Molecular Plant

Papers
(The TQCC of Molecular Plant is 28. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-05-01 to 2024-05-01.)
ArticleCitations
TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data7206
The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation255
TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining178
Toward a “Green Revolution” for Soybean174
WheatOmics: A platform combining multiple omics data to accelerate functional genomics studies in wheat171
Hydrogen Sulfide Positively Regulates Abscisic Acid Signaling through Persulfidation of SnRK2.6 in Guard Cells155
Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level153
Precise Modifications of Both Exogenous and Endogenous Genes in Rice by Prime Editing149
Plant Prime Editors Enable Precise Gene Editing in Rice Cells144
Two gap-free reference genomes and a global view of the centromere architecture in rice141
Toxic metals and metalloids: Uptake, transport, detoxification, phytoremediation, and crop improvement for safer food139
Resequencing of 145 Landmark Cultivars Reveals Asymmetric Sub-genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China135
A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era135
Single-Cell Transcriptome Analysis in Plants: Advances and Challenges132
High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat131
Versatile Nucleotides Substitution in Plant Using an Improved Prime Editing System131
Plant Nutrition for Human Nutrition: Hints from Rice Research and Future Perspectives129
Transcriptional landscape of rice roots at the single-cell resolution129
Cold-Induced CBF–PIF3 Interaction Enhances Freezing Tolerance by Stabilizing the phyB Thermosensor in Arabidopsis128
Plant cytochrome P450 plasticity and evolution125
Global Dynamic Molecular Profiling of Stomatal Lineage Cell Development by Single-Cell RNA Sequencing125
Lipid Metabolism: Critical Roles in Male Fertility and Other Aspects of Reproductive Development in Plants121
The Chromosome-Level Genome Sequence of the Autotetraploid Alfalfa and Resequencing of Core Germplasms Provide Genomic Resources for Alfalfa Research119
MicroTom Metabolic Network: Rewiring Tomato Metabolic Regulatory Network throughout the Growth Cycle116
WGDI: A user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes114
A 2-kb Mycovirus Converts a Pathogenic Fungus into a Beneficial Endophyte for Brassica Protection and Yield Enhancement111
Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus111
A Comprehensive Online Database for Exploring ∼20,000 Public Arabidopsis RNA-Seq Libraries108
Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations97
Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae93
Transcriptional activation and phosphorylation of OsCNGC9 confer enhanced chilling tolerance in rice92
A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis92
The RALF1–FERONIA Complex Phosphorylates eIF4E1 to Promote Protein Synthesis and Polar Root Hair Growth91
A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice91
Highly efficient heritable genome editing in wheat using an RNA virus and bypassing tissue culture90
Zinc in plants: Integrating homeostasis and biofortification89
Genome sequences of five Sitopsis species of Aegilops and the origin of polyploid wheat B subgenome89
Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies87
A Domestication-Associated Gene GmPRR3b Regulates the Circadian Clock and Flowering Time in Soybean86
Variation in cis-regulation of a NAC transcription factor contributes to drought tolerance in wheat86
Plant Immune Mechanisms: From Reductionistic to Holistic Points of View85
The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber83
A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding81
The Soil-Borne Identity and Microbiome-Assisted Agriculture: Looking Back to the Future80
Protein Quality Control in Plant Organelles: Current Progress and Future Perspectives78
Coordinated Transcriptional Regulation by the UV-B Photoreceptor and Multiple Transcription Factors for Plant UV-B Responses78
The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution77
CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis77
Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity77
The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold73
High-efficiency and multiplex adenine base editing in plants using new TadA variants73
Plant adaptation to low phosphorus availability: Core signaling, crosstalks, and applied implications72
ζ-Carotene Isomerase Suppresses Tillering in Rice through the Coordinated Biosynthesis of Strigolactone and Abscisic Acid71
Lipidomic Analysis Reveals the Importance of GIPCs in Arabidopsis Leaf Extracellular Vesicles71
The GW2-WG1-OsbZIP47 pathway controls grain size and weight in rice69
Hydrogen sulfide-linked persulfidation of ABI4 controls ABA responses through the transactivation of MAPKKK18 in Arabidopsis68
Nematode-Encoded RALF Peptide Mimics Facilitate Parasitism of Plants through the FERONIA Receptor Kinase68
The receptor-like cytoplasmic kinase RIPK regulates broad-spectrum ROS signaling in multiple layers of plant immune system68
Creation and judicious application of a wheat resistance gene atlas67
CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement67
Smart breeding driven by big data, artificial intelligence, and integrated genomic-enviromic prediction67
Counteraction of ABA-Mediated Inhibition of Seed Germination and Seedling Establishment by ABA Signaling Terminator in Arabidopsis66
Hybrid speciation via inheritance of alternate alleles of parental isolating genes66
Regulation of Rice Tillering by RNA-Directed DNA Methylation at Miniature Inverted-Repeat Transposable Elements66
Control of Plant Growth and Defense by Photoreceptors: From Mechanisms to Opportunities in Agriculture65
Nitric oxide regulation of plant metabolism65
Phenylpropanoid Derivatives Are Essential Components of Sporopollenin in Vascular Plants64
A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice64
Molecular Basis of Disease Resistance and Perspectives on Breeding Strategies for Resistance Improvement in Crops62
Chromosome-Level Reference Genome and Population Genomic Analysis Provide Insights into the Evolution and Improvement of Domesticated Mulberry (Morus alba)62
HASTY modulates miRNA biogenesis by linking pri-miRNA transcription and processing61
Nutrient–hormone relations: Driving root plasticity in plants61
Primary carbohydrate metabolism genes participate in heat-stress memory at the shoot apical meristem of Arabidopsis thaliana61
Bacterial Effectors Induce Oligomerization of Immune Receptor ZAR1 In Vivo61
The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis60
A transceptor–channel complex couples nitrate sensing to calcium signaling in Arabidopsis60
Interspecific plant interaction via root exudates structures the disease suppressiveness of rhizosphere microbiomes60
The landscape of gene–CDS–haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement60
An angiosperm NLR Atlas reveals that NLR gene reduction is associated with ecological specialization and signal transduction component deletion59
Efficient Gene Targeting in Maize Using Inducible CRISPR-Cas9 and Marker-free Donor Template59
Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline58
MPK14-mediated auxin signaling controls lateral root development via ERF13-regulated very-long-chain fatty acid biosynthesis57
Harnessing Knowledge from Maize and Rice Domestication for New Crop Breeding57
Mycorrhizal symbiosis modulates the rhizosphere microbiota to promote rhizobia–legume symbiosis57
Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives57
A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies57
Pho-view of Auxin: Reversible Protein Phosphorylation in Auxin Biosynthesis, Transport and Signaling56
A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C4 photosynthesis56
Exploiting Natural Variation in Tomato to Define Pathway Structure and Metabolic Regulation of Fruit Polyphenolics in the Lycopersicum Complex56
An integrated framework reinstating the environmental dimension for GWAS and genomic selection in crops56
An alternative, zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants56
Cell wall β-1,4-galactan regulated by the BPC1/BPC2-GALS1 module aggravates salt sensitivity in Arabidopsis thaliana55
Genome editing mediated by SpCas9 variants with broad non-canonical PAM compatibility in plants55
