Staying hungry:a roadmap to harnessing central regulators of symbiotic nitrogen fixation under fluctuating nitrogen availability

Legumes have evolved specific inventions to enhance nitrogen(N)acquisition by establishing symbiotic interactions with N-fixing rhizobial bacteria.Because symbiotic N fixation is energetically costly,legumes have developed sophisticated mechanisms to ensure carbon-nitrogen balance,in a variable environment,both locally and at the whole plant level,by monitoring nodule number,nodule development,and nodular nitrogenase activity,as well as controlling nodule senescence.Studies of the autoregulation of nodulation and regulation of nodulation by nodule inception(NIN)and NIN-LIKE PROTEINs(NLPs)have provided great insights into the genetic mechanisms underlying the nitrateinduced regulation of root nodulation for adapting to N availability in the rhizosphere.However,many aspects of N-induced pleiotropic regulation remain to be fully explained,such as N-triggered senescence in mature nodules.Wang et al.determined that this process is governed by a transcriptional network regulated by NAC-type transcription factors.Characterization and dissection of these soybean nitrogenassociated NAPs(SNAPs)transcription factor-mastered networks have yielded a roadmap for exploring how legumes rewire nodule functions across a range of N levels,laying the foundation for enhancing the growth of N-deprived crops in agricultural settings.

Two H3K36 methyltransferases differentially associate with transcriptional activity and enrichment of facultative heterochromatin in rice blast fungus

Di-and tri-methylation of lysine 36 on histone H3(H3K36me2/3)is catalysed by histone methyltransferase Set2,which plays an essential role in transcriptional regulation.Although there is a single H3K36 methyltransferase in yeast and higher eukaryotes,two H3K36 methyltransferases,Ash1 and Set2,were present in many filamentous fungi.However,their roles in H3K36 methylation and transcriptional regulation remained unclear.Combined with methods of RNA-seq and ChIP-seq,we revealed that both Ash1 and Set2 are redundantly required for the full H3K36me2/3 activity in Magnaporthe oryzae,which causes the devastating worldwide rice blast disease.Ash1 and Set2 distinguish genomic H3K36me2/3-marked regions and are differentially associated with repressed and activated transcription,respectively.Furthermore,Ash1-catalysed H3K36me2 was co-localized with H3K27me3 at the chromatin,and Ash1 was required for the enrichment and transcriptional silencing of H3K27me3-occupied genes.With the different roles of Ash1 and Set2,in H3K36me2/3 enrichment and transcriptional regulation on the stress-responsive genes,they differentially respond to various stresses in M.oryzae.Overall,we reveal a novel mechanism by which two H3K36 methyltransferases catalyze H3K36me2/3 that differentially associate with transcriptional activities and contribute to enrichment of facultative heterochromatin in eukaryotes.

Publisher Correction: The RNA-binding domain of DCL3 is required for long-distance RNAi signaling

Correction to:aBIOTECH https://doi.org/10.1007/s42994-023-00124-6 The copyright holder for this article was incorrectly given as‘Agricultural Information Institute,Chinese Academy of Agricultural Sciences’but should have been‘The Authors’This article was originally published with the incorrect licence;it should have been:Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,which permits use,sharing,adaptation.

The RNA-binding domain of DCL3 is required for long-distance RNAi signaling

Small RNA(sRNA)-mediated RNA silencing(also known as RNA interference,or RNAi)is a conserved mechanism in eukaryotes that includes RNA degradation,DNA methylation,heterochromatin formation and protein translation repression.In plants,sRNAs can move either cell-to-cell or systemically,thereby acting as mobile silencing signals to trigger noncell autonomous silencing.However,whether and what proteins are also involved in noncell autonomous silencing have not been elucidated.In this study,we utilized a previously reported inducible RNAi plant,PDSi,which can induce systemic silencing of the endogenous PDS gene,and we demonstrated that DCL3 is involved in systemic PDS silencing through its RNA binding activity.We confirmed that the C-terminus of DCL3,including the predicted RNA-binding domain,is capable of binding short RNAs.Mutations affecting RNA binding,but not processing activity,reduced systemic PDS silencing,indicating that DCL3 binding to RNAs is required for the induction of systemic silencing.Cucumber mosaic virus infection assays showed that the RNA-binding activity of DCL3 is required for antiviral RNAi in systemically noninoculated leaves.Our findings demonstrate that DCL3 acts as a signaling agent involved in noncell autonomous silencing and an antiviral effect in addition to its previously known function in the generation of 24-nucleotide sRNAs.

