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Tricyclazole is commonly used to prevent rice blast to meet the carbohydrate intake needs of half of the global population, and a large number of toxicological reports indicate that monitoring of tricyclazole is necessary. Here, we analyzed the structure of tricyclazole and designed different hapten derivatization strategies to prepare a high-performance monoclonal antibody (half inhibition concentration of 1.61 ng/mL), and then a lateral flow immunochromatographic sensor based on gold nanoparticles for the detection of tricyclazole in rice, with a limit of detection of 6.74 μg/kg and 13.58 μg/kg in polished and brown rice, respectively. The recoveries in rice were in the range of 84.6-107.4%, no complex pretreatment was required for comparison with LC-MS/MS, and the comparative analysis demonstrated that our method had good accuracy and precision. Therefore, the developed lateral flow immunochromatographic analysis was a reliable and rapid means for the on-site analysis of tricyclazole in rice., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Molecular basis of rice aroma formation is sparsely known and developmental programs driving biochemical pathways towards aroma is in infancy. Here, discovery and targeted proteo-metabolome of non-aromatic and aromatic rice seeds across developmental stages identified a total of 442 aroma-responsive proteins (ARPs) and 824 aroma-responsive metabolites (ARMs) involved in metabolism, calcium and G-protein signaling. Biochemical examination revealed ARM/Ps were linked to 2-acetylpyrrolidine, γ-aminobutyrate, anthocyanin, tannins, flavonoids and related enzymes. Pairwise correlation and clustering showed positive correlation among ARM/Ps. Consistent with aroma-related QTLs, ARPs were mapped on chromosomes 3,4,5,8 and were mainly compartmentalized in cytoplasm and mitochondria. ARM/P-correlation network identified associations related to metabolism and signaling. Multiple reaction monitoring (MRM) confirmed role of catechins, quinic acid and quercetin in aroma formation. Pathway enrichment, multivariate analysis and qRT-PCR validated that calcium and G-protein signaling, aromatic/branched-chain aminoacid, 2-acetylpyrrolidine, oxylipin, melvonate and prenylpyrophosphate pathways, indole, phenylacetate, flavonoid, cinnamoic ester govern aroma formation in rice., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Three rice varieties underwent the field natural extreme high temperature (EHT) with daily average temperature over 30 °C from 21 to 89 days after sowing, and had transparent, chalky and floury grains. The structures, gelatinization properties and enzyme hydrolyses of starches from transparent and floury grains were investigated. Compared with control transparent grains, floury grains subjected to EHT markedly decreased the contents of amylose molecules, amylopectin A chains and amylopectin B1 chains and increased the contents of amylopectin B2 and B3+ chains and the average branch-chain length of amylopectin. Both transparent and floury grains had A-type starches, but floury grain starches exhibited higher relative crystallinity, gelatinization temperature, retrogradation and pasting viscosities than transparent grain starches. Floury grain starches had lower hydrolysis rates than transparent grain starches. Native starches were more resistant to digestion but gelatinized and retrograded starches were more prone to digestion in floury grains than in transparent grains., Competing Interests: Declaration of competing interest There are no conflicts of interest to declare., (Copyright © 2023. Published by Elsevier Ltd.)

Assessing the bioaccessibility and bioavailability of cadmium (Cd) is crucial for effective evaluation of the exposure risk associated with intake of Cd-contaminated rice. However, limited studies have investigated the influence of gut microbiota on these two significant factors. In this study, we utilized in vitro gastrointestinal simulators, specifically the RIVM-M (with human gut microbial communities) and the RIVM model (without gut microbial communities), to determine the bioaccessibility of Cd in rice. Additionally, we employed the Caco-2 cell model to assess bioavailability. Our findings provide compelling evidence that gut microbiota significantly reduces Cd bioaccessibility and bioavailability (p<0.05). Notably, strong in vivo-in vitro correlations (IVIVC) were observed between the in vitro bioaccessibilities and bioavailabilities, as compared to the results obtained from an in vivo mouse bioassay (R 2  = 0.63-0.65 and 0.45-0.70, respectively). Minerals such as copper (Cu) and iron (Fe) in the food matrix were found to be negatively correlated with Cd bioaccessibility in rice. Furthermore, the results obtained from the toxicokinetic (TK) model revealed that the predicted urinary Cd levels in the Chinese population, based on dietary Cd intake adjusted by in vitro bioaccessibility from the RIVM-M model, were consistent with the actual measured levels (p > 0.05). These results indicated that the RIVM-M model represents a potent approach for measuring Cd bioaccessibility and underscore the crucial role of gut microbiota in the digestion and absorption process of Cd. The implementation of these in vitro methods holds promise for reducing uncertainties in dietary exposure assessment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

A recent study by Sun et al. OsNLP3 enhances grain weight and reduces grain chalkiness in rice sheds new insight on the crucial role of OsNLP3 in regulating grain weight and chalkiness through its interaction with OsCEP6.1 and OsNF-YA8 and suppress their expression. The research reveals a promising pathway for developing strategies to reduce chalkiness while enhancing grain yield, paving the way for improved rice crop productivity., Competing Interests: Declarations. Competing interests: The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Zn as an essential element has the potential to protect against mercury (Hg) toxicity in rice. However, the antagonistic effects between Zn and Hg in rice and their mechanisms remain unknown. This study proposed a promising strategy for Zn application to mitigate Hg accumulation and toxicity in rice and revealed the underlying molecular mechanisms. The findings revealed that Zn supplementation significantly reduced the uptake and transportation of both IHg and MeHg in rice, thereby alleviating Hg phytotoxicity. In particular, Zn profoundly mitigated Hg-induced oxidative damage to rice, which was attributed to the redistribution of Hg and Zn in the root and Zn competing for binding sites on glutathione. The co-binding of Zn 2+ and HgCH 3 within the same active sites of Zn transporters can promote the transfer of regions with a high charge density distribution at the highest occupied molecular orbital (HOMO) level. This process facilitates proton attack on the Hg-C bond, thereby enhancing MeHg demethylation in rice. By elucidating the molecular mechanisms of Zn, IHg, and MeHg interactions in rice, this study offers new insights for developing efficient strategies to mitigate Hg risks while boosting the Zn content in crops, thereby fortifying food safety.+ within the same active sites of Zn transporters can promote the transfer of regions with a high charge density distribution at the highest occupied molecular orbital (HOMO) level. This process facilitates proton attack on the Hg-C bond, thereby enhancing MeHg demethylation in rice. By elucidating the molecular mechanisms of Zn, IHg, and MeHg interactions in rice, this study offers new insights for developing efficient strategies to mitigate Hg risks while boosting the Zn content in crops, thereby fortifying food safety.

