AoB PLANTS

Auxins are a family of plant hormones involved in various processes across plant tissues and species. The Nuclear Auxin Pathway (NAP) consists of interacting transcription factors (ARFs) and repressors (Aux/IAAs), which govern an individual cells response to changes in auxin concentration. These components are present in all land plants, and many species possess multiple copies of each signalling component. We present a general framework for ODE-based models of NAP submodules with the flexibility to model the promotion and repression of target genes by any combination of transcriptional regulators. We analyse published data and show that auxin treatment in Arabidopsis thaliana roots triggers a range of characteristically distinct temporal response profiles--for both target genes and the signalling components themselves. Using our modelling framework, we recapitulate aspects of this behaviour by presenting examples of real and theoretical NAP subnetworks, and by analysing the effect that these network dynamics have on auxin-mediated transcriptional responses. This work demonstrates the utility of our modelling framework as a general-purpose tool for understanding the function of certain protein-protein and protein-DNA interactions through their effects on the NAP. This exploration of the rich dynamics of more complex signalling pathways promises to advance our understanding of the NAP.

Background and aims: Perennial root systems develop over decades and exhibit continuous turnover of structural and absorptive components, yet most root architecture models treat woody roots as permanent and neglect root age structure. We developed an empirically constrained modelling framework that explicitly represents age-structured demography, growth regulation and dormancy in perennial root systems. Methods: We extended the functional-structural plant model CPlantBox to simulate perennial root development over decades by integrating age-dependent survival, secondary radial growth and climate-driven dormancy. The model was parameterised using unique three-dimensional root system data from young and mature grapevines, together with dendrochronological root age measurements, and coupled to root hydraulic properties. Key results: Empirical analyses revealed multi-cohort age distributions and substantial turnover of lignified structural roots, contradicting the assumption of a static woody scaffold. The model reproduced age distributions, order-specific survival probabilities and fine-to-structural root length ratios, and generated realistic, genotype-specific three-dimensional architectures. Simulated uptake profiles and hydraulic scenarios showed strong age- and architecture-driven effects. Conclusions: Explicitly representing woody root age distributions and age-dependent processes may fundamentally change predictions of perennial root system architecture and function. The framework advances root modelling beyond annual paradigms and provides a transferable tool for analysing long-term architectural and hydraulic consequences of genotype x climate interactions in perennial crops.

Seed ecophysiology is essential for understanding plant regeneration and developing effective conservation and ecological restoration strategies, yet knowledge remains scarce for most threatened Cerrado species. We characterised the germination niche, desiccation tolerance and storage behaviour of Xyris paradisiaca (Xyridaceae), an Endangered species endemic to Central Brazil, to assess whether its restricted distribution is associated with narrow germination requirements and to inform seed-based conservation. Germination was tested across light regimes, constant temperatures, decreasing water potentials and short-duration heat shocks, while thermal- and hydro-time models were used to quantify thermal and hydric thresholds. Seeds exhibited an absolute light requirement but broad abiotic tolerances. Germination remained >87% between 15 and 40 {degrees}C, with estimated cardinal temperatures of Tb = 8.94 {degrees}C, To = 33.13 {degrees}C and Tc = 45.53 {degrees}C. Germination remained similar to the control down to -0.6 MPa and exceeded 40% at -1.0 MPa, with a median base water potential of {Psi}b = -1.03 MPa. Germination also remained high after 1-min heat shocks up to 200 {degrees}C. Seeds were desiccation tolerant, with 100% germination after drying and a viability loss index of -0.04, and germination remained >90% after 24 months of ambient storage. Thus, the highly restricted distribution of X. paradisiaca is not driven by a narrow physiological germination niche. Its broad environmental tolerances, desiccation tolerance and favourable storage behaviour also highlight its unexplored potential for seed-based restoration, propagation and ex situ conservation.

