Multiple mutations in BADH2 gene reveal the novel fragrance allele in indica rice (Oryza sativa L.).

The aroma in rice is the most appreciable quality trait, controlled by the loss of function of the betaine aldehyde dehydrogenase 2 (BADH2) gene. In the present study, indica rice cultivars (basmati, nonbasmati aromatic, and nonaromatic) were screened to explore allelic differences in the BADH2 gene using two functional markers (badh2-p-5'UTR and FMbadh2-E7). Notably, the results of the present mutational analysis showed that both markers confirmed a different mutation in indica rice cultivars than earlier reported japonica accessions. It was found that there is 250-bp deletion in the promoter region of aromatic Kagesali and Kalakrishna as compared to nonaromatic Kolamb. The results of FMbadh2-E7 showed 8-bp deletion and six SNPs in exon 7 of the Kalakrishna cultivar. Interestingly, the nonbasmati aromatic Lalbhat rice cultivar did not harbour any reported mutation and showed a novel BADH2 allele carrying 1-bp deletion in exon 7. Among the selected aromatic rice cultivars, eight cultivars showed mutation in the 5' UTR region and interestingly 23 rice cultivars carried the mutation in both 5' UTR and exon 7 of a BADH2 gene. The 2-acetyl-1-pyrroline (2AP) biosynthesis related metabolites, enzyme assay and gene expression supported mutation in BADH2 gene and expression of 2AP in aromatic rice cultivars under study.

DNA methylation remodeling and the functional implication during male gametogenesis in rice.

BACKGROUND: Epigenetic marks are reprogrammed during sexual reproduction. In flowering plants, DNA methylation is only partially remodeled in the gametes and the zygote. However, the timing and functional significance of the remodeling during plant gametogenesis remain obscure. RESULTS: Here we show that DNA methylation remodeling starts after male meiosis in rice, with non-CG methylation, particularly at CHG sites, being first enhanced in the microspore and subsequently decreased in sperm. Functional analysis of rice CHG methyltransferase genes CMT3a and CMT3b indicates that CMT3a functions as the major CHG methyltransferase in rice meiocyte, while CMT3b is responsible for the increase of CHG methylation in microspore. The function of the two histone demethylases JMJ706 and JMJ707 that remove H3K9me2 may contribute to the decreased CHG methylation in sperm. During male gametogenesis CMT3a mainly silences TE and TE-related genes while CMT3b is required for repression of genes encoding factors involved in transcriptional and translational activities. In addition, CMT3b functions to repress zygotic gene expression in egg and participates in establishing the zygotic epigenome upon fertilization. CONCLUSION: Collectively, the results indicate that DNA methylation is dynamically remodeled during male gametogenesis, distinguish the function of CMT3a and CMT3b in sex cells, and underpin the functional significance of DNA methylation remodeling during rice reproduction.

Biochar obtained from eucalyptus, rice hull, and native bamboo as an alternative to decrease mobility of hexazinone, metribuzin, and quinclorac in a tropical soil.

Mobile herbicides have a high potential for groundwater contamination. An alternative to decrease the mobility of herbicides is to apply materials with high sorbent capacity to the soil, such as biochars. The objective of this research was to evaluate the effect of eucalyptus, rice hull, and native bamboo biochar amendments on sorption and desorption of hexazinone, metribuzin, and quinclorac in a tropical soil. The sorption-desorption was evaluated using the batch equilibrium method at five concentrations of hexazinone, metribuzin, and quinclorac. Soil was amended with eucalyptus, rice hull, and native bamboo biochar at a rate of 0 (control-unamended) and 1% (w w-1), corresponding to 0 and 12 t ha-1, respectively. The amount of sorbed herbicides in the unamended soil followed the decreasing order: quinclorac (65.9%) > metribuzin (21.4%) > hexazinone (16.0%). Native bamboo biochar provided the highest sorption compared to rice hull and eucalyptus biochar-amended soils for the three herbicides. The amount of desorbed herbicides in the unamended soil followed the decreasing order: metribuzin (18.35%) > hexazinone (15.9%) > quinclorac (15.1%). Addition of native bamboo biochar provided the lowest desorption among the biochar amendments for the three herbicides. In conclusion, the biochars differently affect the sorption and desorption of hexazinone, metribuzin, and quinclorac mobile herbicides in a tropical soil. The addition of eucalyptus, rice hull, and native bamboo biochars is a good alternative to increase the sorption of hexazinone, metribuzin, and quinclorac, thus, reducing mobility and availability of these herbicides to nontarget organisms in soil.

