Determination of prebiotic properties of rice bran extract.

This research investigated and compared the prebiotic properties of a rice bran extract obtained through commercial xylanase extraction in comparison with water extraction. Prebiotic properties were evaluated by probiotic growth stimulation (Lacticaseibacillus casei and Lactiplantibacillus plantarum) and gastrointestinal pathogen inhibition (Bacillus cereus and Escherichia coli). The rice bran extract obtained with xylanase (RB1) displayed significantly higher total polysaccharide and total reducing sugar contents than those obtained with water (RB2; p<0.05). After extraction for 30 min, RB1 exhibited the highest total polysaccharide and total reducing sugar contents. HPLC (high performance liquid chromatography) analysis revealed that RB1 primarily contained xylose, while RB2 contained less glucose and lacked other sugar derivatives. RB1 proved effective in stimulating the growth of L. casei and L. plantarum, surpassing even inulin (a commercial prebiotic). Furthermore, it demonstrated a high potential for inhibiting the growth of pathogenic B. cereus and E. coli, comparable to inulin. In contrast, RB2 exhibited lower inhibitory capacity against B. cereus and E. coli.

Lot-to-lot variation in the microbiota during the brewing process of kimoto-type Japanese rice wine.

Kimoto-type Japanese rice wine (sake) has a wide variety of flavors, as the predominant microbes, including lactic acid bacteria (LAB) and nitrate-reducing bacteria, that spontaneously proliferate in the fermentation starter vary depending on the brewery. In this study, we traced the microbiota in four lots of starters manufactured in a newly established brewery and evaluated the lot-to-lot variation and characteristics of the microbiota in the brewery. The results of a 16S ribosomal RNA amplicon analysis showed that the starters brewed in the second brewing year had a more diverse microbiota than those in the first brewing year. Among the LAB predominated at the middle production stage, lactococci, including Leuconostoc spp., were detected in all the lots, while lactobacilli predominated for the first time in the second year. These results suggest that repeated brewing increased microbial diversity and altered the microbial transition pattern in the kimoto-style fermentation starters. Phylogenetic analyses for the LAB isolates from each starter identified Leuconostoc suionicum, Leuconostoc citreum, and Leuconostoc mesenteroides as predominant lactococci as well as a unique lactobacillus in place of Latilactobacillus sakei. We also found that a rice koji-derived Staphylococcus gallinarum with nitrate-reducing activity was generally predominant during the early production stage, suggesting that there was a case in which staphylococci played a role in nitrite production in the starters. These findings are expected to contribute to the understanding of the diversity of microbiota in kimoto-type sake brewing and enable control of the microbiota for consistent sake quality.

GCPDFFNet: Small Object Detection for Rice Blast Recognition.

Early detection of rice blast disease is pivotal to ensure rice yield. We collected in situ images of rice blast and constructed a rice blast dataset based on variations in lesion shape, size, and color. Given that rice blast lesions are small and typically exhibit round, oval, and fusiform shapes, we proposed a small object detection model named GCPDFFNet (global context-based parallel differentiation feature fusion network) for rice blast recognition. The GCPDFFNet model has three global context feature extraction modules and two parallel differentiation feature fusion modules. The global context modules are employed to focus on the lesion areas; the parallel differentiation feature fusion modules are used to enhance the recognition effect of small-sized lesions. In addition, we proposed the SCYLLA normalized Wasserstein distance loss function, specifically designed to accelerate model convergence and improve the detection accuracy of rice blast disease. Comparative experiments were conducted on the rice blast dataset to evaluate the performance of the model. The proposed GCPDFFNet model outperformed the baseline network CenterNet, with a significant increase in mean average precision from 83.6 to 95.4% on the rice blast test set while maintaining a satisfactory frames per second drop from 147.9 to 122.1. Our results suggest that the GCPDFFNet model can accurately detect in situ rice blast disease while ensuring the inference speed meets the real-time requirements.

