Plant, Cell & Environment

In the context of global food security challenges and unsustainable agricultural practices, improving crop nutrient use efficiency (NUE) has become pivotal for achieving yield stability and environmental sustainability. Traditional breeding approaches face limitations in dissecting complex traits like NUE due to low genetic resolution and restricted allelic diversity. This review highlights the transformative role of genome‐wide association studies (GWAS) in bridging genomic insights with agricultural innovation. By leveraging high‐throughput sequencing, advanced statistical models, and diverse germplasm resources, GWAS enables precise identification of genetic loci governing nitrogen (N), phosphorus (P), potassium (K), and micronutrient utilization efficiency. We summarize breakthroughs in identification of critical genes (e.g., OsTCP19, ZmNLP3.2, GmPHF1, ZmNAC78) and their regulatory roles in nitrogen‐responsive tillering mechanisms, potassium‐sodium interaction networks, phosphorus starvation adaptation pathways, or micronutrient accumulation in grains. Furthermore, we discuss the integration of GWAS with multi‐omics technologies, epigenetics, and machine learning to overcome challenges such as false positives, genetic heterogeneity, and genotype‐environment interactions. These advancements provide a robust framework for developing nutrient‐efficient crops through precision breeding, ultimately contributing to sustainable intensification of agriculture by optimizing resource use and minimizing ecological footprints.

Plant hydraulics govern water transport linking root to mesophyll surfaces, affecting gas‐exchange, survival and growth. Xylem and leaf structural and functional characteristics vary widely among Pinus species, even when growing under similar conditions. We quantified the variation of xylem anatomy, hydraulic function, and within‐tree hydraulic resistivity distribution, among five widely ranging southern US species: Pinus echinata, Pinus elliottii, Pinus palustris, Pinus taeda and Pinus virginiana. We found that, across species, needle length (NL) explained most of the variation in needle hydraulic properties. Resistivity to water flow in needles through tracheids' bordered‐pits decreased linearly from ~99% to 8% with increasing NL; total tracheid resistivity in branches and roots was partitioned between bordered‐pits and lumens similarly regardless of NL. Mean annual precipitation typical of the species' climatic range (CR) accounted for the variation in root hydraulic properties. Despite strong root‐to‐branch correlations of several attributes, neither NL nor CR explained the variation of any branch attribute. The results suggest that NL dominates needle xylem anatomy and function in a manner consistent with increasing hydraulic efficiency with NL, but CR produces genetic differences resulting in increased resistance to more negative xylem pressures with decreasing precipitation, at a cost of reduced hydraulic efficiency.

Drought serves as a major environmental stress that restricts both the yield and quality of perennial ryegrass. Therefore, it is important to identify the essential genes that determine drought tolerance in perennial ryegrasses. In this paper, we isolated a drought‐induced NAC transcription factor LpNAC22. Transcriptional activity assays in yeast and plant cells indicated that LpNAC22 has transcriptional activation function. Subcellular localization observations revealed that LpNAC22 localized in the nucleus, compatible with its function as a transcription factor. LpNAC22 overexpression plants had enhanced drought tolerance and reduced cell membrane damage, whereas the knockdown of LpNAC22 in perennial ryegrass reduced plant drought tolerance and led to aggravated cell membrane damage. Late embryogenesis abundant (LEA), well‐known stress resistance proteins, can protect the cell membrane from damage during drought conditions. DNA affinity purification sequencing and transcriptional regulation analysis demonstrated that LpNAC22 upregulates two LEA family genes, LpLEA1 and LpLEA2‐1, by directly binding to their promoters. Furthermore, we demonstrated that overexpression of LpLEA1 and LpLEA2‐1 in Arabidopsis enhanced drought tolerance and reduced cell membrane damage under drought conditions. Our findings provide evidence that LpNAC22 improves drought resistance by modulating the transcription of LEA family genes in perennial ryegrass.

