Successful emergence from the soil is a prerequisite for survival of germinating seeds in their natural envi-ronment.In rice,coleoptile elongation facilitates seedling emergence and establishment,and ethylene plays an...Successful emergence from the soil is a prerequisite for survival of germinating seeds in their natural envi-ronment.In rice,coleoptile elongation facilitates seedling emergence and establishment,and ethylene plays an important role in this process.However,the underlying regulatory mechanism remains largely unclear.Here,we report that ethylene promotes cell elongation and inhibits cell expansion in rice coleoptiles,result-ing in longer and thinner coleoptiles that facilitate seedlings emergence from the soil.Transcriptome analysis showed that genes related to reactive oxygen species(ROS)generation are upregulated and genes involved in ROS scavenging are downregulated in the coleoptiles of ethylene-signaling mutants.Further investiga-tions showed that soil coverage promotes accumulation of ETHYLENE INSENSITIVE 3-LIKE 1(OsEIL1)and OsEIL2 in the upper region of the coleoptile,and both OsEIL1 and OsEIL2 can bind directly to the promoters of the GDP-mannose pyrophosphorylase(VTC1)gene OsVTC1-3 and the peroxidase(PRX)genes OsPRX37,OsPRX81,OsPRX82,and OsPRX88 to activate their expression.This leads to increased ascorbic acid content,greater peroxidase activity,and decreased ROS accumulation in the upper region of the coleoptile.Disruption of ROS accumulation promotes coleoptile growth and seedling emergence from soil.Thesendings deepen our understanding of the roles of ethylene and ROS in controlling coleoptile growth,and this information can be used by breeders to produce rice varieties suitable for direct seeding.展开更多
Bacterial leaf streak caused by Xanthomonas oryzae pv.oryzicola(Xoc)is a continuous threat to rice cultivation,leading to substantial yield losses with socioeconomic implications.Iron ions are essential mineral nutrie...Bacterial leaf streak caused by Xanthomonas oryzae pv.oryzicola(Xoc)is a continuous threat to rice cultivation,leading to substantial yield losses with socioeconomic implications.Iron ions are essential mineral nutrients for plant growth,but little information is available on how they influence mechanisms of rice immunity against Xoc.Here,we investigated the role of the myeloblastosis-related(MYB)transcriptional repressor OsMYBxoc1 in modulation of rice resistance through control of iron ion transport.Overexpression of OsMYBxoc1 significantly increased rice resistance,whereas OsMYBxoc1 RNA-interference lines and knockout mutants showed the opposite result.Suppression of OsMYBxoc1 expression dampened the immune response induced by pathogen-associated molecular patterns.We demonstrated that OsMYBxoc1 binds specifically to the OsNRAMP5 promoter and represses transcription of OsNRAMP5.OsNRAMP5,a negative regulator of rice resistance to bacterial leaf streak,possesses metal ion transport activity,and inhibition of OsMYBxoc1 expression increased the iron ion content in rice.Activity of the iondependent H2O2 scavenging enzyme catalase was increased in plants with suppressed expression of OsMYBxoc1 or overexpression of OsNRAMP5.We found that iron ions promoted Xoc infection and interfered with the production of reactive oxygen species induced by Xoc.The type Ⅲ effector XopAK directly inhibited OsMYBxoc1 transcription,indicating that the pathogen may promote its own proliferation by relieving restriction of iron ion transport in plants.In addition,iron complemented the pathogenicity defects of the RS105_DXopAK mutant strain,further confirming that iron utilization by Xoc may be dependent upon XopAK.In conclusion,our study reveals a novel mechanism by which OsMYBxoc1 modulates rice resistance by regulating iron accumulation and demonstrates that Xoc can accumulate iron ions by secreting the effector XopAK to promote its own infection.展开更多
Increasing soil salinization has led to severe reductions in plant yield and quality,and investigating the mo-lecular mechanism of salt stress response is therefore an urgent priority.In this study,we systematically a...Increasing soil salinization has led to severe reductions in plant yield and quality,and investigating the mo-lecular mechanism of salt stress response is therefore an urgent priority.In this study,we systematically analyzed the response of cotton roots to salt stress using single-cell transcriptomics technology;56281 high-quality cells were obtained from 5-day-old lateral root tips of Gossypium arboreum under natural growth conditions and different salt treatments.Ten cell types with an array of novel marker genes were identified and confirmed by in situ RNA hybridization,and pseudotime analysis of some specific cell types revealed their potential differentiation trajectories.Prominent changes in cell numbers under salt stress were observed for outer epidermal and inner endodermal cells,which were significantly enriched in response to stress,amide biosynthetic process,glutathione metabolism,and glycolysis/gluconeogenesis.Analysis of differentially expressed genes identified in multiple comparisons revealed other functional ag-gregations concentrated on plant-type primary cell wall biogenesis,defense response,phenylpropanoid biosynthesis,and metabolic pathways.Some candidate differentially expressed genes encoding transcrip-tion factors or associated with plant hormones also responsive to salt stress were identified,and the func-tion of Ga03G2153,annotated as auxin-responsive GH3.6,was confirmed by virus-induced gene silencing.The GaGH3.6-silenced plants showed a severe stress-susceptible phenotype,and physiological and biochemical measurements indicated that they suffered more significant oxidative damage.These results suggest that GaGH3.6 might participate in cotton salt tolerance by regulating redox processes.We thus construct a transcriptional atlas of salt-stressed cotton roots at single-cell resolution,enabling us to explore cellular heterogeneity and differentiation trajectories and providing valuable insights into the mo-lecular mechanisms that underlie plant stress tolerance.展开更多
Despite recent advances in crop metabolomics,the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown.Here,we performed widely tar-geted metabolit...Despite recent advances in crop metabolomics,the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown.Here,we performed widely tar-geted metabolite profiling of kernels from three developmental stages(grain-filling kernels[FKs],mature kernels[MKs],and germinating kernels[GKs])using a population of 159 recombinant inbred lines.We de-tected 625 annotated metabolites and mapped 3173,3143,and 2644 metabolite quantitative trait loci(mQTLs)in FKs,MKs,and GKs,respectively.Only 52 mQTLs were mapped at all three stages,indicating the high stage specificity of the wheat kernel metabolome.Four candidate genes were functionally vali-dated by in vitro enzymatic reactions and/or transgenic approaches in wheat,three of which mediated the tricin metabolic pathway.Metaboliteflux efficiencies within the tricin pathway were evaluated,and su-perior candidate haplotypes were identified,comprehensively delineating the tricin metabolism pathway in wheat.Finally,additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study.Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.展开更多
