Molecular Mechanism of Rice Necrotic Lesion for Optimized Yield and Disease Resistance

How to balance rice resistance and yield is an important issue in rice breeding.Plants with mutated necrotic lesion genes often have persistent broad-spectrum resistance,but this broad-spectrum resistance usually comes at the expense of yield.Currently,many necrotic lesion mutants in rice have been identified,and these genes are involved in disease resistance pathways.This review provides a detailed introduction to the characteristics,classification,and molecular mechanisms of necrotic lesion formation.Additionally,we review the molecular regulatory pathways of genes involved in rice disease resistance.Concurrently,we summarize the relationship between resistance and yield in rice using newly developed gene editing methods.We discuss a rational and precise breeding strategy to better utilize molecular design technology for breeding disease-resistant and high-yield rice varieties.

Effect of rice cultivar on greenhouse-gas emissions from rice-fish co-culture

In aquaculture,co-culturing rice with fish may mitigate greenhouse-gas emissions.In this study,co-culture of four rice cultivars in a laboratory-scale rice–fish system reduced CH_(4)and N_(2)O emissions relative to fish monoculture.Differences in CH_(4)and N_(2)O emissions among rice cultivars primarily stem from the differential effects of rice plants on plant-mediated CH_(4)transport,CH_(4)oxidation and nitrogen absorption.

Interaction Between Ustilaginoidea virens and Rice and Its Sustainable Control

Ustilaginoidea virens is a common rice pathogen that can easily lead to a decline in rice quality and the production of toxins pose potential risks to human health.In this review,we present a comprehensive literature review of research since the discovery of rice false smut.We provide a comprehensive and,at times,critical overview of the main results and findings from related research,and propose future research directions.Firstly,we delve into the interaction between U.virens and rice,including the regulation of transcription factors,the process of U.virens infecting rice panicles,and the plant immune response caused by rice infection.Following that,we discuss the identification and characterization of mycotoxins produced by the pathogenic fungus,as well as strategies for disease management.We emphasize the importance of comprehensive agricultural prevention and control methods for the sustainable management of U.virens.This knowledge will update our understanding of the interaction between U.virens and rice plants,offering a valuable perspective for those interested in U.virens.

A rice exocyst subunit gene SEC3A is required for anther dehiscence

Anther dehiscence controls optimal interaction between pollen and stigma,thereby determining the successful sexual reproduction.The regulators or mechanisms of this process remain elusive.Here,two CRISPR/Cas9 mutants of a rice exocyst subunit gene SEC3A,sec3a-1 and sec3a-2,showed anther indehiscence at anthesis and male sterility at maturity.Pollen viability and germination in the mutants were partly defective,whereas their female gametes undergone a normal development.Hybrid or self-pollinated seeds could be produced by artificial pollination,suggesting potential use of a weak sec3a mutant as a female line during hybrid breeding.SEC3A is widely expressed in various tissues,including anther walls.Further results showed an excessive IAA accumulation and no endothecium lignification in sec3a-1/2 anthers.Our findings suggest that SEC3A appears to regulate anther dehiscence by modulating auxin signaling,providing insights into regulation of anther dehiscence and function of exocyst in plants.

A polygalacturonase gene OsPG1 modulates water homeostasis in rice

A dynamic plant architecture is the basis of plant adaptation to changing environments.Although many genes regulating leaf rolling have been identified,genes directly associated with water homeostasis are largely unknown.Here,we isolated a rice mutant,dynamic leaf rolling 1(dlr1),characterized by‘leaf unfolding in the morning-leaf rolling at noon-leaf unfolding in the evening’during a sunny day.Water content was decreased in rolled leaves and water sprayed on leaves caused reopening,indicating that in vivo water deficiency induced the leaf rolling.Map-based cloning and expression tests demonstrated that an A1400G single base mutation in Oryza sativa Polygalacturonase 1(OsPG1)/PHOTO-SENSITIVE LEAF ROLLING 1(PSL1)was responsible for the dynamic leaf rolling phenotype in the dlr1 mutant.OsPG1 encodes a polygalacturonase,one of the main enzymes that degrade demethylesterified homogalacturonans in plant cell walls.OsPG1 was constitutively expressed in various tissues and was enriched in stomata.Mutants of the OsPG1 gene exhibited defects in stomatal closure and decreased stomatal density,leading to reduced transpiration and excessive water loss under specific conditions,but had normal root development.Further analysis revealed that mutation of OsPG1 led to reduced pectinase activity in the leaves and increased demethylesterified homogalacturonans in guard cells.Our findings reveal a mechanism by which OsPG1 modulates water homeostasis to control dynamic leaf rolling,providing insights for plants to adapt to environmental variation.

