Physiologia Plantarum

Strigolactones (SLs) are an important class of plant hormones that play crucial roles in regulating plant branching, root architecture, and organ development. However, the regulatory mechanisms underlying the crosstalk between SLs and other plant hormones remain largely unclear, particularly regarding the key regulatory genes that integrate and coordinate multiple hormonal signaling pathways. In this study, secondary cup seedlings of the Pisang Awak banana cultivar Yufen 6 at the eight-leaf stage were used as experimental materials. The roots were treated with a nutrient solution containing 30 mol/L exogenous SLs, while a nutrient solution supplemented with water served as the control. Tissues near the corm growth point were collected at 0, 15, 30, 60, 90, and 120 days after treatment to measure corm weight, height, and diameter, and transcriptome sequencing was performed using the collected tissues. Differentially expressed genes (DEGs) at different treatment stages were identified, followed by Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses to systematically investigate the crosstalk between SLs and endogenous hormone metabolism and signaling during corm development in Pisang Awak banana. The results showed that SL treatment significantly inhibited the weight, height, and diameter of the corm. The regulatory effect of SLs on Pisang Awak banana corm development exhibited a clear temporal dynamic pattern, representing a gradual accumulation process that ultimately triggers key developmental transitions. The highest number of DEGs was detected at 15 days after treatment, including 3943 upregulated genes and 3704 downregulated genes, indicating that this stage represents a critical phase for SL response initiation. GO enrichment analysis revealed that the DEGs were mainly involved in metabolic processes, biological regulation, response to stimulus, and regulation of biological processes. KEGG pathway analysis indicated that these DEGs were significantly enriched in pathways related to plant hormone signal transduction, starch and sucrose metabolism, and secondary metabolite biosynthesis. Further analysis revealed that the crosstalk between SLs and multiple hormone metabolic and signaling pathways is mediated by the SPL15 gene, involving auxin (IAA), cytokinin (CTK), abscisic acid (ABA), brassinosteroids (BRs), gibberellins (GA), and jasmonic acid (JA) pathways. This study reveals the molecular mechanism by which SLs regulate Pisang Awak banana corm development through SPL15-mediated integration of multiple hormonal signals, providing new insights into the role of SLs in regulating the development of underground organs in banana.

While most plant lineages are pigmented by anthocyanins, several families in the Caryophyllales represent a major exception by showing a replacement of anthocyanin pigmentation by betalain pigmentation. The mutual exclusion of anthocyanins and betalains at the family level has been well established for over 50 years and has been mechanistically explained. Chenopodiaceae are a betalain-pigmented lineage lacking a key anthocyanin biosynthesis gene and lacking the key activating transcription factor of the anthocyanin biosynthesis. A publication by Zhang et al., 2024 claims that anthocyanins would be responsible for the red pigmentation in leaves of Chenopodium quinoa. Here, we assessed this study and reanalyzed the RNA-seq datasets generated in this study to demonstrate that there is no evidence for anthocyanin biosynthesis, but activity of the betalain and carotenoid biosynthesis could explain the observed pigmentation of quinoa leaves.

C4 photosynthesis is a CO2-concentration mechanism that separates CO2 fixation between two cell types, thereby reducing photorespiration and making C4 plants more efficient than their C3 counterparts. While the C4 cycle has evolved multiple times across different genera, this study evaluates very closely related C3 and C4 species within the genus Flaveria. Apart from their carbon metabolism, C4 plants also possess adaptations in their mineral nutrition. One key nutrient which is also directly involved in photosynthesis is phosphorus. It is absorbed by the plant in the form of inorganic phosphate and is an essential component of DNA, ATP, lipids, and carbohydrates. In the Flaveria C4 species, but not in the C3 species, phosphate limitation was shown to affect the dark reactions of photosynthesis. This study investigates how phosphate deficiency impacts the light reactions in C3 and C4 Flaveria plants. We observed a differential response in the functionality of photosynthetic energy conversion between the two species. When exposed to a limited phosphate supply, the C3 species reduced its linear electron transport rate while dissipating excess energy through high-energy quenching, which was regulated by a higher pH gradient across the thylakoid membrane. In contrast, the C4 species did not regulate its photosynthetic light reaction under phosphate limitation. Instead, it exhibited increased stress levels, evidenced by a stronger biomass reduction and the induction of stress markers in the leaves. Additionally, this study uncovered an acceleration in NPQ relaxation during phosphate limitation, regardless of the photosynthesis type. HighlightPhosphate deficiency reduced linear electron transport rates and induced dissipation of excess energy through non-photochemical quenching in the C3 Flaveria species, while in the C4 species, despite elevated stress levels, the photosynthetic light reactions were unaffected.

