Precise and scarless DNA insertion and replacement represent two of the major challenges in plant genome editing. Numerous tools have been developed, including homology-directed repair-dependent tools and prime-editing-mediated systems. However, none has fully resolved these challenges. In this study, we develop the "mortise-tenon joint system" (MT), a novel strategy that enables precise and efficient targeted DNA insertion and replacement. By leveraging the APOBEC-Cas9-uracil DNA glycosylase/ (apurinic or apyrimidinic site) lyase within our previously reported APOBEC-Cas9 fusion-induced deletion system, which performs single-strand cleavage on the non-target strand and double-strand cleavage on the target strand, we generated a unique "mortise" structure, consisting of double-strand breaks with single or double non-complementary 5 ' overhangs. We further designed "tenons," double-stranded DNA donors containing 5 ' sticky ends precisely matching the 5 ' overhangs of the mortises. The end-capture interaction between mortises and tenons facilitates precise targeted insertion and replacement, achieving frequencies of 16.30%-59.47% across seven tested targets using 21-85 bp donor inserts in rice. If long DNA donors with sticky ends complementary to the mortise structure can be generated, the MT system may enable highly precise targeted insertion and replacement of large DNA fragments.

Disease resistance often comes with a penalty in growth and yield. The microRNA miR156 and its target, the transcription factor gene IDEAL PLANT ARCHITECTURE 1 (IPA1), regulate developmental processes such as tillering and panicle branching while enhancing disease resistance and abiotic stress tolerance in rice (Oryza sativa). However, how this transcription factor regulates multiple processes remains unclear. Here, we found that IPA1 physically interacts with NON-EXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (OsNPR1) in the nucleus. Under normal conditions, the OsNPR1 expression levels are low, and OsCULLIN3a (OsCUL3a), an E3 ligase responsible for OsNPR1 degradation, keeps the abundance of monomeric OsNPR1 low in the nucleus and prevents IPA1 from transcriptionally regulating defense genes. When the plant is attacked by pathogens, OsNPR1 oligomers dissociate into monomers, which translocate into the nucleus and physically interact with IPA1, facilitating its binding to promoters of downstream genes, thereby activating positive defense regulators and repressing negative defense regulators. Simultaneously, IPA1 abundance increases, and IPA1 interacts with OsNPR1 and OsCUL3a, interfering with the OsCUL3a-OsNPR1 interaction, dampening the ubiquitin-mediated degradation of OsNPR1. The stabilization of OsNPR1 by IPA1 further enhances IPA1 transcriptional activity in disease resistance. Our work demonstrates that OsNPR1 facilitates IPA1 binding to the promoters of genes related to disease resistance and that IPA1 inhibits OsCUL3a-mediated degradation of OsNPR1.

Land plants underpin civilization and planetary health, yet their genomic diversity remains largely uncharted. Current resources are unstandardized and scarce, lacking reference genomes for 95% of genera, 70% of families, and 51% of orders, impeding evolutionary and functional insight. We thus propose the PLANeT initiative, an international effort to generate high-quality, standardized genomes across the plant tree of life. Integrating artificial intelligence (AI) with genomics, we will decode conserved principles to advance fundamental plant biology, biodiversity conservation, crop improvement, and natural product discovery. Engaging around 100 labs to train 1,000 scientists, we will tackle pivotal questions for a sustainable future.

Sunlight fuels life but generates singlet oxygen (1O2), which causes photodamage and triggers signaling and antioxidative defense pathways in chloroplasts where photosynthesis takes place. How cells sense 1O2 and instantaneously mount photoprotection remains elusive. Here, we show that a key mediator of 1O2 responses, METHYLENE BLUE SENSITIVITY1 (MBS1), is conserved from plants to animals and comprises a zinc-finger (ZnF) domain flanked by intrinsically disordered regions. MBS1 plays a critical role in ¹O₂ sensing through ZnF conformational change and phase transition from liquid-like droplets to lower-dynamic condensates. These chloroplast-associated condensates under high light attenuate light penetration to shield chloroplasts from photodamage. In rice, MBS1-overexpressing lines exhibit enhanced high-light tolerance and yield in 4-year field trials. Our findings uncover a "sunscreening" mechanism via MBS1 condensates that confer chloroplast photoprotection, highlighting its value for improving rice yields in the field under high-light stress exacerbated by climate change.