Plant genomic resources at National Genomics Data Center:assisting in data-driven breeding applications

Genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among species.Through various efforts in genomic data archiving,integrative analysis and value-added curation,the National Genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database resources.This dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research efforts.Here,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application tools.We intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

DGS1 improves rice disease resistance by elevating pathogenassociated molecular pattern-triggered immunity

Rice yield and disease resistance are two crucial factors in determining the suitability of a gene for agricultural breeding.Decreased grain size1(DGS1),encoding an RING-type E3 ligase,has been found to have a positive effect on rice yield by regulating rice grain number and 1000-grain weight.However,the role of DGS1 in rice blast resistance is still unknown.In this study,we report that DGS1 enhances disease resistance by improving PTI responses,including stronger ROS burst and MAPK activation,and also increased expression of defense-related genes.Furthermore,DGS1 works in conjunction with ubiquitin conjugating enzyme OsUBC45 as an E2-E3 pair to facilitate the ubiquitin-dependent degradation of OsGSK3 and OsPIP2;1,thereby influencing rice yield and immunity,respectively.Therefore,the DGS1-OsUBC45 module has the potential in facilitating rice agricultural breeding.

Revealing the specific regulations of nitric oxide on the postharvest ripening and senescence of bitter melon fruit

Bitter melon fruit is susceptible to yellowing,softening,and rotting under room-temperature storage conditions,resulting in reduced commercial value.Nitric oxide(NO)is an important signaling molecule and plays a crucial role in regulating the fruit postharvest quality.In this study,we investigated the effects of NO treatment on changes in sensory and firmness of bitter melon fruit during postharvest storage.Moreover,transcriptomic,metabolomic,and proteomic analyses were performed to elucidate the regulatory mechanisms through which No treatment delays the ripening and senescence of bitter melon fruit.Our results show that differentially expressed genes(DEGs)were involved in fruit texture(CSLE,β-Gal,and PME),plant hormone signal transduction(ACS,JAR4,and AUX28),and fruit flavor and aroma(SUS2,LOX,and GDH2).In addition,proteins differentially abundant were associated with fruit texture(PLY,PME,and PGA)and plant hormone signal transduction(PBL15,JAR1,and PYL9).Moreover,No significantly increased the abundance of key enzymes involved in the phenylpropanoid biosynthetic pathway,thus enhancing the disease resistance and alleviating softening of bitter melon fruit.Finally,differential metabolites mainly included phenolic acids,terpenoids,and flavonoids.These results provide a theoretical basis for further studies on the physiological changes associated with postharvest ripening and senescence of bitter melon fruit.

Innovations in functional genomics and molecular breeding of pea:exploring advances and opportunities

The garden pea(Pisum sativum L.)is a significant cool-season legume,serving as crucial food sources,animal feed,and industrial raw materials.The advancement of functional genomics over the past two decades has provided substantial theoretical foundations and progress to pea breeding.Notably,the release of the pea reference genome has enhanced our understanding of plant architecture,symbiotic nitrogen fixation(SNF),flowering time,floral organ development,seed development,and stress resistance.However,a considerable gap remains between pea functional genomics and molecular breeding.This review summarizes the current advancements in pea functional genomics and breeding while highlighting the future challenges in pea molecular breeding.

Innovative computational tools provide new insights into the polyploid wheat genome

Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.

Correction:Co-expression of GR79 EPSPS and GAT generates high glyphosate-resistant alfalfa with low glyphosate residues

Correction:aBIOTECH[2023]4:352-358 https://doi.org/10.1007/s42994-023-00119-3 In the Acknowledgements section of this article the funding number incorrectly given as SQ2022YF F1000033 and should have been 2022YFF1003204.

Correction:Integration of light and hormone signaling pathways in the regulation of plant shade avoidance syndrome

Correction:aBI0TECH(2021)2:131-145 https://doi.0rg/10.1007/s42994-021-00038-1 In this article the author's name Fereshteh Jafari was incorrectly written as Feresheeh Jafari.The original article has been corrected.Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,which permits use,sharing,adaptation,distribution and reproduction in any medium or format.