Recent studies have demonstrated the presence of kynurenine (KYN) and kynurenic acid (KYNA) in several plant species, but the metabolic function of these metabolites remains undefined. We hypothesized that KYN and KYNA are metabolites of auxin and play a role in plant morphogenesis. To test our hypothesis, we developed a plant tissue-culture-based bioassay using Hypericum perforatum (St. Johns wort; SJW), a model system for auxin and indoleamine metabolism and pharmacological inhibitors (PF-04859989, RO-61-8048, and KMO inhibitor II, JM6) of human kynurenine pathways enzymes. SJW is an interesting model system because explants root in the absence of plant growth regulators but supplementation of the culture media with 10 M IAA induces a callus response without de novo root organogenesis. Supplementation of the culture media with 10 M KYN increased root number and internodal length relative to basal media. We used a previously validated high-resolution mass spectrometry analytical method to quantify KYN, KYNA, and 3-hydroxyanthranilic acid (3-HAA). KYN, KYNA and 3-HAA were quantified in roots and shoots of SJW grown on basal media. Supplementation of the culture media with 10 M KYN increased the concentration of KYN, KYNA and 3-HAA in roots and shoots. Treatment with 10 M IAA increased KYN and 3-HAA concentration in shoots. Three pharmaceutical candidates that are kynurenine pathway inhibitors in humans were taken up into the tissues from the culture media and increased KYN content as compared to basal control. Together, these data propose a role for KYN in IAA metabolism, shoot and root organogenesis. HighlightsO_LIKynurenine metabolites are detected and accumulate in H. perforatum tissue culture C_LIO_LIIAA redirects metabolism towards accumulation of KYN and 3-HAA in shoots C_LIO_LIExogenous KYN promotes KYNA accumulation C_LIO_LIPharmacological inhibition alters kynurenine pathway metabolite profiles in a tissue-specific manner C_LIO_LIKynurenine and IAA differentially regulate root development C_LI

Soil salinization threatens global agriculture reducing yields, yet the metabolic signals controlling salt-sensitive root plasticity in alfalfa remain unclear. We hypothesize that salinity transiently uncouples the sucrose-trehalose-6-P (Tre6P)- Sucrose non-fermenting kinase 1 (SnRK1) nexus, aligning with a biphasic root metabolic response and altered root architecture. Alfalfa seedlings were grown in a hydroponic system and exposed to 200 mM NaCl, with root samples collected from 1 h to 7 d. While primary root growth and biomass remained unchanged, lateral root development was enhanced under salinity. Early response (1 h-1 d) was characterized by reduced carbon metabolites, low Tre6P, increased malondialdehyde, and SnRK1 activation, with a decline in glycolytic and TCA intermediates. During this phase, sucrose was negatively correlated with both Tre6P and SnRK1. Late response (3-7 d) showed a SnRK1 reactivation, Tre6P recovery, and osmoprotectant accumulation, including increased antioxidant capacity (+75% at 3dpt), proline (+178%), and sucrose (+18%) and starch depletion (-57%) at 7dpt respect to control. These metabolic changes coincided with the enhanced lateral root emergence. These findings indicate a two-phase response: early metabolic downscaling with transient Suc-Tre6P-SnRK1 disruption, followed by recovery with Tre6P restoration, SnRK1 reactivation, osmoprotection, and sustained root plasticity under salinity. HighlightSalinity triggers a temporary metabolic shift in alfalfa roots: plants first conserve energy, then adapt to stress, maintaining lateral root growth and flexible root architecture.

