Salinity is a severe environmental stressor that reduces crop performance, alters soil microbial communities, and influences greenhouse gas emissions such as methane (CH4). Climate change is expected to further increase salinity globally. Although plants have evolved physiological and molecular mechanisms to cope with salinity, the role of plant-microbiome interactions in salinity tolerance and their link to CH4 emissions remain poorly understood. Here, we investigated the interactions among plant salinity tolerance, rhizobiome, and CH4 emission under salinity stress. We used salt-tolerant and salt-sensitive rice genotypes grown in nutrient-poor paddy field soil and nutrient-rich commercial nursery soil under climate-controlled greenhouse conditions with salinity stress until harvesting. Salt-sensitive genotypes exhibited decreases in early biomass and gas exchange due to salinity stress under nutrient-rich nursery soil. However, salinity effects were mitigated by plant-microbiome interactions, which improved plant growth performance. Rhizosphere microbiome analysis revealed that Rhizobacteria, including Cyanobacteria, were associated with plant development and salinity tolerance. Salinity altered methanogenic archaeal communities, especially Methanobacteria and Methanocellia, with salt-tolerant genotypes releasing more CH4 during stress. Gas exchange and antioxidant enzyme activity were positively correlated with CH4 emissions, suggesting an association between improved physiological performance under salinity and microbial methanogenesis. Gene expression profiling revealed a significant upregulation of hormone- and ion-transport-related genes in paddy soil, which may be associated with stress tolerance, microbial activity, and CH4 emissions. This study proposes a mechanistic framework that links plant salinity tolerance, rhizosphere microbial dynamics, and methane production, illustrating how these interconnected processes shape plant performance and the environmental outcomes. These findings emphasize the necessity of balancing agricultural productivity with CH4 emissions and soil resilience under climate-induced stress.

Maternally inherited extranuclear genomes (ptDNA and mtDNA) and epigenetic mechanisms are known to affect offspring phenotypes; nevertheless, their integrated function in stress adaptation remains incompletely understood. Classical breeding strategies have mostly ignored these non-Mendelian influences by focusing exclusively on nuclear genome inheritance. We developed reciprocal rice hybrids from selected salt-tolerant and salt-sensitive progenitors and utilized a multi-omics strategy-comprising whole-genome sequencing, WGS-derived cytosine content profiling, transcriptomics, and phenotypic evaluations-to understand the maternal contribution to salinity tolerance of rice offspring. Despite sharing a broadly biparental nuclear genetic background, maternal-tolerant rice hybrids demonstrated improved performance, including better growth, photosynthesis, ion homeostasis, and yield relative to maternal-sensitive rice hybrids under salinity stress. Organellar genome sequencing revealed predominantly maternal inheritance. Cytosine profiling indicated CpG and CHG content similarity to the maternal genotype. Transcriptomic data revealed maternal-aligned expression of stress-responsive and organelle-associated genes, consistent with enhanced performance in maternal-tolerant hybrids. Our results from a multi-omics approach support a strong association between maternal cytoplasmic inheritance and differential stress responses in rice hybrids. This non-Mendelian model of stress tolerance, informed by multi-omics integration, provides innovative insights into maternal regulation of stress resilience in rice and proposes an effective strategy for breeding salt-tolerant crops in climate-challenged areas.

Salinity is one of the severe abiotic stress factors that affect approximately 50% of planted and irrigated agricultural fields. The determination of plant response to salinity is the key factor that reduces yield lost in crop production. Transgenerational plasticity is a nongenetic modification that provides a mechanism for plants to "remember" and adapt to environmental conditions experienced by their ancestors, contributing to the phenotypic plasticity and resilience of plant populations over successive generations. This ability to retain stress memory enables plants to respond more effectively to recurring salinity stress, potentially enhancing crop adaptation and productivity. The determination of transgenerational plasticity of salinity tolerance has some key research elements that can be focused on heritable modifications. In this chapter, we explain the methods of transgenerational plasticity of salinity tolerance research.