Determination of trace chelating carboxylic acids in rice by green extraction combined with liquid chromatography-mass spectrometry analysis and its application in the evaluation of old and new rice.

RATIONALE: Accurate identification of old rice samples from new ones benefits their market circulation and consumers. However, the current detection methods are still not satisfactory because of their insufficient accuracy or (and) time-consuming process. METHODS: Chelating carboxylic acids (CCAs) were selectively extracted from rice, by stirring with chelating resin and a dilute Na2CO3 solution. The green analytical chemistry guidelines for sample preparation were investigated by using the green chemistry calculator AGREE prep. The extractant was determined by liquid chromatography-mass spectrometry (LC/MS), and statistical analysis of the analytical data was carried out to evaluate the significance of the difference by ChiPlot. RESULTS: The limit of quantitation for the CCAs is in the range of 1 to 50 ng/mL, with a reasonable reproducibility. The CCAs in 23 rice samples were determined within a wide concentration range from 0.03 to 1174 µg/g. Intriguingly, the content of citric acid, malonic acid, α-ketoglutaric acid and cis-aconite acid in new rice was each found to be distinctively higher than that in old rice by several times. Even mixtures of old and new rice were found to show much difference in the concentration of citric acid and malic acid. CONCLUSION: A green analytical method has been developed for the simultaneous determination of CCAs by LC/MS analysis, and the identification of old rice samples from new ones was easily carried out according to their CCA content for the first time. The results indicated that the described method has powerful potential for the accurate identification of old rice samples from new ones.

Predictive modeling of methylmercury in rice (Oryza sativa L.) and species-sensitivity-distribution-based derivation of the threshold of soil mercury in karst mountain areas.

The bioavailable mercury (Hg) in the soil is highly active and can affect the formulation of methyl-Hg (MeHg) in soil and its accumulation in rice. Herein, we predicted the concentration of MeHg in rice using bioavailable Hg extracted from soils; additionally, we determined the threshold value of soil Hg in karst mountain areas based on species sensitivity distribution. The bioavailable Hg was extracted using calcium chloride, hydrochloric acid (HCl), diethylenetriaminepentaacetic acid mixture, ammonium acetate, and thioglycolic acid. Results showed that HCl is the best extractant, and the prediction model demonstrated good predictability of the MeHg concentration in rice based on the HCl-extractable Hg, pH, and soil organic matter (SOM) data. Compared with the actual MeHg concentration in rice, approximately 99% of the predicted values (n = 103) were within the 95% prediction range, indicating the good performance of the rice MeHg prediction model based on soil pH, SOM, and bioavailable Hg in karst mountain areas. Based on this MeHg prediction model, the safety threshold of soil Hg was calculated to be 0.0936 mg/kg, which is much lower than the soil pollution risk screening value of agricultural land (0.5 mg/kg), suggesting that a stricter standard should be applied regarding soil Hg in karst mountain areas. This study presents the threshold of soil Hg pollution for rice safety in karst mountain areas, and future studies should target this threshold range.

Transcriptional and metabolic profiling of sulfur starvation response in two monocots.

