Flowering time is a key agronomic trait that influences plant reproductive success and crop yield, and its regulation is closely associated with soil nutrient availability. This review summarizes recent advances in understanding the molecular mechanisms through which macronutrients and micronutrients regulate flowering time in plants. An emerging central theme is that nutrient-derived signaling integrates with core flowering regulatory pathways, including the photoperiodic, gibberellin, vernalization, autonomous, and sugar pathways, with nitrogen and phosphorus being the most extensively studied. However, major knowledge gaps remain regarding the regulatory roles of potassium, sulfur, and micronutrients, as well as species-specific nutrient responses and the molecular basis of nutrient-nutrient and nutrient-environment interactions in flowering regulation. In addition, the role of nutrient-derived metabolites and rhizosphere microorganisms in flowering control remains largely unexplored. Addressing these challenges is essential for the rational development of crop varieties with optimized flowering time and enhanced nutrient use efficiency through targeted genetic engineering, molecular breeding, and innovative nutrient management strategies, thereby supporting sustainable agricultural development.

This study introduces an intronic artificial microRNA (IamiRNA) strategy that combines CRISPR-Cas9-mediated knock-in with endogenous miRNA processing for targeted gene silencing in plants. By inserting amiRNA precursors into introns of endogenous genes, this approach enables effective, tissue-specific gene silencing without persistent transgene expression, offering a promising tool for functional genomics and crop improvement.

Phosphorus (P) is an essential macronutrient for plant growth and development, yet its limited availability in soil severely constrains crop productivity. To cope with phosphate (Pi) deficiency, plants have evolved a sophisticated signaling network centered on SPX domain proteins, which serve as central regulators of Pi homeostasis. Recent breakthrough structural studies have revolutionized our understanding of these proteins, revealing their function as cellular Pi sensors through binding of the inositol pyrophosphate InsP8. This review synthesizes current knowledge of SPX protein molecular structures, evolution, and functions within the Pi signaling network. We detail their sensing mechanism, focusing on inositol pyrophosphate binding and the subsequent control of PHR activity and phosphate starvation response (PSR) gene expression. Recent cryo-electron microscopy structures of rice SPX1-PHR2, Arabidopsis PHO1;H1, and human XPR1 have provided unprecedented insights into phosphate transport mechanisms and SPX domain regulation. We also discuss emerging functions of SPX proteins in coordinating arbuscular mycorrhizal symbiosis, plant immunity, nitrogen-phosphorus balance, and cold stress responses, highlighting their broad significance in plant biology. Finally, we discuss key challenges and future research directions crucial for translating these mechanistic insights into innovative strategies to enhance phosphorus use efficiency (PUE) in crops, including structure-guided protein engineering approaches.

Autophagy is an evolutionarily conserved catabolic pathway that maintains cellular homeostasis by degrading and recycling cytoplasmic components in the vacuole or lysosome. In plants, this process is indispensable for nutrient remobilization and stress acclimation, clearing dysfunctional organelles, protein aggregates, and other cytoplasmic material. This review covers current knowledge of plant autophagy, beginning with the core ATG (autophagy-related) machinery and the mechanisms of selective cargo recognition mediated by receptors such as NBR1 and the ATG8 protein family, then extending to organelle-specific degradation pathways including chlorophagy, mitophagy, and ER (endoplasmic reticulum)-phagy. We examine how autophagy supports plant survival under adverse conditions with attention to the regulatory networks governing autophagic activity, including the antagonistic TOR (Target of Rapamycin) and SnRK1 (Sucrose Non-Fermenting Related Kinase 1) kinase pathways that act as central nutrient and energy sensors. Collectively, these findings establish autophagy not merely as a cellular housekeeping mechanism, but as a central regulatory hub that coordinates plant growth with environmental adaptation, with important implications for engineering stress-resilient crops.

