Intraspecific variation in growth response to drought stress across geographic locations and genetic groups in Coffea canephora.

Uganda lies within the drier end of the natural distribution range of Coffea canephora and contains unexplored genetic material that could be drought-adapted and useful for developing climate-resilient varieties. Using water treatment: (i) ample and (ii) restricted-water, the response of 148 genotypes were studied comprising wild, feral and cultivated C. canephora. Biomass allocation, standing leaf area and leaf area growth data were collected. Linear mixed effect models and PCA were used to the analyze effect of water treatment on genotypes from different: (i) cultivation status, (ii) genetic groups and (iii) locations. We also assessed the relationship between drought tolerance for relative growth rate in leaf area (RGRA), total number of leaves (TNL), total leaf area (TLA) and total leaf dry weight (TLDW) of genotypes at final harvest. Restricted-water reduced RGRA across genetic groups (3.2-32.5%) and locations (7.1-36.7%) but not cultivation status. For TNL, TLA and TLDW, genotypes that performed well in ample-water performed worse under restricted-water, indicating growth-tolerance trade-off. Drought tolerance in RGRA and TNL were negatively correlated with wetness index suggesting some degree of adaptation to local climate. Findings indicate a growth-tolerance trade-off within this tropical tree species and drought tolerance of Uganda's C. canephora is somewhat associated with local climate.

Plastic response of leaf traits to N deficiency in field-grown maize.

Nitrogen (N) utilization for crop production under N deficiency conditions is subject to a trade-off between maintaining specific leaf N content (SLN) important for radiation-use efficiency versus maintaining leaf area (LA) development, important for light capture. This paper aims to explore how maize deals with this trade-off through responses in SLN, LA and their underlying traits during the vegetative and reproductive growth stages. In a 10-year N fertilization trial in Jilin province, Northeast China, three N fertilizer levels have been maintained: N deficiency (N0), low N supply (N1) and high N supply (N2). We analysed data from years 8 and 10 of this experiment for two common hybrids. Under N deficiency, maize plants maintained LA and decreased SLN during vegetative stages, while both LA and SLN decreased comparably during reproductive stages. Canopy SLA (specific leaf area, cm2 g-1) decreased sharply during vegetative stages and slightly during reproductive stages, mainly because senesced leaves in the lower canopy had a higher SLA. In the vegetative stage, maize maintained LA at low N by maintaining leaf biomass (albeit hence having N content/mass) and slightly increasing SLA. These responses to N deficiency were stronger in maize hybrid XY335 than in ZD958. We conclude that the main strategy of maize to cope with low N is to maintain LA, mainly by increasing SLA throughout the plant but only during the vegetative growth phase.

Effects of sublethal single, simultaneous and sequential abiotic stresses on phenotypic traits of Arabidopsis thaliana.

Plant responses to abiotic stresses are complex and dynamic, and involve changes in different traits, either as the direct consequence of the stress, or as an active acclimatory response. Abiotic stresses frequently occur simultaneously or in succession, rather than in isolation. Despite this, most studies have focused on a single stress and single or few plant traits. To address this gap, our study comprehensively and categorically quantified the individual and combined effects of three major abiotic stresses associated with climate change (flooding, progressive drought and high temperature) on 12 phenotypic traits related to morphology, development, growth and fitness, at different developmental stages in four Arabidopsis thaliana accessions. Combined sublethal stresses were applied either simultaneously (high temperature and drought) or sequentially (flooding followed by drought). In total, we analysed the phenotypic responses of 1782 individuals across these stresses and different developmental stages. Overall, abiotic stresses and their combinations resulted in distinct patterns of effects across the traits analysed, with both quantitative and qualitative differences across accessions. Stress combinations had additive effects on some traits, whereas clear positive and negative interactions were observed for other traits: 9 out of 12 traits for high temperature and drought, 6 out of 12 traits for post-submergence and drought showed significant interactions. In many cases where the stresses interacted, the strength of interactions varied across accessions. Hence, our results indicated a general pattern of response in most phenotypic traits to the different stresses and stress combinations, but it also indicated a natural genetic variation in the strength of these responses. This includes novel results regarding the lack of a response to drought after submergence and a decoupling between leaf number and flowering time after submergence. Overall, our study provides a rich characterization of trait responses of Arabidopsis plants to sublethal abiotic stresses at the phenotypic level and can serve as starting point for further in-depth physiological research and plant modelling efforts.

