1. Brief Introduction

This summary highlights the importance of rice as a staple food crop for a growing global population and the need to increase rice production to meet future demands. The challenges posed by climate change and abiotic stresses, such as drought, salinity, and flooding, are affecting rice productivity on a significant scale. The fine mapping and cloning of genes related to abiotic stress tolerance in rice have provided a foundation for yield improvement and enriched the genetic resources of the crop. Additionally, omics technologies, such as genomics and genome-wide association studies, have played a crucial role in understanding the molecular mechanisms underlying stress responses and identifying genes responsible for important agronomic traits. The integration of these approaches has paved the way for innovative insights and genetic improvements in rice breeding, offering potential solutions for increasing agricultural productivity while reducing costs and preserving the environment. Addressing food security remains an ongoing challenge, and the achievements in rice genetics and breeding for environmental stress tolerance discussed herein provide valuable information and theoretical support for developing resilient rice varieties with improved yield and stress tolerance. The following sections will present the brief key message of the published review in Plants by Usman et al., 2023 ^[1].

2. Recognition and Signaling of Abiotic Stress

Abiotic stresses, including extreme temperatures, drought, and salinity, have detrimental effects on plant growth and development, leading to reduced crop yields. Plants have evolved complex mechanisms to perceive and respond to these stresses. Signal perception at the plasma membrane triggers secondary signaling molecules and protein phosphorylation cascades, ultimately activating transcription factors (TFs) that regulate stress-responsive target genes. Understanding these mechanisms is crucial for developing stress-tolerant crop varieties and ensuring food security. This discussion focuses on transcriptional networks and candidate genes involved in rice plant responses to abiotic stress, highlighting their roles in conferring stress tolerance.

2.1. Cold Stress

Cold stress significantly affects various aspects of rice growth and development, including germination, seedling vigor, reproduction, and grain maturity. To cope with low temperatures, rice undergoes physiological, biochemical, and molecular changes. The activation of antioxidant systems, synthesis of cryoprotectants, and stabilization of cell membranes are crucial mechanisms during cold acclimation. The perception of cold stress by rice involves the cold sensor COLD1 and CBL-interacting protein kinase 7 (OsCIPK7), which regulate calcium influx. Numerous genes associated with chilling stress have been identified, including those involved in chlorophyll content and fluorescence, membrane stability, oxidative stress defense, osmotic regulation, and hormone signaling. The C-repeat-binding factor/dehydration-responsive element-binding factor (CBF/DREB1) acts as a transcription factor that activates the expression of cold-responsive genes. Other genes related to low-temperature tolerance include those involved in sugar metabolism, proline accumulation, and ABA signaling. Additionally, several genes have been identified to play roles in various aspects of cold stress response, such as seed germination, ubiquitin-proteasome pathway, kinase activity, and chloroplast function. However, there is still a limited understanding of plant responses to cold stress at the single-cell level. Further research is needed to unravel the intricate molecular mechanisms underlying rice's response to cold stress and improve cold tolerance in rice varieties.

2.2. Heat Stress

High temperatures above 35 °C have detrimental effects on plant growth, including reduced pollen viability, fertilization ability, and grain filling. They also inhibit photosynthesis and hinder plant cell division and growth by reducing water content. Several categories of high-temperature-related genes have been identified in rice, such as heat shock proteins (HSPs), heat shock transcription factors (HSTFs), stress-related transcription factors (TFs), and others. HSPs act as molecular chaperones, aiding in protein folding and enhancing stress tolerance. HSTFs are responsible for activating heat shock protein expression and play a role in temperature sensing and stress responses.

Other TFs containing stress elements, such as OsDREB1B, OsWRKY11, OsAREB1, and OsbZIP60, are also involved in high-temperature stress response. Enzymes like glutamate decarboxylase and glutamine synthase contribute to high-temperature tolerance by promoting the synthesis of stress-related amino acids. Ubiquitin ligases and proteasome subunits are involved in protein degradation, which is essential for heat tolerance. Various metabolites, such as stress-related amino acids and flavonoids, contribute to high-temperature tolerance in rice. Calcium ion channels and calcium-binding proteins are involved in calcium influx and redox balance regulation. Additionally, post-transcriptional regulators like RNA helicases and RNA methyltransferases play a role in heat stress response.

The accumulation of soluble sugars can inhibit photosynthesis under heat stress, and manipulating sugar transport and allocation pathways may help alleviate this inhibition. Genes involved in sugar accumulation and photosynthesis regulation under heat stress include sucrose transporters, NAC domain TFs, and trehalose-6-phosphate phosphatase.

