Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

Comparative Analysis of Protein Extraction Protocols for Olive Leaf Proteomics: Insights into Differential Protein Abundance and Isoelectric Point Distribution

Plant proteomics studies face two major challenges: limited databases due to the need for sequenced genomes and the difficulty in obtaining high-quality protein extracts. Olive (Olea europaea), a key species in Mediterranean flora known for its rich biochemical content, presents additional complexity due to its lipidic structure and high levels of inhibitory compounds that hinder protein extraction. Consequently, various studies have focused on optimizing the protein extraction methods for olives. While different extraction protocols exist for leaf proteome analysis, their compatibility with LC-MS/MS has been scarcely studied. This work was carried out to compare three protein extraction protocols for LC-MS/MS analysis using olive (O. europaea L) leaf tissue. Denaturing SDS (Method A), physiological CHAPS (Method B), and phenolic TCA/acetone (Method C) were evaluated with LC-MS/MS data. The quantitative comparisons of the three extraction methods revealed that Protocol A gave the greatest yields. According to the results obtained, Protocol A uniquely identified 77 proteins, Protocol B identified 10 unique proteins, and Protocol C identified 19 unique proteins. Similarly, the peptide sequence analysis showed that Protocol A uniquely identified 208 peptide sequences, Protocol B identified 29, and Protocol C identified 36. Moreover, reversed-phase high-performance liquid chromatography (RP-HPLC) results suggest that Method A may be more efficient in removing and retaining hydrophobic proteins. Overall, Protocol A demonstrated greater sensitivity, efficiency, and reproducibility in LC-MS/MS analysis.

Recent Progress in Rice-Xanthomonas oryzae Interactions

Rice bacterial blight (BB) and bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively, are among the most devastating bacterial diseases threatening global rice production. The interactions between rice and Xanthomonas oryzae are complex and dynamic, involving recognition, attack, defense, and adaptation mechanisms enacted by both the rice host and the pathogens. This review summarizes recent advances in understanding rice-Xanthomonas oryzae interactions, focusing on infection models, pathogenic mechanisms, and immune responses elicited by Xanthomonas oryzae. Special attention is devoted to the roles of transcription activator-like effectors (TALEs) and non-TALE effectors in pathogenicity, the functions of resistance (R) genes in defense, and the interconnected molecular networks of interactions derived from multi-omics approaches. Understanding these interactions is essential for developing effective disease-resistance strategies and creating elite disease-resistant rice varieties.

Can the molecular and transgenic breeding of crops be an alternative and sustainable technology to meet food demand?

The gradual increase in the worldwide population represents various challenges, and one of the most alarming being the food demand. Historically technological advances led to the development of crops that meets the requirements and demands. Currently, molecular breeding unlocks the genetic potential of crops for their improvement, positioning it as a key technology for the development of new crops. The implementation of OMICs sciences, such spatial and single cell transcriptomics is providing a large and precise information, which can be exploited for crop improvement related to increasing yield, improving the nutritional value; designing new strategies for diseases resistance and management and for conserving biodiversity. Furthermore, the use of new technologies such CRISPR/CAS9 brought us the ability to modify the selected regions of the genome to select the superior's genotypes at a short time and the use of artificial intelligence aid in the analysis of big data generated by OMICS sciences. On the other hand, the application of molecular improvement technologies open up discussion on global regulatory measures, the socio-economic and socio-ethics, as the frameworks on its global regulation and its impact on the society create the public perception on its acceptance. In this review, the use and impact of OMICs sciences and genetic engineering in crops development, the regulatory measures, the socio-economic impact and as well as the mediatic information on genetically modified crops worldwide is discussed along with comprehensive insights on the potential of molecular plant breeding as an alternative and sustainable technology to meet global food demand.

