Grain size is an important yield trait in cereal crops and understanding the mechanisms that control grain size is essential for precise breeding and improving cereal crop yields. Epigenetics plays a crucial role in plant growth and development, but how it is involved in grain size regulation remains largely unclear. Here we report that the histone-binding protein LARGE3 associates with the histone deacetylase OsHDT1 (HD-tuins 1) to control grain length by influencing histone H4 acetylation in rice (Oryza sativa). The large3 mutants form large and heavy grains because of increased cell proliferation. LARGE3 physically interacts with OsHDT1 to negatively regulate grain length. LARGE3 and OsHDT1 repress the expression of an important grain size gene, OsMKKK10, by decreasing its histone H4 acetylation level and increasing its nucleosome density. Importantly, genome editing of LARGE3 homolog in foxtail millet (Setaria italica) causes large grains and increased grain yield. These findings reveal a molecular mechanism for LARGE3-OsHDT1-mediated epigenetic modulation of grain length by regulating histone H4 acetylation of OsMKKK10, suggesting that this module has potential applications in improving grain size and yield in key cereal crops.

The rice coleoptile, a key protective structure during seed development, is crucial for safeguarding the plumule and facilitating seed germination. It plays a pivotal role in seedling emergence from soil, with its elongation characteristics being particularly important in direct-seeding systems. Coleoptile elongation is a complex biological process coordinately regulated by environmental factors, genetic background, plant hormones, and other signaling molecules, all of which interact to modulate elongation dynamics. This review systematically summarizes the mechanisms underlying coleoptile elongation, explores the regulatory roles of environmental and physiological factors, and synthesizes recent research progress on the identification of coleoptile-related QTLs, gene mining, and molecular regulatory mechanisms. Furthermore, we discuss the potential applications of coleoptile research in rice genetic improvement, aiming to provide a theoretical basis and novel insights for leveraging coleoptile traits in future breeding strategies.

Rice (Oryza sativa L.) grain quality is a critical determinant of market value, consumer acceptance, and nutritional security. This multifaceted trait is governed by the dynamic interaction of genotype (G), environment (E), and management practices (M). In this review, we synthesize recent advances in understanding these multifaceted determinants. We first delineate the genetic architecture, emphasizing key genes and quantitative trait loci (QTLs) such as Wx, ALK, Chalk5, and the GS3/GW families, which control starch composition, gelatinization temperature, chalkiness, and grain dimensions, forming the foundational blueprint for quality potential. We examine how this genetic potential is influenced by environmental factors, focusing on the detrimental impacts of abiotic stresses, particularly high temperatures during grain filling and drought, which impair milling yield, increase chalkiness, and modify starch and protein profiles. Furthermore, we discuss how optimized agronomic strategies—including precision water management (e.g., alternate wetting and drying), balanced nitrogen fertilization, and targeted micronutrient (e.g., silicon) application—can mitigate these adverse effects and potentially improve specific quality parameters. Post-harvest handling is identified as the final determinant of product quality. We conclude that achieving high and stable rice quality under climate variability requires an integrated G × E × M approach. Prospects include next-generation breeding for climate-resilient quality, precision agronomy guided by real-time sensing, synergistic soil health management, and the integration of systems biology with digital agriculture to design sustainable, high-quality rice production systems.