Understanding how root phenotypic plasticity enhances resource-use efficiency can help understand the outcomes of plant competition and identify suitable genotypes for medium- to low-input agricultural systems. Auxin regulates multiple root growth processes, including the root architectural responses to nitrogen (N). We explored the extent to which auxin-mediated local and systemic responses to external and internal N influences plant N uptake and use, using a functional-structural-plant (FSP) modelling approach. A simplified auxin module was developed at the level of the organ and integrated into an FSP model to represent physiological plastic root responses to N. Model performance was evaluated against experimental data. We then ran simulations under various N conditions with local or systemic responses enabled or disabled, to quantify their contribution to N uptake and use. Simulations showed that local auxin responses enhanced N uptake by distributing more roots towards deeper soil layers and increased N forage, thereby avoiding N stress. Systemic auxin responses reduced N uptake by distributing more roots near the top soil layers, which reduced plant size and N demand, thereby enhancing stress tolerance. This points to a trade-off in N uptake between the tolerance and avoidance strategies, which can be traced back to biomass and N investment resulting from source-sink relationships in the plant. Representing hormone-mediated root plasticity in an FSP model provides mechanistic insights into plant strategies for resource capture.

Carbon allocation governs how plants partition assimilates among leaves, roots, stems, and reproductive organs, directly shaping growth and yield. Most crop models represent this partitioning using fixed or empirically derived coefficients, which limits their ability to predict how allocation responds to genotype, environment, or their interaction. Eco-evolutionary optimality theory offers an alternative where the allocation strategy is allowed to emerge from the marginal costs and benefits of investing carbon in each organ. While this approach has been applied successfully to trees, it has not previously been developed for herbaceous plants. Here, we present DAESIM2-Plant, a mechanistic plant growth model that couples physiological processes including photosynthesis, stomatal conductance, plant hydraulics, and canopy radiative transfer, with an eco-evolutionary optimal allocation scheme for leaves and roots. This is applied to wheat by coupling it to a source-sink grain production module. Using a series of idealized sensitivity experiments, we show that the model reproduces well-documented patterns of plasticity in carbon allocation: diminishing returns on leaf investment as canopy closure and water limitation are approached, a shift in allocation toward roots under drier conditions, and a root:shoot response that depends jointly on soil moisture and the plant's existing root:leaf balance. Simulating a full growing season across a gradient of soil moisture levels reveals a threshold-like response in canopy development, biomass accumulation, and grain yield, with yield constrained by the same assimilate supply that governs vegetative growth during the critical period and grain filling. This provides a promising basis for generalizing model behaviour across a wide range of environmental conditions. Evaluating these results against experimental and field trial data remains an important next step.

Many angiosperm species possess self-incompatibility (SI) systems that prevent self-fertilization. Because empirical studies often report higher selfing rates in tetraploids than in diploids, we investigate whether sporophytic self-incompatibility (SSI) is more likely to break down after the introduction of a self-compatible (SC) allele in tetraploid populations. To address this question, we use analytical models and individual-based simulations to compare diploid and tetraploid populations under two main scenarios: (1) all SI alleles are codominant, and (2) SI alleles are structured into dominance classes. Overall, our results indicate that SSI is more difficult to maintain in tetraploids than in diploids, with dominance relationships playing a key role in the invasion success of an SC allele. When SI alleles are organized into dominance classes, increasing the dominance of the SC allele generally favors SSI breakdown in tetraploids, while diploids show weaker sensitivity to dominance, with SSI maintained across all dominance scenarios for the SC allele under sufficiently high inbreeding depression. However, when the SC allele is dominant over all SI alleles, SSI is more readily maintained in both the codominant and dominance-class models.

