Census of breeding birds in the Pyrenees in the early 1980s: A publicly available dataset for ecological research.

The Pyrenees is a mountain range in south-western Europe that supports a rich diversity of bird species. In 1981, point count surveys of breeding birds (passerines and picidae) were carried out in the Vanera valley, a valley in the eastern Pyrenees, resulting in a data set of 228 counts. These data provide valuable information on the distribution and abundance of bird populations on 5350 ha of heterogeneous land (including cropland, grasslands, heaths and river banks, and pine forest) at altitudes ranging from 1100 to 2600 meters. Additional point count surveys were carried out in the pine forest from 1982 to 1985, resulting in a data set of 144 counts. Habitat descriptors (percentage of herbaceous and ligneous plant cover at different heights - 0-1m, 1-4m and more than 8m; vegetation type) and altitude were assessed around each point count. This dataset provides a complete picture of the breeding bird community in a typical valley of eastern Pyrenees in the early 1980s, which could be compared with future censuses to contribute to a variety of research questions, such as quantifying changes in birds between the early 1980s and now in mountain areas, understanding the effects of climate change on bird populations, examining the effects of habitat fragmentation and land-use change, and identifying priority areas for conservation and management. These data could inspire new research and contribute to our collective understanding of bird ecology in the Pyrenees.

Model-assisted analysis for tuning anthocyanin composition in grape berries.

Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.

Integrated model simulates bigger, sweeter tomatoes under changing climate under reduced nitrogen and water input.

When simulating the response of fruit growth and quality to environmental factors and cultivation practices, the interactions between the mother plant and fruit need to be considered as a whole system. Here, we developed the integrative Tomato plant and fruit Growth and Fruit Sugar metabolism (TGFS) model by coupling equations describing the biophysical processes of leaf gas exchange, water transport, carbon allocation, organ growth and fruit sugar metabolism. The model also accounts for effects of soil nitrogen and atmospheric CO2 concentration on gaseous exchange of water and carbon by the leaf. With different nitrogen and water input values, TGFS performed well at simulating the dry mass of the tomato leaf, stem, root, and fruit, and the concentrations of soluble sugar and starch in fruit. TGFS simulations showed that increasing air temperature and CO2 concentration has positive effects on fruit growth, but not on sugar concentrations. Further model-based analyses of cultivation scenarios suggest that, in the context of climate change, decreasing N by 15%-25% and decreasing irrigation by 10%-20% relative to current levels would increase tomato fresh weight by 27.8%-36.4% while increasing soluble sugar concentration by up to 10%. TGFS provides a promising tool to optimise N and water inputs for sustainable high-quality tomatoes.

Resource Translocation Modelling Highlights Density-Dependence Effects in Fruit Production at Various Levels of Organisation.

The size of fruit cells, seeds and fruits depends on their number. Could this density-dependence effect result from sugar resource sharing and, if so, does it involve phloem sugar flow or the intensity of sugar unloading to the sink? A density-dependence model (DDM) describing these processes was designed and parameterised for six species at five levels of organisation: cells and seeds within fruits, fruits within clusters, fruits within plants and plants within plots. Sugar flow was driven by phloem conductance, determined by parameters α, governing the shape of its relationship to population size, and κ, its value for a population size of one. Sugar unloading followed Michaelis-Menten kinetics with parameters Vm (maximal unloading rate) and Km (Michaelis constant). The DDM effectively reproduced the observed individual mass dynamics, the undercompensating density dependence observed in most species at all sub-plant levels and the undercompensating, exact and overcompensating density dependence observed at the plant level. Conductance (κ) was a scaling factor varying with the level of organisation. Vm was positively correlated with density dependence, and α was negatively correlated with density dependence only if the plant-within-plot level was not considered. Analysis of the model's behaviour indicates that density dependence of fruit growth could be a result of sugar sharing, and that both phloem sugar flow and sugar unloading contribute to these effects.

Pedicel anatomy and histology in tomato vary according to genotype and water-deficit environment, affecting fruit mass.