A hybrid CNN-LSTM model for diagnosing rice nutrient levels at the rice panicle initiation stage

Nitrogen(N)and potassium(K)are two key mineral nutrient elements involved in rice growth.Accurate diagnosis of N and K status is very important for the rational application of fertilizers at a specific rice growth stage.Therefore,we propose a hybrid model for diagnosing rice nutrient levels at the early panicle initiation stage(EPIS),which combines a convolutional neural network(CNN)with an attention mechanism and a long short-term memory network(LSTM).The model was validated on a large set of sequential images collected by an unmanned aerial vehicle(UAV)from rice canopies at different growth stages during a two-year experiment.Compared with VGG16,AlexNet,GoogleNet,DenseNet,and inceptionV3,ResNet101 combined with LSTM obtained the highest average accuracy of 83.81%on the dataset of Huanghuazhan(HHZ,an indica cultivar).When tested on the datasets of HHZ and Xiushui 134(XS134,a japonica rice variety)in 2021,the ResNet101-LSTM model enhanced with the squeeze-and-excitation(SE)block achieved the highest accuracies of 85.38 and 88.38%,respectively.Through the cross-dataset method,the average accuracies on the HHZ and XS134 datasets tested in 2022 were 81.25 and 82.50%,respectively,showing a good generalization.Our proposed model works with the dynamic information of different rice growth stages and can efficiently diagnose different rice nutrient status levels at EPIS,which are helpful for making practical decisions regarding rational fertilization treatments at the panicle initiation stage.

Drought-Tolerant Rice at Molecular Breeding Eras:An Emerging Reality

Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental stress.Drought stress impacts about 45%of the world’s rice area,affecting plants at molecular,biochemical,physiological,and phenotypic levels.The conventional breeding method,predominantly employing single pedigree selection,has been widely utilized in breeding numerous drought-tolerant rice varieties since the Green Revolution.With rapid progress in plant molecular biology,hundreds of drought-tolerant QTLs/genes have been identified and tested in rice crops under both indoor and field conditions.Several genes have been introgressed into elite germplasm to develop commercially accepted drought-tolerant varieties,resulting in the development of several drought-tolerant rice varieties through marker-assisted selection and genetically engineered approaches.This review provides up-to-date information on proof-of-concept genes and breeding methods in the molecular breeding era,offering guidance for rice breeders to develop drought-tolerant rice varieties.

OsbZIP01 Affects Plant Growth and Development by Regulating OsSD1 in Rice

As the‘Green Revolution’gene,SD1(encoding GA20ox2),has been widely applied to improve yield in rice breeding.However,research on its transcriptional regulation is limited.Here,we identified a transcription factor OsbZIP01,which can suppress the expression of SD1 and regulate gibberellin(GA)biosynthesis in rice.Knockout mutants of OsbZIP01 exhibited increased plant height,while the overexpression lines showed a semi-dwarf phenotype and diminished germination rate.Furthermore,the semi-dwarf phenotype of OE-bZIP01,was caused by the reduced internode length,which was accompanied by a thin stem width.The predominant expression of OsbZIP01 was observed in leaves and sheaths.OsbZIP01 protein was localized in the nucleus and showed transcriptional repression activity.In addition,OsbZIP01 could directly bind to the promoter of the OsSD1 gene,and inhibit its transcription.The semi-dwarf phenotype of OE-bZIP01 could be rescued by exogenous GA_(3).Meanwhile,the bzip01 sd1 double mutant showed a shorter shoot length compared with the wild type,indicating that OsbZIP01 regulated plant growth mainly through the GA biosynthesis pathway.Collectively,OsbZIP01 negatively regulates GA biosynthesis by restraining SD1 transcription,thereby affecting plant growth and development.

Oriented Generation of Novel Thermo-Sensitive Genic Male Sterile Lines with Improved Grain Shape and Outcrossing Rate in Early-Season Rice

Two-line hybrid rice with excellent quality is preferred in the Chinese market.However,there is a trade-off between reducing costs for hybrid seed production and lowering the outcrossing rate of the sterile line,which is largely determined by the stigma exsertion rate(SER).In this study,we constructed mutants of male sterility lines with improved grain length(GL)and SER in three elite early-season indica rice varieties through targeted manipulation of the TMS5 and GS3 genes using CRISPR/Cas9-mediated multiplex systems.We obtained a series of marker-free gs3 single mutants and gs3tms5 double mutants with significantly higher SER,longer grains,and increased 1000-grain weight compared with the wild type(WT).Importantly,the typically thermo-sensitive genic male sterile(TGMS)trait with a higher SER was observed in gs3tms5 mutants,and their F1 hybrids exhibited remarkable improvements in grain shape and yield-related traits.Our findings provided an efficient method to generate new valuable TGMS germplasm with improved SER through the mutagenesis of GS3 and TMS5 synergistically,and demonstrated that GS3 had pleiotropic effects on grain size,SER,and grain quality in early-season indica rice.

