Integrated Phylogenomics and Expression Profiling of the Peptide Deformylase Gene Family in Oryza sativa Reveals Their Role in Development and Stress Tolerance.

Drought, cold, high-salinity and heat are major abiotic stresses that severely reduce the yield of food crops worldwide. Traditional plant breeding approaches to improve abiotic stress tolerance of crops had limited success due to multigenic nature of stress tolerance. In the last decade, molecular techniques have been used to understand the mechanisms by which plants perceive environmental signals and further their transmission to cellular machinery to activate adaptive responses. This knowledge is critical for the development of rational breeding and transgenic strategies to impart stress tolerance in crops. Studies on physiological and molecular mechanisms of abiotic stress tolerance have led to characterisation of a number of genes associated with stress adaptation. Techniques like microarrays have proven to be invaluable in generating a list of stress-related genes. Some of these genes are specific for a particular stress while others are shared between various stresses. Interestingly, a number of genes are shared in abiotic and biotic stress responses. This highlights the complexity of stress response and adaptation in plants. There is a whole cascade of genes involved in abiotic stress tolerance; starting from stress perception to transcriptional activation of downstream genes leading to stress adaptation and tolerance. A number of these genes have been discovered but we still do not have the complete list with all interactions. There is also significant number of genes with unknown functions found to be regulated by abiotic stresses. Understanding the function of these genes and their interaction with other known genes to effect stress adaptation is required.

Although most studies have indicated that biochar can boost rice ( Oryza sativa ) growth, the material may also suppress it, depending on ratios of carbon (C) to nitrogen (N) and available N to available phosphorous (P). The current study sought to examine the impacts of biochar on rice growth and to identify underlying mechanisms. A pot experiment was conducted using two soils of high (3.05%) and low (0.54%) organic carbon (OC) content, mixed with 0, 1.5, 3, 6, and 12% biochar and planted with rice. Rice growth components, five rice tissue nutrients, and nine soil properties were measured. The results showed that the response of rice growth to biochar rates could be described using an exponential‐growth function in high‐OC soil but an inverted U‐shaped curve in low‐OC soil. In high‐OC soil, the 12% biochar rate led to the greatest total biomass, increased by 47%, whereas in low‐OC soil, the 3 and 6% rates exhibited the highest total biomass, increased by 44%, compared to the no‐biochar added soils. Biochar elevated the C:N ratio from 11.5 to 39.1, with an optimal range of 20–30 corresponding to the highest rice growth. Biochar declined the ratio of NH 4 ‐N to Mehlich‐1 P, causing N deficiency. In brief, high biochar rates may suppress rice growth when the soil C:N ratio exceeds 30. The applied biochar rate should be considered based on soil properties typically OC and N content to obtain the C:N ratio between 20 and 30 for optimal rice growth.

Surjan system (alternating bed system) is an agricultural system that combines dry and wet bedding system. It integrates food crop culture in the sunken-bed and annual crops in the raised-bed of the rainfed rice field. In Bantul, farmers commonly apply Surjan system in rice field by growing shallot (Allium cepa L. aggregatum group) and chili (Capsicum annuum L.) in the raised-bed, whereas no crop is grown in the sunken-bed. This present experiment evaluated the utilization of the sunken-bed for rice cultivation by utilizing fertilizer runoff from the raised-bed. Rice plants in the sunken-bed were not fertilized due to the expectation that it could utilize the fertilizer runoff from the raised-bed. The cropping pattern and the fertilizer dose in the raised-bed are suspected to affect the growth and yield of rice in the sunken-bed. The purpose of this study was to determine the effect of cropping pattern and fertilizer dose applied in raised-bed on the growth and yield of rice in sunken-bed of the Surjan rice field. This study were laid out in a split plot design with three replication. The main plot consists of two cropping pattern, namely shallot monoculture and intercropping shallot with chili. The fertilizer dose applied in raised-bed, namely 100% farmer's habit; 50% farmer’s habit; and 25% farmers' habit, occupying the sub plot. Dose of fertilizer applied in riased- bed according to the farmer's habit in research locatin is 622 kg NPK/ha (16-16-16) ; 228 kg ZA/ha and 76 kg KCl/ha. The results showed that there was no interaction between the cropping pattern and the fertilizer dose applied in the raised-bed on the growth and yield of rice in the sunken-bed. Compared with shallot monoculture, intercropping shallot with chili in raised-bed decreased the growth of rice in the sunken-bed. Compared with the 100% fertilizer dosage of farmer's habits, the fertilizer dose of 50% of the farmer's habits in the raised-bed increased the growth of rice in the sunken-bed. Cropping pattern and fertilizer dose in the raised-bed did not significantly affect the rice yield grown in the sunken-bed of the Surjan rice field.