BACKGROUND: Sulfur (S) is a mineral nutrient essential for plant growth and development, which is incorporated into diverse molecules fundamental for primary and secondary metabolism, plant defense, signaling, and maintaining cellular homeostasis. Although, S starvation response is well documented in the dicot model Arabidopsis thaliana, it is not clear if the same transcriptional networks control the response also in the monocots. RESULTS: We performed series of physiological, expression, and metabolite analyses in two model monocot species, one representing the C3 plants, Oryza sativa cv. kitaake, and second representing the C4 plants, Setaria viridis. Our comprehensive transcriptomic analysis revealed twice as many differentially expressed genes (DEGs) in S. viridis than in O. sativa under S-deficiency, consistent with a greater loss of sulfur and S-containing metabolites under these conditions. Surprisingly, most of the DEGs and enriched gene ontology terms were species-specific, with an intersect of only 58 common DEGs. The transcriptional networks were different in roots and shoots of both species, in particular no genes were down-regulated by S-deficiency in the roots of both species. CONCLUSIONS: Our analysis shows that S-deficiency seems to have different physiological consequences in the two monocot species and their nutrient homeostasis might be under distinct control mechanisms.

Comparative miRNome and transcriptome analyses reveal the expression of novel miRNAs in the panicle of rice implicated in sustained agronomic performance under terminal drought stress.

MAIN CONCLUSION: Differential expression of 128 known and 111 novel miRNAs in the panicle of Nagina 22 under terminal drought stress targeting transcription factors, stress-associated genes, etc., enhances drought tolerance and helps sustain agronomic performance under terminal drought stress. Drought tolerance is a complex multigenic trait, wherein the genes are fine-tuned by coding and non-coding components in mitigating deleterious effects. MicroRNA (miRNA) controls gene expression at post-transcriptional level either by cleaving mRNA (transcript) or by suppressing its translation. miRNAs are known to control developmental processes and abiotic stress tolerance in plants. To identify terminal drought-responsive novel miRNA in contrasting rice cultivars, we constructed small RNA (sRNA) libraries from immature panicles of drought-tolerant rice [Nagina 22 (N 22)] and drought-sensitive (IR 64) cultivars grown under control and terminal drought stress. Our analysis of sRNA-seq data resulted in the identification of 169 known and 148 novel miRNAs in the rice cultivars. Among the novel miRNAs, 68 were up-regulated while 43 were down-regulated in the panicle of N 22 under stress. Interestingly, 31 novel miRNAs up-regulated in N 22 were down-regulated in IR 64, whereas 4 miRNAs down-regulated in N 22 were up-regulated in IR 64 under stress. To detect the effects of miRNA on mRNA expression level, transcriptome analysis was performed, while differential expression of miRNAs and their target genes was validated by RT-qPCR. Targets of the differentially expressed miRNAs include transcription factors and stress-associated genes involved in cellular/metabolic/developmental processes, response to abiotic stress, programmed cell death, photosynthesis, panicle/seed development, and grain yield. Differential expression of the miRNAs could be validated in an independent set of the samples. The findings might be useful in genetic improvement of drought-tolerant rice.

Chinese organic rice transition spatial econometrics empirical analysis.

Based on the integrated model of Super-SBM model, spatial Durbin model (SDM) and Grey neural network model, this paper analyzes the panel data of various provinces in China from multiple angles and dimensions. It was found that there were significant differences in eco-efficiency between organic rice production and conventional rice production. The response of organic rice to climate change, the spatial distribution of ecological and economic benefits and the impact on carbon emission were analyzed. The results showed that organic rice planting not only had higher economic benefits, but also showed a rising trend of ecological benefits and a positive feedback effect. This finding highlights the importance of organic rice farming in reducing carbon emissions. Organic rice farming effectively reduces greenhouse gas emissions, especially carbon dioxide and methane, by improving soil management and reducing the use of fertilizers and pesticides. This has important implications for mitigating climate change and promoting soil health and biodiversity. With the acceleration of urbanization, the increase of organic rice planting area shows the trend of organic rice gradually replacing traditional rice cultivation, further highlighting the potential of organic agriculture in emission reduction, environmental protection and sustainable agricultural production. To this end, it is recommended that the Government implement a diversified support strategy to encourage technological innovation, provide guidance and training, and raise public awareness and demand for organic products. At the same time, private sector participation is stimulated to support the development of organic rice cultivation through a public-private partnership model. Through these measures, further promote organic rice cultivation, achieve the dual goals of economic benefits and environmental benefits, and effectively promote the realization of double carbon emission reduction targets.