The auxin transporter OsAUX1 regulates tillering in rice(Oryza sativa)

Tillering is an important agronomic trait of rice(Oryza sativa)that affects the number of effective panicles,thereby affecting yields.The phytohormone auxin plays a key role in tillering.Here we identified the high tillering and semi-dwarf 1(htsd1)mutant with auxin-deficiency root characteristics,such as shortened lateral roots,reduced lateral root density,and enlarged root angles.htsd1 showed reduced sensitivity to auxin,but the external application of indole-3-acetic acid(IAA)inhibited its tillering.We identified the mutated gene in htsd1 as AUXIN1(OsAUX1,LOC_Os01g63770),which encodes an auxin influx transporter.The promoter sequence of OsAUX1 contains many SQUAMOSA PROMOTER BINDING PROTEIN-LIKE(SPL)binding sites,and we demonstrated that SPL7 binds to the OsAUX1 promoter.TEOSINTE BRANCHED1(OsTB1),a key gene that negatively regulates tillering,was significantly downregulated in htsd1.Tillering was enhanced in the OsTB1 knockout mutant,and the external application of IAA inhibited tiller elongation in this mutant.Overexpressing OsTB1 restored the multi-tiller phenotype of htsd1.These results suggest that SPL7 directly binds to the OsAUX1 promoter and regulates tillering in rice by altering OsTB1 expression to modulate auxin signaling.

Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ morphogenesis.Here,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice cultivar.Of 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific genes.Marker genes of multiple cell types were expressed in several clusters,suggesting a complex developmental system.Some genes for signaling by phytohormones such as abscisic acid were highly expressed in specific clusters.Various cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain clusters.Spatial expression patterns of genes involved in rapid seed germination,seedling growth,and development were identified.These findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

A 48-bp deletion upstream of LIGULELESS 1 alters rice panicle architecture

Panicle architecture is an agronomic determinant of crop yield and a target for cereal crop improvement.To investigate its molecular mechanisms in rice,we performed map-based cloning and characterization of OPEN PANICLE 1(OP1),a gain-of-function allele of LIGULELESS 1(LG1),controlling the spread-panicle phenotype.This allele results from a 48-bp deletion in the LG1 upstream region and promotes pulvinus development at the base of the primary branch.Increased OP1 expression and altered panicle phenotype in chimeric transgenic plants and upstream-region knockout mutants indicated that the deletion regulates spread-panicle architecture in the mutant spread panicle 1(sp1).Knocking out BRASSINOSTEROID UPREGULATED1(BU1)gene in the background of OP1 complementary plants resulted in compact panicles,suggesting OP1 may regulate inflorescence architecture via the brassinosteroid signaling pathway.We regard that manipulating the upstream regulatory region of OP1 or genes involved in BR signal pathway could be an efficient way to improve rice inflorescence architecture.

OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in Rice

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic stresses.OsbZIP53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic plants.To further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic plants.Comprehensive analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid pathway.Specifically,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting OsMYBS1.In addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

Rice AGL1 determines grain size and sterile lemma identity

The grass spikelet is a unique inflorescence structure that determines grain size.Although many genetic factors have been well characterized for grain size and glume development,the underlying molecular mechanisms in rice are far from established.Here,we isolated rice gene,AGL1 that controlled grain size and determines the fate of the sterile lemma.Loss of function of AGL1 produced larger grains and reduced the size of the sterile lemma.Larger grains in the agl1 mutant were caused by a larger number of cells that were longer and wider than in the wild type.The sterile lemma in the mutant spikelet was converted to a rudimentary glume-like organ.Our findings showed that the AGL1(also named LAX1)protein positively regulated G1 expression,and negatively regulated NSG1 expression,thereby affecting the fate of the sterile lemma.Taken together,our results revealed that AGL1 played a key role in negative regulation of grain size by controlling cell proliferation and expansion,and supported the opinion that rudimentary glume and sterile lemma in rice are homologous organs.

