Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice

Soil volatilomics uncovers tight linkage between soybean presence and soil omics profiles in agricultural fields

Securing a stable food supply and achieving sustainable agricultural production are essential for mitigating future food insecurity. Soil metabolomics is a promising tool for capturing soil status, which is a critical issue for future sustainable food security. This study aims to provide deeper insights into the status of soybean-grown fields under varying soil conditions over three years by employing comprehensive soil volatile organic compound (VOC) profiling, also known as soil volatilomics. Profiling identified approximately 200 peaks in agricultural fields. The soil of soybean-presented plots exhibited markedly higher VOC levels than those of non-soybean plots during the flowering season. Pentanoic acid, 2,2,4-trimethyl-3-carboxyisopropyl, isobutyl ester, a discriminative soil VOC, was identified through multivariate data analysis as a distinctively present VOC in fields with or without soybean plants during the flowering period. Soil VOC profiles exhibited strong correlations with soil-related omics datasets (soil ionome, microbiome, metabolome, and physics) and no significant correlations with root microbiome and rhizosphere chemicals. These findings indicate that soil VOC profiles could serve as a valuable indicator for assessing soil status, thereby supporting efforts to ensure future global food security.

CropMetabolome: a comprehensive metabolome database for major crops cross eight categories

Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.

Raising root zone temperature improves plant productivity and metabolites in hydroponic lettuce production

While it is commonly understood that air temperature can greatly affect the process of photosynthesis and the growth of higher plants, the impact of root zone temperature (RZT) on plant growth, metabolism, essential elements, as well as key metabolites like chlorophyll and carotenoids, remains an area that necessitates extensive research. Therefore, this study aimed to investigate the impact of raising the RZT on the growth, metabolites, elements, and proteins of red leaf lettuce. Lettuce was hydroponically grown in a plant factory with artificial light at four different air temperatures (17, 22, 27, and 30°C) and two treatments with different RZTs. The RZT was raised 3°C above the air temperature in one group, while it was not in the other group. Increasing the RZT 3°C above the air temperature improved plant growth and metabolites, including carotenoids, ascorbic acids, and chlorophyll, in all four air temperature treatments. Moreover, raising the RZT increased Mg, K, Fe, Cu, Se, Rb, amino acids, and total soluble proteins in the leaf tissue at all four air temperatures. These results showed that raising the RZT by 3°C improved plant productivity and the metabolites of the hydroponic lettuce by enhancing nutrient uptake and activating the metabolism in the roots at all four air temperatures. Overall, this research demonstrates that plant growth and metabolites can be improved simultaneously with an increased RZT relative to air temperature. This study serves as a foundation for future research on optimizing RZT in relation to air temperature. Further recommended studies include investigating the differential effects of multiple RZT variations relative to air temperature for increased optimization, examining the effects of RZT during nighttime versus daytime, and exploring the impact of stem heating. This research has the potential to make a valuable contribution to the ongoing growth and progress of the plant factory industry and fundamental advancements in root zone physiology. Overall, this research demonstrates that plant growth and metabolites can be improved simultaneously with an increased RZT relative to air temperature. This study serves as a foundation for future research on optimizing RZT in relation to air temperature. Further recommended studies include investigating the differential effects of multiple RZT variations relative to air temperature for increased optimization, examining the effects of RZT during nighttime versus daytime, and exploring the impact of stem heating. This research has the potential to make a valuable contribution to the ongoing growth and progress of the plant factory industry and fundamental advancements in root zone physiology.

Application of ethanol alleviates heat damage to leaf growth and yield in tomato

Chemical priming has emerged as a promising area in agricultural research. Our previous studies have demonstrated that pretreatment with a low concentration of ethanol enhances abiotic stress tolerance in Arabidopsis and cassava. Here, we show that ethanol treatment induces heat stress tolerance in tomato (Solanum lycopersicon L.) plants. Seedlings of the tomato cultivar 'Micro-Tom' were pretreated with ethanol solution and then subjected to heat stress. The survival rates of the ethanol-pretreated plants were significantly higher than those of the water-treated control plants. Similarly, the fruit numbers of the ethanol-pretreated plants were greater than those of the water-treated ones. Transcriptome analysis identified sets of genes that were differentially expressed in shoots and roots of seedlings and in mature green fruits of ethanol-pretreated plants compared with those in water-treated plants. Gene ontology analysis using these genes showed that stress-related gene ontology terms were found in the set of ethanol-induced genes. Metabolome analysis revealed that the contents of a wide range of metabolites differed between water- and ethanol-treated samples. They included sugars such as trehalose, sucrose, glucose, and fructose. From our results, we speculate that ethanol-induced heat stress tolerance in tomato is mainly the result of increased expression of stress-related genes encoding late embryogenesis abundant (LEA) proteins, reactive oxygen species (ROS) elimination enzymes, and activated gluconeogenesis. Our results will be useful for establishing ethanol-based chemical priming technology to reduce heat stress damage in crops, especially in Solanaceae.

Controlling root zone temperature improves plant growth and pigments in hydroponic lettuce

BACKGROUND AND AIMS

Air and root zone temperatures are important environmental factors affecting plant growth and yield. Numerous studies have demonstrated that air temperature strongly affects plant growth and development. Despite the extensive literature on air temperature, comprehensive studies on the effects of root zone temperature (RZT) on plant growth, elemental composition, and pigments are limited. In this study, we carefully observed the effects of RZT in red leaf lettuce to understand its effect on lettuce growth and pigment content.

METHODS

Lettuce (Lactuca sativa, red leaf cultivar 'Red Fire') was grown hydroponically in a plant factory with artificial light under three RZT treatments (15, 25, or 35 °C) for 13 days. We investigated the comprehensive effects of RZT on the production of red leaf lettuce by metabolome and ionome analyses.

KEY RESULTS

The 25 °C RZT treatment achieved maximum shoot and root dry weight. The 35 °C RZT decreased plant growth but significantly increased pigment contents (e.g. anthocyanins, carotenoids). In addition, a RZT heating treatment during plant cultivation that changed from 25 to 35 °C RZT for 8 days before harvest significantly increased shoot dry weight compared with the 35 °C RZT and significantly increased pigments compared with the 25 °C RZT. The 15 °C RZT resulted in significantly less pigment content relative to the 35 °C RZT. The 15 °C RZT also resulted in shoot and root dry weights greater than the 35 °C RZT but less than the 25 °C RZT.

