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:tho...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.展开更多
Doubled haploid(DH)technology has revolutionized crop breeding by enabling the production of homozygous lines in a single generation.In vivo haploid induction(HI)offers a more widely applicable approach that can signi...Doubled haploid(DH)technology has revolutionized crop breeding by enabling the production of homozygous lines in a single generation.In vivo haploid induction(HI)offers a more widely applicable approach that can significantly improve DH breeding efficiency.ToPAR,a parthenogenesis gene,originally identified in dandelion(Taraxacum officinale),has been characterized.Researchers have successfully induced haploid embryo-like structures and haploid offspring in lettuce and foxtail millet,respectively.展开更多
The genetic mechanism determining amylose content(AC)and its impact on eating and cooking quality(ECQ)of rice is highly complex.To elucidate the genetic basis of AC in rice,the Ting’s core collection was used to iden...The genetic mechanism determining amylose content(AC)and its impact on eating and cooking quality(ECQ)of rice is highly complex.To elucidate the genetic basis of AC in rice,the Ting’s core collection was used to identify novel AC genes/loci through genome-wide association analysis(GWAS)using more than 5.0 million single nucleotide polymorphisms(SNPs).In this study,12 genes related to AC,including the major gene Wx and 11 minor genes,were detected using the EMMAX method.A novel gene,LR,encoding a nucleotide-binding leucine-rich-repeat(LRR)receptor(NLR)family protein,was selected for functional study.When LR was knocked out using CRISPR/Cas9,the AC decreased significantly.Furthermore,the AC in varieties was significantly higher with Haplotype A compared to Haplotypes B and C of LR.Notably,two natural variations,SNP-385(Thr-Hap.A vs Ala-Haps.B and C)and SNP-758(Ser-Hap.A vs Asn-Haps.B and C),in the coding region of LR might play critical roles in regulating AC and serve as potential targets for cultivating rice with diverse amylose contents.展开更多
The width of rice leaves determines the size of the photosynthetic area.Optimizing rice leaf width can improve the photosynthetic rate,thereby increasing rice yield.In this study,a genome-wide association study(GWAS)w...The width of rice leaves determines the size of the photosynthetic area.Optimizing rice leaf width can improve the photosynthetic rate,thereby increasing rice yield.In this study,a genome-wide association study(GWAS)was conducted by 225 rice germplasm resources to explore the genetic basis of rice flag leaf width(FLW).We identified nine QTLs associated with FLW(qFLWs),with phenotypic contribution rates ranging from 3.17%to 14.37%.Near-isogenic lines(NILs)were developed for fine-mapping of qFLW11,and the function of FLW11 was further verified.We narrowed down q FLW11 to an 87-kb interval,which contains five genes.展开更多
Iron is an essential nutrient for plant growth,development,and disease resistance.Plants absorb iron through their roots,with citrate playing a key role in xylem transport of insoluble Fe3+.In this study,we identified...Iron is an essential nutrient for plant growth,development,and disease resistance.Plants absorb iron through their roots,with citrate playing a key role in xylem transport of insoluble Fe3+.In this study,we identified the cytoplasmic ATP-citrate lyase(ACL)subunit A2 in rice(Oryza sativa L.),OsACL-A2(Os12g0566300),as a critical factor for iron uptake and transport.The osacl-a2 mutant exhibited reduced leaf iron levels,leading to iron deficiency-induced chlorosis,activated defense signaling,and eventual necrosis in mature leaves.Additionally,blast resistance was weakened in immature osacl-a2 leaves.Exogenous iron supplementation rescued these defects.The mutant displayed reduced ATP-citrate lyase activity but increased citric acid levels compared with its wild type(WT),suggesting that the osacl-a2 mutation impairs enzyme activity.Thus,OsACL-A2-mediated citrate lyase activity plays a vital role in promoting iron uptake and associated blast resistance in rice.展开更多
Tiller number is a crucial agronomic trait for achieving high yield in rice.NAC proteins play critical roles in regulating plant growth and development.However,the role of NAC transcription factors in regulating tille...Tiller number is a crucial agronomic trait for achieving high yield in rice.NAC proteins play critical roles in regulating plant growth and development.However,the role of NAC transcription factors in regulating tiller number remains poorly understood.In this study,we isolated a rice NAC gene,OsNAC022,which is conserved in cereal crops and functions as a transcriptional activator.To investigate the role of this gene in rice,we used CRISPR/Cas9 technology to generate a homozygous mutant named CR-osnac022,which exhibited increased tiller number.展开更多
Bakanae disease,induced by the pathogen Fusarium fujikuroi,poses a significant stress on rice cultivation.However,the key resistance genes to this disease remain largely unknown.In this study,we reported that the plas...Bakanae disease,induced by the pathogen Fusarium fujikuroi,poses a significant stress on rice cultivation.However,the key resistance genes to this disease remain largely unknown.In this study,we reported that the plasma membrane intrinsic protein,OsPIP2;2,positively regulated to bakanae disease resistance in rice.展开更多
Timely identification and forecast of maize tasseling date(TD)are very important for agronomic management,yield prediction,and crop phenotype estimation.Remote sensing-based phenology monitoring has mostly relied on t...Timely identification and forecast of maize tasseling date(TD)are very important for agronomic management,yield prediction,and crop phenotype estimation.Remote sensing-based phenology monitoring has mostly relied on time series spectral index data of the complete growth season.A recent development in maize phenology detection research is to use canopy height(CH)data instead of spectral indices,but its robustness in multiple treatments and stages has not been confirmed.Meanwhile,because data of a complete growth season are needed,the need for timely in-season TD identification remains unmet.This study proposed an approach to timely identify and forecast the maize TD.We obtained RGB and light detection and ranging(Li DAR)data using the unmanned aerial vehicle platform over plots of different maize varieties under multiple treatments.After CH