Pre-harvest sprouting (PHS) is a major problem in cereal production, severely reducing yield and grain quality, particularly under high-temperature (HT) and excessive-rainfall conditions during grain filling. However, the molecular mechanisms by which HT triggers seed dormancy breakdown and promotes PHS remain largely unknown. In this study, we reveal that the rice transcription factor OsbZIP58, previously implicated in seed storage reserve accumulation, integrates HT-induced sugar depletion into precocious seed dormancy release. By combining DNA affinity purification sequencing, chromatin immunoprecipitation-qPCR, and genetic epistasis analyses, we show that OsbZIP58 directly activates the abscisic acid-responsive gene RAB16A while repressing the α-amylase gene OsAmy3D, thereby maintaining seed dormancy under normal conditions. Meanwhile, the energy-sensing sucrose non-fermenting-1-related protein kinase 1-family kinase OSK3, a direct upstream regulator, phosphorylates OsbZIP58 at Ser46 to promote its proteasomal degradation, consequently derepressing OsAmy3D expression. Mechanistically, HT accelerates grain filling and causes premature sugar depletion, which activates OSK3 to trigger OsbZIP58 degradation, thereby releasing OsAmy3D activity to increase starch hydrolysis and soluble sugar levels in seeds, ultimately leading to PHS. Elevated soluble sugar levels restrain OSK3 hyperactivation under HT through a negative-feedback mechanism. Furthermore, haplotype analysis reveals that natural variation in the OsbZIP58 locus is associated with variation in PHS susceptibility among rice accessions. Collectively, our work uncovers the OSK3-OsbZIP58-OsAmy3D module in regulating PHS in response to HT and establishes a previously unrecognized signaling cascade that integrates cellular energy status with developmental timing and thermal stress, providing genetic targets for breeding climate-resilient PHS-resistant cereals.

The rice coleoptile, a key protective structure during seed development, is crucial for safeguarding the plumule and facilitating seed germination. It plays a pivotal role in seedling emergence from soil, with its elongation characteristics being particularly important in direct-seeding systems. Coleoptile elongation is a complex biological process coordinately regulated by environmental factors, genetic background, plant hormones, and other signaling molecules, all of which interact to modulate elongation dynamics. This review systematically summarizes the mechanisms underlying coleoptile elongation, explores the regulatory roles of environmental and physiological factors, and synthesizes recent research progress on the identification of coleoptile-related QTLs, gene mining, and molecular regulatory mechanisms. Furthermore, we discuss the potential applications of coleoptile research in rice genetic improvement, aiming to provide a theoretical basis and novel insights for leveraging coleoptile traits in future breeding strategies.

Plants balance resource energy allocation between growth and immunity to ensure survival and reproduction under limited availability. This study reveals that rice cultivars with elevated sucrose levels boost resistance to the fungal pathogen Magnaporthe oryzae by accumulating the phytoalexin sakuranetin, regulated by the transcription factor STOREKEEPER (OsSTK). OsSTK binds to the promoter region of OsNOMT (Naringenin-7-O-Methyltransferase) to drive sakuranetin biosynthesis. Rice overexpressing OsSTK exhibits enhanced resistance to M. oryzae and improved growth, with greater plant height and higher grain yield, achieved through optimised resource allocation and carbon flow supporting both primary and secondary metabolite production. Moreover, the identification of OsSTK haplotypes linked to functional divergence in sakuranetin-mediated resistance, particularly in high-sucrose rice cultivars, underscores OsSTK's capacity to overcome the traditional growth-defence trade-off. This work highlights OsSTK as a valuable molecular target for breeding resilient, high-yielding rice varieties capable of withstanding environmental stresses. By advancing our understanding of resource allocation through carbon flow regulation, this study offers a sustainable strategy to improve food security and promote agricultural resilience in the face of climate change.

Defensin-like proteins are conserved in multicellular organisms and contribute to innate immune responses against fungal pathogens. In rice, defensins play a novel role in regulating cadmium (Cd) efflux from the cytosol. However, whether the antifungal activity of defensins correlates with Cd-efflux function remains unknown. In this study, we isolated an endophytic Fusarium, designed Fo10, by a comparative microbiome analysis of rice plants grown in a paddy contaminated with Cd. Fo10 is tolerant to high levels of Cd, but is sensitive to the defensin-like protein OsCAL1, which mediates Cd efflux to the apoplast. We found that Fo10 symbiosis in rice is regulated by OsCAL1 dynamics, and Fo10 coordinates multiple plant processes, including Cd uptake, vacuolar sequestration, efflux to the environment, and formation of Fe plaques in the rhizosphere. These processes are dependent on the salicylic acid signaling pathway to keep Cd levels low in the cytosol of rice cells and to decrease Cd levels in rice grains without any yield penalty. Fo10 also plays a role in Cd tolerance in the poaceous crop maize and wheat, but has no observed effects in the eudicot plants Arabidopsis and tomato. Taken together, these findings provide insights into the mechanistic basis underlying how a fungal endophyte and host plant interact to control Cd accumulation in host plants by adapting defense responses to promote the establishment of a symbiosis that permits adaptation to high-Cd environments.