Deciphering nutrient stress in plants: integrative insight from metabolomics and proteomics

To comprehend the responses and resilience of plants under unfavorable environmental conditions, it is crucial to study the metabolomics and proteomic insights into nutrient stress. Nutrient stress substantially challenges agriculture, impacting plant growth, development, and productivity due to a lack or imbalance of essential nutrients, which can happen due to poor soil quality, limited nutrient availability, or unfavorable climatic conditions. Although there has been significant progress in the study of plant nutrient stress using metabolomics and proteomics, several challenges and research gaps still need to be addressed, such as the standardized experimental protocols, data integration strategies, and bioinformatic tools are necessary for comparative analysis and interpretation of omics data. Hence, this review explores the theoretical frameworks of metabolomics and proteomics as powerful tools to decode plant responses to nutrient stress, addressing critical knowledge gaps in the field. This review highlights the advantages of integrative analyses, combining metabolomics, proteomics, and transcriptomics, to uncover the molecular networks governing nutrient stress resilience. Key findings underscore the potential of these techniques to enhance breeding strategies and genetic engineering efforts aimed at developing nutrient-efficient crops. Through metabolomics and proteomic analyses, novel molecular components and regulatory networks have been revealed as responsive to nutrient stress, and this breakthrough has the potential to bolster plant resilience and optimize nutrient utilization. Understanding the synergistic roles of metabolites and proteins in nutrient stress resilience has profound implications for crop improvement and agricultural sustainability. Future research should focus on refining integrative methodologies and exploring their applications across diverse plant species and environmental conditions, paving the way for innovative solutions to nutrient stress challenges.

Decrypting proteomics, transcriptomics, genomics, and integrated omics for augmenting the abiotic, biotic, and climate change stress resilience in plants

As our planet faces increasing environmental challenges, such as biotic pressures, abiotic stressors, and climate change, it is crucial to understand the complex mechanisms that underlie stress responses in crop plants. Over past few years, the integration of techniques of proteomics, transcriptomics, and genomics like LC-MS, IT-MS, MALDI-MS, DIGE, ESTs, SAGE, WGS, GWAS, GBS, 2D-PAGE, CRISPR-Cas, cDNA-AFLP, HLS, HRPF, MPSS, CAGE, MAS, IEF, MudPIT, SRM/MRM, SWATH-MS, ESI have significantly enhanced our ability to comprehend the molecular pathways and regulatory networks, involved in balancing the ecosystem/ecology stress adaptation. This review offers thorough synopsis of the current research on utilizing these multi-omics methods (including metabolomics, ionomics) for battling abiotic (salinity, temperature (chilling/freezing/cold/heat), flood (hypoxia), drought, heavy metals/loids), biotic (pathogens like fungi, bacteria, virus, pests, and insects (aphids, caterpillars, moths, mites, nematodes) and climate change stress (ozone, ultraviolet radiation, green house gases, carbon dioxide). These strategies can expedite crop improvement, and act as powerful tools with high throughput and instant database generation rates. They also provide a platform for interpreting intricate, systematic signalling pathways and knowing how different environmental stimuli cause phenotypic responses at cellular and molecular level by changing the expression of stress-responsive genes like RAB18, KIN1, RD29B, OsCIPK03, OsSTL, SIAGL, bZIP, SnRK, ABF. This review discusses various case studies that exemplify the successful implementation of these omics tools to enhance stress tolerance in plants. Finally, it highlights challenges and future prospects of utilizing these approaches in combating stress, emphasizing the need for interdisciplinary collaborations and bio-technological advancements for sustainable agriculture and food security.

A Cytosolic Phosphoglucose Isomerase, OsPGI1c, Enhances Plant Growth and Herbivore Resistance in Rice

Glucose-6-phosphate isomerase (PGI), a key enzyme that catalyzes the reversible conversion of glucose-6-phosphate and fructose-6-phosphate, plays an important role in plant growth, development, and responses to abiotic stresses and pathogen infections. However, whether and how PGI modulates herbivore-induced plant defenses remain largely unknown. The Brown planthopper (BPH, Nilaparvata lugens) is a devastating insect pest of rice, causing significant damage to rice plants through feeding, oviposition, and disease transmission, resulting in great yield losses. Here, we isolated a rice cytosolic PGI gene, OsPGI1c, which is ubiquitously expressed in rice plants; the highest transcript levels are found in leaves, outer leaf sheaths, and seeds. The expression of OsPGI1c was induced by infestation by gravid females of the BPH, mechanical wounding, and treatment with jasmonic acid (JA). Overexpressing OsPGI1c in rice (oePGI) enhanced both the masses of plant shoots and roots and basal levels of trehalose; however, when infested by gravid BPH females for 2 days, trehalose levels were significantly lower in oePGI plants than in wild-type (WT) plants. Additionally, the overexpression of OsPGI1c increased the BPH-induced levels of JA, jasmonoyl-L-isoleucine, and abscisic acid, but decreased the levels of ethylene and H2O2. Bioassays revealed that gravid BPH females preferred WT plants over oePGI plants for laying eggs; moreover, BPH eggs exhibited lower hatching rates and required longer developmental durations on oePGI plants than WT plants. These results indicate that OsPGI1c positively modulates both rice growth and BPH resistance.