Rice is a staple food for a significant portion of the global population. Arsenic (As) accumulated in rice grains influences rice quality which threatens human health. In this study, we used three machine learning models to predict arsenic accumulation in rice based on over 300 surveys. The prediction results of soil arsenic indicate that high-arsenic soil areas are mainly distributed in South and Southeast Asia such as India, China, and Thailand. In addition, higher bioaccumulation factors (BAF), associated with higher temperature, are predominantly observed in eastern India and southern Myanmar. However, arsenic content in soil is relatively lower in these areas. About 5.5 billion population may be threatened by the consumption of high-arsenic rice. It can be concluded that temperatures may influence the BAF except for soil arsenic, and soil physicochemical properties. Further research on the relationship between climate parameters and BAF should be conducted to address and adapt to future climate change. Additionally, understanding the mechanism of arsenic accumulation under different climatic conditions is crucial for developing agricultural technologies to reduce arsenic accumulation in rice., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: The brown planthopper (BPH) is an economically significant pest of rice. Bph3 is a key BPH resistance gene. However, the proteomic response of rice to BPH infestation, both in the presence and absence of Bph3, remains largely unexplored., Results: In this study, we employed tandem mass tag labeling in conjunction with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis to identify differentially expressed proteins (DEPs) in rice samples. We detected 265 and 125 DEPs via comparison of samples infected with BPH for 2 and 4 days with untreated samples of the BPH-sensitive line R582. For the Bph3 introgression line R373, we identified 29 and 94 DEPs in the same comparisons. Bioinformatic analysis revealed that Bph3 significantly influences the abundance of proteins associated with metabolic pathways, secondary metabolite biosynthesis, microbial metabolism in diverse environments, and phenylpropanoid biosynthesis. Moreover, Bph3 regulates the activity of proteins involved in the calcium signaling pathway, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signal transduction., Conclusions: Our results indicate that Bph3 enhances the resistance of rice to BPH mainly by inhibiting the down-regulation of proteins associated with metabolic pathways; calcium signaling, the MAPK signaling pathway, and plant hormone signal transduction might also be involved in BPH resistance induced by Bph3., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Conflict of interest The authors declare no conflict of interest., (© 2024. The Author(s).)

This study was conducted to combine two physical (ultrasonic) and biological (Saccharomyces cerevisiae) methods to reduce heavy metals such as Arsenic (As), Cadmium (Cd), and Lead (Pb) in rice, which is the most widely consumed grain. The concentrations of As, Cd, and Pb were found to be significantly affected after different treatments, were on uncooked rice samples (R1-R9): As R 9 (2.05 ± 0.01) Cd R 1 , R 3 , R 5 , R 8 (1.20 ± 0.01), Pb R 6 (3.04 ± 0.173) (µgkg - 1 ) and in cooked rice samples were (C1-C10): As C 10 (0.35 ± 0.27) Cd C 9 , C 10 (1.00 ± 0.02), Pb C 1 (3.52 ± 0.17) (µgkg - 1 ). The results showed that using ultrasound treatment combined with yeast (C 10 ) had the greatest effect on reducing As among all treatments. In addition, C 9 , and C 10 treatments were effective in reducing Cd concentration in cooked rice samples, and R 6 treatment was effective in reducing Pb concentration in uncooked samples. The rice's thermal qualities and specific textural traits were also affected by some or all of these treatments. The samples with modified particle sizes had the greatest sensory evaluation scores (C 9 ). Moreover, sensory evaluation results showed that a specific treatment combining yeast and ultrasound (C 3 ) maintained good sensory qualities and did not negatively affect the sensory qualities without sacrificing texture. Overall, this approach provides a promising method for the reduction of heavy metals in rice. A combination of biological and physical treatments can be used to reduce the heavy metals content (As, Cd, Pb) in rice. Stakeholders can use the aforementioned actions to optimize heavy metal content in the food chain, which requires the support of policymakers to promote public health., Competing Interests: Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Rice consumption is a pathway for human exposure to toxic elements. Although rice is a major staple in the Kingdom of Saudi Arabia (KSA) there is limited published data about its toxic element composition. Both imported and locally grown Hassawi rice in Saudi Arabia were collected, digested then analysed by HPLC-ICP-MS for inorganic arsenic (i-As) and by ICP-MS for As, Cd, Pb and Hg. Of these toxic elements, i-As was present at concentrations that might give rise to material concerns about human exposure and public health. Hassawi rice (mean 43 ± 5 µg/kg) was found to have significantly lower concentrations of i-As than imported rice (mean 73 ± 8 µg/kg). The estimated exposure of adults consuming imported rice in one KSA city reached 0.3 µg/kg-bw/day, within the margin of safety of the recently withdrawn WHO PTWI for i-As of 2.1 µg/kg-bw/day and higher than EFSA's 0.06 µg/kg-bw/day skin cancer BMDL 05 ., Competing Interests: Declarations Conflict of interest The authors report there are no competing interests to declare., (© 2024. The Author(s).)

Hydroponics combined with fugacity model was employed to investigate the kinetics of uptake, accumulation, and metabolism of organophosphate esters (OPEs) by japonica rice. The time-dependent process for uptake and accumulation of 5 OPEs and their diester-metabolites in both rice root and shoot fitted well with the pseudo-first-order kinetic model. The peak OPE accumulations in rice root and shoot were significantly positively or negatively correlated with their octanol-water partition coefficient (logK ow ) respectively, but not for their apparent accumulation rates. Root concentration factors (RCFs) and root-to-shoot translocation factors (TFs) of OPEs were found to be positively and negatively correlated with their logK ow , respectively. Triphenyl phosphate with benzene ring substituents showed the highest RCF, but the lowest TF, because of its high potential for root adsorption due to the π electron-rich structures. Sterilized root exudates can hinder the root adsorption and absorption of OPEs from solution probably through competitive adsorption of OPEs with root surface. The first-hand transport and metabolism rates were also obtained by generating these rates to fit the dynamic fugacity model with the measurement values. The simulation indicated that the kinetics of OPE accumulation in rice plants may be controlled by multiple processes and physicochemical properties besides K ow ., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

This study explores the integration of crop phenology models and machine learning approaches for predicting rice phenology across China, to gain a deeper understanding of rice phenology prediction. Multiple approaches were used to predict heading and maturity dates at 337 locations across the main rice growing regions of China from 1981 to 2020, including crop phenology model, machine learning and hybrid model that integrate both approaches. Furthermore, an interpretable machine learning (IML) using SHapley Additive exPlanation (SHAP) was employed to elucidate influence of climatic and varietal factors on uncertainty in crop phenology model predictions. Overall, the hybrid model demonstrated a high accuracy in predicting rice phenology, followed by machine learning and crop phenology models. The best hybrid model, based on a serial structure and the eXtreme Gradient Boosting (XGBoost) algorithm, achieved a root mean square error (RMSE) of 4.65 and 5.72 days and coefficient of determination (R 2 ) values of 0.93 and 0.9 for heading and maturity predictions, respectively. SHAP analysis revealed temperature to be the most influential climate variable affecting phenology predictions, particularly under extreme temperature conditions, while rainfall and solar radiation were found to be less influential. The analysis also highlighted the variable importance of climate across different phenological stages, rice cultivation patterns, and geographic regions, underscoring the notable regionality. The study proposed that a hybrid model using an IML approach would not only improve the accuracy of prediction but also offer a robust framework for leveraging data-driven in crop modeling, providing a valuable tool for refining and advancing the modeling process in rice., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