Prime editing(PE)technology enables precise alterations in the genetic code of a genome of interest.PE offers great potential for identifying major agronomically important genes in plants and editing them into superio...Prime editing(PE)technology enables precise alterations in the genetic code of a genome of interest.PE offers great potential for identifying major agronomically important genes in plants and editing them into superior variants,ideally targeting multiple loci simultaneously to realize the collective effects of the edits.Here,we report the development of a modular assembly-based multiplex PE system in rice and demon-strate its efficacy in editing up to four genes in a single transformation experiment.The duplex PE(DPE)system achieved a co-editing efficiency of 46.1%in the T0 generation,converting TFIIAg5 to xa5 and xa23 to Xa23SW11.The resulting double-mutant lines exhibited robust broad-spectrum resistance against multiple Xanthomonas oryzae pathovar oryzae(Xoo)strains in the T1 generation.In addition,we success-fully edited OsEPSPS1 to an herbicide-tolerant variant and OsSWEET11a to a Xoo-resistant allele,achieving a co-editing rate of 57.14%.Furthermore,with the quadruple PE(QPE)system,we edited four genes—two for herbicide tolerance(OsEPSPS1 and OsALS1)and two for Xoo resistance(TFIIAg5 and OsSWEET11a)—using one construct,with a co-editing efficiency of 43.5%for all four genes in the T0 gen-eration.We performed multiplex PE usingfive more constructs,including two for triplex PE(TPE)and three for QPE,each targeting a different set of genes.The editing rates were dependent on the activity of pegRNA and/or ngRNA.For instance,optimization of ngRNA increased the PE rates for one of the targets(OsSPL13)from 0%to 30%but did not improve editing at another target(OsGS2).Overall,our modular assembly-based system yielded high PE rates and streamlined the cloning of PE reagents,making it feasible for more labs to utilize PE for their editing experiments.Thesefindings have significant implications for advancing gene editing techniques in plants and may pave the way for future agricultural applications.展开更多
Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and...Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum(TM-1)and Gossypium barbadense(3-79).Compared with previously published reference genomes,our assemblies show substantial improvements,with the contig N50 improved by 4.6-fold and 5.6-fold,respectively,and thus represent the most complete cotton genomes to date.These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G.hirsutum and G.barbadense,respectively.Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize(CRM)and Tekay long terminal repeat families,and the CRM family reshapes the centromere structure of the At subgenome after polyploidization.These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes,ensuring centromere function and genome stability.In addition,the reposi-tioning and high sequence divergence of centromeres between G.hirsutum and G.barbadense have contributed to speciation and centromere diversity.This study sheds light on centromere evolution in a sig-nificant crop and provides an alternative approach for exploring the evolution of polyploid plants.展开更多
Dear Editors,Soybeans are a global commodity for their edible protein and vegetable oil.The global population is predicted to be 9.7 billion by 2050(UN,2022),with a concomitant drastic increase in protein demand.With ...Dear Editors,Soybeans are a global commodity for their edible protein and vegetable oil.The global population is predicted to be 9.7 billion by 2050(UN,2022),with a concomitant drastic increase in protein demand.With already 2.4 billion people suffering from food insecurity(FAO et al.,2023),there is an urgent need to meet future production demands for plant-based proteins.展开更多
Bananas(Musa spp.)are one of the world’s most important fruit crops and play a vital role in food security for many developing countries.Most banana cultivars are triploids derived from inter-and intraspecific hybrid...Bananas(Musa spp.)are one of the world’s most important fruit crops and play a vital role in food security for many developing countries.Most banana cultivars are triploids derived from inter-and intraspecific hybrid-izations between the wild diploid ancestor species Musa acuminate(AA)and M.balbisiana(BB).We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types,Plantain and Silk,and precisely characterize ancestral contributions by examining ancestry mosaics across the genome.Widespread asymmetric evolution is observed in their subgenomes,which can be linked to frequent homol-ogous exchange events.We reveal the genetic makeup of triploid banana cultivars and verify that subge-nome B is a rich source of disease resistance genes.Only 58.5%and 59.4%of Plantain and Silk genes,respectively,are present in all three haplotypes,with>50%of genes being differentially expressed alleles in different subgenomes.We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4(Foc TR4),which con-firms that Plantain can initiate defense responses faster than Silk.Additionally,we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk.Our study provides resources for better understanding the genomic architecture of culti-vated bananas and has important implications for Musa genetics and breeding.展开更多
Multilayered defense responses are activated upon pathogen attack.Viruses utilize a number of strategies to maximize the coding capacity of their small genomes and produce viral proteins for infection,including suppre...Multilayered defense responses are activated upon pathogen attack.Viruses utilize a number of strategies to maximize the coding capacity of their small genomes and produce viral proteins for infection,including suppression of host defense.Here,we reveal translation leakage as one of these strategies:two viral effec-tors encoded by tomato golden mosaic virus,chloroplast-localized C4(cC4)and membrane-associated C4(mC4),are translated from two in-frame start codons and function cooperatively to suppress defense.cC4 localizes in chloroplasts,to which it recruits NbPUB4 to induce ubiquitination of the outer membrane;as a result,this organelle is degraded,and chloroplast-mediated defenses are abrogated.However,chloroplast-localized cC4 induces the production of singlet oxygen(^(1)O_(2)),which in turn promotes translo-cation of the ^(1)O_(2) sensor NbMBS1 from the cytosol to the nucleus,where it activates expression of the CERK1 gene.Importantly,an antiviral effect exerted by CERK1 is countered by mC4,localized at the plasma membrane.mC4,like cC4,recruits NbPUB4 and promotes the ubiquitination and subsequent degradation of CERK1,suppressing membrane-based,receptor-like kinase-dependent defenses.Importantly,this translation leakage strategy seems to be conserved in multiple viral species and is related to host range.Thisfinding suggests that stacking of different cellular antiviral responses could be an effective way to abrogate viral infection and engineer sustainable resistance to major crop viral diseases in thefield.展开更多
The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Her...The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Here,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell resolution.We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis seedlings.We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers.We further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity.In addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs.The analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://biobigdata.nju.edu.cn/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.展开更多
The shoot apical meristem(SAM)is responsible for overall shoot growth by generating all aboveground structures.Recent research has revealed that the SAM displays an autonomous heat stress(HS)memory of a previous non-l...The shoot apical meristem(SAM)is responsible for overall shoot growth by generating all aboveground structures.Recent research has revealed that the SAM displays an autonomous heat stress(HS)memory of a previous non-lethal HS event.Considering the importance of the SAM for plant growth,it is essential to determine how its thermomemory is mechanistically controlled.Here,we report that HEAT SHOCK TRAN-SCRIPTION FACTOR A7b(HSFA7b)plays a crucial role in this process in Arabidopsis,as the absence of functional HSFA7b results in the temporal suppression of SAM activity after thermopriming.We found that HSFA7b directly regulates ethylene response at the SAM by binding to the promoter of the key ethylene signaling gene ETHYLENE-INSENSITIVE 3 to establish thermotolerance.Moreover,we demonstrated that HSFA7b regulates the expression of ETHYLENE OVERPRODUCER 1(ETO1)and ETO1-LIKE 1,both of which encode ethylene biosynthesis repressors,thereby ensuring ethylene homeostasis at the SAM.Taken together,these results reveal a crucial and tissue-specic role for HSFA7b in thermomemory at the Arabidopsis SAM.展开更多