estimation,the feature points(inflection point)from the Logistic curve of the CH time series were extracted as TD.We examined the impact of various independent variables(day of year vs.accumulated growing degree days(AGDD)),sensors(RGB and Li DAR),time series denoise methods,different feature points,and temporal resolution on TD identification.Lastly,we used early CH time series data to predict height growth and further forecast TD.The results showed that using the 99th percentile of plot scale digital surface model and the minimum digital terrain model from Li DAR to estimate maize CH was the most stable across treatments and stages(R~2:0.928 to0.943).For TD identification,the best performance was achieved by using Li DAR data with AGDD as the independent variable,combined with the knee point method,resulting in RMSE of 2.95 d.The high accuracy was maintained at temporal resolutions as coarse as 14 d.TD forecast got more accurate as the CH time series extended.The optimal timing for forecasting TD was when the CH exceeded half of its maximum.Using only Li DAR CH data below 1.6 m and empirical growth rate estimates,the forecasted TD showed an RMSE of 3.90 d.In conclusion,this study exploited the growth characteristics of maize height to provide a practical approach for the timely identification and forecast of maize TD.展开更多
Rice grain size is a primary characteristic essential for artificial domestication and breeding,governed by grain length,width,and thickness.In this study,we cloned Grain Size 10(GS10),a novel gene via mapbased clonin...Rice grain size is a primary characteristic essential for artificial domestication and breeding,governed by grain length,width,and thickness.In this study,we cloned Grain Size 10(GS10),a novel gene via mapbased cloning.Biochemical,molecular,and genetic studies were performed to elucidate the GS10 involved grain size mechanism in rice.Mutant of GS10 lead to reduced grain size due to alterations in cell expansion.Additionally,GS10 is responsible for the formation of notched-belly grains,especially in smaller grain varieties possessing loss-function mutations.Overexpression of GS10 in Nipponbare results in increasing grain length,grain weight and improve the appearance quality of rice.GS10 encodes conserved protein with uncharacterized function.Furthermore,GS10 regulates the grain size by interacting OsBRICK1,a subunit of the WAVE complex that governs actin nucleation and affects the assembly of microfilaments in rice.Together,our study demonstrates that,GS10 positively regulates the grain length and grain weight,which is beneficial for further improvements in yield characteristics.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Plant pathogens secrete various cell wall-degrading enzymes that compromise host cell wall integrity and facilitate pathogen invasion.This study identified VdGH7a,a glycoside hydrolase family 7(GH7)cellobiohydrolase f...Plant pathogens secrete various cell wall-degrading enzymes that compromise host cell wall integrity and facilitate pathogen invasion.This study identified VdGH7a,a glycoside hydrolase family 7(GH7)cellobiohydrolase from Verticillium dahliae,which demonstrated hydrolytic activity against 1,4-β-glucan.Notably,VdGH7a induced cell death in Nicotiana benthamiana when signal peptides were present,though this effect was inhibited by the carbohydrate-binding type-1(CBM1)protein domain.The deletion of VdGH7a substantially reduced V.dahliae pathogenicity in cotton plants,as demonstrated by the mutants’inability to penetrate cellophane membrane.These knockout mutants also exhibited reduced carbon source utilization capacity and increased sensitivity to osmotic and cell wall stresses.Through yeast two-hybrid screening,bi-molecular fluorescence complementation(BiFC),and luciferase complementation imaging(LCI),we identified that VdGH7a interacts with an osmotin-like protein(GhOLP1)in cotton.Virus-induced gene silencing of GhOLP1 resulted in decreased salicylic acid(SA)content and reduced resistance to V.dahliae in cotton,while heterologous overexpression of GhOLP1 in Arabidopsis enhanced both resistance and SA signaling pathway gene expression.These results reveal a virulence mechanism wherein the secreted protein VdGH7a from V.dahliae interacts with GhOLP1 to activate host immunity and contribute significantly to plant resistance against V.dahliae.展开更多
RNA interference(RNAi)has been used for agricultural insect pest control based on silencing of targeted insect genes.However,the effectiveness of RNAi and its applications in insect pest control remain challenging.Her...RNA interference(RNAi)has been used for agricultural insect pest control based on silencing of targeted insect genes.However,the effectiveness of RNAi and its applications in insect pest control remain challenging.Here we review factors that may affect the effectiveness of RNAi application,including the variability in RNAi efficacy among different insect species,a limited understanding of double-stranded RNA(dsRNA)uptake and systemic RNAi mechanisms,and the effective delivery of dsRNA in field conditions.Furthermore,we summarize recent progress in RNAi strategies for crop protection,discuss the advantages and disadvantages of RNAi-based insect control,and propose potential strategies to increase the effectiveness of RNAi in insect control.展开更多
Accurate evaluation of disease levels in wild rice germplasm and identification of disease resistance are critical for developing rice varieties resistant to blast disease.However,existing evaluation methods face limi...Accurate evaluation of disease levels in wild rice germplasm and identification of disease resistance are critical for developing rice varieties resistant to blast disease.However,existing evaluation methods face limitations that hinder progress in breeding.To address these challenges,we proposed an AI-powered method for evaluating blast disease levels and identifying resistance in wild rice.A lightweight segmentation model for diseased leaves and lesions was developed,incorporating an improved federated learning approach to enhance robustness and adaptability.Based on the segmentation results and resistance identification technical specifications,wild rice materials were evaluated into 10 disease levels(L0 to L9),further enabling disease-resistance identification through multiple replicates of the same materials.The method was successfully implemented on augmented reality glasses for real-time,first-person evaluation.Additionally,high-speed scanners and edge computing devices were integrated to enable continuous,precise,and dynamic evaluation.Experimental results demonstrate the outstanding performance of the proposed method,achieving effective segmentation of diseased leaves and lesions with only 0.22 M parameters and 5.3 G floating-point operations per second(FLOPs),with a mean average precision(mAP@0.5)of 96.3%.The accuracy of disease level evaluation and disease-resistance identification reached 99.7%,with a practical test accuracy of 99.0%,successfully identifying three highly resistant wild rice materials.This method provides strong technical support for efficiently identifying wild rice materials resistant to blast disease and advancing resistance breeding efforts.展开更多