Foliar insect herbivory could affect arbuscular mycorrhizal fungi (AMF), yet the underlying mechanisms remain understudied. Here, we examined the response of AMF symbiosis signals to foliar herbivory, using six herbaceous plant species and a generalist herbivorous insect. We found AMF colonisation was suppressed by foliar herbivory. After insect attack, plants allocated more biomass to belowground parts and the attack induced defence responses in aboveground parts. Notably, foliar herbivory increased shoot flavonoid concentrations but decreased root flavonoid concentrations. Moreover, quercetin and strigol concentrations in the root exudates were reduced by foliar herbivory. We further tested effect of the root exudates on the in‐vitro germination of spores of two common AMF species. Spore germination was lower in treatments with herbivore‐induced root exudates than in treatments with no‐herbivore root exudates. Moreover, addition of herbivory‐modified root exudates reduced AMF colonisation of healthy plants when compared to addition of root exudates from non‐herbivory plants. Our results suggest that foliar herbivory weakened symbiosis signalling in root exudates, which could have contributed to the observed lower AMF colonisation following herbivory. Therefore, herbivore‐induced symbiosis signalling needs to be considered when studying plant‐mediated interactions between foliar herbivores and root microbes.

Gas exchange measurement is the gold standard method for determining leaf CO2 assimilation rate (An). However, conventional systems for measuring An often require time and/or effort to collect numerous samples in the field owing to their high weight and large size. Here, we present an efficient and convenient method for estimating An using a handheld porometer with a chlorophyll fluorometer, facilitating on‐the‐go assessment of An in the field. This porometer‐fluorometer method integrates the measured stomatal conductance and quantum yield of photochemistry in PSII into a biochemical photosynthesis model, incorporating model uncertainties into a single calibrated parameter. Using this method, we successfully estimated An variations in 12 species under field conditions, with a root mean square error of 2.0 μmol m⁻² s⁻¹, despite using the common parameter set. In contrast, without calibration (i.e., with the often‐assumed parameter value), this method greatly overestimated An. These results highlight the importance of appropriate calibration depending on prevailing conditions, particularly the light source. In summary, this method demonstrates the potential for accessible, high‐throughput, and accurate estimation of An in diverse plants, thereby addressing a key bottleneck in field‐based phenotyping of photosynthesis. However, further studies are required to reduce the uncertainties imposed on the calibrated parameter.

Salinity and drought are major global challenges threatening crop productivity and ecosystem diversity, causing annual losses exceeding US$100 billion. These stresses share a common factor: osmotic stress imposed on plants. While extensive research has explored plant osmotic adjustment mechanisms, the processes underlying osmosensing in plant roots and how this sensing translates into adaptive responses remain poorly understood. This study aims to bridge this gap by examining the structure and function of various putative osmosensors (e.g., histidine kinases, mechanosensitive ion channels, phospholipase enzymes, and receptor‐like kinases) across halophytes and glycophytes—two plant groups with contrasting salinity tolerance. We conducted a thorough bioinformatics analysis to explore the molecular evolution and structural diversity of these osmosensors in both plant groups. Our findings reveal that the evolution of putative osmosensors is highly conserved between glycophytes and halophytes, with notable divergence between monocot and dicot species within both groups. While halophytes do not exhibit distinct protein families during their evolutionary process, differences in conserved amino acids between glycophytes and halophytes may significantly influence osmosensing, signaling, and stress adaptation. Importantly, halophytes possess more copies of osmosensor‐related genes compared to glycophytes. These findings offer valuable insights for breeding climate‐resilient crops, highlighting potential pathways to enhance stress tolerance through genetic improvements.

statement In sulfur‐deficient soils resulting from continuous soybean cropping, inoculation with arbuscular mycorrhizal fungi (AMF) significantly promotes soybean root growth and activity. This inoculation induces the expression of key sulfur‐assimilation pathway genes in soybean roots (such as Sat4 and Sat5) and their encoded proteins (such as SAT4 and SAT5). By enhancing the synergistic effects within the gene‐protein regulatory network, the sulfur and cysteine content in the roots is increased. Thus, AMF effectively alleviates sulfur deficiency in continuously cropped soybean soils by activating root sulfur‐assimilation pathways, thereby providing a theoretical basis for using AMF inoculants to remediate sulfur‐poor soils.