Soybean, a widely cultivated leguminous crop valued for its protein, amino acids, and oil, faces the challenge of maintaining protein levels, which have an inverse correlation with yield. Reducing leaf chlorophyll levels could increase seed protein levels without compromising yield; however, this is yet to be tested. Therefore, to understand the impacts of low chlorophyll mutations on soybean yield and seed composition, we screened and compared 25 low chlorophyll soybean mutants to their 11 dark green parents. PI548210 (Lincoln mutant) demonstrates a higher concentration of protein without affecting yield compared to its dark green parent PI548362 (Lincoln), suggesting it as a good candidate for further large-scale field trials. PI547555 (Y11/y11, Clark mutant) demonstrates a lower concentration of oil without impacting yield, alongside lower gross photosynthesis, but with chlorophyll levels in the pod and seed tissues that are comparable to its dark green parent PI548533 (Clark). These findings are consistent with the oil concentration of the soybean being influenced by pod and seed photosynthesis, which is correlated with pod height and row spacing. Chlorophyll levels in the leaf do not necessarily correlate with those in the pod and seed of low chlorophyll mutants, possibly due to substantially lower expression of chlorophyll synthesis genes in the pod and seed. SIGNIFICANCEO_LIPI548210 (Lincoln mutant), one of twenty-five low chlorophyll soybean mutants, demonstrates a higher concentration of soybean protein without affecting yield compared to its dark green parent (Figure 1 and Table 1). C_LIO_LIPI547555 (Y11/y11, Clark mutant), a low chlorophyll soybean mutant, demonstrates a reduced concentration of soybean oil without impacting yield, alongside lower gross photosynthesis in pod and seed tissues compared to its dark green parent (Figures 3 and Table 2). These findings suggest that the oil concentration of the soybean is influenced by pod and seed photosynthesis, which is in turn influenced by pod height and row spacing (Figure 2). C_LIO_LIChlorophyll levels in the leaf do not necessarily correlate with those in the pod and seed of low chlorophyll mutants, possibly due to substantially lower expression of chlorophyll synthesis genes in the pod and seed (Figure 5-6). C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/744892v1_fig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@4282dcorg.highwire.dtl.DTLVardef@9d565forg.highwire.dtl.DTLVardef@1918292org.highwire.dtl.DTLVardef@1359b1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Two low chlorophyll mutants are as healthy as their dark green parents. Lincoln and its low chlorophyll mutant, left; Clark and its low chlorophyll mutant, known as Y11/y11, right. It can be seen by eye that the plants have low chlorophyll (light green/yellow leaves) but a similar growth habit to their dark green parents. See Supplemental Figures 1-4 for contrast, where low chlorophyll mutants are stunted in growth compared to their dark green parents. C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@657ec9org.highwire.dtl.DTLVardef@166e75borg.highwire.dtl.DTLVardef@df23c7org.highwire.dtl.DTLVardef@1a60124org.highwire.dtl.DTLVardef@194ed96_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONComparison of seed yield, weight, seed composition between low chlorophyll mutants and their dark green parents. ANOVA is used with linear mixed model (random effect = block, fixed effect = variety). Least squares mean is used to compare. For yield and seed composition, N=4 blocks. For leaf chlorophyll (SPAD), N=40. Yield is average yield per plant (g). n.s. = not significant. C_TABLECAPTION C_TBL O_FIG O_LINKSMALLFIG WIDTH=179 HEIGHT=200 SRC="FIGDIR/small/744892v1_fig3.gif" ALT="Figure 3"> View larger version (26K): org.highwire.dtl.DTLVardef@7a368aorg.highwire.dtl.DTLVardef@192b8f0org.highwire.dtl.DTLVardef@1abb738org.highwire.dtl.DTLVardef@89e978_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 3.C_FLOATNO Light response curve of low chlorophyll mutant (Y11/y11, PI547555) and its parent (Clark, PI548533). Rates of net and gross photosynthesis of low chlorophyll (white) and dark green parents (black) pods under