CONCLUSIONS

This study demonstrated that plant growth and pigments can be enhanced by adjusting RZT during different stages of plant growth to attain enhanced pigment contents while minimizing yield loss. This suggests that controlling RZT could be a viable method to improve lettuce quality via enhancement of pigment content quality while maintaining acceptable yields.

Using the organelle glue technique to engineer the plant cell metabolome

By using the organelle glue technique, we artificially manipulated organelle interactions and controlled the plant metabolome at the pathway level. Plant cell metabolic activity changes with fluctuating environmental conditions, in part via adjustments in the arrangement and interaction of organelles. This hints at the potential for designing plants with desirable metabolic activities for food and pharmaceutical industries by artificially controlling the interaction of organelles through genetic modification. We previously developed a method called the organelle glue technique, in which chloroplast-chloroplast adhesion is induced in plant cells using the multimerization properties of split fluorescent proteins. Here, we generated transgenic Arabidopsis (Arabidopsis thaliana) plants in which chloroplasts adhere to each other and performed metabolome analysis to examine the metabolic changes in these lines. In plant cells expressing a construct encoding the red fluorescent protein mCherry targeted to the chloroplast outer envelope by fusion with a signal sequence (cTP-mCherry), chloroplasts adhered to each other and formed chloroplast aggregations. Mitochondria and peroxisomes were embedded in the aggregates, suggesting that normal interactions between chloroplasts and these organelles were also affected. Metabolome analysis of the cTP-mCherry-expressing Arabidopsis shoots revealed significantly higher levels of glycine, serine, and glycerate compared to control plants. Notably, these are photorespiratory metabolites that are normally transported between chloroplasts, mitochondria, and peroxisomes. Together, our data indicate that chloroplast-chloroplast adhesion alters organellar interactions with mitochondria and peroxisomes and disrupts photorespiratory metabolite transport. These results highlight the possibility of controlling plant metabolism at the pathway level by manipulating organelle interactions.

Ethanol induces heat tolerance in plants by stimulating unfolded protein response

Ethanol priming induces heat stress tolerance by the stimulation of unfolded protein response. Global warming increases the risk of heat stress-related yield losses in agricultural crops. Chemical priming, using safe agents, that can flexibly activate adaptive regulatory responses to adverse conditions, is a complementary approach to genetic improvement for stress adaptation. In the present study, we demonstrated that pretreatment of Arabidopsis with a low concentration of ethanol enhances heat tolerance without suppressing plant growth. We also demonstrated that ethanol pretreatment improved leaf growth in lettuce (Lactuca sativa L.) plants grown in the field conditions under high temperatures. Transcriptome analysis revealed a set of genes that were up-regulated in ethanol-pretreated plants, relative to water-pretreated controls. Binding Protein 3 (BIP3), an endoplasmic reticulum (ER)-stress marker chaperone gene, was among the identified up-regulated genes. The expression levels of BIP3 were confirmed by RT-qPCR. Root-uptake of ethanol was metabolized to organic acids, nucleic acids, amines and other molecules, followed by an increase in putrescine content, which substantially promoted unfolded protein response (UPR) signaling and high-temperature acclimation. We also showed that inhibition of polyamine production and UPR signaling negated the heat stress tolerance induced by ethanol pretreatment. These findings collectively indicate that ethanol priming activates UPR signaling via putrescine accumulation, leading to enhanced heat stress tolerance. The information gained from this study will be useful for establishing ethanol-mediated chemical priming strategies that can be used to help maintain crop production under heat stress conditions.

Differential metabolic rearrangements in the roots and leaves of Cicer arietinum caused by single or double nitrate and/or phosphate deficiencies

Nitrate (NO₃ ^- ) and phosphate (Pi) deficiencies are the major constraints for chickpea productivity, significantly impacting global food security. However, excessive fertilization is expensive and can also lead to environmental pollution. Therefore, there is an urgent need to develop chickpea cultivars that are able to grow on soils deficient in both NO₃ ^- and Pi. This study focused on the identification of key NO₃ ^- and/or Pi starvation-responsive metabolic pathways in the leaves and roots of chickpea grown under single and double nutrient deficiencies of NO₃ ^- and Pi, in comparison with nutrient-sufficient conditions. A global metabolite analysis revealed organ-specific differences in the metabolic adaptation to nutrient deficiencies. Moreover, we found stronger adaptive responses in the roots and leaves to any single than combined nutrient-deficient stresses. For example, chickpea enhanced the allocation of carbon among nitrogen-rich amino acids (AAs) and increased the production of organic acids in roots under NO₃ ^- deficiency, whereas this adaptive response was not found under double nutrient deficiency. Nitrogen remobilization through the transport of AAs from leaves to roots was greater under NO₃ ^- deficiency than double nutrient deficiency conditions. Glucose-6-phosphate and fructose-6-phosphate accumulated in the roots under single nutrient deficiencies, but not under double nutrient deficiency, and higher glycolytic pathway activities were observed in both roots and leaves under single nutrient deficiency than double nutrient deficiency. Hence, the simultaneous deficiency generated a unique profile of metabolic changes that could not be simply described as the result of the combined deficiencies of the two nutrients.

Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava

Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid, and indole-3-acetic acid conjugated with aspartic acid on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.

A Review of Integrative Omic Approaches for Understanding Rice Salt Response Mechanisms

Soil salinity is one of the most serious environmental challenges, posing a growing threat to agriculture across the world. Soil salinity has a significant impact on rice growth, development, and production. Hence, improving rice varieties’ resistance to salt stress is a viable solution for meeting global food demand. Adaptation to salt stress is a multifaceted process that involves interacting physiological traits, biochemical or metabolic pathways, and molecular mechanisms. The integration of multi-omics approaches contributes to a better understanding of molecular mechanisms as well as the improvement of salt-resistant and tolerant rice varieties. Firstly, we present a thorough review of current knowledge about salt stress effects on rice and mechanisms behind rice salt tolerance and salt stress signalling. This review focuses on the use of multi-omics approaches to improve next-generation rice breeding for salinity resistance and tolerance, including genomics, transcriptomics, proteomics, metabolomics and phenomics. Integrating multi-omics data effectively is critical to gaining a more comprehensive and in-depth understanding of the molecular pathways, enzyme activity and interacting networks of genes controlling salinity tolerance in rice. The key data mining strategies within the artificial intelligence to analyse big and complex data sets that will allow more accurate prediction of outcomes and modernise traditional breeding programmes and also expedite precision rice breeding such as genetic engineering and genome editing.

