Anne Clément-Vidal

EcoMeristem, a model of morphogenesis and competition among sinks in rice. 1. Concept, validation and sensitivity analysis

Because of rapid advances in functional genomics there is an increasing demand for models simulating complex traits, such as the physiological and environmental controls of plant morphology. This paper describes, validates and explores the behaviour of the structural-functional model EcoMeristem, developed for cereals in the context of the Generation Challenge Program (GCP; CGIAR). EcoMeristem constructs the plant on the basis of an organogenetic body plan, driven by intrinsic (genetic) behavioural norms of meristems. These norms consist of phenological-topological rules for organ initiation and pre-dimensioning (sink creation) and rules enabling feedbacks of the plants resource status on the organogenetic processes. Plant resource status is expressed by a state variable called Internal Competition Index (Ic) calculated daily as the ratio of assimilate source (supply) over the sum of active sinks (demand). Ic constitutes an internal signal analogous to sugar signalling. Ic affects potential phytomer size, tiller initiation, leaf senescence, and carbohydrate storage and mobilisation. The model was calibrated and tested on IR64 rice grown in controlled environments, and validated with field observations for the same cultivar (Philippines). Observed distributions and dynamics of soluble sugars and starch in plant organs supported the model concepts of internal competition and the role of reserves as a buffer for Ic fluctuations. Model sensitivity analyses suggested that plant growth and development depend not only on assimilate supply, but also on organogenesis-based demand. If true, this conclusion has important consequences for crop improvement strategies.

EcoMeristem, a model of morphogenesis and competition among sinks in rice. 2. Simulating genotype responses to phosphorus deficiency

Phenotypic plasticity enables plants to adjust their morphology and phenology to variable environments. Although potentially important for crop breeding and management, the physiology and genetics of plasticity traits are poorly understood, and few models exist for their study. In the previous paper of this series, the structural-functional model EcoMeristem was described and field validated for vegetative-stage rice. This study applies the model to an experimental study on phosphorus deficiency effects on two morphologically contrasting rice cultivars, IR64 and Azucena, grown in controlled environments under hydroponics culture. Phosphorus deficiency caused severe biomass growth reductions in the shoot but not in the root, thus increasing the root / shoot weight ratio. It also inhibited tiller formation and leaf elongation, prolonged the phyllochron, and increased carbohydrate reserve pools in the plant. Analysis aided by the model identified inhibition of leaf extension and tillering as primary effects of the stress. Physiological feedback probably led to longer phyllochron, greater reserve accumulation and root growth stimulation. The main effect of P deficiency appeared to be a reduction in demand for assimilates in the shoot while photosynthetic radiation use efficiency remained nearly constant, resulting in spill-over of excess assimilates into reserve compartments and root growth. The results are discussed in the light of future applications of EcoMeristem for phenotyping and genetic analyses of phenotypic plasticity.

Phenotypic Plasticity of Rice Seedlings: Case of Phosphorus Deficiency

Abstract The aim of this study is to characterize the plasticity of root and shoot morphology in rice, the genomic model plant for cereals, using P deficiency as environmental factor causing variability. A phytotron study on Nipponbare (Oryza Sativa L.) seedlings was conducted to analyze the effects of P deficiency on plant organogenesis (tiller and leaf appearance, root apex number) and allometric relationships (root/shoot weight ratio, specific leaf area (SLA) and specific root length (SRL), blade/sheath weight ratio). The results confirmed that the main effect of P deficiency is a reduction of shoot growth for the benefit of the root system. Reduced shoot growth was associated with reduced tiller production, longer phyllochron and reduced leaf elongation rate while final leaf size remained unchanged. The reduced leaf elongation rate might be a primary response to P deficiency and this caused lower phyllochron and tillering by feedback. Allometric parameters such as SLA, SRL, root apex number per unit length and leaf blade/sheath weight ratio remained largely stable under P deficiency. Increased root growth relative to shoot was associated with increased sucrose concentration in roots, and thus possibly resulted from assimilates liberated by shoot growth inhibition. The simple theory of multiple morphological changes resulting from slow leaf expansion under P deficiency requires further experimental confirmation, after which it may serve as a basis for a mechanistic model of rice phenotypic plasticity and certain genotype X environment interactions on morphology.