Sustainable soil management under drought stress through biochar application: Immobilizing arsenic, ameliorating soil quality, and augmenting plant growth.

Rise in climate change-induced drought occurrences have amplified pollution of metal(loid)s, deteriorated soil quality, and deterred growth of crops. Rice straw-derived biochars (RSB) and cow manure-enriched biochars (CEB) were used in the investigation (at doses of 0%, 2.5%, 5%, and 7.5%) to ameliorate the negative impacts of drought, improve soil fertility, minimize arsenic pollution, replace agro-chemical application, and maximize crop yields. Even in soils exposed to severe droughts, 3 months of RSB and CEB amendment (at 7.5% dose) revealed decreased bulk density (13.7% and 8.9%), and increased cation exchange capacity (6.0% and 6.3%), anion exchange capacity (56.3% and 28.0%), porosity (12.3% and 7.9%), water holding capacity (37.5% and 12.5%), soil respiration (17.8% and 21.8%), and nutrient contents (especially N and P). Additionally, RSB and CEB decreased mobile (30.3% and 35.7%), bio-available (54.7% and 45.3%), and leachable (55.0% and 56.5%) fractions of arsenic. Further, pot experiments with Bengal gram and coriander plants showed enhanced growth (62-188% biomass and 90-277% length) and reduced arsenic accumulation (49-54%) in above ground parts of the plants. Therefore, biochar application was found to improve physico-chemical properties of soil, minimize arsenic contamination, and augment crop growth even in drought-stressed soils. The investigation suggests utilisation of cow manure for eco-friendly fabrication of nutrient-rich CEB, which could eventually promote sustainable agriculture and circular economy. With the increasing need for sustainable agricultural practices, the use of biochar could provide a long-term solution to enhance soil quality, mitigate the effects of climate change, and ensure food security for future generations. Future research should focus on optimizing biochar application across various soil types and climatic conditions, as well as assessing its long-term effectiveness.

Flavor assessment of a lactic fermented vinegar described in Japanese books from the Edo period (1603-1867).

Aims: Rice vinegar is a traditional fermented seasoning in Japan, and its production remained unchanged for over 800 years until the Edo period. However, based on the available information regarding rice vinegar production methods from this period and the results of reproduction experiments, we speculated that unlike the modern-day acetic fermented vinegar, rice vinegar produced during the Edo period was lactic fermented. Main methods: To verify this assumption, we analyzed the flavor components of Honcho, a lactic fermented product prepared using a method described in books, including "Honchoshokkan" from the Edo period, by capillary electrophoresis/time-of-flight mass spectrometry, high-performance liquid chromatography, gas chromatography mass spectrometry, and taste sensor analysis. Sensory evaluation was also conducted to assess validation as a seasoning. Results: Honcho contains 2 % lactic acid, which gives it its acidity, and small amounts of other nonvolatile acids, but significantly lower levels of acetic acid (0.188 ± 0.015 g/100 mL, p < 0.01). It contains more than double the free amino acids of Kurozu, a modern rice vinegar, and more glutamic acid. Boiling to remove ethanol from yeast fermentation concentrated the free amino acids 1.5 times. Sensor taste analysis showed Honcho had weaker acidity but stronger umami taste than commercial rice vinegar. The volatile compounds related to acetic acid fermentation were significantly different between Honcho and Kurozu. Boiling increased Honcho's acidity, mainly through non-volatile acids. Significance: These findings provide evidence to indicate that Honcho was an acidic seasoning for heat-cooking, which is uncommon in Japanese cuisine today and is mentioned in Edo period books. This seasoning contains many amino acids, implying that it adds umami flavor, not only the sourness of modern vinegar.

Alfin-like (AL) transcription factor family in Oryza sativa L.: Genome-wide analysis and expression profiling under different stresses.