The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development.Here we report a graph-based pan-genome of B.oleracea constructed from high-quality genome...The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development.Here we report a graph-based pan-genome of B.oleracea constructed from high-quality genome assemblies of different morphotypes.The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin-andflowering-related genes.Population genomic analyses revealed that early domestication of B.oleracea focused on leaf or stem development.Geneflows resulting from agricultural practices and variety improvement were detected among different morphotypes.Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAV-ATA3/ESR-RELATED family gene as crucial players in leaf–stem differentiation during the early stage of B.oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts.Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization andflowering characteristics among different morphotypes,and variations in thefirst intron of BoFLC3 are involved infine-tuning theflowering process in cauliflower.This study provides a comprehensive understanding of the pan-genome of B.oleracea and sheds light on the domestication and differential organ development of this globally important crop species.展开更多
Transitory starch is an important carbon source in leaves,and its biosynthesis and metabolism are closely related to grain quality and yield.The molecular mechanisms controlling leaf transitory starch biosynthesis and...Transitory starch is an important carbon source in leaves,and its biosynthesis and metabolism are closely related to grain quality and yield.The molecular mechanisms controlling leaf transitory starch biosynthesis and degradation and their effects on rice(Oryza sativa)quality and yield remain unclear.Here,we show that OsLESV and OsESV1,the rice orthologs of AtLESV and AtESV1,are associated with transitory starch biosynthesis in rice.The total starch and amylose contents in leaves and endosperms are significantly reduced,and the final grain quality and yield are compromised in oslesv and osesv1 single and oslesv esv1 double mutants.Furthermore,we found that OsLESV and OsESV1 bind to starch,and this binding depends on a highly conserved C-terminal tryptophan-rich region that acts as a starch-binding domain.Importantly,OsLESV and OsESV1 also interact with the key enzymes of starch biosynthesis,granule-bound starch synthase I(GBSSI),GBSSII,and pyruvate orthophosphote dikiase(PPDKB),to maintain their protein stability and activity.OsLESV and OsESV1 also facilitate the targeting of GBSSI and GBSSII from plastid stroma to starch granules.Overexpression of GBSSI,GBSSII,and PPDKB can partly rescue the phenotypic defects of the oslesv and osesv1 mutants.Thus,we demonstrate that OsLESV and OsESV1 play a key role in regulating the biosynthesis of both leaf transitory starch and endosperm storage starch in rice.These findings deepen our understanding of the molecular mechanisms underlying transitory starch biosynthesis in rice leaves and reveal how the transitory starch metabolism affects rice grain quality and yield,providing useful information for the genetic improvement of rice grain quality and yield.展开更多
Plant organ size is an important agronomic trait that makes a significant contribution to plant yield.Despite its central importance,the genetic and molecular mechanisms underlying organ size control remain to be full...Plant organ size is an important agronomic trait that makes a significant contribution to plant yield.Despite its central importance,the genetic and molecular mechanisms underlying organ size control remain to be fully clarified.Here,we report that the trithorax group protein ULTRAPETALA1(ULT1)interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15(TCP14/15)transcription factors by antagonizing the LIN-11,ISL-1,and MEC-3(LIM)peptidase DA1,thereby regulating organ size in Arabidopsis.Loss of ULT1 function significantly increases rosette leaf,petal,silique,and seed size,whereas overexpression of ULT1 results in reduced organ size.ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication.Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development.ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes,activating their expression to determinefinal cell size.Furthermore,we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation.Collectively,ourfindings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.展开更多
Pigmented rice stands out for its nutritional value and is gaining more and more attention.Wild rice,domes-ticated red rice,and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the...Pigmented rice stands out for its nutritional value and is gaining more and more attention.Wild rice,domes-ticated red rice,and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype.We performed population genetic analyses using 5104 worldwide rice acces-sions,including 2794 accessions with red or black pericarps,85 of which were newly sequenced in this study.The results suggested an evolutionary trajectory of red landraces originating from wild rice,and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years.Cultivated red rice was found to feralize to weedy rice,and weedy rice could be further re-domesticated to cultivated red rice.A genome-wide association study based on the 2794 accessions with pigmented peri-carps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization.Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.展开更多
Roseiflexus castenholzii is a gram-negativefilamentous phototrophic bacterium that carries out anoxygenic photosynthesis through a cyclic electron transport chain(ETC).The ETC is composed of a reaction center(RC)–lig...Roseiflexus castenholzii is a gram-negativefilamentous phototrophic bacterium that carries out anoxygenic photosynthesis through a cyclic electron transport chain(ETC).The ETC is composed of a reaction center(RC)–light-harvesting(LH)complex(rcRC–LH);an alternative complex III(rcACIII),which functionally re-places the cytochrome bc1/b6f complex;and the periplasmic electron acceptor auracyanin(rcAc).Although compositionally and structurally different from the bc1/b6f complex,rcACIII plays similar essential roles in oxidizing menaquinol and transferring electrons to the rcAc.However,rcACIII-mediated electron transfer(which includes both an intraprotein route and a downstream route)has not been clearly elucidated,nor have the details of cyclic ETC.Here,we identify a previously unknown monoheme cytochrome c(cyt c551)as a novel periplasmic electron acceptor of rcACIII.It reduces the light-excited rcRC–LH to complete a cyclic ETC.We also reveal the molecular mechanisms involved in the ETC using electron paramagnetic resonance(EPR),spectroelectrochemistry,and enzymatic and structural analyses.Wefind that electrons released from rcACIII-oxidized menaquinol are transferred to two alternative periplasmic electron acceptors(rcAc and cyt c551),which eventually reduce the rcRC to form the complete cyclic ETC.This work serves as a foundation for further studies of ACIII-mediated electron transfer in anoxygenic photosynthesis and broadens our under-standing of the diversity and molecular evolution of prokaryotic ETCs.展开更多
Invasive alien species are primary drivers of biodiversity loss and species extinction.Smooth cordgrass(Spartina alterniflora)is one of the most aggressive invasive plants in coastal ecosystems around the world.Howeve...Invasive alien species are primary drivers of biodiversity loss and species extinction.Smooth cordgrass(Spartina alterniflora)is one of the most aggressive invasive plants in coastal ecosystems around the world.However,the genomic bases and evolutionary mechanisms underlying its invasion success have remained largely unknown.Here,we assembled a chromosome-level reference genome and performed phenotypic and population genomic analyses between native US and introduced Chinese populations.Our phenotypic comparisons showed that introduced Chinese populations have evolved competitive traits,such as earlyflowering time and greater plant biomass,during secondary introductions along China’s coast.Population genomic and transcriptomic inferences revealed distinct evolutionary trajectories of low-and high-latitude Chinese populations.In particular,genetic mixture among different source populations,together with in-dependent natural selection acting on distinct target genes,may have resulted in high genome dynamics of the introduced Chinese populations.Our study provides novel phenotypic and genomic evidence showing how smooth cordgrass rapidly adapts to variable environmental conditions in its introduced ranges.Moreover,candidate genes related toflowering time,fast growth,and stress tolerance(i.e.,salinity and submergence)provide valuable genetic resources for future improvement of cereal crops.展开更多