Trichomes in plants serve not only to secrete secondary metabolites and defend against biotic and abiotic stresses, but also influence the quality of processed products in species such as tea plants (Camellia sinensis). However, the distribution patterns of plant trichomes and the environmental adaptability of tea plant trichomes remain poorly characterized. This study reveals a distinct polar distribution of trichomes along the adaxial-abaxial, proximal-distal, and medial-lateral axes of tea plant leaves. Trichome density on both leaves and stems decreases with developmental maturation, while trichomes on leaves exhibit greater length but lower density compared to those on stems. The broad-sense heritability of trichome diameter, length, and density is remarkably high, although their coefficients of variation differ significantly. Tea plant cultivars can be classified into three categories: low trichome abundance, moderate abundance, and high abundance. Long-term drought significantly increased trichome length and density, whereas long-term shading exposure produced the opposite effect. Key trichome development genes exhibited differential responsiveness to tissue type, drought, and shade treatments in tea plants. These findings provide insights into the distributional principles of plant trichomes and facilitate the scientific utilization and genetic improvement of trichomes in tea plants.

Strigolactones (SLs) are a class of plant hormones essential for tiller development and yield under diverse environmental conditions. Drought is a major limiting factor for rice yields. Although SLs contribute to drought resistance, mechanisms and practical applications of SL pathway in drought acclimation of rice remain poorly understood. Our study shows that short-term dehydration represses SL biosynthesis in rice roots. Genetic assays indicate that disruption of SL biosynthesis or signaling elevates rice drought resistance, whereas SL signaling activation or supplementation with the SL analog GR244DO impairs drought resistance. SLs negatively regulate drought acclimation by promoting degradation of the repressor protein DWARF53 (D53). D53 interacts with the transcription factor OsWRKY31 via its N-terminal domain and suppresses the protein level of OsWRKY31, which binds to and represses transcription of the ZFP36 promoter. ZFP36 encodes a zinc-finger transcription factor that promotes H2O2 scavenging to sustain reactive oxygen species (ROS) homeostasis during drought stress. Notably, the drought-resistant upland rice variety IRAT109 exhibits lower SL levels in root exudates than the lowland rice variety Nipponbare (NP). Genome editing of key components in SL pathway enhances drought resistance in NP, Huazhan (HZ), and IRAT109. The agronomic potential of tuning SL biosynthesis is further supported by the elite D17/HTD1 allele, which weakens SL biosynthesis and improves drought resistance and grain yield in Nekken 2 (NK2) under field conditions. These findings uncover a key mechanism underlying SL-repressed drought acclimation in rice and provide an effective strategy to improve drought resistance in diverse rice varieties amid ongoing climate change.

Cadmium (Cd) is a toxic and carcinogenic heavy metal, and rice, as a staple food, is a major source of dietary Cd intake. Therefore, limiting the transfer of Cd from soil to rice grain without compromising grain yield is a critical issue for human health. In this study, through base-editing-mediated mutagenesis screening targeting OsNramp5, a major transporter gene for manganese (Mn) and Cd uptake, we identified a single amino acid substitution at position 441 (Ile to Thr) that significantly reduced Cd accumulation in both shoots and grains without affecting the accumulation of other essential metals. Functional analysis revealed that this point mutation did not alter gene expression, protein abundance, subcellular localization, or Cd and Mn transport activity in yeast. However, we found that OsNramp5 also transports zinc (Zn), and the point mutation increased its selectivity for Zn. It is likely that elevated Zn levels in root cells competitively inhibit Cd release into the xylem, thereby reducing root-to-shoot Cd translocation. A field trial confirmed that the mutated OsNramp5 did not affect grain yield or essential micronutrient concentration but significantly decreased Cd accumulation in grains. Our findings suggest that precise editing of this key residue in OsNramp5 offers an effective strategy to reduce Cd transfer from soil to rice grain without yield penalty.