Defective cytokinin signaling reprograms lipid and flavonoid gene-to-metabolite networks to mitigate high salinity in Arabidopsis

Cytokinin (CK) in plants regulates both developmental processes and adaptation to environmental stresses. Arabidopsis histidine phosphotransfer ahp2,3,5 and type-B Arabidopsis response regulator arr1,10,12 triple mutants are almost completely defective in CK signaling, and the ahp2,3,5 mutant was reported to be salt tolerant. Here, we demonstrate that the arr1,10,12 mutant is also more tolerant to salt stress than wild-type (WT) plants. A comprehensive metabolite profiling coupled with transcriptome analysis of the ahp2,3,5 and arr1,10,12 mutants was conducted to elucidate the salt tolerance mechanisms mediated by CK signaling. Numerous primary (e.g., sugars, amino acids, and lipids) and secondary (e.g., flavonoids and sterols) metabolites accumulated in these mutants under nonsaline and saline conditions, suggesting that both prestress and poststress accumulations of stress-related metabolites contribute to improved salt tolerance in CK-signaling mutants. Specifically, the levels of sugars (e.g., trehalose and galactinol), amino acids (e.g., branched-chain amino acids and γ-aminobutyric acid), anthocyanins, sterols, and unsaturated triacylglycerols were higher in the mutant plants than in WT plants. Notably, the reprograming of flavonoid and lipid pools was highly coordinated and concomitant with the changes in transcriptional levels, indicating that these metabolic pathways are transcriptionally regulated by CK signaling. The discovery of the regulatory role of CK signaling on membrane lipid reprogramming provides a greater understanding of CK-mediated salt tolerance in plants. This knowledge will contribute to the development of salt-tolerant crops with the ability to withstand salinity as a key driver to ensure global food security in the era of climate crisis.

Functional disruption of cell wall invertase inhibitor by genome editing increases sugar content of tomato fruit without decrease fruit weight

Sugar content is one of the most important quality traits of tomato. Cell wall invertase promotes sucrose unloading in the fruit by maintaining a gradient of sucrose concentration between source leaves and fruits, while invertase inhibitor (INVINH) regulates this process. In this study, knock-out of cell wall INVINH in tomato (SlINVINH1) was performed by genome editing using, CRISPR/Cas9 and Target-AID technologies. Most of the genome-edited lines set higher soluble solid content (SSC) fruit than the original cultivar ‘Suzukoma’, while fruit weight was different among the genome-edited lines. From these genome-edited lines, three lines (193–3, 199–2, and 247–2), whose SSC was significantly higher than ‘Suzukoma’ and fruit weight were almost the same as the original cultivar, were selected. The fruit weight and overall plant growth of the two lines were comparable to those of the original cultivar. In contrast, the fructose and glucose contents in the mature fruits of the two lines were significantly higher than those of the original cultivar. The mature fruits of genome edited line 193–3 showed the highest sugar content, and the fructose and glucose contents were 29% and 36% higher than that of the original cultivar, respectively. Whole genome sequence data showed no off-target mutations in the genome-edited lines. Non-target metabolome analysis of mature fruits revealed that fructose was the highest loading factor in principal component analysis (PCA) between the genome-edited line and the original cultivar, and no unexpected metabolites appeared in the genome-edited line. In this study, we succeeded in producing tomato lines with high sugar content without a decrease in fruit weight and deterioration of plant growth by knock-out of SlINVINH1 using genome editing technology. This study showed that functional disruption of SlINVINH1 is an effective approach to produce tomato cultivars with high sugar content.

Metabolomic Analysis of Germinated Brown Rice at Different Germination Stages

Brown rice (BR) is unpolished rice containing many bioactive compounds in addition to the basic nutrients of the rice grain. Herein, BR was germinated for up to 48 h to prepare germinated brown rice (GBR). The physiological and chemical changes in the GBR during germination were analyzed. GBR samples germinated for 48 h were in the radicle-emergence stage, but root formation was not observed. The change in the GBR metabolite profile during germination was analyzed to determine the effect of germination on the chemical profiles of the GBR samples. Twenty-five metabolites including acidic compounds, amino acids, sugars, lipid metabolites, and secondary metabolites were identified as the components that contributed to the variations in the GBR groups germinated for different time periods. Among the metabolites, the carbohydrates associated with energy production and lipid metabolites changed significantly. Based on the identified metabolites, a metabolomic pathway was proposed. Carbohydrate metabolism, citric acid cycle, and lipid metabolism were the main processes that were affected during germination. Although further studies on the relationship between the metabolite profile and nutritional quality of the GBR are needed, these results are useful for understanding the effect of germination on the physiological and chemical changes in BR.

Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress

Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.

Transcriptome Analysis of the Hierarchical Response of Histone Deacetylase Proteins That Respond in an Antagonistic Manner to Salinity Stress

Acetylation in histone and non-histone proteins is balanced by histone acetyltransferase and histone deacetylase (HDAC) enzymatic activity, an essential aspect of fine-tuning plant response to environmental stresses. HDACs in Arabidopsis are composed of three families (RPD3-like, SIRT, and HD-tuins). A previous study indicated that class I (HDA19) and class II (HDA5/14/15/18) RPD3-like family HDACs control positive and negative responses to salinity stress, respectively. Furthermore, quintuple hda5/14/15/18/19 mutants (quint) exhibit salinity stress tolerance, suggesting that hda19 suppresses the sensitivity to salinity stress present in quadruple hda5/14/15/18 mutants (quad). In the present study, transcriptome analysis of the quint mutant was conducted to elucidate the hierarchical control of salinity stress response operated by RPD3-like family HDACs (HDA5/14/15/18/19). The analysis identified 4,832 salt-responsive genes in wild-type (Col-0), hda19-3, quad, and quint plants and revealed that 56.7% of the salt-responsive genes exhibited a similar expression pattern in both the hda19-3 and quint plants. These results indicate that deficiency in HDA19 has a bigger impact on salinity stress response than in class II HDACs. Furthermore, the expression pattern of genes encoding enzymes that metabolize phytohormones raises the possibility that a drastic change in the homeostasis of phytohormones, such as abscisic acid, brassinosteroid, and gibberellin, may contribute to increasing stress tolerance in hda19-3 and quint plants. Among these phytohormones, abscisic acid accumulation actually increased in hda19-3 and quint plants, and decreased in quad, compared with wild-type plants. Importantly, 7.8% of the salt-responsive genes in quint plants exhibited a similar expression pattern in quad plants, suggesting that some gene sets are regulated in an HDA5/14/15/18-dependent manner. The transcriptome analysis conducted in the present study revealed the hierarchical and independent regulation of salt stress response that is mediated through HDA19 and class II HDACs.