Other genes related to high temperatures in rice are involved in processes like seed size regulation, grain enlargement, RNA modification, lipid metabolism, ROS scavenging, hormone signaling, and stomatal regulation. However, the molecular mechanisms and regulatory networks underlying high-temperature sensing and signaling pathways in rice are still poorly understood and require further research.

2.3. Drought Stress

Drought is a significant factor that limits the growth and production of rice, with a large portion of global rice production being severely affected by it. Breeding drought-resistant rice varieties is a practical approach to combat drought stress. However, drought tolerance in rice is a complex trait influenced by multiple genes and environmental factors, making it a complicated process to understand. Drought tolerance-related genes can be categorized into transcriptional control, stress signaling, and membrane transport, and they play a role in the molecular, physiological, and biochemical mechanisms of plants under drought stress.

The root system of rice plays a crucial role in absorbing water and nutrients, making it essential for drought-escaping strategies. Drought-tolerant rice varieties have a well-developed root system that helps maintain a higher water potential under drought conditions by increasing the root-shoot ratio, enhancing root penetration, and improving cuticle resistance, root hair density, and depth. Genes associated with root traits in rice, such as DRO1, DRO2, and DRO3, control deep rooting and contribute to drought tolerance. Overexpressing genes like OsDREB2B, CYP735A, and OsDREB1F can improve root morphological adaptations under drought conditions.

Controlling stomatal aperture is an efficient strategy for developing drought-tolerant plants. Stomata are responsible for regulating water loss through transpiration. Under drought stress, plants close their stomata to reduce water loss and improve water-use efficiency. ABA (abscisic acid) plays a role in regulating stomatal movement in response to drought stress. In rice, ABA receptors PYR1 and PYL proteins are involved in stomatal movement control. Mutations in these receptors affect stomatal movement but can promote grain productivity. Other genes like OsASR5, DST, OsSRO1, and OsJAZ1 regulate stomatal closure through ABA-independent and ABA-dependent pathways.

Improving stomatal density, size, and index is essential for enhancing drought tolerance. Genes like OsEPF1 and OsDRAP1 can influence stomatal characteristics and improve drought tolerance. Introducing various genes such as OsLEA3-1, OsNAC5, OsWRKY47, and OsMIOX into rice can enhance its drought tolerance by improving water-use efficiency, antioxidant activity, photosynthesis, and osmolyte accumulation. TFs (transcription factors) like the WRKY F family, OsMUTE, OsSPCHs, OsICEs, and OsFAMA also play a role in controlling stomatal movement and development.

Understanding the mechanisms behind drought tolerance in rice, particularly related to root systems and stomatal control, is crucial for developing drought-resistant rice varieties. Genetic studies and the manipulation of specific genes have provided valuable insights into enhancing drought tolerance in rice.

2.4. Salt Stress

Salt stress has a significant impact on rice growth and grain quality, affecting its market value and economic importance. When rice plants are exposed to excessive salt in the soil, their ability to absorb water is compromised due to reduced water potential, leading to physiological drought. Salt stress also disrupts cell membrane integrity and causes electrolyte leakage. To cope with salt stress, rice plants employ various mechanisms such as regionalizing intracellular salts, absorbing inorganic ions, and synthesizing organic osmotic regulators like sugars, betaine, and proline. Potassium ion uptake is increased, while sodium ion uptake is reduced to maintain cell osmotic regulation and enhance water absorption capacity.

Under salt stress, nutrient imbalances occur as excessive sodium accumulation hampers the absorption of essential nutrients like potassium, magnesium, phosphorus, and calcium. This imbalance negatively affects plant growth, chlorophyll synthesis, and metabolic processes. Transcription factors (TFs) play a crucial role in regulating salt tolerance in rice. Some TFs, such as OsDREB2A, OsCOIN, OsbZIP71, OsMYB2, and OsbZIP23, promote salt tolerance by inducing the accumulation of antioxidants and osmoprotectants and enhancing ion transporter activity. On the other hand, negative regulatory TFs like OsWRKY13 and OsWRKY45-2 can inhibit the expression of salt-responsive genes, resulting in reduced salt tolerance.

The expression of salt-responsive genes in rice is controlled by specific DNA sequences called cis-acting elements. These elements interact with TFs and regulate gene transcription. For example, the ABRE element binds to zinc finger TFs like OsBZ8 and OsABI5 to control gene expression under salt stress. Other cis-acting elements like DRE and AH2 also contribute to salt-responsive gene regulation.