To cope with changing external conditions, plants undergo dynamic acclimation processes that adjust their photosynthetic machinery, optimising energy use while minimising damage to photosystems (PS). Key photoprotective mechanisms include non‐photochemical quenching (NPQ), which dissipates excess excitation energy, and alternative electron transport (AET) pathways, which prevent over‐reduction of the photosynthetic electron transport chain. This study provides a comprehensive analysis of how various photoprotective mechanisms contribute to long‐term acclimation to high and fluctuating light in Physcomitrium patens, a moss that exhibits well‐conserved photoprotective responses that can provide valuable insights into the adaptation of these mechanisms during evolution. Our results demonstrate that modulation of photoprotection at the level of both PSII and PSI is critical for maintaining photosynthetic efficiency and enabling acclimation to variable light conditions. P. patens mutants deficient in NPQ or AET, when exposed to high or fluctuating light all displayed growth defects, reduced photosynthetic efficiency and unbalanced PSI and PSII activity compared to WT plants. These findings indicate that photosynthetic response to varying light conditions depends on the complementary action of multiple protective strategies, rather than a single dominant photoprotective mechanism.

Tea plants with distinct leaf colours, such as purple, have attracted attention for their potential economic and flavour‐related benefits. To investigate how purple mutations influence aroma composition, we analyzed 64 tea germplasms (Camellia sinensis) with varying degrees of purple pigmentation, integrating microenvironmental data, volatile metabolomics and transcriptomics. Purple tea exhibited reduced accumulation of volatile phenylpropanoids/benzenoids (VPBs), higher surface temperatures and enrichment of stress‐responsive genes, leading to increased levels of fatty acid‐derived volatiles (FADVs) and volatile terpenoids (VTs). We identified CsWRKY70 as a central regulator of aroma biosynthesis, with its expression upregulated under heat stress, activating CsLOX3 and CsTPS13 to promote FADVs and VTs accumulation. These findings demonstrate that purple leaf mutations influence aroma composition by modulating the phenylpropanoid pathway and altering the leaf microenvironment, providing new insights into the interplay between leaf colour, environmental stress and flavour potential in tea plants.

Floral transition is crucial for crop productivity and environmental adaptability. As a photoperiod‐sensitive crop, the flowering time of soybean is intricately regulated by environmental signals. Here, we show that short‐term changes of photoperiod or temperature significantly affected soybean flowering time. Through an integrative analysis of transcriptomic and epigenomic data, we revealed that short‐term exposure to inductive short day promoted floral transition via suppressing the expression of a bHLH family gene, GmbHLH68, along with the alteration of H3K27me3 modification on the locus, while short‐term high temperature had contrary effects. We establish that GmbHLH68 directly binds to and activates GmFT2a (FLOWERING LOCUS T2a) expression, forming a critical regulatory module through which short‐term photoperiod and temperature changes control flowering time in soybean. Genetic knockout of either gene abolished photothermal signal responsiveness. Interestingly, GmbHLH68 could as well bind to and promote the expression of GmRGA2L (RGA2‐like) and GmFT4, two inhibitors of floral transition. This bidirectional regulation may fine‐tune the impact of short‐term environmental changes, enabling exquisite control of flowering time. Thus, GmbHLH68 is a central regulator of flowering in response to provisional photothermal changes. Our findings may shed light on soybean cultivar improvement for stable yield during a changing environment.