field conditions. Each dot represents a value (n=4) {+/-}SE. We assumed that the seeds greatly inhibited the transmittance of light through the pod and used photosynthetic photon flux density for a single-side. C_FIG O_TBL View this table: org.highwire.dtl.DTLVardef@3f0528org.highwire.dtl.DTLVardef@16ba712org.highwire.dtl.DTLVardef@a5ab2aorg.highwire.dtl.DTLVardef@889254org.highwire.dtl.DTLVardef@3efa4f_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2.C_FLOATNO O_TABLECAPTIONPod photosynthetic parameters for low chlorophyll mutant (Y11/y11, PI547555) and its parent (Clark, PI548533). Photosynthesis was measured 1 September through 15 September 2021 at the University of Illinois Energy Farm in Urbana, IL, USA. The statistical analysis was done using ANOVA with linear mixed model (alpha=0.05). N=4 {+/-} SEM for Clark and N=3 {+/-} SEM for Y11. C_TABLECAPTION C_TBL O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/744892v1_fig2.gif" ALT="Figure 2"> View larger version (23K): org.highwire.dtl.DTLVardef@a36c26org.highwire.dtl.DTLVardef@1116c8forg.highwire.dtl.DTLVardef@ee5e61org.highwire.dtl.DTLVardef@1766712_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2.C_FLOATNO Low chlorophyll mutant (Y11/y11, PI547555) and its parent (Clark, PI548533) differ in concentration of seed oil, which interacts with height of pod and row spacing. The box plots show the median (central line), the lower and upper quartiles (box) and the minimum and maximum values (whiskers). The statistical analysis was done using ANOVA with linear mixed model (n=3 blocks, alpha=0.05). Least squares mean is used to compare. N.s., non- significant in the analysis. A. Concentration of oil in low chlorophyll mutant seeds from the upper canopy decreased by 4% compared to the dark green parent (18.2% vs 19%) while there was no difference between them in the seeds from the lower canopy (20.2% vs 20.6%). B. Schematic layout of 2013 field setting showing two different row spacings. C. Concentration of oil in low chlorophyll mutant decreased by 2% in 38cm spacing (21.4% vs 22%) while there was no difference in 19cm spacing (21.3% vs 21.7%) in 2013 field. C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/744892v1_fig5.gif" ALT="Figure 5"> View larger version (22K): org.highwire.dtl.DTLVardef@68e508org.highwire.dtl.DTLVardef@94a6ccorg.highwire.dtl.DTLVardef@152a187org.highwire.dtl.DTLVardef@1eae137_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 5C_FLOATNO (greenhouse). Correlation between the level of leaf chlorophyll (x-axis: SPAD reading) and the level of immature pod or seed chlorophyll (y-axis, mg/g DW). Line represents the linear regression model. R-squared is a coefficient of determination, the percentage of the response variable variation that is explained by the linear model. Pod is labeled by the fresh weight of seeds it contained. A. Level of chlorophyll of 25-100mg pod (n=18). B. Level of chlorophyll of 100-200mg pod (n=17) . C. Level of chlorophyll of 25-100mg seed (n=17). D. Level of chlorophyll of 100-200mg seed (n=20). C_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/744892v1_fig6.gif" ALT="Figure 6"> View larger version (28K): org.highwire.dtl.DTLVardef@167fd88org.highwire.dtl.DTLVardef@361472org.highwire.dtl.DTLVardef@786325org.highwire.dtl.DTLVardef@1b53855_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 6.C_FLOATNO Levels of gene expression in chlorophyll synthesis pathway. A. CHL common pathway genes; Glutamyl-tRNA reductase (GluTR). Glutamate 1- semialdehyde aminotransferase (GSA-AT). ALA dehydratase (ALAD). Uroporphyrinogen III synthase (UROS). Uroporphyrinogen III decarboxylase (UROD). Protoporphyrinogen IX oxidase (PPO). B. Mg branch; Mg-chelatase (Mgch). Magnesium-protoporphyrin IX monomethyl ester cyclase (MPEC). Protochlorophyllide reductase (POR). 3,8-divinyl protochlorophyllide a 8-vinyl-reductase (4VCR). Heme pathway; Ferrochelatase (FECH). Heme oxygenase (HO). Phytochromobilin synthase (HY). Data come from Severin et al (2010). RPKM, reads per kilobase per million mapped reads. DAF, days after flowering. The source seed is experimental line A81-356022 which was generated by introgressing G. soja (PI468916) into G. max (A81-356022). C_FIG