Sakuranetin plays a key role as a phytoalexin in plant resistance to biotic and abiotic stresses, and possesses diverse health-promoting benefits. However, mature rice seeds do not contain detectable levels of sakuranetin. In the present study, a transgenic rice plant was developed in which the promoter of an endosperm-specific glutelin gene OsGluD-1 drives the expression of a specific enzyme naringenin 7-O-methyltransferase (NOMT) for sakuranetin biosynthesis. The presence of naringenin, which serves as the biosynthetic precursor of sakuranetin made this modification feasible in theory. Liquid chromatography tandem mass spectrometry (LC-MS/MS) validated that the seeds of transgenic rice accumulated remarkable sakuranetin at the mature stage, and higher at the filling stage. In addition, the panicle blast resistance of transgenic rice was significantly higher than that of the wild type. Specially, the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) imaging was performed to detect the content and spatial distribution of sakuranetin and other nutritional metabolites in transgenic rice seeds. Notably, this genetic modification also did not change the nutritional and quality indicators such as soluble sugars, total amino acids, total flavonoids, amylose, total protein, and free amino acid content in rice. Meanwhile, the phenotypes of the transgenic plant during the whole growth and developmental periods and agricultural traits such as grain width, grain length, and 1000-grain weight exhibited no significant differences from the wild type. Collectively, the study provides a conceptual advance on cultivating sakuranetin-rich biofortified rice by metabolic engineering. This new breeding idea may not only enhance the disease resistance of cereal crop seeds but also improve the nutritional value of grains for human health benefits.

When considering the contradictions between river management and protection in a typical plain river network, it is always confirmed that the river area has usually been encroached upon due to the development of human society. Based on the analysis of multiple attributes of the river network, a statistical model has been proposed in this study in order to determine the river network protection indices such as river area ratio, storage capacity and flux. In this study, a numerical method is proposed to improve the structure and connectivity of the river network by calculating the occupation and supplement balance. According to the principle of water area dynamic balance, the river network structure and its connectivity are improved through water area adjustment in a typical coastal city. As the simulation results show, the water surface ratio equals 8.17%, the storage capacity equals 112.6 million m3 and the water flux equals to 656.06 m3/s in the selected study area. The flood drainage capacity is introduced as the priority function, other functions are also improved due to river management and protection. The harmonious and sustainable coexistence between human society and the river network is then promoted. This comprehensive statistical model proved to be a good tool for the coastal area to enhance the comprehensive attributes of the coastal plain river network and the sustainable development of the local area in the future.

Sakuranetin, a flavonoid phytoalexin in rice, plays a crucial role in defense against pathogen infection. While MYB-type transcription factors are well-known to regulate plant growth, development, secondary metabolism, and adaptation to environmental stresses, the function of rice MYB-related transcription factors in sakuranetin biosynthesis and sakuranetin-mediated defense remains unclear. In this study, we identified and characterized OsMYB1R, a novel single repeat MYB transcription factor that acts as a transcriptional activator in sakuranetin biosynthesis. Protein-DNA binding and activation assays revealed that OsMYB1R directly regulates the gene promoter of OsNOMT, a key enzyme in sakuranetin synthesis. Molecular analyses and infection studies using OsMYB1R-overexpressing (OsMYB1R-OE) and OsMYB1R-knockout (Osmyb1r, generated using CRISPR/Cas9) plants demonstrated that OsMYB1R increases sakuranetin production and decreases Magnaporthe oryzae infection by transcriptionally regulating OsNOMT expression. This finding indicates a positive regulation of sakuranetin biosynthesis and antifungal resistance by the OsMYB1R-OsNOMT crosstalk. Interestingly, the alteration of OsMYB1R expression did not affect yield-related agronomic traits. Our results reveal a novel and positive role of 1R-MYB in secondary metabolite biosynthesis and pathogen defense, suggesting that OsMYB1R is a potential gene for effectively enhancing rice resistance without compromising yield.

