Towards modelling the flexible timing of shoot development: simulation of maize organogenesis based on coordination within and between phytomers

Pervasive G × E interactions shape adaptive trajectories and the exploration of the phenotypic space in artificial selection experiments

Quantitative genetics models have shown that long-term selection responses depend on initial variance and mutational influx. Understanding limits of selection requires quantifying the role of mutational variance. However, correlative responses to selection on nonfocal traits can perturb the selection response on the focal trait; and generations are often confounded with selection environments so that genotype by environment (G×E) interactions are ignored. The Saclay divergent selection experiments (DSEs) on maize flowering time were used to track the fate of individual mutations combining genotyping data and phenotyping data from yearly measurements (DSEYM) and common garden experiments (DSECG) with four objectives: (1) to quantify the relative contribution of standing and mutational variance to the selection response, (2) to estimate genotypic mutation effects, (3) to study the impact of G×E interactions in the selection response, and (4) to analyze how trait correlations modulate the exploration of the phenotypic space. We validated experimentally the expected enrichment of fixed beneficial mutations with an average effect of +0.278 and +0.299 days to flowering, depending on the genetic background. Fixation of unfavorable mutations reached up to 25% of incoming mutations, a genetic load possibly due to antagonistic pleiotropy, whereby mutations fixed in the selection environment (DSEYM) turned to be unfavorable in the evaluation environment (DSECG). Global patterns of trait correlations were conserved across genetic backgrounds but exhibited temporal patterns. Traits weakly or uncorrelated with flowering time triggered stochastic exploration of the phenotypic space, owing to microenvironment-specific fixation of standing variants and pleiotropic mutational input.

A successive time-to-event model of phyllochron dynamics for hypothesis testing: application to the analysis of genetic and environmental effects in maize

BACKGROUND

The time between the appearance of successive leaves, or phyllochron, characterizes the vegetative development of annual plants. Hypothesis testing models, which allow the comparison of phyllochrons between genetic groups and/or environmental conditions, are usually based on regression of thermal time on the number of leaves; most of the time a constant leaf appearance rate is assumed. However regression models ignore auto-correlation of the leaf number process and may lead to biased testing procedures. Moreover, the hypothesis of constant leaf appearance rate may be too restrictive.

METHODS

We propose a stochastic process model in which emergence of new leaves is considered to result from successive time-to-events. This model provides a flexible and more accurate modeling as well as unbiased testing procedures. It was applied to an original maize dataset collected in the field over three years on plants originating from two divergent selection experiments for flowering time in two maize inbred lines.

RESULTS AND CONCLUSION

We showed that the main differences in phyllochron were not observed between selection populations but rather between ancestral lines, years of experimentation and leaf ranks. Our results highlight a strong departure from the assumption of a constant leaf appearance rate over a season which could be related to climate variations, even if the impact of individual climate variables could not be clearly determined.

Interactions Between Environment and Genetic Diversity in Perennial Grass Phenology: A Review of Processes at Plant Scale and Modeling

In perennial grasses, the reproductive development consists of major phenological stages which highly determine the seasonal variations of grassland biomass production in terms of quantity and quality. The reproductive development is regulated by climatic conditions through complex interactions subjected to high genetic diversity. Understanding these interactions and their impact on plant development and growth is essential to optimize grassland management and identify the potential consequences of climate change. Here, we review the main stages of reproductive development, from floral induction to heading, i.e., spike emergence, considering the effect of the environmental conditions and the genetic diversity observed in perennial grasses. We first describe the determinants and consequences of reproductive development at individual tiller scale before examining the interactions between plant tillers and their impact on grassland perenniality. Then, we review the available grassland models through their ability to account for the complexity of reproductive development and genetic × environmental interactions. This review shows that (1) The reproductive development of perennial grasses is characterized by a large intraspecific diversity which has the same order of magnitude as the diversity observed between species or environmental conditions. (2) The reproductive development is determined by complex interactions between the processes of floral induction and morphogenesis of the tiller. (3) The perenniality of a plant is dependent on the reproductive behavior of each tiller. (4) Published models only partly explain the complex interactions between morphogenesis and climate on reproductive development. (5) Introducing more explicitly the underlying processes involved in reproductive development in models would improve our ability to anticipate grassland behavior in future growth conditions.