As rice has no physiological capacity of fixing nitrogen in the soil, its production had always been reliant on the external application of nitrogen (N) to ensure enhanced productivity. In the light of improving nitrogen use efficiency (NUE) in rice, several advanced agronomic strategies have been proposed. However, the soared increase of the prices of N fertilizers and subsequent environmental downfalls caused by the excessive use of N fertilizers, reinforces the prerequisite adaptation of other sustainable, affordable, and globally acceptable strategies. An appropriate alternative approach would be to develop rice cultivars with better NUE. Conventional breeding techniques, however, have had only sporadic success in improving NUE, and hence, this paper proposes a new schema that employs the wholesome benefits of the recent advancements in omics technologies. The suggested approach promotes multidisciplinary research, since such cooperation enables the synthesis of many viewpoints, approaches, and data that result in a comprehensive understanding of NUE in rice. Such collaboration also encourages innovation that leads to developing rice varieties that use nitrogen more effectively, facilitate smart technology transfer, and promotes the adoption of NUE practices by farmers and stakeholders to minimize ecological impact and contribute to a sustainable agricultural future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Rice, has long been an inseparable part of the human diet all over the world. As one of the most rapidly growing crops, rice has played a key role in securing the food chain of low-income food-deficit countries. Starch is the main component in rice granules which other than its nutritional essence, plays a key role in defining the physicochemical attributes of rice-based products. However, rice starch suffers from weak techno-functional characteristics (e.g., retrogradability of pastes, opacity of gels, and low shear/temperature resistibility. Green modification techniques (i.e. Non-thermal methods, Novel thermal (e.g., microwave, and ohmic heating) and enzymatic approaches) were shown to be potent tools in modifying rice starch characteristics without the exertion of unfavorable chemical reagents. This study corroborated the potential of green techniques for rice starch modification and provided deep insight for their further application instead of unsafe chemical methods., Competing Interests: Declaration of competing interest None., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

While it is known that temperature sensors trigger calcium (Ca 2+ ) signaling to confer cold tolerance in cells, less is known about sensors that couple with other secondary messengers. Here, we identify a cold sensor complex of CHILLING-TOLERANCE DIVERGENCE 6 (COLD6) and osmotin-like 1 (OSM1), which triggers 2',3'-cyclic adenosine monophosphate (2',3'-cAMP) production to enhance cold tolerance in rice. COLD6, which is encoded by a major quantitative trait locus (QTL) gene, interacts with the rice G protein α subunit (RGA1) at the plasma membrane under normal conditions. Upon exposure to chilling, cold-induced OSM1 binds to COLD6, kicking out RGA1 from interaction. This triggers an elevation of 2',3'-cAMP levels for enhancing chilling tolerance. Genetic data show that COLD6 negatively regulates cold tolerance and functionally depends on OSM1 in chilling stress. COLD6 alleles were selected during rice domestication. Knockout and natural variation of COLD6 in hybrid rice enhanced chilling tolerance, hinting design potential for breeding. This highlighted a module triggering 2',3'-cAMP to improve chilling tolerance in crops., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

OsGADD45a1, a member of the growth arrest and DNA damage-inducible 45 (GADD45) family in rice, has a newly identified homologue, OsGADD45a2, which differs from OsGADD45a1 in only three amino acids. The role and function of the OsGADD45a2 in DNA demethylation are not well-understood and were investigated in this study. Osgadd45a2 mutants exhibited reduced height, shorter panicle length, fewer grains per panicle, and a lower seed setting rate compared with wild-type plants. Moreover, the results showed that OsGADD45a2 negatively regulates rice blast fungus resistance and exhibited high expression in various tissues. Using the 3000 Rice Genomes Project database, we identified four major haplotypes (each with over 100 cultivars) based on single-nucleotide polymorphisms in the coding sequence of OsGADD45a2 . Among these, Hap4 was associated with a significantly greater plant height than Hap1-3, possibly due to a functional alteration of OsGADD45a2 linked to the SNP at position 2614993. In OsGADD45a2 overexpression lines, significant decreases in CG and CHG methylation levels were observed in protein-coding genes, leading to their upregulation. Overall, our findings indicate that OsGADD45a2 acts as a methylation regulator, mediating the expression of genes essential for plant growth and development and blast resistance.

Characterization of arsenic (As)-responsive genes is fundamental to solving the issue of As contamination in rice. Herein, we establish the involvement of an RAV transcription factor OsAAT1 ( Arsenic Accumulation and Tolerance 1 ) in regulating As response in rice. The expression of OsAAT1 is significantly higher in roots and stems of rice seedlings and is clearly upregulated by higher concentrations of arsenite [As(III)]. Compared with wild-type (WT) plants, OsAAT1 -overexpressed transgenic lines (OE- OsAAT1 ) exhibit tolerance, while OsAAT1 -knockout mutants ( Osaat1 ) are sensitive to As(III) stress. Notably, the application of exogenous 1-naphthylacetic acid (NAA) greatly enhances the As tolerance of WT and transgenic lines, with stronger effects on OE- OsAAT1 . The change in OsAAT1 expression leads to the alteration of As and auxin accumulation in transgenic plants by regulating the expression of OsLsi1 , OsLsi2 , OsCRL4 , and OsAUX1 genes. Moreover, overexpression of OsAAT1 accelerates ROS scavenging and phytochelatins (PCs) synthesis, especially with the addition of exogenous NAA. OsAAT1 localizes in the nucleus and works as a transcriptional suppressor. OsGH3-12, belonging to the auxin-responsive GH3 gene family, is the downstream target gene of OsAAT1, whose expression is extensively downregulated by As(III). These findings provide new insights into As response via auxin signaling pathway in rice.

Background: Nilaparvata lugens is one of the most destructive pests of rice. RNAi-based N. lugens control offers one alternative strategy to traditional chemical insecticides. However, selection of potential target for RNAi against N. lugens remains a major challenge. Only two target genes for nuclear transgenic N. lugens-resistant plants have been screened. Importantly, only one or few potential target genes against N. lugens were screened every time by knowledge of essential genes from model organisms in previous study., Results: Here, in silico genome-wide selection of potential target genes against N. lugens through homology comparison was performed. Through genome synteny comparisons, about 3.5% of Drosophila melanogaster genome was found to have conserved genomic synteny with N. lugens genome. By using N. lugens proteins to search D. melanogaster homologs defining lethal or sterile phenotype, 358 N. lugens genes were first screened as putative target genes. Transgenic rice lines expressing dsRNA of randomly selected gene (NlRan or NlSRP54) from 358 putative target genes enhanced resistance to N. lugens. After expression check and safety check, 115 N. lugens genes were screened as potential target candidates., Conclusion: The combined efforts in this study firstly provide one in silico genome-wide homology-based screening approach for RNAi-based target genes against N. lugens, which not only offer one new opportunity to batch select potential target candidates in pests of interest, but also will facilitate the selection of RNAi target in many pest species by providing more than one hundred potential target candidates., (© 2024. The Author(s).)

Lipid remodeling is crucial for various cellular activities and the stress tolerance of plants; however, little is known about the lipid dynamics induced by the heavy metal cadmium (Cd). In this study, we investigated the phospholipid profiles in rice (Oryza sativa) under Cd exposure. We observed a significant decline in the total amounts of phosphatidylcholine and phosphatidylserine, contrasted with an elevation in phosphatidic acid (PA) due to Cd stress. Additionally, Cd stress prompted the activation of phospholipase D (PLD) and induced the expression of PLDα1. OsPLDα1 knockout mutants (Ospldα1) showed increased sensitivity to Cd, characterized by a heightened accumulation of hydrogen peroxide in roots and diminished PA production following Cd treatment. Conversely, PLDα1-overexpressing (OsPLDα1-OE) lines demonstrated enhanced tolerance to Cd, with suppressed transcription of the respiratory burst oxidase homolog (Rboh) genes. The transcription levels of genes associated with Cd uptake and transport were accordingly modulated in Ospldα1 and OsPLDα1-OE plants relative to the wild-type. Taken together, our findings underscore the pivotal role of OsPLDα1 in conferring tolerance to Cd by modulating reactive oxygen species homeostasis and lipid remodeling in rice., Competing Interests: Declaration of Competing Interest The authors have no competing interests (financial or personal) to declare., (Copyright © 2024. Published by Elsevier B.V.)

