Rice最新文献

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.

The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated protein (Cas)9 genome-editing technology has become a cornerstone for generating knockout mutations in plant functional genomics. To obtain genetically stable CRISPR-edited plants, the removal of exogenous CRISPR constructs through genetic segregation is imperative. However, current transgene-free strategies lack universality and operational simplicity. Here, we developed a modular CRISPR toolkit integrated with the widely applicable visual RUBY marker. This system achieved 100% editing efficiency in three independent CRISPR-Cas9 editing events in rice (cv. Zhonghua 11), enabled rapid visual identification of transgene-free progeny, and may provide a framework for future adaptation of CRISPR vectors to other plant species. Our design significantly accelerates the identification of edited lines while bypassing laborious molecular validation steps.

The plant cell wall serves as the primary structural barrier against herbivorous insect damage. Calcium ions (Ca²⁺) play a crucial role as a second messenger in plants. Exogenous calcium application has been demonstrated to enhance plant resistance to both biotic and abiotic stresses, thereby promoting sustainable crop production. This study investigates the mechanisms by which exogenous calcium induces resistance in rice. Our results show that calcium chloride (CaCl₂) promotes the biosynthesis of cellulose, pectin, and callose within the rice cell wall. It also up-regulates the expression of genes associated with cell wall component synthesis (OsCESA8, OsPME15, and OsGRP0.9) and callose synthesis (OsGSL1, OsGSL10, and OsGSL12). These biochemical modifications strengthen the cell wall structure, resulting in reduced nutrient availability for the female brown planthopper (BPH), Nilaparvata lugens. Consequently, the growth and development of BPH are hindered, ovarian development is delayed, and the expression levels of NlVg and NlVgR genes are reduced. These physiological alterations lead to a shortened oviposition period, reduced longevity, and decreased fecundity in female BPH. Our findings indicate that CaCl₂ strengthens the cell wall structure and promotes callose deposition as a critical defense mechanism in rice. This research provides a foundation for further exploration of the molecular mechanisms and cellular processes underlying exogenous calcium-induced resistance in rice and offers a promising strategy for environmentally friendly BPH management.

Rising food demand has led to heavy use of chemical fertilizers, which are costly and pose serious threats to soil health and the environment. This two-year field study evaluated whether integrating beneficial bacteria with reduced nitrogen (N) fertilizer could improve soil health, wheat productivity, and N use efficiency (NUE), thereby reducing dependence on chemical N inputs. Nine treatments were tested, including combinations of no N (CK), 50% (N50) and 100% (N100) recommended N rates, with or without soil application and seed inoculation using beneficial bacteria (SAB and SIB). Results demonstrated that seed inoculation with beneficial bacteria (particularly N50 + SIB and N100 + SIB) significantly enhanced soil ammonium and nitrate contents, microbial biomass carbon (MBC), dissolved organic carbon (DOC), and soil enzyme activities at critical growth stages compared to uninoculated controls. These improvements in soil health translated into better plant physiological functioning, evidenced by increased chlorophyll content, higher antioxidant enzyme activities (CAT, POD, SOD, GSH), and reduced membrane injury. Consequently, beneficial bacteria inoculated treatments improved N accumulation and translocation efficiencies, with N100 + SIB showing the highest N accumulation at maturity and its contribution to grain. Grain N content and 1000-grain weight were substantially improved with bacterial treatments, with N100 + SIB achieving a 15-20% increase in protein content and the highest grain yield (5705-5760 kg/ha). Notably, N50 + SIB achieved comparable grain yield and quality improvements as N100 alone, highlighting a promising reduction in chemical N dependency. Moreover, bacterial treatments enhanced PFPN, NUPE, and NIE by 16-34% over conventional N treatments, and the N harvest index (NHI) exceeded 67% in N100 + SIB, indicating efficient N partitioning into grain. In summary, seed inoculation with beneficial bacteria significantly improved soil health, plant growth, and N utilization, allowing for reduced application of synthetic N fertilizers without compromising wheat yield or grain quality. This suggests a sustainable and eco-friendly strategy for enhancing N use efficiency in wheat production.

The 14-3-3 proteins are highly conserved and widely distributed across eukaryotes. Some 14-3-3 proteins have been identified as regulators of phosphorus (Pi) deficiency tolerance in rice, but their diverse functions remain largely unexplored. In this study, we characterized the role of rice plant-specific non-ε group 14-3-3 proteins (OsGF14a-f) in response to Pi starvation by mutating these genes. We found that the expression of OsGF14a decreased in response to Pi starvation, while the expression of other non-ε group genes was induced. Subcellular localization studies transiently expressing them in tobacco leaves showed that OsGF14a was present in both the cytoplasm and nucleus, whereas the other proteins were predominantly localized in the cytoplasm. By developing single and multiple mutants, we demonstrated that OsGF14a plays a negative role in Pi homeostasis and root growth, while OsGF14b, OsGF14c and OsGF14f may act as positive regulators of Pi homeostasis and root growth in rice. However, all non-ε group 14-3-3 genes positively regulated rhizosphere acidification. Furthermore, the mutation of OsGF14a enhanced Pi accumulation and plant growth under various Pi supply conditions, likely due to the induction of OsPHR3, OsPT2 and OsPHO1;2 in the roots. Overall, this study highlights the diverse functions of plant-specific non-ε group 14-3-3 proteins in response to Pi starvation in rice and identifies the mutation of OsGF14a as a potential strategy to improve rice tolerance to Pi deficiency.