Weeds pose a significant threat to crop production,resulting in substantial yield reduction.In addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human con-trol.In ...Weeds pose a significant threat to crop production,resulting in substantial yield reduction.In addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human con-trol.In recent years,the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits.In this review,we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology,including the origins of weed spe-cies,weed classification,and the underlying genetic and molecular bases of important weedy traits such as crop–weed interactions,adaptability to different environments,photoperiodicflowering responses,and herbicide resistance.In addition,we discuss limitations to the application of multi-omics techniques in weed science,particularly compared with their extensive use in model plants and crops.In this regard,we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research.These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits.The resulting advances will facilitate the development of sustainable and highly effective weed management strategies,promoting greener practices in agriculture.展开更多
The expression of double-stranded RNAs(dsRNAs)from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes.However,there are limitations to th...The expression of double-stranded RNAs(dsRNAs)from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes.However,there are limitations to the efficiency of plastid-mediated RNA interference(PM-RNAi)due to the initial damage caused by the insects and their slow response to RNA interference.In this study,we developed transplastomic poplar plants that express dsRNAs targeting the b-Actin(dsACT)and Srp54k(dsSRP54K)genes of Plagiodera versicolora.Feeding experiments showed that transplastomic poplar plants can cause significantly higher mortality in P.versicolora larvae compared with nuclear transgenic or wild-type poplar plants.The efficient killing effect of PM-RNAi on P.versicolora larvae was found to be dependent on the presence of gut bacteria.Importantly,foliar application of a gut bacterial strain,Pseudomonas putida,will induce dysbiosis in the gut bacteria of P.versicolora larvae,leading to a significant acceleration in the speed of killing by PM-RNAi.Overall,our findings suggest that interfering with gut bacteria could be a promising strategy to enhance the effectiveness of PM-RNAi for insect pest control,offering a novel and effective approach for crop protection based on RNAi technology.展开更多
Rice blast is a devastating disease worldwide,threatening rice production and food security.The blast fun-gus Magnaporthe oryzae invades the host via the appressorium,a specialized pressure-generating struc-ture that ...Rice blast is a devastating disease worldwide,threatening rice production and food security.The blast fun-gus Magnaporthe oryzae invades the host via the appressorium,a specialized pressure-generating struc-ture that generates enormous turgor pressure to penetrate the host cuticle.However,owing to ongoing evolution of fungicide resistance,it is vitally important to identify new targets and fungicides.Here,we show that Trs85,a subunit of the transport protein particle III complex,is essential for appressorium-mediated infection in M.oryzae.We explain how Trs85 regulates autophagy through Ypt1(a small guano-sine triphosphatase protein)in M.oryzae.We then identify a key conserved amphipathic a helix within Trs85 that is associated with pathogenicity of M.oryzae.Through computer-aided screening,we identify a lead compound,SP-141,that affects autophagy and the Trs85–Ypt1 interaction.SP-141 demonstrates a substantial capacity to effectively inhibit infection caused by the rice blast fungus while also exhibiting wide-ranging potential as an antifungal agent with broad-spectrum activity.Taken together,our data show that Trs85 is a potential new target and that SP-141 has potential for the control of rice blast.Ourfindings thus provide a novel strategy that may help in thefight against rice blast.展开更多
基金funded by National Natural Science Foundation of China grants 32272019 to R.Q.and 32030079 to R.H.the Agricultural Science and Technology Innovation Program (ASTIP No.CAAS-ZDRW202201)of the Chinese Academy of Agricultural Sciences.
文摘Successful emergence from the soil is a prerequisite for survival of germinating seeds in their natural envi-ronment.In rice,coleoptile elongation facilitates seedling emergence and establishment,and ethylene plays an important role in this process.However,the underlying regulatory mechanism remains largely unclear.Here,we report that ethylene promotes cell elongation and inhibits cell expansion in rice coleoptiles,result-ing in longer and thinner coleoptiles that facilitate seedlings emergence from the soil.Transcriptome analysis showed that genes related to reactive oxygen species(ROS)generation are upregulated and genes involved in ROS scavenging are downregulated in the coleoptiles of ethylene-signaling mutants.Further investiga-tions showed that soil coverage promotes accumulation of ETHYLENE INSENSITIVE 3-LIKE 1(OsEIL1)and OsEIL2 in the upper region of the coleoptile,and both OsEIL1 and OsEIL2 can bind directly to the promoters of the GDP-mannose pyrophosphorylase(VTC1)gene OsVTC1-3 and the peroxidase(PRX)genes OsPRX37,OsPRX81,OsPRX82,and OsPRX88 to activate their expression.This leads to increased ascorbic acid content,greater peroxidase activity,and decreased ROS accumulation in the upper region of the coleoptile.Disruption of ROS accumulation promotes coleoptile growth and seedling emergence from soil.Thesendings deepen our understanding of the roles of ethylene and ROS in controlling coleoptile growth,and this information can be used by breeders to produce rice varieties suitable for direct seeding.
基金supported by the National Natural Science Foundation of China(32272557 and 32072500)the Major Basic Research Project of the Natural Science Foundation of Shandong Province(ZR2022ZD23)+2 种基金the National Key Research and Development Program(2022YFD 1402100 and 2022YFD1401500)the Shandong Province Key Research and Development Plan(2022TZXD0025 and 2021TZXD007-04-4)the Taishan Scholar Program of Shandong Province(tstp20221117).
文摘Bacterial leaf streak caused by Xanthomonas oryzae pv.oryzicola(Xoc)is a continuous threat to rice cultivation,leading to substantial yield losses with socioeconomic implications.Iron ions are essential mineral nutrients for plant growth,but little information is available on how they influence mechanisms of rice immunity against Xoc.Here,we investigated the role of the myeloblastosis-related(MYB)transcriptional repressor OsMYBxoc1 in modulation of rice resistance through control of iron ion transport.Overexpression of OsMYBxoc1 significantly increased rice resistance,whereas OsMYBxoc1 RNA-interference lines and knockout mutants showed the opposite result.Suppression of OsMYBxoc1 expression dampened the immune response induced by pathogen-associated molecular patterns.We demonstrated that OsMYBxoc1 binds specifically to the OsNRAMP5 promoter and represses transcription of OsNRAMP5.OsNRAMP5,a negative regulator of rice resistance to bacterial leaf streak,possesses metal ion transport activity,and inhibition of OsMYBxoc1 expression increased the iron ion content in rice.Activity of the iondependent H2O2 scavenging enzyme catalase was increased in plants with suppressed expression of OsMYBxoc1 or overexpression of OsNRAMP5.We found that iron ions promoted Xoc infection and interfered with the production of reactive oxygen species induced by Xoc.The type Ⅲ effector XopAK directly inhibited OsMYBxoc1 transcription,indicating that the pathogen may promote its own proliferation by relieving restriction of iron ion transport in plants.In addition,iron complemented the pathogenicity defects of the RS105_DXopAK mutant strain,further confirming that iron utilization by Xoc may be dependent upon XopAK.In conclusion,our study reveals a novel mechanism by which OsMYBxoc1 modulates rice resistance by regulating iron accumulation and demonstrates that Xoc can accumulate iron ions by secreting the effector XopAK to promote its own infection.