This study utilized hyperspectral imaging technology combined with mathematical modeling methods to predict the protein content of rice grains. Firstly, the Kjeldahl method was used to determine the protein content of rice grains, and different preprocessing techniques were applied to the spectral information. Then, a prediction model for rice grain protein content was developed by combining the spectral data with the protein content. After performing multiplicative scatter correction (MSC) preprocessing and selecting feature wavelengths based on successive projections algorithm (SPA), the multivariate linear regression (MLR) model showed the best prediction performance, with a calibration set R 2 C of 0.8998, an RMSEV of 0.1725, and an RPD of 3.16. Finally, the quantitative protein content model was mapped pixel by pixel to visualize the distribution of rice protein, providing possibilities for non-destructive protein content detection.2 V of 0.8998, an RMSEV of 0.1725, and an RPD of 3.16. Finally, the quantitative protein content model was mapped pixel by pixel to visualize the distribution of rice protein, providing possibilities for non-destructive protein content detection., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Rice (Oryza sativa L.) is susceptible to various abiotic stresses, such as salt, cold, and drought. Therefore, there is an urgent need to explore the relevant genes that enhance tolerance to these stresses. In this study, we identified a gene, OsNCED4 (9-cis-epoxycarotenoid dioxygenase 4), which regulates tolerance to multiple abiotic stresses. OsNCED4 encodes a chloroplast-localized abscisic acid (ABA) biosynthetic enzyme. The expression of OsNCED4 gene was significantly induced by 150 mM NaCl and cold stress. Disruption of OsNCED4 by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9-mediated mutagenesis resulted in significant sensitivity to NaCl and cold stress. The salt and cold sensitivity of osnced4 mutant was due to the reduction of ABA content and the excessive accumulation of reactive oxygen species (ROS) under stress. Moreover, OsNCED4 also regulates drought stress tolerance of rice seedlings. Taken together, these results indicate that OsNCED4 is a new regulator for multiple abiotic stress tolerance in rice, and provided a potential target gene for enhancing multiple stress tolerance in the future., (© 2024. The Author(s).)

Rice (Oryza sativa) provides >20% of the consumed calories in the human diet. However, rice is also a leading source of dietary cadmium (Cd) that seriously threatens human health. Deciphering the genetic network that underlies the grain-Cd accumulation will benefit the development of low-Cd rice and mitigate the effects of Cd accumulation in the rice grain. In this study, we identified a QTL gene, OsCS1, which is allelic to OsMTP11 and encodes a protein sequestering Cd in the leaf during vegetative growth and preventing Cd from being translocated to the grain after heading in rice. OsCS1 is predominantly expressed in leaf vascular parenchyma cells, where it binds to a vacuole-sorting receptor protein OsVSR2 and is translocated intracellularly from the trans-Golgi network to pre-vacuolar compartments and then to the vacuole. In this trafficking process, OsCS1 actively transports Cd into the endomembrane system and sequesters it in the vacuoles. There are natural variations in the promoter of OsCS1 between the indica and japonica rice subspecies. Duplication of a G-box-like motif in the promoter region of the superior allele of OsCS1 from indica rice enhances the binding of the transcription factor OsIRO2 to the OsCS1 promoter, thereby promoting OsCS1 expression. Introgression of this allele into commercial rice varieties could significantly lower grain-Cd levels compared to the inferior allele present in japonica rice. Collectively, our findings offer new insights into the genetic control of leaf-to-grain Cd translocation and provide a novel gene and its superior allele for the genetic improvement of low-Cd variety in rice., (Copyright © 2024 The Author. Published by Elsevier Inc. All rights reserved.)

Plant root system is significantly influenced by high soil levels of ammonium nitrogen, leading to reduced root elongation and enhanced lateral root branching. In Arabidopsis, these processes have been reported to be mediated by phytohormones and their downstream signaling pathways, while the controlling mechanisms remain elusive in crops. Through a transcriptome analysis of roots subjected to high/low ammonium treatments, we identified a cytokinin oxidase/dehydrogenase encoding gene, CKX3, whose expression is induced by high ammonium. Knocking out CKX3 and its homologue CKX8 results in shorter seminal roots, fewer lateral roots, and reduced sensitivity to high ammonium. Endogenous cytokinin levels are elevated by high ammonium or in ckx3 mutants. Cytokinin application results in shorter seminal roots and fewer lateral roots in wild-type, mimicking the root responses of ckx3 mutants to high ammonium. Furthermore, CKX3 is transcriptionally activated by type-B RR25 and RR26, and ckx3 mutants have reduced auxin content and signaling in roots under low ammonium. This study identified RR25/26-CKX3-cytokinin as a signal module that mediates root responses to external ammonium by modulating of auxin signaling in the root meristem and lateral root primordium. This highlights the critical role of cytokinin metabolism in regulating rice root development in response to ammonium., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

In recent decades, plants enduring abiotic stresses such as drought and chemical stresses. Currently, the mechanism of combined antibiotic and drought stress response and its impact on crop growth and food security remains poorly understood. Here, the mechanism of stress responses under the exposure of norfloxacin (NF) and drought (D) individually and in combination (DNF) were explored on rice (Oryza sativa) cultivar Hanyou73 through proteomics and metabolomic analysis. All treatments adversely affected chlorophyll fluorescence kinetics, antioxidant enzyme activities, rice grain composition and yield. The results showed that in DNF the antibiotic was accumulated 627% more than NF treatment in rice grains while in leaves there was no significant difference under both treatments. The proteomic revealed that differentially expressed identified proteins were involved in carbohydrate metabolism, amino acid metabolism, photosynthesis and mRNA binding. However, the metabolomics results showed that the abundance of metabolites related to RNA biosynthesis and amino acid metabolism were more affected. The disruptions caused in rice plant under DNF treatment become more severe, this makes it more susceptible than individual D and NF treatment. These findings improve our knowledge about the response of rice plant to cope with antibiotic contamination alone and in combination with drought., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

