Whole-grain rice has gained significant attention for its potential health benefits, particularly because of its antioxidant and antibacterial properties. Despite this growing interest, there remains a pressing need for a comprehensive evaluation of the methods used to analyze these bioactive compounds, considering the diversity of rice types and the influence of environmental factors. This review aims to provide an in-depth overview of recent analytical methods, particularly those employed over the last five years, to assess the antioxidant and antibacterial properties of rice. It focuses on commonly used antioxidant assays, such as the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity assay, which encompasses both single electron transfer and hydrogen atom transfer mechanisms. Other antioxidant assays are also discussed, alongside methods used to evaluate antibacterial properties, including disc diffusion, well diffusion, broth or agar dilution, and advanced techniques such as flow cytofluorometric and bioluminescent assays. The review further explores the bacterial strains most frequently studied, including Bacillus cereus, Listeria monocytogenes, Escherichia coli, and Salmonella species. It highlights the key techniques and parameters employed to ascertain and quantify the antioxidant and antibacterial potential of rice, while critically analysing the strengths and limitations of these approaches. By synthesizing current methods and offering insights into their application, this review can be served as a guide for future research aimed at standardizing and improving the assessment of rice’s bioactive properties, paving the way for broader scientific and practical applications.

The leucine-rich repeat (LRR) protein family is involved in a variety of fundamental metabolic and signaling processes in plants, including growth and defense responses. LRR proteins can be divided into two categories: those containing LRR domains along with other structural elements, which are further subdivided into five groups, LRR receptor-like kinases, LRR receptor-like proteins, nucleotide-binding site LRR proteins, LRR-extensin proteins, and polygalacturonase-inhibiting proteins, and those containing only LRR domains. Functionally, various LRR proteins are primarily involved in plant development and responses to environmental stress. Notably, the LRR protein family plays a central role in signal transduction pathways related to stress adaptation. In this review, we classify and analyze the functions of LRR proteins in plants. While extensive research has been conducted on the roles of LRR proteins in disease resistance signaling, these proteins also play important roles in abiotic stress responses. This review highlights recent advances in understanding how LRR proteins mediate responses to biotic and abiotic stresses. Building upon these insights, further exploration of the roles of LRR proteins in abiotic stress resistance may aid efforts to develop rice varieties with enhanced stress and disease tolerance.

In rice fields, rice plants usually grow alongside wild weeds and are attacked by various invertebrate species. Viruses are abundant in plants and invertebrates, playing crucial ecological roles in controlling microbial abundance and maintaining community structures. To date, only 16 rice viruses have been documented in rice-growing regions. These viruses pose serious threats to rice production and have traditionally been identified only from rice plants and insect vectors by isolation techniques. Advances in next-generation sequencing (NGS) have made it feasible to discover viruses on a global scale. Recently, numerous viruses have been identified in plants and invertebrates using NGS technologies. In this review, we discuss viral studies in rice plants, invertebrate species, and weeds in rice fields. Many novel viruses have been discovered in rice ecosystems through NGS technologies, with some also detected using metatranscriptomic and small RNA sequencing. These analyses greatly expand our understanding of viruses in rice fields and provide valuable insights for developing efficient strategies to manage insect pests and virus-mediated rice diseases.

The tolerance of rice to drought and saline stress is crucial for maintaining yields and promoting widespread cultivation. From an ethyl methanesulfonate (EMS)-mutagenized mutant library, we identified a mutant that is susceptible to osmotic stress, named Osmotic Stress Sensitivity 1 (Oss1). Using MutMap sequencing, we characterized the role of a choline transporter-related family gene, CTR4 (Choline Transporter-Related 4), in rice’s tolerance to drought and salt stress. CTR4 plays a critical role in regulating membrane lipid synthesis. In knockout mutants, the total membrane lipid content, especially unsaturated fatty acids, was significantly reduced. Compared with the wild type, knockout mutants exhibited decreased membrane lipid stability under drought and salt stress, faster water loss, higher relative electrolyte leakage, and lower levels of proline and soluble sugars, leading to impaired tolerance to drought and salt stress. In contrast, the overexpression of CTR4 enhanced seedling tolerance to drought and saline stress. The overexpression lines displayed lower malondialdehyde levels, reduced relative electrolyte leakage, and slower rates of leaf water loss under stress conditions, thereby improving seedling survival rates during stress. Moreover, lipid synthesis gene expression was down-regulated in CTR4 mutants, potentially exacerbating membrane permeability defects and further compromising stress resistance. These findings suggest that CTR4 mediates choline transport and influences cell membrane formation, thereby enhancing rice defenses against drought and salt stress by maintaining lipid homeostasis.