A later heading date generally leads to higher grain yield in favorable ecological regions;however,grain yield reaches a limit as the heading date exceeds a certain threshold.Ghd7 is the first cloned major gene that r...A later heading date generally leads to higher grain yield in favorable ecological regions;however,grain yield reaches a limit as the heading date exceeds a certain threshold.Ghd7 is the first cloned major gene that regulates heading date,plant height and grain number.Here,we investigated the relationship between Ghd7 and florigen genes Hd3a and RFT1,to determine their roles in regulating heading date and grain number under different photoperiods.Our results revealed that under long-day(LD)conditions,Hd3a acts prior to RFT1 to promote heading while negatively regulating plant height and grain number.In contrast,Ghd7 positively regulates heading date,plant height,and grain number by inhibiting both Hd3a and RFT1.Under short-day(SD)conditions,the functions of Hd3a and RFT1 remain consistent with those under LD conditions,but Ghd7 does not inhibit their expression,resulting in a weaker phenotypic effect compared to Hd3a.Additionally,under both LD and SD conditions,increased Ghd7 expression enhances its inhibitory effect on Hd3a and RFT1,leading to later heading and increased grain number;however,once the heading date exceeds 94 d,grain number no longer increases.Moreover,the gn1a allele increased grain number by 16.5%to 42.5%,while combinations of the elite alleles from Ghd7,Hd3a,RFT1,and Gn1a significantly increased grain number by up to 240.9%.Therefore,we propose a new breeding strategy to optimize the heading date and grain number using the Ghd7Hd3aRFT1gn1a combination of Ghd7,Hd3a,RFT1,and Gn1a under LD conditions,and the Ghd7hd3aRFT1gn1a combination under SD conditions.This strategy improved the yield of the high-quality Northeast variety Kongyu 131(KY131)by 69.1%in Beijing and 93.7%in Hainan.This strategy will greatly improve the efficiency of north-to-south adaptation in rice,providing theoretical guidance for expanding the geographical adaptability of rice varieties.展开更多
Background The bromodomain(BRD) proteins play a pivotal role in regulating gene expression by recognizing acetylated lysine residues and acting as chromatin-associated post-translational modification-inducing proteins...Background The bromodomain(BRD) proteins play a pivotal role in regulating gene expression by recognizing acetylated lysine residues and acting as chromatin-associated post-translational modification-inducing proteins. Although BRD proteins have been extensively studied in mammals, they have also been characterized in plants like Arabidopsis thaliana and Oryza sativa, where they regulate stress-responsive genes related to drought, salinity, and cold. However, their roles in cotton species remain unexplored.Results In this genome-wide comparative analysis, 145 BRD genes were identified in the tetraploid species(Gossypium hirsutum and G. barbadense), compared with 82 BRD genes in their diploid progenitors(G. arboreum and G. raimondii), indicating that polyploidization significantly influenced BRD gene evolution. Gene duplication analysis revealed 78.85% of duplications were segmental and 21.15% were tandem among 104 in-paralogous gene pairs, contributing to BRD gene expansion. Gene structure, motif, and domain analyses demonstrated that most genes were intron-less and conserved throughout evolution. Syntenic analysis revealed a greater number of orthologous gene pairs in the Dt sub-genome than in the At sub-genome. The abundance of regulatory, hormonal, and defense-related cis-regulatory elements in the promoter region suggests that BRD genes play a role in both biotic and abiotic stress responses. Protein-protein interaction analysis indicated that global transcription factor group E(GTE) transcription factors regulate BRD genes. Expression analysis revealed that BRD genes are predominantly involved in ovule development, with some genes displaying specific expression patterns under heat, cold, and salt stress. Furthermore, qRT-PCR analysis demonstrated significant differential expression of BRD genes between the tolerant and sensitive genotype, underscoring their potential role in mediating drought and salinity stress responses.Conclusions This study provides valuable insights into the evolution of BRD genes across species and their roles in abiotic stress tolerance, highlighting their potential in breeding programs to develop drought and salinity tolerant cotton varieties.展开更多
The germination process of seeds is influenced by the interplay between two opposing factors,pectin methylesterase(PME)and pectin methylesterase inhibitor(PMEI),which collectively regulate patterns of pectin methylest...The germination process of seeds is influenced by the interplay between two opposing factors,pectin methylesterase(PME)and pectin methylesterase inhibitor(PMEI),which collectively regulate patterns of pectin methylesterification.Despite the recognized importance of pectin methylesterification in seed germination,the specific mechanisms that govern this process remain unclear.In this study,we demonstrated that the overexpression of GhPMEI53is associated with a decrease in PME activity and an increase in pectin methylesterification.This leads to seed cell wall softening,which positively regulates cotton seed germination.AtPMEI19,the homologue in Arabidopsis thaliana,plays a similar role in seed germination to GhPMEI53,indicating a conserved function and mechanism of PMEI in seed germination regulation.Further studies revealed that GhPMEI53 and AtPMEI19 directly contribute to promoting radicle protrusion and seed germination by inducing cell wall softening and reducing mechanical strength.Additionally,the pathways of abscicic acid(ABA)and gibberellin(GA)in the transgenic materials showed significant changes,suggesting that GhPMEI53/AtPMEI19-mediated pectin methylesterification serves as a regulatory signal for the related phytohormones involved in seed germination.In summary,GhPMEI53 and its homologs alter the mechanical properties of cell walls,which influence the mechanical resistance of the endosperm or testa.Moreover,they impact cellular phytohormone pathways(e.g.,ABA and GA)to regulate seed germination.These findings enhance our understanding of pectin methylesterification in cellular morphological dynamics and signaling transduction,and contribute to a more comprehensive understanding of the PME/PMEI gene superfamily in plants.展开更多