Tallo: A global tree allometry and crown architecture database.

Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research-from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non-forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC-BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599. To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology-from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle.

Adaptive potential of Coffea canephora from Uganda in response to climate change.

Understanding vulnerabilities of plant populations to climate change could help preserve their biodiversity and reveal new elite parents for future breeding programmes. To this end, landscape genomics is a useful approach for assessing putative adaptations to future climatic conditions, especially in long-lived species such as trees. We conducted a population genomics study of 207 Coffea canephora trees from seven forests along different climate gradients in Uganda. For this, we sequenced 323 candidate genes involved in key metabolic and defence pathways in coffee. Seventy-one single nucleotide polymorphisms (SNPs) were found to be significantly associated with bioclimatic variables, and were thereby considered as putatively adaptive loci. These SNPs were linked to key candidate genes, including transcription factors, like DREB-like and MYB family genes controlling plant responses to abiotic stresses, as well as other genes of organoleptic interest, such as the DXMT gene involved in caffeine biosynthesis and a putative pest repellent. These climate-associated genetic markers were used to compute genetic offsets, predicting population responses to future climatic conditions based on local climate change forecasts. Using these measures of maladaptation to future conditions, substantial levels of genetic differentiation between present and future diversity were estimated for all populations and scenarios considered. The populations from the forests Zoka and Budongo, in the northernmost zone of Uganda, appeared to have the lowest genetic offsets under all predicted climate change patterns, while populations from Kalangala and Mabira, in the Lake Victoria region, exhibited the highest genetic offsets. The potential of these findings in terms of ex situ conservation strategies are discussed.

No neighbour-induced increase in root growth of soybean and sunflower in mesh-divider experiments after controlling for nutrient concentration and soil volume.

Root competition is a key factor determining plant performance, community structure and ecosystem productivity. To adequately estimate the extent of root proliferation of plants in response to neighbours independently of nutrient availability, one should use a set-up that can simultaneously control for both nutrient concentration and soil volume at plant individual level. With a mesh-divider design, which was suggested as a promising solution for this problem, we conducted two intraspecific root competition experiments: one with soybean (Glycine max) and the other with sunflower (Helianthus annuus). We found no response of root growth or biomass allocation to intraspecific neighbours, i.e. an 'ideal free distribution' (IFD) norm, in soybean; and even a reduced growth as a negative response in sunflower. These responses are all inconsistent with the hypothesis that plants should produce more roots even at the expense of reduced fitness in response to neighbours, i.e. root over-proliferation. Our results suggest that neighbour-induced root over-proliferation is not a ubiquitous feature in plants. By integrating the findings with results from other soybean studies, we conclude that for some species this response could be a genotype-dependent response as a result of natural or artificial selection, or a context-dependent response so that plants can switch from root over-proliferation to IFD depending on the environment of competition. We also critically discuss whether the mesh-divider design is an ideal solution for root competition experiments.

Genetic diversity of native and cultivated Ugandan Robusta coffee (Coffea canephora Pierre ex A. Froehner): Climate influences, breeding potential and diversity conservation.

