Rice最新文献

Rice blast disease is one of the most destructive rice diseases worldwide. Rice MicroRNAs (miRNAs) play an essential role in immunity against blast fungus Magnaporthe oryzae. However, it remains unclear which miRNAs are involved in the three layers of rice-M. oryzae interaction, including pathogen associated molecular patterns (PAMPs)-triggered immunity (PTI), effector-triggered susceptibility (ETS), and effector-triggered immunity (ETI). In this study, we performed small RNA-sequencing to systemically identify miRNAs regulating PTI, ETS, and ETI in rice-M. oryzae interaction. A totally 441 miRNAs were identified, with 13, 30, and 14 miRNAs screened out and classified as regulators of PTI, ETS, and ETI, respectively. We investigated and confirmed the roles of 9 previously reported miRNAs and an uncharacterized miRNA, miR408-5p, in the three interaction processes. We demonstrated that miR1320-5p positively regulated PTI; miR396 family members and miR164a improved, whereas miR171b and miR172a suppressed ETS; miR166a enhanced, whereas miR169a and miR396 family members suppressed ETI. Moreover, we demonstrated that miR397b and miR408-5p enhanced rice susceptibility by promoting ETS and suppressing ETI; miR398b enhanced rice resistance by promoting both PTI and ETI while suppressing ETS. Our findings figured a miRNA-mediated regulatory network in which distinct miRNAs modulate PTI, ETS, and ETI against M. oryzae. This study provides new sight into the regulation mechanism of plant disease resistance.

Background: Fragrance is a premium trait of grain quality in the traditional, Jasmine-style rice (Oryza sativa L.) variety Phka Rumduol (PRD). Rice fragrance is a combination of various volatile compounds with characteristic odours and flavours that can be traced back to fatty acids. Given the complexity of fragrance phenotype, the use of a robust phenotyping platform in identifying metabolite quantitative trait loci (mQTL) is essential to providing the most suitable set of genetic markers associated with desirable fragrance metabolites and their fatty acid origins in PRD-derived rice breeding lines.

Results: Using combined untargeted metabolomics via GC×GC-TOF-MS, targeted fatty acid analysis with GC-MS, mQTL for individual volatile compounds and fatty acids were identified in a SNP-genotyped F₆ recombinant-inbred rice population developed from a cross between PRD and Thmar Krem (TMK; non-fragrant). This study confirmed the genetic link between 2-acetyl-1-pyrroline and its derivatives with SNPs on chromosomes 8, 3, 4, and 1 and revealed novel mQTLs on chromosomes 2 and 6. MQTLs identified for saturated aldehydes, alcohols, ketones and alkylfurans co-localised on chromosomes 1, 3, and 6 were mainly contributed by PRD, whereas sulfur-containing compounds were contributed by TMK and associated with mQTLs on chromosomes 5 and 6. Oleic and linoleic acid composition were associated with a common QTL on chromosome 7.

Conclusion: Our results demonstrate the ability of untargeted metabolomics to reveal the uniqueness of the fragrance profile of individual rice breeding lines in a mapping population which would allow for improved precision in marker-assisted selection. The various mQTLs verified in this study reaffirm the need for more in-depth metabolite-based selection incorporated in rice breeding. The information from this research is valuable for rice breeding and food quality improvement programs.

The limited availability of ideal cadmium (Cd) hyperaccumulating plants remains a significant challenge for phytoremediating Cd-contaminated soils. This study aims to find out if the high biomass giant rice can be a suitable phytoremediation candidate for Cd-contaminated paddy fields and to elucidate physiological mechanisms relative to low or high Cd accumulation. Soil column and lysimeter tests were conducted with giant and normal species of rice under different water conditions. Cd distribution in different parts of root and shoots were determined. Under sustained flooding in column tests or keeping soil moist after the tillering stage in lysimeter tests, Cd contents in the grain of giant rice were very low. The Cd bioconcentration factor (BCF) of grain of giant rice (0.015-0.034) were significantly lower than those of normal rice (0.088-0.099), while BCF of root was in the reversed trend. Of the Cd in giant rice roots, 23.5% was trapped by the iron plaque on the root surface, compared 11.7% for normal rice. More Fe-O, -COOH functional groups in giant rice roots were confirmed by FTIR spectra. Under semi-dry condition, Cd contents in giant rice were very significantly increased, BCF straw in regenerated giant rice reached 13.4. Cd in shoots were accumulated in basal stems of the giant rice, the phytoextraction rate reached 18.7% of total Cd in topsoil, compared to 9.6% for giant Napier grass (Pennisetum hybridum). Therefore, the giant rice is a unique crop who can highly produce safe rice under wet conditions in the first half year and meanwhile by regenerating it can efficiently phytoextract Cd in the soil under semi-dry condition with a low labor input and carbon emission.