Rice blast,caused by the fungus Magnaporthe oryzae,reduces rice yields by 10%to 35%.Incorporating blast resistance genes into breeding programs is an effective strategy to combat this disease.Understanding the genetic...Rice blast,caused by the fungus Magnaporthe oryzae,reduces rice yields by 10%to 35%.Incorporating blast resistance genes into breeding programs is an effective strategy to combat this disease.Understanding the genetic variants that confer resistance is crucial to this strategy.The gene Bsr-d1 encodes a C2H2-like transcription factor,and its recessive allele confers broad-spectrum resistance against infections by various strains of M.oryzae.In this study,we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice accessions.Our results revealed that wild rice exhibited significantly higher nucleotide diversity,with polymorphic regions primarily concentrated in the promoter region,in contrast to indica and japonica rice varieties.The Bsr-d1 gene displayed significant differentiation between indica and japonica rice varieties,with the bsr-d1 resistance allele being unique to indica rice.Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula.Moreover,we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene.In summary,our study uncovering the origin and evolution of bsr-d1 will enhance our understanding of resistance gene variation and expedite the resistance breeding process.展开更多
Brassinosteroids(BRs)are vital plant steroid hormones involved in numerous aspects of plant life including growth,development,and responses to various stresses.However,the underlying mechanisms of how BR regulates abi...Brassinosteroids(BRs)are vital plant steroid hormones involved in numerous aspects of plant life including growth,development,and responses to various stresses.However,the underlying mechanisms of how BR regulates abiotic stress responses in wheat(Triticum aestivum L.)remain to be elucidated.Here,we find that BR signal core transcription factor BRASSINAZOLE-RESISTANT1(TaBZR1)is significantly up-regulated by salt treatment.Overexpression of Tabzr1-1D(a gain-of-function TaBZR1 mutant protein)improves wheat salt tolerance.Furthermore,we show that TaBZR1 binds directly to the G-box motif in the promoter of ABA biosynthesis gene TaNCED3 to activate its expression and promotes ABA accumulation.Moreover,TaBZR1 associates with the promoters of ROS-scavenging genes TaGPX2 and TaGPX3 to activate their expression.Taken together,our results elucidate that TaBZR1 improves salt-stress tolerance by activating some genes involved in the biosynthesis of ABA and ROS scavenging in wheat,which gives us a new strategy to improve the salt tolerance of wheat.展开更多
The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and ha...The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance.展开更多
Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-d...Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.32072048 and U2004204)National Key Research and Development Program of China(Grant No.2023YFF1001200)+2 种基金China Rice Research Institute Basal Research Fund(Grant No.CPSIBRF-CNRRI-202404)Academician Workstation of National Nanfan Research Institute(Sanya),Chinese Agricultural Academic Science(CAAS),(Grant Nos.YBXM2422 and YBXM2423)Agricultural Science and Technology Innovation Program of CAAS,China.
文摘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.
基金supported by the Nanfan Special Project of the Chinese Academy of Agricultural Sciences(Grant Nos.YBXM2320 and YBXM2433)the Project of Sanya Yazhou Bay Science and Technology City,China(Grant No.SCKJ-JYRC-2024-58)the Agricultural Science and Technology Innovation Program,China(Grant No.CAAS-ASTIP-2021-CNRRI).
文摘Doubled haploid(DH)technology has revolutionized crop breeding by enabling the production of homozygous lines in a single generation.In vivo haploid induction(HI)offers a more widely applicable approach that can significantly improve DH breeding efficiency.ToPAR,a parthenogenesis gene,originally identified in dandelion(Taraxacum officinale),has been characterized.Researchers have successfully induced haploid embryo-like structures and haploid offspring in lettuce and foxtail millet,respectively.
基金supported by the Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City,China(Grant No.2021JJLH0041)the Zhejiang Provincial Natural Science Foundation,China(Grant No.LY23C130006)+3 种基金the National Natural Science Foundation of China(Grant No.32472207)Nanfan Special Project,Chinese Academy of Agricultural Sciences(Grant Nos.YBXM2436 and YBXM2326)the Hainan Province Science and Technology Special Fund,China(Grant No.ZDYF2022XDNY256)the Innovational Fund for Scientific and Technological Personnel of Hainan Province,China(Grant No.KJRC2023B24).
文摘The genetic mechanism determining amylose content(AC)and its impact on eating and cooking quality(ECQ)of rice is highly complex.To elucidate the genetic basis of AC in rice,the Ting’s core collection was used to identify novel AC genes/loci through genome-wide association analysis(GWAS)using more than 5.0 million single nucleotide polymorphisms(SNPs).In this study,12 genes related to AC,including the major gene Wx and 11 minor genes,were detected using the EMMAX method.A novel gene,LR,encoding a nucleotide-binding leucine-rich-repeat(LRR)receptor(NLR)family protein,was selected for functional study.When LR was knocked out using CRISPR/Cas9,the AC decreased significantly.Furthermore,the AC in varieties was significantly higher with Haplotype A compared to Haplotypes B and C of LR.Notably,two natural variations,SNP-385(Thr-Hap.A vs Ala-Haps.B and C)and SNP-758(Ser-Hap.A vs Asn-Haps.B and C),in the coding region of LR might play critical roles in regulating AC and serve as potential targets for cultivating rice with diverse amylose contents.
