Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice

Bacillus velezensis GH1-13 enhances drought tolerance in rice by reducing the accumulation of reactive oxygen species

Plant growth-promoting rhizobacteria colonize the rhizosphere through dynamic and intricate interactions with plants, thereby providing various benefits and contributing to plant growth. Moreover, increasing evidence suggests that plant growth-promoting rhizobacteria affect plant tolerance to abiotic stress, but the underlying molecular mechanisms remain largely unknown. In this study, we investigated the effect of Bacillus velezensis strain GH1-13 on drought stress tolerance in rice. Phenotypical analysis, including the measurement of chlorophyll content and survival rate, showed that B. velezensis GH1-13 enhances rice tolerance to drought stress. Additionally, visualizing ROS levels and quantifying the expression of ROS-scavenging genes revealed that GH1-13 treatment reduces ROS accumulation under drought stress by activating the expression of antioxidant genes. Furthermore, the GH1-13 treatment stimulated the jasmonic acid response, which is a key phytohormone that mediates plant stress tolerance. Together with the result that jasmonic acid treatment promotes the expression of antioxidant genes, these findings indicate that B. velezensis GH1-13 improves drought tolerance in rice by reducing ROS accumulation and suggest that activation of the jasmonic acid response is deeply involved in this process.

Physiological and Molecular Mechanisms of Rice Tolerance to Salt and Drought Stress: Advances and Future Directions

Rice, a globally important food crop, faces significant challenges due to salt and drought stress. These abiotic stresses severely impact rice growth and yield, manifesting as reduced plant height, decreased tillering, reduced biomass, and poor leaf development. Recent advances in molecular biology and genomics have uncovered key physiological and molecular mechanisms that rice employs to cope with these stresses, including osmotic regulation, ion balance, antioxidant responses, signal transduction, and gene expression regulation. Transcription factors such as DREB, NAC, and bZIP, as well as plant hormones like ABA and GA, have been identified as crucial regulators. Utilizing CRISPR/Cas9 technology for gene editing holds promise for significantly enhancing rice stress tolerance. Future research should integrate multi-omics approaches and smart agriculture technologies to develop rice varieties with enhanced stress resistance, ensuring food security and sustainable agriculture in the face of global environmental changes.

A review on strategies for crop improvement against drought stress through molecular insights

The demand for food goods is rising along with the world population growth, which is directly related to the yield of agricultural crops around the world. However, a number of environmental factors, including floods, salinity, moisture, and drought, have a detrimental effect on agricultural production around the world. Among all of these stresses, drought stress (DS) poses a constant threat to agricultural crops and is a significant impediment to global agricultural productivity. Its potency and severity are expected to increase in the future years. A variety of techniques have been used to generate drought-resistant plants in order to get around this restriction. Different crop plants exhibit specific traits that contribute to drought resistance (DR), such as early flowering, drought escape (DE), and leaf traits. We are highlighting numerous methods that can be used to overcome the effects of DS in this review. Agronomic methods, transgenic methods, the use of sufficient fertilizers, and molecular methods such as clustered regularly interspaced short palindromic repeats (CRISPRs)-associated nuclease 9 (Cas9), virus-induced gene silencing (VIGS), quantitative trait loci (QTL) mapping, microRNA (miRNA) technology, and OMICS-based approaches make up the majority of these techniques. CRISPR technology has rapidly become an increasingly popular choice among researchers exploring natural tolerance to abiotic stresses although, only a few plants have been produced so far using this technique. In order to address the difficulties imposed by DS, new plants utilizing the CRISPR technology must be developed.

Impact of Drought Stress on Plant Growth and Its Management Using Plant Growth Promoting Rhizobacteria

Drought stress is a significant environmental challenge affecting global agriculture, leading to substantial reductions in crop yields and overall plant productivity. It induces a cascade of physiological and biochemical changes in plants, including reduced water uptake, stomatal closure, and alterations in hormonal balance, all of which contribute to impaired growth and development. Drought stress diminishes crop production by impacting crucial plant metabolic pathways. Plants possess the ability to activate or deactivate specific sets of genes, leading to changes in their physiological and morphological characteristics. This adaptive response enables plants to evade, endure, or prevent the effects of drought stress. Drought stress triggers the activation of various genes, transcription factors, and signal transduction pathways in plants. In this context, imposing plant growth-promoting rhizobacteria (PGPR) emerges as a promising strategy. PGPR, employing diverse mechanisms such as osmotic adjustments, antioxidant activity, and phytohormone production, not only ensures the plant's survival during drought conditions but also enhances its overall growth. This comprehensive review delves into the various mechanisms through which PGPR enhances drought stress resistance, offering a thorough exploration of recent molecular and omics-based approaches to unravel the role of drought-responsive genes. The manuscript encompasses a detailed mechanistic analysis, along with the development of PGPR-based drought stress management in plants.

