in M. sextelata and new clues for optimizing the methods for its cultivation application.

The Potential of Fermented Food from Southeast Asia as Biofertiliser

The intensive amount of chemical usage in agricultural practices could contribute to a significant impact on food safety issues and environmental health. Over-usage of chemical fertilisers may alter soil characteristics and contaminate water sources, leading to several human and animal health issues. Recently, there have been efforts to use microbial biofertilisers as a more sustainable and environmentally friendly agricultural practice in the common household of Southeast Asia. Traditionally, this method tends to utilise leftover food materials and readily available bacterial cultures, such as yoghurt drinks, and ferment them under a specific period in either solid or liquid form. So far, most of the testimonial-based feedbacks from local communities have been positive, but only limited information is available in the literature regarding the usage of biofertiliser fermented food (BFF). Previously, raw food waste has been used in the agriculture system to promote plant growth, however, the functional role of fermented food in enhancing plant growth have yet to be discovered. An understanding of the symbiotic relationship between fermented food and plants could be exploited to improve agricultural plant production more sustainably. Fermented food is known to be rich in good microbial flora (especially lactic acid bacteria (LAB)). LAB exist in different sources of fermented food and can act as a plant growth-promoting agent, improving the nutrient availability of food waste and other organic materials. Therefore, in this review, the potential use of seafood-based, plant-based, and animal-based fermented food as biofertiliser, especially from Southeast Asia, will be discussed based on their types and microbial and nutritional contents. The different types of fermented food provide a wide range of microbial flora for the enrichment of proteins, amino acids, vitamins, and minerals content in enhancing plant growth and overall development of the plant. The current advances of biofertiliser and practices of BFF will also be discussed in this review.

The Arabidopsis electron-transfer flavoprotein:ubiquinone oxidoreductase is required during normal seed development and germination

The importance of the alternative donation of electrons to the ubiquinol pool via the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex has been demonstrated. However, the functional significance of this pathway during seed development and germination remains to be elucidated. To assess the function of this pathway, we performed a detailed metabolic and transcriptomic analysis of Arabidopsis mutants to test the molecular consequences of a dysfunctional ETF/ETFQO pathway. We demonstrate that the disruption of this pathway compromises seed germination in the absence of an external carbon source and also impacts seed size and yield. Total protein and storage protein content is reduced in dry seeds, whilst sucrose levels remain invariant. Seeds of ETFQO and related mutants were also characterized by an altered fatty acid composition. During seed development, lower levels of fatty acids and proteins accumulated in the etfqo-1 mutant as well as in mutants in the alternative electron donors isovaleryl-CoA dehydrogenase (ivdh-1) and d-2-hydroxyglutarate dehydrogenase (d2hgdh1-2). Furthermore, the content of several amino acids was increased in etfqo-1 mutants during seed development, indicating that these mutants are not using such amino acids as alternative energy source for respiration. Transcriptome analysis revealed alterations in the expression levels of several genes involved in energy and hormonal metabolism. Our findings demonstrated that the alternative pathway of respiration mediated by the ETF/ETFQO complex affects seed germination and development by directly adjusting carbon storage during seed filling. These results indicate a role for the pathway in the normal plant life cycle to complement its previously defined roles in the response to abiotic stress.

Effects of Fruit Shading on Gene and Protein Expression During Starch and Oil Accumulation in Developing Styrax tonkinensis Kernels