基金supported by the Zhejiang Provincial Natural Science Foundation,China(Grant No.LD24C130001)the National Natural Science Foundation of China(Grant Nos.W2412006 and 32372125)+3 种基金the Hainan Provincial Natural Science Foundation,China(Grant Nos.GHYF2025029 and YBXM2422)the Innovation Platform for Academicians of Hainan Province,China(Grant No.YSPTZX202502)the National Modern Agricultural Industry Technology System Project,China(Grant No.CARS-01-18)the Special Support Program of Chinese Academy of Agricultural Sciences(Grant Nos.NKYCLJ-C-2021-015 and CAAS-ZDRW202401)。
文摘The width of rice leaves determines the size of the photosynthetic area.Optimizing rice leaf width can improve the photosynthetic rate,thereby increasing rice yield.In this study,a genome-wide association study(GWAS)was conducted by 225 rice germplasm resources to explore the genetic basis of rice flag leaf width(FLW).We identified nine QTLs associated with FLW(qFLWs),with phenotypic contribution rates ranging from 3.17%to 14.37%.Near-isogenic lines(NILs)were developed for fine-mapping of qFLW11,and the function of FLW11 was further verified.We narrowed down q FLW11 to an 87-kb interval,which contains five genes.
基金supported by the Basic Public Welfare Research Program of Zhejiang Province,China(Grant No.LY23C130003)the Fund of the State Key Laboratory of Rice Biology and Breeding,China(Grant No.2023ZZKT20203)+5 种基金the Major Science and Technology Project of Guangxi,China(Grant No.AA23062015)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences,China(Grant No.CAAS-ASTIP-2013-CNRRI)the China Rice Research System,China(Grant No.CARS-01-011)the Central Public-Interest Scientific Institution Basal Research Fund,China(Grant No.CPSIBRF-CNRRI-202301)High-Quality and Resistant Hybrid Rice Germplasm Creation and New Varieties Development with International Competitiveness,China(Grant Nos.2022KJCX45 and YBXM2437)Xi’nan League Science and Technology Project,China(Grant No.2023DXZD0001).
文摘Iron is an essential nutrient for plant growth,development,and disease resistance.Plants absorb iron through their roots,with citrate playing a key role in xylem transport of insoluble Fe3+.In this study,we identified the cytoplasmic ATP-citrate lyase(ACL)subunit A2 in rice(Oryza sativa L.),OsACL-A2(Os12g0566300),as a critical factor for iron uptake and transport.The osacl-a2 mutant exhibited reduced leaf iron levels,leading to iron deficiency-induced chlorosis,activated defense signaling,and eventual necrosis in mature leaves.Additionally,blast resistance was weakened in immature osacl-a2 leaves.Exogenous iron supplementation rescued these defects.The mutant displayed reduced ATP-citrate lyase activity but increased citric acid levels compared with its wild type(WT),suggesting that the osacl-a2 mutation impairs enzyme activity.Thus,OsACL-A2-mediated citrate lyase activity plays a vital role in promoting iron uptake and associated blast resistance in rice.
基金supported by the National Natural Science Foundation of China(Grant No.32372083)the Fundamental Research Funds for Central Public Welfare Research Institutes of Chinese Rice Research Institute(Grant No.CPSIBRF-CNRRI-202401)+1 种基金the Strategic Cooperation Project between Chongqing Municipal People’s Government and Chinese Academy of Agricultural Sciences‘Introduction,Excavation and Innovative Utilization of High-quality Rice Resources’,the China Agriculture Research System(Grant No.CARS-01-14)the Agricultural Science and Technology Innovation Program,China(Grant No.CAAS‐ASTIP‐2013‐CNRRI).
文摘Tiller number is a crucial agronomic trait for achieving high yield in rice.NAC proteins play critical roles in regulating plant growth and development.However,the role of NAC transcription factors in regulating tiller number remains poorly understood.In this study,we isolated a rice NAC gene,OsNAC022,which is conserved in cereal crops and functions as a transcriptional activator.To investigate the role of this gene in rice,we used CRISPR/Cas9 technology to generate a homozygous mutant named CR-osnac022,which exhibited increased tiller number.
基金supported by the‘Pioneer and Leading Goose’Research and Development Program of Zhejiang Province,China(Grant No.2023C04024)Hainan Province Science and Technology Special Fund,China(Grant No.ZDYF2023XDNY086)the Natural Science Foundation of Zhejiang Province,China(Grant No.LY22C130007).
文摘Bakanae disease,induced by the pathogen Fusarium fujikuroi,poses a significant stress on rice cultivation.However,the key resistance genes to this disease remain largely unknown.In this study,we reported that the plasma membrane intrinsic protein,OsPIP2;2,positively regulated to bakanae disease resistance in rice.
基金supported by National Science and Technology Major Project(2022ZD0115701)Nanfan Special Project,CAAS(YBXM2305,YBXM2401,YBXM2402,PTXM2402)+1 种基金National Natural Science Foundation of China(42071426,42301427)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences。
文摘Timely identification and forecast of maize tasseling date(TD)are very important for agronomic management,yield prediction,and crop phenotype estimation.Remote sensing-based phenology monitoring has mostly relied on time series spectral index data of the complete growth season.A recent development in maize phenology detection research is to use canopy height(CH)data instead of spectral indices,but its robustness in multiple treatments and stages has not been confirmed.Meanwhile,because data of a complete growth season are needed,the need for timely in-season TD identification remains unmet.This study proposed an approach to timely identify and forecast the maize TD.We obtained RGB and light detection and ranging(Li DAR)data using the unmanned aerial vehicle platform over plots of different maize varieties under multiple treatments.After CH estimation,the feature points(inflection point)from the Logistic curve of the CH time series were extracted as TD.We examined the impact of various independent variables(day of year vs.accumulated growing degree days(AGDD)),sensors(RGB and Li DAR),time series denoise methods,different feature points,and temporal resolution on TD identification.Lastly,we used early CH time series data to predict height growth and further forecast TD.The results showed that using the 99th percentile of plot scale digital surface model and the minimum digital terrain model from Li DAR to estimate maize CH was the most stable across treatments and stages(R~2:0.928 to0.943).For TD identification,the best performance was achieved by using Li DAR data with AGDD as the independent variable,combined with the knee point method,resulting in RMSE of 2.95 d.The high accuracy was maintained at temporal resolutions as coarse as 14 d.TD forecast got more accurate as the CH time series extended.The optimal timing for forecasting TD was when the CH exceeded half of its maximum.Using only Li DAR CH data below 1.6 m and empirical growth rate estimates,the forecasted TD showed an RMSE of 3.90 d.In conclusion,this study exploited the growth characteristics of maize height to provide a practical approach for the timely identification and forecast of maize TD.