Compound droughts, i.e. the co-occurrences of heat and drought, represent a serious challenge for temperate forest trees leading to significant losses in forest biomass. We studied the physiological response of Norway spruce (Picea abies) saplings to heat and drought individually, and in combination. Continuous measurements of leaf gas exchange and VOC emission allowed us to identify fast-response reactions, while discrete VOC and root exudate samplings added qualitative information on compositional changes. Additionally, we used 13CO2 and 2H2O label pulses to investigate C-allocation and root water uptake in response to stress. Heat as well as drought reduced assimilation rates in the saplings, whereas transpiration, leaf VOC emission and root exudation rates increased in response to heat. Drought alone increased VOC emission but decreased exudation rates. Combined heat and drought triggered an amplified response in both processes despite negative net CO2 assimilation rates. Label incorporation showed compromised water uptake capacity of drought-stressed plants and illustrated de novo C-allocation to VOC emission and root exudates. The results point at the high susceptibility of Norway spruce saplings to drought and heat. Combined stress resulted in synergistic responses in VOC emissions and root exudates, showing the detrimental effect of compound droughts on Norway spruce. HighlightIn this study, we found synergistic effects of heat and drought on carbon losses from leaf VOC emission and root exudates despite negative assimilation rates in Norway spruce saplings.

Soil salinity is a rapidly intensifying abiotic stress that significantly limits wheat productivity, particularly in coastal and irrigated agroecosystems. Although sodium (Na+) ion exclusion has been recognized as a key tolerance mechanism, the integration of physiological performance with Nax1-mediated molecular regulation among regionally adapted wheat genotypes remains insufficiently characterized. The present study aimed to dissect salinity tolerance by combining hydroponic phenotyping, multivariate trait analysis, molecular marker profiling, and quantitative expression analysis of the Na+ ion transporter gene Nax1. Seventeen spring wheat genotypes were evaluated under four salinity levels (0.0, 10, 12, and 14 dS m-{superscript 1}). Germination and survival rate, shoot and root growth, and biomass accumulation were measured. Principal component analysis (PCA) and hierarchical clustering were performed to classify genotypes, while SSR (simple sequence repeat) and Nax-linked markers assessed genetic diversity. Relative Nax1 expression was quantified using qRT-PCR (quantitative real-time polymerase chain reaction). Salinity significantly reduced germination, survival, elongation, and biomass, with strong genotype-dependent variation. Multivariate analyses clearly separated tolerant and sensitive genotypes, with biomass retention and survival contributing most to total variation. Marker analysis revealed moderate genetic polymorphism. Notably, tolerant genotypes exhibited 3-6-fold induction of Nax1 under severe salinity, positively correlating with biomass maintenance. These findings demonstrate that salinity tolerance in wheat is associated with coordinated physiological resilience and enhanced Nax1-mediated Na ion exclusion, thereby advancing mechanistic understanding and supporting molecular-assisted breeding for salt-affected environments.

During drought, numerous compounds accumulate in plant tissues, but their physiological roles remain unclear - they may function as osmolytes, osmoprotectants, or merely arise as by-products of stress-induced metabolic shifts. We developed an experimental approach to link accumulation patterns with specific functions, using Scots pine (Pinus sylvestris L.) saplings subjected to water deprivation and subsequent rewatering as a model system. We monitored changes in relative water content (RWC) and osmotic adjustment dynamics, employed untargeted primary metabolite profiling for preliminary screening of compounds correlated with water status, and performed quantitative GC-MS and LC-MS analyses of selected metabolites. Major inorganic cations (K, Ca{superscript 2}, Mg{superscript 2}) were also quantified to assess their potential roles. Our results revealed that tryptophan, valine, and lysine - though generally present in low abundance - exhibited selective accumulation under severely reduced RWC ([≤] 70%), suggesting their involvement as osmoprotectants. Major organic acids, particularly shikimic acid, showed trends consistent with osmotic adjustment. Notably, neither sucrose nor inorganic cations appeared to function as primary osmolytes in this context. The proposed approach offers a viable strategy for identifying compounds involved in plant adaptation to water deficit, with potential applications in breeding programs aimed at improving drought tolerance. HighlightsAn approach to identify osmolytes and osmoprotectants was implemented Accumulation of Trp, Val and Lys was consistent with their role in osmoprotection Osmotic adjustment relied predominantly on organic acids than on inorganic ions Monosaccharides but not sucrose correlates with changes in needle water status