Styrax tonkinensis has great potential as a biofuel feedstock source having industrial oilseeds with excellent fatty acids (FAs) composition and good fuel properties. Photosynthesis in the developing pericarp could affect the carbon distribution in kernel. During kernel development, more carbon sources are allocated to starch rather than lipid, when the pericarp photosynthesis is reduced by fruit shading treatment. After shading the fruits at 50 days after flowering (DAF), samples of shaded fruit (FSK) and controls (CK) were collected at 80 DAF and analyzed using the proteomic method. We identified 3,181 proteins, of which 277 were differentially expressed proteins, all downregulated in the FSK group. There were 56 proteins found involved in carbohydrate metabolism and lipid biosynthesis leading to oil accumulation with their iTRAQ ratios of FSK/CK ranging from 0.7123 to 1.1075. According to the qRT-PCR analyses, the key genes related to FA and triacylglycerol (TAG) biosynthesis were significantly downregulated between 60 and 90 DAF especially at 80 DAF, while the key genes involved in starch biosynthesis and FA desaturase had no significant difference between the two groups at 80 DAF. Fruit shading is a negative treatment for lipid accumulation but not starch accumulation by restraining enzymic protein expression involved in FA and TAG biosynthesis during S. tonkinensis kernel development.

The Effects of Different Fertilization Practices in Combination with the Use of PGPR on the Sugar and Amino Acid Content of Asparagus officinalis

The present study examined the effects of different nitrogen (NH4NO3) and potassium (KNO3) fertilization levels in combination with a nitrogen-fixing, plant growth-promoting rhizobacteria (PGPR) inoculation on the carbohydrate (CHO), amino acid content, and nutrient concentrations (N, P, K) in the spears and the root system of asparagus plants. No significant differences were indicated between the different fertilization treatments regarding N, P, and K in the leaves and roots of asparagus. The inoculation of the asparagus fields with PGPR, no matter the type of the inorganic fertilizer, resulted in increased CHO and amino acid content of the foliage and roots of asparagus. The highest CHO content and amino acid content were recorded in the treatment that combined PGPR inoculation along with KNO3 fertilizer, indicating that higher K applications acted synergistically with the added PGPR.

Multi-Omics Analyses Reveal Systemic Insights into Maize Vivipary

Maize vivipary, precocious seed germination on the ear, affects yield and seed quality. The application of multi-omics approaches, such as transcriptomics or metabolomics, to classic vivipary mutants can potentially reveal the underlying mechanism. Seven maize vivipary mutants were selected for transcriptomic and metabolomic analyses. A suite of transporters and transcription factors were found to be upregulated in all mutants, indicating that their functions are required during seed germination. Moreover, vivipary mutants exhibited a uniform expression pattern of genes related to abscisic acid (ABA) biosynthesis, gibberellin (GA) biosynthesis, and ABA core signaling. NCED4 (Zm00001d007876), which is involved in ABA biosynthesis, was markedly downregulated and GA3ox (Zm00001d039634) was upregulated in all vivipary mutants, indicating antagonism between these two phytohormones. The ABA core signaling components (PYL-ABI1-SnRK2-ABI3) were affected in most of the mutants, but the expression of these genes was not significantly different between the vp8 mutant and wild-type seeds. Metabolomics analysis integrated with co-expression network analysis identified unique metabolites, their corresponding pathways, and the gene networks affected by each individual mutation. Collectively, our multi-omics analyses characterized the transcriptional and metabolic landscape during vivipary, providing a valuable resource for improving seed quality.

Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon

BACKGROUND

Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS).

METHODS

The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS).

RESULTS

Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values.

Primary metabolic processes as drivers of leaf ageing

Ageing in plants is a highly coordinated and complex process that starts with the birth of the plant or plant organ and ends with its death. A vivid manifestation of the final stage of leaf ageing is exemplified by the autumn colours of deciduous trees. Over the past decades, technological advances have allowed plant ageing to be studied on a systems biology level, by means of multi-omics approaches. Here, we review some of these studies and argue that these provide strong support for basic metabolic processes as drivers for ageing. In particular, core cellular processes that control the metabolism of chlorophyll, amino acids, sugars, DNA and reactive oxygen species correlate with leaf ageing. However, while multi-omics studies excel at identifying correlative processes and pathways, molecular genetic approaches can provide proof that such processes and pathways control ageing, by means of knock-out and ectopic expression of predicted regulatory genes. Therefore, we also review historic and current molecular evidence to directly test the hypotheses unveiled by the systems biology approaches. We found that the molecular genetic approaches, by and large, confirm the multi-omics-derived hypotheses with notable exceptions, where there is scant evidence that chlorophyll and DNA metabolism are important drivers of leaf ageing. We present a model that summarises the core cellular processes that drive leaf ageing and propose that developmental processes are tightly linked to primary metabolism to inevitably lead to ageing and death.