Wild genetic resources and their ability to adapt to environmental change are critically important in light of the projected climate change, while constituting the foundation of agricultural sustainability. To address the expected negative effects of climate change on Robusta coffee trees (Coffea canephora), collecting missions were conducted to explore its current native distribution in Uganda over a broad climatic range. Wild material from seven forests could thus be collected. We used 19 microsatellite (SSR) markers to assess genetic diversity and structure of this material as well as material from two ex-situ collections and a feral population. The Ugandan C. canephora diversity was then positioned relative to the species' global diversity structure. Twenty-two climatic variables were used to explore variations in climatic zones across the sampled forests. Overall, Uganda's native C. canephora diversity differs from other known genetic groups of this species. In northwestern (NW) Uganda, four distinct genetic clusters were distinguished being from Zoka, Budongo, Itwara and Kibale forests A large southern-central (SC) cluster included Malabigambo, Mabira, and Kalangala forest accessions, as well as feral and cultivated accessions, suggesting similarity in genetic origin and strong gene flow between wild and cultivated compartments. We also confirmed the introduction of Congolese varieties into the SC region where most Robusta coffee production takes place. Identified populations occurred in divergent environmental conditions and 12 environmental variables significantly explained 16.3% of the total allelic variation across populations. The substantial genetic variation within and between Ugandan populations with different climatic envelopes might contain adaptive diversity to cope with climate change. The accessions that we collected have substantially enriched the diversity hosted in the Ugandan collections and thus contribute to ex situ conservation of this vital genetic resource. However, there is an urgent need to develop strategies to enhance complementary in-situ conservation of Coffea canephora in native forests in northwestern Uganda.

Detect thy family: Mechanisms, ecology and agricultural aspects of kin recognition in plants.

The phenomenon that organisms can distinguish genetically related individuals from strangers (i.e., kin recognition) and exhibit more cooperative behaviours towards their relatives (i.e., positive kin discrimination) has been documented in a wide variety of organisms. However, its occurrence in plants has been considered only recently. Despite the concerns about some methodologies used to document kin recognition, there is sufficient evidence to state that it exists in plants. Effects of kin recognition go well beyond reducing resource competition between related plants and involve interactions with symbionts (e.g., mycorrhizal networks). Kin recognition thus likely has important implications for evolution of plant traits, diversity of plant populations, ecological networks and community structures. Moreover, as kin selection may result in less competitive traits and thus greater population performance, it holds potential promise for crop breeding. Exploration of these evo-ecological and agricultural implications requires adequate control and measurements of relatedness, sufficient replication at genotypic level and comprehensive measurements of performance/fitness effects of kin discrimination. The primary questions that need to be answered are: when, where and by how much positive kin discrimination improves population performance.

Light from below matters: Quantifying the consequences of responses to far-red light reflected upwards for plant performance in heterogeneous canopies.

In vegetation stands, plants receive red to far-red ratio (R:FR) signals of varying strength from all directions. However, plant responses to variations in R:FR reflected from below have been largely ignored despite their potential consequences for plant performance. Using a heterogeneous rose canopy, which consists of bent shoots down in the canopy and vertically growing upright shoots, we quantified upward far-red reflection by bent shoots and its consequences for upright shoot architecture. With a three-dimensional plant model, we assessed consequences of responses to R:FR from below for plant photosynthesis. Bent shoots reflected substantially more far-red than red light, causing reduced R:FR in light reflected upwards. Leaf inclination angles increased in upright shoots which received low R:FR reflected from below. The increased leaf angle led to an increase in simulated plant photosynthesis only when this low R:FR was reflected off their own bent shoots and not when it reflected off neighbour bent shoots. We conclude that plant response to R:FR from below is an under-explored phenomenon which may have contrasting consequences for plant performance depending on the type of vegetation or crop system. The responses are beneficial for performance only when R:FR is reflected by lower foliage of the same plants.

TRY plant trait database - enhanced coverage and open access.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Quantifying the contribution of bent shoots to plant photosynthesis and biomass production of flower shoots in rose (Rosa hybrida) using a functional-structural plant model.