Association analysis of phenotypic and metabolomic changes in Arabidopsis accessions and their F1 hybrids affected by different photoperiod and sucrose supply

Photoperiod and sucrose (Suc) assimilation play important roles in the regulation of plant growth and development. However, it remains unclear how natural variation of plants could contribute to metabolic changes under various growth conditions. Here, we investigated the developmental and metabolomic responses of two natural accessions of Arabidopsis thaliana, Columbia (Col) and C24, and their reciprocal F₁ hybrids grown under four carbon source regimens, i.e., two different photoperiods and the presence or absence of exogenous Suc supply. The effect of exogenous Suc clearly appeared in the growth of Col and the F₁ hybrid but not in C24, whereas long-day conditions had significant positive effects on the growth of all lines. Comparative metabolite profiling of Col, C24, and the F₁ hybrid revealed that changes in metabolite levels, particularly sugars, were highly dependent on genotype-specific responses rather than growth conditions. The presence of Suc led to over-accumulation of seven metabolites, including four sugars, a polyamine, and two amino acids in C24, whereas no such accumulation was observed in the profiles of Col and the F₁ hybrid. Thus, the comparative metabolite profiling revealed that the two parental lines of the hybrid show a distinct difference in sugar metabolism.

Bulk Protein and Oil Prediction in Soybeans Using Transmission Raman Spectroscopy: A Comparison of Approaches to Optimize Accuracy

Rapid measurements of protein and oil content are important for a variety of uses, from sorting of soybeans at the point of harvest to feedback during soybean meal production. In this study, our goal is to develop a simple protocol to permit rapid and robust quantitative prediction of soybean constituents using transmission Raman spectroscopy (TRS). To develop this approach, we systematically varied the various elements of the measurement process to provide a diverse test bed. First, we utilized an in-house-built benchtop TRS instrument such that suitable optical configurations could be rapidly deployed and analyzed for experimental data collection for individual soybean grains. Second, we also utilized three different soybean varieties with relatively low (33.97%), medium (36.98%), and high protein (41.23%) contents to test the development process. Third, samples from each variety were prepared using whole bean and three different sample treatments (i.e., ground bean, whole meal, and ground meal). In each case, we modeled the data obtained using partial least squares (PLS) regression and assessed spectral metric-based multiple linear regression (metric-MLR) approaches to build robust prediction models. The metric-MLR models showed lower root mean square errors (RMSEPs), and hence better prediction, compared to corresponding classical PLS regression models for both bulk protein and oil for all treatment types. Comparing different sample preparation approaches, a lower RMSEPs was observed for whole meal treatment and thus the metric-MLR modeling with ground meal treatment was considered to be optimal protocol for bulk protein and oil prediction in soybean, with RMSEP values of 1.15 ± 0.04 (R²= 0.87) and 0.80 ± 0.02 (R²= 0.87) for bulk protein and oil, respectively. These predictions were nearly two- to threefold better (i.e., lower RMSEPs) than the corresponding NIR spectroscopy measurements (i.e., secondary gold standards in grain industry). For content prediction in whole soybean, incorporating physical attributes of individual grains in metric-MLR approach show up to 22% improvement in bulk protein and a relatively mild (up to ∼5%) improvement in bulk oil prediction. The unique combination of metric-MLR modeling approach (which is rare in the field of grain analysis) and sample treatments resulted in improved prediction models; using the physical attributes of individual grains is suggested as a novel measure for improving accuracy in prediction.

Reduction in sucrose contents by downregulation of fructose-1,6-bisphosphatase 2 causes tiller outgrowth cessation in rice mutants lacking glutamine synthetase1;2

BACKGROUND

Our previous transcriptomic analysis revealed that downregulation of nitrogen and carbon metabolism in the basal portions of the shoots inhibited cytosolic glutamine synthetase1;2 (GS1;2), which severely reduced rice tiller number. In the present study, we used rice mutants lacking GS1;2 (gs1;2 mutants) to determine the contribution of carbon metabolism to tiller growth.

RESULTS

Metabolomic analysis indicated the effects of carbon metabolism disorder such as reductions in the levels of sugar metabolites (e.g., sucrose and glucose 6-phosphate) in the shoot basal portions of the gs1;2 mutant seedlings. Decrease in sucrose caused by the lack of GS1;2 was successfully restored to the wild-type levels by introducing OsGS1;2 cDNA into the mutants. In the basal portions of the shoots, the lack of GS1;2 caused low expression of cytosolic fructose 1,6-bisphosphatase2 (OscFBP2), which is a key cytosolic sucrose synthesis enzyme; it is especially important in the phloem companion cells of the nodal vascular anastomoses. NH₄⁺ supply upregulated OscFBP2 expression in the shoot basal portions of the wild type but not in those of the gs1;2 mutants. Rice mutants lacking cFBPase2 presented with ~ 30% reduction in total cFBPase activity in the basal portions of their shoots. These mutants displayed reductions in sucrose levels of the basal portions of their shoots but not in their leaf blades. They also had relatively lower tiller numbers at the early growth stage.

CONCLUSIONS

Metabolomic analysis revealed that the lack of GS1;2 reduced sucrose metabolism in the basal portions of the shoots. Our results indicated that sucrose reduction was caused by the downregulation of OscFBP2 expression in the basal portions of the gs1;2 mutant shoots. The reduction in sucrose content caused by the lack of cFBPase2 resulted in lower tiller number at the early growth stage. Therefore, adequate sucrose supply via cFBPase2 may be necessary for tiller growth in the basal portions of rice shoots.

Effects of different storage conditions on the metabolite and microbial profiles of white rice (Oryza sativa L.)

Microbial populations in white rice (Oryza sativa L.) samples stored for 6 months in open or closed conditions were studied and their metabolite profiles analyzed using GC/MS to elucidate the relationship between storage and rice quality. Rice samples stored in open conditions at 25 °C were contaminated by Aspergillus tritici, Cladosporium cladosporioides, and Penicillium sp., whereas the control stored in closed conditions at 5 °C was mainly contaminated by Hyphopichia burtonii and A. tritici. These differences resulted in significantly different metabolite profiles. Increased mold population decreased the levels of fresh rice flavor-associated volatile metabolites and primary energy sources, but increased the levels of metabolites associated with lipid oxidation, polyols, and energy production. Thus, rice quality, especially flavor, could be significantly influenced by the increased mold population caused by open storage at 25 °C; volatile metabolites and polyols are potential indicators of rice quality.