基金supported by Projects of International Cooperation NSFC(31961143016,31101203)Guizhou Provincial Science and Technology Projects(QKHJC-ZK[2022]YB537)+4 种基金the Fundamental Research Funds of Central Public Welfare Research Institutions(CPSIBRF-CNRRI-202102,Y2020YJ17)Independent Project of State Key Laboratory of Rice Biology(2020Z2KT10201)High-quality and Resistant Hybrid Rice Germplasm Creation and New Varieties Development with International Competitiveness(2022KJCX45,YBXM2437)Zhejiang Provincial Science and Technology Projects(2022R51009)Inner Mongolia Breeding Joint Research Project(YZ2023004).
文摘Rice grain size is a primary characteristic essential for artificial domestication and breeding,governed by grain length,width,and thickness.In this study,we cloned Grain Size 10(GS10),a novel gene via mapbased cloning.Biochemical,molecular,and genetic studies were performed to elucidate the GS10 involved grain size mechanism in rice.Mutant of GS10 lead to reduced grain size due to alterations in cell expansion.Additionally,GS10 is responsible for the formation of notched-belly grains,especially in smaller grain varieties possessing loss-function mutations.Overexpression of GS10 in Nipponbare results in increasing grain length,grain weight and improve the appearance quality of rice.GS10 encodes conserved protein with uncharacterized function.Furthermore,GS10 regulates the grain size by interacting OsBRICK1,a subunit of the WAVE complex that governs actin nucleation and affects the assembly of microfilaments in rice.Together,our study demonstrates that,GS10 positively regulates the grain length and grain weight,which is beneficial for further improvements in yield characteristics.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by the Project of Sanya Yazhou Bay Science and Technology City,China(SCKJ-JYRC-2022-75)the Natural Science Foundation of Hainan Province,China(322QN398).
文摘Plant pathogens secrete various cell wall-degrading enzymes that compromise host cell wall integrity and facilitate pathogen invasion.This study identified VdGH7a,a glycoside hydrolase family 7(GH7)cellobiohydrolase from Verticillium dahliae,which demonstrated hydrolytic activity against 1,4-β-glucan.Notably,VdGH7a induced cell death in Nicotiana benthamiana when signal peptides were present,though this effect was inhibited by the carbohydrate-binding type-1(CBM1)protein domain.The deletion of VdGH7a substantially reduced V.dahliae pathogenicity in cotton plants,as demonstrated by the mutants’inability to penetrate cellophane membrane.These knockout mutants also exhibited reduced carbon source utilization capacity and increased sensitivity to osmotic and cell wall stresses.Through yeast two-hybrid screening,bi-molecular fluorescence complementation(BiFC),and luciferase complementation imaging(LCI),we identified that VdGH7a interacts with an osmotin-like protein(GhOLP1)in cotton.Virus-induced gene silencing of GhOLP1 resulted in decreased salicylic acid(SA)content and reduced resistance to V.dahliae in cotton,while heterologous overexpression of GhOLP1 in Arabidopsis enhanced both resistance and SA signaling pathway gene expression.These results reveal a virulence mechanism wherein the secreted protein VdGH7a from V.dahliae interacts with GhOLP1 to activate host immunity and contribute significantly to plant resistance against V.dahliae.
基金funded by the National Natural Science Foundation of China(32188102 to Lanqin Xia)Natural Science Foundation for Distinguished Young Scholars of Jiangxi province(20212ACB215001 to Xiudao Yu)+1 种基金supported by the China Scholarship Council(202303250062)the GSCAAS-ULg Joint PhD Program。
文摘RNA interference(RNAi)has been used for agricultural insect pest control based on silencing of targeted insect genes.However,the effectiveness of RNAi and its applications in insect pest control remain challenging.Here we review factors that may affect the effectiveness of RNAi application,including the variability in RNAi efficacy among different insect species,a limited understanding of double-stranded RNA(dsRNA)uptake and systemic RNAi mechanisms,and the effective delivery of dsRNA in field conditions.Furthermore,we summarize recent progress in RNAi strategies for crop protection,discuss the advantages and disadvantages of RNAi-based insect control,and propose potential strategies to increase the effectiveness of RNAi in insect control.
基金supported by the National Key Research and Development Program of China(Grant Nos.2022YFF0711805,2022YFF0711801,and 2021YFF0704204)the Project of Sanya Yazhou Bay Science and Technology City,China(Grant No.SCKJ-JYRC-2023-45)+3 种基金the National Natural Science Foundation of China(Grant Nos.31971792 and 32160421)the Innovation Project of the Chinese Academy of Agricultural Sciences(CAAS)(Grant Nos.CAAS-ASTIP-2024-AII and ZDXM23011)the Special Fund of Chinese Central Government for Basic Scientific Research Operations in Commonweal Research Institutes(Grant No.JBYW-AII-2024-05)the Nanfan Special Project,CAAS,China(Grant No.YBXM2312).