GmCRY1s modulate gibberellin metabolism to regulate soybean shade avoidance in response to reduced blue light55
Major episodes of horizontal gene transfer drove the evolution of land plants55
Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes54
Targeted mutagenesis of POLYAMINE OXIDASE 5 that negatively regulates mesocotyl elongation enables the generation of direct-seeding rice with improved grain yield54
The OsNAC23-Tre6P-SnRK1a feed-forward loop regulates sugar homeostasis and grain yield in rice54
ITPK1 is an InsP6/ADP phosphotransferase that controls phosphate signaling in Arabidopsis53
Wheat breeding history reveals synergistic selection of pleiotropic genomic sites for plant architecture and grain yield53
N-terminal truncated RHT-1 proteins generated by translational reinitiation cause semi-dwarfing of wheat Green Revolution alleles52
Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes52
Development of a widely targeted volatilomics method for profiling volatilomes in plants52
PlantscRNAdb: A database for plant single-cell RNA analysis51
Innovations in Agriculture and Food Supply in Response to the COVID-19 Pandemic51
Mobilizing Crop Biodiversity51
Orphan Crops and their Wild Relatives in the Genomic Era51
Bph30 confers resistance to brown planthopper by fortifying sclerenchyma in rice leaf sheaths51
An inferred functional impact map of genetic variants in rice51
A natural variation in Ribonuclease H-like gene underlies Rht8 to confer “Green Revolution” trait in wheat50
Hybrid Rubisco with Complete Replacement of Rice Rubisco Small Subunits by Sorghum Counterparts Confers C4 Plant-like High Catalytic Activity50
Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 920450
Cloning and functional characterization of Rht8, a “Green Revolution” replacement gene in wheat50
Phytophthora Effectors Modulate Genome-wide Alternative Splicing of Host mRNAs to Reprogram Plant Immunity50
Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution50
Unraveling the 3D Genome Architecture in Plants: Present and Future49
The Genomes of the Allohexaploid Echinochloa crus-galli and Its Progenitors Provide Insights into Polyploidization-Driven Adaptation49
A Synthetic Photorespiratory Shortcut Enhances Photosynthesis to Boost Biomass and Grain Yield in Rice49
The LEAFY floral regulator displays pioneer transcription factor properties48
Rice metabolic regulatory network spanning the entire life cycle48
Chromosome-level genome of Himalayan yew provides insights into the origin and evolution of the paclitaxel biosynthetic pathway47
The YDA-MKK4/MKK5-MPK3/MPK6 Cascade Functions Downstream of the RGF1-RGI Ligand–Receptor Pair in Regulating Mitotic Activity in Root Apical Meristem47
Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions47
From Green Super Rice to green agriculture: Reaping the promise of functional genomics research47
Allele-aware chromosome-level genome assembly of Artemisia annua reveals the correlation between ADS expansion and artemisinin yield47
Enhanced Vitamin C Production Mediated by an ABA-Induced PTP-like Nucleotidase Improves Plant Drought Tolerance in Arabidopsis and Maize46
RGF1-RGI1, a Peptide-Receptor Complex, Regulates Arabidopsis Root Meristem Development via a MAPK Signaling Cascade46
Unraveling a genetic roadmap for improved taste in the domesticated apple46
Reconstruction of lateral root formation through single-cell RNA sequencing reveals order of tissue initiation46
TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants45
GSK3-mediated stress signaling inhibits legume–rhizobium symbiosis by phosphorylating GmNSP1 in soybean45
A reciprocal inhibitory module for Pi and iron signaling45
Arabidopsis CHLOROPHYLLASE 1 protects young leaves from long-term photodamage by facilitating FtsH-mediated D1 degradation in photosystem II repair44
Decreasing nitrogen assimilation under drought stress by suppressing DST-mediated activation of Nitrate Reductase 1.2 in rice44
Glycosylation of N-hydroxy-pipecolic acid equilibrates between systemic acquired resistance response and plant growth44
Persulfidation-induced structural change in SnRK2.6 establishes intramolecular interaction between phosphorylation and persulfidation44