基金supported by the National Natural Science Foundation of China (31471548,32272179,and 31801404)the Central Plains Science and Technology Innovation Leader Project (214200510029)+4 种基金the Program for Innovative Research Team (in Science and Technology)in University of Henan Province (20IRTSTHN021)the Science and Technology Development Project of Anyang City (2022C01NY001 and 2022C01NY003)the Doctoral and Postdoctoral Research Fund of Anyang Institute of Technology (BSJ2019014 and BHJ2020002)the Key Scientific Research Project of Henan Higher Education Institutions of China (20A210006)the Zhongyuan Scholars Workstation (224400510020).
文摘Increasing soil salinization has led to severe reductions in plant yield and quality,and investigating the mo-lecular mechanism of salt stress response is therefore an urgent priority.In this study,we systematically analyzed the response of cotton roots to salt stress using single-cell transcriptomics technology;56281 high-quality cells were obtained from 5-day-old lateral root tips of Gossypium arboreum under natural growth conditions and different salt treatments.Ten cell types with an array of novel marker genes were identified and confirmed by in situ RNA hybridization,and pseudotime analysis of some specific cell types revealed their potential differentiation trajectories.Prominent changes in cell numbers under salt stress were observed for outer epidermal and inner endodermal cells,which were significantly enriched in response to stress,amide biosynthetic process,glutathione metabolism,and glycolysis/gluconeogenesis.Analysis of differentially expressed genes identified in multiple comparisons revealed other functional ag-gregations concentrated on plant-type primary cell wall biogenesis,defense response,phenylpropanoid biosynthesis,and metabolic pathways.Some candidate differentially expressed genes encoding transcrip-tion factors or associated with plant hormones also responsive to salt stress were identified,and the func-tion of Ga03G2153,annotated as auxin-responsive GH3.6,was confirmed by virus-induced gene silencing.The GaGH3.6-silenced plants showed a severe stress-susceptible phenotype,and physiological and biochemical measurements indicated that they suffered more significant oxidative damage.These results suggest that GaGH3.6 might participate in cotton salt tolerance by regulating redox processes.We thus construct a transcriptional atlas of salt-stressed cotton roots at single-cell resolution,enabling us to explore cellular heterogeneity and differentiation trajectories and providing valuable insights into the mo-lecular mechanisms that underlie plant stress tolerance.
基金supported by the National Major Program of China (2023ZD0406903)the Natural Science Foundation for Distinguished Young Scientists of Hubei Province (2021CFA058)+2 种基金the Young Topnotch Talent Cultivation Program of Hubei Provincethe National Natural Science Foundation of China (32001541)the China Postdoctoral Science Foundation (2021T140246).
文摘Despite recent advances in crop metabolomics,the genetic control and molecular basis of the wheat kernel metabolome at different developmental stages remain largely unknown.Here,we performed widely tar-geted metabolite profiling of kernels from three developmental stages(grain-filling kernels[FKs],mature kernels[MKs],and germinating kernels[GKs])using a population of 159 recombinant inbred lines.We de-tected 625 annotated metabolites and mapped 3173,3143,and 2644 metabolite quantitative trait loci(mQTLs)in FKs,MKs,and GKs,respectively.Only 52 mQTLs were mapped at all three stages,indicating the high stage specificity of the wheat kernel metabolome.Four candidate genes were functionally vali-dated by in vitro enzymatic reactions and/or transgenic approaches in wheat,three of which mediated the tricin metabolic pathway.Metaboliteflux efficiencies within the tricin pathway were evaluated,and su-perior candidate haplotypes were identified,comprehensively delineating the tricin metabolism pathway in wheat.Finally,additional wheat metabolic pathways were re-constructed by updating them to incorporate the 177 candidate genes identified in this study.Our work provides new information on variations in the wheat kernel metabolome and important molecular resources for improvement of wheat nutritional quality.
基金supported by an NSF award (IOS-2210259 to B.Y.)a subaward to the University of Missouri from the Heinrich Heine University of Dusseldorf funded by the Bill&Melinda Gates Foundation (OPP1155704)supported by the Daniel Millikan Award for Outstanding Research in Plant–Microbe Interactions at the University of Missouri.
文摘Prime editing(PE)technology enables precise alterations in the genetic code of a genome of interest.PE offers great potential for identifying major agronomically important genes in plants and editing them into superior variants,ideally targeting multiple loci simultaneously to realize the collective effects of the edits.Here,we report the development of a modular assembly-based multiplex PE system in rice and demon-strate its efficacy in editing up to four genes in a single transformation experiment.The duplex PE(DPE)system achieved a co-editing efficiency of 46.1%in the T0 generation,converting TFIIAg5 to xa5 and xa23 to Xa23SW11.The resulting double-mutant lines exhibited robust broad-spectrum resistance against multiple Xanthomonas oryzae pathovar oryzae(Xoo)strains in the T1 generation.In addition,we success-fully edited OsEPSPS1 to an herbicide-tolerant variant and OsSWEET11a to a Xoo-resistant allele,achieving a co-editing rate of 57.14%.Furthermore,with the quadruple PE(QPE)system,we edited four genes—two for herbicide tolerance(OsEPSPS1 and OsALS1)and two for Xoo resistance(TFIIAg5 and OsSWEET11a)—using one construct,with a co-editing efficiency of 43.5%for all four genes in the T0 gen-eration.We performed multiplex PE usingfive more constructs,including two for triplex PE(TPE)and three for QPE,each targeting a different set of genes.The editing rates were dependent on the activity of pegRNA and/or ngRNA.For instance,optimization of ngRNA increased the PE rates for one of the targets(OsSPL13)from 0%to 30%but did not improve editing at another target(OsGS2).Overall,our modular assembly-based system yielded high PE rates and streamlined the cloning of PE reagents,making it feasible for more labs to utilize PE for their editing experiments.Thesefindings have significant implications for advancing gene editing techniques in plants and may pave the way for future agricultural applications.
基金supported by the National Natural Science Foundation of China (32170645)the National Key Research and Development Program of China (2021YFF1000900).
