Are high-throughput root phenotyping platforms suitable for informing root system architecture models with genotype-specific parameters? An evaluation based on the root model ArchiSimple and a small panel of wheat cultivars.

Given the difficulties in accessing plant roots in situ, high-throughput root phenotyping (HTRP) platforms under controlled conditions have been developed to meet the growing demand for characterizing root system architecture (RSA) for genetic analyses. However, a proper evaluation of their capacity to provide the same estimates for strictly identical root traits across platforms has never been achieved. In this study, we performed such an evaluation based on six major parameters of the RSA model ArchiSimple, using a diversity panel of 14 bread wheat cultivars in two HTRP platforms that had different growth media and non-destructive imaging systems together with a conventional set-up that had a solid growth medium and destructive sampling. Significant effects of the experimental set-up were found for all the parameters and no significant correlations across the diversity panel among the three set-ups could be detected. Differences in temperature, irradiance, and/or the medium in which the plants were growing might partly explain both the differences in the parameter values across the experiments as well as the genotype × set-up interactions. Furthermore, the values and the rankings across genotypes of only a subset of parameters were conserved between contrasting growth stages. As the parameters chosen for our analysis are root traits that have strong impacts on RSA and are close to parameters used in a majority of RSA models, our results highlight the need to carefully consider both developmental and environmental drivers in root phenomics studies.

Phenotypic plasticity of plant traits contributing to grain and biomass yield of dual-purpose sorghum.

MAIN CONCLUSION: Plant traits of interest for sorghum breeders to develop dual-purpose varieties are stem diameter, flag leaf size, crop cycle, and number of grains per panicle. To develop dual-purpose varieties, breeders need to improve traits linked both to grain and biomass production. To identify these traits, we studied the phenotypic plasticity of eighteen traits and the performance of ten contrasting sorghum genotypes, used in West Africa. Trials were carried out in a randomized complete blocks design with four replicates from 2013 to 2016 in Bambey, Sinthiou Malem and Nioro du Rip in Senegal. The results revealed three plant types. The first type, "biomass production", contained genotypes IS15401 and SK5912, and was linked to cycle duration, leaf area, and plant height. The second type, "grain production", grouped the caudatum race sorghum 621B, F2-20 and Soumba, and was associated with the number of grains per panicle and the width of the flag leaf. The third group, "dual-purpose", corresponding to the genotypes Fadda, Nieleni and Pablo, combined some favourable traits for grain and biomass: stem diameter, internode length, number of green leaves and number of grains per panicle. The study showed that high and stable grain yields were associated with stability in flag leaf size, phenology and number of grains per panicle, and a high and stable biomass yield was associated with stability in stem diameter. Those stable plant traits might be of interest for sorghum breeders selecting to develop dual-purpose varieties.

Plant growth: the What, the How, and the Why.

Growth is a widely used term in plant science and ecology, but it can have different meanings depending on the context and the spatiotemporal scale of analysis. At the meristem level, growth is associated with the production of cells and initiation of new organs. At the organ or plant scale and over short time periods, growth is often used synonymously with tissue expansion, while over longer time periods the increase in biomass is a common metric. At even larger temporal and spatial scales, growth is mostly described as net primary production. Here, we first address the question 'what is growth?'. We propose a general framework to distinguish between the different facets of growth, and the corresponding physiological processes, environmental drivers and mathematical formalisms. Based on these different definitions, we then review how plant growth can be measured and analysed at different organisational, spatial and temporal scales. We conclude by discussing why gaining a better understanding of the different facets of plant growth is essential to disentangle genetic and environmental effects on the phenotype, and to uncover the causalities around source or sink limitations of plant growth.

Physiological roles of Casparian strips and suberin in the transport of water and solutes.

The formation of Casparian strips (CS) and the deposition of suberin at the endodermis of plant roots are thought to limit the apoplastic transport of water and ions. We investigated the specific role of each of these apoplastic barriers in the control of hydro-mineral transport by roots and the consequences on shoot growth. A collection of Arabidopsis thaliana mutants defective in suberin deposition and/or CS development was characterized under standard conditions using a hydroponic system and the Phenopsis platform. Mutants altered in suberin deposition had enhanced root hydraulic conductivity, indicating a restrictive role for this compound in water transport. In contrast, defective CS directly increased solute leakage and indirectly reduced root hydraulic conductivity. Defective CS also led to a reduction in rosette growth, which was partly dependent on the hydro-mineral status of the plant. Ectopic suberin was shown to partially compensate for defective CS phenotypes. Altogether, our work shows that the functionality of the root apoplastic diffusion barriers greatly influences the plant physiology, and that their integrity is tightly surveyed.