Salinity is a major abiotic stress that threatens global food security, particularly in arid and semi-arid regions. Rice (Oryza sativa L.) is a stable food for over half of the world's population. Rising soil salinity, driven by climate change and unsustainable irrigation practices, is expected to affect nearly half of the world's arable lands by 2050. This review focuses on the role of the hst1 gene, a mutant form of OsRR22, in enhancing salinity tolerance in rice. The hst1 gene plays a crucial role in maintaining ion homeostasis, scavenging reactive oxygen species (ROS), and regulating stress-responsive signaling pathways, all of which are critical for mitigating salt-induced damage in rice. Under salt stress, the hst1 mutation enables rice plants to accumulate less sodium (Na+) and more potassium (K+), thus preserving cellular function and enhancing photosynthetic efficiency. Additionally, hst1 activates antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR), which protect cells from oxidative damage caused by ROS. The gene also modulates transcription factors that regulate downstream stress-response genes, contributing to improved growth and yield under saline conditions. By understanding the physiological and molecular mechanisms underlying hst1-mediated salt tolerance, this review provides insights into breeding strategies for developing salt-tolerant rice varieties. Such advancements are essential for sustaining rice production in saline-affected regions and ensuring global food security in the face of climate change and population growth.

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Volatile compounds (VCs) from fungi can promote plant growth, but their application methods are limited. Edible mushroom fungi beds (FBs) provide a readily available alternative source of fungal VCs, although their biostimulatory functions remain unvalidated. In this study, a novel, non-contact exposure method for applying VCs emitted from FBs to rice seedlings was developed. This marks the first evaluation of mushroom FBs as a direct source of bioactive VCs for plant growth promotion. Volatiles from two different edible mushroom FBs promoted shoot growth and increased biomass for rice seedlings. VCs from shiitake FBs significantly increased biomass by 67.4% while VCs from enokitake FBs by 39.5% compared to the control. The biomass-increasing effects were influenced by the quantity of shiitake FBs applied, with significant increases at 15 g, 30 g and 60 g applications. The VCs effects remained significant even when the FBs were covered with two types of gas-permeable polymer film. Chemical analysis of VCs from FBs identified several organic compounds and subsequent bioassays using synthetic VCs determined key bioactive VCs contributing to biomass increase at specific concentrations. This study presents a utilization method of waste mushroom FBs as sustainable, scalable, and cost-effective agricultural biostimulants.

The nitrogen (N) fertilization form and plant energy status are known to significantly influence plant responses to elevated atmospheric carbon dioxide (CO2) concentrations. However, a close examination of the interplay between N sources under contrasting light intensity has been notably absent in the literature. In this study, we conducted a factorial experiment with rice plants involving two different light intensities (150 and 300 µmol m-2 s-1), inorganic N sources [nitrate (N-NO3) or ammonium nitrate (N-NH4NO3)] at varying CO2 levels (410 and 700 parts per million, ppm). The aim was to examine the individual and combined effects of these factors on the allocation of biomass in whole plants, as well as on leaf-level photosynthetic characteristics, chloroplast morphology and development, ATP content, ionomics, metabolomics, and hormone profiles. Our research hypothesis posits that mixed nutrition enhances plant responsiveness to elevated CO2 (eCO2) at both light levels compared to sole N-NO3 nutrition, due to its diminished energy demands for plant assimilation. Our findings indicate that N-NO3 nutrition does not promote the growth of rice, its photosynthetic capacity, or N content when exposed to ambient CO2 (aCO2), and is significantly reduced in low light (LL) conditions. Rice plants with N-NH4NO3 exhibited a higher carboxylation capacity, which resulted in larger biomass (total C, tiller number, and lower root-shoot ratio) supported by higher Calvin-cycle-related sugars. The lower leaf N content and overall amino acid levels at eCO2, particularly pronounced in N-NO3, combined with the lower ATP content (lowest at LL and N-NO3), may reflect the higher energy costs of N assimilation at eCO2. We also observed significant plasticity patterns in leaves under eCO2. Our findings highlight the importance of a thorough physiological understanding to inform innovative management practices aimed at mitigating the negative effects of climate change on plant N use efficiency.

To achieve global goals for sustainable development, such as zero hunger and ensuring food security, the effect of climate change on plant production and overcoming decreasing crop yields caused by environmental stress factors must be understood. Soil salinity is a serious environmental stress factor that threatens food security, combined with global warming, reduced arable land, and the growing human population. Seven percent of the total soil areas of the world are affected by salt, which represents 33% of agricultural land. These areas are getting increased due to unplanned irrigation and aridity. It is reported that 50% of the cultivation areas will be destroyed in 25 years, depending on increased salinity. One of the promising solutions is salt stress-tolerant plant breeding to improve crop yield and quality. Currently, conventional breeding strategies are increasing attention to salt-tolerant rice development. However, it takes a long time, has a relatively low success percentage, and has primitive parental selection progress, so conventional breeding methods must be improved. Combining molecular approaches and conventional breeding methods can be a promising approach to developing salt-tolerant rice to ensure food security. In this chapter, we will explain how conventional breeding methods can be combined with modern molecular methods and new approaches can be developed.