The comprehensive effects of nanoparticles and coexisting heavy metals on plant growth are still unclear, especially in soil medium. The single and combined effects of multiwall carbon nanotubes (MWCNTs) and cadmium (Cd) on rice (Oryza sativa L.) growth were examined in this study through a 4 months pot experiment in 2022. Rice plants were exposed to different concentrations of MWCNTs (100 and 500 mg kg−1) in the presence of 5.0 mg kg−1 Cd stress. At the tillering stage, the 500 mg kg−1 MWCNTs addition reduced plant height by 8.0% and increased soluble protein content in the leaves by 13.7%, demonstrating that a single MWCNTs had a slight negative impact on rice growth. When exposed to Cd stress, the inclusion of 500 mg kg−1 MWCNTs led to a 6.7%–9.0% decrease in bioavailable Cd level in soil, resulting in considerable reductions in Cd content in roots (23.4%–29.9%), shoots (24.5%–28.3%) and grains (28.3%–66.2%). Compared to the single Cd treatment, the O. sativa L. leaves treated with Cd and MWCNTs (500 mg kg−1) had considerably reduced levels of malondialdehyde (MDA), soluble protein, and activities of antioxidant enzymes (POD, CAT, and SOD). The findings of this study indicated that appropriate concentrations of MWCNTs application in soil could alleviate Cd-induced toxicity on rice growth.

Introduction:Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors.Conclusion: This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.

DNA-binding with one finger (DOF)-type transcription factors are involved in many fundamental processes in higher plants, from responses to light and phytohormones to flowering time and seed maturation, but their relation with abiotic stress tolerance is largely unknown. Here, we identify the roles of CDF3, an Arabidopsis DOF gene in abiotic stress responses and developmental processes like flowering time. CDF3 is highly induced by drought, extreme temperatures and abscisic acid treatment. The CDF3 T-DNA insertion mutant cdf3-1 is much more sensitive to drought and low temperature stress, whereas CDF3 overexpression enhances the tolerance of transgenic plants to drought, cold and osmotic stress and promotes late flowering. Transcriptome analysis revealed that CDF3 regulates a set of genes involved in cellular osmoprotection and oxidative stress, including the stress tolerance transcription factors CBFs, DREB2A and ZAT12, which involve both gigantea-dependent and independent pathways. Consistently, metabolite profiling disclosed that the total amount of some protective metabolites including γ-aminobutyric acid, proline, glutamine and sucrose were higher in CDF3-overexpressing plants. Taken together, these results indicate that CDF3 plays a multifaceted role acting on both flowering time and abiotic stress tolerance, in part by controlling the CBF/DREB2A-CRT/DRE and ZAT10/12 modules.

The relationship between plants and beneficial fungi offers a sustainable approach to enhance crop productivity and stress resilience. This study investigated the effects of Leucocalocybe mongolica strain LY9 on rice (Oryza sativa L.) growth, flavonoid metabolism, and transcriptional regulation. Rice plants treated with varying concentrations of LY9-transformed soil (10%, 30%, and 50%) exhibited significant improvements in phenotypic traits, including increased tiller numbers, shoot length (989 mm), and root length (518 mm), alongside elevated chlorophyll content, indicating enhanced photosynthetic efficiency. However, total flavonoid content decreased at the highest LY9 concentration, suggesting a metabolic trade-off between growth promotion and secondary metabolite production. Transcriptomic analysis revealed dose-dependent modulation of MYB, bHLH, and WRKY transcription factor genes such as Os04g0605100-WRKY68 and Os05g0553400-R2R3MYB84, while metabolomic profiling identified selective upregulation of stress-responsive flavonoids, such as chalcones (e.g., 2’,4’-dihydroxy-2,3’,6’-trimethoxychalcone and naringenin chalcone) and isoflavones (e.g., prunetin), while flavones were predominantly suppressed. Pearson correlation analyses underscored negative associations between flavonoid levels and growth traits, highlighting LY9’s role in reallocating resources from defense to growth. These findings demonstrate that LY9 enhances rice productivity by modulating flavonoid metabolism and transcriptional networks, offering insights into sustainable agricultural practices for stress resilience. Additionally, the study underscores the potential of LY9 as a biofertilizer to optimize rice growth while maintaining stress resilience through targeted metabolic adjustments.