CDKs are the master regulator of cell division and their activity is controlled by the regulatory subunit cyclins and phosphorylation by the CAKs. However, the role of MAP kinases in regulating plant cell cycle or CDKs have not been explored. Here, we report that the MAP kinases OsMPK3, OsMPK4, and OsMPK6 physically interact and phosphorylate OsCDKD and its regulatory subunit OsCYCH in rice. MAP kinases phosphorylate CDKD at Ser-168 and Thr-235 residues in OsCDKD. The MAP kinase-mediated phosphorylation of OsCDKD is required for its activation to control the small RNA biogenesis. The phosphodead version of OsCDKD fails to activate the C-terminal domain of RNA Polymerase II, thereby negatively impacting small RNA transcription. Further, the overexpression lines of wild-type (WT) OsCDKD and phosphomimic OsCDKD show increased root growth, plant height, tiller number, panicle number, and seed number in comparison to WT, phosphodead OsCDKD-OE, and kinase-dead OsCDKD-OE plants. In a nutshell, our study establishes a novel regulation of OsCDKD by MAPK-mediated phosphorylation in rice. The phosphorylation of OsCDKD by MAPKs imparts a positive effect on rice growth and development by regulating miRNAs transcription., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Rice plays an important role in the daily diet in China and therefore its quality and safety have been of great concern. However, few systematic studies have investigated Fusarium community and toxins in rice grains. Here, we collected 1381 rice samples from Jiangsu Province in eastern China and found a higher frequency of zearalenone (ZEN), deoxynivalenol (DON), fumonisins (FBs), and beauvericin (BEA). The positive samples were individually contaminated with a minimum of one and a maximum of ten toxins. Fusarium was isolated and identified as the major fungus, which exhibited temporal and geographical distribution. The most prevalent species complexes within this genus were Fusarium incarnatum-equiseti species complex (FIESC), Fusarium fujikuroi species complex (FFSC), and Fusarium sambucinum species complex (FSAMSC). Nevertheless, the amplicon sequence analysis revealed a low relative abundance of Fusarium in the rice panicles, and the fungal community exhibited an irregular change along with the symptom's emergence. In vitro toxigenic profiles of Fusarium strains showed significant complexity and specificity depending on the type and content. FIESC strains were non-pathogenic to wheat heads and weakly pathogenic to maize ears, respectively, accumulating lower amounts of toxins than F. asiaticum and F. fujikuroi. There was no significant variation in the ability to cause panicle blight in rice among the various species tested. Our study provides detailed information about the contamination of Fusarium toxins and community in rice after harvest. This information is valuable for understanding the relationship between Fusarium and rice and for developing effective control strategies., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Jianhong Xu reports financial support was provided by Jiangsu Agriculture Science and Technology. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Salt stress affects the growth of rice, which reduces grain yield. However, the mechanism of the rice response to salt stress is not fully understood. The rice salt tolerance 31 (rst31) mutant exhibits longer shoots and greater dry weight than wild type (WT) plants under salt stress conditions. Through map-based cloning and genetic complementation methods, we determined that RST31 encodes a half-size ABCG transporter protein, ABCG18. We showed that mutation of RST31 reduces DNA damage under salt stress, with less accumulation of reactive oxygen species (ROS). The deficiency of RST31 suppressed the root-to-shoot transport of cytokinin, which resulted in a decrease in cytokinin content in the shoot and an increase in cytokinin content in the root. ROS accumulated abundantly in WT and rst31 mutant plants after exogenous treatment with trans-zeatin, reducing rst31 tolerance of salt stress. Collectively, our results suggest that high cytokinin level in shoots leads to an increase in ROS content and severe DNA damage under salt stress, which lead to sensitivity to salt stress. These findings enhance our understanding of plant responses to salt stress through cytokinin pathways., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Subclass III sucrose nonfermenting1-related protein kinase 2s (SnRK2s) are positive regulators of abscisic acid (ABA) signaling and abiotic stress responses. However, the underlying activation mechanisms of osmotic stress/ABA-activated protein kinase 8/9/10 (SAPK8/9/10) of rice (Oryza sativa) subclass III SnRK2s in ABA signaling remain to be elucidated. In this study, we employed biochemical, molecular biology, cell biology, and genetic approaches to identify the molecular mechanism by which OsPP47, a type one protein phosphatase in rice, regulates SAPK8/9/10 activity in ABA signaling. We found that OsPP47 not only physically interacted with SAPK8/9/10 but also interacted with ABA receptors PYLs. OsPP47 negatively regulated ABA sensitivity in seed germination and root growth. In the absence of ABA, OsPP47 directly inactivated SAPK8/9/10 by dephosphorylation. In the presence of ABA, ABA-bound OsPYL2 formed complexes with OsPP47 and inhibited its phosphatase activity, partially releasing the inhibition of SAPK8/9/10. SAPK8/9/10-mediated H 2 O 2 production inhibited OsPP47 activity by oxidizing Cys-116 and Cys-256 to form OsPP47 oligomers, resulting in not only preventing the OsPP47-SAPK8/9/10 interaction but also blocking the inhibition of SAPK8/9/10 activity by OsPP47. Our results reveal novel pathways for the inhibition of SAPK8/9/10 in the basal state and for the activation of SAPK8/9/10 induced by ABA in rice., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Rice is one of the major food crops, and the study of suitable planting areas for rice plays an important role in improving rice yield and optimizing the production layout. This study used Maximum Entropy (MaxEnt) model to simulate and predict the distribution of suitable rice planting areas in China from 1981 to 2020 by combining the climate, soil, and human activities, analyzed the spatial and temporal changes of suitable rice planting areas in China, and determined the main factors affecting rice planting suitability. The results indicated that the main factors influencing the distribution of suitable planting areas for rice in China were gross domestic product (GDP), population density (Pop), and annual sunshine duration (Sun), with human activities playing a dominant role. The high suitable planting areas of rice were mainly distributed in Hubei, Hunan, Jiangxi, Anhui, Guangdong, southeastern Sichuan and western Guizhou. The total suitable planting areas for rice were 346.00 × 10 4 km 2 , 345.66 × 10 4 km 2 , 347.01 × 10 4 km 2 , and 355.57 × 10 4 km 2 from 1981 to 1990, 1991 to 2000, 2001 to 2010 and 2011 to 2020, respectively. With the passage of time, the area of unsuitable areas for rice gradually decreased, and the area of medium suitable areas increased, with large changes in the area of high- and low-suitable areas. Moreover, due to the transfer of a large number of rural laborers to the cities in recent years, the tension between people and land caused by the population explosion has led to the increasing impact of Pop on rice suitable areas and the relatively weakening of the impact of GDP on rice production interventions. The results can be used to provide scientific evidence for the management of rice cultivation and food production safety, with a view to reducing the impacts of climate change on agricultural production in the context of global climate change., (© 2024. The Author(s) under exclusive licence to International Society of Biometeorology.)

Dual base editors (DBEs) enable simultaneous A-to-G and C-to-T conversions, expanding mutation types. However, low editing efficiency and narrow targeting range limit the widespread use of DBEs in plants. The single-strand DNA binding domain of RAD51 DBD can be fused to base editors to improve their editing efficiency. However, it remains unclear how the DBD affects dual base editing performance in plants. In this study, we generated a series of novel plant DBE-SpGn tools consisting of nine constructs using the high-activity cytidine deaminase evoFERNY, adenosine deaminase TadA8e and DBD in various fusion modes with the PAM-flexible Streptococcus pyogenes Cas9 (SpCas9) nickase variant SpGn (with NG-PAM). By analysing their editing performance on 48 targets in rice, we found that DBE-SpGn constructs containing a single DBD and deaminases located at the N-terminus of SpGn exhibited the highest editing efficiencies. Meanwhile, constructs with deaminases located at the C-terminus and/or multiple DBDs failed to function normally and exhibited inhibited editing activity. We identified three particularly high-efficiency dual base editors (C-A-SpGn, C-A-D-SpGn and A-C-D-SpGn), named PhieDBEs (Plant high-efficiency dual base editors), capable of producing efficient dual base conversions within a narrow editing window (M 5  ~ M 9 , M = A/C). The editing efficiency of C-A-D-SpGn was as high as 95.2% at certain target sites, with frequencies of simultaneous C-to-T and A-to-G conversions as high as 81.0%. In summary, PhieDBEs (especially C-A-D-SpGn) can produce diverse mutants and may prove useful in a wide variety of applications, including plant functional genomics, precise mutagenesis, directed evolution and crop genetic improvement, among others., (© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7 A (allele in cultivar Jin23B) compared with WBR7 G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130) KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B) COM , resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality., (© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Background: Rice is considered a high estimated glycemic index (eGI) food because of its higher starch digestibility, which leads to type II diabetes and obesity as a result of a sedentary life style. Furthermore, the incresaing diabetes cases in rice-consuming populations worldwide need alternative methods to reduce the glycemic impact of rice, with dietary prescriptions based on the eGI value of food being an attractive and practical concept. Rice is often paired with vegetables, pulses, tubers and roots, a staple food group in Africa, Latin America and Asia, which are rich in fibre and health-promoting compounds., Results: Rice from four categories (high protein, scented, general and pigmented) was analyzed for eGI and resistant starch (RS) content. Among the genotypes, Improved Lalat had the lowest eGI (53.12) with a relatively higher RS content (2.17%), whereas Hue showed the lowest RS (0.19%) with the highest eGI (76.3) value. The addition of tuber crops to rice caused a significant lowering of eGI where the maximum beneficial effect was shown by elephant foot yam (49.37) followed by yam bean (53.07) and taro (54.43)., Conclusion: The present study suggests that combining rice with suitable tuber crops can significantly reduce its eGI value, potentially reducing the burden of diet-associated lifestyle diseases particularly diabetics. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