In higher plants, ethylene response factors (ERFs) play crucial roles in orchestrating cold stress signal transduction. This study validated EjERF23 in loquat (Eriobotrya japonica Lindl.) and elucidated its role in cold tolerance. The transcriptional expression of EjERF23 was augmented upon exposure to the ethylene precursor 1‐aminocyclopropane‐1‐carboxylate and low temperatures. Concurrently, it was inhibited by the ethylene inhibitor aminoethoxyvinylglycine under cold conditions. Overexpression of EjERF23 in transgenic tobacco enhanced cold tolerance, exhibiting significantly increased peroxidase (POD) activity, leading to reduced hydrogen peroxide (H2O2) accumulation and improved antioxidant stress tolerance. Further analysis revealed that EjERF23 directly interacts with the EjPOD47 promoter, increasing its transcriptional level. The outcomes of the yeast expression assay indicated that EjPOD47 has notable functions in the response to cold stress. Tobacco lines that were genetically modified and treated with POD inhibitors exhibited elevated content of H2O2 and a remarkable decrease in cold tolerance. The findings indicated that the EjERF23 protein is crucial for enhancing cold tolerance by positively regulating genes that code for POD to eliminate reactive oxygen species. Our findings offer fresh perspectives on the molecular regulatory mechanisms that govern the ethylene signaling pathway related to responses to cold stress.

The amino acid cysteine is the precursor for a wide range of sulfur‐containing functional molecules in plants, including enzyme cofactors and defence compounds. Due to its redox active thiol group cysteine is highly reactive. Synthesis and degradation pathways are present in several subcellular compartments to adjust the intracellular cysteine concentration. However, stress conditions can lead to a transient increase in local cysteine levels. Here we investigate links between cysteine homeostasis and metabolic signalling in Arabidopsis thaliana. The systemic proteome response to cysteine feeding strongly suggests that Arabidopsis seedlings interpret accumulation of cysteine above a certain threshold as a signal for a biotic threat. Cysteine supplementation of Arabidopsis plants via the roots increases their resistance to the hemibiotrophic bacterium Pseudomonas syringae confirming the protective function of the cysteine induced defence pathways. Analysis of mutant plants reveals that the balance of cysteine synthesis between the cytosol and organelles is crucial during Arabidopsis immune response to Pseudomonas syringae. The induction profile of pathogen responsive proteins by cysteine provides insight into potential modes of action. Our results highlight the role of cysteine as a metabolic signal in the plant immune response and add evidence to the emerging concept of intracellular organelles as important players in plant stress signalling.

Cadmium (Cd), an environmentally ubiquitous heavy metal, causes phytotoxic effects to plants even at low concentrations. Plants have evolved sophisticated methods to reduce Cd toxicity. However, the regulatory mechanisms of macroautophagy/autophagy in plant tolerance to Cd remain poorly elucidated. Here, we describe the link between autophagy and Cd response in Arabidopsis, demonstrating that the metallochaperone heavy metal‐associated isoprenylated plant protein 33 (HIPP33) acts as a cargo receptor to modulate the Cd response by facilitating autophagy‐mediated vacuolar sequestration of Cd. In Arabidopsis thaliana, Cd exposure activated autophagy pathway. Consistently, autophagy‐defective (atg) mutants displayed enhanced hypersensitivity with increased reactive oxygen species accumulation and considerably lower Cd concentrations in both roots and shoots. Moreover, we discovered that the core autophagy protein ATG8e associated with HIPP33 and recruited it for autophagic degradation in an AIM (ATG8‐interacting motif)‐dependent manner. Furthermore, purified HIPP33 protein directly bound with Cd in vitro. Accordingly, loss function of HIPP33 exhibited compromised Cd tolerance compared to wild‐type Arabidopsis. Collectively, our findings propose a novel regulatory mechanism where HIPP33 serves as a selective autophagy receptor to target Cd for autophagy‐dependent vacuolar sequestration in response to Cd stress, demonstrating the modulation of Cd detoxification by selective autophagy in plants.