NMR-Based Metabolomic Analysis of Biotic Stress Responses in the Traditional Korean Landrace Red Pepper (Capsicum annuum var. annuum, cv. Subicho)

Korean landrace red peppers (Capsicum annuum var. Subicho), such as the traditional representative Subicho variety, are integral to Korean foods and are often consumed raw or used as a dried powder for cuisine. However, the known vulnerability of local varieties of landrace to biotic stresses can compromise their quality and yield. We employed nuclear magnetic resonance (NMR) spectroscopy coupled with a multivariate analysis to uncover and compare the metabolomic profiles of healthy and biotic-stressed Subicho peppers. We identified 42 metabolites, with significant differences between the groups. The biotic-stressed Subicho red peppers exhibited lower sucrose levels but heightened concentrations of amino acids, particularly branched-chain amino acids (valine, leucine, and isoleucine), suggesting a robust stress resistance mechanism. The biotic-stressed red peppers had increased levels of TCA cycle intermediates (acetic, citric, and succinic acids), nitrogen metabolism-related compounds (alanine, asparagine, and aspartic acid), aromatic amino acids (tyrosine, phenylalanine, and tryptophan), and γ-aminobutyric acid. These findings reveal the unique metabolic adaptations of the Subicho variety, underscoring its potential resilience to biotic stresses. This novel insight into the stress response of the traditional Subicho pepper can inform strategies for developing targeted breeding programs and enhancing the quality and economic returns in the pepper and food industries.

Analysis of drought and heat stress response genes in rice using co-expression network and differentially expressed gene analyses

Studies on Oryza sativa (rice) are crucial for improving agricultural productivity and ensuring global sustenance security, especially considering the increasing drought and heat stress caused by extreme climate change. Currently, the genes and mechanisms underlying drought and heat resistance in rice are not fully understood, and the scope for enhancing the development of new strains remains considerable. To accurately identify the key genes related to drought and heat stress responses in rice, multiple datasets from the Gene Expression Omnibus (GEO) database were integrated in this study. A co-expression network was constructed using a Weighted Correlation Network Analysis (WGCNA) algorithm. We further distinguished the core network and intersected it with differentially expressed genes and multiple expression datasets for screening. Differences in gene expression levels were verified using quantitative real-time polymerase chain reaction (PCR). OsDjC53, MBF1C, BAG6, HSP23.2, and HSP21.9 were found to be associated with the heat stress response, and it is also possible that UGT83A1 and OsCPn60a1, although not directly related, are affected by drought stress. This study offers significant insights into the molecular mechanisms underlying stress responses in rice, which could promote the development of stress-tolerant rice breeds.

Phenazine biosynthesis protein MoPhzF regulates appressorium formation and host infection through canonical metabolic and noncanonical signaling function in Magnaporthe oryzae

Microbe-produced secondary metabolite phenazine-1-carboxylic acid (PCA) facilitates pathogen virulence and defense mechanisms against competitors. Magnaporthe oryzae, a causal agent of the devastating rice blast disease, needs to compete with other phyllosphere microbes and overcome host immunity for successful colonization and infection. However, whether M. oryzae produces PCA or it has any other functions remains unknown. Here, we found that the MoPHZF gene encodes the phenazine biosynthesis protein MoPhzF, synthesizes PCA in M. oryzae, and regulates appressorium formation and host virulence. MoPhzF is likely acquired through an ancient horizontal gene transfer event and has a canonical function in PCA synthesis. In addition, we found that PCA has a role in suppressing the accumulation of host-derived reactive oxygen species (ROS) during infection. Further examination indicated that MoPhzF recruits both the endoplasmic reticulum membrane protein MoEmc2 and the regulator of G-protein signaling MoRgs1 to the plasma membrane (PM) for MoRgs1 phosphorylation, which is a critical regulatory mechanism in appressorium formation and pathogenicity. Collectively, our studies unveiled a canonical function of MoPhzF in PCA synthesis and a noncanonical signaling function in promoting appressorium formation and host infection.