Photosynthesis accounts for most of the final grain yield in rice, making improvements in radiation use efficiency (RUE) a key strategy for enhancing productivity. Agronomically, RUE is defined as the biomass produced per unit of total solar radiation or photosynthetically active radiation intercepted by the canopy. However, the interaction between carbon and nitrogen metabolism plays a critical role in determining plant growth and grain yield. Assimilated nitrogen is required for the synthesis of photosynthetic pigments and enzymes, while the reduction of nitrate (NOLL) and nitrite (NOLL), as well as the assimilation of ammonium (NHLL), depend on the reducing power and carbon skeletons generated by photosynthesis. In this study, two high-yielding rice (Oryza sativa) cultivars--an indica-type (El Paso 144) and a japonica-type (INIA Parao) were subjected to two nitrogen treatments (3 mM and 9 mM NOLL/NHLL) and two light intensities (850 and 1500 mol mL{superscript 2} sL{superscript 1}). A strong interaction between light intensity and nitrogen metabolism was observed, with contrasting responses between subspecies. These differences reflect a coordinated regulation of carbon assimilation and primary nitrogen metabolism. The results provide new insights into the metabolic strategies underlying nitrogen compound accumulation under variable irradiance. Such knowledge is essential for improving nitrogen fertilizer use efficiency and yield performance in elite rice genotypes cultivated under commercial field conditions.

Light wavelengths modulate plant growth, metabolism, and physiology. Amaranthus, a C4 underutilized climate resilient crop with promising nutritional properties remained unexplored in terms of metabolite enrichment under monochromatic light wavelengths of visible spectrum. In current study, two cultivars of Amaranthus tricolor (green and red) were exposed to seven light regimes of photosynthetically active radiation (PAR; 400-700 nm): deep blue, blue, green, amber, red, deep red, far red, and their metabolic responses were captured using Gas Chromatography-Mass Spectrometry. The metabolic analysis revealed wavelength-specific reprogramming in the levels of organic acids, sugars, amino acids, fatty acids as well as phenolics. In both the green and red Amaranthus, branched-chain amino acids and phenylalanine, which are nutritionally essential, were significantly elevated under far-red light. While the phenolics such as caffeic acid and ferulic acid were elevated under green and deep blue light respectively in green Amaranthus, amber light wavelengths enhanced these phenolics in red Amaranthus. The study highlighted cultivar-specific metabolic rewiring triggered by specific wavelengths. Altogether, these findings provides insights into metabolic adaptation and demonstrate the ability of light wavelength to specifically enrich the targeted metabolite of nutritional relevance in Amaranthus. It offers strategies to improve the nutritional value of crops in controlled agriculture systems. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=167 HEIGHT=200 SRC="FIGDIR/small/714947v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@1a4477dorg.highwire.dtl.DTLVardef@518550org.highwire.dtl.DTLVardef@7682dorg.highwire.dtl.DTLVardef@4876e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

Malate and fumarate constitute a significant transient carbon stock that is dynamically synthesized during the photoperiod. These organic acids are diurnally stored and remobilised from the vacuole, and they have a key role in the cellular metabolic regulation. This function is well known in C4 and CAM plants. However, in C3 species that are the majority of terrestrial plants, the importance of the vacuolar accumulation/release and its influence on plant growth is still an open question. In Here we addressed this issue generating multiple knockout mutants in Arabidopsis thaliana lacking vacuolar anion channels of the Aluminium-Activated Malate Transporter (ALMT) family, to impair malate and fumarate transport to the vacuole. We show that in these mutants reducing vacuolar transport of malate and fumarate in mesophyll cells leads to a dramatic growth impairment. Metabolic and fluxomic analysis revealed that vacuolar malate and fumarate transport influences plant carbon and nitrogen metabolism as well as cellular pH and ionic homeostasis. In conclusion, our results show that the transport organic acids like malate and fumarate across the vacuolar membrane is essential for plant growth in a C3 plant too. These results establish the importance of the vacuolar pools of malate and fumarate in plant metabolism.

The production of reactive oxygen species (ROS) in response to cadmium (Cd) has been extensively studied, demonstrating that they play a key role in the plants response to this heavy metal. While the role of enzymes like RBOHs has been thoroughly studied, the function of other ROS-producing enzymes, such as peroxisomal glycolate oxidase (GOX), remains largely overlooked. Peroxisomal GOX is a core metabolic enzyme of the photorespiratory pathway occurring in chloroplasts, mitochondria and peroxisomes. Using Arabidopsis (Arabidopsis thaliana) mutants lacking the main peroxisomal GOX genes, GOX1 (gox1-1) and GOX2 (gox2-1) we explored their function in plant response to Cd. Although photosynthetic capacity appears to be affected to the same extent in both mutants under control and Cd stress conditions, GOX2 seems to play a greater role in ROS production in response to the metal. Transcriptomic analyses on WT and gox2-1 pointed to the mitochondrial electron transport chain (mETC) as a target of Cd stress. We further investigated the individual GOX1 and GOX2 functions in mETC regulation and redox state. Although oxidative ratio of mitochondria was higher in both mutants, it was more pronounced in the absence of GOX1. Furthermore, the mETC is affected in both mutants but the regulation of its components differs in each mutant. These results point out the different functions of the two photorespiratory GOX isoforms in Arabidopsis, leading to a better understanding of the photorespiratory pathway.