BACKGROUND AND AIMS: The success of using bent shoots in cut-rose (Rosa hybrida) production to improve flower shoot quality has been attributed to bent shoots capturing more light and thus providing more assimilates for flower shoot growth. We aimed at quantifying this contribution of photosynthesis by bent shoots to flower shoot growth. METHODS: Rose plants were grown with four upright flower shoots and with no, one or three bent shoots per plant. Plant architectural traits, leaf photosynthetic parameters and organ dry weight were measured. A functional-structural plant (FSP) model of rose was used to calculate photosynthesis of upright shoots and bent shoots separately, taking into account the heterogeneous canopy structure of these plants. KEY RESULTS: Bent shoots contributed to 43-53 % of total assimilated CO2 by the plant. Plant photosynthesis increased by 73 and 117 % in plants with, respectively, one and three bent shoots compared with plants without bent shoots. Upright shoot photosynthesis was not significantly affected by the presence of bent shoots. However, upright shoot dry weight increased by 35 and 59 % in plants with, respectively, one and three bent shoots compared with plants without bent shoots. The increased upright shoot dry weight was entirely due to the contribution of extra photosynthesis by bent shoots, as this was the only source that could induce differences in upright shoot growth apart from their own photosynthesis. At least 47-51 % of the photosynthesis by bent shoots was translocated to upright shoots to support their biomass increase. CONCLUSIONS: Based on model simulations, we conclude that the positive effect of shoot bending on flower shoot growth and quality in cut-rose production system can almost entirely be attributed to assimilate supply from bent shoots. FSP modelling is a useful tool to quantify the contributions of photosynthesis by different parts of heterogeneous canopies.

Disentangling the effects of photosynthetically active radiation and red to far-red ratio on plant photosynthesis under canopy shading: a simulation study using a functional-structural plant model.

BACKGROUND AND AIMS: Shading by an overhead canopy (i.e. canopy shading) entails simultaneous changes in both photosynthetically active radiation (PAR) and red to far-red ratio (R:FR). As plant responses to PAR (e.g. changes in leaf photosynthesis) are different from responses to R:FR (e.g. changes in plant architecture), and these responses occur at both organ and plant levels, understanding plant photosynthesis responses to canopy shading needs separate analysis of responses to reductions in PAR and R:FR at different levels. METHODS: In a glasshouse experiment we subjected plants of woody perennial rose (Rosa hybrida) to different light treatments, and so separately quantified the effects of reductions in PAR and R:FR on leaf photosynthetic traits and plant architectural traits. Using a functional-structural plant model, we separately quantified the effects of responses in these traits on plant photosynthesis, and evaluated the relative importance of changes of individual traits for plant photosynthesis under mild and heavy shading caused by virtual overhead canopies. KEY RESULTS: Model simulations showed that the individual trait responses to canopy shading could have positive and negative effects on plant photosynthesis. Under mild canopy shading, trait responses to reduced R:FR on photosynthesis were generally negative and with a larger magnitude than effects of responses to reduced PAR. Conversely, under heavy canopy shading, the positive effects of trait responses to reduced PAR became dominant. The combined effects of low-R:FR responses and low-PAR responses on plant photosynthesis were not equal to the sum of the separate effects, indicating interactions between individual trait responses. CONCLUSIONS: Our simulation results indicate that under canopy shading, the relative importance of plant responses to PAR and R:FR for plant photosynthesis changes with shade levels. This suggests that the adaptive significance of plant plasticity responses to one shading factor depends on plant responses to the other.

Variation in plastic responses to light results from selection in different competitive environments-A game theoretical approach using virtual plants.

Phenotypic plasticity is a vital strategy for plants to deal with changing conditions by inducing phenotypes favourable in different environments. Understanding how natural selection acts on variation in phenotypic plasticity in plants is therefore a central question in ecology, but is often ignored in modelling studies. Here we present a new modelling approach that allows for the analysis of selection for variation in phenotypic plasticity as a response strategy. We assess selection for shade avoidance strategies of Arabidopsis thaliana in response to future neighbour shading signalled through a decrease in red:far-red (R:FR) ratio. For this, we used a spatially explicit 3D virtual plant model that simulates individual Arabidopsis plants competing for light in different planting densities. Plant structure and growth were determined by the organ-specific interactions with the light environment created by the vegetation structure itself. Shade avoidance plastic responses were defined by a plastic response curve relating petiole elongation and lamina growth to R:FR perceived locally. Different plasticity strategies were represented by different shapes of the response curve that expressed different levels of R:FR sensitivity. Our analyses show that the shape of the selected shade avoidance strategy varies with planting density. At higher planting densities, more sensitive response curves are selected for than at lower densities. In addition, the balance between lamina and petiole responses influences the sensitivity of the response curves selected for. Combining computational virtual plant modelling with a game theoretical analysis represents a new step towards analysing how natural selection could have acted upon variation in shade avoidance as a response strategy, which can be linked to genetic variation and underlying physiological processes.