Joint transcriptomic and metabolomic analysis provides new insights into drought resistance in watermelon (Citrullus lanatus)

Introduction

Watermelon is an annual vine of the family Cucurbitaceae. Watermelon plants produce a fruit that people love and have important nutritional and economic value. With global warming and deterioration of the ecological environment, abiotic stresses, including drought, have become important factors that impact the yield and quality of watermelon plants. Previous research on watermelon drought resistance has included analyzing homologous genes based on known drought-responsive genes and pathways in other species.

Methods

However, identifying key pathways and genes involved in watermelon drought resistance through high-throughput omics methods is particularly important. In this study, RNA-seq and metabolomic analysis were performed on watermelon plants at five time points (0 h, 1 h, 6 h, 12 h and 24 h) before and after drought stress.

Results

Transcriptomic analysis revealed 7829 differentially expressed genes (DEGs) at the five time points. The DEGs were grouped into five clusters using the k-means clustering algorithm. The functional category for each cluster was annotated based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database; different clusters were associated with different time points after stress. A total of 949 metabolites were divided into 10 categories, with lipids and lipid-like molecules accounting for the most metabolites. Differential expression analysis revealed 22 differentially regulated metabolites (DRMs) among the five time points. Through joint analysis of RNA-seq and metabolome data, the 6-h period was identified as the critical period for watermelon drought resistance, and the starch and sucrose metabolism, plant hormone signal transduction and photosynthesis pathways were identified as important regulatory pathways involved in watermelon drought resistance. In addition, 15 candidate genes associated with watermelon drought resistance were identified through joint RNA-seq and metabolome analysis combined with weighted correlation network analysis (WGCNA). Four of these genes encode transcription factors, including bHLH (Cla97C03G068160), MYB (Cla97C01G002440), HSP (Cla97C02G033390) and GRF (Cla97C02G042620), one key gene in the ABA pathway, SnRK2-4 (Cla97C10G186750), and the GP-2 gene (Cla97C05G105810), which is involved in the starch and sucrose metabolism pathway.

Discussion

In summary, our study provides a theoretical basis for elucidating the molecular mechanisms underlying drought resistance in watermelon plants and provides new genetic resources for the study of drought resistance in this crop.

Mapping and Omics Integration: Towards Precise Rice Disease Resistance Breeding

Rice (Oryza sativa), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. The integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with a better understanding of their functional roles in disease resistance. The improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because a better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to a more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can result in a transformative impact on rice breeding for enhancing disease resistance.

Effect of ethyl methanesulfonate mediated mutation for enhancing morpho-physio-biochemical and yield contributing traits of fragrant rice

Background

Chemical mutagenesis has been successfully used for increasing genetic diversity in crop plants. More than 800 novel mutant types of rice (Oryza sativa L.) have been developed through the successful application of numerous mutagenic agents. Among a wide variety of chemical mutagens, ethyl-methane-sulfonate (EMS) is the alkylating agent that is most commonly employed in crop plants because it frequently induces nucleotide substitutions as detected in numerous genomes.

Methods

In this study, seeds of the widely consumed Basmati rice variety (Super Basmati, Oryza sativa L.) were treated with EMS at concentrations of 0.25%, 0.50%, 0.75%, 1.0%, and 1.25% to broaden its narrow genetic base.

Results

Sensitivity to a chemical mutagen such as ethyl methanesulfonate (EMS) was determined in the M1 generation. Results in M1 generation revealed that as the levels of applied EMS increased, there was a significant reduction in the germination percent, root length, shoot length, plant height, productive tillers, panicle length, sterile spikelet, total spikelet, and fertility percent as compared to the control under field conditions. All the aforementioned parameters decreased but there was an increase in EMS mutagens in an approximately linear fashion. Furthermore, there was no germination at 1.25% of EMS treatment for seed germination. A 50% germination was recorded between 0.50% and 0.75% EMS treatments. After germination, the subsequent parameters, viz. root length and shoot length had LD50 between 05.0% and 0.75% EMS dose levels. Significant variation was noticed in the photosynthetic and water related attributes of fragrant rice. The linear increase in the enzymatic attributes was noticed by the EMS mediated treatments. After the establishment of the plants in the M1 generation in the field, it was observed that LD50 for fertility percentage was at EMS 1.0% level, for the rice variety.

Conclusion

Hence, it is concluded that for creating genetic variability in the rice variety (Super Basmati), EMS doses from 0.5% to 0.75% are the most efficient, and effective.