A transcription factor STOP1-centered pathway coordinates ammonium and phosphate acquisition in Arabidopsis43
Normal Structure and Function of Endothecium Chloroplasts Maintained by ZmMs33-Mediated Lipid Biosynthesis in Tapetal Cells Are Critical for Anther Development in Maize43
Two VOZ transcription factors link an E3 ligase and an NLR immune receptor to modulate immunity in rice43
The RING E3 ligase CLG1 targets GS3 for degradation via the endosome pathway to determine grain size in rice43
Citrus Pan-Genome to Breeding Database (CPBD): A comprehensive genome database for citrus breeding43
The vernalization-induced long non-coding RNA VAS functions with the transcription factor TaRF2b to promote TaVRN1 expression for flowering in hexaploid wheat43
Genome Editing Enables Next-Generation Hybrid Seed Production Technology43
Coordination of plant growth and abiotic stress responses by tryptophan synthase β subunit 1 through modulation of tryptophan and ABA homeostasis in Arabidopsis43
CLE14 functions as a “brake signal” to suppress age-dependent and stress-induced leaf senescence by promoting JUB1-mediated ROS scavenging in Arabidopsis42
Genomic insights into the fast growth of paulownias and the formation of Paulownia witches' broom42
A reactive oxygen species burst causes haploid induction in maize42
Pathogen-inducible OsMPKK10.2-OsMPK6 cascade phosphorylates the Raf-like kinase OsEDR1 and inhibits its scaffold function to promote rice disease resistance41
The blue light receptor CRY1 interacts with GID1 and DELLA proteins to repress GA signaling during photomorphogenesis in Arabidopsis41
Genome architecture and tetrasomic inheritance of autotetraploid potato40
Asymmetric epigenome maps of subgenomes reveal imbalanced transcription and distinct evolutionary trends in Brassica napus40
A single-cell morpho-transcriptomic map of brassinosteroid action in the Arabidopsis root39
Pandemics of People and Plants: Which Is the Greater Threat to Food Security?39
Enhancing the light reactions of photosynthesis: Strategies, controversies, and perspectives39
ESCRT-I Component VPS23A Sustains Salt Tolerance by Strengthening the SOS Module in Arabidopsis38
Regulation of the stability and ABA import activity of NRT1.2/NPF4.6 by CEPR2-mediated phosphorylation in Arabidopsis38
IIIVmrMLM: The R and C++ tools associated with 3VmrMLM, a comprehensive GWAS method for dissecting quantitative traits38
The Ghd7 transcription factor represses ARE1 expression to enhance nitrogen utilization and grain yield in rice37
Toward Precision Genome Editing in Crop Plants37
The miR166–SlHB15A regulatory module controls ovule development and parthenocarpic fruit set under adverse temperatures in tomato37
A Bunyavirus-Inducible Ubiquitin Ligase Targets RNA Polymerase IV for Degradation during Viral Pathogenesis in Rice36
A near-complete assembly of an Arabidopsis thaliana genome36
WheatGmap: a comprehensive platform for wheat gene mapping and genomic studies36
Dynamic changes of phosphatidylinositol and phosphatidylinositol 4-phosphate levels modulate H+-ATPase and Na+/H+ antiporter activities to maintain ion homeostasis in Arabidopsis under salt stress36
Transcriptional Regulation of Lipid Catabolism during Seedling Establishment36
Ectopic expression of VRT-A2 underlies the origin of Triticum polonicum and Triticum petropavlovskyi with long outer glumes and grains36
Activation of Mitochondrial orf355 Gene Expression by a Nuclear-Encoded DREB Transcription Factor Causes Cytoplasmic Male Sterility in Maize36
ORHis, a Natural Variant of OR, Specifically Interacts with Plastid Division Factor ARC3 to Regulate Chromoplast Number and Carotenoid Accumulation36
Cell-specific pathways recruited for symbiotic nodulation in the Medicago truncatula legume35
Dynamic spatial reorganization of BSK1 complexes in the plasma membrane underpins signal-specific activation for growth and immunity35
Warm temperature compromises JA-regulated basal resistance to enhance Magnaporthe oryzae infection in rice35
Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding35
Bract suppression regulated by the miR156/529-SPLs-NL1-PLA1 module is required for the transition from vegetative to reproductive branching in rice35
