This Commentary highlights a newly uncovered layer of plant immune regulation, summarizing how surface immune signals license intracellular NLR receptors through alternative RNA splicing. This mechanism enables rapid activation of NLRs upon effector recognition, revealing that surface immunity not only amplifies defense and actively sets the threshold for intracellular immune triggering.
In canonical jasmonate (JA) signaling, MYC2 activity is restrained by JA-inducible JAZ repressors that are rapidly degraded upon JA perception. However, it remains unclear how MYC2 is attenuated during prolonged developmental processes such as leaf senescence, where sustained repression is required independently of acute JA fluctuations. Here, we identify C-type cyclin 1;1 (CycC1;1) as a negative regulator of JA-induced leaf senescence in Arabidopsis. CycC1;1 physically interacts with MYC2 in the nucleus to inhibit MYC2-mediated transcriptional activation of senescence-associated genes (SAGs) by interfering with RNA polymerase II recruitment. Additionally, CycC1;1 interacts with the Mediator subunit MED25 to disrupt its association with MYC2. Disruption of CycC1;1 accelerates JA-dependent leaf yellowing, whereas loss of MYC2 or MED25 fully suppresses this premature-senescence phenotype. Unlike JAZ repressors, CycC1;1 expression and protein stability are uncoupled from JA signaling. Phylogenetic analyses suggest that the CycC1;1-MYC2 interaction may predate the emergence of JAZ repressors in aquatic ancestors, and CycC1;1 shows evolutionarily conserved ability to interact with and inhibit MYC2 across different plant species. Collectively, our findings uncover a CycC1;1-MED25-MYC2-regulatory module wherein CycC1;1 suppresses MYC2 activity by inhibiting MED25 binding to MYC2 and RNA polymerase II recruitment, downregulating SAG expression and thus delaying leaf senescence in plants.
Higher grain weight and stronger seed dormancy are key objectives for improving rice (Oryza sativa) yield and inhibiting pre-harvest sprouting. Therefore, identifying genes that coordinately regulate grain weight and seed dormancy is an urgent priority. Here, we report that knocking out miR1866 (KO1866) increased grain weight and reinforced dormancy. We identified the transcript of ubiquitin-specific processing protease 7 (OsUBP7), which encodes a protein with deubiquitination activity in vitro, as the primary target of miR1866. Consistent with miRNA-directed repression, OsUBP7 transcript abundance generally showed a spatiotemporal pattern opposite to miR1866 accumulation during rice development. Overexpression of native OsUBP7 (UBP7-OE) or a miR1866-resistant form (mUBP7-OE) phenocopied KO1866 by producing heavier grains with stronger dormancy. The miR1866-OsUBP7 module also altered the expression of genes associated with sucrose and starch metabolism, cell-cycle control, grain development, and abscisic acid (ABA) biosynthesis and signaling. Accordingly, KO1866, UBP7-OE, and mUBP7-OE plants contained more ABA and responded more sensitively to exogenous ABA than wild type. OsUBP7 interacted with OsDA1 (encoded by Os06g0182500) and UBIQUITIN-CONJUGATING ENZYME (OsUCE1; encoded by Os02g0833300), thereby affecting hull cell division and ABA signaling and ultimately regulating grain weight and seed dormancy, respectively. Our results indicate that the miR1866-OsUBP7 module regulates grain weight and seed dormancy in rice, highlighting its potential for engineering crops with improved yields and stronger seed dormancy.