Barnyard Grass Stress Triggers Changes in Root Traits and Phytohormone Levels in Allelopathic and Non-Allelopathic Rice

Despite the growing knowledge concerning allelopathic interference with barnyard grass, little is understood regarding the competitive physiological mechanisms of the interaction between allelopathic rice and herbicide-resistant barnyard grass. A hydroponic system was employed to investigate the root morphological traits and different phytohormonal changes in allelopathic and non-allelopathic rice cultivars when co-planted with quinclorac-resistant and -susceptible barnyard grass, respectively. The results show that shoot and root biomass were greater in PI. Barnyard grass stress induced an increase in shoot and root biomass in PI at 7 and 14 days of co-culturing rice and barnyard grass. Especially under the stress of quinclorac-resistant barnyard grass, the shoot biomass of PI increased by 23% and 68%, respectively, and the root biomass increased by 37% and 34%, respectively. In terms of root morphology, PI exhibited a significantly higher fine-root length, in root diameters of <0.5 mm, a greater number of root tips, and longer root tips compared to LE. The response to quinclorac-resistant barnyard grass stress was consistent in terms of the SA and JA content. The obvious accumulation of SA and JA was observed in two rice cultivars under quinclorac-resistant barnyard grass stress, with greater amounts of SA and JA in PI. The significant decrease in auxin (IAA) and abscisic acid (ABA) content in rice was detected from 7 to 14 days under co-culture stress. Additionally, highly significant and positive correlations were found between SA and JA content, and the number of root tips and root tip length at root diameters of 0-0.5 mm in rice.

Molecular Advances to Combat Different Biotic and Abiotic Stresses in Linseed (Linum usitatissimum L.): A Comprehensive Review

Flax, or linseed, is considered a "superfood", which means that it is a food with diverse health benefits and potentially useful bioactive ingredients. It is a multi-purpose crop that is prized for its seed oil, fibre, nutraceutical, and probiotic qualities. It is suited to various habitats and agro-ecological conditions. Numerous abiotic and biotic stressors that can either have a direct or indirect impact on plant health are experienced by flax plants as a result of changing environmental circumstances. Research on the impact of various stresses and their possible ameliorators is prompted by such expectations. By inducing the loss of specific alleles and using a limited number of selected varieties, modern breeding techniques have decreased the overall genetic variability required for climate-smart agriculture. However, gene banks have well-managed collectionns of landraces, wild linseed accessions, and auxiliary Linum species that serve as an important source of novel alleles. In the past, flax-breeding techniques were prioritised, preserving high yield with other essential traits. Applications of molecular markers in modern breeding have made it easy to identify quantitative trait loci (QTLs) for various agronomic characteristics. The genetic diversity of linseed species and the evaluation of their tolerance to abiotic stresses, including drought, salinity, heavy metal tolerance, and temperature, as well as resistance to biotic stress factors, viz., rust, wilt, powdery mildew, and alternaria blight, despite addressing various morphotypes and the value of linseed as a supplement, are the primary topics of this review.