Two maize cultivars of contrasting leaf size show different leaf elongation rates with identical patterns of extension dynamics and coordination

Simulating leaf development from initiation to maturity opens new possibilities to model plant-environment interactions and the plasticity of plant architecture. This study analyses the dynamics of leaf production and extension along a maize (Zea mays) shoot to assess important modelling choices. Maize plants from two cultivars originating from the same inbred line, yet differing in the length of mature leaves were used in this study. We characterized the dynamics of the blade and sheath lengths of all phytomers by dissecting plants every 2-3 days. We analysed how differences in leaf size were built up and we examined the coordination between the emergence of organs and phases of their extension. Leaf extension rates were higher in the cultivar with longer leaves than in the cultivar with shorter leaves; no differences were found in other aspects. We found that (i) first post-embryonic leaves were initiated at a markedly higher rate than upper leaves; (ii) below ear position, sheaths were initiated at a time intermediate between tip emergence and appearance, while above the ear position, sheaths were initiated at a high rate, such that the time interval between the blade and sheath initiations decreased for these leaves; and (iii) ear position also marked a change in the correlation in size between successive phytomers with little correlation of size between upper and lower leaves. Our results identified leaf extension rate as the reason for the difference in size between the two cultivars. The two cultivars shared the same pattern for the timing of initiation events, which was more complex than previously thought. The differences described here may explain some inaccuracies reported in functional-structural plant models. We speculate that genotypic variation in behaviour for leaf and sheath initiation exists, which has been little documented in former studies.

A functional structural model of grass development based on metabolic regulation and coordination rules

Shoot architecture is a key component of the interactions between plants and their environment. We present a novel model of grass, which fully integrates shoot morphogenesis and the metabolism of carbon (C) and nitrogen (N) at organ scale, within a three-dimensional representation of plant architecture. Plant morphogenesis is seen as a self-regulated system driven by two main mechanisms. First, the rate of organ extension and the establishment of architectural traits are regulated by concentrations of C and N metabolites in the growth zones and the temperature. Second, the timing of extension is regulated by rules coordinating successive phytomers instead of a thermal time schedule. Local concentrations are calculated from a model of C and N metabolism at organ scale. The three-dimensional representation allows the accurate calculation of light and temperature distribution within the architecture. The model was calibrated for wheat (Triticum aestivum) and evaluated for early vegetative stages. This approach allowed the simulation of realistic patterns of leaf dimensions, extension dynamics, and organ mass and composition. The model simulated, as emergent properties, plant and agronomic traits. Metabolic activities of growing leaves were investigated in relation to whole-plant functioning and environmental conditions. The current model is an important step towards a better understanding of the plasticity of plant phenotype in different environments.

Contrasting phenotypes emerging from stable rules: A model based on self-regulated control loops captures the dynamics of shoot extension in contrasting maize phenotypes

BACKGROUND AND AIMS

The dynamics of plant architecture is a central aspect of plant and crop models. Most models assume that whole shoot development is orchestrated by the leaf appearance rate, which follows a thermal time schedule. However, leaf appearance actually results from leaf extension and taking it as an input hampers our ability to understand shoot construction. The objective of the present study was to assess a modelling framework for grasses, in which the emergence of leaves and other organs is explicitly calculated as a result of their extension.

METHODS

The approach builds on a previous model, which uses a set of rules co-ordinating the timing of development within and between phytomers. We first assessed rule validity for four experimental datasets, including different cultivars, planting densities and environments, and accordingly revised the equations driving the extension of the upper leaves and of internodes. We then fitted model parameters for each dataset and evaluated the ability to simulate the measured phenotypes across time. Finally, we carried out a sensitivity analysis to identify the parameters that had the greatest impact and to investigate model behaviour.

KEY RESULTS

The modified version of the model simulated correctly the contrasting maize phenotypes. Co-ordination rules accounted for the observations in all studied cultivars. Factors with major impact on model output included extension rates, the time of tassel initiation and initial conditions. A large diversity of phenotypes could be simulated.

CONCLUSIONS

This work provides direct experimental evidence for co-ordination rules and illustrates the capacity of the model to represent contrasting phenotypes. These rules play an important role in patterning shoot architecture and some of them need to be assessed further, considering contrasting growth conditions. To make the model more predictive, several parameters could be considered in the future as internal variables driven by plant status.