Crop metabolomics: from diagnostics to assisted breeding

BACKGROUND

Until recently, plant metabolomics have provided a deep understanding on the metabolic regulation in individual plants as experimental units. The application of these techniques to agricultural systems subjected to more complex interactions is a step towards the implementation of translational metabolomics in crop breeding.

AIM OF REVIEW

We present here a review paper discussing advances in the knowledge reached in the last years derived from the application of metabolomic techniques that evolved from biomarker discovery to improve crop yield and quality.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Translational metabolomics applied to crop breeding programs.

Comparative Rice Bran Metabolomics across Diverse Cultivars and Functional Rice Gene⁻Bran Metabolite Relationships

Rice (Oryza sativa L.) processing yields ~60 million metric tons of bran annually. Rice genes producing bran metabolites of nutritional and human health importance were assessed across 17 diverse cultivars from seven countries using non-targeted metabolomics, and resulted in 378–430 metabolites. Gambiaka cultivar had the highest number and Njavara had the lowest number of metabolites. The 71 rice bran compounds of significant variation by cultivar included 21 amino acids, seven carbohydrates, two metabolites from cofactors and vitamins, 33 lipids, six nucleotides, and two secondary metabolites. Tryptophan, α-ketoglutarate, γ-tocopherol/β-tocopherol, and γ-tocotrienol are examples of bran metabolites with extensive cultivar variation and genetic information. Thirty-four rice bran components that varied between cultivars linked to 535 putative biosynthetic genes using to the OryzaCyc 4.0, Plant Metabolic Network database. Rice genes responsible for bran composition with animal and human health importance is available for rice breeding programs to utilize in crop improvement.

A Systems Analysis With "Simplified Source-Sink Model" Reveals Metabolic Reprogramming in a Pair of Source-to-Sink Organs During Early Fruit Development in Tomato by LED Light Treatments

Tomato (Solanum lycopersicum) is a model crop for studying development regulation and ripening in flesh fruits and vegetables. Supplementary light to maintain the optimal light environment can lead to the stable growth of tomatoes in greenhouses and areas without sufficient daily light integral. Technological advances in genome-wide molecular phenotyping have dramatically enhanced our understanding of metabolic shifts in the plant metabolism across tomato fruit development. However, comprehensive metabolic and transcriptional behaviors along the developmental process under supplementary light provided by light-emitting diodes (LEDs) remain to be fully elucidated. We present integrative omic approaches to identify the impact on the metabolism of a single tomato plant leaf exposed to monochromatic red LEDs of different intensities during the fruit development stage. Our special light delivery system, the "simplified source-sink model," involves the exposure of a single leaf below the second truss to red LED light of different intensities. We evaluated fruit-size- and fruit-shape variations elicited by different light intensities. Our findings suggest that more than high-light treatment (500 μmol m-2 s-1) with the red LED light is required to accelerate fruit growth for 2 weeks after anthesis. To investigate transcriptomic and metabolomic changes in leaf- and fruit samples we used microarray-, RNA sequencing-, and gas chromatography-mass spectrometry techniques. We found that metabolic shifts in the carbohydrate metabolism and in several key pathways contributed to fruit development, including ripening and cell-wall modification. Our findings suggest that the proposed workflow aids in the identification of key metabolites in the central metabolism that respond to monochromatic red-LED treatment and contribute to increase the fruit size of tomato plants. This study expands our understanding of systems-level responses mediated by low-, appropriate-, and high levels of red light irradiation in the fruit growth of tomato plants.

Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs

Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics-based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m-2·s-1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.

Transcriptomic and Metabolomic Reprogramming from Roots to Haustoria in the Parasitic Plant, Thesium chinense

Most plants show remarkable developmental plasticity in the generation of diverse types of new organs upon external stimuli, allowing them to adapt to their environment. Haustorial formation in parasitic plants is an example of such developmental reprogramming, but its molecular mechanism is largely unknown. In this study, we performed field-omics using transcriptomics and metabolomics to profile the molecular switch occurring in haustorial formation of the root parasitic plant, Thesium chinense, collected from its natural habitat. RNA-sequencing with de novo assembly revealed that the transcripts of very long chain fatty acid (VLCFA) biosynthesis genes, auxin biosynthesis/signaling-related genes and lateral root developmental genes are highly abundant in the haustoria. Gene co-expression network analysis identified a network module linking VLCFAs and the auxin-responsive lateral root development pathway. GC-TOF-MS analysis consistently revealed a unique metabolome profile with many types of fatty acids in the T. chinense root system, including the accumulation of a 25-carbon long chain saturated fatty acid in the haustoria. Our field-omics data provide evidence supporting the hypothesis that the molecular developmental machinery used for lateral root formation in non-parasitic plants has been co-opted into the developmental reprogramming of haustorial formation in the linage of parasitic plants.

[Development of Plant Metabolomics and Medicinal Plant Genomics]

 A variety of chemicals produced by plants, often referred to as 'phytochemicals', have been used as medicines, food, fuels and industrial raw materials. Recent advances in the study of genomics and metabolomics in plant science have accelerated our understanding of the mechanisms, regulation and evolution of the biosynthesis of specialized plant products. We can now address such questions as how the metabolomic diversity of plants is originated at the levels of genome, and how we should apply this knowledge to drug discovery, industry and agriculture. Our research group has focused on metabolomics-based functional genomics over the last 15 years and we have developed a new research area called 'Phytochemical Genomics'. In this review, the development of a research platform for plant metabolomics is discussed first, to provide a better understanding of the chemical diversity of plants. Then, representative applications of metabolomics to functional genomics in a model plant, Arabidopsis thaliana, are described. The extension of integrated multi-omics analyses to non-model specialized plants, e.g., medicinal plants, is presented, including the identification of novel genes, metabolites and networks for the biosynthesis of flavonoids, alkaloids, sulfur-containing metabolites and terpenoids. Further, functional genomics studies on a variety of medicinal plants is presented. I also discuss future trends in pharmacognosy and related sciences.