RNase is a kind of RNA hydrolase that widely exists in organisms. RNase T2 in plants functions by hydrolyzing and processing RNA in the cell. However, the mechanism by which RNase T2 acts on intercellular RNA to exert the resistance function has not been studied. Here, we identified the S-like RNase TaRNS4 that positively regulates wheat resistance to stripe rust by degrading the RNA of Puccinia striiformis f. sp. tritici (Pst), the causative agent of stripe rust. Importantly, TaRNS4 phosphorylation mediated by receptor-like kinase TaRLK5 contributes to its degradation of Pst RNA and enhances plant resistance, and changes in a single active site can significantly reduce RNA degradation efficiency. However, the serine/threonine protein phosphatase TaPP2C10 can bind to TaRNS4 and dephosphorylate it to inhibit Pst RNA degradation to promote Pst colonization. Meanwhile, it was found that TaPP2C10, as a negative regulator, can also increase plant susceptibility by binding to TaMAPK6 and dephosphorylating it. Moreover, TaRNS4 was found to increase wheat resistance to Pst by hijacking TaPP2C10 to relieve its dephosphorylation of TaMAPK6. Overall, these findings indicate that the TaRNS4-TaPP2C10 module fine-tunes plant immunity in an antagonistic manner and highlight the versatility of TaRNS4, which enhances plant resistance by synergizing RNA degradation and the MAPK cascade.
This commentary discusses new research showing that CHILLING PHOENIX acts as a transcriptional hub rewiring rice metabolism from cold defense to nitrogen-driven regrowth. Its mechanism, governed by natural variation, functions as a temporal switch, offering a new paradigm for engineering climate-resilient crops with improved recovery.
The prime editing (PE) system is a precise genome editing technology that works efficiently in monocots; however, its application is limited by low editing efficiency in dicots, particularly Cucurbitaceae and Solanaceae plants. Here, we first significantly improved the transformation efficiency by introducing spectinomycin in cucurbits, then used the tomato elongation factor 1-alpha (SlEF1α) promoter to enhance PE protein expression, and incorporated the Csy4 ribonuclease to process pegRNAs, collectively addressing multiple constraints limiting PE efficiency in cucurbits. The optimized PE systems, particularly Csy4-PE6d, achieved an average desired editing frequency of 80.83% at targeted loci in cucumber via stable genetic transformation, with frequencies reaching up to 100% at certain sites. Moreover, Csy4-PE6d generated homozygous edits in 36.43% of transgenic lines and demonstrated robust editing activity in melon, pumpkin, and potato. Using the Csy4-PE6d tool, we generated heritable edited cucumber lines with dual resistance to bacterial angular leaf spot and downy mildew by targeting the CsSGR gene. Collectively, this optimized system substantially enhances PE efficiency in Cucurbit crops, providing an effective solution to common challenges such as low editing efficiency and limited heritability in these species.
The early morphogenesis of the embryo and endosperm sets the upper limit of rice grain yield; yet, the cellular dynamics and regulatory mechanisms underlying this critical stage remain largely elusive. Here, we present a single-cell atlas of developing rice seeds based on single-nucleus RNA sequencing of 67,922 high-quality nuclei from rice caryopses. Integration with bulk RNA-seq, in situ hybridization, and promoter-GUS staining enabled systematic cell-type annotation and revealed a distinct population of embryo-endosperm interface (EEI) cells occupying the boundary between the developing embryo and endosperm. Comparative analyses with maize data sets, together with trajectory inference, suggested that a subset of EEI cells shares molecular features with maize embryo-adjacent scutellum cells and shows transcriptional continuity with starchy endosperm cells. Embryo-endosperm interface cells were enriched in transport-related and developmental regulatory genes with known functions in seed development and embryogenesis. Focusing on the EEI-enriched regulator OsBZR4, we found that loss of OsBZR4 altered cellular composition and transcriptional programs during early seed development, disrupted embryonic developmental progression, and reduced the expression of embryonic genes, including OsCDP3.10 and RINO1. Together, our study provides a single-cell resolution framework for understanding early rice seed development, identifies the embryo-endosperm interface as an important cellular domain associated with embryogenesis, and offers a valuable resource for dissecting the molecular basis of seed formation in rice and related cereals.
