Gain-of-function screens enable the discovery of gene functions and candidate targets for molecular breeding. Here we developed a protoplast-based dCas9-TV-mediated CRISPR activation screen in rice and identified OsTV1, an epidermal papillae-specific receptor kinase, as a positive regulator of fungal resistance. OsTV1 overexpression enhanced silicon deposition, leaf rigidity and basal defence gene expression, conferring broad-spectrum fungal resistance without compromising growth. This study establishes a high-throughput gain-of-function screen adaptable for investigating diverse cellular processes in plants and provides insights into the roles of silicon in rice defence. The authors develop a protoplast-based dCas9-TV-mediated CRISPR activation screen in rice, identifying a papillae-specific receptor kinase that positively regulates fungal resistance via silicon-mediated physical and biochemical defences.
Spontaneous epimutations are stochastic gains and losses of cytosine methylation that arise from imperfect maintenance across cell divisions. At CG sites, such epimutations can be inherited across generations in plants and constitute a major source of CG methylation (mCG) diversity. However, why the fidelity of mCG inheritance varies among genotypes, and how this variation relates to steady-state mCG levels, remains poorly understood. Here we tracked DNA methylation over 10 generations in ~400 mutation-accumulation lines derived from ~70 Arabidopsis thaliana Ler × Cvi recombinant inbred founders. By treating methylation gain and loss rates as quantitative molecular traits, we mapped a major-effect locus to a Cvi-derived deletion between VARIANT IN METHYLATION (VIM)2 and VIM4, two key components of the METHYLTRANSFERASE 1-dependent mCG maintenance pathway. Lines carrying this deletion showed elevated VIM2/4 (VIM2 and VIM4) expression, a rapid shift of genome-wide mCG towards a lower steady state and reduced fidelity of methylation inheritance across generations. Complementary overexpression and loss-of-function experiments identify VIM2/4 as dosage-sensitive negative regulators of mCG maintenance, in contrast to the canonical positive role of VIM-family proteins in mCG. Together, our results support a punctuated-equilibrium model of DNA methylome evolution, in which naturally segregating modifiers of mCG homeostasis can produce abrupt shifts in methylation state and alter the rate at which heritable epigenetic variation accumulates in plant genomes.
A wild population on a drought-stricken Atlantic island and a ten-generation greenhouse experiment converge on the same missing 2.7 kilobases of DNA — and highlight that the potential to change can be an adaptation in itself.
Synthetic apomixis promises to fix hybrid vigour through clonal seeds, yet practical implementation has been limited by low efficiency and reduced fertility. A new study identifies a sperm cell-specific transcription factor, HUAXU, that can trigger fertilization-independent embryogenesis when coupled with clonal gametogenesis, achieving near-complete clonal seed production in hybrid rice with minimal yield penalty. This work provides a mechanistic insight into the paternal activation of embryogenesis and offers a scalable strategy for fixing heterosis in crops.
Reprogramming of plant nucleotide-binding leucine-rich immune receptors has long been limited by natural receptor diversity and hard-to-engineer recognition surfaces. A novel approach combines de novo protein design with directed evolution in planta to build synthetic plant immune receptors that detect diverse pathogen proteins, enabling on-demand design and refinement of resistance genes.
With the approval of the European Council and the European Parliament, Regulation (EU) 2026/1388 on plants obtained by certain new genomic techniques and their products was finally adopted by the European Union on 17 June 2026. This is a remarkable achievement considering that Directive 2001/18/EC, the main legislation on the environmental release of genetically modified organisms, dates back to 2001, and that the first Working Group on New Plant Breeding Techniques was established by the European Commission in 2007 with the aim of identifying legislation more appropriate to technologies developed after 2001.
Domestication has profoundly reshaped the maize genome, yet its impact on abiotic stress resilience remains largely unresolved. Here we show that modern maize exhibits markedly greater salt tolerance than its wild progenitor, teosinte. Using a maize-teosinte (W22-T8759) recombinant inbred line population, we identify the transcriptional repressor MYB28 as a major genetic determinant underlying this divergence. MYB28 negatively regulates salt tolerance by impairing shoot Na+ exclusion. In modern maize (W22), however, salt stress activates CIPK20, which phosphorylates MYB28 to relieve its repression. A non-synonymous single nucleotide polymorphism (SNP1409T) disrupts this regulation in teosinte (T8759), conferring salt sensitivity. We further identify HAK4 as a downstream target of the CIPK20-MYB28 pathway, mediating shoot Na+ exclusion and salt adaptation. Population genomic and cross-species analyses revealed that the salt-tolerant SNP1409T MYB28 allele originated in ancestral teosinte and was positively selected during domestication, increasing yield in salt-affected fields. Together, our findings uncover a domestication-selected CIPK20-MYB28-HAK4 module that provides mechanistic insights into the evolutionary trajectory of salt tolerance, and identifies valuable targets for developing salt-resilient cultivars.