Rice fragrance is a key determinant of grain quality, yet the aroma profile of cultivated rice is highly uniform and largely dominated by the popcorn-like compound 2-acetyl-1-pyrroline. Here we expanded the aromatic repertoire of rice by engineering a rose-like fragrance through reconstruction of the phenylalanine-derived 2-phenylethanol (2-PE) pathway in the endosperm. To increase phenylalanine precursor supply, we co-expressed an engineered G211R/G212S variant of the rice 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase isoform OsDHS2 (LOC_Os08g37790; mOsDHS2) with heterologous phenylacetaldehyde synthase (PAAS) and phenylacetaldehyde reductase (PAR) in the endosperm. As a result, the engineered grains accumulated up to 2014 μg/kg 2-PE, conferring a distinct rose-like aroma. Unexpectedly, metabolic rewiring also reshaped grain composition, resulting in nearly doubled soluble protein content and increased levels of several vitamin B6-related metabolites, including the active coenzyme forms pyridoxal 5'-phosphate and pyridoxamine 5'-phosphate. These findings reveal extensive associated metabolic coordination between aromatic amino acid pathways and central seed metabolism. Our work establishes a strategy for creating designer fragrances in staple crops while simultaneously improving nutritional traits, providing a versatile platform for producing high-value metabolites in cereal grains.

In northern China's tea plantations - where extreme drought is uncommon - subtle yet persistent mild drought increasingly shapes tea yield and quality. However, how tea plants link mild drought-induced secondary metabolite accumulation to drought tolerance remains unknown. By integrating RNA-seq analysis with functional validation and regulatory network characterization of CsTCP14b, we demonstrate that this transcription factor promotes flavonol biosynthesis, thereby enhancing reactive oxygen species (ROS) scavenging and conferring early-stage drought tolerance in tea plants. CsTCP14b is rapidly induced during early drought stress and directly activates CsFLSb transcription by binding to its promoter, leading to increased accumulation of the flavonols kaempferol and quercetin and enhanced ROS detoxification. Yeast library screening and targeted interaction assays further identified HD-ZIP III transcription factor CsREV as an interacting partner. The CsREV-CsTCP14b interaction promotes nuclear retention of CsTCP14b and strengthens its activation of CsFLSb. Cross-cultivar analyses confirmed that the CsTCP14b-CsREV-CsFLSb module is conserved. Under drought stress, the drought-tolerant cultivar Zhongcha 108 (ZC108) shows rapid induction of CsTCP14b and CsREV and increased flavonol accumulation, whereas these responses are weaker in the drought-sensitive cultivar Wuniuzao (WNZ). These findings provide mechanistic insight into tea plant adaptation to mild drought and offer molecular targets for breeding drought-resilient, high-quality tea cultivars.

In the root apical meristem, the stem cell niche (SCN) comprises a mitotically inactive quiescent center (QC) and adjacent, mitotically active stem cells that divide to form root tissues. Auxin dynamics are essential for specification and maintenance of the root SCN; however, the underlying mechanisms remain to be explored. Here, we report that Arabidopsis (Arabidopsis thaliana) AUXIN RESPONSE FACTOR3 (ARF3), ARF3-INTERACTING PROTEIN1/2 (AIP1/2), and SIN3-ASSOCIATED POLYPEPTIDE OF 18 KDA (SAP18) form a protein complex that specifies root SCN cell fate in response to auxin level. In cells proximal to the QC, the ARF3-AIP1/2-SAP18 complex bound the WOX5 promoter and restricted WOX5 expression to the QC by decreasing H3 histone acetylation, thereby maintaining the SCN. Disrupting the ARF3-AIP1/2-SAP18 complex via mutation or exposure to excessive amounts of auxin resulted in proximal and lateral expansion of WOX5 expression and inhibited root elongation by repressing cell division. During de novo specification of the SCN in lateral root primordia or regenerating root tips, accumulated auxin caused the ARF3-AIP1/2-SAP18 complex to dissociate, allowing the induction of WOX5 expression. In the reestablished meristem, the ARF3-AIP1/2-SAP18 complex confines WOX5 expression to the newly formed QC. Our findings provide insights into the roles of auxin dynamics in determining root SCN.