Background: Nitrogen is a key factor affecting the quality of rice. Studying the impact of nitrogen fertilizer on the taste, physicochemical properties, and starch structure of Indica rice with different amylose contents is of great significance for scientifically fertilizing and cultivating high-quality rice varieties for consumption., Results: The results indicate that increasing nitrogen fertilizer application reduces the amylose content and increases the protein content, resulting in a decrease in taste quality. Simultaneously, it reduces the intergranular porosity of starch particles, improving the appearance and milling quality of rice. Compared to the N1 treatment (nitrogen fertilizer application rate of 90 kg ha -1 ), the taste of low-amylose rice (Yixiangyou 2115) and high-amylose rice (Byou 268) decreased by 14.24% and 19.79%, respectively, under N4 treatment (nitrogen fertilizer application rate of 270 kg ha -1 ). The effect of nitrogen fertilizer on low-amylose rice is mainly reflected in increased rice hardness, enthalpy value, and setback viscosity, resulting in a decline in taste. The effect of nitrogen fertilizer on high-amylose rice is mainly reflected in a decrease in peak viscosity, an increase in gelatinization temperature, and crystallinity under high nitrogen levels., Conclusion: Increasing nitrogen fertilizer application can improve the appearance and milling quality of rice, but it also leads to an increase in protein content, hardness, gelatinization enthalpy, decrease in breakdown value, and a decline in palatability. In practical production, different production measures should be taken according to different production goals. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

The storability of rice seeds is crucial for ensuring flexible planting options, agricultural seed security, and global food safety. With the intensification of global climate change and the constant fluctuations in agricultural production conditions, enhancing the storability of rice seeds has become particularly important. Seed storability is a complex quantitative trait regulated by both genetic and environmental factors. This article reviews the main regulatory mechanisms of rice seed storability, including the accumulation of seed storage proteins, late embryogenesis abundant (LEA) proteins, heat shock proteins, sugar signaling, hormonal regulation by gibberellins and abscisic acid, and the role of the ubiquitination pathway. Additionally, this article explores the improvement of storability using wild rice genes, molecular marker-assisted selection, and gene editing techniques such as CRISPR/Cas9 in rice breeding. By providing a comprehensive scientific foundation and practical guidance, this review aims to promote the development of rice varieties with enhanced storability to meet evolving agricultural demands., Competing Interests: Declaration of Competing Interest The authors declare that there are no conflicts of interest regarding the publication of this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Copper (Cu) is an indispensable micronutrient for plants, animals, and microorganisms and plays a vital role in different physiological processes. However, excessive Cu accumulation in agricultural soil, often through anthropogenic action, poses a potential risk to plant health and crop productivity. This review article provided a comprehensive overview of the available information regarding Cu dynamics in agricultural soils, major sources of Cu contamination, factors influencing its mobility and bioavailability, and mechanisms of Cu uptake and translocation in rice plants. This review examined the impact of Cu toxicity on the germination, growth, and photosynthesis of rice plants. It also highlighted molecular mechanisms underlying Cu stress signaling and the plant defense strategy, involving chelation, compartmentalization, and antioxidant responses. This review also identified significant areas that need further research, such as Cu uptake mechanism in rice, Cu signaling process, and the assessment of Cu-polluted paddy soil and rice toxicity under diverse environmental conditions. The development of rice varieties with reduced Cu accumulation through comprehensive breeding programs is also necessary. Regulatory measures, fungicide management, plant selection, soil and environmental investigation are recommended to prevent Cu buildup in agricultural lands to achieve sustainable agricultural goals., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier GmbH. All rights reserved.)

For several decades, a plant-based expression system has been proposed as an alternative platform for the production of biopharmaceuticals including therapeutic monoclonal antibodies (mAbs), but the immunogenicity concerns associated with plant-specific N-glycans attached in plant-based biopharmaceuticals has not been completely solved. To eliminate all plant-specific N-glycan structure, eight genes involved in plant-specific N-glycosylation were mutated in rice (Oryza sativa) using the CRISPR/Cas9 system. The glycoengineered cell lines, PhytoRice®, contained a predominant GnGn (G0) glycoform. The gene for codon-optimized trastuzumab (TMab) was then introduced into PhytoRice® through Agrobacterium co-cultivation. Selected cell lines were suspension cultured, and TMab secreted from cells was purified from the cultured media. The amino acid sequence of the TMab produced by PhytoRice® (P-TMab) was identical to that of TMab. The inhibitory effect of P-TMab on the proliferation of the BT-474 cancer cell line was significantly enhanced at concentrations above 1 μg/mL (****P < 0.0001). P-TMab bound to a FcγRIIIa variant, FcγRIIIa-F158, more than 2.7 times more effectively than TMab. The ADCC efficacy of P-TMab against Jurkat cells was 2.6 times higher than that of TMab in an in vitro ADCC assay. Furthermore, P-TMab demonstrated efficient tumour uptake with less liver uptake compared to TMab in a xenograft assay using the BT-474 mouse model. These results suggest that the glycoengineered PhytoRice® could be an alternative platform for mAb production compared to current CHO cells, and P-TMab has a novel and enhanced efficacy compared to TMab., (© 2024 The Author(s). Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.)

Rice provides poor yields in acidic soils due to several nutrient deficiencies and metal toxicities. The low availability of phosphorus (P) in acidic soils offers a natural condition for screening genotypes for grain yield and phosphorus utilization efficiency (PUE). The objective of this study was to phenotype a subset of indica rice accessions from 3000 Rice Genome Project (3K-RGP) under acidic soils and find associated genes and alleles. A panel of 234 genotypes, along with checks, were grown under low-input acidic soils for two consecutive seasons, followed by a low-P-based hydroponic screening experiment. The heritability of the agro-morphological traits was high across seasons, and Ward's clustering method identified 46 genotypes that can be used as low-P-tolerant donors in acidic soil conditions. Genotypes ARC10145, RPA5929, and K1559-4, with a higher grain yield than checks, were identified. Over 29 million SNPs were retrieved from the Rice SNP-Seek database, and after quality control, they were utilized for a genome-wide association study (GWAS) with seventeen traits. Ten quantitative trait nucleotides (QTNs) for three yield traits and five QTNs for PUE were identified. A set of 34 candidate genes for yield-related traits was also identified. An association study using this indica panel for an already reported 1.84 Mbp region on chromosome 2 identified genes Os02g09840 and Os02g08420 for yield and PUE, respectively. A haplotype analysis for the candidate genes identified favorable allelic combinations. Donors carrying the superior haplotypic combinations for the identified genes could be exploited in future breeding programs.