Transgenerational plasticity in plants enables rapid adaptation to environmental changes, allowing organisms and their offspring to adapt to the environment without altering their underlying DNA. In this study, we investigated the transgenerational plasticity in salinity tolerance of rice plants using a reciprocal transplant experimental strategy. Our aim was to assess whether non-genetic environment-induced phenotypic modifications and transgenerational salinity affect the salinity tolerance of progeny while excluding nuclear genomic factors for two generations. Using salt-tolerant and salt-sensitive rice genotypes, we observed that the parentally salt-stressed salt-sensitive genotype displayed greater growth performance, photosynthetic activity, yield performance, and transcriptional responses than the parentally non-stressed salt-sensitive plants under salt stress conditions. Surprisingly, salt stress-exposed salt-tolerant progeny did not exhibit as much salinity tolerance as salt stress-exposed salt-sensitive progeny under salt stress. Our findings indicate that the phenotypes of offspring plants differed based on the environment experienced by their ancestors, resulting in heritable transgenerational phenotypic modifications in salt-sensitive genotypes via maternal effects. These results elucidated the mechanisms underlying transgenerational plasticity in salinity tolerance, providing valuable insights into how plants respond to changing environmental conditions. Parental environmental experiences induce heritable epigenetic changes in offspring: maternal effects lead to the production of salt-tolerant progeny from salt stress-sensitive rice genotypes, revealing transgenerational phenotypic modifications.

Rice is one of the most important staple foods globally, sustaining over half of the world’s population. However, the sustainability of grain production is increasingly threatened by heat stress, which is intensified by global climate change. Heat stress, characterized by temperatures exceeding crop-specific optimal growth thresholds, significantly impacts the rice yield and quality, particularly during critical reproductive stages. This review synthesizes current research on strategies to mitigate heat stress in rice through genetic and agronomic approaches. It highlights the implementation of advanced genetic tools such as marker-assisted selection (MAS) and genomic selection (GS) to accelerate the breeding of heat-tolerant rice varieties. Additionally, it discusses sustainable agronomic practices, including adjusting planting dates, optimizing water management, and crop rotation, which enhance resilience to heat stress. The objective of this review is to bridge the gap between research findings and practical agricultural applications, providing a comprehensive resource that guides future research directions and informs policy interventions. This review emphasizes the importance of integrating genetic innovations with traditional and modern farming practices to develop rice varieties that can withstand the adverse effects of heat stress, ensuring food security and agricultural sustainability in the face of climatic challenges.

The increasing global population and climate change threaten food security, with the need for sustenance expected to rise by 85% by 2050. Rice, a crucial staple food for over 50% of the global population, is a major source of calories in underdeveloped and developing countries. However, by the end of the century, over 30% of rice fields will become saline due to soil salinity caused by earthquakes, tsunamis, and rising sea levels. Plants have developed strategies to deal with salt stress, such as ion homeostasis, antioxidant defense mechanisms, and morphological adaptations. Proline, an endogenous osmolyte, is the predominant endogenous osmolyte that accumulates in response to salinity, and its overexpression in rice plants has been observed to increase plant salinity tolerance. Exogenously applied proline has been shown to improve plant salt tolerance by reducing the destructive effect of salinity. Recent research has focused on ionic toxicity, nitrogen fixation, and gene expression related to salt tolerance. Exogenous proline has been shown to improve water potential and leaf content, restoring water usage efficiency. It can also ease growth inhibition in salt-sensitive plants. Exogenously applied proline increases antioxidant activities and enhances plant salinity tolerance. This review examines the role and processes of proline in rice plants under salt stress and its relationship with other tolerance mechanisms.

High temperatures, drought, and salt stresses severely inhibit plant growth and production due to the effects of climate change. The Arabidopsis ARR1, ARR10, and ARR12 genes were identified as negative salt and drought stress regulators. However, in rice, the tolerance capacity of the hst1 gene, which is orthologous to the ARR1, ARR10, and ARR12 genes, to drought and multiple high temperature and drought stresses remains unknown. At the seedling and reproductive stages, we investigated the drought (DS) high temperature (HT) and multiple high temperature and drought stress (HT+DS) tolerance capacity of the YNU31−2−4 (YNU) genotype, which carries the hst1 gene, and its nearest genomic relative Sister Line (SL), which has a 99% identical genome without the hst1 gene. At the seedling stage, YNU demonstrated greater growth, photosynthesis, antioxidant enzyme activity, and decreased ROS accumulation under multiple HT+DS conditions. The YNU genotype also demonstrated improved yield potential and grain quality due to higher antioxidant enzyme activity and lower ROS generation throughout the reproductive stage under multiple HT+DS settings. Furthermore, for the first time, we discovered that the B−type response regulator hst1 gene controls ROS generation and antioxidant enzyme activities by regulating upstream and downstream genes to overcome yield reduction under multiple high temperatures and drought stress. This insight will help us to better understand the mechanisms of high temperature and drought stress tolerance in rice, as well as the evolution of tolerant crops that can survive increased salinity to provide food security during climate change.