文摘Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum(TM-1)and Gossypium barbadense(3-79).Compared with previously published reference genomes,our assemblies show substantial improvements,with the contig N50 improved by 4.6-fold and 5.6-fold,respectively,and thus represent the most complete cotton genomes to date.These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G.hirsutum and G.barbadense,respectively.Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize(CRM)and Tekay long terminal repeat families,and the CRM family reshapes the centromere structure of the At subgenome after polyploidization.These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes,ensuring centromere function and genome stability.In addition,the reposi-tioning and high sequence divergence of centromeres between G.hirsutum and G.barbadense have contributed to speciation and centromere diversity.This study sheds light on centromere evolution in a sig-nificant crop and provides an alternative approach for exploring the evolution of polyploid plants.
基金supported by the National Institute of Food and Agriculture award 2014-33522-22531 (to M.A.S.and E.M.H.)the Start-up Fund of the Huazhong Agricultural University (HZAU) (to J.Z.).
文摘Dear Editors,Soybeans are a global commodity for their edible protein and vegetable oil.The global population is predicted to be 9.7 billion by 2050(UN,2022),with a concomitant drastic increase in protein demand.With already 2.4 billion people suffering from food insecurity(FAO et al.,2023),there is an urgent need to meet future production demands for plant-based proteins.
基金funded by the Strategy of Rural Vitalization of Guangdong Provinces (2022-NPY-00-003,2022-NJS-00-001)the National Natural Science Foundation of China (32270712)+4 种基金the earmarked fund for CARS (CARS-31-01)GDAAS (202102TD,R2020PY-JX002)the Ba-Gui Scholar Program of Guangxi (to Z.-G.H)the Laboratory of Lingnan Modern Agriculture Project (NT2021004)the Maoming Branch Grant (2021TDQD003).
文摘Bananas(Musa spp.)are one of the world’s most important fruit crops and play a vital role in food security for many developing countries.Most banana cultivars are triploids derived from inter-and intraspecific hybrid-izations between the wild diploid ancestor species Musa acuminate(AA)and M.balbisiana(BB).We report two haplotype-resolved genome assemblies of the representative AAB-cultivated types,Plantain and Silk,and precisely characterize ancestral contributions by examining ancestry mosaics across the genome.Widespread asymmetric evolution is observed in their subgenomes,which can be linked to frequent homol-ogous exchange events.We reveal the genetic makeup of triploid banana cultivars and verify that subge-nome B is a rich source of disease resistance genes.Only 58.5%and 59.4%of Plantain and Silk genes,respectively,are present in all three haplotypes,with>50%of genes being differentially expressed alleles in different subgenomes.We observed that the number of upregulated genes in Plantain is significantly higher than that in Silk at one-week post-inoculation with Fusarium wilt tropical race 4(Foc TR4),which con-firms that Plantain can initiate defense responses faster than Silk.Additionally,we compared genomic and transcriptomic differences among the genes related to carotenoid synthesis and starch metabolism between Plantain and Silk.Our study provides resources for better understanding the genomic architecture of culti-vated bananas and has important implications for Musa genetics and breeding.
基金funded by grants from the National Natural Science Foundation of China (31930089)the National Key Research and Development Program of China (2021YFD1400400)the Yunnan Zhouxueping Expert Workstation (No.202205AF150047).
文摘Multilayered defense responses are activated upon pathogen attack.Viruses utilize a number of strategies to maximize the coding capacity of their small genomes and produce viral proteins for infection,including suppression of host defense.Here,we reveal translation leakage as one of these strategies:two viral effec-tors encoded by tomato golden mosaic virus,chloroplast-localized C4(cC4)and membrane-associated C4(mC4),are translated from two in-frame start codons and function cooperatively to suppress defense.cC4 localizes in chloroplasts,to which it recruits NbPUB4 to induce ubiquitination of the outer membrane;as a result,this organelle is degraded,and chloroplast-mediated defenses are abrogated.However,chloroplast-localized cC4 induces the production of singlet oxygen(^(1)O_(2)),which in turn promotes translo-cation of the ^(1)O_(2) sensor NbMBS1 from the cytosol to the nucleus,where it activates expression of the CERK1 gene.Importantly,an antiviral effect exerted by CERK1 is countered by mC4,localized at the plasma membrane.mC4,like cC4,recruits NbPUB4 and promotes the ubiquitination and subsequent degradation of CERK1,suppressing membrane-based,receptor-like kinase-dependent defenses.Importantly,this translation leakage strategy seems to be conserved in multiple viral species and is related to host range.Thisfinding suggests that stacking of different cellular antiviral responses could be an effective way to abrogate viral infection and engineer sustainable resistance to major crop viral diseases in thefield.
基金supported by grants from the National Natural Science Foundation of China (grants 32070656,32270709,32070677,and 32000362)the Natural Science Foundation of Jiangsu Higher Education Institutions of China (grant 23KJA210002)+1 种基金the open funds of the Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding (grant PL202105),the Priority Academic Program Development of Jiangsu Higher Education Institutions of Jiangsu Higher Education Institutions (PAPD)the 2023 Postgraduate Research&Practice Innovation Program of Jiangsu Province (grant KYCX23_0131).
文摘The plant genome produces an extremely large collection of long noncoding RNAs(lncRNAs)that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes.Here,we mapped the transcriptional heterogeneity of lncRNAs and their associated gene reg-ulatory networks at single-cell resolution.We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing(scRNA-seq)datasets from juvenile Arabidopsis seedlings.We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers.We further demon-strated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity.In addi-tion,we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs,and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs.The analysis results are available at the single-cell-based plant lncRNA atlas data-base(scPLAD;https://biobigdata.nju.edu.cn/scPLAD/).Overall,this work demonstrates the power of inte-grative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.
基金funding Collaborative Research Centre 973"Priming and Memory of Organismic Responses to Stress" (www.sfb973.de)the European Union’s Horizon 2020 Research and Innovation Programme for funding project PlantaSYST (SGA-CSA No.739582 under FPA No.664620)+1 种基金the European Regional Development Fund for funding project BG05M2OP001-1.003-001-C01 through the Bulgarian"Science and Education for Smart Growth"Operational Programme,and the MPI-MP and the University of Potsdam for financial support.B.M.-R.and S.J.thank the International Max Planck Research School"Primary Metabolism and Plant Growth" (IMPRS-PMPG)for support.J.J.O.thanks the DFG (OL 767/1-1)Leibniz Institute of Vegetable and Ornamental Crops for funding.