Plant cell walls are complex, multifunctional structures, built up of polysaccharides and proteins. The configuration and abundance of cell wall constituents determine cellular elongation and plant growth. The emphasis of this review is on rice, a staple crop with economic importance, serving as model for grasses/cereals. Recent advancements have contributed to a better understanding of the grass/cereal cell wall. This review brings together current knowledge of the organization and metabolism of the rice cell wall, and addresses gaps in the information regarding the cell wall and enzymes involved. Several cell wall fractions, including cellulose, mixed-linkage glucans, and glucuronoarabinoxylans, are well understood in rice and other grasses/grains. Conversely, there are still open questions and missing links in relation to xyloglucans, glucomannans, pectin, lignin, and arabinogalactan proteins. There is still a large and untapped potential to identify carbohydrate-active enzymes (CAZymes), to characterize their activity, and to elucidate their involvement in the metabolism of the mentioned cell wall fractions. This review highlights the involvement of carbohydrate-active enzymes in rice cell wall metabolism, providing an update of current understanding with the aim of demarcating research areas with potential for further investigations., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Rice blast, caused by the fungus Magnaporthe oryzae (syn. Pyricularia oryzae), is a major problem in rice cultivation and ranks among the most severe fungal diseases. Cloning and identifying resistance genes in rice, coupled with a comprehensive examination of the interaction between M. oryzae and rice, may provide insights into the mechanisms of rice disease resistance and facilitate the creation of new rice varieties with improved germplasm. These efforts are essential for protecting food security. This review examines the discovery of genes that confer resistance or susceptiblity to M. oryzae in rice over the last decade. It also discusses how knowledge of molecular mechanisms has been used in rice breeding and outlines key strategies for creating rice varieties resistant to this disease. The strategies discussed include gene pyramiding, molecular design breeding, editing susceptibility genes, and increasing expression of resistance genes through pathogen challenge. We address the prospects and challenges in breeding for rice blast resistance, emphasizing the need to fully exploit germplasm resources, employ cutting-edge methods to identify new resistance genes, and develop innovative breeding cultivars. Additionally, we underscore the importance of understanding the molecular basis of rice blast resistance and developing novel cultivars with broad-spectrum disease resistance., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

The Rho GDP dissociation inhibitor gene OsRhoGDI1 was isolated as the putative partner of OsRac5 from rice young panicles by the yeast two-hybrid screening, but the characterization and functions of the gene remains unknown. In this study, on the basis of the bioinformatics analysis, expression profile chip mining and RT-qPCR were employed to analyze the expression pattern of OsRhoGDI1 , and it was found that the gene was widely expressed in various tissues of rice, especially with high abundance during the development of young panicles, and its expression was regulated by abscisic acid (ABA), brassinolide (BL), salicylic acid (SA), indole-3-acetic acid (IAA), gibberellin (GA) and high salinity. Subcellular localization identification showed that OsRhoGDI1 was distributed in the cytomembrane, cytoplasm, and nucleus. Bimolecular fluorescence completion (BiFC) was further performed to identify the in vivo interaction between OsRhoGDI1 and OsRac5, the results suggested that the interaction occurred in the nucleus, cytomembrane, and cytoplasm. In addition, OsRhoGDI1 interacted with OsRac1 in the cytomembrane. Our results indicated that OsRhoGDI1 may be involved in rice panicle development, and participate in regulating various biological processes such as rice growth and development, hormone response, and abiotic stress by regulating the activities of different Rho/Rop proteins via interactions.

Vitamin B6 (VB6), as an essential component involved in numerous biological activities of animals and plants, reflects the nutritional quality of cereal crops such as rice. Few studies have been conducted to mine the genes controlling the VB6 content in rice grains, and the available studies remain to be deepened. In this study, the recombinant inbred lines created from parents 'HZ' and 'Nekken2' served as the experimental materials. Based on QTL mapping, the initial screening identified ten candidate genes. The expression levels of LOC &#95; Os01g52450 , LOC &#95; Os01g52500 , LOC &#95; Os05g09500 , LOC &#95; Os05g09440 , LOC &#95; Os05g20570 , and LOC &#95; Os05g36270 showed significant differences between the parents. According to the gene expression and parental VB6 content, we hypothesized LOC &#95; Os05g09500 as the key gene affecting the VB6 content in rice grains, and the high expression of this gene significantly influenced the VB6 content. The results of this study fill a gap in the QTL mapping on the VB6 content of rice grains and provide theoretical support for elucidating the molecular genetic mechanisms and cloning the related genes of VB6 synthesis in rice. In addition, the findings have significant implications for identifying, screening, and breeding new rice cultivars with high VB6 content.

Improving the nitrogen use efficiency is an effective way to increase the yield of rice, and maintaining carbon-nitrogen balance is essential for the normal growth and development of rice. To investigate the impact of the sucrose transporter protein OsSTP1 on nitrogen absorption in rice, in this study, we constructed transgenic lines overexpressing the sucrose transporter gene OsSTP1 ( OsSTP1-OE1 , OsSTP1-OE2 ) and mutant transgenic lines ( osstp1-1 , osstp1-2 ) from the wild type TB309. Further, we conducted a hydroponic experiment with four nitrogen supply levels of free nitrogen (FN, 0 mg/L), low nitrogen (LN, 10 mg/L), normal nitrogen (NN, 40 mg/L), and high nitrogen (HN, 80 mg/L) to study the responses of each line to different nitrogen supply levels during the seedling stage. The results showed that compared with the wild type and mutant lines in the LN group, the OsSTP1 -overexpressing lines exhibited significantly increased biomass, root length, and plant height, decreased soluble sugar content in the leaves, and increased soluble sugar content in the roots. The results indicate that the soluble sugars produced by leaf photosynthesis are transported to the roots through the phloem to promote root growth and nitrogen uptake, thus increasing the aboveground biomass. This study has identified that OsSTP1 can affect the long-distance transport of carbohydrates from source to sink to promote root growth, ultimately influencing rice's absorption and accumulation of nitrogen, improving nitrogen use efficiency and providing reference for reducing nitrogen fertilizer application.

Melatonin is a bioactive molecule with an important role in plants responding to various abiotic and biotic stresses. This study aims to determine the role of melatonin in rice under salt stress. This study used a factorial completely randomized design. The first factor was local rice varieties (IR64 and Silaun), and the second factor was plant treatments (control, 1 µM melatonin, 150 mM NaCl, 150 mM NaCl + 1µM melatonin). This study shows that exogenous melatonin can increase plant growth, such as plant height, root length, stem length, leaf length, leaf area, and plant biomass under salt stress compared to treatment without melatonin. Exogenous melatonin can increase the total chlorophyll content, relative water content, and proline content, reduce the total sodium content, and increase potassium absorption under conditions of salinity stress. Melatonin is also able to scavenge ROS in plants, resulted the decrease in ROS and MDA content. In terms of gene expression, OsAPX1 and cytosolic APX exhibited the highest expression in IR64 under combined salt and melatonin treatment, while GPOD, Mn-SOD, and Cu/Zn-SOD were upregulated under various conditions in both varieties. Additionally, OsLEA showed high expression in both varieties under control conditions, and CAT was significantly upregulated under salt stress. Our findings indicate that exogenous melatonin has the potential to enhance various factors under salt stress and helping in the recovery of rice plants from sodium (Na+) damage., (© 2024. The Author(s).)