Metabolomic Evaluation of the Quality of Leaf Lettuce Grown in Practical Plant Factory to Capture Metabolite Signature

Vegetables produce metabolites that affect their taste and nutritional value and compounds that contribute to human health. The quality of vegetables grown in plant factories under hydroponic cultivation, e.g., their sweetness and softness, can be improved by controlling growth factors including the temperature, humidity, light source, and fertilizer. However, soil is cheaper than hydroponic cultivation and the visual phenotype of vegetables grown under the two conditions is different. As it is not clear whether their metabolite composition is also different, we studied leaf lettuce raised under the hydroponic condition in practical plant factory and strictly controlled soil condition. We chose two representative cultivars, "black rose" (BR) and "red fire" (RF) because they are of high economic value. Metabolite profiling by comprehensive gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) resulted in the annotation of 101 metabolites from 223 peaks detected by GC-MS; LC-MS yielded 95 peaks. The principal component analysis (PCA) scatter plot showed that the most distinct separation patterns on the first principal component (PC1) coincided with differences in the cultivation methods. There were no clear separations related to cultivar differences in the plot. PC1 loading revealed the discriminant metabolites for each cultivation method. The level of amino acids such as lysine, phenylalanine, tryptophan, and valine was significantly increased in hydroponically grown leaf lettuce, while soil-cultivation derived leaf lettuce samples contained significantly higher levels of fatty-acid derived alcohols (tetracosanol and hexacosanol) and lettuce-specific sesquiterpene lactones (lactucopicrin-15-oxalate and 15-deoxylactucin-8-sulfate). These findings suggest that the metabolite composition of leaf lettuce is primarily affected by its cultivation condition. As the discriminant metabolites reveal important factors that contribute to the nutritional value and taste characteristics of leaf lettuce, we performed comprehensive metabolite profiling to identify metabolite compositions, i.e., metabolite signature, that directly improve its quality and value.

Effects of Combined Low Glutathione with Mild Oxidative and Low Phosphorus Stress on the Metabolism of Arabidopsis thaliana

Plants possess highly sensitive mechanisms that monitor environmental stress levels for a dose-dependent fine-tuning of their growth and development. Differences in plant responses to severe and mild abiotic stresses have been recognized. Although many studies have revealed that glutathione can contribute to plant tolerance to various environmental stresses, little is known about the relationship between glutathione and mild abiotic stress, especially the effect of stress-induced altered glutathione levels on the metabolism. Here, we applied a systems biology approach to identify key pathways involved in the gene-to-metabolite networks perturbed by low glutathione content under mild abiotic stress in Arabidopsis thaliana. We used glutathione synthesis mutants (cad2-1 and pad2-1) and plants overexpressing the gene encoding γ-glutamylcysteine synthetase, the first enzyme of the glutathione biosynthetic pathway. The plants were exposed to two mild stress conditions-oxidative stress elicited by methyl viologen and stress induced by the limited availability of phosphate. We observed that the mutants and transgenic plants showed similar shoot growth as that of the wild-type plants under mild abiotic stress. We then selected the synthesis mutants and performed multi-platform metabolomics and microarray experiments to evaluate the possible effects on the overall metabolome and the transcriptome. As a common oxidative stress response, several flavonoids that we assessed showed overaccumulation, whereas the mild phosphate stress resulted in increased levels of specific kaempferol- and quercetin-glycosides. Remarkably, in addition to a significant increased level of sugar, osmolytes, and lipids as mild oxidative stress-responsive metabolites, short-chain aliphatic glucosinolates over-accumulated in the mutants, whereas the level of long-chain aliphatic glucosinolates and specific lipids decreased. Coordinated gene expressions related to glucosinolate and flavonoid biosynthesis also supported the metabolite responses in the pad2-1 mutant. Our results suggest that glutathione synthesis mutants accelerate transcriptional regulatory networks to control the biosynthetic pathways involved in glutathione-independent scavenging metabolites, and that they might reconfigure the metabolic networks in primary and secondary metabolism, including lipids, glucosinolates, and flavonoids. This work provides a basis for the elucidation of the molecular mechanisms involved in the metabolic and transcriptional regulatory networks in response to combined low glutathione content with mild oxidative and nutrient stress in A. thaliana.

Metabolomics for Plant Improvement: Status and Prospects

Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

Metabolome Analysis of Oryza sativa (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity

Oryza sativa L. (rice) is an important staple crop across the world. In the previous study, we identified 36 specialized (secondary) metabolites including 28 flavonoids. In the present study, a metabolome analysis using liquid chromatography-mass spectrometry was conducted on the leaf, bran, and brown and polished rice grains to better understand the distribution of these metabolites. Principal component analysis using the metabolome data clearly characterized the accumulation patterns of the metabolites. Flavonoids, e.g., tricin, tricin 7-O-rutinoside, and tricin 7-O-β-D-glucopyranoside, were mainly present in the leaf and bran but not in the polished grain. In addition, anti-inflammatory and anti-oxidant activity of the metabolites were assayed in vitro. Tricin 4'-O-(erythro-β-guaiacylglyceryl)ether and isoscoparin 2″-O-(6‴-(E)-feruloyl)-glucopyranoside showed the strongest activity for inhibiting nitric oxide (NO) production and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging, respectively.

Distribution of Hwc2-1, a causal gene of a hybrid weakness, in the World Rice Core collection and the Japanese Rice mini Core collection: its implications for varietal differentiation and artificial selection

A pair of complementary genes, Hwc1-1 at HWC1 locus and Hwc2-1 at HWC2 locus, cause a weakness phenomenon in rice. For this study, we performed haplotype analysis around the HWC2 locus in two core collections comprising 119 accessions. We also examined reactions to phenol and Xanthomonas oryzae pv. oryzae (Xoo) Japanese race I. To elucidate the genetic relations among all accessions, we analyzed their banding patterns of 40 Indel markers covering the rice genome. The classification by Indel markers was almost consistent with that using 4,357 SNPs. The testcross with Hwc1-1 carrier indicated that 37 accessions carried Hwc2-1 allele, whereas 82 carried hwc2-2 allele. Strong association between HWC2 and Ph genes was observed. Based on 14 DNA markers around HWC2 locus and Ph genotype, the 119 accessions were divided into 50 haplotypes. To examine the HWC2 candidate chromosomal region specifically, the 'haplotype group' characterized by the six DNA markers closely linked with HWC2 were analyzed. Hwc2-1 carriers had the same haplotype group. Some hwc2-2 haplotype groups were associated with resistance against the Xoo race. The relation between varietal differentiation and haplotypes around the HWC2 locus was discussed, along with its breeding significance.