文摘The shoot apical meristem(SAM)is responsible for overall shoot growth by generating all aboveground structures.Recent research has revealed that the SAM displays an autonomous heat stress(HS)memory of a previous non-lethal HS event.Considering the importance of the SAM for plant growth,it is essential to determine how its thermomemory is mechanistically controlled.Here,we report that HEAT SHOCK TRAN-SCRIPTION FACTOR A7b(HSFA7b)plays a crucial role in this process in Arabidopsis,as the absence of functional HSFA7b results in the temporal suppression of SAM activity after thermopriming.We found that HSFA7b directly regulates ethylene response at the SAM by binding to the promoter of the key ethylene signaling gene ETHYLENE-INSENSITIVE 3 to establish thermotolerance.Moreover,we demonstrated that HSFA7b regulates the expression of ETHYLENE OVERPRODUCER 1(ETO1)and ETO1-LIKE 1,both of which encode ethylene biosynthesis repressors,thereby ensuring ethylene homeostasis at the SAM.Taken together,these results reveal a crucial and tissue-specic role for HSFA7b in thermomemory at the Arabidopsis SAM.
基金supported by grants from the National Key Research and Development Program of China (2022YFF1003001)the National Natural Science Foundation of China (32072576)+3 种基金the National Modern Agriculture Industry Technology System (CARS-23-G42)the Jiangsu Provincial Key Research and Development Program (BE2021376)the Innovation Program of the Beijing Academy of Agricultural and Forestry Sciences (KJCX20230121)the Collaborative Innovation Program for Leafy and Root Vegetables of the Beijing Vegetable Research Center,Beijing Academy of Agricultural and Forestry Sciences (XTCX202302).
文摘The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development.Here we report a graph-based pan-genome of B.oleracea constructed from high-quality genome assemblies of different morphotypes.The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin-andflowering-related genes.Population genomic analyses revealed that early domestication of B.oleracea focused on leaf or stem development.Geneflows resulting from agricultural practices and variety improvement were detected among different morphotypes.Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAV-ATA3/ESR-RELATED family gene as crucial players in leaf–stem differentiation during the early stage of B.oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts.Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization andflowering characteristics among different morphotypes,and variations in thefirst intron of BoFLC3 are involved infine-tuning theflowering process in cauliflower.This study provides a comprehensive understanding of the pan-genome of B.oleracea and sheds light on the domestication and differential organ development of this globally important crop species.
基金supported by the"STI2030-Major Project"of China(2023ZD04072)the National Major Agriculture Science and Technolohy Project of China(NK2022050102)+1 种基金the National Natural Science Foundation of China(32372099 and 32188102)the Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-CACB-202402).
文摘Transitory starch is an important carbon source in leaves,and its biosynthesis and metabolism are closely related to grain quality and yield.The molecular mechanisms controlling leaf transitory starch biosynthesis and degradation and their effects on rice(Oryza sativa)quality and yield remain unclear.Here,we show that OsLESV and OsESV1,the rice orthologs of AtLESV and AtESV1,are associated with transitory starch biosynthesis in rice.The total starch and amylose contents in leaves and endosperms are significantly reduced,and the final grain quality and yield are compromised in oslesv and osesv1 single and oslesv esv1 double mutants.Furthermore,we found that OsLESV and OsESV1 bind to starch,and this binding depends on a highly conserved C-terminal tryptophan-rich region that acts as a starch-binding domain.Importantly,OsLESV and OsESV1 also interact with the key enzymes of starch biosynthesis,granule-bound starch synthase I(GBSSI),GBSSII,and pyruvate orthophosphote dikiase(PPDKB),to maintain their protein stability and activity.OsLESV and OsESV1 also facilitate the targeting of GBSSI and GBSSII from plastid stroma to starch granules.Overexpression of GBSSI,GBSSII,and PPDKB can partly rescue the phenotypic defects of the oslesv and osesv1 mutants.Thus,we demonstrate that OsLESV and OsESV1 play a key role in regulating the biosynthesis of both leaf transitory starch and endosperm storage starch in rice.These findings deepen our understanding of the molecular mechanisms underlying transitory starch biosynthesis in rice leaves and reveal how the transitory starch metabolism affects rice grain quality and yield,providing useful information for the genetic improvement of rice grain quality and yield.
基金supported by the National Natural Science Foundation of China (31872805)the Fundamental Research Funds for Central NonProfit of the Chinese Academy of Agricultural Sciences (CAASZDRW202109 and Y2023PT20)the Nanfan Special Project of the Chinese Academy of Agricultural Sciences (YBXM15).
文摘Plant organ size is an important agronomic trait that makes a significant contribution to plant yield.Despite its central importance,the genetic and molecular mechanisms underlying organ size control remain to be fully clarified.Here,we report that the trithorax group protein ULTRAPETALA1(ULT1)interacts with the TEOSINTE BRANCHED1/CYCLOIDEA/PCF14/15(TCP14/15)transcription factors by antagonizing the LIN-11,ISL-1,and MEC-3(LIM)peptidase DA1,thereby regulating organ size in Arabidopsis.Loss of ULT1 function significantly increases rosette leaf,petal,silique,and seed size,whereas overexpression of ULT1 results in reduced organ size.ULT1 associates with TCP14 and TCP15 to co-regulate cell size by affecting cellular endoreduplication.Transcriptome analysis revealed that ULT1 and TCP14/15 regulate common target genes involved in endoreduplication and leaf development.ULT1 can be recruited by TCP14/15 to promote lysine 4 of histone H3 trimethylation at target genes,activating their expression to determinefinal cell size.Furthermore,we found that ULT1 influences the interaction of DA1 and TCP14/15 and antagonizes the effect of DA1 on TCP14/15 degradation.Collectively,ourfindings reveal a novel epigenetic mechanism underlying the regulation of organ size in Arabidopsis.
基金supported by the Department of Science and Technology of Zhejiang Province (2022C02032 and 2020C02002)the National Natural Science Foundation of China (31971865)CIC-MCP to L.F.
文摘Pigmented rice stands out for its nutritional value and is gaining more and more attention.Wild rice,domes-ticated red rice,and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype.We performed population genetic analyses using 5104 worldwide rice acces-sions,including 2794 accessions with red or black pericarps,85 of which were newly sequenced in this study.The results suggested an evolutionary trajectory of red landraces originating from wild rice,and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years.Cultivated red rice was found to feralize to weedy rice,and weedy rice could be further re-domesticated to cultivated red rice.A genome-wide association study based on the 2794 accessions with pigmented peri-carps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization.Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.
基金supported by grants from the National Natural Science Foundation of China (32171227,31870740,and 31570738 to X.X.,21825703 and 21927814 to C.T.)the National Key Research and Development Project of China (2019YFA0405600 and 2019YFA0706900 to C.T.)+2 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37040000)to C.T.,the Youth Innovation Promotion Association CAS (2022455)to L.Y.,the Zhejiang Provincial Natural Science Foundation of China under grant LR22C020002 to X.X.