Orchestration of transpiration, growth and carbohydrate dynamics in rice during a dry-down cycle

The regulation of carbohydrate metabolism and source-sink relationships among organs play a key role in plant adaptation to drought. This study aimed at characterising the dynamics of transpiration, development, growth and carbon metabolism, as well as the expression of invertase genes, in response to drought during a dry-down cycle. Three 1-month experiments were conducted in controlled environment using the rice genotype IR64 (Oryza sativa L., indica). Plant leaf relative transpiration and expansion rates decreased linearly when fraction of transpirable soil water (FTSW) dropped below 0.66 and 0.58, respectively. Hexose and starch concentration responses to FTSW in a given organ were generally linear and opposite: in source leaves, hexose concentration increased and starch decreased, and vice versa in sink leaves and roots. Sucrose remained constant in source leaves and increased slightly in sink leaves. Starch reserves built up during stress in sink organs were rapidly mobilised upon rewatering, indicating its involvement in a mechanism to ensure recovery. Expression of cell-wall and vacuolar invertase genes under stress increased in sink leaves, interpreted as a mechanism to maintain sink activity (cell wall) and osmotic adjustment (vacuolar). It is concluded that carbohydrate metabolism in sink organs under drought is highly regulated, and important for stress adaptation.

Phenotypic and genetic dissection of component traits for early vigour in rice using plant growth modelling, sugar content analyses and association mapping

Highlight Plant-model-assisted phenotyping and metabolomics enable phenotypic and genetic dissection of early vigour traits in a rice diversity panel.

Role of transitory carbon reserves during adjustment to climate variability and source–sink imbalances in oil palm (Elaeis guineensis)

Oil palm (Elaeis guineensis Jacq.) is a perennial, tropical, monocotyledonous plant characterized by simple architecture and low phenotypic plasticity, but marked by long development cycles of individual phytomers (a pair of one leaf and one inflorescence at its axil). Environmental effects on vegetative or reproductive sinks occur with various time lags depending on the process affected, causing source-sink imbalances. This study investigated how the two instantaneous sources of carbon assimilates, CO(2) assimilation and mobilization of transitory non-structural carbohydrate (NSC) reserves, may buffer such imbalances. An experiment was conducted in Indonesia during a 22-month period (from July 2006 to May 2008) at two contrasting locations (Kandista and Batu Mulia) using two treatments (control and complete fruit pruning treatment) in Kandista. Measurements included leaf gas exchange, dynamics of NSC reserves and dynamics of structural aboveground vegetative growth (SVG) and reproductive growth. Drought was estimated from a simulated fraction of transpirable soil water. The main sources of variation in source-sink relationships were (i) short-term reductions in light-saturated leaf CO(2) assimilation rate (A(max)) during seasonal drought periods, particularly in Batu Mulia; (ii) rapid responses of SVG rate to drought; and (iii) marked lag periods between 16 and 29 months of environmental effects on the development of reproductive sinks. The resulting source-sink imbalances were buffered by fluctuations in NSC reserves in the stem, which mainly consisted of glucose and starch. Starch was the main buffer for sink variations, whereas glucose dynamics remained unexplained. Even under strong sink limitation, no negative feedback on A(max) was observed. In conclusion, the different lag periods for environmental effects on assimilate sources and sinks in oil palm are mainly buffered by NSC accumulation in the stem, which can attain 50% (dw:dw) in stem tops. The resulting dynamics of growth and production are complex because several dozen phytomers of different phenological ages develop at any given time and interact with a common pool of reserves.

Phenology, growth and physiological adjustments of oil palm (Elaeis guineensis) to sink limitation induced by fruit pruning

BACKGROUND AND AIMS Despite its simple architecture and small phenotypic plasticity, oil palm has complex phenology and source-sink interactions. Phytomers appear in regular succession but their development takes years, involving long lag periods between environmental influences and their effects on sinks. Plant adjustments to resulting source-sink imbalances are poorly understood. This study investigated oil palm adjustments to imbalances caused by severe fruit pruning. METHODS An experiment with two treatments (control and complete fruit pruning) during 22 months in 2006-2008) and six replications per treatment was conducted in Indonesia. Phenology, growth of above-ground vegetative and reproductive organs, leaf morphology, inflorescence sex differentiation, dynamics of non-structural carbohydrate reserves and light-saturated net photosynthesis (A(max)) were monitored. KEY RESULTS Artificial sink limitation by complete fruit pruning accelerated development rate, resulting in higher phytomer, leaf and inflorescence numbers. Leaf size and morphology remained unchanged. Complete fruit pruning also suppressed the abortion of male inflorescences, estimated to be triggered at about 16 months before bunch maturity. The number of female inflorescences increased after an estimated lag of 24-26 months, corresponding to time from sex differentiation to bunch maturity. The most important adjustment process was increased assimilate storage in the stem, attaining nearly 50 % of dry weight in the stem top, mainly as starch, whereas glucose, which in controls was the most abundant non-structural carbohydrate stored in oil palm, decreased. CONCLUSIONS The development rate of oil palm is in part controlled by source-sink relationships. Although increased rate of development and proportion of female inflorescences constituted observed adjustments to sink limitation, the low plasticity of plant architecture (constant leaf size, absence of branching) limited compensatory growth. Non-structural carbohydrate storage was thus the main adjustment process.

