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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.)

Drought is the primary factor limiting rice production in ecosystems. Wild rice rhizosphere bacteria possess the potential to assist in the stress resistance of cultivated rice. This study examines the impact of wild rice rhizosphere bacteria on cultivated rice under drought conditions. From the rhizosphere soil of wild rice, 20 potential drought-resistant strains were isolated. Subsequent to the screening, the most effective strain b3, was identified as Enterobacter ludwigii. Pot experiments were conducted on the cultivated Changbai 9 rice. It was found that inoculation with the E. ludwigii b3 strain improved the drought resistance of the rice, promotion of rice growth (shoot height increased by 13.47 %), increased chlorophyll content (chlorophyll a, chlorophyll b and carotenoid increased by 168.74 %, 130.68 % and 87.89 %), improved antioxidant system (content of glutathione was increased by 60.35 %), and accumulation of osmotic regulation substances (soluble sugar and soluble protein increased by 70.36 % and 142.03 %). Furthermore, E. ludwigii b3 had a transformative effect on the rhizosphere bacterial community of cultivated rice, increasing its abundance and diversity while simultaneously recruiting beneficial rhizosphere bacteria, resulting in a more complex community. Additionally, E. ludwigii b3 acted directly and indirectly on cultivated rice through its metabolites (organic acids, amino acids, flavonoids and other substances), which helped alleviate drought stress. In conclusion, the E. ludwigii b3 shows promise as a drought-resistant strain and has the potential to improve the growth and productivity of cultivated rice in arid agricultural ecosystems. This study represents the first investigation of E. ludwigii in the rhizosphere of wild rice under drought conditions on cultivated 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. Published by Elsevier Inc.)

The use of reclaimed water from wastewater treatment plants for irrigation has a risk of introducing micropollutants such as microplastics (MPs) and antimicrobials (AMs) into the agroecosystem. This study was conducted to investigate the effects of single and combined treatment of 0.1 % polyamide (PA ∼15 μm), and varying sulfamethoxazole (SMX) levels 0, 10, 50, and 150 mg/L on rice seedlings (Oryza sativa L.) for 12 days. The study aimed to assess the impact of these contaminants on the morphological, physiological, and biochemical parameters of the rice plants. The findings revealed that rice seedlings were not sensitive to PA alone. However, SMX alone or in combination with PA, significantly inhibited shoot and root growth, total biomass, and affected photosynthetic pigments. Higher concentrations of SMX increased antioxidant enzyme activity, indicating oxidative stress. The roots had a higher SMX content than the shoots, and the concentration of minerals such as iron, copper, and magnesium were reduced in roots treated with SMX. RNA-seq analysis showed changes in the expression of genes related to stress, metabolism, and transport in response to the micropollutants. Overall, this study provides valuable insights on the combined impacts of MPs and AMs on food crops, the environment, and human health in future risk assessments and management strategies in using reclaimed water., Competing Interests: Declaration of competing interest All the authors declare that there is no conflict of interest., (Copyright © 2024. Published by Elsevier B.V.)

Background: Early seed germination in crops can confer a competitive advantage against weeds and reduce the time to maturation and harvest. WRKY transcription factors regulate many aspects of plant development including seed dormancy and germination. Both positive and negative regulators of seed germination have been reported in many plants such as rice and Arabidopsis. Using a transient expression system, we previously demonstrated that OsWRKY71 is a negative regulator of gibberellin (GA) signaling in aleurone cells and likely forms a "repressosome" complex with other transcriptional repressors. Hence, it has the potential to impact seed germination properties., Results: In this study, we demonstrate that OsWRKY71, a Group IIa WRKY gene, appeared at the same time as seed-bearing plants. Rice mutants lacking OsWRKY71 have seeds and embryos that germinate earlier than wildtype controls. In oswrky71 aleurone layers, α-amylase activity was hypersensitive to stimulation by GA 3 and hyposensitive to inhibition by abscisic acid (ABA). Early germination in oswrky71 intact seeds was also hyposensitive to ABA. Transcriptomic profiling during embryo germination and early post-germination growth demonstrates that OsWRKY71 influences the expression of 9-17% of genes in dry and imbibing embryos. Compared to wildtype embryos, the mutant transcriptomes have large temporal shifts at 4, 8 and 12 h after imbibition (HAI). Importantly, many genes involved in the ABA-dependent inhibition of seed germination were downregulated in oswrky71-1. This mutant also displayed altered expression of multiple ABA receptors (OsPYLs/RCARs) that control ABA signaling and the VP1-SDR4-DOG1L branch of ABA signaling that promotes seed dormancy. Association studies reveal an OsWRKY71-containing quantitative trait locus involved in low-temperature seed germinability, qLTG-2. Indeed, oswrky71 seeds germinated early at 15 °C., Conclusions: Rice Group-IIa WRKY transcription factor OsWRKY71 is a master regulator of germination that influences the expression of 9-17% of genes in dry and imbibing embryos. It is also most likely the primary candidate of low-temperature seed germinability QTL, qLTG-2. We propose that knockouts of OsWRKY71 can generate rice varieties with improved germination properties under normal or low-temperature conditions., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Hexavalent chromium is a toxic environmental pollutant that damages plants due to disruption of nutrient uptake, photosynthesis metabolism, and oxidative stress, which suppresses the growth and development of the plant. In this work, we have developed a betaine-modified carbon dot (BT@CD) sensor for monitoring Cr(VI) in water and plants. Fluorescent carbon dots have been synthesized using jamun juice ( Syzygium cumini ) as the carbon source subjected to surface modification with betaine (BT@JCD). This BT@JCD exhibits strong blue fluorescence, which significantly decreases in the presence of Cr(VI) due to the inner filter effect in a range of 5-450 nM with a detection limit of 0.033 μM. Due to its easy translocation in the vascular bundles, these fluorescence nanosensors can be applied to detect Cr(VI) in rice plants Oryza sativa ) through fluorescence confocal imaging. The treatment of rice plants with BT@JCDs in the concentration range of 0.2 to 1g/mL not only triggered photophysical parameters such as carbohydrates, chlorophyll, and carotenoids but also enhanced the antioxidant enzyme activity promoting plant growth.