Oryza sativa L. is the world's most essential and economically important food crop. Climate change and ecological imbalances make rice plants vulnerable to abiotic and biotic stresses, threatening global food security. The Alfin-like (AL) transcription factor family plays a crucial role in plant development and stress responses. This study comprehensively analyzed this gene family and their expression profiles in rice, revealing nine AL genes, classifying them into three distinct groups based on phylogenetic analysis and identifying four segmental duplication events. RNA-seq data analysis revealed high expression levels of OsALs in different tissues, growth stages, and their responsiveness to stresses. RT-qPCR data showed significant expression of OsALs in different abiotic stresses. Identification of potential cis-regulatory elements in promoter regions has also unveiled their involvement. Tertiary structures of the proteins were predicted. These findings would lay the groundwork for future research to reveal their molecular mechanism in stress tolerance and plant development.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice.

Transposable elements (TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing data. Coupling the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms (SNPs), such as OsRbohB, and validated OsRbohB's relative expression activity using a dual-Luciferase (LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

Identification and analysis of nine new flo2 allelic mutants in rice.

FLO2 is involved in grain development and storage substance synthesis in rice, and therefore can regulate grain size and quality. In this study, we identified 4 new flo2 allelic mutants with nonsense and frameshift mutation in the exon of 6, 10, 11 and 21 and 5 new flo2 allelic mutants with alternative splicing and frameshift mutation at the splicing site of intron 13, 14, 16 and 17. Compared with wild-type rice, the outer endosperm of flo2 mutants was transparent, and the inner endosperm was floury. Different mutation sites and types of FLO2 significantly decreased kernel width, thickness and weight to some extent. The contents of storage protein, starch, amylose and amylopectin showed significant decrease at different levels among 9 flo2 mutants. The expressions of most storage protein synthesis genes and starch synthesis-related genes were significantly down-regulated, and exhibited different ranges of variation among different flo2 mutants. This study could add helpful information for the roles of flo2 alleles in rice quality regulation and provide abundant germplasm resources for rice quality breeding.

Identification of water transitions using a combination of moisture sorption characteristics and dielectric properties of different parts of jasmine rice (Oryza sativa).

BACKGROUND: In this work, water transition points (first transition: monolayer-multilayer water; and second transition: multilayer-free and solvent water) of different parts of jasmine rice including white rice, brown rice and bran were identified through the integration of sorption isotherm and dielectric properties data. Desorption isotherm data were fitted to four established models to select the optimal model for describing the sorption behaviors. Then, dielectric properties such as dielectric constant (ε') and dielectric loss factor (ε″) were measured across various moisture content levels within the frequency range of 200-20 000 MHz. RESULTS: A type III isotherm was observed for all samples and the Peleg model was the best fit with the experimental data. Monolayer moisture content of the samples, estimated using the GAB model, ranged from 3.25% to 4.17% dry basis. For dielectric properties, frequency and moisture dependencies were evident for all sample types. Moreover, the sorption isotherm models effectively described the relationship between water activity (aw) and dielectric properties as reflected by their goodness of fit, and their strong correlation through principal component analysis and Pearson's correlation results. CONCLUSION: The first water transition occurs at aw values of 0.11, 0.12, and 0.22, while the second transition appears at aw values of 0.9, 0.9 and 0.75-0.85 for white rice, brown rice and bran, respectively. This knowledge will be useful for food processors, providing insights into the optimization of food processing and storage conditions to extend food products' shelf life. © 2024 Society of Chemical Industry.

High surface area biochar for the removal of naphthenic acids from environmental water and industrial wastewater.