The Effects of Insect Infestation on Stored Agricultural Products and the Quality of Food

In this review article, we focus on the effects of insect pests on the quality of stored cereals and legume grains. The changes in the amino-acid content, the quality of proteins, carbohydrates, and lipids, and the technological characteristics of the raw materials when infested by specific insects are presented. The differences reported concerning the rate and kind of infestation effects are related to the trophic habits of the infesting insect species, the variation of the component distribution in the different species of grains, and the length of the storage period. For example, wheat germ and brans feeders such as Trogoderma granarium may cause a higher reduction in proteins than endosperm feeders such as Rhyzopertha dominica, since the germ and brans contain higher concentrations of proteins. Trogoderma granarium may also cause higher reduction in lipids than R. dominica in wheat, maize and sorghum, in which most of the lipids exist in the germ. Furthermore, infestation with insects such as Tribolium castaneum may downgrade the overall quality of wheat flour, by increasing the moisture content, the number of insect fragments, the color change, the concentration of uric acid, the microbial growth, and the prevalence of aflatoxins. Whenever possible, the significance of the insect infestation and the concomitant compositional alterations on human health are presented. It should be highlighted that understanding the impact of insect infestation on stored agricultural products and the quality of food will be crucial for the required food security in the future.

Omics Approaches in Invasion Biology: Understanding Mechanisms and Impacts on Ecological Health

Invasive species and rapid climate change are affecting the control of new plant diseases and epidemics. To effectively manage these diseases under changing environmental conditions, a better understanding of pathophysiology with holistic approach is needed. Multiomics approaches can help us to understand the relationship between plants and microbes and construct predictive models for how they respond to environmental stresses. The application of omics methods enables the simultaneous analysis of plant hosts, soil, and microbiota, providing insights into their intricate relationships and the mechanisms underlying plant-microbe interactions. This can help in the development of novel strategies for enhancing plant health and improving soil ecosystem functions. The review proposes the use of omics methods to study the relationship between plant hosts, soil, and microbiota, with the aim of developing a new technique to regulate soil health. This approach can provide a comprehensive understanding of the mechanisms underlying plant-microbe interactions and contribute to the development of effective strategies for managing plant diseases and improving soil ecosystem functions. In conclusion, omics technologies offer an innovative and holistic approach to understanding plant-microbe interactions and their response to changing environmental conditions.

A Proteomics Insight into Advancements in the Rice-Microbe Interaction

Rice is one of the most-consumed foods worldwide. However, the productivity and quality of rice grains are severely constrained by pathogenic microbes. Over the last few decades, proteomics tools have been applied to investigate the protein level changes during rice-microbe interactions, leading to the identification of several proteins involved in disease resistance. Plants have developed a multi-layered immune system to suppress the invasion and infection of pathogens. Therefore, targeting the proteins and pathways associated with the host's innate immune response is an efficient strategy for developing stress-resistant crops. In this review, we discuss the progress made thus far with respect to rice-microbe interactions from side views of the proteome. Genetic evidence associated with pathogen-resistance-related proteins is also presented, and challenges and future perspectives are highlighted in order to understand the complexity of rice-microbe interactions and to develop disease-resistant crops in the future.

Negative impacts of nanoplastics on the purification function of submerged plants in constructed wetlands: Responses of oxidative stress and metabolic processes

Constructed wetlands (CWs) are an important barrier to prevent nanoplastics (NPs) and microplastics (MPs) from entering receiving streams. However, little is known about how the accumulation of NPs affects the growth, photosynthesis, oxidative stress responses, and metabolism of plants, especially submerged plants that are widely used in CWs for water purification. Herein, we adopted Utricularia vulgaris (U. vulgaris), a typical submerged macrophyte as the model plant to address the above knowledge gaps under exposure to polystyrene NPs (PS-NPs, 500 nm, 0∼10 mg·L^-1). Results showed that PS-NPs were absorbed by insect traps and further transported to stems and leaves of U. vulgaris, which limited plant height (6.8∼72.9%), relative growth rate (7.4∼17.2%), and photosynthesis (3.7∼28.2%). U. vulgaris suffered from oxidative stresses, as evidenced by the increase in malondialdehyde, antioxidant enzymes (catalase, peroxidase, and superoxide dismutase), and H₂O₂, especially under 1 and 10 mg·L^-1. Abundances of 548 metabolites were quantified, and 291 metabolites were detected with altered levels after exposure, in which 25∼34% metabolites were up-regulated, and 32∼40% metabolites were down-regulated in metabolite expression. Metabolic pathways of the tricarboxylic acid cycle and amino acid were disrupted, in which citric acid, threonine, and adenine decreased, while amino acids (like serine, phenylalanine, histidine, etc.) increased first and then decreased with increasing PS-NPs concentrations. Moreover, PS-NPs reduced the removal efficiency of total nitrogen and phosphorus from water by U. vulgaris, bringing potential risks to aquatic ecosystems. These findings have greatly enhanced our understanding of the metabolic mechanisms and interactions of aquatic macrophytes that are heavily used in CWs in response to NPs stress, as well as the impact of NPs on CWs functioning.