文摘Accurate evaluation of disease levels in wild rice germplasm and identification of disease resistance are critical for developing rice varieties resistant to blast disease.However,existing evaluation methods face limitations that hinder progress in breeding.To address these challenges,we proposed an AI-powered method for evaluating blast disease levels and identifying resistance in wild rice.A lightweight segmentation model for diseased leaves and lesions was developed,incorporating an improved federated learning approach to enhance robustness and adaptability.Based on the segmentation results and resistance identification technical specifications,wild rice materials were evaluated into 10 disease levels(L0 to L9),further enabling disease-resistance identification through multiple replicates of the same materials.The method was successfully implemented on augmented reality glasses for real-time,first-person evaluation.Additionally,high-speed scanners and edge computing devices were integrated to enable continuous,precise,and dynamic evaluation.Experimental results demonstrate the outstanding performance of the proposed method,achieving effective segmentation of diseased leaves and lesions with only 0.22 M parameters and 5.3 G floating-point operations per second(FLOPs),with a mean average precision(mAP@0.5)of 96.3%.The accuracy of disease level evaluation and disease-resistance identification reached 99.7%,with a practical test accuracy of 99.0%,successfully identifying three highly resistant wild rice materials.This method provides strong technical support for efficiently identifying wild rice materials resistant to blast disease and advancing resistance breeding efforts.
基金supported by grants from the Chinese Academy of Sciences(XDA24010101)the Biological Breeding-National Science and Technology Major Project(2024ZD04077)+2 种基金the National Key Research and Development Program of China(2023YFF1001200)Natural Science Foundation of Zhejiang Province(LD24C130001)the Agricultural Science and Technology Innovation Program(ASTIP)of CAAS。
文摘A later heading date generally leads to higher grain yield in favorable ecological regions;however,grain yield reaches a limit as the heading date exceeds a certain threshold.Ghd7 is the first cloned major gene that regulates heading date,plant height and grain number.Here,we investigated the relationship between Ghd7 and florigen genes Hd3a and RFT1,to determine their roles in regulating heading date and grain number under different photoperiods.Our results revealed that under long-day(LD)conditions,Hd3a acts prior to RFT1 to promote heading while negatively regulating plant height and grain number.In contrast,Ghd7 positively regulates heading date,plant height,and grain number by inhibiting both Hd3a and RFT1.Under short-day(SD)conditions,the functions of Hd3a and RFT1 remain consistent with those under LD conditions,but Ghd7 does not inhibit their expression,resulting in a weaker phenotypic effect compared to Hd3a.Additionally,under both LD and SD conditions,increased Ghd7 expression enhances its inhibitory effect on Hd3a and RFT1,leading to later heading and increased grain number;however,once the heading date exceeds 94 d,grain number no longer increases.Moreover,the gn1a allele increased grain number by 16.5%to 42.5%,while combinations of the elite alleles from Ghd7,Hd3a,RFT1,and Gn1a significantly increased grain number by up to 240.9%.Therefore,we propose a new breeding strategy to optimize the heading date and grain number using the Ghd7Hd3aRFT1gn1a combination of Ghd7,Hd3a,RFT1,and Gn1a under LD conditions,and the Ghd7hd3aRFT1gn1a combination under SD conditions.This strategy improved the yield of the high-quality Northeast variety Kongyu 131(KY131)by 69.1%in Beijing and 93.7%in Hainan.This strategy will greatly improve the efficiency of north-to-south adaptation in rice,providing theoretical guidance for expanding the geographical adaptability of rice varieties.
文摘Background The bromodomain(BRD) proteins play a pivotal role in regulating gene expression by recognizing acetylated lysine residues and acting as chromatin-associated post-translational modification-inducing proteins. Although BRD proteins have been extensively studied in mammals, they have also been characterized in plants like Arabidopsis thaliana and Oryza sativa, where they regulate stress-responsive genes related to drought, salinity, and cold. However, their roles in cotton species remain unexplored.Results In this genome-wide comparative analysis, 145 BRD genes were identified in the tetraploid species(Gossypium hirsutum and G. barbadense), compared with 82 BRD genes in their diploid progenitors(G. arboreum and G. raimondii), indicating that polyploidization significantly influenced BRD gene evolution. Gene duplication analysis revealed 78.85% of duplications were segmental and 21.15% were tandem among 104 in-paralogous gene pairs, contributing to BRD gene expansion. Gene structure, motif, and domain analyses demonstrated that most genes were intron-less and conserved throughout evolution. Syntenic analysis revealed a greater number of orthologous gene pairs in the Dt sub-genome than in the At sub-genome. The abundance of regulatory, hormonal, and defense-related cis-regulatory elements in the promoter region suggests that BRD genes play a role in both biotic and abiotic stress responses. Protein-protein interaction analysis indicated that global transcription factor group E(GTE) transcription factors regulate BRD genes. Expression analysis revealed that BRD genes are predominantly involved in ovule development, with some genes displaying specific expression patterns under heat, cold, and salt stress. Furthermore, qRT-PCR analysis demonstrated significant differential expression of BRD genes between the tolerant and sensitive genotype, underscoring their potential role in mediating drought and salinity stress responses.Conclusions This study provides valuable insights into the evolution of BRD genes across species and their roles in abiotic stress tolerance, highlighting their potential in breeding programs to develop drought and salinity tolerant cotton varieties.