Process-based tree growth models provide a mechanistic framework for investigating how climate conditions regulate tree growth across daily to annual time scales. Yet, their broader application across species and environments is constrained by the limited accessibility in open-source environments and the difficulty of estimating physiological parameters that are rarely measured directly. Here, we present virtualRings, a new R package integrating the Vaganov-Shashkin model (VSM) and the RINGS3 models, and focus on the implementation and calibration of VSM. Using tree-ring width observations from seven Northern Hemisphere sites across various environmental conditions, we compared the traditional bootstrap-based calibration approach with the Covariance Matrix Adaptation Evolution Strategy (CMA-ES). CMA-ES improved agreement between simulated and observed radial tree growth and provided an efficient approach for model parameter estimation. We further evaluated practical CMA-ES settings to balance computational cost and performance and discussed its potential limitations. The virtualRings package provides an open and reproducible platform for tree growth simulation, facilitating the application of important process-based models across species and environments and the investigation of how temperature and moisture constraints regulate daily tree-ring formation across spatial and temporal scales.

1O_LIEmbolism, the formation of air bubbles in the plant water transport system, is a mechanistic driver of plant death. The Optical Vulnerability Technique (OVT) is an imaging method for non-invasive quantification of embolism (including P50, a common metric for drought vulnerability), which can also provide detailed spatial and temporal information. Its major cost lies in the post-processing of thousands of images. C_LIO_LIHere we designed, tested, trained, and make publicly available a neural network model to automate post-processing of OVT images. Using a dataset of 65 leaves from Senecio pterophorous, we compared our model predictions to results obtained via traditional post-processing by an expert. C_LIO_LIOur model resolved P50 to within 0.027 MPa of the expert-processed data with training taking 30 minutes to 2.5 hours and model-runtime in the order of seconds to minutes, demonstrating its promise for increasing the efficiency and throughput of P50 calculation. The models performance in replicating the pixels that constitute embolism events was lower (mean event-frame IoU of 0.38). C_LIO_LIWe invite the community to utilise our model but emphasise that it does not replace the expert-processing pipeline and that care must be taken when considering applying this and similar approaches to OVT data. C_LI

Yield improvement is a main issue in the oil palm industry. Several ways to achieve this goal are possible, like, for instance, improving fruit set. Here we explore a planting strategy to increase two major factors influencing pollination; i.e. (1) the number of individuals of its main pollinator, Elaeidobius kamerunicus Faust, and (2) pollen availability, by mixing oil palm planting material, usually highly feminine, with a new oil palm material, the "super-male" (SM) planting material, with a high ratio of male inflorescences. We design and study a field trial comprising extremely feminine planting material mixed with different SM densities. Using Mark-Release-Recapture experiments we estimate the average dispersal of the pollinators over three different periods of the year, from 2017 till 2022. Second, using phenological data recorded over the same period, we studied the impact of the SM planting density on the population size of the pollinators. Finally, we assess the impact over time of different SM planting densities on the fruit set, the fruit-to-bunch, and the number of trapped wild pollinators. The combination of SM material with a highly feminine planting material provides very promising results in terms of fruit set, linked with increased pollinator population and pollen availability, demonstrating its potential for application in oil palm plantations.

Reports that the South American climbing vine Boquila trifoliolata modifies its leaf shape to mimic leaves of its host plant have raised considerable attention. Boquila leaf development was proposed to reflect visual inputs perceived in an unknown manner. However, the very existence of Boquila leaf shape mimicry remains inconclusive, since the reported observations are open to alternative explanations. We performed an initial quantitative characterization of leaf shape variability in glasshouse-cultured clonal Boquila plants grown without close host contact, and attempted to reproduce the leaf shape mimicry phenomenon under controlled culture conditions using live olive (Olea europaea) plants, artificial (decoy) olive or artificial ivy plants as supports. While we found leaves of variable shape (including those resembling ivy leaves) both in plants grown without host contact and in those climbing on live or decoy hosts, we did not observe any link between leaf shape and host presence or character. Instead, the leaf shape appears to be affected by environmental conditions including the season. Although our study was limited to a single Boquila genotype and an ecologically unrealistic host selection, our observations suggest that the alleged mimicry might originate from unintentional misinterpretation of intrinsic discontinuous leaf shape plasticity in field observations.