TIR1/AFB proteins: Active players in abiotic and biotic stress signaling

The TIR1/AFB family of proteins is a group of functionally diverse auxin receptors that are only found in plants. TIR1/AFB family members are characterized by a conserved N-terminal F-box domain followed by 18 leucine-rich repeats. In the past few decades, extensive research has been conducted on the role of these proteins in regulating plant development, metabolism, and responses to abiotic and biotic stress. In this review, we focus on TIR1/AFB proteins that play crucial roles in plant responses to diverse abiotic and biotic stress. We highlight studies that have shed light on the mechanisms by which TIR1/AFB proteins are regulated at the transcriptional and post-transcriptional as well as the downstream in abiotic or biotic stress pathways regulated by the TIR1/AFB family.

Combined Proteomic and Metabolomic Analysis of the Molecular Mechanism Underlying the Response to Salt Stress during Seed Germination in Barley

Salt stress is a major abiotic stress factor affecting crop production, and understanding of the response mechanisms of seed germination to salt stress can help to improve crop tolerance and yield. The differences in regulatory pathways during germination in different salt-tolerant barley seeds are not clear. Therefore, this study investigated the responses of different salt-tolerant barley seeds during germination to salt stress at the proteomic and metabolic levels. To do so, the proteomics and metabolomics of two barley seeds with different salt tolerances were comprehensively examined. Through comparative proteomic analysis, 778 differentially expressed proteins were identified, of which 335 were upregulated and 443 were downregulated. These proteins, were mainly involved in signal transduction, propanoate metabolism, phenylpropanoid biosynthesis, plant hormones and cell wall stress. In addition, a total of 187 salt-regulated metabolites were identified in this research, which were mainly related to ABC transporters, amino acid metabolism, carbohydrate metabolism and lipid metabolism; 72 were increased and 112 were decreased. Compared with salt-sensitive materials, salt-tolerant materials responded more positively to salt stress at the protein and metabolic levels. Taken together, these results suggest that salt-tolerant germplasm may enhance resilience by repairing intracellular structures, promoting lipid metabolism and increasing osmotic metabolites. These data not only provide new ideas for how seeds respond to salt stress but also provide new directions for studying the molecular mechanisms and the metabolic homeostasis of seeds in the early stages of germination under abiotic stresses.

Heterologous overexpression of PDH45 gene of pea provides tolerance against sheath blight disease and drought stress in rice

Biotic and abiotic stress tolerant crops are required for sustainable agriculture as well as ensuring global food security. In a previous study, we have reported that heterologous overexpression of pea DNA helicase (PDH45), a DEAD-box family member protein, provides salinity stress tolerance in rice. The improved management of photosynthetic machinery and scavenging of reactive oxygen species (ROS) are associated with PDH45 mediated salinity stress tolerance. However, the role of PDH45 in biotic and other abiotic stress (drought) tolerance remains unexplored. In the present study, we have generated marker-free transgenic IR64 rice lines that overexpress PDH45 under the CaMV35S promoter. The transgenic rice lines exhibited a significant level of tolerance against sheath blight disease, caused by Rhizoctonia solani, a polyphagous necrotrophic fungal pathogen. The defense as well as antioxidant responsive marker genes were significantly upregulated in the PDH45 overexpressing (OE) rice lines, upon pathogen infection. Moreover, the OE lines exhibited tolerance to drought stress and various antioxidant as well as drought responsive marker genes were significantly upregulated in them, upon drought stress. Overall, the current study emphasizes that heterologous overexpression of PDH45 provides abiotic as well as biotic stress tolerance in rice. Tolerance against drought as well as sheath blight disease by overexpression of a single gene (PDH45) signifies the practical implication of the present study. Moreover, considering the conserved nature of the gene in different plant species, we anticipate that PDH45 can be gainfully deployed to impart tolerance against multiple stresses in agriculturally important crops.