Plant biomass can significantly contribute to alternative energy sources. Sorghum bicolor is a promising plant for producing energy, but is susceptible to iron deficiency, which inhibits its cultivation in iron-limiting calcareous soils. The molecular basis for the susceptibility of sorghum to iron deficiency remains unclear. Here, we explored the sorghum genome to identify genes involved in iron uptake and translocation. Iron deficiency-responsive gene expression was comparable to that in other graminaceous plants. A nicotianamine synthase gene, SbNAS1, was induced in response to iron deficiency, and SbNAS1 showed enzyme activity. Sorghum secreted 2'-deoxymugineic acid and other phytosiderophores under iron deficiency, but their levels were relatively low. Intercropping of sorghum with barley or rice rescued iron deficiency symptoms of sorghum. To produce bioengineered sorghum with enhanced tolerance to iron deficiency, we introduced four cassettes into sorghum: 35S promoter-OsIRO2 for activation of iron acquisition-related gene expression, SbIRT1 promoter-Refre1/372 for enhanced ferric-chelate reductase activity, and barley IDS3, and HvNAS1 genomic fragments for enhanced production of phytosiderophores and nicotianamine. The resultant single sorghum line exhibited enhanced secretion of phytosiderophores, increased ferric-chelate reductase activity, and improved iron uptake and leaf greenness compared with non-transformants under iron-limiting conditions. Similar traits were also conferred to rice by introducing the four cassettes. Moreover, these rice lines showed similar or better tolerance in calcareous soils and increased grain iron accumulation compared with previous rice lines carrying two or three comparable cassettes. These results provide a molecular basis for the bioengineering of sorghum tolerant of low iron availability in calcareous soils., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Rice (Oryza sativa L.) is highly sensitive to low temperatures, which can significantly reduce its production. Cold tolerance in rice is a complex trait regulated by multiple mechanisms. OsTZF5, a member of the CCCH-type zinc finger gene family in rice, has been previously reported that overexpressing OsTZF5 under the stress-responsive promoter can confer drought resistance. In this study, we showed that the loss of function mutants of OsTZF5 decreased seed germination rate and chilling tolerance in rice, and influencing normal growth and development. OsTZF5 is expressed in various parts of the rice plant, including roots, stems, leaves and inflorescences, with the highest expression levels observed in leaves. Additionally, the expression of OsTZF5 gene was influenced by various stress conditions and hormone treatments. OsTZF5 knock-out mutants exhibited significantly lower survival rates compared to the wild type (Zhonghua11, ZH11) after cold stress, as well as fewer tillers, lower thousand-grain weight, and reduced grain yield under normal conditions. Transcriptomic analyses revealed that the expression of cold stress-related genes was significantly down-regulated in OsTZF5 knock-out mutants compared to ZH11 after cold stress. This down-regulation likely contributes to the reduced cold stress tolerance observed in OsTZF5 knock-out mutants. Our findings suggest that OsTZF5 is a multifunctional gene that plays a crucial role in regulating cold stress in rice., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Diterpenoid Phytoalexin Factor (DPF) is a key transcription factor involved in diterpenoid phytoalexin (DP) biosynthesis under non-stressed conditions in rice (Oryza sativa L.). Using clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9, DPF knockout rice lines were generated. Treatments with abiotic stresses (copper chloride, ultraviolet light, and jasmonic acid) and biotic stress (blast fungus infection) to the knockout lines revealed that the DPF positively regulates stress-induced DP biosynthesis., (© The Author(s) 2024. Published by Oxford University Press on behalf of Japan Society for Bioscience, Biotechnology, and Agrochemistry.)

The ubiquitin-proteasome system (UPS) plays crucial roles in cellular processes including plant growth, development, and stress responses. In this study, we report that a pair of E3 ubiquitin ligases, AvrPiz-t-interaction protein 6 (APIP6) and IPA1-interaction protein 1 (IPI1), intricately target early flowering3 (ELF3) paralogous proteins to control rice immunity and flowering. APIP6 forms homo-oligomers or hetero-oligomers with IPI1. Both proteins interact with OsELF3-2, promoting its degradation to positively control resistance against the rice blast fungus (Magnaporthe oryzae). Intriguingly, overexpression of IPI1 in Nipponbare caused significantly late-flowering phenotypes similar to the oself3-1 mutant. Except for late flowering, oself3-1 enhances resistance against M. oryzae. IPI1 also interacts with and promotes the degradation of OsELF3-1, a paralog of OsELF3-2. Notably, IPI1 and APIP6 synergistically modulate OsELF3s degradation, finely tuning blast disease resistance by targeting OsELF3-2, while IPI1 controls both disease resistance and flowering by targeting OsELF3-1. This study unravels multiple functions for a pair of E3 ligases in rice., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Immunity and flowering are energy-consuming processes. However, the mechanism underlying the balance between immunity and flowering remains to be elucidated. Here, we report that the E3 ligase ideal plant architecture 1 interactor 1 (IPI1) controls rice immunity and flowering via two different pathways, one dependent on and another independent of its E3 ligase activity. We found that IPI1, a RING-finger E3 ligase, interacts with another E3 ligase, AvrPiz-t-interacting protein 6 (APIP6), and protects APIP6 from degradation by preventing APIP6's self-ubiquitination. Stabilization of APIP6 by IPI1 requires no IPI1 E3 ligase activity and leads to degradation of APIP6 substrates via the ubiquitin-proteasome system (UPS). Meanwhile, IPI1 directly ubiquitinates OsELF3-1 and OsELF3-2, two homologs of EARLY FLOWERING3 (ELF3), targeting them for degradation via the 26S proteasome. IPI1 knockout plants display early flowering but compromised resistance to rice blast. Thus, IPI1 balances rice immunity and flowering via both E3 ligase-dependent and -independent pathways., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Background: Increasing concern has recently been highlighted regarding crop damage due to extreme weather events caused by global warming and the increased production of ground-level ozone. Several studies have investigated rice growth in response to fertilization conditions under various environmental stress conditions; however, studies on growth development in response to fertilization conditions under combined high-temperature/ozone treatment conditions are scarce. In this study, we aimed investigate the growth and physiological development of rice under combined high temperature and ozone treatment conditions and to reveal the damage-mitigation effects of NPK fertilization treatments., Results: The plants were treated with varying levels of NPK [N2 (N-P-K: 9.0-4.5-4.0 kg/a), P2 (4.5-9.0-4.0 kg/a), K2 (4.5-4.5-8.0 kg/a), and control (4.5-4.5-4.0 kg/10a).] under combined high-temperature (35 ℃) and ozone (150 pb) treatment conditions. Analysis of the growth metrics, including plant height, leaf age, dry weight, and the plant height/leaf age (PH/L) ratio were revealed that combined high-temperature/ozone treatment promoted the phenological development indicated by increasing leaf age but decreased the plant height and dry weight indicating its negative effect on quantitative growth. The effects of this combined high-temperature/ozone treatment on growth were alleviated by NPK fertilization, particularly in K2 treatment but worsened in N2 treatment. Visible damage symptoms in rice leaves induced by exposure to the combined stressors was also alleviated by the K2 treatment. At the physiological level, K2 treatment reduced the expression of OsF3H2, which is associated with antioxidant activity, suggesting that potassium improved stress tolerance. Additionally, expression of genes related to abscisic acid (ABA) metabolism showed increased OsNECD (ABA synthesis) and decreased OsCYP707A3 (ABA degradation) in the K2 treatment, promoting a stronger adaptive stress response. Stomatal conductance measurements indicated a slight increase under K2 treatment, reflecting enhanced regulation of stomatal function during stress., Conclusion: The study highlights the potential of potassium fertilization to mitigate combined high-temperature and ozone stress in rice, suggesting it as a strategy to improve crop resilience and optimize fertilization. The findings offer insights into fertilization treatments and can guide future research on stress tolerance in crops., (© 2024. The Author(s).)