Flavonoids are key secondary metabolites involved in plant stress responses. As ultraviolet (UV) radiation intensity increases, plants experience heightened UV stress. To elucidate Ginkgo biloba's molecular adaptation to ultraviolet‐B (UV‐B) stress, we subjected G. biloba seedlings to daily UV‐B irradiation at 10 kJ/m². The total flavonoid glycoside content in leaves increased significantly by Day 13 (2.64‐fold compared to the CK), with quercetin accounting for over 90% of the accumulated flavonoids. Transcriptome analysis identified 3652 differentially expressed genes (DEGs), 209 lncRNAs (DElncRNAs), and 52 miRNAs (DEmiRNAs). Notably, UV‐B radiation upregulated key genes involved in flavonoid biosynthesis, including the F3'H family gene evm.model.chr2.812 and the MYB transcription factor (TF) evm.model.chr11.568. Trans‐regulation analysis suggested lncRNAs modulate target genes: MSTRG.5750.1 and MSTRG.13336.1 potentially enhance evm.model.chr2.812 and evm.model.chr11.568 expression, while UV‐B‐repressed MSTRG.845.1 and MSTRG.3390.1 indirectly upregulated them. A ceRNA network revealed nine regulatory pairs, though associated miRNAs (gbi‐miR‐nov634‐3, gbi‐miR‐nov789‐3p) exhibited low abundance, indicating minor roles in UV‐B response. These findings provide insights into the transcriptional regulation of flavonoid biosynthesis in G. biloba under UV‐B stress, advancing understanding of plant secondary metabolic adaptation.

Wild alfalfa is a ubiquitous legume crop and an important feed for livestock such as cattle and sheep. However, despite its agricultural significance, the potential of alfalfa as a medicinal raw material remains largely untapped, with particularly limited research focusing on the bioactivity of its phenolic compounds. This study aimed to systematically evaluate the phenolic profiles, antioxidant capacities, and antimicrobial effects of three common wild alfalfa species to explore their potential as sustainable sources of phytomedicinal ingredients. A comprehensive analysis was conducted on the growth characteristics, photosynthetic parameters and metabolic profiles of Medicago sativa (M. sativa) L., Medicago falcata (M. falcata) L. and Medicago ruthenica (M. ruthenica) L. collected from Hulunbuir Prairie, China. Phenolic compounds were quantified using HPLC–MS, while antioxidant activities were assessed via FRAP and ABTS assays. Antimicrobial efficacy was tested against gram‐positive (Staphylococcus aureus [S. aureus], Bacillus subtilis) and gram‐negative (Escherichia coli, Acinetobacter baumannii) bacteria using agar diffusion and microdilution techniques. M. falcata L. demonstrated the greatest plant height (81 cm) and basal stem diameter (5.7 mm), while M. sativa L. exhibited the highest photosynthetic rate (9.3 μmol m⁻² s⁻¹) and chlorophyll content, indicating distinct species‐specific adaptations. Phytochemical analysis showed that the leaves were rich in phenolic compounds including isoliquiritigenin and ferulic acid, while roots contained substantial l‐phenylalanine and trigonelline. Leaf and root extracts of three wild alfalfa species exhibited notable antioxidant capacity, with M. ruthenica leaves showing the highest activity (FRAP: 149.2 ± 2.7 mmol Fe (II)/g DW; ABTS: 100.5 ± 2.8 mmol TE/g DW), highlighting their potential as natural antioxidant sources. The extracts exhibited selective antibacterial efficacy against gram‐positive pathogens (S. aureus, etc.), demonstrating inhibition zones of 15.2–18.2 mm and MIC values of 313 mg/mL. Phenolic compounds in alfalfa possess biological activities such as antioxidant and antibacterial properties. Many phenolic compounds are difficult and expensive to synthesize, leading to supply shortages. Alfalfa, as a common and widely distributed crop, can provide a plant source for antioxidants and antimicrobials. This study provides new guidance to meet the demand for phytomedicinal ingredients. It offers data to support the development of medicines for human health.