Land plants must cope with the spatiotemporal heterogeneity of soil nutrients. During evolution, plants have developed sophisticated systems to perceive nutrient distribution and adaptively remodel their root system architecture (RSA) to maximize nutrient acquisition while minimizing energy expenditure. This process, referred to as nutrient foraging, involves local nutrient perception at the root, signal integration in the shoot, and subsequent RSA adjustment. Over the past decade, significant progress has been made in understanding how plants sense spatially heterogeneous nutrient availability and how systemic signals coordinate root development. Nitrogen (N) is a key limiting nutrient, often unevenly distributed in soils. Nitrate (NO3 -), a predominant N source, displays pronounced heterogeneity in soils. To adapt to this heterogeneity, plants use nitrate transporters, small peptides, phytohormones, receptor-like kinases (RLKs), microRNAs (miRNAs), mobile transcription factors, and amino acid signals as central regulators to mediate long-distance bidirectional signaling between the root and the shoot, ultimately guiding RSA modulation to match whole-plant nutritional demands. In legumes, systemic signaling pathways also regulate symbiotic nitrogen fixation. The product of symbiotic nitrogen fixation, ammonia (NH3)/ammonium (NH4 +), represents a nitrogen form fundamentally distinct from nitrate. This review summarizes current understandings of nitrate foraging, from local sensing to systemic signaling, and discusses how these insights can be harnessed to optimize RSA and improve nitrogen use efficiency (NUE) in crops. By integrating these concepts, we provide a framework for designing nitrogen-efficient crops adapted to heterogeneous soil environments.
Plant height and grain number are key factors influencing plant architecture and yield. Although a number of genes regulating rice plant height and grain number have been identified, further elucidation of their regulatory mechanisms remains critical for breeding high-yield rice varieties. In this study, we show that the GRAIN NUMBER AND PLANT HEIGHT 1 (GNH1) gene, which is identical to rice TRYPTOPHAN AMINOTRANSFERASE RELATED 2 (OsTAR2), plays an important role in regulating both rice plant height and grain number. A natural variation located 382 bp upstream of GNH1 impairs the DNA-binding affinity of the C2H2-type transcription factor ZFP36, increasing GNH1 transcript abundance and auxin accumulation in the indica cultivar T5 and ultimately leading to increased plant height and grain number. Haplotype analysis revealed that GNH1 has undergone differentiation between indica and japonica subspecies. Increasing the expression level of GNH1 significantly boosts rice yield in two elite rice varieties: Zhonghua 11 and Jigeng 88. Collectively, these findings not only deepen our understanding of the molecular mechanisms underlying plant architecture and yield regulation but also offer a favorable gene for rice genetic improvement.
In apple, the nitrate signaling-responsive factor MdLBD36 and the phosphate signaling-responsive factor MdPHR1 recruit the transcription factor MdBZR1 to enhance its transcriptional activation of the target gene MdMYC2, thereby improving resistance to Botryosphaeria dothidea.
Multiplex CRISPR editing of prolamin genes and phenotype-based screening revealed that reducing prolamin content in rice can increase lysine content and digestibility, improve taste. PROLM25 and PROLM26 are key genes for reducing prolamin content, and knocking out these two genes can achieve the same effect.
This Commentary defines five interconnected biophysical parameters of cellular water status and proposes a hierarchical framework integrating cell-surface osmosensors with intracellular liquid-liquid phase separation-based sensing mechanisms. It highlights how two recent studies expand our understanding of plant water sensing through distinct condensation-driven pathways.
Most orchid species require fungi for natural germination, but the molecular mechanism of this symbiosis is poorly understood. Cremastra appendiculata seeds secrete phenolic acids before fungal contact, acting as nutrient molecules to chemically attract its symbiotic fungus Coprinellus disseminatus.
Reconstruction of a robust phylogeny of Medicago using genome-scale nuclear data from the Angiosperms353 probe set sheds light on the origin of the genus and provides evidence that pod morphological traits acted as key innovations, playing a central role in the adaptive radiation of Medicago.