Quinoa (Chenopodium quinoa Willd.) has emerged as a compelling model for understanding plant resilience to environmental adversity. As a facultative halophyte native to the Andean highlands, quinoa tolerates drought, salinity, temperature extremes, and nutrient-poor soils through a multi-layered molecular defense system that is both conserved with other plants and enriched with quinoa-specific innovations. This review synthesizes current knowledge of three interconnected regulatory tiers that underpin quinoa’s stress resilience. First, a suite of functional proteins provides the immediate cellular defense against stress-induced damage. Second, a diverse repertoire of transcription factor families orchestrates the transcriptional reprogramming required for stress adaptation, with several families showing quinoa-specific expansions and functionally validated members. Third, interconnected signaling networks integrate stress perception with adaptive responses through extensive crosstalk and feedback regulation. We further highlight how multi-omics approaches are revealing stress-specific regulatory hubs and genotype-dependent adaptive strategies. Finally, we identify critical knowledge gaps and propose research priorities that will be essential for translating mechanistic insights into climate-adaptive crop improvement.

CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are key regulators of cell division in root, shoot, and vascular meristems. However, their roles in the regulation of root hair growth remain poorly understood. Here, we report that SlCLE10 expression is rapidly induced by hyperosmotic stress in tomato. Overexpression of SlCLE10 increases root hair length and enhances drought tolerance, whereas the slcle10 knockout mutant exhibits shorter root hairs than the wild type. We further demonstrate that SlCLE10-mediated promotion of root hair growth under osmotic stress depends on ethylene biosynthesis and signaling. Mechanistically, SlCLE10 enhances the activation of SlMAPK6 and promotes its interaction with SlACS2. Activated SlMAPK6 subsequently phosphorylates SlACS2, thereby stabilizing the protein and increasing ethylene production. These findings define an SlCLE10-SlMAPK6-SlACS2 signaling module that regulates root hair formation under hyperosmotic stress. Notably, exogenous application of the SlCLE10 peptide promotes root hair growth across a range of dicot species, including pepper, eggplant, cucumber, oilseed rape, leafy greens, and tobacco. Collectively, our results establish a molecular framework linking environmental stress to CLE-peptide-mediated root hair development and propose a potential strategy for improving crop drought resistance through genetic enhancement of root hair growth.

Alternative polyadenylation (APA) generates transcript diversity by producing mRNA isoforms with distinct 3' ends. Despite the critical roles that APA plays in various biological processes, the mechanisms regulating APA in response to stresses have remained poorly understood in plants. Here, we perform comprehensive analysis of APA in tomato, and focus on a phosphate (Pi)- regulated APA gene SlSPX5, encoding a putative Pi sensor protein. SlSPX5 interacts with and sequesters the transcription factor SlPHL1 in the cytosol, thereby inhibiting the expression of Pi starvation inducible genes. We discover that a cis-natural antisense RNA (cis-NAT) is activated from SlSPX5 to promote its proximal polyadenylation under Pi-depleted conditions. The transcription of this cis-NAT induces RNA Polymerase II pausing, generating Ser2 phosphorylation signals that recruit polyadenylation machinery to the 5' end of SlSPX5. Our findings demonstrate that a cis-NAT regulates APA of its cognate gene in response to Pi starvation.

XPR1 is emerging as the only known inorganic phosphate (Pi) exporter in humans, critical for Pi homeostasis, with its activity stimulated by inositol pyrophosphate InsP8 and regulated by neuronal scaffold protein KIDINS220. Our structural studies reveal that InsP8 specifically activates XPR1 in a stepwise manner, involving profound SYG1/PHO/XPR1 (SPX) domain movements. Each XPR1 subunit functions with four gating states, in which Pi permeates a constriction site via a "knock-kiss-kick" process. By contrast, KIDINS220 delicately stabilizes XPR1 in a closed conformation through multiple mechanisms, one of which involves trapping the XPR1 α1 helix-critical for InsP8 binding-within an interaction hub. InsP8 serves as a key to release KIDINS220's restraint, reinforcing a "key-to-locks" mechanism to safeguard the stepwise activation. Additionally, our study provides direct structural insights into XPR1-associated neuronal disorders and highlights the evolutionary conservation and divergence among XPR1 orthologs, offering a comprehensive understanding of Pi homeostasis across species.