Effects of warming on rice production and metabolism process associated with greenhouse gas emissions.

Evaluating the impact of global warming on rice production and greenhouse gas (GHG) emissions is critical for ensuring food security and mitigating the consequences of climate change. Nonetheless, the impacts of warming on crop production, GHG emissions, and microbial mechanisms in the single-cropping rice systems remain unclear. Here, a two-year field experiment was conducted to explore the effects of warming (increased by 2.7-3.0 °C on average) in the rice growing season on crop production and functional microorganisms associated with GHG emissions. Results showed that warming resulted in significant reduction (p < 0.01) in the aboveground biomass and grain yield as well as in grain weight, the number of spikelets per panicle, and the seed-setting rate. However, it caused a significant increase (p < 0.01) in the number of panicles by 15.6 % and 34.9 %, respectively. Furthermore, warming significantly increased (p < 0.01) seasonal methane (CH4) emissions but reduced nitrous oxide (N2O) emissions, particularly in 2022.The relative abundance of genes associated with CH4 metabolism and nitrogen metabolism was increased by 40.7 % and 32.7 %, respectively, in response to warming. Moreover, warming had a positive impact on the abundance of genes related to CH4 production and oxidation processes but did not affect the denitrification processes associated with N2O production. These results showed that warming decreased rice yield and biomass in the single cropping rice system but increased CH4 emissions and global warming potential. Taken together, to address the increasing food demand of a growing population and mitigate the impacts of global warming, it is imperative to duce GHG emissions and enhance crop yields.

Leaching Approach for ß-Glucosidase Extraction from Fermented Rice Husk in Solid State Cultivation by Aspergillus protuberus.

Environmental problems are caused by the disposal of agrowastes in developing countries. It is imperative to convert such wastes into useful products, which require enzymes such as ß-glucosidase. ß-Glucosidase has variety of applications in biotechnology including food, textile, detergents, pulp and paper, pharmaceutical and biofuel industries. ß-Glucosidase production was performed using the locally isolated Aspergillus protuberus using best growth circumstances on rice husk in solid-state fermentation (SSF). Leaching of ß-glucosidase from fermented rice husk with number of solvents to evaluate their extraction efficacy. Among the different solvents examined, acetate buffer (0.02 M, pH 5.0) proved to be the best solvent. The subsequent parameters were optimized with acetate buffer. Two washes with acetate buffer each by shaking (30 min) in a ratio of 1 g of rice husk: 5 ml of acetate buffer together attained maximum recovery of ß-glucosidase with 41.95 U/g of rice husk.

Soil redox status governs within-field spatial variation in microbial arsenic methylation and rice straighthead disease.

Microbial arsenic (As) methylation in paddy soil produces mainly dimethylarsenate (DMA), which can cause physiological straighthead disease in rice. The disease is often highly patchy in the field, but the reasons remain unknown. We investigated within-field spatial variations in straighthead disease severity, As species in rice husks and in soil porewater, microbial composition and abundance of arsM gene encoding arsenite S-adenosylmethionine methyltransferase in two paddy fields. The spatial pattern of disease severity matched those of soil redox potential, arsM gene abundance, porewater DMA concentration, and husk DMA concentration in both fields. Structural equation modelling identified soil redox potential as the key factor affecting arsM gene abundance, consequently impacting porewater DMA and husk DMA concentrations. Core amplicon variants that correlated positively with husk DMA concentration belonged mainly to the phyla of Chloroflexi, Bacillota, Acidobacteriota, Actinobacteriota, and Myxococcota. Meta-omics analyses of soil samples from the disease and non-disease patches identified 5129 arsM gene sequences, with 71% being transcribed. The arsM-carrying hosts were diverse and dominated by anaerobic bacteria. Between 96 and 115 arsM sequences were significantly more expressed in the soil samples from the disease than from the non-disease patch, which were distributed across 18 phyla, especially Acidobacteriota, Bacteroidota, Verrucomicrobiota, Chloroflexota, Pseudomonadota, and Actinomycetota. This study demonstrates that even a small variation in soil redox potential within the anoxic range can cause a large variation in the abundance of As-methylating microorganisms, thus resulting in within-field variation in rice straighthead disease. Raising soil redox potential could be an effective way to prevent straighthead disease.