Plant gray mold disease, caused by the necrotrophic fungus Botrytis cinerea, threatens global food security by infecting over 1,400 species. The resistance of B. cinerea to fungicides poses a major challenge for its control. RNA interference (RNAi) shows promise for pathogen management, but high production costs, poor stability, and inefficient delivery of double-stranded RNA (dsRNA) restrict its practical use. In this study, we developed Yarrowia lipolytica strain MP181-2 as a novel RNAi platform, leveraging its ability to colonize the phyllosphere of crop plants (tomato and alfalfa) to enable simultaneous dsRNA production and pathogen targeting via microbe-induced gene silencing (MIGS). Through target screening, we identified three essential fungal genes, BcRpd3, BcNat1, and BcArd1, whose silencing significantly reduced the pathogenicity of B. cinerea. We further constructed a chimeric dsRNA molecule (BcANR-dsRNA) targeting these three genes, which demonstrated superior disease suppression compared to single-gene targeting. The engineered Y. lipolytica strains that produce dsRNA could effectively interfere with the expression of target genes in B. cinerea, and the strain expressing BcANR-dsRNA (designated Yl-dsANR) acquired the ability to suppress the growth of B. cinerea. In planta tests confirmed that Yl-dsANR successfully interfered with the expression of three target genes, leading to decreased fungal biomass and reduced lesion development on different hosts. Notably, foliar application of Yl-dsANR provided durable protection (over 70% efficacy for 5 d) in potted plants. Our integrated approach combines the advantages of microbial biocontrol with RNAi precision, establishing Y. lipolytica as a versatile chassis for sustainable crop protection. This study also provides an effective solution to current limitations in RNA pesticide development and offers a scalable, eco-friendly alternative to chemical fungicides for gray mold management.
As global temperatures increase, heat stress has become a key limiting factor affecting crop yield and quality. Against the backdrop of growing global food demand and increasingly frequent extreme high-temperature events, this dual pressure poses a threat to global food security. This review systematically analyzes the physiological effects of heat on major crops, focusing on source-sink relationships and nutrient transport processes. We summarize key heat-related genes identified in these crops through forward and reverse genetic approaches, elucidating the mechanisms underlying heat signal perception and transduction across genetic, transcriptional, protein, metabolic, cell membrane, nuclear, and organellar levels. Furthermore, we explore the complex crosstalk between heat and other abiotic/biotic stresses in crops. Finally, we discuss current challenges and future avenues for breeding heat-resilient crops to ensure stable agricultural productivity.
Using a new restorer line for rapeseed Ogura cytoplasmic male sterility, with a shorter foreign DNA fragment, higher fertility stability, and seed color as a marker, established a fully mechanized hybrid seed production system that greatly reduces labor costs and improves hybrid seed purity.
Engineering rice endosperm with modules for vitamin binding, lipid storage, and antioxidant protection enriched water- and fat-soluble vitamins without compromising key agronomic traits and maintained vitamin higher levels after cooking, demonstrating its potential to improve crop nutrition.
Sugarcane (Saccharum spp.) is a globally important C4 crop that contributes substantially to sugar production and renewable bioenergy systems. Modern sugarcane cultivars were derived from interspecific hybridization between high-sucrose S. officinarum and stress-resilient wild S. spontaneum, followed by extensive backcrossing and selection. Such breeding trajectory has generated an extremely complex polyploid genome marked by high ploidy, pervasive aneuploidy, mosaic subgenome composition, and a reticulate evolution history. For decades, this complexity has resulted in persistent taxonomic ambiguities, constrained genomic analyses, complicated genetic dissection of agronomic traits, and limited breeding efficiency. The rapid development of third-generation long-read sequencing, haplotype-resolved assembly, and polyploid-aware computational approaches has fundamentally revolutionized sugarcane research. This review synthesizes recent progress in Saccharum taxonomy, polyploid genome architecture and evolution, high-quality genomic resource development, germplasm exploration, and genome-informed breeding strategies. We propose an integrated framework connecting taxonomic refinement, genome biology, and breeding applications. Critical challenges are elaborated, including the taxonomy-genomics disconnect, diploid-centric analytical bias, insufficient haplotype resolution, the lack of polyploid-aware genetic models, and underutilization of wild germplasm. Finally, we outline future priorities toward predictive and design-oriented sugarcane improvement by addressing unresolved core questions. This review provides a comprehensive and forward-looking perspective for accelerating genetic improvement in sugarcane and other highly complex polyploid crops.