Common bermudagrass (Cynodon dactylon) is a highly resilient and cosmopolitan grass widely used for turf, forage, and soil stabilization. Although its genome has been sequenced, little study has focused on characterizing genes underlying its resilience, including the NAC transcription factor family, which is well known for its physiological and stress-related functions. This study aimed to systematically characterize NAC TF genes in the bermudagrass genome and assess their potential roles in abiotic stress tolerance. A total of 237 CdNAC genes were identified and phylogenetically classified into 14 groups, including 40 members in the NAM/NAC1 class, which is associated with plant growth and development, and 23 members in the SNAC class, which is associated with stress responses. Tissue-specific RNA-seq analysis indicated that about one-fourth of CdNAC genes were expressed across all tissues, whereas 13 genes showed relatively higher expression in roots and 9 in inflorescence, suggesting both essential and specialized functions. Stress-responsive expression profiling revealed that 35 CdNAC genes were upregulated in response to drought, 43 to heat, 10 to salt, and 42 to submergence stress. Notably, CdNAC122, 149, and 155, the members of SNAC class, were consistently upregulated across all stress conditions, while others exhibited stress-specific expression, such as CdNAC37, 130, 145, and 199 in drought, CdNAC7, 12, 18, and 29 in heat, CdNAC46 and 151 in salt, and CdNAC9 and 31 in submergence. In contrast, 53 genes were downregulated during different stresses, with most belonging to NAM/NAC1, TERN, or OsNAC7 classes, possibly reflecting suppression of photosynthesis and development-related processes under stress. These results provide the first comprehensive characterization of CdNAC genes, reveal their distinct regulatory roles in abiotic stress responses, and establish a foundation for future functional validation and applications in breeding of stress-resilient bermudagrass.

Improving photosynthesis is a promising approach to enhance sugar beet productivity. However, genetic variation in leaf photosynthesis and its relationship with disease resistance remain underexplored. We evaluated 98 sugar beet genotypes representing different breeding categories, including commercial F1 hybrids, seed-parent lines, and pollinator lines, in Hokkaido, northern Japan. Leaf gas exchange was measured during early growth under field conditions around the infection period of Cercospora leaf spot (CLS). To account for fluctuating irradiance during large-scale phenotyping, we applied a multilevel mixed-effects light-response model to estimate genotype-specific photosynthetic characteristics. Substantial genotypic variations in photosynthetic characteristics were detected. F1 hybrids exhibited higher photosynthetic capacity than breeding lines, whereas differences among breeding categories were unclear due to large within-category variation. Some breeding lines exhibited photosynthetic rates higher than those of hybrids, indicating exploitable genetic resources within the present genetic panel. We did not detect statistically significant trade-off between leaf photosynthesis and CLS resistance among 98 genotypes; in a subset of 19 genotypes analysed in detail, the relationship was even synergistic. Our results highlight the genetic diversity of leaf photosynthesis and its category-dependent structure, and suggest that selection for enhanced photosynthesis can proceed without substantial trade-off with CLS resistance. HighlightLeaf photosynthesis of 98 sugar beet genotypes showed significant genetic variation and dependence on breeding category. Active photosynthesis incurred minimal trade-off with Cercospora leaf spot resistance.