Rice (Oryza sativa L.) is a staple crop for over half of the global population, yet its cultivation faces significant threats from biotic stresses, particularly root-knot nematodes (Meloidogyne spp.). Among these, M. graminicola poses a major challenge in rice-growing regions, leading to substantial yield losses. This study evaluated the resistance of 348 rice varieties to M. graminicola through controlled pot and field experiments over two years (2023 and 2024). Varieties were classified based on gall index, revealing a spectrum of susceptibility from highly susceptible to highly resistant. Notably, varieties such as JR-1124 and JR-403 exhibited high gall index, while others like RP-5219-9-7-3-2-1-1, NPT-10, MTU 1390 (IR17M1172), Kushiari, RP 6750-RMS-2-23-67-91, Sonkharchi, Sugandha-3, HRT-183, and HR-12 demonstrated significant resistance. Resistant rice genotypes exhibited significantly higher PAL, POX, and total phenolic content at all intervals, indicating a strong biochemical defense response against Meloidogyne graminicola. Advanced techniques, including confocal microscopy, revealed distinct histopathological responses to M. graminicola infection, with susceptible rice varieties exhibiting extensive giant cell formation and root tissue degradation, while a resistant variety displayed restricted giant cell development, enhanced callose deposition, and maintained vascular integrity-highlighting robust defense mechanisms against nematode invasion. The findings underscore the potential for breeding programs to enhance resistance traits in rice, contributing to sustainable agricultural practices and improved food security. As nematode populations evolve, ongoing research is essential to adapt breeding strategies and maintain effective management of this significant pest in rice production systems.

Rice is an important human staple food providing calories and useful elements, even though vulnerable to heavy metal contamination. Breeding tools for improving the concentration of nutrient and reduce levels of toxic compounds can improve the nutritional value and safety of rice grains. This work presents a comprehensive analysis of the genetic bases controlling variation in the rice ionome employing genome-wide association studies (GWAS) with a diversity panel of 294 temperate and tropical japonica accessions, each genotyped with 36,830 SNP loci. GWAS was performed for brown rice content of 13 elements: As, Ca, Cd, Cu, Fe, K, Mg, Mn, Mo, Na, Ni, P, Zn for rice plants grown under two diverse water management regimes, permanent flooding and limited watering. GWAS identified 232 significant marker-traits associations (MTAs); 87 of which had high R² and low p-values and were selected for further analysis. Among them, 32 MTAs were consistently identified under both environments. These can represent valuable candidates for marker-assisted selection to improve the composition of essential mineral nutrients and reduce the concentration of toxic elements in the rice grain. Furthermore, co-localization regions for 60 MTAs were highlighted for two or more traits. Potential candidate genes were identified for 14 MTAs with -log₁₀(p) value < 5 and R² > 6; among them, gene functions that were related to transport/uptake, accumulation, detoxification, metal binding and root architecture, coherent with the traits of interest, were highlighted. The study provides relevant insights into the genetic basis of ionomic variations in rice and may serve as an important foundation for improvement in breeding, as well as for further studies on the genetic bases and molecular mechanisms controlling the rice grain ionome.

Herbicides are pivotal for modern agriculture, but challenges like weed resistance and crop rotation issues necessitate the development of herbicide-resistant genetic resources. This study focused on acetolactate synthase (ALS), a key enzyme targeted by numerous herbicides. Using CRISPR/Cas9-mediated non-homologous end joining (NHEJ) and combining with whole-stage selection, we induced mutations in the OsALS gene of indica rice and identified novel in-frame mutations at the P171 and S627 sites, respectively. Among them, one mutation at the P171 site, the triple mutation P171T/R172G/M174L (ALS-TM) conferred broad-spectrum resistance to Imidazolinones Pyrimidinylthiobenzoates Sulfonylaminocarbonyltriazolinones and Sulfonylureas herbicides. Compared to wild-type (WT) rice, ALS-TM showed 1153-fold higher resistance to imazethapyr (IMT) than WT based on GR₅₀ values (The herbicide dose causing a 50% reduction in growth), with minimal growth inhibition at 10-fold IMT treatment. Enzymatic assays revealed that ALS-TM maintained catalytic efficiency while reducing herbicide binding, which validated the resistance at the protein level. Field trials showed that ALS-TM mutant retained normal agronomic traits even after IMT spraying, indicating no yield penalty. Additionally, ALS mutations were validated as effective transgenic selection markers, enabling efficient rice transformation under different selection systems. These results demonstrated that ALS-TM could also serve as a reliable tool in basic research, facilitating the selection and identification of transgenic materials in laboratory studies. This study provided a robust method for generating herbicide-resistant rice germplasm and highlighted the potential of CRISPR-mediated NHEJ for creating novel resistant mutations.