Cadmium (Cd) is a potentially harmful metal with significant biological toxicity that adversely affects plant growth and physiological metabolism. Excessive Cd exposure in plants leads to stunted plant growth owing to its negative impact on physiological functions such as photosynthesis, nutrient uptake, and water balance. Potassium-enriched biochar (KBC) and Bacillus altitudinis rhizobacteria (RB) can effectively overcome this problem. Potassium-enriched biochar (KBC) significantly enhances plant growth by improving the soil structure, encouraging water retention, and enhancing microbial activity as a slow-release nutrient. Rhizobacteria promote plant growth by improving root ion transport and nutrient availability while promoting soil health and water conservation through RB production. This study examined the effects of combining RB + KBC as an amendment to rice, both with and without Cd stress. Four treatments (control, KBC, RB, and RB + KBC) were applied using a completely randomized design (CRD) in four replications. The results showed that the combination of RB + KBC increased rice plant height (38.40%), shoot length (53.90%), and root length (12.49%) above the control under Cd stress. Additionally, there were notable improvements in chlorophyll a (15.31%), chlorophyll b (25.01%), and total chlorophyll (19.37%) compared to the control under Cd stress, which also showed the potential of RB + KBC treatment. Moreover, increased N, P, and K concentrations in the roots and shoots confirmed that RB + KBC could improve rice plant growth under Cd stress. Consequently, these findings suggest that RB + KBC is an effective amendment to alleviate Cd stress in rice. Farmers should use RB + KBC to achieve better rice growth under cadmium stress., Competing Interests: Declarations Ethics approval and consent to participate I declare that manuscript reporting studies do not involve human participants, data, or tissue. So, it is not applicable. Experimental research and field studies on plants (cultivated or wild), including the collection of plant material, must comply with relevant institutional, national, and international guidelines and legislation I confirmed that all methods were performed according to the relevant guidelines/regulations/legislation. The seeds were purchased from a local certified seed dealer of the Government of Punjab, Pakistan. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Oriented cell divisions are crucial for determining the overall morphology and size of plants, but what controls the onset and duration of this process remains largely unknown. Here, we identified a small molecule that activates root apical meristem (RAM) expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13 (SPL13) a known player in the shoot's juvenile-to-adult transition. This expression leads to oriented cell divisions in the RAM through SHORT ROOT (SHR) and cell cycle regulators. We further show that the RAM has distinct juvenile and adult phases typed by morphological and molecular characteristics and that SPL factors are crucially required for this transition in Arabidopsis and rice ( Oryza sativa ). In summary, we provide molecular insights into the age-dependent morphological changes occurring in the RAM during phase change.

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.)

Key Message: Key message A major quantitative trait locus (qGW12) for grain shape and weight has been isolated in rice, corresponding to LOC_Os12g17900/OsPUB23, and its encoded protein interacts with OsMADS1. Grain shape in rice is an important trait that influences both yield and quality. The primary determinants of grain shape are quantitative trait loci (QTLs) inherited from natural variation in crops. In recent years, much attention has been paid to the molecular role of QTLs in regulating grain shape and weight. In this study, we report the cloning and characterization of qGW12, a major QTL regulating grain shape and weight in rice, using a series of chromosome fragment substitution lines (CSSLs) derived from Oryza sativa indica cultivar 9311 (acceptor) and Oryza rufipogon Griff (donor). One CSSL line, Q187, harboring the introgression of qGW12, exhibited a significant decrease in grain-shape-related traits (including grain length and width) and thousand-grain weight compared to the cultivar 9311. Subsequent backcrossing of Q187 with 9311 resulted in the generation of secondary segregating populations, which were used to fine-map qGW12 to a 24-kb region between markers Seq-44 and Seq-48. Our data indicated that qGW12 encodes a previously unreported U-box type E3 ubiquitin ligase, designated OsPUB23, which exhibited E3 ubiquitin ligase activity. Overexpression of OsPUB23 in rice resulted in higher plant yield than the wild type due to an increase in grain size and weight. Conversely, loss of OsPUB23 function resulted in the opposite tendency. Yeast two-hybrid screening and split luciferase complementation assays revealed that OsPUB23 interacts with OsMADS1. The functional characterization of OsPUB23 provides new genetic resources for improving of grain yield and quality in crops., Competing Interests: Declarations Conflicts of interest The authors declare no conflict of interest., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

In the current industrial scenario, vanadium (V) as a metal is of great importance but poses a major threat to the ecosystem. In the present study, the effect of a toxic concentration of V, i.e., 10 µM in the soil on growth, photosynthetic pigments, gas exchange characteristics, oxidative stress biomarkers, antioxidants machinery (enzymatic and non-enzymatic antioxidants), ions uptake, proline metabolism, and V uptake in different parts of the plant was investigated with and without the exogenous application of selenium (Se) i.e., 5 µM in V-stressed rice (Oryza sativa L.). Our results depicted that V addition to the soil significantly (P < 0.05) decreased plant growth and biomass, gas exchange attributes, and minerals uptake by O. sativa as compared to the plants grown without the addition of V. However, V toxicity boosted the production of reactive oxygen species (ROS) by increasing the contents of malondialdehyde (MDA), which is the indication of oxidative stress in O. sativa and was also manifested by hydrogen peroxide (H 2 O 2 ) contents to the membrane-bounded organelles. Although activities of various antioxidative enzymes like superoxidase dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) and their gene expression Fe-SOD, POD, CAT, and APX and also non-enzymatic antioxidants like phenolic, flavonoid, and ascorbic acid, anthocyanin contents and also the proline metabolism i.e., proline, pyrroline5-carboxylate, pyrroline-5-carboxylate reductase, and pyrroline-5-carboxylate dehydrogenase were increased due to V stress. Although results also illustrated that the application of Se also decreased V toxicity in O. sativa seedlings by increasing antioxidant capacity and, thus, improved the plant growth and biomass, photosynthetic pigments, gas exchange characteristics, and decreased oxidative stress in the O. sativa seedlings, compared to those plants which were not artificially supplied by Se. Research findings, therefore, suggested that the Se application can ameliorate V toxicity in O. sativa seedlings and result in improved plant growth and composition under metal stress as depicted by balanced exudation of nutrient effluxes. This study provides novel insights into the role of selenium in mitigating vanadium-induced oxidative stress in rice, thereby offering a promising approach to enhancing crop resilience in metal-contaminated soils and advancing sustainable agricultural practices., Competing Interests: Declarations Ethics approval and consent to participate Healthy and mature seeds of rice (variety name: Ruz Al Bukhari) were collected from Jouf University. All the experiments were performed in accordance with relevant guidelines and regulations. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

Sogatella furcifera is a migratory pest that harms rice cultivation. Triflumezopyrim (TFM), a novel insecticide, effectively controls S. furcifera . To guide its scientific application, we studied the TFM resistance mechanisms in resistant strains. Through cross-resistance determination, we found that the strain had cross-resistance to clothianidin. Synergistic and enzyme activities also demonstrated that the TFM resistance was related to the enhancement of glutathione S -transferases and UDP-glycosyltransferases. Meanwhile, SfGSTd2 , SfUGT2, and SfUGT35A1 were invariably upregulated in the TFM-resistant strain. RNAi revealed that SfGSTd2 (mortality increasing 33.3-53.3%) and SfUGT35A1 (increasing 33.3-46.7%) significantly increased sensitivity on TFM, while SfUGT35A1 (increasing 40.0-46.7%) also clearly promoted sensitivity toward clothianidin in S. furcifera . The GAL4/UAS system further verified that the overexpression of SfUGT35A1 is involved in the formation of TFM (mortality descending 2.8-52.8%) and clothianidin resistance (mortality descending 11.1-41.7%). Therefore, all results showed that the overexpression of SfGSTd2- and SfUGT35A1- mediated resistance to TFM in S. furcifera .

Metolachlor, the chiral herbicide, inhibits the very-long-chain fatty acid (VLCFA) synthesis; elucidating the enantioselectivity between R - and S -metolachlor in the toxicological difference will facilitate the understanding of the site of action. We found that the endogenous accumulation of C22 VLCFAs decreased in both R -/ S -metolachlor -treated plants by 6, 12, and 24 h after treatment, with more significant reduction in the S isomer group. Gene expression of glutathione S -transferase OsGST Tau members were obviously induced upon treatments with S or R isomer; both OsGSTU1 and OsGSTU4 can metabolize metolachlor effectively, with S isomer as the preference by directly catalyzing the conjugation between S -metolachlor and glutathione. In the current study, we provide the first evidence in rice seedlings that S -metolachlor showed herbicidal toxicity by blocking the synthesis of C22-type fatty acid, which eventually affects the whole elongation chain of (V)LCFA. Meanwhile, OsGSTU1 and 4 metabolize the metolachlor with the S isomer as preference. All of these discoveries broaden our knowledge about metolachlor toxicology and enantioselectivity.