The growth and composition of fleshy fruits depend on resource acquisition and distribution in the plant. In tomato, the pedicel serves as the final connection between plant and fruit. However, very few quantitative data are available for the conducting tissues of the pedicel, nor is their genetic variability known. In the present study, a histological approach was combined with process-based modeling to evaluate the potential contribution made by the anatomy and histology of the pedicel to variations in fruit mass. Eleven genotypes were characterized and the impact of water deficit was studied for a single genotype using stress intensity and stage of application as variables. The results highlighted extensive variations in the relative proportions of the different pedicel tissues and in the absolute areas of xylem and phloem between genotypes. The model suggests that the variations in the area of the pedicel's vascular tissues induced by differences in genotype and water-deficit environments partly contributed to fruit mass variability. They therefore warrant phenotyping for use in the development of plant strains adapted to future environmental constraints. The results also demonstrated the need to develop non-invasive in vivo measurement methods to establish the number and size of active vessels and the flow rates in these vessels to improve prediction of water fluxes in plant architecture.

Brown Rot Disease in Stored Nectarines: Modeling the Combined Effects of Preharvest and Storage Conditions.

Brown rot in stored stone fruits, caused by Monilinia spp., may be due to preharvest and storage factors, but the combined effect of these factors has yet to be investigated. We set up two experiments to monitor the progression of brown rot during the storage of nectarines subjected to various preharvest and storage conditions. We assessed the effects of different agricultural practices (irrigation regimen × fruit load) and harvest dates on brown rot progress during storage in 2018 and the effect of different storage temperatures in 2019. We found that the cumulative incidence of brown rot during storage increased with individual fruit mass, which was influenced by agricultural practices, and for later harvest dates. It also increased with storage temperature. We observed that during storage no secondary infections developed in nectarines not in direct contact with fruits infected with Monilinia laxa. These findings led to the identification of candidate variables describing the brown rot risk on nectarines during storage, such as individual fruit mass, meteorological conditions before fruit harvest, prevalence of brown rot at harvest, and storage temperature. We used these variables to build a mathematical model for estimating the time-to-appearance of brown rot symptoms in stored nectarines. This model fitted the experimental data well, highlighting the need to pay greater attention to the interaction between preharvest and storage conditions. This model could be used to evaluate management strategies for reducing the impact of brown rot in nectarines during storage.

A parsimonious mechanistic model of reproductive and vegetative growth in fruit trees predicts consequences of fruit thinning and branch pruning.

Productivity of fruit tree crops depends on the interaction between plant physiology, environmental conditions and agricultural practices. We develop a mechanistic model of fruit tree crops that reliable simulates the dynamics of variables of interest for growers and consequences of agricultural practices while relying on a minimal number of inputs and parameters. The temporal dynamics of carbon content in the different organs (i.e., shoots-S, roots-R and fruits-F) are the result of photosynthesis by S, nutrient supply by R, respiration by S, R and F, competition among different organs, photoperiod and initial system conditions partially controlled by cultural practices. We calibrate model parameters and evaluate model predictions using unpublished data from a peach (Prunus persica) experimental orchard with trees subjected to different levels of branch pruning and fruit thinning. Fiinally, we evaluate the consequences of different combinations of pruning and thinning intensities within a multi-criteria analysis. The predictions are in good agreement with the experimental measurements and for the different conditions (pruning and thinning). Our simulations indicate that thinning and pruning practices actually used by growers provide the best compromise between total shoot production, which impacts next year's abundance of shoots and fruits, and current year's fruit production in terms of quantity (yield) and quality (average fruit size). This suggests that growers are not only interested in maximizing current year's yield but also in its quality and its durability. The present work provides for modelers a system of equations based on acknowledged principles of plant science easily modifiable for different purposes. For horticulturists, it gives insights on the potentialities of pruning and thinning. For ecologists, it provides a transparent quantitative framework that can be coupled with biotic and abiotic stressors.

Modelling predicts tomatoes can be bigger and sweeter if biophysical factors and transmembrane transports are fine-tuned during fruit development.

The trade-off between yield and quality, a major problem for the production of fleshy fruits, involves fruit expansive growth and sugar metabolism. Here we developed an integrative model by coupling a biophysical model of fleshy fruit growth processes, including water and carbon fluxes and organ expansion, with an enzyme-based kinetic model of sugar metabolism to better understand the interactions between these two processes. The integrative model was initially tested on tomato fruit, a model system for fleshy fruit. The integrative model closely simulated the biomass and major carbon metabolites of tomato fruit developing under optimal or stress conditions. The model also performed robustly when simulating the fruit size and sugar concentrations of different tomato genotypes including wild species. The validated model was used to explore ways of uncoupling the size-sweetness trade-off in fruit. Model-based virtual experiments suggested that larger sweeter tomatoes could be obtained by simultaneously manipulating certain biophysical factors and transmembrane transports. The integrative fleshy fruit model provides a promising tool to facilitate the targeted bioengineering and breeding of tomatoes and other fruits.