Presence of Belowground Neighbors Activates Defense Pathways at the Expense of Growth in Tobacco Plants.

Plants can detect the presence of their neighbors belowground, often responding with changes in root growth for resource competition. Recent evidence also implies that perception of neighbors may also elicit defense responses, however, the associated metabolic activities are unclear. We investigated primary and defense-related secondary metabolisms and hormone expressions in tobaccos (Nicotiana rustica) grown either with own roots or roots of another conspecifics in hydroponic condition. The results showed that non-self root interaction significantly reduced photosynthetic activity and assimilate production, leading to a reduction of growth. Non-self interaction also modified plant phenylpropanoids metabolism, yielding higher lignin content (i.e., structural resistance) at whole plant level and higher phenolics accumulation (i.e., chemical defense) in roots. All these metabolic responses were associated with enhanced expressions of phytohormones, particularly jasmonic acid, salicylic acid and cytokinin in roots and abscisic acid in leaves, at the early stage of non-self interaction. Since the presence of neighbors often increase the probability of attacks from, e.g., pathogens and pests, this defense activation may act as an adaptation of plants to these possible upcoming attacks.

Heritability of growth and leaf loss compensation in a long-lived tropical understorey palm.

INTRODUCTION: Defoliation and light competition are ubiquitous stressors that can strongly limit plant performance. Tolerance to defoliation is often associated with compensatory growth, which could be positively or negatively related to plant growth. Genetic variation in growth, tolerance and compensation, in turn, plays an important role in the evolutionary adaptation of plants to changing disturbance regimes but this issue has been poorly investigated for long-lived woody species. We quantified genetic variation in plant growth and growth parameters, tolerance to defoliation and compensation for a population of the understorey palm Chamaedorea elegans. In addition, we evaluated genetic correlations between growth and tolerance/compensation. METHODS: We performed a greenhouse experiment with 711 seedlings from 43 families with twelve or more individuals of C. elegans. Seeds were collected in southeast Mexico within a 0.7 ha natural forest area. A two-third defoliation treatment (repeated every two months) was applied to half of the individuals to simulate leaf loss. Compensatory responses in specific leaf area, biomass allocation to leaves and growth per unit leaf area were quantified using iterative growth models. RESULTS: We found that growth rate was highly heritable and that plants compensated strongly for leaf loss. However, genetic variation in tolerance, compensation, and the individual compensatory responses was low. We found strong correlations between family mean growth rates in control and defoliation treatments. We did not find indications for growth-tolerance/compensation trade-offs: genetic correlation between tolerance/compensation and growth rate were not significant. IMPLICATIONS: The high genetic variation in growth rate, but low genetic variation in tolerance and compensation observed here suggest high ability to adapt to changes in environment that require different growth rates, but a low potential for evolutionary adaptation to changes in damage or herbivory. The strong correlations between family mean growth rates in control and defoliation treatments suggest that performance differences among families are also maintained under stress of disturbance.

Ecological significance of light quality in optimizing plant defence.

Plants balance the allocation of resources between growth and defence to optimize fitness in a competitive environment. Perception of neighbour-detection cues, such as a low ratio of red to far-red (R:FR) radiation, activates a suite of shade-avoidance responses that include stem elongation and upward leaf movement, whilst simultaneously downregulating defence. This downregulation is hypothesized to benefit the plant either by mediating the growth-defence balance in favour of growth in high plant densities or, alternatively, by mediating defence of individual leaves such that those most photosynthetically productive are best protected. To test these hypotheses, we used a 3D functional-structural plant model of Brassica nigra that mechanistically simulates the interactions between plant architecture, herbivory, and the light environment. Our results show that plant-level defence expression is a strong determinant of plant fitness and that leaf-level defence mediation by R:FR can provide a fitness benefit in high densities. However, optimal plant-level defence expression does not decrease monotonically with plant density, indicating that R:FR mediation of defence alone is not enough to optimize defence between densities. Therefore, assessing the ecological significance of R:FR-mediated defence is paramount to better understand the evolution of this physiological linkage and its implications for crop breeding.