Dispersal enables species to track climate change by facilitating range shifts and colonization, yet successful post-dispersal establishment is often constrained by ecological niche mismatches. The mechanisms underlying...Dispersal enables species to track climate change by facilitating range shifts and colonization, yet successful post-dispersal establishment is often constrained by ecological niche mismatches. The mechanisms underlying this constraint remain poorly understood due to a lack of molecular evidence, limiting our ability to predict climate-induced range dynamics. Here, we integrate biogeographic analysis with macroecological insights to investigate how ecology shapes genomic divergence, local adaptation, and climate resilience in Debregeasia orientalis C. J. Chen, a dominant riparian shrub distributed across multiple biodiversity hotspots in southwestern China. Based on whole genome sequencing data from 332 individuals, we identify three genetically distinct groups: two diverged during the early Last Glacial period, and one originated through hybridization more recently. Despite both historical and ongoing opportunities for gene flow, strong genetic differentiation persists among the three groups. This differentiation is supported by clear niche divergence among the three groups and by genomic signatures of local adaptation, including selective sweeps related to hypoxia tolerance, thermal adaptation, and anthropogenic pressures. Together, these findings indicate that post-dispersal niche filtering limits the merging of these lineages. Genomic offset projections reveal asymmetric vulnerabilities to future climate scenarios, with one lineage particularly maladapted under projected shifts. These findings highlight niche-driven adaptation as a primary determinant of both historical divergence and contemporary resilience. Collectively, this study presents a framework linking post-dispersal ecological filtering to long-term genomic divergence, offering new insights into how niche filtering maintains genetic structure under rapid environmental change.
Ubiquitination is a common protein modification, mostly targeting protein substrates for degradation. As E3 ligases serve critical roles in substrate recognition, their biological functions are of special interest. Throu...Ubiquitination is a common protein modification, mostly targeting protein substrates for degradation. As E3 ligases serve critical roles in substrate recognition, their biological functions are of special interest. Through a targeted reverse genetic screen, we discovered a novel E3, SNIPER8 (snc1-influencing plant E3 ligase reverse genetic, 8), that negatively regulates immunity in Arabidopsis. Overexpression of SNIPER8 suppressed the phenotypes of the autoimmune mutant snc1, which carries a gain-of-function mutation in a TIR-type NLR (Toll/Interleukin-1 Receptor-like nucleotide-binding leucine-rich repeat receptor). Conversely, knocking out sniper8 enhanced the dwarfism of snc1. SNIPER8 and its three paralogs function redundantly, and knocking out all four genes in wild-type background yielded strong autoimmunity. To search for the substrates of SNIPER8, a suppressor screen with the sniper8 quadruple mutant was carried out, which yielded many loss-of-function alleles of SNC1. As the transcriptional corepressor TPR1 (Topless-related protein 1) was known to be required for SNC1-mediated immunity, its relationship with SNIPER8 was examined. SNIPER8 was found to directly interact with TPR1 and negatively regulate its protein levels. In addition, SNIPER8 overexpression can suppress TPR1-mediated autoimmunity, whereas the autoimmunity of sniper8 quadruple mutant fully depends on both the SNC1 locus and three redundant TPL/TPR genes. Taken together, SNIPER8 is a negative regulatory E3 ligase in plant immunity that promotes TPR1 turnover. This regulation is essential for maintaining immune homeostasis and preventing autoimmune activation.