Pepino mosaic virus antagonizes plant m^(6)A modification by promoting the autophagic degradation of the m^(6)A writer HAKAI

Autophagy plays an active anti-viral role in plants.Increasing evidence suggests that viruses can inhibit or manipulate autophagy,thereby winning the arms race between plants and viruses.Here,we demonstrate that overexpression of an m^(6)A writer from Solanum lycopersicum,SlHAKAI,could negatively regulate pepino mosaic virus(PepMV)infection,inhibit viral RNA and protein accumulations by affecting viral m^(6)A levels in tomato plants and vice versa.The PepMV-encoded RNA-dependent RNA polymerase(RdRP)directly interacts with SlHAKAI and reduces its protein accumulation.The RdRP-mediated decreased protein accumulation of SlHAKAI is sensitive to the autophagy inhibitor 3-methyladenine and is compromised by knocking down a core autophagy gene.Furthermore,PepMV RdRP could interact with an essential autophagy-related protein,SlBeclin1.RdRP,SlHAKAI,and SlBeclin1 interaction complexes form bright granules in the cytoplasm.Silencing of Beclin1 in Nicotiana benthamiana plants abolishes the RdRP-mediated degradation of SlHAKAI,indicating the requirement of Beclin1 in this process.This study uncovers that the PepMV RdRP exploits the autophagy pathway by interacting with SlBeclin1 to promote the autophagic degradation of the SlHAKAI protein,thereby inhibiting the m^(6)A modification-mediated plant defense responses.

Recent advances in understanding of the epigenetic regulation of plant regeneration

Ever since the concept of"plant cell totipotency"was first proposed in the early twentieth century,plant regeneration has been a major focus of study.Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture.Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration.The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation.Here,we summarize how various aspects of epigenetic regulation,including histone modifications and variants,chromatin accessibility dynamics,DNA methylation,and microRNAs,modulate plant regeneration.As the mechanisms of epigenetic regulation are conserved in many plants,research in this field has potential applications in boosting crop breeding,especially if coupled with emerging single-cell omics technologies.

Deoxynivalenol accumulation and detoxification in cereals and its potential role in wheat-Fusarium graminearum interactions

Deoxynivalenol(DON)is a prominent mycotoxin showing significant accumulation in cereal plants during infection by the phytopathogen Fusarium graminearum.It is a virulence factor that is important in the spread of F.graminearum within cereal heads,and it causes serious yield losses and significant contamination of cereal grains.In recent decades,genetic and genomic studies have facilitated the characterization of the molecular pathways of DON biosynthesis in F.graminearum and the environmental factors that influence DON accumulation.In addition,diverse scab resistance traits related to the repression of DON accumulation in plants have been identified,and experimental studies of wheat–pathogen interactions have contributed to understanding detoxification mechanisms in host plants.The present review illustrates and summarizes the molecular networks of DON mycotoxin production in F.graminearum and the methods of DON detoxification in plants based on the current literature,which provides molecular targets for crop improvement programs.This review also comprehensively discusses recent advances and challenges related to genetic engineering-mediated cultivar improvements to strengthen scab resistance.Furthermore,ongoing advancements in genetic engineering will enable the application of these molecular targets to develop more scab-resistant wheat cultivars with DON detoxification traits.

Co-expression of GR79 EPSPS and GAT generates highglyphosate-resistant alfalfa with low glyphosate residues

Weed competition seriously threatens the yield of alfalfa, the most important forage legume worldwide,thus generating herbicide-resistant alfalfa varieties is becoming a necessary cost-effective strategy toassist farmers for weed control. Here, we report the co-expression of plant codon-optimized forms ofGR79 EPSPS (pGR79 EPSPS) and N-acetyltransferase (pGAT) genes, in alfalfa, via Agrobacterium-mediated transformation. We established that the pGR79 EPSPS-pGAT co-expression alfalfa lines were able totolerate up to tenfold higher commercial usage of glyphosate and produced approximately ten timeslower glyphosate residues than the conventional cultivar. Our findings generate an elite herbicideresistant germplasm for alfalfa breeding and provide a promising strategy for developing high-glyphosate-resistant and low-glyphosate-residue forages.