The rice- S. rugosoannulata pattern is a rapidly growing agricultural practice for straw disposal and mushroom production in China. However, different S. rugosoannulata strains show a large variation in rice straw degradability. Here, we constructed a core collection of S. rugosoannulata containing 14 strains with rich genetic diversity. The molecular profiling of the lignocellulose degradability discrepancy of S. rugosoannulata strains was then explored using enzyme activity assays and transcriptome analysis. The results indicated that mycelial growth rate, lignocellulolytic enzyme activities, and rice straw degradability differed widely among the S. rugosoannulata core strains. The genes encoding lignin modifying and degrading auxiliary enzymes, oxidases, glycoside hydrolases, and detoxification proteins were differentially expressed between two representative S. rugosoannulata strains, resulting in differences in their lignocellulolytic enzyme activities and further causing differences in lignocellulose degradability. This study is useful to improve the production efficiency of S. rugosoannulata and promote the recycling of rice straw.

Sulfate fertilization has been proposed to limit arsenic (As) mobility in paddy soils and accumulation in rice grains. However, As and sulfur (S) have complex biogeochemical interactions. Besides the desired precipitation of sulfides that sorb or incorporate As, S can enhance As biotic methylation and abiotic thiolation. Incubating 50- to 2000-year-old paddy soil chronosequence samples without and with S-addition showed the highest relative increases in the formation of low-sorbing, phytotoxic methylated oxyarsenates, and low-sorbing, cyto-, and phytotoxic thioarsenates in the youngest soil. These increases were related to low soil organic carbon (SOC) and iron (Fe) availability, high pH, and As methylation driven by sulfate-reducing bacteria. In older paddy soils, higher SOC and Fe availability buffered these net increases but only in healthy soils. Two paddy soils, where microbial activity and Fe availability had been anthropogenically disturbed, lacked this buffering effect. Therefore, soil history should be considered prior to sulfate fertilization.

The lower Chao Phraya River Basin (CPRB) in Thailand, a major rice-producing area, is grappling with increased water scarcity alongside more frequent floods and droughts, necessitating effective adaptation strategies to sustain agricultural productivity. This study assesses the impacts of climate change on rice yield and irrigation water use, using the DSSAT-CERES-Rice model. Based on these findings, potential genotype- and management-based adaptation strategies were recommended. The model was calibrated and evaluated using the data from field experiments conducted at the Asian Institute of Technology, Thailand during 2017-2018 and 2021-2022. The grain yield and irrigation water use between baseline (2010-2022) and future climate periods (early-century: 2023-2040, mid-century: 2041-2070, and late-century: 2071-2100) were compared. Future climate projections were based on five Global Climate Models (GCMs) from the NEX-GDDP-CMIP6 project under three scenarios (SSP126, SSP245, and SSP585). The model calibration and evaluation demonstrated very good performance statistics, with a d-index of 0.85 during both calibration and evaluation. The model simulations indicated that the maximum and minimum temperatures in the lower CPRB are projected to increase by ~ 2 °C and ~ 4 °C in the late century under SSP245 and SSP585, respectively. Consequently, rice yields are projected to decline by up to 33%, and irrigation water usage to increase by 53% under SSP585 by the late century. Based on the findings, the following major genotype- and management-based adaptation strategies are recommended: (1) Developing heat-tolerant rice cultivars to mitigate yield losses under future climate scenarios, (2) Developing rice cultivars with extended grain-filling duration to enhance both irrigation water use and yield, (3) Shifting the planting date 1-2 weeks earlier (from baseline planting date of 20 July), and shifting fertilizer application date 1-2 weeks earlier (from baseline fertilizer application date of 20 September) for the panicle initiation stage to improve yield, and (4) Optimizing irrigation thresholds (remaining soil water at which to irrigate) to reduce irrigation water use without compromising yield. Overall, the findings highlight the importance of genotype improvement and adaptive management practices in mitigating the adverse effects of climate change on rice production in the lower CPRB., Competing Interests: Declarations Ethical approval All authors have read, understood, and have complied as applicable with the statement on “Ethical responsibilities of Authors” as found in the Instructions for Authors. Consent to participate The authors consent to participate in this research. Consent for publication The authors consent to the publication of this research work. Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

This study is the first attempt to assess rice cultivation under alternate wetting and drying (AWD) and continuous flooding (CF) using the latest scenarios from the Intergovernmental Panel on Climate Change (IPCC), utilizing AquaCrop Model. Field experiments were conducted during the dry season 2023 to get the model calibration and validation input. We used two shared socioeconomic pathways scenarios (SSP3-7.0 and SSP5-8.5) developed within Coupled Model Intercomparison Project Phase 6 (CMIP6) and projected the rice growth during 2040-2070. The simulation results demonstrated the effectiveness of AquaCrop in capturing crop development across treatments and varieties. This model's accuracy in simulating canopy cover (nRMSE = 14-32.5%), time series biomass (nRMSE = 22-42.5%), grain yield (Pd = 4.36-24.38%), and total biomass (nRMSE = 0.39-18.98%) was generally acceptable. The analysis of future climate shows an increasing trend in the monthly average temperature by 0.8 °C (Tmin) and 1.3 °C (Tmax) in both scenarios. While ETo values were not anticipated, rainfall was expected to increase with average values of 5.62 mm to 11.25 mm. In addition, the study found that varieties with growing periods longer than 93 days after transplanting (DAT), such as CAR15 and Sen Kra Ob, were most impacted by heat stress conditions, leading to reduced yield, harvest index (HI), and water use efficiency (WUE). In our case, CAR15 and Sen Kra Ob grain yields were reduced by 53% and 8%, respectively. AWD maintains superior WUE compared with CF regardless of the type of varieties, suggesting this technique is a drought-adaptive strategy., Competing Interests: Declarations Competing interests The authors declare no competing interests., (© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

The lack of obvious difference between germinated seeds and non-germinated seeds will cause the low accuracy of detecting rice seed germination rate, remains a challenging issue in the field. In view of this, a new model named Rice Seed Germination-YOLOV8 (RSG-YOLOV8) is proposed in this paper. This model initially incorporates CSPDenseNet to streamline computational processes while preserving accuracy. Furthermore, the BRA, a dynamic and sparse attention mechanism is integrated to highlight critical features while minimizing redundancy. The third advancement is the employment of a structured feature fusion network, based on GFPN, aiming to reconfigure the original Neck component of YOLOv8, thus enabling efficient feature fusion across varying levels. An additional detection head is introduced, improving detection performance through the integration of variable anchor box scales and the optimization of regression losses. This paper also explores the influence of various attention mechanisms, feature fusion techniques, and detection head architectures on the precision of rice seed germination rate detection. Experimental results indicate that RSG-YOLOV8 achieves a mAP50 of 0.981, marking a 4% enhancement over the mAP50 of YOLOv8 and setting a new benchmark on the RiceSeedGermination dataset for the detection of rice seed germination rate., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Li et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