Biomass composition explains fruit relative growth rate and discriminates climacteric from non-climacteric species.

Fleshy fruits are very varied, whether in terms of their composition, physiology, or rate and duration of growth. To understand the mechanisms that link metabolism to phenotypes, which would help the targeting of breeding strategies, we compared eight fleshy fruit species during development and ripening. Three herbaceous (eggplant, pepper, and cucumber), three tree (apple, peach, and clementine) and two vine (kiwifruit and grape) species were selected for their diversity. Fruit fresh weight and biomass composition, including the major soluble and insoluble components, were determined throughout fruit development and ripening. Best-fitting models of fruit weight were used to estimate relative growth rate (RGR), which was significantly correlated with several biomass components, especially protein content (R=84), stearate (R=0.72), palmitate (R=0.72), and lignocerate (R=0.68). The strong link between biomass composition and RGR was further evidenced by generalized linear models that predicted RGR with R-values exceeding 0.9. Comparison of the fruit also showed that climacteric fruit (apple, peach, kiwifruit) contained more non-cellulosic cell-wall glucose and fucose, and more starch, than non-climacteric fruit. The rate of starch net accumulation was also higher in climacteric fruit. These results suggest that the way biomass is constructed has a major influence on performance, especially growth rate.

Cuticular waxes of nectarines during fruit development in relation to surface conductance and susceptibility to Monilinia laxa.

The cuticle is composed of cutin and cuticular waxes, and it is the first protective barrier to abiotic and biotic stresses in fruit. In this study, we analysed the composition of and changes in cuticular waxes during fruit development in nectarine (Prunus persica L. Batsch) cultivars, in parallel with their conductance and their susceptibility to Monilinia laxa. The nectarine waxes were composed of triterpenoids, mostly ursolic and oleanolic acids, phytosterols, and very-long-chain aliphatics. In addition, we detected phenolic compounds that were esterified with sugars or with triterpenoids, which are newly described in cuticular waxes. We quantified 42 compounds and found that they changed markedly during fruit development, with an intense accumulation of triterpenoids during initial fruit growth followed by their decrease at the end of endocarp lignification and a final increase in very-long-chain alkanes and hydroxylated triterpenoids until maturity. The surface conductance and susceptibility to Monilinia decreased sharply at the beginning of endocarp lignification, suggesting that triterpenoid deposition could play a major role in regulating fruit permeability and susceptibility to brown rot. Our results provide new insights into the composition of cuticular waxes of nectarines and their changes during fruit development, opening new avenues of research to explore brown rot resistance factors in stone fruit.

Model-assisted analysis of the peach pedicel-fruit system suggests regulation of sugar uptake and a water-saving strategy.

We develop a model based on the biophysical representation of water and sugar flows between the pedicel, fruit xylem and phloem, and the fruit apoplast and symplast in order to identify diurnal patterns of transport in the pedicel-fruit system of peach. The model predicts that during the night water is mainly imported to the fruit through the xylem, and that fruit phloem-xylem transfer of water allows sugar concentrations in the phloem to be higher in the fruit than in the pedicel. This results in relatively high sugar transport to the fruit apoplast, leading to relatively high sugar uptake by the fruit symplast despite low sugar concentrations in the pedicel. At midday, the model predicts a xylem backflow of water driven by a lower pressure potential in the xylem than in the fruit apoplast. In addition, fruit xylem-to-phloem transfer of water decreases the fruit phloem sugar concentration, resulting in moderate sugar uptake by the fruit symplast, despite the high sugar concentration in the pedicel. Globally, the predicted fruit xylem-phloem water transfers buffer the sugar concentrations in the fruit phloem and apoplast, leading to a diurnally regulated uptake of sugar. A possible fruit xylem-to-apoplast recirculation of water through the fruit phloem reduces water lost by xylem backflow at midday.

Fruit water content as an indication of sugar metabolism improves simulation of carbohydrate accumulation in tomato fruit.

Although fleshy fruit is mainly made up of water, little is known about the impact of its water status on sugar metabolism and its composition. In order to verify whether fruit water status is an important driver of carbohydrate composition in tomato fruit, an adaptation of the SUGAR model proposed previously by M. Génard and M. Souty was used. Two versions of the model, with or without integrating the influence of fruit water content on carbohydrate metabolism, were proposed and then assessed with the data sets from two genotypes, Levovil and Cervil, grown under different conditions. The results showed that, for both genotypes, soluble sugars and starch were better fitted by the model when the effects of water content on carbohydrate metabolism were taken into consideration. Water content might play a regulatory role in the carbon metabolism from sugars to compounds other than sugars and starch in Cervil fruit, and from sugars to starch in Levovil fruit. While water content influences tomato fruit carbohydrate concentrations by both metabolism and dilution/dehydration effects in the early developmental stage, it is mainly by dilution/dehydration effects in the late stage. The possible mechanisms underlying the effect of the fruit water content on carbohydrate metabolism are also discussed.