PhieCBEs: Plant High-Efficiency Cytidine Base Editors with Expanded Target Range35
Wheat leaf rust resistance gene Lr13 is a specific Ne2 allele for hybrid necrosis34
Pyramiding favorable alleles in an elite wheat variety in one generation by CRISPR-Cas9-mediated multiplex gene editing34
A cell wall-localized NLR confers resistance to Soybean mosaic virus by recognizing viral-encoded cylindrical inclusion protein34
Verticillium dahliae secretory effector PevD1 induces leaf senescence by promoting ORE1-mediated ethylene biosynthesis34
A bacterial effector protein uncovers a plant metabolic pathway involved in tolerance to bacterial wilt disease34
Redox sensor QSOX1 regulates plant immunity by targeting GSNOR to modulate ROS generation33
Tanned or Sunburned: How Excessive Light Triggers Plant Cell Death33
A virus-derived siRNA activates plant immunity by interfering with ROS scavenging33
Multi-omics analyses of 398 foxtail millet accessions reveal genomic regions associated with domestication, metabolite traits, and anti-inflammatory effects33
miR395-regulated sulfate metabolism exploits pathogen sensitivity to sulfate to boost immunity in rice33
Hetero-trans-β-Glucanase Produces Cellulose–Xyloglucan Covalent Bonds in the Cell Walls of Structural Plant Tissues and Is Stimulated by Expansin33
Tonoplast-associated calcium signaling regulates manganese homeostasis in Arabidopsis32
Molecular basis underlying rice tiller angle: Current progress and future perspectives32
Regulation of Leaf Longevity by DML3-Mediated DNA Demethylation32
Importers Drive Leaf-to-Leaf Jasmonic Acid Transmission in Wound-Induced Systemic Immunity31
The RppC-AvrRppC NLR-effector interaction mediates the resistance to southern corn rust in maize31
High-efficiency plastome base editing in rice with TAL cytosine deaminase31
Optimized prime editing efficiently generates glyphosate-resistant rice plants carrying homozygous TAP-IVS mutation in EPSPS30
Engineering broad-spectrum resistance to bacterial blight by CRISPR-Cas9-mediated precise homology directed repair in rice30
A teosinte-derived allele of a MYB transcription repressor confers multiple disease resistance in maize30
Breeding with dominant genic male-sterility genes to boost crop grain yield in the post-heterosis utilization era30
Genome-wide identification of agronomically important genes in outcrossing crops using OutcrossSeq30
PDX1.1-dependent biosynthesis of vitamin B6 protects roots from ammonium-induced oxidative stress30
DNA demethylases remodel DNA methylation in rice gametes and zygote and are required for reproduction29
Construction of a high-density mutant population of Chinese cabbage facilitates the genetic dissection of agronomic traits29
Natural variations of ZmSRO1d modulate the trade-off between drought resistance and yield by affecting ZmRBOHC-mediated stomatal ROS production in maize29
The IBI1 Receptor of β-Aminobutyric Acid Interacts with VOZ Transcription Factors to Regulate Abscisic Acid Signaling and Callose-Associated Defense28
Differentiation trajectories and biofunctions of symbiotic and un-symbiotic fate cells in root nodules of Medicago truncatula28
Direct acetylation of a conserved threonine of RIN4 by the bacterial effector HopZ5 or AvrBsT activates RPM1-dependent immunity in Arabidopsis28
Speed vernalization to accelerate generation advance in winter cereal crops28
The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution28
Two mitochondrial phosphatases, PP2c63 and Sal2, are required for posttranslational regulation of the TCA cycle in Arabidopsis28
Reshaping of the Arabidopsis thaliana Proteome Landscape and Co-regulation of Proteins in Development and Immunity28
A potato late blight resistance gene protects against multiple Phytophthora species by recognizing a broadly conserved RXLR-WY effector28
High-temperature wheat leaf rust resistance gene Lr13 exhibits pleiotropic effects on hybrid necrosis28
Ca2+-dependent successive phosphorylation of vacuolar transporter MTP8 by CBL2/3-CIPK3/9/26 and CPK5 is critical for manganese homeostasis in Arabidopsis28
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