Hypoxic conditions caused by submergence or soil waterlogging constrain plant growth and productivity. To survive, plants coordinately reprogram both sugar metabolism and phytohormone signaling to trigger adaptive respon...Hypoxic conditions caused by submergence or soil waterlogging constrain plant growth and productivity. To survive, plants coordinately reprogram both sugar metabolism and phytohormone signaling to trigger adaptive responses; yet, the integrative regulatory frameworks governing this interaction remain unresolved. Here, we synthesize current knowledge on how sugars, acting as both metabolites and signals, intersect with phytohormone networks to regulate growth and survival under low-oxygen stress. Under hypoxia, ethylene and auxin reshape root architecture, while cytokinin mediates sugar-dependent regulation of shoot branching to optimize resource allocation. The dynamic interplay between abscisic acid and sugars is central to maintaining energy balance under cyclic day-night hypoxia. This interaction modulates the stomatal aperture, facilitates controlled starch degradation, and coordinates sucrose transport to sustain metabolism. Furthermore, crosstalk between primary sugars, gibberellin, and brassinosteroid fine-tunes critical developmental transitions, including seed germination and internode elongation. Although individual signaling pathways under hypoxia have been well studied, their integration via sugar-hormone crosstalk remains elusive. To address these issues, we propose integrating synthetic low-oxygen sensors that initially detect hypoxic stress with engineered sugar-hormone balancing circuits that subsequently fine-tune metabolic and hormonal responses, thereby creating closed-loop feedback systems for adaptive stress resilience. Such systems could enable "Sensing, Metabolism, Adaptation, and Regulation Technology" (SMART) crops to autonomously sense and adapt to hypoxia stress. By synthesizing current knowledge and existing gaps, our work proposes future directions to advance the development of hypoxia-resilient crops through optimizing growth and yield stability under stress.
Editing the watermelon EPSPS gene using a prime editing platform with visible markers created a non-transgenic glyphosate-resistant line. These robust heterozygous mutants tolerate field-level herbicide doses without gro...Editing the watermelon EPSPS gene using a prime editing platform with visible markers created a non-transgenic glyphosate-resistant line. These robust heterozygous mutants tolerate field-level herbicide doses without growth penalties, serving as ideal parental lines for crop breeding.
Abscisic acid (ABA) promotes sugar accumulation during the ripening and quality formation of non-climacteric fruits; however, the underlying molecular mechanisms remain incompletely understood. Here, we identified that C...Abscisic acid (ABA) promotes sugar accumulation during the ripening and quality formation of non-climacteric fruits; however, the underlying molecular mechanisms remain incompletely understood. Here, we identified that CsSWEET16, a plasma membrane-localized transporter, was upregulated during the late developmental stages of citrus fruit and contributes to enhanced sugar accumulation in juice sacs under ABA regulation. The regulatory mechanism revealed that two transcription factors in the ABA signaling pathway, CsABF3 and CsABI5, synergistically activated CsSWEET16 expression. Conversely, during the early stage of fruit development, the transcription of CsSWEET16 was repressed by the transcription factor CsMYB35, which was dephosphorylated and stabilized by phosphatase CsPP2C58. However, during fruit ripening and with the increase in endogenous ABA levels, the expression of CsPP2C58 was downregulated, whereas CsSnRK2.6 phosphorylated CsMYB35, resulting in its degradation and thereby alleviating the suppression on CsSWEET16 transcription. Two cooperation pathways, phosphorylation dynamics for CsMYB35 stability and CsABF3/CsABI5 transcriptional activity, were elucidated through which ABA signaling enhances CsSWEET16 expression and promotes sugar accumulation in citrus. These findings not only expand our understanding of novel cooperative regulatory mechanisms within the ABA signaling network but also offer valuable insights for optimizing the sweetness and taste quality of citrus and other non-climacteric fruits.
This commentary highlights a new study revealing a fungal RNA decoy strategy that interferes with plant microRNA-mediated immune regulation. By blocking key microRNA activity, fungal RNAs reprogram host gene expression a...This commentary highlights a new study revealing a fungal RNA decoy strategy that interferes with plant microRNA-mediated immune regulation. By blocking key microRNA activity, fungal RNAs reprogram host gene expression and weaken immune responses, thereby enhancing pathogen virulence and disease susceptibility in rice.