α-Ketol octadecadienoic acid (KODA), an oxylipin, has stimulatory effects on flowering, rooting, and resistance to pathogens. It also increases the yield of rice, Oryza sativa L. Here we examined the effects of KODA on the early growth of rice under various temperature conditions. KODA was applied by imbibing seeds in 1 µM KODA solution overnight. KODA treatment did not promote the growth at 25°C or 28°C, which are appropriate temperatures for rice cultivation. At a constant temperature of 15°C, seedling growth was poor, and KODA application did not promote seedling growth. On the other hand, at a night temperature of 15°C and day temperature of 25°C, KODA prominently enhanced the growth. We analyzed the transcript levels of several marker genes associated with chilling signaling and stress tolerance in rice. The expression of the dehydration-responsive-element-binding protein 1/C-repeat binding factor (DREB1/CBF), which regulate the expression of many stress-responsive genes was promoted. The expression of the late embryogenesis abundant (LEA), which has a DRE/CRT cis-element, was also increased by KODA treatment. Additionally, the expression of the b-amylase 4 (OsBMY4), which is important for starch degradation during cold-stress adaptation in rice, and that of the probenazole-induced protein 1 (PBZ1), a molecular marker in the rice immune response, were significantly elevated in KODA-treated rice. Thus, the enhanced growth of KODA-treated rice under chilling stress may be attributed, at least in part, to the enhanced transcriptional regulatory network mediated by DREB1/CBF genes and sugar metabolism, including starch degradation mediated by abscisic acid.

Chapter 8 - Abiotic stress responses and tolerance in wheat under climate change

A pot experiment was conducted to measure the effect of silicon on phosphorus uptake and on the growth of rice at different P levels. Rice (Oryza sativa L. cv. Akebono) was cultured in Kimura B nutrient solution without and with silicon (1.66 mM Si) and with three phosphorus levels (0.014 mM P, low; 0.21 mM, medium; and 0.70 mM, high). Shoot dry weight with Si (+Si) in solution increased with increasing P level, while shoot weight without Si (−Si) was maximum at 0.21 mM P, suggesting that +Si raised the optimum P level for rice. +Si increased shoot weight more when P was low or high than when P was medium. The concentration and amount of inorganic P in shoots increased with increasing P level. +Si did not significantly decrease P uptake by rice at 0.014 mM P, however, uptake at 0.21 and 0.70 mM P was 27 and 30 percent less than uptake with −Si, respectively. In −Si with 0.21 and 0.70 mM P, inorganic P in shoots was more than double the concentration in shoots grown in +Si solutions. The Si concentration in shoots decreased slightly with increasing P level, although Si uptake was not significantly affected by P. +Si decreased the uptake of Fe and Mn by an average of 20 and 50 percent, respectively, thus P/Mn and P/Fe ratios increased in the shoot when P was low. From the results above, the beneficial effect of Si on the growth of rice was clearly shown when P was low or high. This effect may have resulted from decreased Mn and Fe uptake, and thus increased P availability within P deficient plants, or from reduced P uptake when P was high.

The better growth of rice in a flooded soil as compared to an upland soil has been attributed to the reducing conditions caused by submergence. No study has been carried out, however, in which the effects of the soil moisture status has been separated from the effect of the oxidation‐reduction conditions of the soil.In the study reported here, the effect of soil oxidation‐reduction conditions on early growth and mineral composition of lowland rice (Oryza sativa L. ‘Saturn’) was determined by growing plants in artificially packed soil columns maintained under different soil moisture tension and oxygen conditions. Since soil aeration is largely governed by the moisture status of the soil, this study was designed to separate these effects by subjecting the rice plant to different aeration conditions while at the same time attempting not to limit moisture supply. In one experiment different redox conditions were established by maintaining soil columns at soil moisture tensions ranging from 0 to 80 cm during growth of the plants. In a second experiment plants were grown at soil oxygen levels of 0, 3, 8, and 12% while soil moisture was maintained at 10 cm moisture tension. Vegetative growth of rice was greater under reduced conditions than under oxidized conditions in both experiments. The P concentration of the plant was much higher under reduced conditions than under oxidized conditions. Reduced conditions increased the solubility of P, Fe, and Mn in the soil although no consistent effect of reducing conditions on plant uptake of Fe and Mn was observed.