A genome-wide association study reveals that the 2-oxoglutarate/malate translocator mediates seed vigor in rice

Seed vigor is an important trait for the direct seeding of rice (Oryza sativa L.). In this study, we examined the genetic architecture of variation in the germination rate using a diverse panel of rice accessions. Four quantitative trait loci for germination rate were identified using a genome-wide association study during early germination. One candidate gene, encoding the 2-oxoglutarate/malate translocator (OsOMT), was validated for qGR11. Disruption of this gene (Osomt mutants) reduced seed vigor, including seed germination and seedling growth, in rice. Functional analysis revealed that OsOMT influences seed vigor mainly by modulating amino acid levels and glycolysis and tricarboxylic acid cycle processes. The levels of most amino acids, including the Glu family (Glu, Pro, Arg, and GABA), Asp family (Asp, Thr, Lys, Ile, and Met), Ser family (Ser, Gly, and Cys), and others (His, Ala, Leu, and Val), were significantly reduced in the mature grains and the early germinating seeds of Osomt mutants compared to wild type (WT). The glucose and soluble sugar contents, as well as adenosine triphosphate levels, were significantly decreased in germinating seeds of Osomt mutants compared to WT. These results provide important insights into the role of OsOMT in seed vigor in rice.

Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination

Magnolia sieboldii K. Koch (M. sieboldii) is a deciduous Chinese tree species of the Magnoliaceae family with high ornamental, medicinal, and economic benefits. The germination of M. sieboldii seeds under natural conditions is extremely difficult, thereby hindering the cultivation and breeding of this important species. The molecular mechanisms underlying M. sieboldii seed germination remain unclear due to the lack of genomic and transcriptomic resources. Here, we integrated both mRNA and miRNA sequencing to identify the genes and pathways related to M. sieboldii germination. A comprehensive full-length transcriptome containing 158,083 high-quality unigenes was obtained by single-molecule real-time (SMRT) sequencing technology. We identified a total of 13,877 genes that were differentially expressed between non-germinated and germinated seeds. These genes were mainly involved in plant hormone signal transduction and diverse metabolic pathways such as those involving lipids, sugars, and amino acids. Our results also identified a complex regulatory network between miRNAs and their target genes. Taken together, we present the first transcriptome of M. sieboldii and provide key genes and pathways associated with seed germination for further characterization. Future studies of the molecular basis of seed germination will facilitate the genetic improvement M. sieboldii.

High-Throughput LC-ESI-MS/MS Metabolomics Approach Reveals Regulation of Metabolites Related to Diverse Functions in Mature Fruit of Grafted Watermelon

Grafting has been reported as a factor regulating the metabolome of a plant. Therefore, a comprehensive metabolic profile and comparative analysis of metabolites were conducted from fully mature fruit of pumpkin-grafted watermelon (PGW) and a self-rooted watermelon (SRW). Widely targeted LC-ESI-MS/MS metabolomics approach facilitated the simultaneous identification and quantification of 339 metabolites across PGW and SRW. Regardless of grafting, delta-aminolevulinic acid hydrochloride, sucrose, mannose-6-phosphate (carbohydrates), homocystine, 2-phenylglycine, s-adenosyl-L-homocysteine (amino acids and derivatives), malic, azelaic, H-butanoic acid ethyl ester-hexoside isomer 1, (organic acids), MAG (18:3) isomer1, LysoPC 16:0, LysoPC 18:2 2n isomer (lipids) p-coumaric acid, piperidine, and salicylic acid-o-glycoside (secondary metabolites) were among the dominant metabolite. Dulcitol, mono-, and disaccharide sugars were higher in PGW, while polysaccharides showed complex behavior. In PGW, most aromatic and nitrogen-rich amino acids accumulated greater than 1.5- and 1-fold, respectively. Intermediates of the tricarboxylic acid cycle (TCA), stress-related metabolites, vitamin B5, and several flavonoids were significantly more abundant in PGW. Most lipids were also significantly higher in grafted watermelon. This is the first report providing a comprehensive picture of watermelon metabolic profile and changes induced by grafting. Hence, the untargeted high-throughput LC-ESI-MS/MS metabolomics approach could be suitable to provide significant differences in metabolite contents between grafted and ungrafted plants.