A Lycopene ε-Cyclase TILLING Allele Enhances Lycopene and Carotenoid Content in Fruit and Improves Drought Stress Tolerance in Tomato Plants

In the scenario of climate change, the availability of genetic resources for tomato cultivation that combine improved nutritional properties and more tolerance to water deficiency is highly desirable. Within this context, the molecular screenings of the Red Setter cultivar-based TILLING platform led to the isolation of a novel lycopene ε-cyclase gene (SlLCY-E) variant (G/3378/T) that produces modifications in the carotenoid content of tomato leaves and fruits. In leaf tissue, the novel G/3378/T SlLCY-E allele enhances β,β-xanthophyll content at the expense of lutein, which decreases, while in ripe tomato fruit the TILLING mutation induces a significant increase in lycopene and total carotenoid content. Under drought stress conditions, the G/3378/T SlLCY-E plants produce more abscisic acid (ABA) and still conserve their leaf carotenoid profile (reduction of lutein and increase in β,β-xanthophyll content). Furthermore, under said conditions, the mutant plants grow much better and are more tolerant to drought stress, as revealed by digital-based image analysis and in vivo monitoring of the OECT (Organic Electrochemical Transistor) sensor. Altogether, our data indicate that the novel TILLING SlLCY-E allelic variant is a valuable genetic resource that can be used for developing new tomato varieties, improved in drought stress tolerance and enriched in fruit lycopene and carotenoid content.

Insights from a Multi-Omics Integration (MOI) Study in Oil Palm (Elaeis guineensis Jacq.) Response to Abiotic Stresses: Part Two-Drought

Drought and salinity are two of the most severe abiotic stresses affecting agriculture worldwide and bear some similarities regarding the responses of plants to them. The first is also known as osmotic stress and shows similarities mainly with the osmotic effect, the first phase of salinity stress. Multi-Omics Integration (MOI) offers a new opportunity for the non-trivial challenge of unraveling the mechanisms behind multigenic traits, such as drought and salinity resistance. The current study carried out a comprehensive, large-scale, single-omics analysis (SOA) and MOI studies on the leaves of young oil palm plants submitted to water deprivation. After performing SOA, 1955 DE enzymes from transcriptomics analysis, 131 DE enzymes from proteomics analysis, and 269 DE metabolites underwent MOI analysis, revealing several pathways affected by this stress, with at least one DE molecule in all three omics platforms used. Moreover, the similarities and dissimilarities in the molecular response of those plants to those two abiotic stresses underwent mapping. Cysteine and methionine metabolism (map00270) was the most affected pathway in all scenarios evaluated. The correlation analysis revealed that 91.55% of those enzymes expressed under both stresses had similar qualitative profiles, corroborating the already known fact that plant responses to drought and salinity show several similarities. At last, the results shed light on some candidate genes for engineering crop species resilient to both abiotic stresses.

Melatonin Enhances Drought Tolerance in Rice Seedlings by Modulating Antioxidant Systems, Osmoregulation, and Corresponding Gene Expression

Rice is the third largest food crop in the world, especially in Asia. Its production in various regions is affected to different degrees by drought stress. Melatonin (MT), a novel growth regulator, plays an essential role in enhancing stress resistance in crops. Nevertheless, the underlying mechanism by which melatonin helps mitigate drought damage in rice remains unclear. Therefore, in the present study, rice seedlings pretreated with melatonin (200 μM) were stressed with drought (water potential of −0.5 MPa). These rice seedlings were subsequently examined for their phenotypes and physiological and molecular properties, including metabolite contents, enzyme activities, and the corresponding gene expression levels. The findings demonstrated that drought stress induced an increase in malondialdehyde (MDA) levels, lipoxygenase (LOX) activity, and reactive oxygen species (ROS, e.g., O₂⁻ and H₂O₂) in rice seedlings. However, the melatonin application significantly reduced LOX activity and the MDA and ROS contents (O₂⁻ production rate and H₂O₂ content), with a decrease of 29.35%, 47.23%, and (45.54% and 49.33%), respectively. It activated the expression of ALM1, OsPOX1, OsCATC, and OsAPX2, which increased the activity of antioxidant enzymes such as superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX), respectively. Meanwhile, the melatonin pretreatment enhanced the proline, fructose, and sucrose content by inducing OsP5CS, OsSUS7, and OsSPS1 gene expression levels. Moreover, the melatonin pretreatment considerably up-regulated the expression levels of the melatonin synthesis genes TDC2 and ASMT1 under drought stress by 7-fold and 5-fold, approximately. These improvements were reflected by an increase in the relative water content (RWC) and the root-shoot ratio in the drought-stressed rice seedlings that received a melatonin application. Consequently, melatonin considerably reduced the adverse effects of drought stress on rice seedlings and improved rice’s ability to tolerate drought by primarily boosting endogenous antioxidant enzymes and osmoregulation abilities.