Over-expression of a cytosolic isoform of the HbCuZnSOD gene in Hevea brasiliensis changes its response to a water deficit

Hevea brasiliensis is the main commercial source of natural rubber. Reactive oxygen species (ROS) scavenging systems are involved in various biotic and abiotic stresses. Genetic engineering was undertaken to study the strengthening of plant defences by antioxidants. To that end, Hevea transgenic plant lines over-expressing a Hevea brasiliensis cytosolic HbCuZnSOD gene were successfully established and regenerated. Over-expression of the HbCuZnSOD gene was not clearly related to an increase in SOD activity in plant leaves. The impact of HbCuZnSOD gene over-expression in somatic embryogenesis and in plant development are presented and discussed. The water deficit tolerance of two HbCuZnSOD over-expressing lines was evaluated. The physiological parameters of transgenic plantlets subjected to a water deficit suggested that plants from line TS4T8An displayed lower stomatal conductance and a higher proline content. Over-expression of the HbCuZnSOD gene and activation of all ROS-scavenging enzymes also suggested that protection against ROS was more efficient in the TS4T8An transgenic line.

Model-assisted physiological analysis of Phyllo, a rice architectural mutant

Studies of phenotype of knockout mutants can provide new insights into physiological, phenological and architectural feedbacks in the plant system. Phyllo, a mutant of Nippon Bare rice (Oryza sativa L.) producing small leaves in rapid succession, was isolated during multiplication of a T-DNA insertion library. Phyllo phenotype was compared with the wild type (WT) during vegetative development in hydroponics culture using a wide range of physiological and biometric measurements. These were integrated with the help of the functional-structural model EcoMeristem, explicitly designed to study interactions between morphogenesis and carbon assimilation. Although the phenotype of the mutant was caused by a single recessive gene, it differed in many ways from the WT, suggesting a pleiotropic effect of this mutation. Phyllochron was 25 (1-4 leaf stage) to 38% (>>4 leaf stage) shorter but showed normal transition from juvenile to adult phase after leaf 4. Leaf size also increased steadily with leaf position as in WT. The mutant had reduced leaf blade length : width and blade : sheath length ratios, particularly during the transition from heterotrophic to autotrophic growth. During the same period, root : shoot dry weight ratio was significantly diminished. Specific leaf area (SLA) was strongly increased in the mutant but showed normal descending patterns with leaf position. Probably related to high SLA, the mutant had much lower light-saturated leaf photosynthetic rates and lower radiation use efficiency (RUE) than the WT. Leaf extension rates were strongly reduced in absolute terms but were high in relative terms (normalised by final leaf length). The application of the EcoMeristem model to these data indicated that the mutant was severely deficient in assimilate, resulting from low RUE and high organ initiation rate causing high assimilate demand. This was particularly pronounced during the heterotrophic-autotrophic transition, probably causing shorter leaf blades relative to sheaths, as well as a temporary reduction of assimilate partitioning to roots. The model accurately simulated the mutants high leaf mortality and absence of tillering. The simulated assimilate shortage was supported by observed reductions in starch storage in sheaths. Soluble sugar concentrations differed between mutant and WT in roots but not in shoots. Specifically, the hexose : sucrose ratio was 50% lower in the roots of the mutant, possibly indicating low invertase activity. Furthermore, two OsCIN genes coding for cell wall invertases were not expressed in roots, and others were expressed weakly. This was interpreted as natural silencing via sugar signalling. In summary, the authors attributed the majority of observed allometric and metabolic modifications in the mutant to an extreme assimilate shortage caused by hastened shoot organogenesis and inefficient leaf morphology.

Grain, sugar and biomass accumulation in photoperiod-sensitive sorghums. II. Biochemical processes at internode level and interaction with phenology.

Sugar accumulation in sorghum (Sorghum bicolor (L.) Moench) stems is a complex trait that is particularly plastic in response to photoperiod. This study investigated sucrose accumulation in a sterile (no grain filling) and fertile near-isogenic line of the photoperiod-sensitive cultivar IS2848 in two greenhouse experiments. Variable phenology was induced by applying a short (12-h PP) and a long (13-h PP) photoperiod. Dynamics of plant growth, phenology, sugar accumulation and related enzyme activities in internodes were investigated. Under 13-h PP, plants flowered 28 days later and attained threefold higher sucrose concentration at anthesis compared with those under 12-h PP. Sucrose accumulation in individual internodes was driven by organ physiological age, not by plant phenology. Competition with grain filling was marginal but greater under 12-h PP (i.e. when sucrose accumulation in internodes occurred after flowering). Enzyme activities showed marked developmental patterns but contributed little to explaining differences between treatments and genotypes. The study demonstrates that sucrose storage physiology in sweet sorghum resembles that of sugarcane (Saccharum spp.) but is more complex due to photoperiod effects on phenology. It confirms the field results on 14 sorghum genotypes contrasting for phenology and photoperiod sensitivity presented in a companion paper. Perspectives for developing sorghum ideotype concepts for food and fuel crops are discussed.