TiO2 nanoparticles induced sugar impairments and metabolic pathway shift towards amino acid metabolism in wheat

TiO₂-nanoparticles (TiO₂-NP) have the potential to impair plant development. Nevertheless, the metabolic processes behind the physiological responses to TiO₂-NP are still far from being fully understood. In this study, Triticum aestivum plants were exposed for 21 days to different concentrations (0; 5; 50; 150 mg L^-1) of TiO₂-NP (P25). After treatment, the metabolite profiles of roots and leaves were analysed. The content of >70 % of the identified metabolites changed in response to P25 and the impact on metabolic pathways increased with TiO₂-NP dose, with leaves showing higher alterations. Roots up-regulated monosaccharides, azelaic acid, and γ-aminobutanoic acid and triggered the tyrosine metabolism, whereas leaves up-regulated the metabolisms of reserve sugars and tocopherol, and the phenylalanine and tryptophan pathways. Both organs (mainly leaves) up-regulated the aspartate family pathway together with serine, alanine and valine metabolisms and the glycerolipids' biosynthesis. In addition, the citrate and glyoxylate metabolisms were down-regulated in both organs (highest dose). Sugar biosynthesis breakdown, due to photosynthetic disturbances, shifted the cell metabolism to use amino acids as an alternative energy source, and both ROS and sugars worked as signalling molecules activating organ dependent antioxidant responses. Concluding, these NP-pollutants severely impact multiple crop metabolic pathways and may ultimately compromise plant performance.

Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in Dry Arabidopsis Seeds

Plant growth, development, and nutritional quality depends upon amino acid homeostasis, especially in seeds. However, our understanding of the underlying genetics influencing amino acid content and composition remains limited, with only a few candidate genes and quantitative trait loci identified to date. Improved knowledge of the genetics and biological processes that determine amino acid levels will enable researchers to use this information for plant breeding and biological discovery. Toward this goal, we used genomic prediction to identify biological processes that are associated with, and therefore potentially influence, free amino acid (FAA) composition in seeds of the model plant Arabidopsis thaliana. Markers were split into categories based on metabolic pathway annotations and fit using a genomic partitioning model to evaluate the influence of each pathway on heritability explained, model fit, and predictive ability. Selected pathways included processes known to influence FAA composition, albeit to an unknown degree, and spanned four categories: amino acid, core, specialized, and protein metabolism. Using this approach, we identified associations for pathways containing known variants for FAA traits, in addition to finding new trait-pathway associations. Markers related to amino acid metabolism, which are directly involved in FAA regulation, improved predictive ability for branched chain amino acids and histidine. The use of genomic partitioning also revealed patterns across biochemical families, in which serine-derived FAAs were associated with protein related annotations and aromatic FAAs were associated with specialized metabolic pathways. Taken together, these findings provide evidence that genomic partitioning is a viable strategy to uncover the relative contributions of biological processes to FAA traits in seeds, offering a promising framework to guide hypothesis testing and narrow the search space for candidate genes.

Roles of metabolic regulation in developing Quercus variabilis acorns at contrasting geologically-derived phosphorus sites in subtropical China

BACKGROUND

Phosphorus (P) -rich soils develop in phosphorite residing areas while P-deficient soils are ubiquitous in subtropical regions. Little has been reported that how metabolites participate in the seed development and the processes involved in their coping with contrasting-nutrient environments.