This study reports the production of biochar adsorbents from two major crop residues (i.e., rice and wheat straw) to remove naphthenic acids from water. The alkali treatment approach was used for biochar activation that resulted in a tremendous increase in their surface area, i.e., up to 2252 and 2314 m2/g, respectively, for rice and wheat straw biochars. Benzoic acid was used as a model compound to optimize critical adsorption parameters. Its maximum monolayer adsorption capacity of 459.55 and 357.64 mg/g was achieved for activated rice and wheat straw biochars. The adsorption of benzoic acid was exothermic (∆H° = - 7.06 and - 3.89 kJ/mol) and identified possibly as physisorption (Gibbs free energy ranges 3.5-4.0 kJ/mol). The kinetic study suggested that adsorption follows pseudo-second-order kinetics with qe2 for rice straw and wheat straw-derived adsorbents at 200 and 194 mg/g, respectively. As adsorbent, the recyclability of activated biochars was noticed with no significant loss in their efficiency for up to ten successive regeneration cycles. The adsorption results were validated using a commercial naphthenic acid mixture-spiked river water and paper/pulp industrial effluent. The activated rice and wheat straw biochars exhibited excellent adsorption efficiency of 130.3 and 74.6 mg/g, respectively. The naphthenic acid adsorption on biochar surface was due to various interactions, i.e., weak van der Waal's, pore filling, π-π stacking, and ionic interactions. This study offers a cost-effective and eco-friendly approach to valorizing agricultural residues for pollutant removal from industrial wastewater, including petroleum refineries.

An integrated approach through controlled experiment and LCIA to evaluate water quality and ecological impacts of irrigated paddy rice.

This study used an integrated approach to mainly assess the water quality of paddy field during cultivation and quantify its equivalent ecological damages. Accordingly, an isolated pilot area with 0.6 ha and subsurface drainage pipes was prepared for flow measurement and multiple pollutant examination (DO, EC, pH, COD, TKN, TN, TP, NO3, butachlor) under controlled condition during 94 days of rice cultivation. Based on life cycle impact assessment (LCIA) database, the indices of ReCiPe (2016) were used to convert the examined nutrient and herbicide pollution. Results showed that TKN and TP were significant pollutants and reached the maximum concentrations of 7.2 and 4.9 mg/L in pilot outflow, respectively. Here, their average discharged loads were 56.2 gN/day and 45.3 gP/day. These loads equal leaching 8.5% and 9.4% of applied urea and phosphate fertilizers, respectively. The nutrient export coefficients were 8.4 kgN/ha and 6.8 kgP/ha. Nevertheless, the majority of this pollution was transferred by inflow. The net export coefficients were 0.3 kgN/ha and 2.6 kgP/ha while net leaching rates were 0.3%TN and 3.3%TP. The trend of combined ecological damages also showed that the 11-17th day of cultivation imposed the highest ecological risks. The state-of-the-art index of ecological footprint per food production estimates the equivalent ratio of lost lives by impaired ecosystem against lives saved from starvation. This index showed that 7% of the potential of produced paddy rice in this area for saving lives would be spoiled by releasing pollution to the terrestrial ecosystem in the long term. Yet, it can be enhanced as a matter of direct discharge to the freshwater. Therefore, using suitable agricultural operations or improving farm management practices for pollution abatement or assimilation potential is highly recommended.

Symptoms and management of cow's milk allergy: perception and evidence.

Introduction: The diagnosis and management of cow's milk allergy (CMA) is a topic of debate and controversy. Our aim was to compare the opinions of expert groups from the Middle East (n = 14) and the European Society of Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN) (n = 13). Methods: These Expert groups voted on statements that were developed by the ESPGHAN group and published in a recent position paper. The voting outcome was compared. Results: Overall, there was consensus amongst both groups of experts. Experts agreed that symptoms of crying, irritability and colic, as single manifestation, are not suggestive of CMA. They agreed that amino-acid based formula (AAF) should be reserved for severe cases (e.g., malnutrition and anaphylaxis) and that there is insufficient evidence to recommend a step-down approach. There was no unanimous consensus on the statement that a cow's milk based extensively hydrolysed formula (eHF) should be the first choice as a diagnostic elimination diet in mild/moderate cases. Although the statements regarding the role for hydrolysed rice formula as a diagnostic and therapeutic elimination diet were accepted, 3/27 disagreed. The votes regarding soy formula highlight the differences in opinion in the role of soy protein in CMA dietary treatment. Generally, soy-based formula is seldom available in the Middle-East region. All ESPGHAN experts agreed that there is insufficient evidence that the addition of probiotics, prebiotics and synbiotics increase the efficacy of elimination diets regarding CMA symptoms (despite other benefits such as decrease of infections and antibiotic intake), whereas 3/14 of the Middle East group thought there was sufficient evidence. Discussion: Differences in voting are related to geographical, cultural and other conditions, such as cost and availability. This emphasizes the need to develop region-specific guidelines considering social and cultural conditions, and to perform further research in this area.