As soil acidification occurs due to industrial and agricultural production processes, it can induce the release of rhizotoxic aluminium ions (Al³⁺) into the soil, ultimately causing aluminium (Al) stress. Excessive Al content in soil exhibits significant phytotoxicity, inhibiting the growth of roots and stems. In this study, we conducted an investigation into the Al stress tolerance of two apple rootstocks, namely ‘YZ3’ and ‘YZ6’, and discovered that ‘YZ3’ exhibited a superior ability to alleviate the inhibitory effects of Al stress on plant growth. By comparing the transcriptomes of two rootstocks, a differentially expressed gene, MdDUF506, containing an unknown functional (DUF) domain, was identified. Overexpression of MdDUF506 in apple and calli enhances the ability to scavenge reactive oxygen species (ROS), subsequently mitigating the oxidative damage induced by Al stress on plant growth and development. Furthermore, MdDUF506 regulates Al stress tolerance by modulating the expression of genes related to Al stress (MdSTOP1, MdRSL1, MdRSL4, MdGL2, and MdRAE1). MdDUF506 interacts with MdCNR8, positively regulating Al stress tolerance. Taken together, these discoveries offer crucial candidate genes for targeted breeding as well as fresh insights into resistance to Al stress.

Climate change increases extreme weather events like heat waves and cold waves. Understanding plant thermal tolerance is essential for assessing their safety. Measuring the Fv/Fm after dark thermal treatments is a common way to evaluate photosynthetic thermal tolerance, but it differs from real‐world conditions with light–temperature covariation. To investigate how light influences thermal tolerance measurement, we tested the photosynthetic thermal tolerance of 20 naturally growing canopy species from Xishuangbanna Tropical Botanical Garden under various light intensities. We found that weak light (300 μmol·m⁻²·s⁻¹) triggered species‐specific responses in heat tolerance, while strong light (1000 μmol·m⁻²·s⁻¹) reduced heat tolerance across all tested species, except for Psidium guajava in T50_h. Weak light (200 μmol·m⁻²·s⁻¹) significantly reduced the cold tolerance of all 10 tested species. The species with higher gas exchange rate (Emax and Amax) were more resistant to light‐induced damage under heat stress. Leaf thickness mitigated the reduction of heat tolerance caused by strong light and provided physical photoprotection under cold stress. These findings highlight the importance of considering both species‐specific photoprotective capacities and ecological realism when evaluating photosynthetic thermal limits. This study helps us understand plant adaptation strategies and predict ecosystem responses to climate change.

Accumulation of anthocyanin is a protective response to high light in plants, by absorbing excess energy and serving as antioxidant. Our study in Arabidopsis revealed that GOLDEN2‐LIKE 2 (GLK2), a key transcription factor regulating chloroplast development, plays a crucial role in anthocyanin biosynthesis during seedling photomorphogenesis, especially under high light stress. We demonstrate that GLK2 acts as a transcriptional activator by directly binding to the promoters of anthocyanin late biosynthetic genes (LBGs) and TRANSPARENT TESTA GLABRA 1 (TTG1) gene, that encodes a key component of the regulatory MYB‐bHLH‐WD40 (MBW) complex (which also activates LBGs). Another component of MBW complex, TT8, interacts with GLK2 and may take part in GLK2‐mediated anthocyanin accumulation. DE‐ETIOLATED 1 (DET1) facilitates the degradation of ELONGATED HYPOCOTYL5 (HY5) and GLKs in darkness by forming a ubiquitin ligase complex. Loss of DET1 resulted in increased anthocyanin production, while mutations of HY5 or GLK2 each partially suppresses the expression of anthocyanin biosynthetic genes in det1 mutant. In addition, HY5 and GLKs appear to regulate anthocyanin early and late biosynthesis with different preferences. We therefore propose the involvement of GLK2, partially independent of HY5, in promoting anthocyanin production as a protective measure against excessive light during seedling greening.

statement In this commentary, we highlight the importance of LDH in the modulation of several crucial metabolic pathways for submergence tolerance in rice

statement Tree weatherproofing during senescence is imprinted in trees' stemflow chemistry. We supply novel data on stemflow neutral sugars leaching and propose a conceptual model to explain the interplay between higher stemflow neutral sugar concentrations during senescence and ecophysiological changes in bark/wood chemistry that initiate cold hardiness.