RESULTS

Here we quantified the metabolites of Quercus variabilis acorns in the early (July), middle (August), late (September) development stages, and determined element (C, H, O, N, P, K, Ca, Mg, S, Fe, Al, Mn, Na, Zn, and Cu) concentrations of acorns in the late stage, at geologically-derived contrasting-P sites in subtropical China. The primary metabolic pathways included sugar metabolism, the TCA cycle, and amino acid metabolism. Most metabolites (especially C- and N-containing metabolites) increased and then decreased from July to September. Acorns between the two sites were significantly discriminated at the three stages, respectively, by metabolites (predominantly sugars and organic acids). Concentrations of P, orthophosphoric acid and most sugars were higher; erythrose was lower in late-stage acorns at P-rich sites than those at P-deficient sites. No significant differences existed in the size and dry mass of individual acorns between oak populations at the two sites.

CONCLUSIONS

Oak acorns at the two sites formed distinct metabolic phenotypes related to their distinct geologically-derived soil conditions, and the late-stage acorns tended to increase P-use-efficiency in the material synthesis process at P-deficient sites, relative to those at P-rich sites.

Comparative proteomic analysis of mitochondrial proteins from maize CMS-C sterile, maintainer and restorer anthers

The maize C system of cytoplasmic male sterility (CMS) and its fertility restoration gene Rf4 have been widely used for maize hybrid production; however, the underlying mechanism is still uncertain. The sterility factor functions in mitochondria, where it interacts directly or indirectly with the restorer. Mitoproteomics can capture all participants involved in CMS and restoration at the organelle level. In the present study, we identified and quantified anther mitochondrial proteins from CMS, maintainer and restorer lines. We obtained 14,528 unique peptides belonging to 3,369 proteins. Comparative analysis of 1840 high-confidence proteins revealed 68 were differentially accumulated proteins likely involved in CMS or its restoration within mitochondria. These proteins were mainly associated with fatty acid metabolism, amino acid metabolism and protein-processing pathways. These results suggest that an energy deficiency caused by the sterility factor hinders other proteins or protein complexes required for pollen development through nuclear-mitochondrial interaction. The restorer factor may boost the energy generation by activating alternative metabolic pathways and by improving the post-translation processing efficiency of proteins in energy-producing complexes to restore pollen fertility. Our findings may aid detailed molecular analysis and contribute to a better understanding of maize CMS-C restoration and sterility.

In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis

Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.

Identification of key genes related to seedlessness by genome-wide detection of structural variation and transcriptome analysis in 'Shijiwuhe' pear

Seedless fruits are highly marketable because they are easier to eat than fruits with seeds. 'Shijiwuhe' is a seedless pear cultivar that is a mutant derived from an F1 hybridization population ('Bartlett' x 'Yali'). Little is known about the key genes controlling seedless pear fruit. In this study, field experiments revealed that seedless 'Shijiwuhe' pear was not due to parthenocarpy, and that it was self-incompatible. Single nucleotide polymorphisms (SNPs), small insertions and deletions (InDels) and structural variations (SVs) were characterized using DNA sequencing data between 'Shijiwuhe' and parental cultivars. A total of 1498 genes were found to be affected by SV and over 50% of SVs were located in promoter regions. Transcriptome analysis was conducted at three time points (4, 8, and 12 days after cross-pollination) during early fruit development of 'Shijiwuhe', 'Bartlett', and 'Yali'. In total, 1438 differentially expressed genes (DEGs) were found between 'Shijiwuhe' and parental cultivars 'Bartlett' and 'Yali'. We found 1193 SVs that caused differential expression of genes at 4 DACP. Among them, over 100 genes were in pathways related to seed nutrition and energy storage and 41 candidate genes encoded several important transcription factors, such as MYB, WRKY, NAC, and bHLH, which might play important roles in seed development. The qRT-PCR results also confirmed that the candidate genes with SVs showed differential expression between 'Shijiwuhe' pear and 'Bartlett' or 'Yali'. This study, which combined field experiments, SV detection, and transcriptome analysis might provide an effective way to predict the candidate genes regulating the seedless trait and important gene resources for genetic improvement of pear.