Model-assisted comparison of sugar accumulation patterns in ten fleshy fruits highlights differences between herbaceous and woody species.

BACKGROUND AND AIMS: Sugar concentration is a key determinant of fruit quality. Soluble sugars and starch concentrations in fruits vary greatly from one species to another. The aim of this study was to investigate similarities and differences in sugar accumulation strategies across ten contrasting fruit species using a modelling approach. METHODS: We developed a coarse-grained model of primary metabolism based on the description of the main metabolic and hydraulic processes (synthesis of compounds other than sugar and starch, synthesis and hydrolysis of starch, and water dilution) involved in the accumulation of soluble sugars during fruit development. KEY RESULTS: Statistical analyses based on metabolic rates separated the species into six groups according to the rate of synthesis of compounds other than sugar and starch. Herbaceous species (cucumber, tomato, eggplant, pepper and strawberry) were characterized by a higher synthesis rate than woody species (apple, nectarine, clementine, grape and kiwifruit). Inspection of the dynamics of the processes involved in sugar accumulation revealed that net sugar importation, metabolism and dilution processes were remarkably synchronous in most herbaceous plants, whereas in kiwifruit, apple and nectarine, processes related to starch metabolism were temporally separated from other processes. Strawberry, clementine and grape showed a distinct dynamic compared with all other species. CONCLUSIONS: Overall, these results provide fresh insights into species-specific regulatory strategies and into the role of starch metabolism in the accumulation of soluble sugars in fleshy fruits. In particular, inter-specific differences in development period shape the co-ordination of metabolic processes and affect priorities for carbon allocation across species. The six metabolic groups identified by our analysis do not show a clear separation into climacteric and non-climacteric species, possibly suggesting that the metabolic processes related to sugar concentration are not greatly affected by ethylene-associated events.

Model-based QTL detection is sensitive to slight modifications in model formulation.

Classical crop models have been developed to predict crop yield and quality, and they are based on physiological and environmental inputs. After molecular discoveries, models should integrate genetic variation to allow predictions that are more genotype-dependent. An interesting approach, Quantitative Trait Locus (QTL)-based ecophysiological modeling, has shown promising results for the design of ideotypes that are adapted to biotic and abiotic stresses, but there are still limitations to attaining a fully integrated model. The aim of this case study is to clarify the impact of choosing different model equations (closely related and with different numbers of parameters) and optimization methods on the detection of QTLs controlling the parameters of crop growth. Different growth equations were parameterized based on a genetic population by following different approaches. The correlations between parameters were analyzed, and two different strategies were adopted to address the correlation issue. QTL analysis was performed on the optimized values of the parameters of the growth equations and on the observed dry mass (DM) data to validate the QTLs detected. Overall, models and strategies resulted in different QTLs being detected. Similar LOD profiles but with peaks of different heights were observed, some of which were significant, resulting in different numbers of QTLs. In some cases, peaks had slightly different positions or were absent. Even closely related growth models led to the detection of different QTLs. The goodness of fit and complexity of the growth models were found to be insufficient to select the best model. Calculating parameters independently of observed data may not be a good strategy, whereas setting parameters independent of the genotype is recommended. Given the large-scale global optimization problem and the strong correlations between parameters, the two algorithms tested showed poor performance. Currently, the lack of effective algorithms is the main obstacle to answering the question posed. The authors therefore suggest testing different model formulations and comparing the QTLs detected before choosing the best formulation to use in an ecophysiological modeling approach based on QTLs.

Organ-wide and ploidy-dependent regulation both contribute to cell-size determination: evidence from a computational model of tomato fruit.

The development of a new organ is the result of coordinated events of cell division and expansion, in strong interaction with each other. This study presents a dynamic model of tomato fruit development that includes cell division, endoreduplication, and expansion processes. The model is used to investigate the potential interactions among these developmental processes within the context of the neo-cellular theory. In particular, different control schemes (either cell-autonomous or organ-controlled) are tested and compared to experimental data from two contrasting genotypes. The model shows that a pure cell-autonomous control fails to reproduce the observed cell-size distribution, and that an organ-wide control is required in order to get realistic cell-size variations. The model also supports the role of endoreduplication as an important determinant of the final cell size and suggests that a direct effect of endoreduplication on cell expansion is needed in order to obtain a significant correlation between size and ploidy, as observed in real data.