Background The number of grains per panicle is an important factor in determining rice yield. The DST-OsCKX2 module has been demonstrated to regulate panicle development in rice by controlling cytokinin content. However, to date, how the function of DST-OsCKX2 module is regulated during panicle development remains obscure. Result In this study, the ABNORMAL PANICLE 1 ( ABP1 ), a severely allele of FRIZZY PANICLE ( FZP ), exhibits abnormal spikelets morphology. We show that FZP can repress the expression of DST via directly binding to its promotor. Consistently, the expression level of OsCKX2 increased and the cytokinin content decreased in the fzp mutant, suggesting that the FZP acts upstream of the DST-OsCKX2 to maintain cytokinin homeostasis in the inflorescence meristem. Conclusions Our results indicate that FZP plays an important role in regulating spikelet development and grain number through mediating cytokinin metabolism.

氮肥是影响水稻产量和品质的关键因素之一.本试验以浙江省 3 个具有代表性的籼粳杂交稻品种嘉丰优 2 号、甬优 7850、嘉优中科 13-1 为材料,研究 75、150、225 和 300 kg·hm-2 氮肥施用水平对其产量和品质的影响.结果表明,3 个品种在产量和品质上都存在显著差异,氮肥对株高、穗数、单株重、结实率和每穗粒数、胶稠度、垩白率等有极显著影响.不同品种对氮肥的响应存在差异,整体而言,各品种的单株穗数均随施氮量增加而上升,每穗粒数则相反.单株产量、结实率、千粒重随施氮量增加基本呈上升或先升后降的趋势.整精米率、直链淀粉含量对氮肥的响应因品种而异,胶稠度和垩白率基本随氮肥增加而下降,消减值随施氮量增加上升,峰值黏度随施氮量增加而下降,崩解值随施氮量增加先降再升.综合考虑产量和品质因素,认为嘉丰优 2 号和甬优 7850 的适宜氮肥水平是 150～225 kg·hm-2,嘉优中科 13-1 的适宜氮肥水平为 300 kg·hm-2,嘉丰优 2 号垩白率最低、甬优 7850 整精米率最高,较适合作商品米生产.

Grain cadmium (Cd) is translocated from source to sink tissues exclusively via phloem, though the phloem Cd unloading transporter has not been identified yet. Here, we isolated and functionally characterized a defensin-like gene DEFENSIN 8 (DEF8) highly expressed in rice (Oryza sativa) grains and induced by Cd exposure in seedling roots. Histochemical analysis and subcellular localization detected DEF8 expression preferentially in pericycle cells and phloem of seedling roots, as well as in phloem of grain vasculatures. Further analysis demonstrated that DEF8 is secreted into extracellular spaces possibly by vesicle trafficking. DEF8 bound to Cd in vitro, and Cd efflux from protoplasts as well as loading into xylem vessels decreased in the def8 mutant seedlings compared with the wild type. At maturity, significantly less Cd accumulation was observed in the mutant grains. These results suggest that DEF8 is a dual function protein that facilitates Cd loading into xylem and unloading from phloem, thus mediating Cd translocation from roots to shoots and further allocation to grains, representing a phloem Cd unloading regulator. Moreover, essential mineral nutrient accumulation as well as important agronomic traits were not affected in the def8 mutants, suggesting DEF8 is an ideal target for breeding low grain Cd rice.