Stump sprouts may originate from pre-existing preventitious buds or adventitious buds, but whether these developmental origins produce distinguishable whole-shoot phenotypes remains unclear. We examined all visible sprouts on a single stump of an ornamental cherry (Prunus sp.) and measured four preselected traits: fresh weight, basal diameter, shoot length, and node number. The initial census comprised 35 sprouts. These traits were strongly correlated and were dominated by a common multivariate growth axis. Unsupervised mixture modelling identified statistical components within the morphological distribution, but these components could not be assigned to preventitious or adventitious developmental origins. During subsequent examination, we identified an unexpected basal longitudinal cavity and recorded its presence and axial length. The cavity occurred in 23 of 31 sectioned sprouts (74%). After complete removal of the initial sprout population, all visible sprouts were collected again seven days later. This second cohort comprised 22 substantially smaller sprouts but reproduced the coordinated whole-shoot growth structure. Remarkably, the basal longitudinal cavity occurred in 16 of 22 sprouts (73%), nearly identical to its initial frequency despite the marked difference in shoot size. Cavity presence was largely independent of overall shoot size, whereas cavity length increased with size among cavity-positive sprouts. Thus, gross quantitative morphology did not discriminate the hypothesized developmental origins, whereas basal anatomy revealed a reproducible feature potentially informative of developmental history. Direct anatomical and ontogenetic analyses are required to determine whether the basal longitudinal cavity is associated with sprout origin.

Photosynthetic carbon assimilation is sensitive to heat stress, with a key component being the thermal sensitivity of Rubisco activase (RCA). One approach to increasing heat tolerance of photosynthesis is to increase the thermotolerance of RCA. Here, we have used a transgenic approach to express RCA{beta} from Agave tequilana (AtRCA) in Setaria viridis. A second line was created where the endogenous SvRCA{beta} was substituted for AtRCA{beta} through complementation of a null mutant, {triangleup}rcaB (AtRCA[bKO]). In vitro assays showed that Agave RCA readily activates Setaria Rubisco, and that its thermostability is higher than that of Setaria RCA. AtRCA[bKO] plants exhibited higher CO2 assimilation at 25{degrees}C compared to WT and AtRCA plants, although Rubisco content and activation did not change. After six hours of heat stress, AtRCA[bKO] plants retained higher CO2 assimilation rates than AtRCA, however, after 24 hours CO2 assimilation declined to similar levels in all lines, suggesting that RCA may not limit carbon assimilation at the conditions tested. Taken together, our results show that substitution of RCA from a CAM plant into a C4 model allows normal growth and supports slightly increased carbon assimilation under control and short-term heat conditions.

A strategy to improve agricultural water productivity is to increase water use efficiency (WUE) at the level of plant transpiration through genetic selection. This requires detectable genetic variability in WUE and the ability to phenotype and select plants with higher WUE within a population. A proxy for phenotyping leaf level WUE by measuring carbon isotope signature ({delta}13Cleaf) has been supported by theory and data in C4 species. However, the functional relationship of {delta}13Cleaf and WUE in C4 species can be driven by genetics and environment. Therefore, a wide survey of existing natural variation is needed to quantify the heritability and identify various genetic factors that influence {delta}13Cleaf and WUE. In this study a genome-wide association panel was used to quantify the heritability of {delta}13Cleaf. We measured {delta}13Cleaf across a population of 360 genetically diverse lines of the C4 species Sorghum bicolor with single nucleotide polymorphic (SNP) markers determined from whole-genome resequencing. This analysis was conducted on two independent field environments where heritability of {delta}13Cleaf was evident and was driven by small genetic effects from loci that were consistently identified across environments. Candidate genes are presented that offer insights on future targets to manipulate and explore the functional relationship between {delta}13Cleaf and WUEi in C4 plants.