Web Server for Peak Detection, Baseline Correction, and Alignment in Two-Dimensional Gas Chromatography Mass Spectrometry-Based Metabolomics Data

Two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC/TOF-MS) is superior for chromatographic separation and provides great sensitivity for complex biological fluid analysis in metabolomics. However, GC×GC/TOF-MS data processing is currently limited to vendor software and typically requires several preprocessing steps. In this work, we implement a web-based platform, which we call GC²MS, to facilitate the application of recent advances in GC×GC/TOF-MS, especially for metabolomics studies. The core processing workflow of GC²MS consists of blob/peak detection, baseline correction, and blob alignment. GC²MS treats GC×GC/TOF-MS data as pictures and clusters the pixels as blobs according to the brightness of each pixel to generate a blob table. GC²MS then aligns the blobs of two GC×GC/TOF-MS data sets according to their distance and similarity. The blob distance and similarity are the Euclidean distance of the first and second retention times of two blobs and the Pearson's correlation coefficient of the two mass spectra, respectively. GC²MS also directly corrects the raw data baseline. The analytical performance of GC²MS was evaluated using GC×GC/TOF-MS data sets of Angelica sinensis compounds acquired under different experimental conditions and of human plasma samples. The results show that GC²MS is an easy-to-use tool for detecting peaks and correcting baselines, and GC²MS is able to align GC×GC/TOF-MS data sets acquired under different experimental conditions. GC²MS is freely accessible at http://gc2ms.web.cmdm.tw .

Adaptation of the symbiotic Mesorhizobium-chickpea relationship to phosphate deficiency relies on reprogramming of whole-plant metabolism

Low inorganic phosphate (Pi) availability is a major constraint for efficient nitrogen fixation in legumes, including chickpea. To elucidate the mechanisms involved in nodule acclimation to low Pi availability, two Mesorhizobium-chickpea associations exhibiting differential symbiotic performances, Mesorhizobium ciceri CP-31 (McCP-31)-chickpea and Mesorhizobium mediterranum SWRI9 (MmSWRI9)-chickpea, were comprehensively studied under both control and low Pi conditions. MmSWRI9-chickpea showed a lower symbiotic efficiency under low Pi availability than McCP-31-chickpea as evidenced by reduced growth parameters and down-regulation of nifD and nifK These differences can be attributed to decline in Pi level in MmSWRI9-induced nodules under low Pi stress, which coincided with up-regulation of several key Pi starvation-responsive genes, and accumulation of asparagine in nodules and the levels of identified amino acids in Pi-deficient leaves of MmSWRI9-inoculated plants exceeding the shoot nitrogen requirement during Pi starvation, indicative of nitrogen feedback inhibition. Conversely, Pi levels increased in nodules of Pi-stressed McCP-31-inoculated plants, because these plants evolved various metabolic and biochemical strategies to maintain nodular Pi homeostasis under Pi deficiency. These adaptations involve the activation of alternative pathways of carbon metabolism, enhanced production and exudation of organic acids from roots into the rhizosphere, and the ability to protect nodule metabolism against Pi deficiency-induced oxidative stress. Collectively, the adaptation of symbiotic efficiency under Pi deficiency resulted from highly coordinated processes with an extensive reprogramming of whole-plant metabolism. The findings of this study will enable us to design effective breeding and genetic engineering strategies to enhance symbiotic efficiency in legume crops.

Integrated metabolomics and phytochemical genomics approaches for studies on rice

Metabolomics is widely employed to monitor the cellular metabolic state and assess the quality of plant-derived foodstuffs because it can be used to manage datasets that include a wide range of metabolites in their analytical samples. In this review, we discuss metabolomics research on rice in order to elucidate the overall regulation of the metabolism as it is related to the growth and mechanisms of adaptation to genetic modifications and environmental stresses such as fungal infections, submergence, and oxidative stress. We also focus on phytochemical genomics studies based on a combination of metabolomics and quantitative trait locus (QTL) mapping techniques. In addition to starch, rice produces many metabolites that also serve as nutrients for human consumers. The outcomes of recent phytochemical genomics studies of diverse natural rice resources suggest there is potential for using further effective breeding strategies to improve the quality of ingredients in rice grains.

Amyloplast Membrane Protein SUBSTANDARD STARCH GRAIN6 Controls Starch Grain Size in Rice Endosperm

Starch is a biologically and commercially important polymer of glucose. Starch is organized into starch grains (SGs) inside amyloplasts. The SG size differs depending on the plant species and is one of the most important factors for industrial applications of starch. There is limited information on genetic factors regulating SG sizes. In this study, we report the rice (Oryza sativa) mutant substandard starch grain6 (ssg6), which develops enlarged SGs in endosperm. Enlarged SGs are observed starting at 3 d after flowering. During endosperm development, a number of smaller SGs appear and coexist with enlarged SGs in the same cells. The ssg6 mutation also affects SG morphologies in pollen. The SSG6 gene was identified by map-based cloning and microarray analysis. SSG6 encodes a protein homologous to aminotransferase. SSG6 differs from other rice homologs in that it has a transmembrane domain. SSG6-green fluorescent protein is localized in the amyloplast membrane surrounding SGs in rice endosperm, pollen, and pericarp. The results of this study suggest that SSG6 is a novel protein that controls SG size. SSG6 will be a useful molecular tool for future starch breeding and applications.

Unbiased profiling of volatile organic compounds in the headspace of Allium plants using an in-tube extraction device

BACKGROUND

Plants produce and emit important volatile organic compounds (VOCs), which have an essential role in biotic and abiotic stress responses and in plant-plant and plant-insect interactions. In order to study the bouquets from plants qualitatively and quantitatively, a comprehensive, analytical method yielding reproducible results is required.

RESULTS

We applied in-tube extraction (ITEX) and solid-phase microextraction (SPME) for studying the emissions of Allium plants. The collected HS samples were analyzed by gas chromatography-time-of-flight-mass spectrometry (GC-TOF-MS), and the results were subjected to multivariate analysis. In case of ITEX-method Allium cultivars released more than 300 VOCs, out of which we provisionally identified 50 volatiles. We also used the VOC profiles of Allium samples to discriminate among groups of A. fistulosum, A. chinense (rakkyo), and A. tuberosum (Oriental garlic). As we found 12 metabolite peaks including dipropyl disulphide with significant changes in A. chinense and A. tuberosum when compared to the control cultivar, these metabolite peaks can be used for chemotaxonomic classification of A. chinense, tuberosum, and A. fistulosum.