Bacterial blight (BB) of rice caused by Xanthomonas oryzae pv. oryzae ( Xoo ) is one of the most serious bacterial diseases that hinder the normal growth and production of rice, which greatly reduces the quality and yield of rice. The effect of traditional methods such as chemical control is often not ideal. A series of production practices have shown that among the numerous methods for BB controlling, breeding and using resistant varieties are the most economical, effective, and environmentally friendly, and the important basis for BB resistance breeding is the exploration of resistance genes and their functional research. So far, 44 rice BB resistance genes have been identified and confirmed by international registration or reported in journals, of which 15 have been successfully cloned and characterized. In this paper, research progress in recent years is reviewed mainly on the identification, map-based cloning, molecular resistance mechanism, and application in rice breeding of these BB resistance genes, and the future influence and direction of the remained research for rice BB resistance breeding are also prospected.

Herbicides and heavy metals are hazardous substances of environmental pollution, resulting in plant stress and harming humans and animals. Identification of stress types can help trace stress sources, manage plant growth, and improve stress-resistant breeding. In this research, hyperspectral imaging (HSI) and chlorophyll fluorescence imaging (Chl-FI) were adopted to identify the rice plants under two types of herbicide stresses (butachlor (DCA) and quinclorac (ELK)) and two types of heavy metal stresses (cadmium (Cd) and copper (Cu)). Visible/near-infrared spectra of leaves (L-VIS/NIR) and stems (S-VIS/NIR) extracted from HSI and chlorophyll fluorescence kinetic curves of leaves (L-Chl-FKC) and stems (S-Chl-FKC) extracted from Chl-FI were fused to establish the models to detect the stress of the hazardous substances. Novel end-to-end deep fusion models were proposed for low-level, middle-level, and high-level information fusion to improve identification accuracy. Results showed that the high-level fusion-based convolutional neural network (CNN) models reached the highest detection accuracy (97.7%), outperforming the models using a single data source (<94.7%). Furthermore, the proposed end-to-end deep fusion models required a much simpler training procedure than the conventional two-stage deep learning fusion. This research provided an efficient alternative for plant stress phenotyping, including identifying plant stresses caused by hazardous substances of environmental pollution.

With the acceleration of industrialization and urbanization, the flood control ability and water environment of most Chinese coastal cities become worse than before, the current river network water system layout and river scale can no longer meet the regional flood discharge and drainage requirements. Yuhuan city is a typical coastal city located close to the east offshore area of China, which also suffered from the flood control and water environment problems. According to the planning reconstruction project of river network in Yuhuan city, the layout of river networks will transform. In this study, a river network model is introduced to simulate different conditions of the planning project. A comprehensive study of flood control and water environment method is utilized in order to ensure the regional water security and social development.

The successful implementation of heterosis in rice has significantly enhanced rice productivity, but the genetic basis of heterosis in rice remains unclear. To understand the genetic basis of heterosis in rice, main-effect and epistatic quantitative trait loci (QTLs) associated with heterosis for grain yield-related traits in the four related rice mapping populations derived from Xiushui09 (XS09) ( japonica ) and IR2061 ( indica ), were dissected using single nucleotide polymorphism bin maps and replicated phenotyping experiments under two locations. Most mid-parent heterosis of testcross F 1 s (TCF 1 s) of XS09 background introgression lines (XSILs) with Peiai64S were significantly higher than those of TCF 1 s of recombinant inbred lines (RILs) with PA64S at two locations, suggesting that the effects of heterosis was influenced by the proportion of introgression of IR2061’s genome into XS09 background. A total of 81 main-effect QTLs (M-QTLs) and 41 epistatic QTLs were identified for the phenotypic variations of four traits of RILs and XSILs, TCF 1 s and absolute mid-parent heterosis in two locations. Furthermore, overdominance and underdominance were detected to play predominant effects on most traits in this study, suggesting overdominance and underdominance as well as epistasis are the main genetic bases of heterosis in rice. Some M-QTLs exhibiting positive overdominance effects such as qPN1.2 , qPN1.5 and qPN4.3 for increased panicle number per plant, qGYP9 and qGYP12.1 for increased grain yield per plant, and qTGW3.4 and qTGW8.2 for enhanced 1000-grain weight would be highly valuable for breeding to enhance grain yield of hybrid rice by marker-assisted selection.