A New Phenotyping Pipeline Reveals Three Types of Lateral Roots and a Random Branching Pattern in Two Cereals.

Recent progress in root phenotyping has focused mainly on increasing throughput for genetic studies, while identifying root developmental patterns has been comparatively underexplored. We introduce a new phenotyping pipeline for producing high-quality spatiotemporal root system development data and identifying developmental patterns within these data. The SmartRoot image-analysis system and temporal and spatial statistical models were applied to two cereals, pearl millet (Pennisetum glaucum) and maize (Zea mays). Semi-Markov switching linear models were used to cluster lateral roots based on their growth rate profiles. These models revealed three types of lateral roots with similar characteristics in both species. The first type corresponds to fast and accelerating roots, the second to rapidly arrested roots, and the third to an intermediate type where roots cease elongation after a few days. These types of lateral roots were retrieved in different proportions in a maize mutant affected in auxin signaling, while the first most vigorous type was absent in maize plants exposed to severe shading. Moreover, the classification of growth rate profiles was mirrored by a ranking of anatomical traits in pearl millet. Potential dependencies in the succession of lateral root types along the primary root were then analyzed using variable-order Markov chains. The lateral root type was not influenced by the shootward neighbor root type or by the distance from this root. This random branching pattern of primary roots was remarkably conserved, despite the high variability of root systems in both species. Our phenotyping pipeline opens the door to exploring the genetic variability of lateral root developmental patterns.

Experimental and modeling evidence of carbon limitation of leaf appearance rate for spring and winter wheat.

Accurate predictions of the timing of physiological stages and the development rate are crucial for predicting crop performance under field conditions. Plant development is controlled by the leaf appearance rate (LAR) and our understanding of how LAR responds to environmental factors is still limited. Here, we tested the hypothesis that carbon availability may account for the effects of irradiance, photoperiod, atmospheric CO2 concentration, and ontogeny on LAR. We conducted three experiments in growth chambers to quantify and disentangle these effects for both winter and spring wheat cultivars. Variations of LAR observed between environmental scenarios were well explained by the supply/demand ratio for carbon, quantified using the photothermal quotient. We therefore developed an ecophysiological model based on the photothermal quotient that accounts for the effects of temperature, irradiance, photoperiod, and ontogeny on LAR. Comparisons of observed leaf stages and LAR with simulations from our model, from a linear thermal-time model, and from a segmented linear thermal-time model corrected for sowing date showed that our model can simulate the observed changes in LAR in the field with the lowest error. Our findings demonstrate that a hypothesis-driven approach that incorporates more physiology in specific processes of crop models can increase their predictive power under variable environments.

The dual effect of abscisic acid on stomata.

The classical view that the drought-related hormone ABA simply acts locally at the guard cell level to induce stomatal closure is questioned by differences between isolated epidermis and intact leaves in stomatal response to several stimuli. We tested the hypothesis that ABA mediates, in addition to a local effect, a remote effect in planta by changing hydraulic regulation in the leaf upstream of the stomata. By gravimetry, porometry to water vapour and argon, and psychrometry, we investigated the effect of exogenous ABA on transpiration, stomatal conductance and leaf hydraulic conductance of mutants described as ABA-insensitive at the guard cell level. We show that foliar transpiration of several ABA-insensitive mutants decreases in response to ABA. We demonstrate that ABA decreases stomatal conductance and down-regulates leaf hydraulic conductance in both the wildtype Col-0 and the ABA-insensitive mutant ost2-2. We propose that ABA promotes stomatal closure in a dual way via its already known biochemical effect on guard cells and a novel, indirect hydraulic effect through a decrease in water permeability within leaf vascular tissues. Variability in sensitivity of leaf hydraulic conductance to ABA among species could provide a physiological basis to the isohydric or anisohydric behaviour.

Upland rice varietal mixtures in Madagascar: evaluating the effects of varietal interaction on crop performance.