Phosphate (Pi) homeostasis is important for plant growth and adaptation to the dynamic environment, which requires the precise regulation of phosphate transporter (PHT) trafficking from the endoplasmic reticulum to the plasma membrane. LIPOYL SYNTHASE 1p (LIP1p) is known as a key enzyme in plastids to catalyze lipoylation of pyruvate dehydrogenase complex for de novo fatty acid synthesis. It is unknown whether this process is involved in regulating Pi homeostasis. Here, we demonstrate a new role of LIP1p in controlling Pi homeostasis by regulating PHT1 trafficking. We recovered a weak mutant allele of LIP1p in Arabidopsis that accumulates much less Pi and has enhanced expression of phosphate starvation-induced genes. LIP1p mutation alters the lipid profile and compromises vesicle trafficking of PHT1 to the plasma membrane to impair Pi uptake. Beside phosphorus, the homeostasis of a series of mineral nutrients was also perturbed in lip1p mutant. Our findings provide powerful genetic evidence to support the linkage between lipoylation and ion homeostasis in plants.

Phosphorus nutrition has been known for a long time to influence floral transition in plants, but the underlying mechanism is unclear. Arabidopsis phosphate transporter PHOSPHATE1 (PHO1) plays a critical role in phosphate translocation from roots to shoots, but whether and how it regulates floral transition is unknown. Here, we show that knockout mutation of PHO1 delays flowering under both long- and short-day conditions. The late flowering of pho1 mutants can be partially rescued by Pi supplementation in rosettes or shoot apices. Grafting assay indicates that the late flowering of pho1 mutants is a result of impaired phosphate translocation from roots to shoots. Knockout mutation of SPX1 and SPX2, two negative regulators of the phosphate starvation response, partially rescues the late flowering of pho1 mutants. PHO1 is epistatic to PHO2, a negative regulator of PHO1, in flowering time regulation. Loss of PHO1 represses the expression of some floral activators, including FT encoding florigen, and induces the expression of some floral repressors in shoots. Genetic analyses indicate that at least jasmonic acid signaling is partially responsible for the late flowering of pho1 mutants. In addition, we find that rice PHO1;2, the homolog of PHO1, plays a similar role in floral transition. These results suggest that PHO1 integrates phosphorus nutrition and flowering time, and could be used as a potential target in modulating phosphorus nutrition-mediated flowering time in plants.

Plants need nutrients for survival. Of the macronutrients, phosphorus (P), the second most important after nitrogen, is obtained by plants as phosphate (Pi) from the soil for sustained plant growth and development. Low Pi levels, therefore, could limit crop production, and it is imperative that adaptive mechanisms of plants to such conditions are deciphered to harness these mechanisms to engineer crops with traits enhanced for Pi acquisition and utilisation. There have been grand advances in the recent past, particularly in how plants sense Pi and maintain Pi homeostasis. In this chapter, we assess the recent findings on local and systemic Pi sensing with a focus on the molecular mechanisms behind root system architectural changes, Pi uptake and redistribution, and plant-microbiome interactions. We also focus on the recent advances in the discovery of the inositol pyrophosphate InsP8 as a signalling molecule in a plant's response to Pi fluctuation and the mechanism of its interaction with SPX domain proteins, which play significant roles in regulating PHR proteins, master regulators of the Pi starvation response.

Discovery of the Clustered Regularly Interspaced Short Palindromic Repeats / CRISPR-associated (CRISPR/Cas) system and its repurposing into a powerful genome editing tool has revolutionized genome engineering and generated excitement for innovative breeding technology. CRISPR/Cas can perform genetic operations such as targeted insertion, deletion and replacement of genes in plants by its simple two-component system comprising a Cas protein and a guide RNA. Here, we focus on the recent advances in CRISPR/Cas technologies that are available for genome editing, among which Cas9, Cas12, and Cas13 systems are widely used in the areas of botany and agriculture. We also describe the new high-precision genome editing tools, base editors and prime editors that are derived from the Cas9 system and beyond for altering the genome in living cells, without generating double-stranded breaks in DNA or requiring a donor. In addition, we summarize the differences between the different CRISPR/Cas systems and their broad applications in plants. We also discuss the challenges facing the use of CRISPR/Cas technologies and the future directions of CRISPR/Cas systems in plant genome editing.