Photosynthesis in non-foliar tissues: implications for yield

Photosynthesis is currently a focus for crop improvement. The majority of this work has taken place and been assessed in leaves, and limited consideration has been given to the contribution that other green tissues make to whole-plant carbon assimilation. The major focus of this review is to evaluate the impact of non-foliar photosynthesis on carbon-use efficiency and total assimilation. Here we appraise and summarize past and current literature on the substantial contribution of different photosynthetically active organs and tissues to productivity in a variety of different plant types, with an emphasis on fruit and cereal crops. Previous studies provide evidence that non-leaf photosynthesis could be an unexploited potential target for crop improvement. We also briefly examine the role of stomata in non-foliar tissues, gas exchange, maintenance of optimal temperatures and thus photosynthesis. In the final section, we discuss possible opportunities to manipulate these processes and provide evidence that Triticum aestivum (wheat) plants genetically manipulated to increase leaf photosynthesis also displayed higher rates of ear assimilation, which translated to increased grain yield. By understanding these processes, we can start to provide insights into manipulating non-foliar photosynthesis and stomatal behaviour to identify novel targets for exploitation in continuing breeding programmes.

Combined Kinetin and Spermidine Treatments Ameliorate Growth and Photosynthetic Inhibition in Vigna angularis by Up-Regulating Antioxidant and Nitrogen Metabolism under Cadmium Stress

Pot experiments were conducted to investigate the probable beneficial role of the individual as well as combined application of kinetin (50 μM Kn) and spermidine (200 μM Spd) on Vigna angularis under cadmium (Cd) stress. Cd treatment reduced growth by declining the content of chlorophylls and carotenoids, photosynthesis, and gas exchange parameters. Exogenously, Kn and Spd application enhanced the photosynthetic parameters and up-regulated the antioxidant system by improving the activities of antioxidant enzymes and the content of non-enzymatic components. In addition, the application of Kn and Spd resulted in significant improvement in the content of sugars, proline, and glycine betaine, ameliorating the decline in relative water content. Oxidative stress parameters including hydrogen peroxide, superoxide, lipid peroxidation, lipoxygenase activity, and electrolyte leakage increased due to Cd stress; however, the application of Kn and Spd imparted a significant decline in all these parameters. Further, reduced Cd uptake was also observed due to Kn and Spd application. Total phenols and flavonoids also increased due to Kn and Spd treatments under normal as well as Cd stress conditions, which may have further helped with the elimination of reactive oxygen species. Reduction in the activity of nitrate reductase and the content of nitrogen was ameliorated due to the exogenous application of Kn and Spd. Therefore, the exogenous application of Kn and Spd benefited Vigna angularis counteracting the damaging effects of Cd stress by up-regulating the tolerance mechanisms, including antioxidant and osmolyte metabolism.

Enzymatic Reaction-Related Protein Degradation and Proteinaceous Amino Acid Metabolism during the Black Tea (Camellia sinensis) Manufacturing Process

Amino acids contribute to the nutritional value and quality of black tea. Fermentation is the most important stage of the black tea manufacturing process. In this study, we investigated protein degradation and proteinaceous amino acid metabolism associated with enzymatic reactions during fermentation in the black tea manufacturing process. The results showed that the concentrations of both protein and free amino acids decreased during fermentation. We also confirmed that proteins were broken down into free amino acids by artificially synthesized dipeptide benzyloxycarbonyl glutamyl-tyrosine (Z-Glu-Tyr). Metabolites of the amino acid metabolic pathway increased significantly during fermentation. Furthermore, we confirmed that free amino acids were degraded to volatile compounds in a tracer experiment with the isotope precursor. These results provide information that will help black tea manufacturers improve the quality of black tea.