Cannabis is well known for its pungent, skunk-like aroma. Recent chemical studies have identified prenylated and C6 volatile sulfur compounds as contributors to its skunky and citrus-like aromas, but the pathways that produce these compounds remain unknown. This gap limits efforts to explain variation in sulfur-aroma traits and to selectively enhance or reduce those traits. To address this gap, we used the known chemistry of sulfur-containing volatiles in Cannabis and characterized sulfur and volatile biosynthetic pathways in other plant species to select candidate enzyme groups. Because the GMO cultivar is anecdotally associated with a pronounced sulfurous aroma, reference protein sequences and profile hidden Markov models were used to search its version 1 (v1) primary high-confidence protein set of 55,790 sequences. These searches recovered 975 unique proteins. Sequence screening retained 941 candidates across 20 reporting categories; 939 contained all expected domains, while the two candidates assigned to the methionine gamma-lyase (MGL)-nearest category had no category-specific expected-domain rule. The largest reporting category comprised 359 proteins containing a cytochrome P450 domain, recovered through a search motivated by cytochrome P450 family 74 (CYP74) enzymes involved in oxylipin and plant volatile formation. Thirteen of these proteins were also recovered by at least one full-length CYP74 reference search. Other large reporting categories included 218 sugar-transferase, 83 glutathione-transferase, and 61 alcohol dehydrogenase candidates. Comparison with the Cannabis Expression Atlas linked 168 candidates to 128 annotated genes through 100%-identity amino-acid matches spanning at least 80% of each GMO v1 candidate protein. Twenty-nine genes were tissue-specific, including 13 root-specific and 6 trichome-specific genes. These results define candidates for biochemical testing and direct searches for additional enzymes acting upstream and downstream in Cannabis sulfur-volatile pathways.

Chlorophyll fluorescence imaging is a powerful tool used to characterize abiotic and biotic stress response of photosynthesis in plants. However, extracting metrics such as Fv/Fm (maximum quantum yield of photosystem II) from chlorophyll fluorescence images remains a substantial bottleneck in large measurement campaigns, often requiring significant manual effort. To resolve this issue, we developed fvfmPy, a user-friendly program which enables rapid analysis of chlorophyll fluorescence images of arrays of leaf discs. fvfmPy uses algorithmic image segmentation to identify regions of interest and extract fluorescence metrics from tens or hundreds of leaf samples per image with little to no manual input. fvfmPy is developed in Python and includes a graphical user interface enabling intuitive parameter adjustment and real-time quality control checking. We additionally developed fvfmR, an R wrapper package for fvfmPy. Fv/Fm values extracted with fvfmPy were indistinguishable from those obtained using manual methods (r2 > 0.99) but required 94% less time to complete (13 s vs. 200 s per 100 measurements). fvfmPy and fvfmR were built to directly integrate with existing fluorescence software packages and can greatly increase throughput of fluorescence measurements to help address key challenges in agriculture and ecology.

Common bean (Phaseolus vulgaris L.) yields are strongly impacted by water deficit, yet there is substantial within-species diversity in how development, biomass accumulation, gas exchange, and photosynthetic performance are coordinated under stress. Based on this variation within a diversity panel, we characterise response profiles, define drought-response strategies, assess how these strategies relate to population structure and gene flow, and identify associated loci. A panel of 142 common bean accessions representing diverse genetic backgrounds was grown outdoors under controlled water-deficit conditions. Over five weeks, plants were monitored for phenology, biomass, pod production, and leaf traits related to stomatal and photosynthetic performance, including a brief recovery period. Genome-wide association analyses were then performed for developmental, physiological and recovery-related traits. Declining soil water availability revealed marked variation among accessions in developmental progression, biomass partitioning, stomatal behaviour and photosynthetic performance. We combined developmental and physiological traits to define above-ground response profiles and classify drought-response strategies in common bean, which were distributed across the diversity panel. GWAS identified multiple QTL and candidate loci associated with developmental, physiological and recovery-related traits. Common bean exhibits extensive diversity in overall above-ground responses to water deficit, likely reflecting local adaptation rather than population structure. Developmental data were essential for differentiating response strategies and, when combined with porometer and fluorometer measurements indicating the level of water stress experienced by the plants, for connecting traits and strategies to genomic variation. These results provide trait relationships, candidate loci and testable hypotheses for validation across environments and for future breeding-oriented studies.