文摘Roseiflexus castenholzii is a gram-negativefilamentous phototrophic bacterium that carries out anoxygenic photosynthesis through a cyclic electron transport chain(ETC).The ETC is composed of a reaction center(RC)–light-harvesting(LH)complex(rcRC–LH);an alternative complex III(rcACIII),which functionally re-places the cytochrome bc1/b6f complex;and the periplasmic electron acceptor auracyanin(rcAc).Although compositionally and structurally different from the bc1/b6f complex,rcACIII plays similar essential roles in oxidizing menaquinol and transferring electrons to the rcAc.However,rcACIII-mediated electron transfer(which includes both an intraprotein route and a downstream route)has not been clearly elucidated,nor have the details of cyclic ETC.Here,we identify a previously unknown monoheme cytochrome c(cyt c551)as a novel periplasmic electron acceptor of rcACIII.It reduces the light-excited rcRC–LH to complete a cyclic ETC.We also reveal the molecular mechanisms involved in the ETC using electron paramagnetic resonance(EPR),spectroelectrochemistry,and enzymatic and structural analyses.Wefind that electrons released from rcACIII-oxidized menaquinol are transferred to two alternative periplasmic electron acceptors(rcAc and cyt c551),which eventually reduce the rcRC to form the complete cyclic ETC.This work serves as a foundation for further studies of ACIII-mediated electron transfer in anoxygenic photosynthesis and broadens our under-standing of the diversity and molecular evolution of prokaryotic ETCs.
基金supported by the National Key Research and Development Program of China (2022YFC2601100 to B.L.)the Natural Science Foundation of China (32030067 to J.-H.W.,31970235 to L.-F.L.,32171661 to R.-T.J.,and 31961133028 to B.L.).
文摘Invasive alien species are primary drivers of biodiversity loss and species extinction.Smooth cordgrass(Spartina alterniflora)is one of the most aggressive invasive plants in coastal ecosystems around the world.However,the genomic bases and evolutionary mechanisms underlying its invasion success have remained largely unknown.Here,we assembled a chromosome-level reference genome and performed phenotypic and population genomic analyses between native US and introduced Chinese populations.Our phenotypic comparisons showed that introduced Chinese populations have evolved competitive traits,such as earlyflowering time and greater plant biomass,during secondary introductions along China’s coast.Population genomic and transcriptomic inferences revealed distinct evolutionary trajectories of low-and high-latitude Chinese populations.In particular,genetic mixture among different source populations,together with in-dependent natural selection acting on distinct target genes,may have resulted in high genome dynamics of the introduced Chinese populations.Our study provides novel phenotypic and genomic evidence showing how smooth cordgrass rapidly adapts to variable environmental conditions in its introduced ranges.Moreover,candidate genes related toflowering time,fast growth,and stress tolerance(i.e.,salinity and submergence)provide valuable genetic resources for future improvement of cereal crops.
基金supported by grants from the National Natural Science Foundation of China (no.32272564 and no.32302387)the National Key R&D Program of China (no.2023YFD1401100 and no.2021YFD1700101)+3 种基金the Science and Technology Innovation Program of Hunan Province (no.2022RC1017)Hunan Outstanding Youth Fund Project (no.2023JJ10025)the Training Program for Excellent Young Innovators of Changsha (kq2106079)the Hunan Agricultural Science and Technology Innovation Fund Project (2022CX01 and 2023CX02).
文摘Weeds pose a significant threat to crop production,resulting in substantial yield reduction.In addition,they possess robust weedy traits that enable them to survive in extreme environments and evade human con-trol.In recent years,the application of multi-omics biotechnologies has helped to reveal the molecular mechanisms underlying these weedy traits.In this review,we systematically describe diverse applications of multi-omics platforms for characterizing key aspects of weed biology,including the origins of weed spe-cies,weed classification,and the underlying genetic and molecular bases of important weedy traits such as crop–weed interactions,adaptability to different environments,photoperiodicflowering responses,and herbicide resistance.In addition,we discuss limitations to the application of multi-omics techniques in weed science,particularly compared with their extensive use in model plants and crops.In this regard,we provide a forward-looking perspective on the future application of multi-omics technologies to weed science research.These powerful tools hold great promise for comprehensively and efficiently unraveling the intricate molecular genetic mechanisms that underlie weedy traits.The resulting advances will facilitate the development of sustainable and highly effective weed management strategies,promoting greener practices in agriculture.
基金supported by grants from the National Natural Science Foundation of China(32271912,32272634,32101484)。
文摘The expression of double-stranded RNAs(dsRNAs)from the plastid genome has been proven to be an effective method for controlling herbivorous pests by targeting essential insect genes.However,there are limitations to the efficiency of plastid-mediated RNA interference(PM-RNAi)due to the initial damage caused by the insects and their slow response to RNA interference.In this study,we developed transplastomic poplar plants that express dsRNAs targeting the b-Actin(dsACT)and Srp54k(dsSRP54K)genes of Plagiodera versicolora.Feeding experiments showed that transplastomic poplar plants can cause significantly higher mortality in P.versicolora larvae compared with nuclear transgenic or wild-type poplar plants.The efficient killing effect of PM-RNAi on P.versicolora larvae was found to be dependent on the presence of gut bacteria.Importantly,foliar application of a gut bacterial strain,Pseudomonas putida,will induce dysbiosis in the gut bacteria of P.versicolora larvae,leading to a significant acceleration in the speed of killing by PM-RNAi.Overall,our findings suggest that interfering with gut bacteria could be a promising strategy to enhance the effectiveness of PM-RNAi for insect pest control,offering a novel and effective approach for crop protection based on RNAi technology.
基金supported by the Key Research and Development Project of Zhejiang Province,China (2021C02010)the National Natural Science Foundation of China (32270201,31972216,and 31970140)+1 种基金the Special Project for the Selection and Breeding of New Agricultural Varieties in Zhejiang Province,China (2021C02064)supported by a grant,Organism Interaction,from Zhejiang Xianghu Laboratory (to F.-C.L.).
文摘Rice blast is a devastating disease worldwide,threatening rice production and food security.The blast fun-gus Magnaporthe oryzae invades the host via the appressorium,a specialized pressure-generating struc-ture that generates enormous turgor pressure to penetrate the host cuticle.However,owing to ongoing evolution of fungicide resistance,it is vitally important to identify new targets and fungicides.Here,we show that Trs85,a subunit of the transport protein particle III complex,is essential for appressorium-mediated infection in M.oryzae.We explain how Trs85 regulates autophagy through Ypt1(a small guano-sine triphosphatase protein)in M.oryzae.We then identify a key conserved amphipathic a helix within Trs85 that is associated with pathogenicity of M.oryzae.Through computer-aided screening,we identify a lead compound,SP-141,that affects autophagy and the Trs85–Ypt1 interaction.SP-141 demonstrates a substantial capacity to effectively inhibit infection caused by the rice blast fungus while also exhibiting wide-ranging potential as an antifungal agent with broad-spectrum activity.Taken together,our data show that Trs85 is a potential new target and that SP-141 has potential for the control of rice blast.Ourfindings thus provide a novel strategy that may help in thefight against rice blast.