Natural antisense transcripts (NATs) correspond to nearly 60% of annotated rice loci, however their functions are largely unknown. In this study, we characterise a rice cis-NAT (NAT1850) that completely overlaps with a rice-specific primary miRNA, pri-miR1850. Pri-miR1850, but not its mature miR1850 products, promotes the accumulation of NAT1850, while NAT1850 overexpression in turn reduces the accumulation of pri-miR1850 transcripts. A 21-nt siRNA (siR1850) derived from the pri-miR1850 transcripts is generated by cleavage of pri-miR1850-NAT1850 dsRNA and overlaps in sequence with miR1850.1 and miR1850.2. Both NAT1850 and siR1850 negatively regulate cold tolerance at both the young-seedling and booting stages. Interestingly, siR1850 targets and represses NPR3, which is also a target of miR1850.1. NPR3 interacts with the WRKY76 transcription factor and acts as a co-transcriptional activator of WRKY76 to trigger DREB1B under cold stress. Genetic evidence shows the NAT1850-siR1850 module functions in cold stress response via an NPR3-dependent manner. Furthermore, NAT1850 and siR1850 control nitrogen assimilation and rice yield in a miR1850.1-NPR3-independent pathway. Our findings reveal a regulatory mode for a pri-miRNA and its cis-NAT, and uncover their roles in balancing the cold-stress response and rice yields.

Rice serves as a cornerstone of global food security, feeding over half of the world’s population, yet it faces increasingly severe challenges from population growth, climate change, biotic stresses, and resource limitations. In the past 60 years, remarkable achievements have been made in fundamental research and rice breeding, supporting the quadrupled global rice production. However, the current growth rate of rice yield has stagnated at ∼0.5% annually, insufficient to meet projected food demand for 2050 or beyond. In this Perspective article, we briefly summarizes the developmental trajectories of rice fundamental research and breeding, and retrace the shift in rice breeding goals and research stages, encompassing the milestone events in Green Revolution, hybrid rice breeding, and molecular design breeding. We then emphasize the persistent challenges in limited genetic diversity, trade-offs between yield and resistance, and nutrient utilization and articulate the breeding objectives of “Two Increases and Two Decreases” for the next decade in enhancing yield and quality while reducing fertilizer and pesticide inputs and yield loss in response to disasters. To address these challenges, we overview and prospect current and future cutting-edge technologies, research methodologies, and breeding approaches, focusing on expanding genetic diversity, deciphering the molecular basis of key traits, and improving breeding efficiency. These efforts aim to facilitate the realization of the “Rice 2035” breeding goals, thereby ensuring global food security.

The establishment of arbuscular mycorrhizal symbiosis (AMS) is crucial for the survival of many terrestrial plants in nutrient-poor environments. This symbiotic relationship begins with complex chemical communication that reprograms transcriptional responses in host plants to facilitate it. However, the precise mechanisms regulating mutual recognition and commitment between arbuscular mycorrhizal fungi (AMF) and host plants remain largely unknown. In this study, we identified the NSP1-NSP2-SLR1-SMAX1 module as a central regulatory hub operating downstream of the phosphate starvation response, gibberellin (GA), and karrikin (KAR) signaling pathways to control presymbiotic transcriptional responses necessary for AMS establishment. Phosphorus starvation upregulates the transcription of NSP1 and NSP2, which control the expression of genes involved in strigolactone production and mycorrhizal factor recognition. We found that SLR1, the DELLA protein in the GA signaling pathway in rice, interacts with NSP2 and enhances the transcriptional activity of the NSP1-NSP2 complex. In addition, SLR1 interacts with SMAX1, a repressor of the KAR signaling pathway. The presence of AMF activates the KAR signaling pathway, which relieves the SMAX1-mediated repression of the transcriptional activity of NSP1-NSP2-SLR1, thereby triggering transcriptional host response signatures at the presymbiotic stage of AMS. Our findings reveal the function of the NSP1-NSP2-SLR1-SMAX1 module in integrating multiple signals to establish a permissive state for AMS in rice. While activation of the KAR signaling pathway by AMF is necessary, it alone is not sufficient to ensure successful root mycorrhizal colonization; activation of the common symbiosis signaling pathway by AMF is also required. This study advances our understanding of how molecular communication between AMF and host plants orchestrates the establishment of AMS.