To address rising global food demand, the development of sustainable technologies to increase productivity is urgently needed. This study revealed that foliar application of zinc oxide nanoparticles (ZnO NPs; 30 to 80 nm, 0.67 mg/d per plant, 6 d) to rice leaves under heatwave (HW) stress increased the grain yield and nutritional quality. Compared with the HW control, the HWs+ZnO group presented increases in the grain yield, grain protein content, and amino acid content of 22.1%, 11.8%, and 77.5%, respectively. Nanoscale ZnO aggregated on the leaf surface and interacted with leaf surface molecules. Compared with that at ambient temperature, HW treatment increased the dissolution of ZnO NPs on the leaf surface by 25.9% and facilitated their translocation to mesophyll cells. The Zn in the leaves existed as both ionic Zn and particulate ZnO. Compared with the HW control, foliar application of ZnO NPs under HW conditions increased leaf nutrient levels (Zn, Mn, Cu, Fe, and Mg) by 15.8 to 416.9%, the chlorophyll content by 22.2 to 24.8%, Rubisco enzyme activity by 21.2%, and antioxidant activity by 26.7 to 31.2%. Transcriptomic analyses revealed that ZnO NPs reversed HW-induced transcriptomic dysregulation, thereby enhancing leaf photosynthesis by 74.4%. Additionally, ZnO NPs increased the diversity, stability, and enrichment of beneficial microbial taxa and protected the phyllosphere microbial community from HW damage. This work elucidates how NPs interact with the phyllosphere, highlighting the potential of NPs to promote sustainable agriculture, especially under extreme climate events (e.g., HWs)., Competing Interests: Competing interests statement:The authors declare no competing interest.

Salt stress has strongly impacted the long-term growth of eco-friendly farming worldwide. By targeting the oxidative stress induced by salt, the utilization of biomass-derived carbon dots (CDs) that possess high-efficiency antioxidant properties, are nontoxic, and have excellent biocompatibility represents a viable and effective approach for enhancing the salt tolerance of plants. In this study, we blended magnesium oxide nanoparticles with carbon sources derived from durian shells to construct Mg-doped carbon dots (Mg-CDs) through a hydrothermal reaction. We demonstrated that the foliar application of 150 μg/mL Mg-CDs to rice plants after treatment with 100 mM salt effectively increased the plant height (9.52%), fresh weight (22.41%), dry weight (33.33%), K + content (21.46%), chlorophyll content (36.21%), and carotenoid content (16.21%); decreased the malondialdehyde (MDA) (9.43%), Na + (25.75%), H 2 O 2 (17.50%), and O 2 •- contents (37.99%); and promoted the photosynthetic system and antioxidant activity. Transcriptome analysis revealed that Mg-CD pretreatment triggered transcriptional reprogramming in rice seedlings. The enrichment analysis of the Kyoto Encyclopedia of Genes and Genomes pathways based on trend groups of gene expression patterns of Profile 8 and Profile 15 indicated that priming with Mg-CDs activated stress signaling- and defense-related pathways, such as metabolic pathways, biosynthesis of secondary metabolites, and photosynthesis pathways. These activations subsequently prompted the expression of genes related to the mitogen-activated protein kinase signaling pathway, hormone signal transduction, the oxidative stress response, and the photosynthetic system. This study demonstrated that the use of Mg-CDs represents a potential strategy to increase plant salt tolerance, creating the possibility for the regulation of crop salinity stress and offering valuable advancements in sustainable agriculture.

Anther development involves a series of important biological events that are precisely regulated by many genes. Although several important genes involved in rice anther development have been identified, the regulatory network involved in tapetal development and pollen wall formation is still largely unclear. PERSISTENT TAPETAL CELL 1 (PTC1) encodes a PHD-Finger protein, which plays a critical role in the regulation of tapetal cell death and pollen development in rice. Here, we report the isolation and characterization of a new allele ptc1-2 with 2-base deletion in the third exon, causing the absent of the PHD domain due to the sequence change. Cytological analysis revealed delayed tapetal PCD, defective pollen exine formation and abnormal ubisch bodies development. Transcriptome analysis revealed that genes related to pollen wall formation (secondary metabolism, phenylalanine synthesis, and cutin and wax biosynthesis pathways), cell death (cysteine and methionine metabolism and DNA repair pathways), and carbohydrate synthesis (starch and sucrose metabolism pathways) were significantly altered in ptc1-2 mutant. A total of 13 reported anther development genes exhibited significant expression changes in the ptc1-2 mutant. Yeast two-hybrid and BiFC analyses showed that PTC1 could interact with API5, an inhibitor of apoptosis, and the citrin-binding enzyme EDT1. This work is helpful in deepening the understanding of the regulatory network of male reproductive development in rice., Competing Interests: Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests., (© 2024. The Author(s).)

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.

Fatty acids play a putative role as second messengers of phytohormones and regulate the rice grain weight. However, the inner mechanism is still unclear and needs to be further studied. In this study, we identified that oleic acid (C18:1) negatively correlates while linoleic acid (C18:2) positively correlates with rice grain weight. Field trials showed that 1000-grain weight was significantly reduced when treated with the fatty acid synthesis inhibitor, Firsocostat S enantiomer (FSE), at the heading and flowering stages. RNA-seq analysis revealed that FSE affects grain weight by modulating processes, such as glycolysis, sucrose metabolism, and hormone signaling. Notably, FSE inhibited the expression of OsLIN6 , which is responsible for transporting C18:1 to the phosphatidylcholine pool for C18:2 synthesis. Compared with the wild type (WT), the OsLIN6 knockout mutant exhibited a lower grain weight, an increased C18:1 content, and a decreased C18:2 content. Importantly, OsARF12 was shown to bind to the OsLIN6 promoter and activate its expression. In summary, this study highlights the crucial role of the fatty acid synthesis gene, OsLIN6 , which was regulated by OsARF12, in rice grain weight determination, thus establishing the molecular link between fatty acid synthesis and auxin signaling.

Decabromodiphenyl ethane (DBDPE) and cadmium (Cd) are typical pollutants in e-waste, seriously threatening crop growth. This study investigated the bioaccumulation and toxicity mechanisms of DBDPE and Cd in a soil-rice system. The results showed that 50 mg/kg DBDPE could reduce the level of accumulation of Cd in rice roots. DBDPE and Cd induced the antioxidant system (SOD, POD, and MDA) in rice seedlings. The combined exposure reduced the contents of carbohydrates, lipids, amino acids, and organic acids. Phenylalanine and phenylpropanoid metabolisms were identified as the key detoxification metabolic pathways under combined exposure. DBDPE and Cd disrupted the functional cycling of carbon and nitrogen in rhizosphere soil, while Gemmatimonadetes, Actinobacteria, and Bacteroidetes were the key bacterial groups responding to DBDPE and Cd stress. This work provides data for the toxicity risk evaluation of DBDPE and Cd combined exposure to food crops.