An integrated model for rice supplier selection strategies and a comparative analysis of fuzzy multicriteria decision-making approaches based on the fuzzy entropy weight method for evaluating rice suppliers.

Rice, being a staple food in many countries, necessitates the identification of reliable suppliers to ensure a steady supply. Consequently, it is vital to establish trustworthy vendors for various types of this essential grain who can meet stringent product quality standards. This study aims to identify, analyze, rank, and select primary rice suppliers. The study emphasizes the importance of selecting and managing suitable providers to meet customer demands, proposes a ranking model for rice suppliers, and introduces developed fuzzy MCDM techniques. It proposes an integrated model for selecting rice suppliers, considering factors related to the processes before, during, and after selecting providers within a defined framework. The outcomes shows that rice supplier selection strategy can efficiently identify reliable rice suppliers, improve buyer value, reduce procurement risk, enhance efficiency, and establish strong supply chain relationships in complex decision-making processes. To assess suppliers, the study introduces two advanced integrated approaches and compares them. The fuzzy entropy weight method (EWM) was used to determine the criteria weights. The ranking of rice suppliers was achieved using a fuzzy multi-objective optimization based on ratio analysis (MOORA), fuzzy complex proportional assessment (COPRAS), and combinations of these two methods in different approaches. The methodology supports decision-makers in a rapidly evolving global environment by assisting importers, traders, suppliers, procurement, and logistics management, particularly for non-rice-cultivating countries in rice importation and supplier selection. The numerical analysis is grounded in a real-world case study of selecting rice suppliers in Jordan. The findings reveal that the various strategies yield both similar and different results. Furthermore, the integrated method is considered the most accurate for evaluating rice imports and suppliers, aligning closely with the reality of the current situation.

Influence of rice husk ash on the mechanical properties of ultra-high strength engineered cementitious composites (UHS-ECC).

Generally, UHS-ECC should consume massive cement, which is negative to its sustainability as cement production leads to 8% of global CO2 emissions. To decrease the cost of production and carbon emissions of UHS-ECC, rice husk ash was employed to replace the cement as a supplementary cementitious material in this study. Experiment results illustrate that blending rice husk ash (RHA) would decrease the fluidity of mortar. Furthermore, the green UHS-ECC shows a maximum compressive strength of 130.3 MPa at 28 days when RHA content was 20% of cement. The ultimate tensile strength of UHS-ECCs first increased and then decreased, while both tensile strain and strain energy presented an opposite tendency. At the micro-scale, if RHA content was lower than 20% of cement, incorporating RHA can significantly decreasing fiber bridging complementary energy of UHS-ECC, thus reducing pseudo strain hardening energy (PSHenergy) index, which finely agrees with the degradation of ductility of UHS-ECCs. To guarantee the features of ultra-high strength, acceptable workability, and high tensile ductility, the RHA dosage should not be in excess 20% of cement. These researched results are prospected to the contribution of pozzolanic RHA on the efficient usage of sustainable UHS-ECC.

Identification of biochemical indices for brown spot (Bipolaris oryzae) disease resistance in rice mutants and hybrids.