Introduction: Rice plays a critical role in human livelihoods and food security. However, its cultivation requires inputs that are not accessible to all farming communities and can have negative effects on ecosystems. simultaneously, ecological research demonstrates that biodiversity management within fields contributes to ecosystem functioning. Methods: This study aims to evaluate the mixture effect of four functionally distinct rice varieties in terms of characteristics and agronomic performance and their spatial arrangement on the upland rice performance in the highlands of Madagascar. The study was conducted during the 2021-2022 rainfall season at two close sites in Madagascar. Both site differ from each other's in soil properties and soil fertility management. The experimental design at each site included three modalities: i) plot composition, i.e., pure stand or binary mixture; ii) the balance between the varieties within a mixture; iii) and for the balanced mixture (50% of each variety), the spatial arrangement, i.e., row or checkerboard patterns. Data were collected on yields (grain and biomass), and resistance to Striga asiatica infestation, Pyricularia oryzea and bacterial leaf blight (BLB) caused by Xanthomonas oryzae-pv from each plot. Results and discussion: Varietal mixtures produced significantly higher grain and biomass yields, and significantly lower incidence of Pyricularia oryzea compared to pure stands. No significant differences were observed for BLB and striga infestation. These effects were influenced by site fertility, the less fertilized site showed stronger mixture effects with greater gains in grain yield (60%) and biomass yield (42%). The most unbalanced repartition (75% and 25% of each variety) showed the greatest mixture effect for grain yield at both sites, with a strong impact of the varietal identity within the plot. The mixture was most effective when EARLY_MUTANT_IAC_165 constituted 75% of the density associated with other varieties at 25% density. The assessment of the net effect ratio of disease, an index evaluating the mixture effect in disease reduction, indicated improved disease resistance in mixtures, regardless of site conditions. Our study in limited environments suggests that varietal mixtures can enhance rice productivity, especially in low-input situations. Further research is needed to understand the ecological mechanisms behind the positive mixture effect.

Improving crop yield potential: Underlying biological processes and future prospects.

The growing world population and global increases in the standard of living both result in an increasing demand for food, feed and other plant-derived products. In the coming years, plant-based research will be among the major drivers ensuring food security and the expansion of the bio-based economy. Crop productivity is determined by several factors, including the available physical and agricultural resources, crop management, and the resource use efficiency, quality and intrinsic yield potential of the chosen crop. This review focuses on intrinsic yield potential, since understanding its determinants and their biological basis will allow to maximize the plant's potential in food and energy production. Yield potential is determined by a variety of complex traits that integrate strictly regulated processes and their underlying gene regulatory networks. Due to this inherent complexity, numerous potential targets have been identified that could be exploited to increase crop yield. These encompass diverse metabolic and physical processes at the cellular, organ and canopy level. We present an overview of some of the distinct biological processes considered to be crucial for yield determination that could further be exploited to improve future crop productivity.

Coming of leaf age: control of growth by hydraulics and metabolics during leaf ontogeny.

Leaf growth is the central process facilitating energy capture and plant performance. This is also one of the most sensitive processes to a wide range of abiotic stresses. Because hydraulics and metabolics are two major determinants of expansive growth (volumetric increase) and structural growth (dry matter increase), we review the interaction nodes between water and carbon. We detail the crosstalks between water and carbon transports, including the dual role of stomata and aquaporins in regulating water and carbon fluxes, the coupling between phloem and xylem, the interactions between leaf water relations and photosynthetic capacity, the links between Lockhart's hydromechanical model and carbon metabolism, and the central regulatory role of abscisic acid. Then, we argue that during leaf ontogeny, these interactions change dramatically because of uncoupled modifications between several anatomical and physiological features of the leaf. We conclude that the control of leaf growth switches from a metabolic to a hydromechanical limitation during the course of leaf ontogeny. Finally, we illustrate how taking leaf ontogeny into account provides insights into the mechanisms underlying leaf growth responses to abiotic stresses that affect water and carbon relations, such as elevated CO2, low light, high temperature and drought.

Control of leaf expansion: a developmental switch from metabolics to hydraulics.