Arsenic (As) mobilization in paddy fields poses significant health risks, necessitating a thorough understanding of the controlling factors and mechanisms to safeguard human health. We conducted a comprehensive investigation of the soil-porewater-rice system throughout the rice life cycle, focusing on monitoring arsenic distribution and porewater characteristics in typical paddy field plots. Soil pH ranged from 4.79 to 7.98, while porewater pH was weakly alkaline, varying from 7.2 to 7.47. Total arsenic content in paddy soils ranged from 6.8 to 17.2 mg/kg, with arsenic concentrations in porewater during rice growth ranging from 2.97 to 14.85 μg/L. Specifically, arsenite concentrations in porewater ranged from 0.48 to 7.91 μg/L, and arsenate concentrations ranged from 0.73 to 5.83 μg/L. Through principal component analysis (PCA) and analysis of redox factors, we identified that arsenic concentration in porewater is predominantly influenced by the interplay of reduction and desorption processes, contributing 43.5 % collectively. Specifically, the reductive dissolution of iron oxides associated with organic carbon accounted for 23.3 % of arsenic concentration dynamics in porewater. Additionally, arsenic release from the soil followed a sequence starting with nitrate reduction, followed by ferric ion reduction, and subsequently sulfate reduction. Our findings provide valuable insights into the mechanisms governing arsenic mobilization within the paddy soil-porewater-rice system. These insights could inform strategies for irrigation management aimed at mitigating arsenic toxicity and associated health risks., 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.)

Green agriculture faced challenges due to the shortage of efficient cadmium (Cd)-resistant plant growth-promoting bacteria (CdR-PGPB) and their low survival rate and activity during application. In this study, a diverse range of efficient CdR-PGPB were isolated from the rhizosphere soil of Desmodium elegans, especially those with high phosphate-solubilizing capabilities (272.87-450.45 mg L -1 ). Two highly efficient CdR-PGPB namely, XH1 and XH3 were loaded on to rice husk biochar (RHB) and pig bone biochar (PBB), labelled as RHBM and PBBM respectively. This study aimed to explore their effectiveness and mechanisms in promoting maize growth in a Cd-contaminated planting system. Results showed that PBBM performed best among all treatments. It significantly decreased soil phytoavailable Cd by 53.19 % and Cd content in maize shoot by 85.89 %. It also increased soil available phosphorus by 145.72 %, soil alkaline phosphatase activity by 76.34 %, maize shoot/root biomass by 47.06 %/67.98 %, Chlorophyll (a/b) content by 66.80 %/134.13 % and peroxidase activity by 171.96 %. These results were achieved through the synergistic action of efficient CdR-PGPB and PBB. Therefore, PBBM proved to be a promising and innovative application technique for sustainable agricultural development in Cd-contaminated farmland ecosystems., 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 The Authors. Published by Elsevier B.V. All rights reserved.)

The microbiome plays a crucial role in soil nitrogen (N) cycling and in regulating its bioavailability. However, the functional and genomic information of microorganisms encoding N cycling in response to copper (Cu) and cadmium (Cd) contamination is largely unknown. Here, metagenomics and genome binning were used to examine microbial N cycling in Cu and Cd co-contaminated red paddy soils collected from a polluted watershed in southern China. The results showed that soil Cu and Cd concentrations induced more drastic changes in microbial N functional and taxonomic traits than soil general properties. Soil Cu and Cd co-contamination stimulated microbial nitrification, denitrification, and dissimilatory nitrate reduction processes mainly by increasing the abundance of Nitrospira (phylum Nitrospirota), while inhibiting N fixation by decreasing the abundance of Desulfobacca. These contrasting changes in microbial N cycling processes suggested a potential risk of N loss in paddy soils. A high-quality genome was identified as belonging to Nitrospirota with the highest abundance in heavily contaminated soils. This novel Nitrospirota strain possessed metabolic capacities for N transformation and metal resistance. These findings elucidate the genetic mechanisms underlying soil N bioavailability under long-term Cu and Cd contamination, which is essential for maintaining agricultural productivity and controlling heavy metal pollution., 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.)

Chlormequat (CCC) is widely used in agricultural production to increase the crop yield. However, the effects of CCC on transfer of ARGs in agricultural system are still unclear. In this study, using E.coli DH5α (carrying RP4 plasmid with Amp R , Tet R , Kan R ) as the donor bacterium, E.coli HB101, endophytic Pseudomonas sp. Ph6 or rhizosphere Pseudomonas putida KT2440 as the recipient strain, three conjugative systems were designed to investigate the effects of CCC on ARG transfer. Meanwhile, hydroponics experiments were designed to study the ARG spread in the rice-nutrient solution system after CCC application. The results showed that CCC significantly promoted the RP4 conjugation by expanding cell membrane permeability and improving the relative transcription levels of trfAp, trbBp, traA and traL genes in RP4. Furthermore, the conjugation frequency between E. coli and Pseudomonas was much higher than that between E. coli cells. Compared with spraying foliage with 2500 mg·L -1 of CCC, soaking seeds with 250 mg·L -1 of CCC was more beneficial to the colonization of ARB in rice, and also increased the abundance of ARGs in rice cultivation system. These results remind that the use of CCC in agricultural production might promote the ARG transmission in agro-ecosystems; however, foliage spraying with 2500 mg·L -1 of CCC could control its spread., 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 aimed at isolation of native plant growth-promoting bacteria (PGPB) associated with organic tea plantations. Most research on tea and associated microbes have been on Darjeeling and Assam, known for their world-class tea. However, emerging tea plantations in remote Northeast India are gaining prominence due to their unique geographical location, favorable climate, and organic practices. This study investigated PGBP associated with these organic tea plantations, aimed to assess their potential cross-infectivity on non-host plants. A total of 58 PGP bacterial isolates were isolated from four organic tea plantations. Six potential isolates were further evaluated individually and as consortium for their PGP on rice and maize. Bacillus, Pseudomonas, and Serratia spp. as individual and in consortium were found to have potent cross-infectivity with significant growth promotion in non-host plants indicated by plant height, root length, shoot, and root weight. The present findings suggest that PGPB native to organic tea plantations have potential cross-infectivity for use as a biofertilizers to improve the growth and productivity of non-host crops. This provides prospectives of using native bacteria on non-host plants paving the way for their potential application in sustainable agriculture practices for growth promotion of staple food crops., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

The extensive use of nitrogen fertilizer boosts rice (Oryza sativa) production but also harms ecosystems. Therefore, enhancing crop nitrogen use efficiency is crucial. Here, we performed map-based cloning and identified the EARLY FLOWERING3 (ELF3) like protein-encoding gene OsELF3-1, which confers enhanced nitrogen uptake in rice. OsELF3-1 forms a ternary complex (OsEC) with OsELF4s and OsLUX, the putative orthologs of ELF4 and LUX ARRHYTHMO (LUX) in Arabidopsis (Arabidopsis thaliana), respectively. OsEC directly binds to the promoter of Grain number, plant height, and heading date7 (Ghd7) and represses its expression. Ghd7 encodes a transcription factor that has major effects on multiple agronomic traits. Ghd7 is also a transcriptional repressor and directly suppresses the expression of ABC1 REPRESSOR1 (ARE1), a negative regulator of nitrogen use efficiency. Therefore, targeting the OsEC-Ghd7-ARE1 module offers an approach to enhance nitrogen uptake, presenting promising avenues for sustainable agriculture., Competing Interests: Conflict of interest statement. The authors declare no conflict of interest., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists. 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.)