Extremely high temperatures resulting from climate change have become a major challenge for increasing rice production. Therefore, our objective was to develop heat-tolerant aromatic rice varieties using the pedigree method, focusing on selecting for seed-setting ability under extremely high temperatures along with the use of single nucleotide polymorphism/insertion and deletion (SNP/InDel) markers to improve aromatic properties and grain quality. Furthermore, the QTL-seq approach was utilized to identify QTLs for seed-setting rate in an F₂ population subjected to heat stress. The candidate QTL regions were then aligned to confirm SNPs/InDels in synonymous F₇ candidate heat-tolerant lines. The results revealed that four promising lines, namely 84-7-1-9, 84-7-1-10, 159-3-3-1, and 159-3-3-10, were classified as heat-tolerant with low amylose content. In addition, lines 84-7-1-9 and 84-7-1-10 were identified as aromatic rice encompassing the aroma gene (badh2). Regarding the QTL-seq results, the qSF2.1 region ranged from 311 051 to 3 929 422 bp on chromosome 2, was identified based on the highest contrasting SNP index between the heat-susceptible and tolerant bulks. The candidate genes within this region include two genes related to heat shock proteins, three genes associated with pollen fertility, and four genes involved in heat stress and other abiotic stress responses. These genes are proposed as potential candidates for heat tolerance and could serve as targets in rice breeding programs aimed at enhancing heat tolerance.

Honglian type-cytoplasmic male sterility (HL-CMS) is caused by the inter-communication between the nucleus and mitochondria. However, the mechanisms by which sterility genes regulate metabolic alterations and changes in mitochondrial morphology in the pollen of HL-CMS remain unclear. In this study, we compared the morphological differences between the pollen of the male sterile line YA and the near-isogenic line NIL-Rf6 using hematoxylin-eosin staining and 4ʹ,6-diamidino-2-phenylindole (DAPI) staining. HL-CMS is characterized by gametophytic sterility, where the aborted pollen grains are empty, and the tapetal layer remains intact. Transmission electron microscopy was employed to observe mitochondrial morphological changes at the microspore stage, revealing significant mitochondrial alterations, characterized by the formation of 'large spherical mitochondria', occurred at the binucleate stage in the YA line. Additionally, metabolomics analysis revealed decreased levels of metabolites associated with the carbohydrate and flavonoid pathways. Notably, the decrease in flavonoids was found to contribute to an elevation in reactive oxygen species (ROS) levels. Therefore, we propose a model in which rice fertility is modulated by the levels of pollen carbohydrates and flavonoid metabolites, with impaired mitochondrial energy production and reduced flavonoid biosynthesis as the main causes of ROS accumulation and pollen abortion in rice.