Integrated omics approaches for flax improvement under abiotic and biotic stress: Current status and future prospects

Flax (Linum usitatissimum L.) or linseed is one of the important industrial crops grown all over the world for seed oil and fiber. Besides oil and fiber, flax offers a wide range of nutritional and therapeutic applications as a feed and food source owing to high amount of α-linolenic acid (omega-3 fatty acid), lignans, protein, minerals, and vitamins. Periodic losses caused by unpredictable environmental stresses such as drought, heat, salinity-alkalinity, and diseases pose a threat to meet the rising market demand. Furthermore, these abiotic and biotic stressors have a negative impact on biological diversity and quality of oil/fiber. Therefore, understanding the interaction of genetic and environmental factors in stress tolerance mechanism and identification of underlying genes for economically important traits is critical for flax improvement and sustainability. In recent technological era, numerous omics techniques such as genomics, transcriptomics, metabolomics, proteomics, phenomics, and ionomics have evolved. The advancements in sequencing technologies accelerated development of genomic resources which facilitated finer genetic mapping, quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection in major cereal and oilseed crops including flax. Extensive studies in the area of genomics and transcriptomics have been conducted post flax genome sequencing. Interestingly, research has been focused more for abiotic stresses tolerance compared to disease resistance in flax through transcriptomics, while the other areas of omics such as metabolomics, proteomics, ionomics, and phenomics are in the initial stages in flax and several key questions remain unanswered. Little has been explored in the integration of omic-scale data to explain complex genetic, physiological and biochemical basis of stress tolerance in flax. In this review, the current status of various omics approaches for elucidation of molecular pathways underlying abiotic and biotic stress tolerance in flax have been presented and the importance of integrated omics technologies in future research and breeding have been emphasized to ensure sustainable yield in challenging environments.

Plant Proteome Dynamics

Proteins are intimately involved in executing and controlling virtually all cellular processes. To understand the molecular mechanisms that underlie plant phenotypes, it is essential to investigate protein expression, interactions, and modifications, to name a few. The proteome is highly dynamic in time and space, and a plethora of protein modifications, protein interactions, and network constellations are at play under specific conditions and developmental stages. Analysis of proteomes aims to characterize the entire protein complement of a particular cell type, tissue, or organism-a challenging task, given the dynamic nature of the proteome. Modern mass spectrometry-based proteomics technology can be used to address this complexity at a system-wide scale by the global identification and quantification of thousands of proteins. In this review, we present current methods and technologies employed in mass spectrometry-based proteomics and provide examples of dynamic changes in the plant proteome elucidated by proteomic approaches.

Adverse Effects of Arsenic Uptake in Rice Metabolome and Lipidome Revealed by Untargeted Liquid Chromatography Coupled to Mass Spectrometry (LC-MS) and Regions of Interest Multivariate Curve Resolution

Rice crops are especially vulnerable to arsenic exposure compared to other cereal crops because flooding growing conditions facilitates its uptake. Besides, there are still many unknown questions about arsenic’s mode of action in rice. Here, we apply two untargeted approaches using liquid chromatography coupled to mass spectrometry (LC-MS) to unravel the effects on rice lipidome and metabolome in the early stages of growth. The exposure is evaluated through two different treatments, watering with arsenic-contaminated water and soil containing arsenic. The combination of regions of interest (ROI) and multivariate curve resolution (MCR) strategies in the ROIMCR data analyses workflow is proposed and complemented with other multivariate analyses such as partial least square discriminant analysis (PLS-DA) for the identification of potential markers of arsenic exposure and toxicity effects. The results of this study showed that rice metabolome (and lipidome) in root tissues seemed to be more affected by the watering and soil treatment. In contrast, aerial tissues alterations were accentuated by the arsenic dose, rather than with the watering and soil treatment itself. Up to a hundred lipids and 40 metabolites were significantly altered due to arsenic exposure. Major metabolic alterations were found in glycerophospholipids, glycerolipids, and amino acid-related pathways.

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.