Several genes in rice have been identified as sensors and mediators of salt stress signals, improving salt tolerance. Overexpression of genes like SAPK4, OsCPK12, OsMAPK44, and OsSRK1 enhances ion balance, reduces oxidative damage, and improves salt tolerance. Ion transporters such as OVP1 and SKC1 help maintain ion homeostasis, while genes involved in osmoprotectant synthesis, such as OsTPP1, OsTPS1, OsP5CS, and OsCMO, play crucial roles in rice salt tolerance. Additionally, genes associated with ROS regulation, protein chaperones, and molecular stabilizers contribute to improved salt tolerance in rice.

In summary, rice plants employ a variety of mechanisms to cope with salt stress, including osmotic regulation, ion balance maintenance, and gene expression regulation through TFs and cis-acting elements. Understanding these molecular mechanisms can aid in the development of salt-tolerant rice varieties with improved growth and grain quality.

2.5. Osmotic Stress

Plants respond to osmotic stress caused by low temperatures, drought, and salinity by adjusting their ion transport and increasing permeability to water. This leads to the accumulation of small organic molecules with osmoprotective effects, such as sugars, proline, and betaine, as well as an increase in ABA concentration, triggering physiological and biochemical changes in proteins. To maintain osmotic pressure balance, plants regulate ion absorption, enhance water intake, boost antioxidant defense systems, and alter photosynthetic pathways. Osmotic regulation involves inorganic ions (Na+, K+, Cl-) and small organic molecules like polyols, nitrogen-containing compounds, sugars, and organic acids.

Proline, a water-soluble amino acid, acts as an intracellular osmotic regulator and has multiple functions in plant cells. Its biosynthesis is regulated by the enzyme δ-pyrroline-5-carboxylate synthase (P5CS). Overexpression of P5CS genes in rice improves osmotic tolerance by increasing proline content. Other genes like Ta-UnP and TaPUB15 from wheat also induce proline synthesis and enhance osmotic and salt stress tolerance in rice.

Calcium-binding proteins, annexins, and proteins involved in cell wall polysaccharide synthesis play important roles in osmotic stress responses. For example, OsCCD1, an annexin gene in rice, regulates oxidative damage and membrane protection under osmotic stress. OsCSLD4, involved in cell wall polysaccharide synthesis, positively contributes to osmotic stress tolerance by regulating ABA content.

The balance between hormonal signaling and osmotic stress tolerance is crucial for plant growth and development. Genes like OsGA2ox8 and OsNF-YA3 influence this balance by regulating GA and ABA levels, affecting osmotic stress tolerance in rice. OsPP65, a type 2C protein phosphatase, modulates JA and ABA signaling pathways, and its knockout enhances osmotic and salt stress tolerance.

Other genes and proteins like OsHSP50.2, OsOSCA1.2, and OsRLCK241 also contribute to osmotic stress tolerance in rice by regulating water loss, ion transport, and ROS scavenging.

Although progress has been made in understanding the signaling pathways and interactions involved in osmotic stress responses in rice, there is still much to learn compared to other stress types.

2.6. Submergence Tolerance

Submergence or flooding can have detrimental effects on plant growth, including inhibition of photosynthesis, energy consumption, and even plant death. Rice has developed specific traits to adapt to excess water conditions, such as aerenchyma, oxygen barriers, adventitious roots, and leaf gas films. These adaptations allow the rice to regulate gas exchange and undergo programmed cell death to cope with submergence. However, these strategies are insufficient for prolonged submergence, leading to stunted growth or death. Rice plants respond to submergence by accumulating gibberellic acid (GA), which triggers rapid internode elongation.

Rice plants can form a radial oxygen loss (ROL) barrier around their roots under submergence to prevent oxygen loss. The main component of this barrier is suberin, but the exact mechanism of its formation is not yet fully understood. Some rice varieties have developed additional traits, such as aerobic germination and quiescence of leaf elongation, to tolerate submergence for around 15 days. A major genetic factor, known as Sub1, on chromosome 9 of submergence-tolerant rice varieties, plays a crucial role in conferring submergence tolerance without affecting grain yield and quality. SUB1A, SUB1B, and SUB1C genes encode ETHYLENE RESPONSIVE FACTOR (ERF) transcription factors that control submergence escape and tolerance.