Tuber crops could be a potential food component for lowering starch digestibility and estimated glycemic index in rice.

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

A NAC transcription factor MNAC3-centered regulatory network negatively modulates rice immunity against blast disease.

NAC transcription factors (TFs) are pivotal in plant immunity against diverse pathogens. Here, we report the functional and regulatory network of MNAC3, a novel NAC TF, in rice immunity. MNAC3, a transcriptional activator, negatively modulates rice immunity against blast and bacterial leaf blight diseases and pathogen-associated molecular pattern (PAMP)-triggered immune responses. MNAC3 binds to a CACG cis-element and activates the transcription of immune-negative target genes OsINO80, OsJAZ10, and OsJAZ11. The negative function of MNAC3 in rice immunity depends on its transcription of downstream genes such as OsINO80 and OsJAZ10. MNAC3 interacts with immunity-related OsPP2C41 (a protein phosphatase), ONAC066 (a NAC TF), and OsDjA6 (a DnaJ chaperone). ONAC066 and OsPP2C41 attenuate MNAC3 transcriptional activity, while OsDjA6 promotes it. Phosphorylation of MNAC3 at S163 is critical for its negative functions in rice immunity. OsPP2C41, which plays positive roles in rice blast resistance and chitin-triggered immune responses, dephosphorylates MNAC3, suppressing its transcriptional activity on the target genes OsINO80, OsJAZ10, and OsJAZ11 and promoting the translocation of MNAC3 from nucleus to cytoplasm. These results establish a MNAC3-centered regulatory network in which OsPP2C41 dephosphorylates MNAC3, attenuating its transcriptional activity on downstream immune-negative target genes in rice. Together, these findings deepen our understanding of molecular mechanisms in rice immunity and offer a novel strategy for genetic improvement of rice disease resistance.

Novel trans-Resveratrol Derivatives: Design, Synthesis, Antibacterial Activity, and Mechanisms.

Rice bacterial leaf blight and rice bacterial leaf streak have induced tremendous damage to production of rice worldwide. To discover an effective novel antibacterial agent, a series of novel trans-resveratrol (RSV) derivatives containing 1,3,4-oxadiazole and amide moieties were designed and synthesized for the first time. Most of them showed excellent antibacterial activities against Xanthomonas oryzae pv oryzicola and Xanthomonas oryzae pv oryzae. Especially, compound J12 had the best inhibitory with the half-maximal effective concentration values of 4.2 and 5.0 mg/L, respectively, which were better than that of RSV (63.7 and 75.4 mg/L), bismerthiazol (79.5 and 89.6 mg/L), and thiodiazole copper (105.4 and 112.8 mg/L). Furthermore, compound J12 had an excellent control effect against rice bacterial leaf streak and rice bacterial leaf blight, with protective activities of 46.2 and 42.1% and curative activities of 44.5 and 41.7%, respectively. Preliminary mechanisms indicated that compound J12 could not only remarkably decrease biofilm formation, extracellular polysaccharide production, and the synthesis of extracellular enzymes but also destroy bacterial cell surface morphology, thereby reducing the pathogenicity of bacteria. In addition, compound J12 could increase the activity of defense-related enzymes and affect the expression of multiple pathogenic-related genes including plant-pathogen interaction, the MAPK signaling pathway, and phenylpropanoid biosynthesis, and this could improve the defense of rice against rice bacterial leaf streak infection. The present work indicates that the RSV derivatives can be used as promising candidates for the development of antibacterial agents.