Leaf expansion is the central process by which plants colonize space, allowing energy capture and carbon acquisition. Water and carbon emerge as main limiting factors of leaf expansion, but the literature remains controversial about their respective contributions. Here, we tested the hypothesis that the importance of hydraulics and metabolics is organized according to both dark/light fluctuations and leaf ontogeny. For this purpose, we established the developmental pattern of individual leaf expansion during days and nights in the model plant Arabidopsis (Arabidopsis thaliana). Under control conditions, decreases in leaf expansion were observed at night immediately after emergence, when starch reserves were lowest. These nocturnal decreases were strongly exaggerated in a set of starch mutants, consistent with an early carbon limitation. However, low-light treatment of wild-type plants had no influence on these early decreases, implying that expansion can be uncoupled from changes in carbon availability. From 4 d after leaf emergence onward, decreases of leaf expansion were observed in the daytime. Using mutants impaired in stomatal control of transpiration as well as plants grown under soil water deficit or high air humidity, we gathered evidence that these diurnal decreases were the signature of a hydraulic limitation that gradually set up as the leaf developed. Changes in leaf turgor were consistent with this pattern. It is concluded that during the course of leaf ontogeny, the predominant control of leaf expansion switches from metabolics to hydraulics. We suggest that the leaf is better armed to buffer variations in the former than in the latter.

Arabidopsis growth under prolonged high temperature and water deficit: independent or interactive effects?

High temperature (HT) and water deficit (WD) are frequent environmental constraints restricting plant growth and productivity. These stresses often occur simultaneously in the field, but little is known about their combined impacts on plant growth, development and physiology. We evaluated the responses of 10 Arabidopsis thaliana natural accessions to prolonged elevated air temperature (30 °C) and soil WD applied separately or in combination. Plant growth was significantly reduced under both stresses and their combination was even more detrimental to plant performance. The effects of the two stresses were globally additive, but some traits responded specifically to one but not the other stress. Root allocation increased in response to WD, while reproductive allocation, hyponasty and specific leaf area increased under HT. All the traits that varied in response to combined stresses also responded to at least one of them. Tolerance to WD was higher in small-sized accessions under control temperature and HT and in accessions with high biomass allocation to root under control conditions. Accessions that originate from sites with higher temperature have less stomatal density and allocate less biomass to the roots when cultivated under HT. Independence and interaction between stresses as well as the relationships between traits and stress responses are discussed.

Identifying Developmental Patterns in Structured Plant Phenotyping Data.

Technological breakthroughs concerning both sensors and robotized plant phenotyping platforms have totally renewed the plant phenotyping paradigm in the last two decades. This has impacted both the nature and the throughput of data with the availability of data at high-throughput from the tissular to the whole plant scale. Sensor outputs often take the form of 2D or 3D images or time series of such images from which traits are extracted while organ shapes, shoot or root system architectures can be deduced. Despite this change of paradigm, many phenotyping studies often ignore the structure of the plant and therefore loose the information conveyed by the temporal and spatial patterns emerging from this structure. The developmental patterns of plants often take the form of succession of well-differentiated phases, stages or zones depending on the temporal, spatial or topological indexing of data. This entails the use of hierarchical statistical models for their identification.The objective here is to show potential approaches for analyzing structured plant phenotyping data using state-of-the-art methods combining probabilistic modeling, statistical inference and pattern recognition. This approach is illustrated using five different examples at various scales that combine temporal and topological index parameters, and development and growth variables obtained using prospective or retrospective measurements.

Arabidopsis plants acclimate to water deficit at low cost through changes of carbon usage: an integrated perspective using growth, metabolite, enzyme, and gene expression analysis.

Growth and carbon (C) fluxes are severely altered in plants exposed to soil water deficit. Correspondingly, it has been suggested that plants under water deficit suffer from C shortage. In this study, we test this hypothesis in Arabidopsis (Arabidopsis thaliana) by providing an overview of the responses of growth, C balance, metabolites, enzymes of the central metabolism, and a set of sugar-responsive genes to a sustained soil water deficit. The results show that under drought, rosette relative expansion rate is decreased more than photosynthesis, leading to a more positive C balance, while root growth is promoted. Several soluble metabolites accumulate in response to soil water deficit, with K(+) and organic acids as the main contributors to osmotic adjustment. Osmotic adjustment costs only a small percentage of the daily photosynthetic C fixation. All C metabolites measured (not only starch and sugars but also organic acids and amino acids) show a diurnal turnover that often increased under water deficit, suggesting that these metabolites are readily available for being metabolized in situ or exported to roots. On the basis of 30 enzyme activities, no in-depth reprogramming of C metabolism was observed. Water deficit induces a shift of the expression level of a set of sugar-responsive genes that is indicative of increased, rather than decreased, C availability. These results converge to show that the differential impact of soil water deficit on photosynthesis and rosette expansion results in an increased availability of C for the roots, an increased turnover of C metabolites, and a low-cost C-based osmotic adjustment, and these responses are performed without major reformatting of the primary metabolism machinery.