On the Inverse Correlation of Protein and Oil: Examining the Effects of Altered Central Carbon Metabolism on Seed Composition Using Soybean Fast Neutron Mutants

Protein and oil levels measured at maturity are inversely correlated across soybean lines; however, carbon is in limited supply during maturation resulting in tradeoffs for the production of other reserves including oligosaccharides. During the late stages of seed development, the allocation of carbon for storage reserves changes. Lipid and protein levels decline while concentrations of indigestible raffinose family oligosaccharides (RFOs) increase, leading to a decreased crop value. Since the maternal source of carbon is diminished during seed maturation stages of development, carbon supplied to RFO synthesis likely comes from an internal, turned-over source and may contribute to the reduction in protein and lipid content in mature seeds. In this study, fast neutron (FN) mutagenized soybean populations with deletions in central carbon metabolic genes were examined for trends in oil, protein, sugar, and RFO accumulation leading to an altered final composition. Two lines with concurrent increases in oil and protein, by combined 10%, were identified. A delayed switch in carbon allocation towards RFO biosynthesis resulted in extended lipid accumulation and without compromising protein. Strategies for future soybean improvement using FN resources are described.

Simultaneous and sequential based co-fermentations of Trichoderma asperellum GDFS1009 and Bacillus amyloliquefaciens 1841: a strategy to enhance the gene expression and metabolites to improve the bio-control and plant growth promoting activity

BACKGROUND

The consequence of simultaneous and sequential inoculation of T. asperellum and B. amyloliquefaciens cultures with respect to growth rate, differential expression of vital genes and metabolites were examined.

RESULTS

The competition was observed between T. asperellum and B. amyloliquefaciens under co-cultivation. The proliferation of Trichoderma was reduced in the simultaneous inoculation (TB1) method, possibly due to the fastest growth of Bacillus. Both T. asperellum and B. amyloliquefaciens were proliferated in sequential inoculation method (TB2). The sequential inoculation method (TB2) upregulated the expression of metabolites and vital genes (sporulation, secondary metabolites, mycoparasitism enzymes and antioxidants) in Trichoderma and downregulated in Bacillus and vice versa in co-inoculation method (TB1). The metabolic changes in the co-culture promoted the maize plant growth and defense potential under normal and biotic stress conditions.

CONCLUSION

The metabolites produced by the co-culture of T. asperellum and B. amyloliquefaciens improved the maize plant growth and defense potential under normal and biotic stress conditions.

Nitric Oxide Increases the Physiological and Biochemical Stability of Soybean Plants under High Temperature

Thermal stress reduces plant growth and development, resulting in considerable economic losses in crops such as soybeans. Nitric oxide (NO) in plants is associated with tolerance to various abiotic stresses. Nevertheless, there are few studies of the range of observed effects of NO in modulating physiological and metabolic functions in soybean plants under high temperature. In the present study, we investigated the effects of sodium nitroprusside (SNP, NO donor), on anatomical, physiological, biochemical, and metabolic processes of soybean plants exposed to high temperature. Soybean plants were grown in soil: sand (2:1) substrate in acclimatized growth chambers. At developmental V3 stage, plants were exposed to two temperatures (25 °C and 40 °C) and SNP (0 and 100 μM), in a randomized block experimental design, with five replicates. After six days, we quantified NO concentration, leaf anatomy, gas exchange, chlorophyll a fluorescence, photosynthetic pigments, lipid peroxidation, antioxidant enzyme activity, and metabolite profiles. Higher NO concentration in soybean plants exposed to high temperature and SNP showed increased effective quantum yields of photosystem II (PSII) and photochemical dissipation, thereby maintaining the photosynthetic rate. Under high temperature, NO also promoted greater activity of ascorbate peroxidase and peroxidase activity, avoiding lipid peroxidation of cell membranes, in addition to regulating amino acid and organic compound levels. These results suggest that NO prevented damage caused by high temperature in soybean plants, illustrating the potential to mitigate thermal stress in cultivated plants.