Irrigation with microcystins-contaminated water threatens growth and yield of crops and human health. Growth of rice at booting stage is crucial for the yield of rice at mature stage. Hence, we studied growth, yield and grains quality of rice as well as accumulation of microcystins in different tissues of rice at booting stage exposed to 1, 100, 1000, and 3000 μg L−1 microcystins solution and then recovered (without microcystins). After a 7-day exposure, microcystins content in tissues was positively correlated with microcystins concentrations, and microcystins content in roots was the highest. In addition, microcystins content in grains of rice treated with 1, 100, 1000 and 3000 μg L−1 microcystins was 4.9, 7.1, 12.6 and 21.2 μg kg−1 dry weight, indicating that the microcystins in grains of rice treated with microcystins (≥1000 μg L−1) could pose a threat to human health through food chain. Low concentration microcystins (1 μg L−1) did not affect growth and photosynthesis, but high concentration microcystins (≥100 μg L−1) inhibited growth and photosynthesis. After a 7-day restoration, growth and photosynthesis in rice treated with microcystins (≥1000 μg L−1) were even worse than those during the exposure period. After maturity, yield of rice as well as protein and amylose content in grains of rice treated with microcystins (≥100 μg L−1) were all lower than those of the control. Our results imply that irrigation with microcystins-contaminated water must be monitored and controlled to avoid harmful accumulation of microcystins and damage to crops yield.

Heterotrimeric guanine-nucleotide-binding proteins (G-proteins) play key roles in responses to various abiotic stress responses and tolerance in plants. However, the detailed mechanisms behind these roles remain unclear. Mulberry (Morus alba L.) can adapt to adverse abiotic stress conditions; however, little is known regarding the associated molecular mechanisms. In this study, mulberry G-protein genes, MaGα, MaGβ, MaGγ1, and MaGγ2, were independently transformed into tobacco, and the transgenic plants were used for resistance identification experiments. The ectopic expression of MaGα in tobacco decreased the tolerance to drought and salt stresses, while the overexpression of MaGβ, MaGγ1, and MaGγ2 increased the tolerance. Further analysis showed that mulberry G-proteins may regulate drought and salt tolerances by modulating reactive oxygen species’ detoxification. This study revealed the roles of each mulberry G-protein subunit in abiotic stress tolerance and advances our knowledge of the molecular mechanisms underlying G-proteins’ regulation of plant abiotic stress tolerance.

ABSTRACTSalt-affected soil induces detrimental influences on paddy rice (Oryza sativa L.) growth and ameliorating the influences could be done with organic amendments, such as animal manure and biochar. The aims of the current study are: (1) to examine the interactive effects of biochar and cow manure on rice growth and on selected properties of salt-affected soil, and (2) to identify potential mechanisms related to the amendments. Saline-sodic soil was used for a net house experiment with two experimental factors: biochar (no-biochar, rice-husk, and -straw biochar) and cow manure (with and without cow manure). Without the manure, addition of both rice-hush and – straw biochar significantly increased rice growth, whereas a combination of individual biochar with manure did not show a positive synergistic effect. The interactive effect of two factors was not significant on available P and exchangeable K concentrations, but the main effects of the two factors were significant. Biochar addition resulted in higher soil cation exchange capacity (CEC) (28.8 to 29.0 cmolc kg−1) than the control (25.6 cmolc kg−1), but manure addition did not. Improved nutrient availabilities such as P and K, as well as CEC are among the potential mechanisms accounting for the enhanced rice growth with biochar.

OsANN1 is a member of the annexin protein family in rice. The function of this protein and the mechanisms of its involvement in stress responses and stress tolerance are largely unknown. Here it is reported that OsANN1 confers abiotic stress tolerance by modulating antioxidant accumulation under abiotic stress. OsANN1-knockdown [RNA interference (RNAi)] plants were more sensitive to heat and drought stresses, whereas OsANN1-overexpression (OE) lines showed improved growth with higher expression of OsANN1 under abiotic stress. Overexpression of OsANN1 promoted SOD (superoxide dismutase) and CAT (catalase) activities, which regulate H2O2 content and redox homeostasis, suggesting the existence of a feedback mechanism between OsANN1 and H2O2 production under abiotic stress. Higher expression of OsANN1 can provide overall cellular protection against abiotic stress-induced damage, and a significant accumulation of OsANN1-green fluorescent protein (GFP) signals was found in the cytosol after heat shock treatment. OsANN1 also has calcium-binding and ATPase activities in vitro, indicating that OsANN1 has multiple functions in rice growth. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays demonstrated that OsANN1 interacts with OsCDPK24. This cross-talk may provide additional layers of regulation in the abiotic stress response.