The exopolysaccharide matrix of diazotrophic cyanobacteria was used to integrate phosphorus (P) and potassium (K) solubilizing bacteria, enhancing the survival of plant growth-promoting rhizobacteria, and ultimately the survival of bacteria in the rhizosphere for better plant growth. A new biofilm-based formulation comprising the diazotrophic cyanobacteria Anabaena AMP2, P-solubilizing Bacillus megaterium var. phosphaticum PB1, and K-solubilizing Rhizobium pusense KRBKKM1 was tested for efficacy in rice. The growth medium with half-strength BG-11 medium supplemented with 3% glucose showed best for biofilm formation under in vitro conditions. Analysis of the methanolic extract of the cyanobacterial- bacterial biofilm (CBB) showed the activity of antioxidants, such as 2-methoxy phenol and pentadecane, which are proven to improve plant-microbe interactions and plant growth, respectively. Treatment of rice seeds with CBB extract at 100 mL/kg or 200 mL/kg showed significant enhancement in germination rate and seedling length. Therefore, a pot culture experiment with the CBB formulations was carried out, and different growth and yield parameters were recorded. Principal component analysis showed that plant growth, yield, soil dehydrogenase activity, and soil chlorophyll content were positively correlated with rice plants amended with vermiculite-based CBB at 2 kg/hm² followed by a spray with aqueous CBB formulation at 5 mL/L at 15 and 30 d after rice transplanting grown with a 25% reduced level of nitrogen/phosphorus/potassium chemical fertilizers than the recommended dose. Further, Pearson correlation analysis showed that yield was positively correlated with soil dehydrogenase (r = 0.92**) and soil chlorophyll content (r = 0.96**). We concluded that CBB could be used as a novel biofilm-based bio-inoculant to increase rice productivity and crop fitness as a component in integrated nutrient management and sustainable organic farming strategies with reduced chemical fertilizers.

The application of fungicides is an effective strategy for controlling plant diseases. Among these agents, plant-derived antifungal metabolites are particularly promising due to their eco-friendly and sustainable nature. Plant secondary metabolites typically exhibit broad-spectrum antifungal activity without selective toxicity against pathogens. However, only a small fraction of antifungal metabolites have been identified from the tens of thousands of known plant secondary metabolites. In this study, we conducted a metabolomic analysis on both blast-resistant (Digu) and -susceptible (Lijiangxintuanheigu) rice varieties to uncover novel metabolites that enhance blast resistance. We found that 24 and 48 h post-inoculation with Magnaporthe oryzae were critical time points for metabolomic profiling, based on the infected status of M. oryzae in rice and the observed differences in shikimate accumulation between the two varieties. Following metabolomic analysis, we identified nine flavonoids that were differentially accumulated and are considered potential candidates for disease control. Among these, apigenin-7-glucoside, rhamnetin, and spireoside were found to be effective in controlling blast disease, with spireoside demonstrating the most pronounced efficacy. We discovered that spireoside controlled blast disease by inhibiting both spore germination and appressorium formation in M. oryzae, primarily through disrupting cell membrane integrity. However, spireoside did not induce rice immunity. Furthermore, spireoside was also effective in controlling sheath blight disease. Thus, spireoside shows considerable promise as a candidate for the development of a fungicide for controlling plant diseases.

Rice seedling blight, caused by various fungi, including Fusarium oxysporum, poses a severe threat to rice production. As awareness grows regarding the environmental and safety hazards associated with the application of fungicides for managing rice seedling blight, there has been a shift in focus towards biological control agents. In this study, we isolated biocontrol bacteria from paddy fields that significantly inhibited the growth of F. oxysporum in vitro and identified the strains as Bacillus amyloliquefaciens T40 and Bacillus pumilus T208. Additionally, our findings indicated that the combined application of these Bacillus strains in soil was more effective in reducing the incidence of rice seedling blight than their individual use. Analysis of 16S and internal transcribed spacer rRNA gene sequencing data revealed that the mixture of the T40 and T208 strains exhibited the lowest average clustering coefficients, which were negatively correlated with the biomass of F. oxysporum-inoculated rice seedlings. Furthermore, this mixture led to higher stochastic assembly (average |βNTI| < 2) and reduced selection pressures on rice rhizosphere bacteria compared with individual strain applications. The mixture of the T40 and T208 strains also significantly increased the expression of defense-related genes. In conclusion, the mixture of the T40 and T208 strains effectively modulates microbial community structures, enhances microbial network stability, and boosts the resistance against rice seedling blight. Our study supports the development and utilization of biological resources for crop protection.