A Model of Leaf Coordination to Scale-Up Leaf Expansion from the Organ to the Canopy

Process-based crop growth models are popular tools with which to analyze and understand the impact of crop management, genotype-by-environment interactions, or climate change. The ability to predict leaf area development is critical to predict crop growth, particularly under conditions of limited resources. Here, we aimed at deciphering growth coordination rules between wheat (Triticum aestivum) plant organs (i.e. between leaves within a stem, between laminae and sheaths, and between the mainstem and axillary tillers) to model the dynamics of canopy development. We found a unique relationship between laminae area and leaf rank for the mainstem and its tillers, which was robust across a range of sowing dates and plant densities. Robust relationships between laminae and sheath areas also were found, highlighting the tight control of organ growth within and between phytomers. These relationships identified at the phytomer scale were used to develop a simulation model of leaf area dynamics at the canopy level that was integrated in the wheat model SiriusQuality. The model was then evaluated using several independent experiments. The model accurately predicts leaf area dynamics under different scenarios of nitrogen and water limitations. It accounted for 85%, 64%, and 73% of the variability of the surface area of leaf cohorts, total leaf area index, and total green area index, respectively. The process-based model of the dynamics of leaf area described here is a key element to quantify the value of candidate traits for use in plant breeding and to project the impact of climate change on wheat growth.

Effects of nitrogen and vapour pressure deficit on phytomer growth and development in a C4 grass

Phytomers are basic morphological units of plants. Knowledge of phytomer development is essential for understanding morphological plasticity, functional-structural modelling of plant growth and the usage of leaf characteristics to indicate growth conditions at the time of production (e.g. stable isotope signals). Yet, systematic analysis on the process of phytomer development is unavailable for wild or perennial C4 grasses. Also, effects of environmental factors, such as nitrogen nutrition or vapour pressure deficit (VPD), on coordination events of developmental processes of C4 grasses have not been studied. This study investigates phytomer growth and development in Cleistogenes squarrosa, a predominant C4 grass in the Eurasian steppe, grown at low (0.63 kPa) or high (1.58 kPa) VPD with low or high nitrogen supply in controlled environments. Elongation of phytomers on marked tillers was measured daily for 13 days. Then lengths of immature and mature phytomer components (blade, sheath and internode) of all phytomers were measured following dissection. Nitrogen nutrition and VPD had no effects on coordination of growth within and between phytomers: phytomer tips emerged when phytomers reached 26 % of their final length, coincident with the acceleration phase of its elongation; blade elongation stopped when phytomers reached ∼75 % of their final length and elongation of the preceding phytomer was confined to the internode. The relationship between fraction of final phytomer length and days after tip emergence for all treatments was well described by a sigmoidal function: y = 1/{1 + exp[(1.82 - x)/1.81]}. C. squarrosa exhibited little morphological plasticity at phytomer-level in response to nitrogen supply and VPD, but a clear increase in tillering under high N supply. Also, the invariant coordination of elongation within and between phytomers was a stable developmental feature, thus the quantitative coordination rules are applicable for predicting morphological development of C. squarrosa under contrasting levels of nitrogen nutrition or VPD.

A Conserved Potential Development Framework Applies to Shoots of Legume Species with Contrasting Morphogenetic Strategies

A great variety of legume species are used for forage production and grown in multi-species grasslands. Despite their close phylogenetic relationship, they display a broad range of morphologies that markedly affect their competitive abilities and persistence in mixtures. Little is yet known about the component traits that control the deployment of plant architecture in most of these species. During the present study, we compared the patterns of shoot organogenesis and shoot organ growth in contrasting forage species belonging to the four morphogenetic groups previously identified in herbaceous legumes (i.e., stolon-formers, rhizome-formers, crown-formers tolerant to defoliation and crown-formers intolerant to defoliation). To achieve this, three greenhouse experiments were carried out using plant species from each group (namely alfalfa, birdsfoot trefoil, sainfoin, kura clover, red clover, and white clover) which were grown at low density under non-limiting water and soil nutrient availability. The potential morphogenesis of shoots characterized under these conditions showed that all the species shared a number of common morphogenetic features. All complied with a generalized classification of shoot axes into three types (main axis, primary and secondary axes). A common quantitative framework for vegetative growth and development involved: (i) the regular development of all shoot axes in thermal time and a deterministic branching pattern in the absence of stress; (ii) a temporal coordination of organ growth at the phytomer level that was highly conserved irrespective of phytomer position, and (iii) an identical allometry determining the surface area of all the leaves. The species differed in their architecture as a consequence of the values taken by component traits of morphogenesis. Assessing the relationships between the traits studied showed that these species were distinct from each other along two main PCA axes which explained 68% of total variance: the first axis captured a trade-off between maximum leaf size and the ability to produce numerous phytomers, while the second distinguished morphogenetic strategies reliant on either petiole or internode expansion to achieve space colonization. The consequences of this quantitative framework are discussed, along with its possible applications regarding plant phenotyping and modeling.