Salinity poses a significant challenge to global wheat production. The screening of wheat cultivars for salt tolerance is essential for developing new varieties resilient to salinity and advancing breeding strategies. Identifying key traits from a myriad of morphological, physiological, and molecular markers in screening studies can enhance selection efficiency and expedite the process. In this study, 16 common wheat cultivars were subjected to 0 and 150 mM NaCl stress for ten days during the seedling stage. To assess the salinity tolerance of wheat cultivars comprehensively, we employed a diverse array of morpho-physiological, biochemical, and molecular markers, coupled with multivariate analysis. Salt stress resulted in reduced germination and seedling growth across most wheat cultivars. Notably, the ‘Ikizce-96’ and ‘Demir-2000’ genotypes exhibited a higher salinity tolerance index, with the least reduction in morpho-physiological parameters. These cultivars demonstrated elevated osmoregulator proline content and enhanced activity of reactive oxygen species-scavenging antioxidant enzymes. Under 150 mM NaCl, tolerant cultivars exhibited up-regulated transcript expression levels of TaHKT1;4, TaP5CS, and TaDHN marker genes compared to salt-sensitive cultivars. The accuracy of our findings was validated through principal component analysis, hierarchical clustering analysis, and a correlation network. Proline content, glutathione reductase, catalase, and superoxide dismutase activity emerged as the most reliable indicators of salt tolerance in wheat under saline conditions. The identified salt-tolerant cultivars hold promise as donor parents in salinity tolerance breeding programs.

The objective of this study was to characterize the endosperm starch in rice that ectopically overexpressed the α-amylase. Transgenic rice plants, transformed with cauliflower mosaic virus 35S promoter driven AmyI-1 (35S::AmyI-1) and AmyII-4 (35S::AmyII-4), and 10 kDa prolamin promoter driven AmyI-1 (P10::AmyI-1), were cultivated under standard conditions (23 °C, 12 h in the dark/ 26 °C, 12 h in the light), and brown grains were subsequently harvested. Each grain displayed characteristic chalkiness, while electron microanalyzer (EPMA)-SEM images disclosed numerous small pits on the surface of the starch granules, attributable to α-amylase activity. Fluorescence labeling and capillary electrophoresis analysis of starch chain length distribution revealed no significant alterations in the starches of 35S::AmyI-1 and 35S::AmyII-4 transgenic rice compared to the wild-type. Conversely, the extremely short α-glucan chains (DP 2-8) exhibited a dramatic increase in the P10::AmyI-1 starch. Rapid visco-analyzer analysis also identified variations in the chain length distribution of P10::AmyI-1 starch, manifesting as changes in viscosity. Moreover, 1H-NMR analysis uncovered dynamic modifications in the molecular structure of starch in rice grain transformed with P10::AmyI-1, which was found to possess unprecedented structural characteristics.

Biofertilizers offer a sustainable method for improving rice growth and productivity, yet their effects on the interaction between plant growth, photosynthetic activity, and gene expression remain under-researched. This study examines how biofertilizer influences rice physiology, focusing on photosynthetic regulation and expression of chlorophyll-related genes. Eight fertilizer treatments were applied: control (CNT), biofertilizer (BF), deactivated biofertilizer (DABF), rice straw (RS), rice straw with biofertilizer (RS+BF), organic fertilizer (OF), organic fertilizer with biofertilizer (OF+BF), and inorganic fertilizer (IOF). Plant height, tiller number, SPAD, NDVI, chlorophyll content, and photosynthesis rates were measured, while gene expression analysis was conducted using RT-qPCR. The OF+BF treatment produced the most significant results, leading to a 31% increase in plant height, a 135% increase in tiller number, and a 42% increase in chlorophyll content (SPAD values) compared to the control. Additionally, OF+BF enhanced photosynthetic efficiency by 74%, with the highest net photosynthetic rate of 48.23 μmol CO2 m−2 s−1. Gene expression analysis revealed that OF+BF upregulated key photosynthesis-related genes, such as OsChlD and OsCHLM, showing a 70% and 90% increase in expression. These findings highlight the potential of integrating biofertilizers with organic fertilizers to sustainably boost rice growth and productivity, contributing to global food security and climate change mitigation.