Unlike microbe-associated molecular patterns（MAMPs） that are readily targeted by host immunity,microbial non-pathogenic factors（NPFs） appear negligible as they do not elicit defense. Little is known about whether and how NPFs may be monitored by hosts to control compatibility. Herein, a forward genetic screening isolated an Arabidopsis mutant with a loss of plant-rhizobacteria mutualism, leading to the disclosure of a plant latent defense response（LDR） to NPFs. The activation of LDR in the mutant,named rol1 for regulator of LDR 1, is triggered by several non-pathogenic volatile organic compounds and antagonizes plant compatibility with the beneficial bacterium Bacillus amyloliquefaciens GB03. The activation of LDR in rol1 is mediated through the prokaryotic pathway of chloroplastic lipid biosynthesis.The rol1 root microbiome showed a reduced proportion of the Bacillaceae family. We propose that, parallel to the forefront immunity to MAMPs, LDR to certain NPFs provides a hidden layer of defense for controlling compatibility with commensal or beneficial microbes.

Phosphorus (P) is obtained by plants as phosphate (Pi) from the soil and low Pi levels affects plant growth and development. Adaptation to low Pi condition entails sensing internal and external Pi levels and translating those signals to molecular and morphophysiological changes in the plant. In this review, we present findings related to local and systemin Pi sensing with focus the molecular mechanisms behind root system architectural changes and the impact of hormones and epigenetic mechanisms affecting those changes. We also present some of the recent advances in the Pi sensing and signaling mechanisms focusing on inositol pyrophosphate InsP8 and its interaction with SPX domain proteins to regulate the activity of the central regulator of the Pi starvation response, PHR.

KEY MESSAGE:An efficient Agrobacterium-mediated transient expression method was developed, which contributed to the functional characterization of the transcription factor CqPHR1, and demonstrates the potential application of gene editing in quinoa. Chenopodium quinoa is a crop expected to ensure global food security in future due to its high resistance to multiple abiotic stresses and nutritional value. We cloned one of the paralogous genes of the Arabidopsis homolog PHR1 (PHOSPHATE STARVATION RESPONSE 1) in quinoa-inbred lines by reverse genetic approach. Overexpression of CqPHR1 driven by the constitutive CaMV 35S promoter in Arabidopsis phr1 mutant can complement its phenotypes, including the induction of phosphate starvation-induced (PSI) genes and anthocyanin accumulation in leaves. By Agrobacterium-mediated gene transient expression, we found that CqPHR1 localized in the nucleus of quinoa cells, and overexpression of CqPHR1 in quinoa cells promoted PSI genes expression, which further revealed the function of CqPHR1 as a transcription factor. We have also shown that the transient expression system can be used to express Cas9 protein in various quinoa-inbred lines and perform effective gene editing in quinoa tissue. The method developed in this study will be useful for verifying the effectiveness of gene-editing systems in quinoa cells and has potential application in the generation of gene-edited quinoa with heritable traits.

Arsenic is a metalloid toxic to plants, animals and human beings. Small ubiquitin-like modifier (SUMO) conjugation is involved in many biological processes in plants. However, the role of SUMOylation in regulating plant arsenic response is still unclear. In this study, we found that dysfunction of SUMO E3 ligase SIZ1 improves arsenite resistance in Arabidopsis. Overexpression of the dominant-negative SUMO E2 variant resembled the arsenite-resistant phenotype of siz1 mutant, indicating that SUMOylation plays a negative role in plant arsenite detoxification. The siz1 mutant accumulated more glutathione (GSH) than the wild type under arsenite stress, and the arsenite-resistant phenotype of siz1 was depressed by inhibiting GSH biosynthesis. The transcript levels of the genes in the GSH biosynthetic pathway were increased in the siz1 mutant comparing with the wild type in response to arsenite treatment. Taken together, our findings revealed a novel function of SIZ1 in modulating plant arsenite response through regulating the GSH-dependent detoxification.