miR168a, a plant-specific microRNA (miRNA) derived from the MIR168a gene, plays a pivotal role in modulating rice blast disease resistance and critical agronomic traits such as flowering time and yield. However, the regulatory mechanisms governing the MIR168a promoter remain poorly understood. This study identified a 1661 bp upstream fragment of the mature miR168a as highly active in promoter function. Sequence alignments revealed substantial variation in MIR168 promoters across plant species. Analysis of over 4000 rice accessions showed that while the MIR168a promoter exhibited abundant SNPs and InDels, miR168a itself had no such polymorphisms. Based on promoter polymorphisms, the MIR168a promoter was classified into three haplotypes, with Hap2 and Hap3 showing higher activity than Hap1. Through DNA fragment swapping and site-directed mutagenesis, the T site in Hap2 and the A site in Hap3 were identified as critical determinants of promoter activity. Rice accessions containing these sites exhibited significantly higher miR168a abundance compared to Hap1 accessions. Population genetic and evolutionary analyses revealed that highly active MIR168a promoters in Hap2 and Hap3 predominantly occur in indica accessions and trace their origins to wild rice. Furthermore, the nucleotide diversity of the MIR168a promoter in cultivated rice was markedly lower than in wild rice, likely reflecting artificial selection during domestication and artificial selection. Breeders may have favored rice lines harboring MIR168a promoter variants with reduced activity, such as Hap1 accessions, underscoring its potential for breeding programs. Additionally, miR168a expression was induced in all three haplotypes following infection with Magnaporthe oryzae. These findings illuminate the natural variation in MIR168a promoter sequences and their influence on miR168a expression activity, offering new insights for rice improvement strategies.

Gibberellins (GAs) are crucial in the regulation of plant growth and development, and in responses to adverse environments. Here, we report that a Cys2 /His2 zinc finger protein in rice, HSTL (heat stress tolerance like), participates in the control of stem elongation and salt stress response by affecting GA homeostasis. Knockdown of HSTL increased plant height, internode elongation and bioactive GAs levels in rice plants. Comparative transcriptome showed that HSTL plays a critical role in rice GA pathway through regulation of genes involved in GA biosynthesis and metabolism. In addition, HSTL knockdown seedlings maintained higher relative water content and lower accumulation of H₂O₂ as well as higher tolerance to salt stress compared with the wild-type (WT). These results suggest that HSTL plays an important role in regulating internode elongation and stress response by coordinating GAs homeostasis, thus providing a useful target for engineering stress-tolerant rice varieties.

Powdery mildew (PM) is one of the most devastating and widespread foliar diseases globally. Despite the critical need for developing a durable PM resistance, the number of cloned genes remains limited, along with a shortage of Mildew Locus O (MLO) resistance-conferring genes in wheat breeding programs. Here, utilizing the latest wheat reference genome data, we comprehensively identified and characterized 47 MLO genes through a genome-wide search approach. These genes are randomly distributed among 21 wheat chromosomes, harbor seven transmembrane domains, and are predicted to be primarily localized in the plasma membrane. Comparative phylogenetic analysis with model plants classified wheat MLOs into four clades (I-IV) harboring 6, 28, 6, and 7 genes, respectively. The phylogenetic grouping was strongly supported by gene structures and motif distribution among members of different clades. Evolution analysis revealed that the MLO gene arsenal expanded through segmental duplications, and purifying selection is potentially conserving their stress-associated functions. In-silico expression analysis highlighted at least 10 genes with overlapping expression patterns among different growth and development stages and under abiotic and biotic stress conditions. The quantitative real-time polymerase chain reaction (qRT-PCR) validated the differential expression patterns of these 10 overlapping genes in PM-resistant and susceptible wheat genotypes after challenging these with a PM pathogen strain at different time intervals. The identified wheat MLO genes, especially the 10 overlapping genes, highlight untapped genetic diversity for engineering a durable and broad-spectrum tolerance/resistance against abiotic and biotic stresses, especially the PM resistance. Collectively, this study provides a compendium of wheat MLO genes, which could be functionally characterized to confirm their roles in PM resistance and further exploited in wheat breeding programs for the development of climate-resilient cultivars for sustainable wheat production.