Nitrogen pollution represents a critical challenge in the 21st century, highlighting the urgent need for sustainable alternatives to industrial nitrogen fixation. Diazotrophic bacteria, which uniquely convert dinitrogen...Nitrogen pollution represents a critical challenge in the 21st century, highlighting the urgent need for sustainable alternatives to industrial nitrogen fixation. Diazotrophic bacteria, which uniquely convert dinitrogen (N) into bioavailable forms, offer a promising solution through biological nitrogen fixation (BNF). These bacteria typically perform nitrogen fixation under nitrogen-limited conditions. Over the past 50 years, extensive research has elucidated the molecular mechanisms and regulatory pathways governing BNF. Recent microbiome studies have revealed that wild rice accessions harbor a greater abundance of diazotrophic bacteria, whereas a substantial proportion of these beneficial microbes have been lost in modern cultivated varieties. Advancements in synthetic biology have enabled the engineering of nitrogen‑exporting diazotrophs, potentially reducing dependence on industrial nitrogen fertilizers. This review emphasizes the importance of targeted research to develop customized diazotrophic microbes in conjunction with synthetic microbial community that can serve as nitrogen exporters for rice. Furthermore, it highlights the necessity of identifying rice cultivars that are particularly responsive to these microbial interventions. Finally, it provides a comprehensive roadmap addressing key challenges and opportunities in deploying BNF to supplement plant nitrogen nutrition and advance sustainable agriculture.
Engineered nanoparticles (ENPs) are increasingly recognized as promising tools for modulating plant stress responses; however, their underlying mechanisms and associated risks remain under debate. This review integrates...Engineered nanoparticles (ENPs) are increasingly recognized as promising tools for modulating plant stress responses; however, their underlying mechanisms and associated risks remain under debate. This review integrates recent advances showing that ENPs can reprogram plant redox homeostasis through multiple pathways, including direct surface redox activity, nanozyme-like catalysis, ion release, and disruption of organellar electron transport. In addition, ENPs influence membrane physicochemical properties, transcriptional regulation, metabolic fluxes, hormonal crosstalk, epigenetic modifications, and the structure of the plant-associated microbiome. These processes produce distinct reactive oxygen and nitrogen species (ROS/RNS) signatures that activate Ca fluxes, mitogen-activated protein kinase (MAPK) cascades, and downstream transcriptional networks. We emphasize the importance of dose-dependent-often hormetic-responses, the critical role of the rhizosphere microbiome, and the application of spatially resolved techniques (e.g., μ-XRF, NanoSIMS, and spatial omics) to link NP fate with localized redox dynamics. Finally, we propose a safe-by-design framework that incorporates standardized NP characterization, appropriate ionic and inert controls, and predictive modeling approaches. This framework aims to facilitate the risk-informed and sustainable deployment of ENPs in agriculture.
An optimized Cas12i3 genome-editing system enables highly efficient and predictable editing of regulatory sequences in rice. Precise promoter engineering fine-tunes gene expression, improves grain size, and enhances prod...An optimized Cas12i3 genome-editing system enables highly efficient and predictable editing of regulatory sequences in rice. Precise promoter engineering fine-tunes gene expression, improves grain size, and enhances production potential, demonstrating a powerful new approach for crop improvement through targeted regulation rather than gene disruption.
Seed germination is a complex, multistep developmental process that is critical for plant growth and regulated by intricate polygenic networks. Despite its agronomic significance, the precise mechanism underlying this pr...Seed germination is a complex, multistep developmental process that is critical for plant growth and regulated by intricate polygenic networks. Despite its agronomic significance, the precise mechanism underlying this process in rice remains incompletely understood. In this study, we determined a seed-specific gene OsDOG1L1, the ortholog of Arabidopsis DOG1, as an essential regulator that inhibits germination while promoting seed dormancy in rice. Overexpression of OsDOG1L1 led to delayed germination and enhanced dormancy, whereas loss-of-function mutants showed accelerated germination and reduced dormancy. Temporal analysis showed a progressive decline in OsDOG1L1 transcript and protein levels during germination. Furthermore, we identified two C2H2-type zinc finger transcription factors, ZFP36 (also known as Bsr-d1) and ZFP252, as direct regulators of OsDOG1L1, functioning upstream to repress OsDOG1L1 expression. Molecular and genetic analyses demonstrated that OsDOG1L1 interacts with and suppresses the phosphatase activity of clade A protein phosphatase 2Cs (PP2Cs), OsPP2C09 and OsPP2C30, thereby enhancing ABA signaling to inhibit seed germination. Together, our findings uncover a ZFP36/ZFP252-OsDOG1L1-OsPP2Cs regulatory module that governs rice seed germination, providing insights into the molecular regulation of germination control in rice.