Brown spot caused by Bipolaris oryzae is a major damaging fungal disease of rice which can decrease the yield and value of produce due to grain discoloration. The objectives of the current study were to investigate and understand the biochemical indices of brown spot disease resistance in rice. A total of 108 genotypes (mutant and hybrid) along with Super Basmati and parent RICF-160 were evaluated against brown spot disease. The genotypes exhibiting resistant and susceptible responses to brown spot disease according to the IRRI standard disease rating scale were screened and selected. To study the biochemical response mechanism, forty five selected genotypes along with Super Basmati and RICF-160 were analyzed using the biochemical markers. The physiological and biochemical analysis provided valuable insights and confirmed the resistance of rice hybrids and mutants against brown spot disease. Positive correlations were observed among stress bio-markers and disease response. Rice genotypes i.e. Mu-AS-8, Mu-AS-19, Mu-AS-20 and Mu-AS-35 exhibited moderate resistant response while Hy-AS-92, Hy-AS-98, Hy-AS-99, Hy-AS-101, Hy-AS-102 and Hy-AS-107 showed resistant response to brown spot disease. Brown spot resistant rice genotypes had lesser values of malondialdehyde and total oxidant status and higher antioxidant activities i.e. superoxide dismutase, peroxidase, total phenolic content and lycopene. The selected resistant rice genotypes had resistance capacity against Bipolaris oryzae stress. In conclusion, identified resistant mutants i.e. Mu-AS-8, Mu-AS-19, Mu-AS-20 and Mu-AS-35 and hybrids i.e. Hy-AS-92, Hy-AS-98, Hy-AS-99, Hy-AS-101, Hy-AS-102 and Hy-AS-107 could be used in rice breeding program to achieve sustainable rice production by coping the emerging challenge of brown spot disease under variable climate conditions.

Identification of responsive genes to multiple abiotic stresses in rice (Oryza sativa): a meta-analysis of transcriptomics data.

Abiotic stresses limit the quantity and quality of rice grain production, which is considered a strategic crop in many countries. In this study, a meta-analysis of different microarray data at seedling stage was performed to investigate the effects of multiple abiotic stresses (drought, salinity, cold situation, high temperature, alkali condition, iron, aluminum, and heavy metal toxicity, nitrogen, phosphorus, and potassium deficiency) on rice. Comparative analysis between multiple abiotic stress groups and their control groups indicated 561 differentially expressed genes (DEGs), among which 422 and 139 genes were up-regulated and down-regulated, respectively. Gene Ontology analysis showed that the process of responding to stresses and stimuli was significantly enriched. In addition, pathways such as metabolic process and biosynthesis of secondary metabolites were identified by KEGG pathway analysis. Weighted correlation network analysis (WGCNA) uncovered 17 distinct co-expression modules. Six modules were significantly associated with genes involved in response to abiotic stresses. Finally, to validate the results of the meta-analysis, five genes, including TIFY9 (JAZ5), RAB16B, ADF3, Os01g0124650, and Os05g0142900 selected for qRT-PCR analysis. Expression patterns of selected genes confirmed the results of the meta-analysis. The outcome of this study could help introduce candidate genes that may be beneficial for use in genetic engineering programs to produce more tolerant crops or as markers for selection.

CRISPR/Cas9 targeted mutations of OsDSG1 gene enhanced salt tolerance in rice.

Salinization is one of the leading causes of arable land shrinkage and rice yield decline, recently. Therefore, developing and utilizing salt-tolerant rice varieties have been seen as a crucial and urgent strategy to reduce the effects of saline intrusion and protect food security worldwide. In the current study, the CRISPR/Cas9 system was utilized to induce targeted mutations in the coding sequence of the OsDSG1, a gene involved in the ubiquitination pathway and the regulation of biochemical reactions in rice. The CRISPR/Cas9-induced mutations of the OsDSG1 were generated in a local rice cultivar and the mutant inheritance was validated at different generations. The OsDSG1 mutant lines showed an enhancement in salt tolerance compared to wild type plants at both germination and seedling stages indicated by increases in plant height, root length, and total fresh weight as well as the total chlorophyll and relative water contents under the salt stress condition. In addition, lower proline and MDA contents were observed in mutant rice as compared to wild type plants in the presence of salt stress. Importantly, no effect on seed germination and plant growth parameters was recorded in the CRISRP/Cas9-induced mutant rice under the normal condition. This study again indicates the involvement of the OsDSG1 gene in the salt resistant mechanism in rice and provides a potential strategy to enhance the tolerance of local rice varieties to the salt stress.

Transcriptomic analysis of salt-tolerant and sensitive high-yield japonica rice (Oryza sativa L.) reveals complicated salt-tolerant mechanisms.