RNA-seq datasets from medicinal yews are crucial for studying paclitaxel biosynthesis. However, cross-study data analyses are hindered by pronounced batch effects. Here, we compiled 45 RNA-seq samples from three studies across four tissues (bark, leaf, root, stem) and assessed 35 preprocessing pipelines combining six normalization strategies with five batch-effect correction approaches. Unsupervised clustering (HCA, k-means, Grade-of-Membership), evaluated using Jaccard and Adjusted Rand indices, revealed significant variability in batch effect removal. Supervised classification of tissue and project labels (Random Forest and linear/radial SVM) demonstrated improved accuracy in tissue type prediction, highlighting the effectiveness of correction methods. The processed data facilitated the identification of 189 putative ABC transporters across samples, six of which showing a strong correlation to the gene encoding 10-deacetylbaccatin-III-10{beta}-O-acetyltransferase, a key biosynthetic enzyme in the taxol pathway. High expression levels in leaf and bark further support their role in taxane intermediates trafficking in taxol biosynthesis. Structural analysis and molecular docking further supported the selection of these candidates, and the agreement between transcriptomic ranking and docking-based prioritization suggests that these transporters may participate in taxane intermediate recognition, trafficking, or export. These findings demonstrate the importance of normalization and batch effect correction in RNA-seq analysis to advance gene discovery in Taxus species and, more broadly, in plant research. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/723993v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1469162org.highwire.dtl.DTLVardef@1f2c4deorg.highwire.dtl.DTLVardef@15ad821org.highwire.dtl.DTLVardef@123676d_HPS_FORMAT_FIGEXP M_FIG C_FIG

AO_SCPLOWBSTRACTC_SCPLOWNitrogen fertilizers are essential for crop productivity but cause environmental harm, necessitating the development of cultivars that thrive under limited nitrogen. This study investigates the transcriptomic response to nitrate in Arabidopsis thaliana (a model dicot), Brachypodium distachyon (a model Pooideae), and Hordeum vulgare (barley, a domesticated Pooideae) to identify conserved and species-specific molecular mechanisms. Using RNA-seq after 1.5 and 3 hours of nitrate treatment, we found that core nitrate-responsive biological processes - such as nitrate transport, assimilation, carbon metabolism, and hormone signaling - are largely conserved across species. However, comparative analysis at gene level based on orthology revealed specificities between the species. For instance, rRNA processing was uniquely stimulated in Arabidopsis, while cysteine biosynthesis from serine and gibberellin biosynthesis were specifically regulated in Brachypodium and barley. Orthologs of key nitrate-responsive genes (e.g., NRT, NLP, TCP20) exhibited variable regulation, reflecting potential adaptations linked to domestication or nutrient acquisition strategies. These findings highlight the importance of integrating model and crop species to uncover targets for improving nitrogen use efficiency in cereals. The study provides a pipeline integrating gene ontology and orthology analyses to compare transcriptomic responses between species.

Cyclic electron transport (CET) around photosystem I (PSI) is essential for maintaining photosynthetic efficiency by balancing ATP/NADPH production and protecting PSI from photoinhibition. Although the PROTON GRADIENT REGULATION 5 (PGR5)-dependent CET pathway is known to be critical under high or fluctuating light conditions, its role under fluctuating low light remains poorly understood. In natural environments, plants frequently experience prolonged low irradiance interspersed with brief sunflecks, making fluctuating low light a physiologically relevant condition. Here, we investigated Arabidopsis thaliana lines with graded PGR5 expression levels to evaluate the dose-dependent contribution of PGR5 to CET activity, photosynthetic regulation, and growth performance under both low light and fluctuating low light conditions. Moderate increase in the PGR5 protein level enhanced CET activity, accelerated photosynthetic induction, improved PSI protection and increased biomass accumulation under fluctuating low light. In contrast, excessive PGR5 accumulation impaired photosynthetic performance and reduced plant growth, indicating that optimal CET capacity requires precise tuning of PGR5 abundance. These results reveal a non-linear relationship between PGR5 protein levels and photosynthetic performance and demonstrate that moderate enhancement of CET improves plant productivity under fluctuating low light. Our findings highlight the importance of optimizing CET capacity to match dynamic light environments and suggest that fine-tuning PGR5 expression could be a promising strategy for improving crop performance under natural canopy conditions. Significance statementModerate increase in the PGR5 improves plant productivity, whereas excessive PGR5 accumulation impaired photosynthetic performance and reduced plant growth. Therefore, optimizing CET capacity by the fine-tuning PGR5 expression is important for improving crop productivity.