Natural genetic variation for morphological and molecular determinants of plant growth and yield

The rates of increase in yield of the main commercial crops have been steadily falling in many areas worldwide. This generates concerns because there is a growing demand for plant biomass due to the increasing population. Plant yield should thus be improved in the context of climate change and decreasing natural resources. It is a major challenge which could be tackled by improving and/or altering light-use efficiency, CO2 uptake and fixation, primary metabolism, plant architecture and leaf morphology, and developmental plant processes. In this review, we discuss some of the traits which could lead to yield increase, with a focus on how natural genetic variation could be harnessed. Moreover, we provide insights for advancing our understanding of the molecular aspects governing plant growth and yield, and propose future avenues for improvement of crop yield. We also suggest that knowledge accumulated over the last decade in the field of molecular physiology should be integrated into new ideotypes.

A unique approach to demonstrating that apical bud temperature specifically determines leaf initiation rate in the dicot Cucumis sativus

MAIN CONCLUSION

Leaf initiation rate is largely determined by the apical bud temperature even when apical bud temperature largely deviates from the temperature of other plant organs. We have long known that the rate of leaf initiation (LIR) is highly sensitive to temperature, but previous studies in dicots have not rigorously demonstrated that apical bud temperature controls LIR independent of other plant organs temperature. Many models assume that apical bud and leaf temperature are the same. In some environments, the temperature of the apical bud, where leaf initiation occurs, may differ by several degrees Celsius from the temperature of other plant organs. In a 28-days study, we maintained temperature differences between the apical bud and the rest of the individual Cucumis sativus plants from -7 to +8 °C by enclosing the apical buds in transparent, temperature-controlled, flow-through, spheres. Our results demonstrate that LIR was completely determined by apical bud temperature independent of other plant organs temperature. These results emphasize the need to measure or model apical bud temperatures in dicots to improve the prediction of crop development rates in simulation models.

Measurement of plant growth in view of an integrative analysis of regulatory networks

As the regulatory networks of growth at the cellular level are elucidated at a fast pace, their complexity is not reduced; on the contrary, the tissue, organ and even whole-plant level affect cell proliferation and expansion by means of development-induced and environment-induced signaling events in growth regulatory processes. Measurement of growth across different levels aids in gaining a mechanistic understanding of growth, and in defining the spatial and temporal resolution of sampling strategies for molecular analyses in the model Arabidopsis thaliana and increasingly also in crop species. The latter claim their place at the forefront of plant research, since global issues and future needs drive the translation from laboratory model-acquired knowledge of growth processes to improvements in crop productivity in field conditions.

Functional-structural plant models: a growing paradigm for plant studies

A number of research groups in various areas of plant biology as well as computer science and applied mathematics have addressed modelling the spatiotemporal dynamics of growth and development of plants. This has resulted in development of functional-structural plant models (FSPMs). In FSPMs, the plant structure is always explicitly represented in terms of a network of elementary units. In this respect, FSPMs are different from more abstract models in which a simplified representation of the plant structure is frequently used (e.g. spatial density of leaves, total biomass, etc.). This key feature makes it possible to build modular models and creates avenues for efficient exchange of model components and experimental data. They are being used to deal with the complex 3-D structure of plants and to simulate growth and development occurring at spatial scales from cells to forest areas, and temporal scales from seconds to decades and many plant generations. The plant types studied also cover a broad spectrum, from algae to trees. This special issue of Annals of Botany features selected papers on FSPM topics such as models of morphological development, models of physical and biological processes, integrated models predicting dynamics of plants and plant communities, modelling platforms, methods for acquiring the 3-D structures of plants using automated measurements, and practical applications for agronomic purposes.