The coordinated distribution of inorganic phosphate (Pi) between roots and shoots is an important process that plants use to maintain Pi homeostasis. SHORT-ROOT (SHR) is well characterized for its function in root radial patterning. Here we demonstrate a role of SHR in controlling Pi allocation from root to shoot by regulating PHOSPHATE1 in the root differentiation zone. We recovered a weak mutant allele of SHR in Arabidopsis that accumulates much less Pi in the shoot and shows a constitutive Pi starvation response under Pi-sufficient conditions. In addition, Pi starvation suppresses SHR protein accumulation and releases its inhibition on the HD-ZIP III transcription factor PHB. PHB accumulates and directly binds the promoter of PHOSPHATE2 to upregulate its transcription, resulting in PHOSPHATE1 degradation in the xylem-pole pericycle cells. Our findings reveal a previously unrecognized mechanism of how plants regulate Pi translocation from roots to shoots.

Phosphorus is a building block in various biomolecules such as nucleic acids,proteins,and phospholipids.It also plays pivotal roles in many metabolic pathways,including photosynthesis and respiration(Bowler et al.,2010).Plants take up phosphorus as inorganic phosphate(Pi),which is limited in most soils,and Pi constraints affect plant growth and development and hence agricultural productivity.To cope with low Pi availability in soil,plants have evolved complex mechanisms to maintain Pi homeostasis at the whole-plant and cellular level,which includes Pi uptake,storage,and redistribution.

Plasticity in root system architecture(RSA) allows plants to adapt to changing nutritional status in the soil.Phosphorus availability is a major determinant of crop yield,and RSA remodeling is critical to increasing the efficiency of phosphorus acquisition.Although substantial progress has been made in understanding the signaling mechanism driving phosphate starvation responses in plants,whether and how epigenetic regulatory mechanisms contribute is poorly understood.Here,we report that the Switch defective/sucrose non-fermentable(SWI/SNF) ATPase BRAHMA(BRM) is involved in the local response to phosphate(Pi) starvation.The loss of BRM function induces iron(Fe) accumulation through increased LOW PHOSPHATE ROOT1(LPR1) and LPR2 expression,reducing primary root length under Pi deficiency.We also demonstrate that BRM recruits the histone deacetylase(HDA) complex HDA6-HDC1 to facilitate histone H3 deacetylation at LPR loci,thereby negatively regulating local Pi deficiency responses.BRM is degraded under Pi deficiency conditions through the 26 S proteasome pathway,leading to increased histone H3 acetylation at the LPR loci.Collectively,our data suggest that the chromatin remodeler BRM,in concert with HDA6,negatively regulates Fe-dependent local Pi starvation responses by transcriptionally repressing the RSA-related genes LPR1 and LPR2 in Arabidopsis thaliana.

DNA methylation,a conserved epigenetic mark,is critical for tuning temporal and spatial gene expression.The Arabidopsis thaliana DNA glycosylase/lyase REPRESSOR OF SILENCING 1(ROS1) initiates active DNA demethylation and is required to prevent DNA hypermethylation at thousands of genomic loci.However,how ROS1 is recruited to specific loci is not well understood.Here,we report the discovery of Arabidopsis AGENET Domain Containing Protein 3(AGDP3) as a cellular factor that is required to prevent gene silencing and DNA hypermethylation.AGDP3 binds to H3K9me2 marks in its target DNA via its AGD12 cassette.Analysis of the crystal structure of the AGD12 cassette of AGDP3 in complex with an H3K9me2 peptide revealed that dimethylated H3 K9 and unmodified H3 K4 are specifically anchored into two different surface pockets.A histidine residue located in the methyllysine binding aromatic cage provides AGDP3 with pH-dependent H3K9me2 binding capacity.Our results uncover a molecular mechanism for the regulation of DNA demethylation by the gene silencing mark H3K9me2.