Blue Economy models position aquaculture as a key pathway to securing global food security. Species selected for aquaculture typically show rapid growth, high stress tolerance and fast biomass accumulation, but these same traits may increase their potential to become invasive when introduced beyond their native range. We investigated the invasion history and current status of the commercially important red seaweed Kappaphycus alvarezii in the Palk Bay-Gulf of Mannar region of India. This is one of the worlds largest cultivation hubs, a climatically vulnerable marine biodiversity hotspot, and one of the three regions to report invasion. We combined in-water surveys, interviews with wild seaweed collectors, and a review of published literature to reconstruct the history of invasion and assess current status. Invasion has declined substantially, with interviews indicating that the disappearance of invasive populations began around 2014. We discuss several non-mutually exclusive explanations for this decline, including climate change, loss of coral substrate, herbivory, and reduced vitality of the seaweed. Although the decline in invasion is encouraging for coral reefs, our findings raise questions about the ecological and socioeconomic consequences of introducing non-native aquaculture species under Blue Economy initiatives, particularly in ecologically sensitive regions vulnerable to climate change.

Climate change is increasing the frequency and intensity of heatwaves and droughts, threatening medicinal and aromatic plants (MAP) production. Temporary shading during the hottest part of the day may reduce heat and radiative stress while limiting the reduction in light availability. We evaluated this strategy in a field experiment using three MAP species with contrasting ecological requirements and harvested organs: lavandin (Lavandula x intermedia), curly parsley (Petroselinum crispum) and valerian (Valeriana officinalis). Vertical shade nets provided midday shading and effects on crop microclimate, leaf temperature, water status, PSII photochemical efficiency, plant growth and biomass and essential oil production were assessed over two growing seasons. Midday shading reduced daily photosynthetically active radiation by 19.9-55.9 %, with weak effects on air temperature and vapor pressure deficit. In contrast, leaf temperature at solar noon decreased by 6.9 degrees C, 5.6 degrees C and 3.0 degrees C in lavandin, valerian and parsley, respectively. Midday shading improved light-adapted and maximum PSII photochemical efficiencies in all three species and reduced branch dehydration in lavandin during heatwave periods. However, agronomic responses were species-dependent. Floral biomass decreased in lavandin, whereas parsley leaf biomass and valerian root biomass increased. Essential oil concentration was unaffected in lavandin and valerian. Overall, our results show that midday shading primarily reduced leaf-level thermal and radiative stress rather than modifying the surrounding air microclimate, and suggest that its agronomic effects may reflect a balance between stress alleviation and reduced carbon acquisition, that varies with species ecology and production objectives.

{middle dot} Comparing maize canopies is confounded by two problems: plants differ in the number of phytomers they produce, and phytomer size scales with that number. Position along the shoot is therefore an unreliable basis for comparison, confounding shape with size. {middle dot} We first position the floral transition (tassel initiation, T.I.) within shoot development, revealing it as the landmark that organizes a conserved canopy shape. This provides the foundation for aligning canopies that differ in phytomer number. {middle dot} Focusing on the leaf blade, we used functional data analysis on a maize panel across controlled and field environments to decompose variation in blade-length profiles, which was dominated (77%) by overall amplitude, identifying scaling as the major source of size variation. Because blades enlarge with each phytomer until the transition, later T.I. yields a larger maximum; this T.I.-linked component explains up to one-third of scaling variation, reinforced by a shared genetic association between T.I. and blade size with the flowering-time gene ZmCCT10. {middle dot} Regressing out this component leaves a residual that defines a new, heritable axis of intrinsic scaling, independent of flowering time. It distinguishes hyper- and hypo-scaling genotypes consistently across environments, offering a selection target decoupled from phenology.