Heterosis, commonly referred to as hybrid vigor, describes the biological phenomenon by which F1 hybrids outperform their parents. The exploitation of rice heterosis has made a great contribution to yield improvements and global food security. However, a unified molecular theory explaining heterosis remains elusive. This review consolidates recent advances in rice heterosis research, focusing on genetic and multi-omics. We discuss the contribution of key genes, non-additive gene expression patterns, and metabolic changes that underpin hybrid performance. The genomic, transcriptomic, epigenetic, and metabolomic evidence supporting dominance, overdominance, and epistasis hypotheses for heterosis are highlighted and integrated. The collective evidence suggests that heterosis is not governed by a single universal mechanism but is a complex consequence of synergistic interactions from sequence variation to regulatory networks across multiple omics. We also highlight emerging applications of artificial intelligence (AI) driven prediction in the breeding of next-generation super-hybrid rice. We propose that key points of future heterosis research should extend beyond static omics snapshots to dynamic, developmental, and metabolic pathways related to yield formation, such as energy metabolism, which decode the ontogenetic basis and the mechanistic understanding of heterosis. Progress in this area will accelerate the breeding of high-yielding, resilient hybrid rice cultivars.

Plant branching plasticity represents a critical adaptive strategy that enables dynamic architectural adjustments in response to environmental fluctuations. This review focuses on the current understanding of the molecular mechanisms underlying shoot branching regulation, emphasizing the interplay among hormone networks, sugar signaling, and transcriptional control. It also summarizes how environmental cues, such as nutrients, light, and abiotic stresses, influence shoot branching, offering a deeper understanding into the role of shoot branching plasticity in terms of plant fitness and agricultural productivity. Finally, this review highlights key areas for future research and explores the potential of advanced technologies for optimizing crop architecture.

Salinization affects over 800 million hectares of irrigated land globally.As a typical salt-sensitive crop,rice(Oryza sativa L.)suffers from high ionic stress,elevated osmotic pressure,and excessive accumulation of reactive oxygen species(ROS)in saline soils,result-ing in growth inhibition(Goyal et al.,2021;Jia et al.,2022).Salt toler-ance in rice involves complex mechanisms across morphological,physiological,and molecular levels(Zhu,2016;Alkahtani and Dwiningsih,2023;Li et al.,2024).

Rice has made a significant contribution to global food security over the past half-century. However, the continuous increase in grain yield potential per unit area remains a critical challenge. Recent advances in functional genomics have provided unprecedented opportunities to overcome current barriers to yield enhancement. This review briefly introduces current high-yielding rice varieties by analyzing their key characteristics across China's six major rice cropping zones. It primarily focuses on the breeding value of major yield-related genes and their complex regulatory networks by outlining designs to optimize heading date, ideal plant architecture, and photosynthetic efficiency for source enhancement; to coordinate tiller number, panicle structure, and grain shape for sink expansion; to improve the smooth flow of assimilates for optimal yield; and to increase nitrogen and phosphorus utilization efficiency to boost biomass. A breeding design is developed to create interspecific hybrids by producing superior wide-compatible lines that increase hybrid seed production by synchronizing Xian-Geng parental diurnal floret-opening times. Furthermore, we propose a strategy that integrates major-gene-based breeding design with recurrent selection to fully utilize minor genes, thereby enhancing breeding efficiency and overcoming barriers to high-yield breeding. Ultimately, artificial intelligence-driven prediction and discovery of cis-regulatory elements will facilitate the development of advanced, stress-resilient smart varieties.

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.