Water deficits uncouple growth from photosynthesis, increase C content, and modify the relationships between C and growth in sink organs.

In plants, carbon (C) molecules provide building blocks for biomass production, fuel for energy, and exert signalling roles to shape development and metabolism. Accordingly, plant growth is well correlated with light interception and energy conversion through photosynthesis. Because water deficits close stomata and thus reduce C entry, it has been hypothesised that droughted plants are under C starvation and their growth under C limitation. In this review, these points are questioned by combining literature review with experimental and modelling illustrations in various plant organs and species. First, converging evidence is gathered from the literature that water deficit generally increases C concentration in plant organs. The hypothesis is raised that this could be due to organ expansion (as a major C sink) being affected earlier and more intensively than photosynthesis (C source) and metabolism. How such an increase is likely to interact with C signalling is not known. Hence, the literature is reviewed for possible links between C and stress signalling that could take part in this interaction. Finally, the possible impact of water deficit-induced C accumulation on growth is questioned for various sink organs of several species by combining published as well as new experimental data or data generated using a modelling approach. To this aim, robust correlations between C availability and sink organ growth are reported in the absence of water deficit. Under water deficit, relationships weaken or are modified suggesting release of the influence of C availability on sink organ growth. These results are interpreted as the signature of a transition from source to sink growth limitation under water deficit.

The case for improving crop carbon sink strength or plasticity for a CO2-rich future.

Atmospheric CO2 concentration [CO2] has increased from 260 to 280µmolmol-1 (level during crop domestication up to the industrial revolution) to currently 400 and will reach 550µmolmol-1 by 2050. C3 crops are expected to benefit from elevated [CO2] (e-CO2) thanks to photosynthesis responsiveness to [CO2] but this may require greater sink capacity. We review recent literature on crop e-CO2 responses, related source-sink interactions, how abiotic stresses potentially interact, and prospects to improve e-CO2 response via breeding or genetic engineering. Several lines of evidence suggest that e-CO2 responsiveness is related either to sink intrinsic capacity or adaptive plasticity, for example, involving enhanced branching. Wild relatives and old cultivars mostly showed lower photosynthetic rates, less downward acclimation of photosynthesis to e-CO2 and responded strongly to e-CO2 due to greater phenotypic plasticity. While reverting to such archaic traits would be an inappropriate strategy for breeding, we argue that substantial enhancement of vegetative sink vigor, inflorescence size and/or number and root sinks will be necessary to fully benefit from e-CO2. Potential ideotype features based on enhanced sinks are discussed. The generic 'feast-famine' sugar signaling pathway may be suited to engineer sink strength tissue-specifically and stage-specifically and help validate ideotype concepts. Finally, we argue that models better accounting for acclimation to e-CO2 are needed to predict which trait combinations should be targeted by breeders for a CO2-rich world.

Lateral Roots: Random Diversity in Adversity.

Lateral roots are essential for soil foraging and uptake of minerals and water. They feature a large morphological diversity that results from divergent primordia or root growth and development patterns. Besides a structured diversity, resulting from the hierarchical and developmental organization of root systems, there exists a random diversity, occurring between roots of similar age, of the same hierarchical order, and exposed to uniform conditions. The physiological bases and functional consequences of this random diversity are largely ignored. Here we review the evidence for such random diversity throughout the plant kingdom, present innovative approaches based on statistical modeling to account for such diversity, and set the list of its potential benefits in front of a variable and unpredictable soil environment.

The Physiological Basis of Drought Tolerance in Crop Plants: A Scenario-Dependent Probabilistic Approach.

Drought tolerance involves mechanisms operating at different spatial and temporal scales, from rapid stomatal closure to maintenance of crop yield. We review how short-term mechanisms are controlled for stabilizing shoot water potential and how long-term processes have been constrained by evolution or breeding to fit into acclimation strategies for specific drought scenarios. These short- or long-term feedback processes participate in trade-offs between carbon accumulation and the risk of deleterious soil water depletion. Corresponding traits and alleles may therefore have positive or negative effects on crop yield depending on drought scenarios. We propose an approach that analyzes the genetic architecture of traits in phenotyping platforms and of yield in tens of field experiments. A combination of modeling and genomic prediction is then used to estimate the comparative interests of combinations of alleles depending on drought scenarios. Hence, drought tolerance is understood probabilistically by estimating the benefit and risk of each combination of alleles.