CONCLUSIONS

Compared to SPME-method our ITEX-based VOC profiling technique contributes to automatic and reproducible analyses. Hence, it can be applied to high-throughput analyses such as metabolite profiling.

Metabolic Effects of the pksCT Gene on Monascus aurantiacus Li As3.4384 Using Gas Chromatography--Time-of-Flight Mass Spectrometry-Based Metabolomics

Monascus spp. have been used for the production of natural pigments and bioactive compounds in China for several centuries. Monascus can also produce the mycotoxin citrinin, restricting its use. Disruption of the pksCT gene in Monascus aurantiacus Li AS3.4384 reduces citrinin production capacity of this strain (Monascus PHDS26) by over 98%. However, it is unclear how other metabolites of M. aurantiacus Li AS3.4384 (the wild-type strain) are affected by the pksCT gene. Here, we used metabolomic analyses to compare red yeast rice (RYR) metabolite profiles of the wild-type strain and Monascus PHDS26 at different stages of solid-state fermentation. A total of 18 metabolites forming components within the glycolysis, acetyl-CoA, amino acid, and tricarboxylic acid (TCA) cycle metabolic processes were found to be altered between the wild-type strain and Monascus PHDS26 at different stages of solid-state fermentation. Thus, these findings provide important insights into the metabolic pathways affected by the pksCT gene in M. aurantiacus.

Understanding salinity responses and adopting 'omics-based' approaches to generate salinity tolerant cultivars of rice

Soil salinity is one of the main constraints affecting production of rice worldwide, by reducing growth, pollen viability as well as yield of the plant. Therefore, detailed understanding of the response of rice towards soil salinity at the physiological and molecular level is a prerequisite for its effective management. Various approaches have been adopted by molecular biologists or breeders to understand the mechanism for salinity tolerance in plants and to develop salt tolerant rice cultivars. Genome wide analysis using 'omics-based' tools followed by identification and functional validation of individual genes is becoming one of the popular approaches to tackle this task. On the other hand, mutation breeding and insertional mutagenesis has also been exploited to obtain salinity tolerant crop plants. This review looks into various responses at cellular and whole plant level generated in rice plants toward salinity stress thus, evaluating the suitability of intervention of functional genomics to raise stress tolerant plants. We have tried to highlight the usefulness of the contemporary 'omics-based' approaches such as genomics, proteomics, transcriptomics and phenomics towards dissecting out the salinity tolerance trait in rice. In addition, we have highlighted the importance of integration of various 'omics' approaches to develop an understanding of the machinery involved in salinity response in rice and to move forward to develop salt tolerant cultivars of rice.

The Stable Level of Glutamine synthetase 2 Plays an Important Role in Rice Growth and in Carbon-Nitrogen Metabolic Balance

Glutamine synthetase 2 (GS2) is a key enzyme involved in the ammonium metabolism in plant leaves. In our previous study, we obtained GS2-cosuppressed plants, which displayed a normal growth phenotype at the seedling stage, while at the tillering stage they showed a chlorosis phenotype. In this study, to investigate the chlorosis mechanism, we systematically analyzed the plant growth, carbon-nitrogen metabolism and gene expressions between the GS2-cosuppressed rice and wild-type plants. The results revealed that the GS2-cosuppressed plants exhibited a poor plant growth phenotype and a poor nitrogen transport ability, which led to nitrogen accumulation and a decline in the carbon/nitrogen ratio in the stems. Interestingly, there was a higher concentration of soluble proteins and a lower concentration of carbohydrates in the GS2-cosuppressed plants at the seedling stage, while a contrasting result was displayed at the tillering stage. The analysis of the metabolic profile showed a significant increase of sugars and organic acids. Additionally, gene expression patterns were different in root and leaf of GS2-cosuppressed plants between the seedling and tillering stage. These results indicated the important role of a stable level of GS2 transcription during normal rice development and the importance of the carbon-nitrogen metabolic balance in rice growth.

Effect of genetic and climatic variability on the metabolic profiles of black gram (Vigna mungo L.) seeds and sprouts

BACKGROUND

Black gram is becoming increasingly of interest for consumers worldwide. The metabolomics have been conducted to reflect the life history of each individual plant. The metabolic pattern of black gram seeds and sprouts was profiled to investigate genetic and climatic influences on a broad range of chemical constituents.

RESULTS

Distinct differences in metabolite profiles among three black gram varieties for both intact seeds and sprouts were observed. The differential impact of climate on metabolite profiles of the variety Chai Nat 80 during both dry and rainy seasons was investigated. Univariate statistical analysis demonstrated that greater maturity due to adequate moisture in the rainy season led to a higher content of nutritionally relevant polar metabolites, whereas the dry season resulted in a high relative amount of storage lipid because of immaturity due to insufficient rain and water supply.

CONCLUSION

The investigation confirmed the potential of metabolite profiling to assist in breeding and farming practices.

Overexpressing of OsAMT1-3, a High Affinity Ammonium Transporter Gene, Modifies Rice Growth and Carbon-Nitrogen Metabolic Status

AMT1-3 encodes the high affinity NH₄⁺ transporter in rice roots and is predominantly expressed under nitrogen starvation. In order to evaluate the effect of AMT1-3 gene on rice growth, nitrogen absorption and metabolism, we generated AMT1-3-overexpressing plants and analyzed the growth phenotype, yield, carbon and nitrogen metabolic status, and gene expression profiles. Although AMT1-3 mRNA accumulated in transgenic plants, these plants displayed significant decreases in growth when compared to the wild-type plants. The nitrogen uptake assay using a 15N tracer revealed poor nitrogen uptake ability in AMT1-3-overexpressing plants. We found significant decreases in AMT1-3-overexpressing plant leaf carbon and nitrogen content accompanied with a higher leaf C/N ratio. Significant changes in soluble proteins and carbohydrates were also observed in AMT1-3-overexpressing plants. In addition, metabolite profile analysis demonstrated significant changes in individual sugars, organic acids and free amino acids. Gene expression analysis revealed distinct expression patterns of genes that participate in carbon and nitrogen metabolism. Additionally, the correlation between the metabolites and gene expression patterns was consistent in AMT1-3-overexpressing plants under both low and high nitrogen growth conditions. Therefore, we hypothesized that the carbon and nitrogen metabolic imbalance caused by AMT1-3 overexpressing attributed to the poor growth and yield of transgenic plants.