Enhancing the valorization of pulping black liquors in production effective aerogel-carbon nanostructure as adsorbents toward cationic and ionic dyes.

This work deals with promoting the efficiency of removing the cationic and ionic dyes by new aerogel-carbon nanostructures. For cleaner production the rice straw-pulping black liquors, which regards serious environmental risk during routine disposing, is used in preparing the aerogel precursors. These aerogels (AGBs) depend on using pulping black liquor in hybrid with resorcinol and the less carcinogenic formaldehyde butyraldehyde. Black liquors from five pulping processes are used, Elemental, thermogravimetric (TGA and DTG), and FTIR-ATR analyses are used to characterize the carbon precursors. While their adsorption behavior toward cationic and anionic dyes are accessed via iodine-value, adsorption capacity and kinetic models, textural characterization, and SEM. The TGA measurements reveal that AGBs from BLs of neutral sulfite and soda-borohydride pulping reagents have higher activation and degradation energies than other aerogels. In terms of cationic and anionic dyes adsorption as well as textural characterization, the AGB-CNSs surpass that made from BLs. The discarded KOH/NH4OH black liquor is used to synthesize the best aerogel precursor for producing cationic methylene blue dye (MB) adsorbent, where it provides an adsorption capacity 242.1 mg/g. The maximum anionic brilliant blue dye (BB) adsorption capacity, 162.6 mg/g, is noticed by Kraft BL-aerogel-CNSs. These finding data overcome the literature carbon adsorbents based on lignin precursors. All examined CNSs toward MB dye follow the Langmuir adsorption equilibrium; while primarily the Freundlich model for BB dye. The pseudo-second-order kinetic model well fits the adsorption kinetics of investigated AGB-CNSs. The textural characterization and SEM revealed a mixture of mesoporous and micro porous features in the CNSs.

Comparative Field Evaluation and Transcriptome Analysis Reveals that Chromosome Doubling Enhances Sheath Blight Resistance in Rice.

Rice sheath blight, caused by Rhizoctonia solani Kihn (R. solani), poses a significant threat to rice production and quality. Autotetraploid rice, developed through chromosome doubling of diploid rice, holds great potential for enhancing biological and yield traits. However, its resistance to sheath blight in the field has remained unclear. In this study, the field resistance of 35 autotetraploid genotypes and corresponding diploids was evaluated across three environments from 2020 to 2021. The booting stage was optimal for inoculating period based on the inoculation and analysis of R. solani at five rice growth stages. We found autotetraploids generally exhibited lower disease scores than diploids, indicating enhanced resistance after chromosome doubling. Among the 35 genotypes, 16 (45.71%) displayed increased resistance, 2 (5.71%) showed decreased resistance, and 17 (48.57%) displayed unstable resistance in different sowing dates. All combinations of the genotype, environment and ploidy, including the genotype-environment-ploidy interaction, contributed significantly to field resistance. Chromosome doubling increased sheath blight resistance in most genotypes, but was also dependent on the genotype-environment interaction. To elucidate the enhanced resistance mechanism, RNA-seq revealed autotetraploid recruited more down-regulated differentially expressed genes (DEGs), additionally, more resistance-related DEGs, were down-regulated at 24 h post inoculation in autotetraploid versus diploid. The ubiquinone/terpenoid quinone and diterpenoid biosynthesis pathways may play key roles in ploidy-specific resistance mechanisms. In summary, our findings shed light on the understanding of sheath blight resistance mechanisms in autotetraploid rice.

Effect of silicon spraying on rice photosynthesis and antioxidant defense system on cadmium accumulation.