基金funded by the National Natural Science Foundation of China(32072022)the Nanfan Special Project,CAAS(YBXM07)the Hainan Yazhou Bay Seed Laboratory,China(B23CJ0208)。
文摘The germination process of seeds is influenced by the interplay between two opposing factors,pectin methylesterase(PME)and pectin methylesterase inhibitor(PMEI),which collectively regulate patterns of pectin methylesterification.Despite the recognized importance of pectin methylesterification in seed germination,the specific mechanisms that govern this process remain unclear.In this study,we demonstrated that the overexpression of GhPMEI53is associated with a decrease in PME activity and an increase in pectin methylesterification.This leads to seed cell wall softening,which positively regulates cotton seed germination.AtPMEI19,the homologue in Arabidopsis thaliana,plays a similar role in seed germination to GhPMEI53,indicating a conserved function and mechanism of PMEI in seed germination regulation.Further studies revealed that GhPMEI53 and AtPMEI19 directly contribute to promoting radicle protrusion and seed germination by inducing cell wall softening and reducing mechanical strength.Additionally,the pathways of abscicic acid(ABA)and gibberellin(GA)in the transgenic materials showed significant changes,suggesting that GhPMEI53/AtPMEI19-mediated pectin methylesterification serves as a regulatory signal for the related phytohormones involved in seed germination.In summary,GhPMEI53 and its homologs alter the mechanical properties of cell walls,which influence the mechanical resistance of the endosperm or testa.Moreover,they impact cellular phytohormone pathways(e.g.,ABA and GA)to regulate seed germination.These findings enhance our understanding of pectin methylesterification in cellular morphological dynamics and signaling transduction,and contribute to a more comprehensive understanding of the PME/PMEI gene superfamily in plants.
基金supported by the National Key Research and Development Program of China (Grant No.2023YFD1202600)the Zhejiang Lab independently establishes research projects (Research and Development of Intelligent Technologies and Platforms for Rice Breeding,Grant No.2021PE0AC05)the Natural Science Foundation of Zhejiang Province,China (Grant No.LQ22C130006)。
文摘Rice blast,caused by the fungus Magnaporthe oryzae,reduces rice yields by 10%to 35%.Incorporating blast resistance genes into breeding programs is an effective strategy to combat this disease.Understanding the genetic variants that confer resistance is crucial to this strategy.The gene Bsr-d1 encodes a C2H2-like transcription factor,and its recessive allele confers broad-spectrum resistance against infections by various strains of M.oryzae.In this study,we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice accessions.Our results revealed that wild rice exhibited significantly higher nucleotide diversity,with polymorphic regions primarily concentrated in the promoter region,in contrast to indica and japonica rice varieties.The Bsr-d1 gene displayed significant differentiation between indica and japonica rice varieties,with the bsr-d1 resistance allele being unique to indica rice.Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula.Moreover,we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene.In summary,our study uncovering the origin and evolution of bsr-d1 will enhance our understanding of resistance gene variation and expedite the resistance breeding process.
基金supported by the Hainan Yazhou Bay Seed Laboratory(B21HJ0215)an open project of the State Key Laboratory of Crop Stress Adaptation and Improvement at Henan University(2021KF03)+1 种基金the Central Public-interest Scientific Institution Basal Research Fund(S2022ZD02)Agricultural Science and Technology Innovation Program of CAAS.
文摘Brassinosteroids(BRs)are vital plant steroid hormones involved in numerous aspects of plant life including growth,development,and responses to various stresses.However,the underlying mechanisms of how BR regulates abiotic stress responses in wheat(Triticum aestivum L.)remain to be elucidated.Here,we find that BR signal core transcription factor BRASSINAZOLE-RESISTANT1(TaBZR1)is significantly up-regulated by salt treatment.Overexpression of Tabzr1-1D(a gain-of-function TaBZR1 mutant protein)improves wheat salt tolerance.Furthermore,we show that TaBZR1 binds directly to the G-box motif in the promoter of ABA biosynthesis gene TaNCED3 to activate its expression and promotes ABA accumulation.Moreover,TaBZR1 associates with the promoters of ROS-scavenging genes TaGPX2 and TaGPX3 to activate their expression.Taken together,our results elucidate that TaBZR1 improves salt-stress tolerance by activating some genes involved in the biosynthesis of ABA and ROS scavenging in wheat,which gives us a new strategy to improve the salt tolerance of wheat.
基金supported by the Guangxi Major Project of Science and Technology(Guike AA18118027)the Postdoctoral Project of Hainan Yazhou Bay Seed Laboratory Program(B21Y10203)the Scientific Research and Development Fund of the College of Agriculture,Guangxi University(EE101731).
文摘The lemon(Citrus limon;family Rutaceae)is one of the most important and popular fruits worldwide.Lemon also tolerates huan-glongbing(HLB)disease,which is a devastating citrus disease.Here we produced a gap-free and haplotype-resolved chromosome-scale genome assembly of the lemon by combining Pacific Biosciences circular consensus sequencing,Oxford Nanopore 50-kb ultra-long,and high-throughput chromatin conformation capture technologies.The assembly contained nine-pair chromosomes with a contig N50 of 35.6 Mb and zero gaps,while a total of 633.0 Mb genomic sequences were generated.The origination analysis identified 338.5Mb genomic sequences originating from citron(53.5%),147.4Mb frommandarin(23.3%),and 147.1Mb frompummelo(23.2%).The genome included 30528 protein-coding genes,and most of the assembled sequences were found to be repetitive sequences.Several significantly expanded gene families were associated with plant-pathogen interactions,plant hormone signal transduction,and the biosynthesis of major active components,such as terpenoids and f lavor compounds.Most HLB-tolerant genes were expanded in the lemon genome,such as 2-oxoglutarate(2OG)/Fe(II)-dependent oxygenase and constitutive disease resistance 1,cell wall-related genes,and lignin synthesis genes.Comparative transcriptomic analysis showed that phloem regeneration and lower levels of phloem plugging are the elements that contribute to HLB tolerance in lemon.Our results provide insight into lemon genome evolution,active component biosynthesis,and genes associated with HLB tolerance.
基金supported by the National Natural Science Foundation of China(31971927 and U21A20214)the Science and Technology Major Project of Anhui Province(2021d06050002)+4 种基金the Improved Varieties Joint Research(Rice)Project of Anhui Province(the 14th five-year plan)the National Key Research and Development Program of China(2020YFE0202300)the CAAS Innovative Team Awardthe Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City(B21HJ0215,B21HJ0223,and B21HJ0508)Nanfan Special Project,CAAS(YBXM04)。
文摘Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.