Epigenetic regulation of plant immunity:from chromatin codes to plant disease resistance

Facing a deteriorating natural environment and an increasing serious food crisis,bioengineering-based breeding is increasing in importance.To defend against pathogen infection,plants have evolved multiple defense mechanisms,including pathogen-associated molecular pattern(PAMP)-triggered immunity(PTI)and effector-triggered immunity(ETI).A complex regulatory network acts downstream of these PTI and ETI pathways,including hormone signal transduction and transcriptional reprogramming.In recent years,increasing lines of evidence show that epigenetic factors act,as key regulators involved in the transcriptional reprogramming,to modulate plant immune responses.Here,we summarize current progress on the regulatory mechanism of DNA methylation and histone modifications in plant defense responses.In addition,we also discuss the application of epigenetic mechanism-based resistance strategies in plant disease breeding.

Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development

Development of wheat(Triticum aestivum L.)grain mainly depends on the processes of starch synthesis and storage protein accumulation,which are critical for grain yield and quality.However,the regulatory network underlying the transcriptional and physiological changes of grain development is still not clear.Here,we combined ATAC-seq and RNA-seq to discover the chromatin accessibility and gene expression dynamics during these processes.We found that the chromatin accessibility changes are tightly associated with differential transcriptomic expressions,and the proportion of distal ACRs was increased gradually during grain development.Specific transcription factor(TF)binding sites were enriched at different stages and were diversified among the 3 subgenomes.We further predicted the potential interactions between key TFs and genes related with starch and storage protein biosynthesis and found different copies of some key TFs played diversified roles.Overall,our findings have provided numerous resources and illustrated the regulatory network during wheat grain development,which would shed light on the improvement of wheat yields and qualities.

Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways

Plants are the most important sources of food for humans,as well as supplying many ingredients that are of great importance for human health.Developing an understanding of the functional components of plant metabolism has attracted considerable attention.The rapid development of liquid chromatography and gas chromatography,coupled with mass spectrometry,has allowed the detection and characterization of many thousands of metabolites of plant origin.Nowadays,elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding.Recently,the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways.Here,we review the recent research which integrates metabolomic with different omics methods,to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways.Finally,we discuss other novel methods that can accelerate the process of identification of metabolic pathways and,ultimately,identify metabolite function(s).

Predicting rice diseases using advanced technologies at different scales: present status and future perspectives

The past few years have witnessed significant progress in emerging disease detection techniques foraccurately and rapidly tracking rice diseases and predicting potential solutions. In this review we focuson image processing techniques using machine learning (ML) and deep learning (DL) models related tomulti-scale rice diseases. Furthermore, we summarize applications of different detection techniques,including genomic, physiological, and biochemical approaches. In addition, we also present the state-ofthe-art in contemporary optical sensing applications of pathogen–plant interaction phenotypes. Thisreview serves as a valuable resource for researchers seeking effective solutions to address the challenges of high-throughput data and model recognition for early detection of issues affecting rice cropsthrough ML and DL models.

Lipidomic insights into the response of Arabidopsis sepals to mild heat

Arabidopsis sepals coordinate flower opening in the morning as ambient temperature rises;however,the underlying molecular mechanisms are poorly understood. Mutation of one heat shock proteinencoding gene, HSP70-16, impaired sepal heat stress responses (HSR), disrupting lipid metabolism,especially sepal cuticular lipids, leading to abnormal flower opening. To further explore, to what extent,lipids play roles in this process, in this study, we compared lipidomic changes in sepals of hsp70-16 andvdac3 (mutant of a voltage-dependent anion channel, VDAC3, an HSP70-16 interactor) grown underboth normal (22 C) and mild heat stress (27 C, mild HS) temperatures. Under normal temperature,neither hsp70-16 nor vdac3 sepals showed significant changes in total lipids;however, vdac3 but nothsp70-16 sepals exhibited significant reductions in the ratios of all detected 11 lipid classes, except themonogalactosyldiacylglycerols (MGDGs). Under mild HS temperature, hsp70-16 but not vdac3 sepalsshowed dramatic reduction in total lipids. In addition, vdac3 sepals exhibited a significant accumulationof plastidic lipids, especially sulfoquinovosyldiacylglycerols (SQDGs) and phosphatidylglycerols (PGs),whereas hsp70-16 sepals had a significant accumulation of triacylglycerols (TAGs) and simultaneousdramatic reductions in SQDGs and phospholipids (PLs), such as phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), and phosphatidylserines (PSs). These findings revealed that the impact ofmild HS on sepal lipidome is influenced by genetic factors, and further, that HSP70-16 and VDAC3differently affect sepal lipidomic responses to mild HS. Our studies provide a lipidomic insight intofunctions of HSP and VDAC proteins in the plant’s HSR, in the context of floral development.