Temperature plays a pivotal role in plant growth and development, with flowering time being particularly sensitive to thermal changes. Understanding the molecular mechanisms of temperature‐regulated flowering is crucial for enhancing plant adaptability and improving productivity. This review systematically summarised the molecular mechanisms underlying flowering regulation by ambient temperature fluctuations (excluding vernalisation treatments typically requiring prolonged exposure to 0°C–6°C for weeks or months) in Arabidopsis and three key short‐day crops: soybean (Glycine max), rice (Oryza sativa), and maize (Zea mays). We provide a comprehensive overview of the temperature sensors involved in flowering regulation, focusing on how key molecular components, including photoreceptors, transcription factors, chromatin modifiers, miRNAs, and hormone, mediate temperature responses that regulate flowering time. Although significant insights have been gained from Arabidopsis, understanding of these mechanisms in crops remains limited, hindering advances in developing temperature‐adaptive varieties. We discuss the limitations of the current study and propose future research directions, including uncovering crop‐specific temperature regulation mechanisms, studying flowering responses under dynamic conditions, and exploring strategies for breeding temperature‐adaptive crops. By clarifying the flowering mechanisms that respond to non‐vernalisation temperatures, this review aims to guide future efforts to improve crop resilience and adaptation strategies in the face of climate change.

Shading is a widely applied strategy to increase theanine and chlorophyll levels in tea leaves during matcha production. However, the regulatory mechanism of theanine accumulation under shading conditions remains elusive. Through visualization analysis of PIF genes under shading conditions, we identified a homologue of AtPIF7 gene, CsPIF7, highly responsive to shading treatment. Through co‐expression analysis, we found that CsPIF7 expression patterns exhibited a high correlation with those of the key theanine biosynthesis genes, CsTSⅠ and CsGSⅠ. Silencing of CsPIF7 significantly reduced the expression of CsTSⅠ and CsGSⅠ and theanine content. On the contrary, overexpression of CsPIF7 increased the expression levels of CsTSⅠ and CsGSⅠ and theanine content. Yeast one‐hybrid (Y1H), dual‐luciferase reporter assay and Electrophoretic Mobility Shift Assay (EMSA) further demonstrated that CsPIF7 could bind to the promoters of CsTSⅠ and CsGSⅠ, and activate the expression of CsTSⅠ and CsGSⅠ. In conclusion, CsPIF7 could mediate the shading‐induced biosynthesis of theanine by directly binding to and activating the expression of CsTSⅠ and CsGSⅠ. This study provides new insights into molecular mechanisms for the production of greener and fresher matcha under shading conditions.

statement J3 regulates flowering by antagonising AFP2 and protecting CO stability in Arabidopsis.

Deep sequencing of ribosome footprints, also known as ribosome profiling (Ribo‐seq), enables the quantification of mRNA translation and a comprehensive view of the translatome landscape. Here, we report an optimised Ribo‐seq protocol and analysis pipeline for the model green alga, Chlamydomonas reinhardtiii (Chlamydomonas). Compared to the previously published data sets, the ribosome‐protected fragments generated by our protocol showed improved mapping rates to the main open reading frames, reduced bias mapping to the gene coding regions and high 3‐nt footprint periodicity. Using this optimised protocol, we employed Ribo‐seq alongside RNA‐seq to compute translation efficiency and identify genes with differential translation during the diurnal cycle. Interestingly, we found that the translation efficiency of many core cell cycle genes was significantly enhanced in cells at the early synthesis/mitosis (S/M) stage. This result suggests that translational regulation plays a role in cell cycle regulation in C. reinhardtii. Furthermore, the high periodicity of ribosome footprints allowed us to identify potential C. reinhardtii upstream open reading frames (uORFs). Further analysis revealed that some of these uORFs are differentially regulated and may play a role in diurnal regulation. In summary, we used an optimised Ribo‐seq protocol to generate a high‐quality Ribo‐seq data set that constitutes a valuable resource for Chlamydomonas genomics. The ribosome profile data is linked to the Chlamydomonas reference genome and accessible to the scientific community.