Developing and cultivating rice varieties is a potent strategy for reclaiming salinity-affected soils for rice production. Nevertheless, the molecular mechanisms conferring salt tolerance, especially in conventional high-yield japonica rice varieties, remain obscure. In this study, Zhendao 23309 (ZD23309) exhibited significantly less grain yield reduction under a salt stress gradient than the control variety Wuyunjing 30 (WYJ30). High positive correlations between grain yield and dry matter accumulation at the jointing, heading and maturity stages indicated that early salt tolerance performance is a crucial hallmark for yield formation. After a mild salt stress (85 mM NaCl) of young seedlings, RNA sequencing (RNA-seq) of shoot and root separately identified a total of 1952 and 3647 differentially expressed genes (DEGs) in ZD23309, and 2114 and 2711 DEGs in WYJ30, respectively. Gene ontology (GO) analysis revealed numerous DEGs in ZD23309 that play pivotal roles in strengthening salt tolerance, encompassing the response to stimulus (GO:0050896) in shoots and nucleoside binding (GO:0001882) in roots. Additionally, distinct expression patterns were observed in a fraction of genes in the two rice varieties under salt stress, corroborating the efficacy of previously reported salt tolerance genes. Our research not only offers fresh insights into the differences in salt stress tolerance among conventional high-yield rice varieties but also unveils the intricate nature of salt tolerance mechanisms. These findings lay a solid groundwork for deciphering the mechanisms underlying salt tolerance.

Methionine biosynthetic genes and methionine sulfoxide reductase A are required for Rhizoctonia solani AG1-IA to cause sheath blight disease in rice.

Rhizoctonia solani is a polyphagous necrotrophic fungal pathogen that causes sheath blight disease in rice. It deploys effector molecules as well as carbohydrate-active enzymes and enhances the production of reactive oxygen species for killing host tissues. Understanding R. solani ability to sustain growth under an oxidative-stress-enriched environment is important for developing disease control strategies. Here, we demonstrate that R. solani upregulates methionine biosynthetic genes, including Rs_MET13 during infection in rice, and double-stranded RNA-mediated silencing of these genes impairs the pathogen's ability to cause disease. Exogenous treatment with methionine restores the disease-causing ability of Rs_MET13-silenced R. solani and facilitates its growth on 10 mM H2O2-containing minimal-media. Notably, the Rs_MsrA gene that encodes methionine sulfoxide reductase A, an antioxidant enzyme involved in the repair of oxidative damage of methionine, is upregulated upon H2O2 treatment and also during infection in rice. Rs_MsrA-silenced R. solani is unable to cause disease, suggesting that it is important for the repair of oxidative damage in methionine during host colonization. We propose that spray-induced gene silencing of Rs_MsrA and designing of antagonistic molecules that block MsrA activity can be exploited as a drug target for effective control of sheath blight disease in rice.

Health of Holochilus chacarius (Rodentia: Cricetidae) in rice agroecosystem in a neotropical wetland assessed by histopathology.

Small mammals have a short lifetime and are strictly associated with their environment. This work aimed to use histopathology to assess the health of Holochilus chacarius in a rice agroecosystem in the Pantanal of Mato Grosso do Sul. During necropsy, fragments of the lung, kidney, skin, liver, and reproductive system of 33 animals were collected and submitted to histological processing. Tissue damages were evaluated as mild, moderate, and severe and arranged in a matrix for further statistical analysis. Furthermore, we used generalized linear models to verify the influence of tissue changes on the body condition, obtained by a regression between body mass and length. In the lungs, we found an intense inflammatory infiltrate associated with anthracosis that had a negative influence on the body's condition. Also, we observed degenerative and inflammatory changes in the liver, kidneys, skin, and reproductive system that ranged from mild to moderate. The histopathological lesions observed in this study may be associated with environmental alterations of anthropic origin such as the exposure to soot from wildfires and heavy metals, evidenced by lesions in the lung, kidney, and liver. The present study provided a histopathological matrix as a new approach that allows to classify and quantify the tissue alterations. Tissue changes when associated with body condition demonstrated to be an effective tool to assess the health of small free-living mammals, showing that these animals can be used as bioindicators of environmental condition.

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice.

BACKGROUND: Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS: In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION: This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.