Dynamic Transcriptome Changes Related to Oil Accumulation in Developing Soybean Seeds

Soybean is one of the most important oil crops in the world. Revealing the molecular basis and exploring key candidate genes for seed oil synthesis has great significance for soybean improvement. In this study, we found that oil accumulation rates and gene expression levels changed dynamically during soybean seed development. The expression levels of genes in metabolic pathways such as carbon fixation, photosynthesis, glycolysis, and fatty acid biosynthesis were significantly up-regulated during the rapid accumulation of oil in developing soybean seeds. Through weighted correlation network analysis, we identified six co-expression modules associated with soybean seed oil content and the pink module was the most positively correlated (r = 0.83, p = 7 × 10-4) network. Through the integration of differential expression and co-expression analysis, we predicted 124 candidate genes potentially affecting soybean seed oil content, including seven genes in lipid metabolism pathway, two genes involved in glycolysis, one gene in sucrose metabolism, and 12 genes belonged to transcription factors as well as other categories. Among these, three genes (GmABI3b, GmNFYA and GmFAD2-1B) have been shown to control oil and fatty acid content in soybean seeds, and other newly identified candidate genes would broaden our knowledge to understand the molecular basis for oil accumulation in soybean seeds.

Influence of isopropylmalate synthase OsIPMS1 on seed vigour associated with amino acid and energy metabolism in rice

Seed vigour is an imperative trait for the direct seeding of rice. Isopropylmalate synthase (IPMS) catalyses the committed step of leucine (Leu) biosynthesis, but its effect on seed vigour remains unclear. In this study, rice OsIPMS1 and OsIPMS2 was cloned, and the roles of OsIPMS1 in seed vigour were mainly investigated. OsIPMS1 and OsIPMS2 catalyse Leu biosynthesis, and Leu feedback inhibits their IPMS activities. Disruption of OsIPMS1 resulted in low seed vigour under various conditions, which might be tightly associated with the reduction of amino acids in germinating seeds. Eleven amino acids that associated with stress tolerance, GA biosynthesis and tricarboxylic acid (TCA) cycle were significantly reduced in osipms1 mutants compared with those in wide type (WT) during seed germination. Transcriptome analysis indicated that a total of 1209 differentially expressed genes (DEGs) were altered in osipms1a mutant compared with WT at the early germination stage, wherein most of the genes were involved in glycolysis/gluconeogenesis, protein processing, pyruvate, carbon, fructose and mannose metabolism. Further analysis confirmed that the regulation of OsIPMS1 in seed vigour involved in starch hydrolysis, glycolytic activity and energy levels in germinating seeds. The effects of seed priming were tightly associated with the mRNA levels of OsIPMS1 in priming seeds. The OsIPMS1 might be used as a biomarker to determine the best stop time-point of seed priming in rice. This study provides novel insights into the function of OsIPMS1 on seed vigour and should have practical applications in seed priming of rice.

On the role of the tricarboxylic acid cycle in plant productivity

The tricarboxylic acid (TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were reduced or knocked out in order to ascertain their in vivo function. Some of the resultant plants exhibited improved photosynthesis and plant growth, under controlled greenhouse conditions. In addition, overexpression of the endogenous genes, or heterologous forms of a number of the enzymes, has been carried out in tomato fruit and the roots of a range of species, and in some instances improvement in fruit yield and postharvest properties and plant performance, under nutrient limitation, have been reported, respectively. Given a number of variants, in nature, we discuss possible synthetic approaches involving introducing these variants, or at least a subset of them, into plants. We additionally discuss the likely consequences of introducing synthetic metabolons, wherein certain pairs of reactions are artificially permanently assembled into plants, and speculate as to future strategies to further improve plant productivity by manipulation of the core metabolic pathway.