Polar tip growth in plants occurs only in root hairs and pollen tubes. In particular, root hair growth is considered very important in the growth of plants, as it is critical for water and nutrient absorption. Polar tip growth is regulated by various factors, including plant hormones such as abscisic acid (ABA) and gibberellin (GA) and cell wall modifications. We aimed to elucidate the effects and mechanisms on tip growth of a novel gene containing the domain of unknown function (DUF) 3511. We found that Protein Involved in Tip Elongation (PITE) is involved in root hair development in rice (Oryza sativa L.). PITE protein was observed in the plasma membrane and cytoplasm of root hairs. Pite mutants generated by the CRISPR/Cas9 system showed a shorter root hair phenotype compared to the wild type. Through RNA sequencing and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis, we found that the expression of genes that affect cell wall rigidity and GA metabolism-related genes were differently regulated in pite mutants. PITE could interact with acyl transferase and haloacid dehalogenase-like hydrolase (HAD9) in the nucleus and cytoplasm. Our study suggests that PITEs containing the DUF3511 domain regulate root hair growth in rice by mediating the expression of genes that can regulate cell wall rigidity or cause changes in GA metabolism through interactors such as HAD9., (© 2024 Scandinavian Plant Physiology Society.)

The abounding variations in wild rice provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we report wild rice GL12 W improves grain length and salt tolerance in both indica and japonica genetic backgrounds. GL12 W alters cell length by regulating grain size related genes including GS2, and positively regulates the salt tolerance related genes, such as NAC5, NCED3, under salt stresses. We find that a G/T variation in GL12 promoter determined its binding to coactivator GIF1 and transcription factor WRKY53. GIF1 promotes GL12 W expression in young panicle and WRKY53 represses GL12 W expression under salt stresses. The G/T variation also contributes to the divergence of indica and japonica subspecies. Our results provide useful resources for modern rice breeding and shed insights for understanding yield and salt tolerance trade-off mechanism., (© 2024. The Author(s).)

Rice growth and yield response to salinity can be influenced by the duration and the timing of salt stress. The present study tested the effects of saline water irrigation from vegetative growth to maturity on rice growth and yield and ion concentrations in the straw and root and related them to changes in soil salinity and soil solute potential. The treatments consisted of five levels of saline water irrigation (electrical conductivity ~0.25 (control), 4, 6, 8, and 10 dS m-1) with two rice cultivars (BRRI dhan67 and BRRI dhan99) grown in pots in a rain shelter. Grain weight per pot, dry straw weight, and root weight were significantly reduced with increasing water salinity, but BRRI dhan99 was less affected. With prolonged saline water irrigation, salt concentration increased in the soil and lowered the soil solute potential. Increased saline water induced higher concentrations of Na+ in the straw (527-1200 mmol kg-1 at 4-10 dS m-1) relative to the root. By contrast, higher Cl- concentrations accumulated in the root than in the straw. The decrease of K+ in the straw and root for increasing salinity was inconsistent, but the Na+/K+ ratio sharply increased in the straw with higher water salinity. The increased Na+/K+ explained most grain weight loss due to higher salinity (R2 = 0.93) followed by Na+ (R2 = 0.87) and Cl-1 (R2 = 0.53). We conclude that the prolonged saline water irrigation has a cumulative effect on root zone salinity and solute potential that depresses grain yield in rice by increasing the Na+/K+ ratio in plants., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Rice is an important agricultural crop that faces serious challenges from pathogens, pests, and weeds during growth stages. Meanwhile, these organisms would interact with each other to increase the level of destruction. The previous studies showed that barnyard grass (Echinochloa spp) could be used as a temporary host to increase infestation of small brown planthopper (SBPH, Laodelphax striatellus), which is one of the main polyphagous pests. Herbicides are widely used to control weeds that induce resistance development. However, little is known about the effects of increased weed resistance on insect species. In this study, we investigated the effect of quinclorac-resistant and sensitive biotypes of barnyard grass (Echinochloa crus-galli var. zelayensis; Echinochloa crus-pavonis Schult) and rice plants (Wuyujing 3) on the ecological fitness of SBPH and examined physiological indicators of plants and SBPH to explore the mechanism. Our results showed that the growth and reproduction of SBPH promoted significantly reared on quinclorac-resistant barnyard grass. From the perspectives of oxidative stress response, the activities of peroxidase (POD) increased and the activities of catalase (CAT), mixed-functional oxidase (MFO), and carboxylesterase (CarE) decreased in SBPH reared on resistant barnyard grass. Combined with the increased amino acid contents (threonine, serine, methionine, and alanine) of resistant barnyard grass E. crus-pavonis, we speculate that quinclorac-resistant barnyard grass probably provides SBPH with a more suitable environment, thus increasing the risk of SBPH., 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 Inc. All rights reserved.)

Calcium plays a crucial role in regulating plant senescence. However, the specific effects of increased intranuclear calcium versus cytoplasmic calcium on aging remain unclear. Cyclic nucleotide-gated channels (CNGCs), which manage Ca 2 ⁺ levels in plant cells, are particularly significant in this context. These channels are known to relocate between the nuclear envelope and the plasma membrane in response to stress and developmental signals. Through this movement, CNGCs help regulate the balance of cytosolic and intranuclear Ca 2 ⁺. In this study, we categorized the 16 CNGC genes in rice into five subgroups. OsCNGCs are notably expressed in leaves, especially during the reproductive stage. Both OsCNGC6 and OsCNGC7 exhibit dual localization to the plasma membrane and the nuclear envelope. Knockdown of OsCNGC7 led to reduced levels of Ca 2 ⁺ and K⁺ in plants. Conversely, yeast expressing the OsCNGC7 gene showed increased sensitivity to Ca 2 ⁺. Additionally, while the [Ca 2 ⁺] cyt was maintained at relatively low levels in both wild-type and OsCNGC7-RNAi lines, the fluorescence intensity was significantly higher in OsCNGC7-overexpressing lines, particularly in the nucleus of root tips. Overexpression of OsCNGC7 resulted in enhanced stomatal opening and accelerated leaf senescence from the tillering stage to grain filling in rice. Treatment with MeJA rapidly induced OsCNGC7 expression, while knockdown of OsCNGC7 delayed both MeJA-induced and dark-induced leaf senescence. Further analysis revealed that OsCNGC7 interacts with OsKAT2 and OsALMT2. In conclusion, our findings highlight the distinct roles of OsCNGCs in regulating senescence. This knowledge could provide new strategies for manipulating plant senescence and enhancing crop productivity., Competing Interests: Declaration of competing interest The authors have no conflict of interest., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Kam sweet rice is a cultural treasure in Qiandongnan, Guizhou Province. However, the situation with low yield and economic value in Kam sweet rice urgently requires improved mechanistic understanding of tillering to increase its yield. In this study, we found that the rate of axillary bud elongation differed significantly among Kam sweet rice varieties, which was positively correlated with tiller number. Transcriptome analysis suggests that genes involved in nitrogen metabolism and plant hormone signaling pathways could be the main reasons for the differences in tillering among these varieties. The amino acid transporter OsAAP11 in the transcriptome was essential for bud outgrowth and rice tillering based on the phenotypic performance of its transgenic plants. Further results found that OsAAP11 was able to transport amino acids such as proline, glycine, and alanine in rice. Natural variations were found in the promoter region of this gene in different Kam sweet rice varieties, which may lead to differences in the transcription levels of OsAAP11. Overall, the results suggest that the natural variations of OsAAP11 in rice might lead to variations in its expression levels, further affecting bud outgrowth and tillering through regulating the transport and accumulation of amino acids., 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.)