Cadmium (Cd) pollution is a serious threat to food safety and human health. Minimizing Cd uptake and enhancing Cd tolerance in plants are vital to improve crop yield and reduce hazardous effects to humans. In this study, we designed three Cd concentration stress treatments (Cd1: 0.20 mg·kg-1, Cd2: 0.60 mg·kg-1, and Cd3: 1.60 mg·kg-1) and two foliar silicon (Si) treatments (CK: no spraying of any material, and Si: foliar Si spraying) to conduct pot experiments on soil Cd stress. The results showed that spraying Si on the leaves reduced the Cd content in brown rice by 4.79-42.14%. Si application increased net photosynthetic rate (Pn) by 1.77-4.08%, stomatal conductance (Gs) by 5.27-23.43%, transpiration rate (Tr) by 2.99-20.50% and intercellular carbon dioxide (CO2) concentration (Ci) by 6.55-8.84%. Foliar spraying of Si significantly increased the activities of superoxide dismutase (SOD) and peroxidase (POD) in rice leaves by 9.84-14.09% and 4.69-53.09%, respectively, and reduced the content of malondialdehyde (MDA) by 7.83-48.72%. In summary, foliar Si spraying protects the photosynthesis and antioxidant system of rice canopy leaves, and is an effective method to reduce the Cd content in brown rice.

Genome editing in plants using the TnpB transposase system.

The widely used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas) system is thought to have evolved from IS200/IS605 transposons. TnpB proteins, encoded by one type of IS200/IS605 transposon, are considered to be the evolutionary ancestors of Cas12 nucleases, which have been engineered to function as RNA-guided DNA endonucleases for genome editing in bacteria and human cells. TnpB nucleases, which are smaller than Cas nucleases, have been engineered for use in genome editing in animal systems, but the feasibility of this approach in plants remained unknown. Here, we obtained stably transformed genome-edited mutants in rice (Oryza sativa) by adapting three recently identified TnpB genome editing vectors, encoding distinct TnpB nucleases (ISAam1, ISDra2, and ISYmu1), for use in plants, demonstrating that the hypercompact TnpB proteins can effectively edit plant genomes. ISDra2 and ISYmu1 precisely edited their target sequences, with no off-target mutations detected, showing that TnpB transposon nucleases are suitable for development into a new genome editing tool for plants. Future modifications improving the genome-editing efficiency of the TnpB system will facilitate plant functional studies and breeding programs. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-024-00172-6.

Efficient genome editing in rice with miniature Cas12f variants.

Genome editing, particularly using the CRISPR/Cas system, has revolutionized biological research and crop improvement. Despite the widespread use of CRISPR/Cas9, it faces limitations such as PAM sequence requirements and challenges in delivering its large protein into plant cells. The hypercompact Cas12f, derived from Acidibacillus sulfuroxidans (AsCas12f), stands out due to its small size of only 422 amino acids and its preference for a T-rich motif, presenting advantageous features over SpCas9. However, its editing efficiency is extremely low in plants. Recent studies have generated two AsCas12f variants, AsCas12f-YHAM and AsCas12f-HKRA, demonstrating higher editing efficiencies in mammalian cells, yet their performance in plants remains unexplored. In this study, through a systematic investigation of genome cleavage activity in rice, we unveiled a substantial enhancement in editing efficiency for both AsCas12f variants, particularly for AsCas12f-HKRA, which achieved an editing efficiency of up to 53%. Furthermore, our analysis revealed that AsCas12f predominantly induces deletion in the target DNA, displaying a unique deletion pattern primarily concentrated at positions 12, 13, 23, and 24, resulting in deletion size mainly of 10 and 11 bp, suggesting significant potential for targeted DNA deletion using AsCas12f. These findings expand the toolbox for efficient genome editing in plants, offering promising prospects for precise genetic modifications in agriculture. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-024-00168-2.