Salinity is one of the limiting factors that reduce crop production and yield. The salinity tolerance response of plants varies depending on the growth stages. Although the previous studies showed salinity tolerance responses of plants at early or late stages, the common early and late salinity tolerance response of rice plants has yet to be discovered. We investigated the common early (6-h salt exposure) and late (30-days salt exposure) physiological, biochemical, and transcriptome responses associated with salinity tolerance in salt-tolerant (ST) and sensitive (SS) rice genotypes with almost 99

Salinity is a critical environmental stress factor that significantly reduces crop productivity and yield. A mutant B-type response regulator gene (hst1) has been shown to promote salinity tolerance in the YNU genotype. Previous studies on the hst1 gene showed a higher proline production capacity under salt stress. Using almost identical genetic backgrounded salt-tolerant (YNU) and salt-sensitive (Sister line) rice genotypes, we tested the function of proline in the hst1 gene salinity-tolerance mechanism by applying exogenous proline under control and salt-stress conditions. Morpho-physiological, biochemical, and molecular analysis of ST and SS plants was performed to clarify the salinity tolerance mechanism mediated by the exogenous proline. The ST and SS genotypes accumulated exogenous proline, and the ST genotype has higher proline levels than the SS genotype. However, exogenous proline improved salt tolerance only in the SS genotype. Exogenous proline promotes plant and root growth by stimulating photosynthetic pigments and photosynthesis. The exogenous proline has a reductive effect on MDA, and H2O2 protects plants against ROS. Interestingly, exogenous proline lowers Na+ and raises K+ accumulations under salt stress. In the SS genotype, exogenous proline increases the activity of antioxidant enzymes (SOD, CAT, and APX) to protect against salinity-induced damage. The exogenous proline application down-regulates proline-synthesis genes (OsP5CS1 and OsP5CR) and up-regulates proline-degradation genes. Also, exogenous proline increases the expression of the OsSalT and OsGRAS29 genes, improving salinity tolerance in the SS genotype. Our study has demonstrated that proline plays a significant role in conferring salt tolerance with the salinity-tolerance-related hst1 mechanisms.

Environmental stresses are posing a danger to global food security due to worldwide reductions in the productivity and yield of cereals under climate change pressure. Food security is an issue of great concern when the demand for food is projected to increase by 85% by the end of 2050. Soil salinity is one of the significant problems to solve in improving the productivity of cereals in arid and semi-arid regions. Crop improvement via classical breeding techniques needs a long timescale, and the success rate is not high. With the developing sequencing technology, markers based on the detection of associated morphological features that reference nucleic acid sequence differences in the plant genome have enabled the development of modern breeding approaches. Currently, newly developed methods such as GWAS based on NGS form the foundation for next-generation breeding. Also, the discovery of CRISPR/Cas 9 systems gives the unprecedented prospect of manipulating the plant genomes with more accuracy and precision. Performing genome editing under rapid breeding conditions provides a controlled system to accelerate crop growing cycles at minimal cost and is a technological breakthrough for non-transgenic salt stress–tolerant plants. The development and widespread use of this technology are essential steps that will affect the success and speed of breeding studies in the future. Using integrated next-generation approaches, this technology will achieve substantial success in ensuring future food security and meeting the food demands of a rapidly increasing population in the coming decades.

The yield-reduction effect of abiotic stressors such as salinity and heat stresses with the growing world population threatens food security. Although adverse effects of salinity and heat stress on plant growth and production parameters have been documented, in nature, abiotic stresses occur sequentially or simultaneously. In this study, the stress tolerance and yield capacity of Yukinkomai, YNU31-2-4, and YNU SL rice genotypes tested under control (26 °C, 0 mM NaCl), salinity (26 °C, 75 mM NaCl), heat (31 °C, 0 mM NaCl), and heat and salinity (31 °C, 75 mM NaCl) stress combinations at vegetative and reproductive stages with six different scenarios. The results show that salinity and the heat and salinity combination stresses highly reduce plant growth performance and yield capacity. Heat stress during reproduction does not affect the yield but reduces the grain quality. The YNU31-2-4 genotype performs better under heavy salt and heat and salinity stress then the Yukinkomai and YNU SL genotypes. YNU31-2-4 genotypes accumulate less Na+ and more K+ under salt and multiple stresses. In the YNU31-2-4 genotype, low Na+ ion accumulation increases photosynthetic activity and pigment deposition, boosting the yield. Stress lowers the glucose accumulation in dry seeds, but the YNU31-2-4 genotype has a higher glucose accumulation.