During anaerobic germination, rice coleoptiles elongate to reach the water surface and secure oxygen. Ethanol fermentation and starch decomposition provide energy for coleoptile elongation. Genetic factors, such as OsTPP7, are involved in anaerobic respiration by promoting trehalose 6-phosphate metabolism. Submergence-tolerant rice exhibits growth atrophy to reduce energy consumption and ensure survival under flooding stress. SUB1A negatively regulates genes involved in starch and sucrose degradation, while promoting genes like ADH and pyruvate. It also inhibits ethylene synthesis and cell wall expansion proteins, maintaining high chlorophyll levels and regulating metabolic processes.

SNORKEL1 and SNORKEL2 genes respond to submergence by inducing internode elongation through ethylene signaling. SNORKEL1/2 and SUB1A belong to the same ERF subgroup. GWAS studies have identified other genetic factors involved in floating rice, including GA20oxidase2, SD1, ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1), and DEC1. These genes play roles in GA synthesis, internode elongation, and cell division inhibition during submergence.

Understanding the molecular mechanisms behind rice adaptations to submergence can provide insights into improving flood tolerance in crops.

3. Utilization of Integrative Omics Analyses to Identify Potential Candidate Genes Associated with Abiotic Stress

Recent advances in transcriptomic, proteomic, and metabolomic technologies have opened up new possibilities for identifying candidate genes that can be used in plant breeding to improve global food security. By utilizing these technologies, researchers have been able to identify candidate genes underlying abiotic stress tolerance in rice and other crops. Transcriptomic studies have provided insights into gene expression patterns in response to different environmental conditions. For example, RNA-seq analysis has identified numerous differentially expressed genes (DEGs) related to chilling stress in rice. These DEGs include genes encoding oxidoreductases, thioredoxins, glutathione S-transferases, death-associated protein kinase 1, calcium homeostasis regulator CHoR1, and various other proteins involved in stress response and metabolism. Additionally, transcriptomic studies have identified candidate genes associated with heat stress tolerance in rice, such as OsCML4, genes involved in plant hormone signal transduction, metabolic pathways, and survival rate.

Proteomic analysis, which focuses on the protein level, has provided valuable information about plant stress responses. Through proteomics, researchers have identified candidate proteins involved in various stress responses, including cold, drought, heat, and salt stress. These candidate proteins play roles in defense response, transport, energy metabolism, signal transduction, and transcript regulation, among other functions. For instance, proteomics analysis has identified heat-responsive proteins, such as small heat shock proteins (HSPs), glycolysis-related proteins, and proteins involved in the ubiquitin-proteasome system.

Metabolomic studies have revealed changes in the metabolic composition of plants under stress conditions. By comparing the metabolomes of stress-tolerant and stress-sensitive rice varieties, researchers have identified metabolites associated with stress tolerance. These metabolites include glutathione, putrescine, asparagine, β-Alanine, γ-Glutamylleucine, and various other compounds involved in different metabolic pathways.

Integration of transcriptomic, proteomic, and metabolomic data has provided a comprehensive understanding of the molecular mechanisms underlying stress tolerance in rice. By identifying candidate genes, proteins, and metabolites involved in stress responses, researchers can develop strategies for breeding stress-tolerant crops. These advancements in omics technologies offer promising prospects for enhancing global food security by improving crop resilience to environmental stresses.

4. Conclusion

Recent research in rice has focused on understanding the molecular mechanisms involved in the plant's response to abiotic stress. Studies have explored signal transduction pathways, gene expression regulation, and the roles of hormones and transcription factors in stress tolerance. While progress has been made in identifying transcription factors and their binding sites, further research is needed to understand how multiple transcription factors act as negative feedback regulators during stress signaling. Additionally, alternative approaches such as epigenetic modifications and small RNA regulations require more exploration. Epigenetic regulation has been shown to play a role in plant stress response, but its mechanisms and regulatory networks are not fully understood. Understanding the interaction between epigenetic regulation and plant hormones is also important. Big data analysis and new methods can aid in identifying key players for stress tolerance and studying their regulatory mechanisms. Genomics, transcriptomics, and proteomics techniques are crucial for unraveling the molecular basis of stress responses. Co-expression networks and advanced microscopy techniques can provide valuable insights into gene interactions and cellular responses to stress. By combining cutting-edge technologies with stress-tolerant plants, precision breeding,^[1] and data analytics can help meet global food targets by producing rice for the global market.

This entry is adapted from the peer-reviewed paper 10.3390/plants12102019