Phosphate (Pi) is essential to plant growth and crop yield. However, it remains unknown how Pi homeostasis is maintained during cereal grain filling. Here, we identified a rice grain-filling-controlling PHO1-type Pi transporter, OsPHO1;2, through map-based cloning. Pi efflux activity and its localization to the plasma membrane of seed tissues implicated a specific role for OsPHO1;2 in Pi reallocation during grain filling. Indeed, Pi over-accumulated in developing seeds of the Ospho1;2 mutant, which inhibited the activity of ADP-glucose pyrophosphorylase (AGPase), important for starch synthesis, and the grain-filling defect was alleviated by overexpression of AGPase in Ospho1;2 -mutant plants. A conserved function was recognized for the maize transporter ZmPHO1;2. Importantly, ectopic overexpression of OsPHO1;2 enhanced grain yield, especially under low-Pi conditions. Collectively, we discovered a mechanism underlying Pi transport, grain filling and P-use efficiency, providing an efficient strategy for improving grain yield with minimal P-fertilizer input in cereals.

The insertion position of the exogenous fragment sequence in a genetically modified organism (GMO) is important for the safety assessment and labeling of GMOs. SK12-5 is a newly developed transgenic maize line transformed with two trait genes [i.e., G10evo -5-enolpyrul-shikimate-3-phosphate synthase (EPSPS) and Cry1Ab/Cry2Aj ] that was recently approved for commercial use in China. In this study, we tried to determine the insertion position of the exogenous fragment for SK12-5. The transgene–host left border and right border integration junctions were obtained from SK12-5 genomic DNA by using the thermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) and next-generation Illumina sequencing technology. However, a Basic Local Alignment Search Tool (BLAST) analysis revealed that the flanking sequences in the maize genome are unspecific and that the insertion position is located in a repetitive sequence area in the maize genome. To locate the fine-scale insertion position in SK12-5, we combined the methods of genetic mapping and nanopore-based sequencing technology. From a classical bulked-segregant analysis (BSA), the insertion position in SK12-5 was mapped onto Bin9.03 of chromosome 9 between the simple sequence repeat (SSR) markers umc2337 and umc1743 (26,822,048–100,724,531 bp). The nanopore sequencing results uncovered 10 reads for which one end was mapped onto the vector and the other end was mapped onto the maize genome. These observations indicated that the exogenous T-DNA fragments were putatively integrated at the position from 82,329,568 to 82,379,296 bp of chromosome 9 in the transgenic maize SK12-5. This study is helpful for the safety assessment of the novel transgenic maize SK12-5 and shows that the combined method of genetic mapping and the nanopore-based sequencing technology will be a useful approach for identifying the insertion positions of transgenic sequences in other GM plants with relatively large and complex genomes.

The eutrophication of lake water bodies has been emphasized for decades in our country due to its severe environmental effects. Indeed, 85.4% of lakes have met the eutrophication standard, and 40.1% of the lakes have met the severe eutrophication standard in China nowadays. Taihu lake, as the most important freshwater lake in eastern China, has been embarrassed because of the serious cyanobacteria outbreak problem every year. In this study, a statistic analysis of cyanobacteria outbreak in the offshore area of Taihu lake is conducted. Both the satellite image and field monitoring data are cited and analyzed. As a result, it is confirmed that the cyanobacteria outbreak effects are serious in spring and summer due to the high temperature and the high ratio of TN/TP. Additionally, the variations of TN/TP and cyanobacteria density are both computed and compared to show the environmental issues close to the Taihu lake.