Orchidaceae, one of the largest and most morphologically diverse angiosperm families, showcases unique evolutionary adaptations in morphology, ecology, and function. Recent advances in molecular and genomic research have...Orchidaceae, one of the largest and most morphologically diverse angiosperm families, showcases unique evolutionary adaptations in morphology, ecology, and function. Recent advances in molecular and genomic research have greatly reshaped our understanding of orchid evolution, revealing how genome dynamics, ecological interactions, and developmental plasticity jointly shaped their exceptional diversification. Phylogenomic frameworks derived from various genomic datasets have reconstructed the evolutionary history, revealing the influence of geological, climatic, and biotic factors on ancient divergences and global distributions. Comprehensive genomic studies have uncovered substantial variation in genome size, structure, and composition, largely driven by repetitive elements and whole-genome duplication events that facilitated adaptive radiations. Key innovations, including epiphytism, mycoheterotrophy, and deceptive pollination, are linked to gene family evolution and modifications in pathways related to CAM photosynthesis, mycorrhizal symbiosis, and floral morphogenesis. Integrative multi-omics approaches further illuminate mechanisms underlying speciation hotspots, coevolution with pollinators and fungi, and the molecular basis of developmental diversity. Overall, this review synthesizes current genomic, phylogenetic, and functional insights into orchid evolution, providing a theoretical foundation and future research framework for understanding their molecular diversification.
The Seed and Seedling Marker Method double-screening system for maize hybrid seed production integrates Ms45-mediated fertility restoration, Mn1/Sh1-RNAi-based seed selection, and Lc-based seedling selection. It thus ena...The Seed and Seedling Marker Method double-screening system for maize hybrid seed production integrates Ms45-mediated fertility restoration, Mn1/Sh1-RNAi-based seed selection, and Lc-based seedling selection. It thus enables efficient, high-purity propagation of male-sterile lines by combining fertility maintenance with sequential visual selection at the seed and seedling stages.
This Commentary highlights a study revealing that adaptation to cold climates indirectly drove the loss of bacterial blight resistance in japonica rice. Rebuilding the lost immune module restores strong disease resistanc...This Commentary highlights a study revealing that adaptation to cold climates indirectly drove the loss of bacterial blight resistance in japonica rice. Rebuilding the lost immune module restores strong disease resistance without yield penalty, opening new opportunities for crop breeding.
The tonoplast-localized ABCG transporter SmABCG11 directly transports long-chain hydroxy fatty acids, the core structural precursors of sporopollenin, to regulate pollen wall development and male fertility in eggplant.The tonoplast-localized ABCG transporter SmABCG11 directly transports long-chain hydroxy fatty acids, the core structural precursors of sporopollenin, to regulate pollen wall development and male fertility in eggplant.
This commentary interprets recent findings on how plants decode heat at the plasma membrane. By discussing FERONIA-mediated membrane nanoclusters, it highlights how receptor activation, lipid organization, and signaling...This commentary interprets recent findings on how plants decode heat at the plasma membrane. By discussing FERONIA-mediated membrane nanoclusters, it highlights how receptor activation, lipid organization, and signaling compartmentalization work together to distinguish adaptive warming from damaging heat, offering new perspectives on plant thermosensing and crop heat resilience.