Phenotypic plasticity is a key mechanism by which plants adjust their traits to environmental changes. These phenotypic adjustments are driven by plastic changes in gene expression regulated by gene regulatory networks. Drought, a major selective force in Mediterranean ecosystems, provides a powerful context to examine how genomic plasticity translates into phenotypic responses. Here, we used Dianthus inoxianus, a drought-tolerant Mediterranean carnation, in order to characterize the phenotypic and transcriptomic plasticity in response to drought stress combining ecophysiological measurements with RNA-seq, gene co-expression and gene regulatory network analyses. Most of the phenotypic traits exhibited low plasticity in response to drought, except water and osmotic potential. At transcriptome level, we identified 57 plastic genes, suggesting that drought tolerance in D. inoxianus relies predominantly on constitutive gene expression. These plastic genes were enriched in processes typically related to drought response, such as cell wall components and abscisic acid (ABA) signaling. Some plastic genes belonged to drought-responsive modules, while others were hubs in different modules acting as inter-modular connectors. Furthermore, the regulatory network revealed that these plastic genes were strongly regulated by multiple stress-responsive transcription factors, and that drought-associated modules were regulated through both ABA-dependent and ABA-independent pathways. In addition, we identified contrasting patterns of canalization and decanalization, with immune and post-transcriptional regulation remaining canalized under drought, whereas photosynthesis and amino acid metabolism became decanalized, potentially releasing cryptic genetic variation. Overall, our results emphasise that drought tolerance in D. inoxianus emerges from a strategy combining preadaptation with targeted plasticity in key molecular pathways.

Indica rice, being a tropical crop, is highly sensitive to cold temperature. Cold stress affects vegetative growth, photosynthetic efficiency, along with reproductive features. Genetic resource screening in diverse landraces is an approach for identifying cold-tolerant traits. Here, we have characterised a boro germplasm, CB1, with an efficient germination rate and growth vigour when treated at chilling temperatures. CB1 seedlings show a higher survival rate compared to IR36 when subjected to prolonged chilling stress. Biochemical analyses indicated efficient ROS modulation, higher chlorophyll content, enhanced photosystem II efficiency and unique stomatal traits, leading to higher relative water content in CB1 plants during stress and recovery. Transcriptome analysis supported upregulation of chlorophyll biosynthesis, photosystem, & light harvesting complex and ROS scavenger genes in CB1 seedlings. Interestingly, high D1 protein turnover in CB1 promotes damage-repair of PSII for efficient photosynthesis. Furthermore, key transcription factors for stomatal development and expression of photosynthetic genes were upregulated in CB1 during stress recovery. Notably, higher expression of OsGLK1 and enrichment of GLK1 targets were observed in CB1 plants during chilling stress and recovery. Taken together, our results suggested that CB1 plants exhibit cold tolerance by modulating photosynthesis efficiency and stomatal behavior for better adaptability and survival against chilling temperature. HIGHLIGHTSThe efficient photosynthetic recovery, active ROS scavenging system and maintenance of water content through regulating stomatal traits, enhance the survival of indica germplasm CB1 against chilling stress.

Low temperature stress causes significant damage to the strawberry plant. During cold stress, plants undergo morphological and physiological changes often regulated at the genetic and/or epigenetic levels. Some strawberry cultivars are more cold-hardy than others. Using the diploid woodland strawberry as a model, we analyzed the effects of cold acclimation on methylome and transcriptome dynamics in the crowns and leaves of three ecotypes with contrasting cold tolerance. Alta, which was the most cold-tolerant ecotype, exhibited the highest genetic and epigenetic plasticity in response to cold. CHH-context methylation dominated the differentially methylated regions (DMRs) with more hypomethylation in crowns and hypermethylation in leaves. CG methylation was enriched in gene bodies, while non-CG methylation was prevalent in upstream and downstream regions. Our study revealed that less than a quarter of differentially methylated genes (DMGs) showed changes in transcript accumulation levels. This finding indicates that universal cold response in Fragaria vesca, as reflected by gene expression, cannot be mechanistically attributed to DNA methylation. The majority of differentially expressed differentially methylated genes (DEDMGs) were ecotype- and tissue-specific. Enrichment analysis revealed that these genes were involved in pathways related to stress tolerance, such as carbohydrate metabolism, lipid metabolism, ATP hydrolysis, and cellular detoxification. Each ecotype responded to cold through mobilization of its own set of differentially expressed genes (DEGs), DMGs, and DEDMGs, and variation in expression and methylation patterns exhibited by Alta, FDP817, and NCGR1363 suggest that cold signaling processes and survival depend on the tissue, ecotype, and geographical origin of the plants exposed to cold stress. Therefore, this study highlights the potential of both genetic markers and epialleles as molecular markers for the development of cold-tolerant octoploid strawberry cultivars that are better suited for propagation in Nordic climates.