Coupling epidemiological and tree growth models to control fungal diseases spread in fruit orchards.

Agronomic practices can alter plant susceptibility to diseases and represent a promising alternative to the use of pesticides. Yet, they also alter crop quality and quantity so that the evaluation of their efficacy is not straightforward. Here we couple a compartmental epidemiological model for brown rot diffusion in fruit orchards with a fruit-tree growth model explicitly considering the role of agronomic practices over fruit quality. The new modelling framework permits us to evaluate, in terms of quantity and quality of the fruit production, management scenarios characterized by different levels of regulated deficit irrigation and crop load. Our results suggest that a moderate water stress in the final weeks of fruit development and a moderate fruit load provide effective control on the brown rot spreading, and eventually guarantee monetary returns similar to those that would be obtained in the absence of the disease.

Coupling water fluxes with cell wall mechanics in a multicellular model of plant development.

The growth of plant organs is a complex process powered by osmosis that attracts water inside the cells; this influx induces simultaneously an elastic extension of the walls and pressure in the cells, called turgor pressure; above a threshold, the walls yield and the cells grow. Based on Lockhart's seminal work, various models of plant morphogenesis have been proposed, either for single cells, or focusing on the wall mechanical properties. However, the synergistic coupling of fluxes and wall mechanics has not yet been fully addressed in a multicellular model. This work lays the foundations of such a model, by simplifying as much as possible each process and putting emphasis on the coupling itself. Its emergent properties are rich and can help to understand plant morphogenesis. In particular, we show that the model can display a new type of lateral inhibitory mechanism that amplifies growth heterogeneities due e.g to cell wall loosening.

A simulation study of synergies and tradeoffs between multiple ecosystem services in apple orchards.

In this study, we analyzed the patterns of relationships between multiple ecosystem services in apple orchards by considering the cascade that links agricultural practices to ecosystem functions and then to ecosystem services. Five major ecosystem services were considered: fruit production, soil nitrogen availability, climate regulation, water cycle maintenance and regulation, including water quality, and pest and disease control. We derived indicators of ecosystem functions and of ecosystem services from model simulations of orchards driven by virtual cropping systems combining various modalities of nitrogen fertilization, irrigation, and pest control. We deciphered the links between practices and ecosystem functions and between those functions and ecosystem services and clustered cropping systems according to their ecosystem service supply. Noticeable synergies were found between yield, fruit mass and sequestrated carbon. The contribution of carbon allocation to fruit in sequestrated carbon was considerable. Nitrogen absorption, impacted by fertilization and irrigation, was a major driver of these relationships. The typology built from these virtual cropping systems clearly followed a gradient of provisioning and regulating ecosystem services. Five cropping systems optimized the compromise between provisioning and regulating services and were essentially characterized by organo-mineral fertilization, comfort irrigation, apple scab-resistant cultivars and exclusion nets against codling moth. Our approach could contribute to the design of cropping systems that would provide an acceptable compromise between multiple ecosystem services in orchards.

Modelling grape growth in relation to whole-plant carbon and water fluxes.

The growth of fleshy fruits is still poorly understood as a result of the complex integration of water and solute fluxes, cell structural properties, and the regulation of whole plant source-sink relationships. To unravel the contribution of these processes to berry growth, a biophysical grape (Vitis vinifera L.) berry growth module was developed and integrated with a whole-plant functional-structural model, and was calibrated on two varieties, Cabernet Sauvignon and Sangiovese. The model captured well the variations in growth and sugar accumulation caused by environmental conditions, changes in leaf-to-fruit ratio, plant water status, and varietal differences, with obvious future application in predicting yield and maturity under a variety of production contexts and regional climates. Our analyses illustrated that grapevines strive to maintain proper ripening by partially compensating for a reduced source-sink ratio, and that under drought an enhanced berry sucrose uptake capacity can reverse berry shrinkage. Sensitivity analysis highlighted the importance of phloem hydraulic conductance, sugar uptake, and surface transpiration on growth, while suggesting that cell wall extensibility and the turgor threshold for cell expansion had minor effects. This study demonstrates that this integrated model is a useful tool in understanding the integration and relative importance of different processes in driving fleshy fruit growth.