Profiling transcriptome isoforms in their spatial context is instrumental for deciphering plant embryogenesis. By combining high-throughput full-length isoform sequencing and spatial transcriptomics (spatial MAS-IsoSeq) in maize embryogenesis, we identified 285,639 isoforms, 72.87% of which were previously uncharacterized. Gene models based on these full-length isoforms increased short-read exon mapping by 5.52%. Furthermore, spatial transcription expression detection improved by up to 97.45% in an extreme example. Using these isoforms, we constructed a new gene-model database (MaizeV5_IsoAnn) by integrating 5,228 novel genes and 1,674 genes with 5'- and/or 3'-flanking region extensions into the current maize reference gene models. Leveraging MaizeV5_IsoAnn, we reanalysed embryonic leaf cell transcriptomes to construct a refined time-ordered regulatory network and integrated it into multi-omics analyses with chromatin accessibility dynamics profiling, providing new insights into maize embryonic leaf development. Moreover, we propose LBD26 as an essential transcription factor in maize embryonic vein development. This study underscores the power of spatial MAS-IsoSeq to construct gene-model databases and elucidate developmental processes and mechanisms.
Plant peptide hormones orchestrate growth, development and immunity by engaging membrane-resident receptor kinases. GmSubPEP, a defence-eliciting peptide derived from a subtilase precursor, was initially isolated from soybean leaf extracts. Here we uncover an unexpected expansion of GmSubPEP variants with highly diverse sequences, yet each capable of triggering robust, tissue-specific pathogen resistance. Integrated transcriptomic and phosphoproteomic profiling shows that individual GmSubPEPs differentially activate overlapping and unique immune pathways, enabling fine-tuned defence modulation. Strikingly, genes generating these peptides and their receptors, termed GmSubPEP Receptors (GSPRs), are physically interspersed within a genomic cluster, and GSPRs exhibit differential binding affinities for their cognate peptide ligands. By unveiling how conserved subtilase precursor scaffolds diversify into specialized ligand-receptor pairs across legume lineages, our work reveals the role of SubPEP-GSPR modules in plant-microbe interactions and provides a framework for mining and engineering peptide-receptor modules to strengthen crop immunity.
Drought stress threatens global wheat productivity, yet the genetic and molecular mechanisms underlying drought resilience remain incompletely understood. Here we identify TaSCE1-A1, which encodes a SUMO-conjugating enzyme, as a positive regulator of drought resistance through genome-wide association studies. In arid regions, an evolutionary G-to-A transition in the promoter confers elevated TaSCE1-A1 expression through disruption of TaBPC1-mediated transcriptional repression. Prime-edited and near-isogenic lines harbouring elite alleles show improved drought resilience, confirming its functional significance. Moreover, TaSCE1-A1 mediates SUMOylation of TaBAP1/2, thereby enhancing its protein stability, which in turn modulates the ABA pathway to facilitate stomatal closure under drought conditions. Evolutionarily, this adaptive allele originated in tetraploid wheat and underwent positive selection during hexaploid wheat domestication. Our findings reveal a drought resistance pathway shaped by evolutionary selection, offering molecular targets for breeding drought-resilient wheat varieties.
Plant cells are enclosed by a semi-rigid cell wall with a complex biochemical composition and architecture. The poorly understood process of remodelling the cell wall is crucial for controlling growth and development and for regulating abiotic and biotic stress responses. Cell wall remodelling upon disruption of cell wall integrity through inhibition of cellulose biosynthesis depends on the receptor kinase STRUBBELIG (SUB) and its binding partner QUIRKY (QKY). Here, we identify NON-RACE SPECIFIC DISEASE RESISTANCE/HIN1 HAIRPIN-INDUCED-LIKE protein 3 (NHL3) as an additional factor involved in the SUB-dependent cellulose biosynthesis inhibition response. Collectively, our data indicate that NHL3 maintains SUB at the plasma membrane by physically interacting with SUB. SUB signalling is attenuated by receptor-mediated endocytosis initiated by release of first the SUB-NHL3 and later the SUB-QKY interaction. Our results further suggest a diverse set of biochemically and functionally distinct SUB complexes involved in regulating cell wall integrity and development.