Labile organic carbon (C) substrates could accelerate microbial transformation of soil N pool by stimulating the decomposition of large molecule organic N. However, it remains unclear how gross N transformation processes (protein depolymerization, amino acid uptake, microbial N mineralization and NH 4 + -N uptake rates) in response to individual C substrates. Typical paddy soil was incubated with the supplement of oxalic acid or glucose under simulated field water conditions for 16 days to assess the gross N transformation rates by 15 N pool dilution assays. A mixture of 15 N labeled amino acid was applied to gross protein depolymerization and amino acid uptake rates measurement, and 15 N-(NH 4 ) 2 SO 4 was used to gross microbial N mineralization and NH 4 + -N uptake rates analyses. Oxalic acid supplement promoted the gross protein depolymerization, gross microbial uptake of amino acid, and gross N mineralization rates at the early stage. It was attributed that oxalic acid supplement urged microbes to decompose large molecular organic N to acquire amino acid derived C and excluded the superfluous N via mineralization as evidenced by the increase of NH 4 + -N. By contrast, glucose supplement diminished the gross N transformation processes, since microbes prefer to utilize the native NH 4 + -N to meet their N demand supported by the decreasing NH 4 + -N concentration in soil, and consequently inhibited the decomposition for the large molecule organic N. With the increase of microbial growth, especially for bacteria, glucose amendment stimulated the large molecular organic N depolymerization to acquire amino acid to maintain the microbial C/N stoichiometric balance. Compared to glucose treatment, oxalic acid supplement stimulated more N allocation into microbial growth but not for mineralization, and thus led to higher microbial N use efficiency, which was adverse for available inorganic N supply for rice growth in paddy ecosystem. Overall, this study emphasizes that low molecular organic C substrates of organic acid and glucose exerted contrasting influences on gross N transformation, and help to improve our understanding of the mechanism of the coupling biotransformation of C and N in paddy soil., 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.)

Drought hampers agricultural production by constraining crop growth and development. Nevertheless, there has been limited exploration regarding the effect of biochar coating in enhancing seed germination under drought conditions and understanding its underlying mechanisms. To fill this gap and clarify the pathway to drought resistance, the current research investigated the protective effectiveness of BC on seedling establishment and subsequent growth of rice under drought conditions. Results showed that BC notably elevated emergence rate (5.5%), shoot length (27.4%), root length (33.4%), plant height (19.6/10.3%), leaf area (69.8/71.7%), and plant biomass (85.7/67.9%) after 15/30 days under drought conditions compared to the control. Biochar coating facilitated the maintenance of a stable chloroplast structure, reduced chlorophyll degradation, and sustained cell expansion. This contributed to the improvement of stomatal characteristics on both adaxial and abaxial leaf surfaces during drought stress, encompassing enhancements in stomatal density and aperture. The preservation of stomatal opening led to an increased photosynthetic capacity, thereby fostering elevated photosynthetic activity and heightened plant biomass under stressful conditions. Simultaneously, BC treatment significantly diminished the production of reactive oxygen species, preserved cell membrane integrity, and augmented the accumulation of osmotic protectants. These outcomes signify that biochar coating mitigates the deleterious impacts of drought stress on photosynthesis, stomatal aperture, chloroplast ultrastructure, osmotic regulation, and redox homeostasis in plants through specific water and nutrient regulation. Consequently, this enhances the tolerance and growth of rice under drought stress., 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.)

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.)

The developmental changes in the granular surface structure and functional properties of starch during the entire grain filling period of rice (around 40 days) were investigated. The specific surface area of rice starch significantly decreased firstly then stabilized during growth due to increasing granular size. The pore volume decreased from 5.40 cm 3 /g at 6th day after anthesis (DAA-6) to 3.02 cm 3 /g (DAA-46). More starch granule-associated proteins (SGAPs) accumulated on the surface and in channels. Swelling power decreased by 46 %, whereas the flow behavior index (n) decreased by 32 % in upward curve during starch development from DAA-6 to DAA-30. Tan δ first dropped then remained steady at DAA 22-34 and lightly rebounded at the final stage, indicating that starch in the middle stage tended to have greater viscoelastic gel behavior at all sweeps. Mature starch showed lower in vitro hydrolysis rate and exhibited stronger enzymatic resistance. The results showed that granular surface features of rice starch may be an essential factor in determining rheological behavior and resistance to hydrolysis., 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.)

Excess antimony (Sb) has been shown to damage plant growth. Rice plants readily absorb a large amount of Sb after a long period of flooding, yet the mechanisms underlying Sb toxicity in plants have not been solved. This study was conducted to explore the effects of Sb on the uptake of N and S, and monitor the concentrations of reduced glutathione (GSH) and enzymes associated with these processes. In addition, we analyzed differentially expressed metabolites (DEMs) correlated with amino acids (AAs) and oligopeptides, specifically DEMs containing sulfur (S), GSH and indole-3-acetic acid (IAA). The results showed that antimonite [Sb(III)] inhibited shoot growth whereas antimonate [Sb(V)] stimulated shoot growth. Interestingly, Sb(III) 5/10 enhanced shoot concentrations of total nitrogen (N), NH 4 + -N [only at Sb(III) 10 ] and S; but reduced the shoot concentrations of NO 3 -N and soluble protein. Sb(III) 5/10 addition significantly increased oxidized glutathione (GSSG) concentration and activities of glutathione peroxidase (GSH-Px) and glutathione S-transferase (GST) but non-significantly affected concentration of reduced glutathione (GSH) and activities of γ-glutamylcysteine synthetase (GCL) and glutathione reductase (GR), suggesting Sb(III) restricted GSH recycling. Addition of Sb (1) increased the abundance of DEMs associated with lignins, Ca uptake, toxicity/detoxification, and branched chain AAs; (2) decreased the abundance of AAs inclcuding isoleucine (Ile), leucine (Leu), tryptophan (Trp), tyrosine (Tyr) and histidine (His); (3) increased the abundance of arginine (Arg), putrescine (Put) and spermidine (Spd); and (4) affected methylation and acetylation of many AAs, especially acetylation., Competing Interests: Declaration of competing interest We declare that no conflict of interest exits in this manuscript, and manuscript is approved by all authors for publication. This manuscript was original and has not been published in whole or in part previously. We do not have any commercial or associative interest that represents a conflict of interest in connection with the work submitted., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

The rice albumin (RAG) gene family belongs to the Tryp&#95;alpha&#95;amyl family. RAG2, specifically expressed in 14-21 DAP (days after pollination) seeds, regulates grain yield and quality. In this study, we identified another RAG family gene, RAL6, which exhibits specific expression in developing seeds, particularly in 7, 10, and 15 DAP seeds. Employing the CRISPR/Cas9 system, we analyzed functions of RAL6 and found that the ral6 lines (ral6-1, ral6-2, ral6-3, and ral6-4) displayed thinner seeds with significantly decreased 1000-grain weight and grain thickness compared to ZH11. Additionally, the cell width of spikelet cells, total protein and glutelin contents were significantly reduced in ral6. The germination assay and 1% TTC staining revealed a significant decrease in seed vigor among the ral6 lines. The alpha-amylase activity in ral6 mutant seeds was also markedly lower than in ZH11 seeds after 2 days of imbibition. Furthermore, co-expression analysis and GO annotation showed that co-expressed genes were involved in immune response, oligopeptide transport, and the glucan biosynthetic process. Collectively, our findings suggest that RAL6 plays a coordinating role in regulating grain weight and seed germination in rice., (© 2024. The Author(s) under exclusive licence to The Botanical Society of Japan.)