Tension wood formation enables angiosperm trees to maintain upright growth through asymmetric secondary xylem development; yet, the primary physical signal that initiates this process remains unclear. Here, using Populus...Tension wood formation enables angiosperm trees to maintain upright growth through asymmetric secondary xylem development; yet, the primary physical signal that initiates this process remains unclear. Here, using Populus as a model system, we experimentally decoupled gravitational orientation from mechanical strain through clinostat rotation and controlled stem bending. We show that a persistent gravity vector is essential for tension wood (TW) induction, whereas mechanical strain alone is insufficient. Gravity perception in secondary growth stems is associated with endodermal amyloplast sedimentation and coincides with gravity-dependent lateral repolarization of the auxin efflux carrier PIN3b. This polarity shift establishes a sustained auxin maximum on the upper side of the cambial cylinder and leads to coordinated transcriptional repression of regulators controlling cambial cell proliferation, vessel differentiation, and lignification. Targeted reactivation of individual auxin-repressed transcription factors in TW-forming tissues selectively restores these developmental outputs, demonstrating that tension wood formation is genetically modular rather than governed by a single unified program. Together, these findings define a gravity-driven signaling pathway linking gravity perception to hormone transport polarity and cambial fate specification, extending classical models of gravitropism to secondary growth and providing a molecular basis for adaptive wood formation and the engineering of wood properties.
Strigolactones (SLs) were initially identified as rhizosphere signals that trigger germination of parasitic weeds and promote branching in arbuscular mycorrhizal fungi. More recently, SLs have been characterized as a cla...Strigolactones (SLs) were initially identified as rhizosphere signals that trigger germination of parasitic weeds and promote branching in arbuscular mycorrhizal fungi. More recently, SLs have been characterized as a class of carotenoid-derived plant hormones that regulate plant architecture and stress responses. This review systematically summarizes their diverse functions in shaping shoot architecture and root development, as well as their ability to mediate acclimation to various abiotic and biotic stresses. It also discusses the canonical signaling module composed of D14, MAX2/D3, and D53/SMXLs and its extensive interactions with other hormonal pathways. Finally, this review suggests that future research should focus on elucidating the dynamic responses to environmental stress mediated by the SL pathway, decoding the functional diversification of SLs in different plant species, and leveraging SLs as rhizosphere signals to control parasitic weeds. Precise spatiotemporal modulation of SL activity is crucial for balancing its functional complexity and will contribute to designing crops with optimized plant architectures and enhanced stress resilience.
MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression in eukaryotes. Among them, miR396 targets GROWTH-REGULATING FACTOR (GRF) transcription factors and forms one of the most highly conse...MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression in eukaryotes. Among them, miR396 targets GROWTH-REGULATING FACTOR (GRF) transcription factors and forms one of the most highly conserved regulatory modules in plants. Recent studies have greatly expanded the functional landscape of the miR396-GRF module, showing that, beyond its canonical role in leaf morphogenesis, it also participates in root meristem regulation, reproductive development, yield formation, tissue regeneration, and responses to diverse abiotic and biotic stresses. In crop plants, this module further controls agronomically important traits. Here, we summarize current knowledge of the evolutionary conservation and diversification of the MIR396 loci, the upstream pathways that control miR396 expression, and the developmental and stress-related outputs mediated by the miR396-GRF module. We also discuss evidence that miR396 functions as a context-dependent regulator rather than a simple growth suppressor, and highlight how precise manipulation of the miR396-GRF module may provide new opportunities for crop improvement by optimizing growth, regeneration, and stress resilience.
The serine/threonine protein kinase LlSAPK2 enhances thermotolerance in lily (Lilium longiflorum) by phosphorylating and stabilizing the transcription factor LlbZIP46, which activates heat shock factor genes, thereby red...The serine/threonine protein kinase LlSAPK2 enhances thermotolerance in lily (Lilium longiflorum) by phosphorylating and stabilizing the transcription factor LlbZIP46, which activates heat shock factor genes, thereby reducing heat-induced cellular damage.