Root hairs (RHs) are cellular outgrowths of plant root epidermal cells that are important for water uptake, nutrient acquisition and rhizosphere dynamics. Key genes controlling RH development have been identified, but the regulatory mechanisms of RH growth during drought stress remain largely elusive. Here we show that the bacterial root endophyte Flavobacterium sp. 98 (Flavo98) modulates root system architecture with a pronounced promotion of RH formation and cell elongation that is maintained under low-water conditions. We also show that Flavo98 improves plant performance under drought in diverse plant species, including Arabidopsis and wheat, and mitigates drought-associated seed yield loss. Using cellular, molecular and genetic analyses in Arabidopsis, we identified root stele-expressed ERF transcription factors, ERF115 and ERF114, as key mediators of Flavo98-induced RH development and plant drought responses. We show that both ERFs operate, in part, by inducing the expression of the small signalling peptide C-TERMINALLY ENCODED PEPTIDE 5 (CEP5). In addition, we present evidence for enhanced ethylene biosynthesis and signalling in Flavo98-induced ERF115 and ERF114 expression, revealing a new pathway that integrates ethylene signalling into RH regulation under drought. Together, our findings uncover a pathway that regulates RH growth as part of a broader, microorganism-dependent root system architecture plasticity under low-water conditions. This study highlights the potential of uncovering plant-microorganism mechanisms to strengthen crop resilience in a changing climate.
Plants employ non-photochemical quenching (NPQ) to protect their photosynthetic apparatus from photodamage. The response latency of NPQ following changes in light intensity is thought to significantly decrease photosynthetic efficiency. The amount of NPQ is commonly quantified from chlorophyll-fluorescence techniques using the Stern-Volmer equation, which requires fully closed reaction centres (RCs) of photosystem II, yielding NPQ in the absence of photochemical quenching ( NPQ Closed ). However, in nature, NPQ and photochemical quenching are normally present simultaneously. Therefore, to obtain a full understanding of this process, NPQ should also be explored when the RCs are open. Here we developed two methodologies to obtain NPQ in the presence of photochemistry ( NPQ Open ) using both fluorescence lifetime and fluorescence yield measurements. A detailed comparison in Arabidopsis thaliana plants reveals that the value of NPQ Open is ~35% lower than that of NPQ Closed . This difference is consistently observed across all measurements and is seen both upon closing ( NPQ Open → NPQ Closed ) and upon reopening ( NPQ Closed → NPQ Open ) of the RCs. We show that this difference can be explained by the presence of RC-induced 'instantaneous' switching of the NPQ quenching rate. This means that, in plants, NPQ is much more economical than is widely believed, it is large when its presence is needed, and it decreases instantaneously when the need disappears.
Ancient trees are in global decline and face increasing conservation challenges. Their exceptional longevity has fostered the view that they are genetic reservoirs, yet whether old age is synonymous with unique genetic variation remains unclear. Here we assembled a ~8-Gb chromosome-level reference genome for the critically endangered conifer Glyptostrobus pensilis, now largely restricted to southern China with scattered populations in Vietnam and Laos, and resequenced 147 individuals, including 64 ancient (>100 years old and persisting in human-dominated landscapes), 33 wild and 50 recently cultivated individuals. Ancient individuals comprised both likely natural relics and historically introduced individuals and formed two deeply divergent lineages and one ancestral-admixed group, each with distinct demographic histories of prolonged contraction and genomic erosion. Lineage identity explained more variation in genome-wide diversity, inbreeding and genetic load than the three conservation types, despite broad differences in age structure. Rare-allele analyses revealed pronounced heterogeneity among ancient trees: only relic and ancestral-origin individuals from high-diversity lineages contributed substantial unique variation, much of which is poorly represented in wild and cultivated populations. Together, our findings suggest that ancient trees are not uniformly genetically irreplaceable and that, at least in this conifer, evolutionary importance is shaped more strongly by population history than by age alone.