Background: The invasive freshwater snail Pomacea canaliculata is an agricultural pest with a certain level of tolerance to abiotic stress. After the harvest of late rice, the snails usually burrow themselves into the soil surface layers to overwinter and pose a renewed threat to rice production in the following year. Revealing the response of snails to environmental stresses is crucial for developing countermeasures to control their damage and spread., Results: In this study, we conducted a 120-day in situ experiment during the winter to investigate the survival and physiological changes of hibernating snails in 0-5 and 5-10 cm soil depths, aiming to explore their overwintering strategies. Our results showed that 73.61%, 87.50%, and 90.28% of male, female, and juvenile snails survived after hibernation for 120 days in 0-10 cm soil depth, respectively. The differences in survival rates based on sex and size of snails potentially reflect the countermeasures of snails to rapidly reproduce after hibernation. Simultaneously, the hibernating snails exhibited the ability to maintain a certain level of body weight. During this period, the snails increased their antioxidant enzyme activities to cope with oxidative stress, and enhanced their lipid storage. The hibernation survival of snails was not significantly affected by different soil depths, indicating that they have the potential to hibernate into deeper soils. Furthermore, snails were capable of increasing their contents of bound water and glycerol to cope with sudden cold spells during hibernation., Conclusion: Our findings emphasize the adaptive changes of P. canaliculata snails overwintering in paddy soils. In future studies, the vulnerabilities of P. canaliculata during hibernation (e.g. shell characteristics, nutrient reserves, and dehydration tolerance, etc.,) should be investigated to develop effective control methods for this period. © 2024 Society of Chemical Industry., (© 2024 Society of Chemical Industry.)

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.)

Rice is one of the world's major food crops. Changes in major climatic factors such as temperature, rainfall, solar radiation and carbon dioxide (CO 2 ) concentration have an important impact on rice growth and yield. However, many of the current studies that predict the impact of future climate change on rice yield are affected by uncertainties such as climate models, climate scenarios, model parameters and structure, and showing great differences. This study was based on the assessment results of the impact of climate change on rice in the future of 111 published literature, and comprehensively analyzed the impact and uncertainty of climate change on rice yield. This study utilized local polynomial (Loess) regression analysis to investigate the impact of changes in mean temperature, minimum temperature, maximum temperature, solar radiation, and precipitation on relative rice yield variations within a complete dataset. A linear mixed-effects model was used to quantitatively analyze the relationships between the restricted datasets. The qualitative analysis based on the entire dataset revealed that rice yields decreased with increasing average temperature. The precipitation changed between 0 and 25 %, it was conducive to the stable production of rice, and when the precipitation changed >25 %, it would cause rice yield reduction. The change of solar radiation was less than -1.15 %, the rice yield increases with the increase of solar radiation, and when the change of solar radiation exceeds -1.15 %, the rice yield decreases. Elevated CO 2 concentrations and management practices could mitigate the negative effects of climate change. The results of a quantitative analysis utilizing the mixed effects model revealed that average temperature, precipitation, CO 2 concentration, and adaptation methods all had a substantial impact on rice production, and elevated CO 2 concentrations and management practices could exert positive influences on rice production. For every 1 °C and 1 % increase in average temperature and precipitation, rice yield decreased by 3.85 % and 0.56 %, respectively. For every 100 ppm increase in CO 2 concentration, rice yield increased by 7.1 %. The variation of rice yield under different climate models, study sites and climate scenarios had significant variability. Elevated CO 2 concentrations and management practices could compensate for the negative effects of climate change, benefiting rice production. This study comprehensively collected and analyzed a wide range of literature and research, which provides an in-depth understanding of the impacts of climate change on rice production and informs future research and policy development., 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.)

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.)

Weed infestation is the major biological threat in direct-seeded rice production and can cause significant yield losses. The effective use of herbicides is particularly important in direct-seeded rice production. Anilofos, a pre-emergence herbicide, has been shown to be effective against the weed barnyardgrass. However, its impacts on crop yield and the direct-seeded rice production ecosystem remain underexplored. In this study, we conducted field trials and used untargeted metabolomics to investigate systemic effects of two different treatments (40 g/acre and 60 g/acre) on rice shoot and root as well as the rhizosphere soil during the critical tillering stage. Here, a total of 400 metabolites were determined in the crop and soil, with differential metabolites primarily comprising lipids and lipid-like molecules as well as phenylpropanoids and polyketides. Spearman correlation network analysis and a Zi-Pi plot revealed 7 key differential metabolites with significant topological roles, including succinic acid semialdehyde and riboflavin. KEGG pathway analysis showed that anilofos downregulated the amino acid metabolism while mainly promoted carbohydrate metabolism and secondary metabolites biosynthesis of the crop, which made minimal disruption on soil metabolism. Notably, we found 40 g/acre anilofos application could significantly improve the rice yield, potentially linked to the improved activity of flavonoid biosynthesis and starch and sucrose metabolism. This research provides a comprehensive evaluation of anilofos effects in the direct-seeded rice production system, offering new insights into optimizing herbicide use to improve agricultural sustainability and productivity., 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.)

Background: Nanotechnology has been widely applied in agricultural science. During the process of reducing metal toxicity and accumulation in rice, nanomaterials exhibit size effects. However, there is limited knowledge regarding these size effects. We aim to explore the impact of fertilizer with various sizes of ZnO nanoparticles (ZnO-NPs) on rice growth and cadmium (Cd) accumulation and to elucidate the potential mechanism of Cd reduction in rice. Foliar applications of different concentrations (0.5 and 2 mmol L -1 ) and different sizes (30 and 300 nm ZnO-NPs) of zinc (Zn) fertilizer (Zn(NO 3 ) 2 ) were performed to investigate the effects on rice growth, Cd accumulation and subcellular distribution, and the expression of Zn-Cd transport genes., Results: The results suggested that all the foliar sprayings can significantly reduce the Cd concentrations in rice grains by 41-61% with the highest reduction in the application of ZnO-NPs with large size and low concentration. This is related to the enhancement of Cd fixation in leaf cell walls and downregulation of Cd transport genes (OsZIP7, OsHMA2, OsHMA3) in stem nodes. Foliar ZnO-NPs applications can increase the Zn concentration in grains by 9-21%. Foliar applications of Zn(NO 3 ) 2 and small-sized ZnO-NPs promoted plant growth and rice yield, while the application of large-sized ZnO-NPs significantly reduced rice growth and yield., Conclusion: The study suggests that the rice yield and Cd reduction are dependent on the size and concentration of foliar spraying and the use of large-sized ZnO-NPs is the most effective strategy when considering both yield and Cd reduction comprehensively. © 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.)

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.