Leaf Morphology Genes SRL1 and RENL1 Co-Regulate Cellulose Synthesis and Affect Rice Drought Tolerance

The morphological development of rice(Oryza sativa L.)leaves is closely related to plant architecture,physiological activities,and resistance.However,it is unclear whether there is a co-regulatory relationship between the morphological development of leaves and adaptation to drought environment.In this study,a drought-sensitive,roll-enhanced,and narrow-leaf mutant(renl1)was induced from a semi-rolled leaf mutant(srl1)by ethyl methane sulfonate(EMS),which was obtained from Nipponbare(NPB)through EMS.Map-based cloning and functional validation showed that RENL1 encodes a cellulose synthase,allelic to NRL1/OsCLSD4.The RENL1 mutation resulted in reduced vascular bundles,vesicular cells,cellulose,and hemicellulose contents in cell walls,diminishing the water-holding capacity of leaves.In addition,the root system of the renl1 mutant was poorly developed and its ability to scavenge reactive oxygen species(ROS)was decreased,leading to an increase in ROS after drought stress.Meanwhile,genetic results showed that RENL1 and SRL1 synergistically regulated cell wall components.Our results revealed a theoretical basis for further elucidating the molecular regulation mechanism of cellulose on rice drought tolerance,and provided a new genetic resource for enhancing the synergistic regulation network of plant type and stress resistance,thereby realizing simultaneous improvement of multiple traits in rice.

Identification of the BTA8 gene reveals the contribution of natural variation to tiller angle in rice

Plant architecture is a collection of major agronomic traits that determines rice grain production,and it is mainly influenced by tillering,tiller angle,plant height and panicle morphology(Wang and Li 2006).Tiller angle is one of the critical components that determines rice plant architecture,which in turn influences grain yield mainly due to its large impact on plant density(Wang et al.2022).

The UDP-glycosyltransferase OsUGT706D2 positively regulates cold and submergence stress tolerance in rice

In a genome-wide association study,we identified a rice UDP-glycosyltransferase gene,OsUGT706D2,whose transcription was activated in response to cold and submergence stress and to exogenous abscisic acid(ABA).OsUGT706D2 positively regulated the biosynthesis of tricin-4’-O-(syringyl alcohol)ether-7-O-glucoside at both the transcriptional and metabolic levels.OsUGT706D2 mediated cold and submergence tolerance by modulating the expression of stress-responsive genes as well as the abscisic acid(ABA)signaling pathway.Gain of function of OsUGT706D2 increased cold and submergence tolerance and loss of function of OsUGT706D2 reduced cold tolerance.ABA positively regulated OsUGT706D2-mediated cold tolerance but reduced submergence tolerance.These findings suggest the potential use of OsUGT706D2 for improving abiotic stress tolerance in rice.

Direct-Seeded Rice: Genetic Improvement of Game-Changing Traits for Better Adaption

The sustainability of rice production continues to be a subject of uncertainty and inquiry attributed to shifts in climatic conditions. In light of the impending climate change crisis and the high labor and water costs accompanying it, direct-seeded rice(DSR) is unquestionably one of the most practical solutions. Despite its resource and climate-friendly advantages, early maturing rice faces weed competitiveness and seedling establishment challenges. Resolving these issues is crucial for promoting its wider adoption among farmers, presenting it as a more effective sustainable rice cultivation method globally. Diverse traditional and contemporary breeding methods are employed to mitigate the limitations of the DSR approach, leveraging advanced techniques such as speed breeding and genome editing. Focusing on key traits like mesocotyl length elongation, early seedling vigor, root system architecture, and weed competitiveness holds promise for transformative improvements in DSR adaptation at a broader scale within farming communities. This review aims to summarize how these features contribute to increased crop production in DSR conditions and explore the research efforts focusing on enhancing DSR adaptation through these traits. Emphasizing the pivotal role of these game-changing traits in DSR adaptation, our analysis sheds light on their potential transformative impact and offers valuable insights for advancing DSR practices.

Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

The Magnaporthe oryzae effector Avr-PikD suppresses rice immunity by inhibiting an LSD1-like transcriptional activator

Avirulence effectors(Avrs),encoded by plant pathogens,can be recognized by plants harboring the corresponding resistance proteins,thereby initiating effector-triggered immunity(ETI).In susceptible plants,however,Avrs can function as effectors,facilitating infection via effector-triggered susceptibility(ETS).Mechanisms of Avr-mediated ETS remain largely unexplored.Here we report that the Magnaporthe oryzae effector Avr-PikD enters rice cells via the canonical cytoplasmic secretion pathway and suppresses rice basal defense.Avr-PikD interacts with an LSD1-like transcriptional activator AKIP30 of rice,and AKIP30 is also a positive regulator of rice immunity,whereas Avr-PikD impedes its nuclear localization and suppresses its transcriptional activity.In summary,M.oryzae delivers Avr-PikD into rice cells to facilitate ETS by inhibiting AKIP30-mediated transcriptional regulation of immune response against M.oryzae.