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Crop health management systems can be designed according to practices that help to reduce crop losses by restricting pathogen development and promoting host plant growth. A good understanding of pathogen and host dynamics, which are interdependent, is therefore needed. In this article, we used a holistic approach to explain the behavior of coffee leaf rust (CLR), a major coffee disease. We monitored coffee plant and CLR dynamics simultaneously in plots under different disease management and agroforestry systems. Diseased leaves were also collected to characterize inoculum stock and rust life stages (latent rust area, area with uredospores, necrosis due to rust) through picture analysis. We used structural equation modeling to obtain an overview of CLR pathosystem functioning on a plant scale. This overview integrates processes such as disease dilution by host leaf renewal, direct and indirect effects of fruit load on CLR development, antagonistic effects of shading depending on rust life stages, the tonic effect of copper-based fungicides on leaf retention, and effects on rust life stages depending on fungicide types. From our results, we also deduced that the inoculum stock could be calculated in unsprayed plots from the rust area with uredospores, with uredospores at 58 × 103 cm−2, on average.

International audience; The vulnerability of forest species and tree populations to climate change is related to the exposure of the ecosystem to extreme climatic conditions and to the adaptive capacity of the population to cope with those conditions. Adaptive capacity is a relatively under-researched topic within the forest science community and there is an urgent need to understand to what extent particular combinations of traits have been shaped by natural selection under climatic gradients, potentially resulting in adaptive multi-trait associations. Thus, our aim was to quantify genetic variation in several leaf and woody traits that may contribute to multi-trait associations in which intraspecific variation could represent a source for species adaptation to climate change. A multi-trait approach was performed using nine Quercus petraea provenances originating from different locations that cover most of the species' distribution range over Europe and that were grown in a common garden. Multiple adaptive differences were observed between oak provenances but also some evolutionary stasis. Also, our results revealed higher genetic differentiation in traits related to phenology and growth than in those related to xylem anatomy, physiology and hydraulics for which no genetic differentiation was observed. The multiple associations between those traits and climate variables resulting from multivariate and path analyses suggest a multi-trait association largely involving phenological and growth traits for Quercus petraea. © The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Correction added on 07 May 2021, after first online publication: some minor wording changes have been made in the article; International audience; PREMISE: The expression of shade adaptation traits is expected to be stronger in low light and can be detrimental to flowering and yield. Our study focused on the expression of shade adaptation traits of apple trees (Malus domestica Borkh. ‘Dalinette’) in an agroforestry system.METHODS: The architecture of 45 apple trees in their third and fourth year was extensively described and analyzed at the tree scale and compared depending on the light quantity received during the growing season. Flower cluster phenology and the relation between leaf area and floral initiation were also investigated.RESULTS: The number of growing shoots and the leaf area were reduced by shade even if specific leaf area increased with increasing shade. Shade did not modify primary growth but did decrease secondary growth, so that apple tree shoots in shade were slender, with a lower taper and reduced number and proportion of flower clusters. The correlation between floral initiation and leaf area was high both in full and moderate light but not for apple trees in low light. Shade did not impact the date of bud burst and the early phenological stages of flower clusters, but it reduced the number of days at full bloom.CONCLUSIONS: Our results suggest that while the architecture of apple trees is modified by a reduction in light intensity, it is not until a reduction of 65% that the capability to produce fruit is impeded. These results could help optimize the design of apple-tree-based agroforestry systems.

Dacryodes edulis (G. Don) H.J. Lam is an underexploited oil-bearing fruit tree highly appreciated in the Central Africa rainforest. To improve horticultural management and provide relevant data to scientists for physiological studies, the reproductive phenology of D. edulis as well as their fruit (safou) development and ripening indexes has been defined and correlated to climatic conditions. Changes in safou were assessed in four production localities in Cameroon. Fruit-set-to-ripening time was evaluated over 2 consecutive production years. Four fruits developmental and ripening stages and their durations were determined as follows: The putative cell division (1–2 weeks); putative elongation (10–14 weeks); pre-ripening (2–7 weeks); and ripening phases (3–5 weeks). Rainfall, average, and cumulative temperatures were found to be correlated with the chronology of reproductive phenophases. The average temperature during the period ranging from the floral bud emergence to the fruit set can be used to predict the thermal time. Similarly, the average ambient temperature during the period from floral bud emergence to anthesis can help to determine the temperature to be cumulated during the ripening phase. These findings are considerable contributions that could help producers to enhance the industrial management of safou sector, reduce fruit perishability, and better control their harvesting time.

International audience; Rubber powdery mildew disease (Oidium heveae) is a serious threat to natural rubber production (Hevea brasiliensis) in some rubber developing regions of the world. Both phenological- and meteorological-related factors have been reported influencing the powdery mildew disease. However, few studies have investigated the effects of both phenological- and meteorological-related factors on the disease. The objective of this study is to quantify the contributions of phenological- and meteorological-related factors to affect the disease. We used the partial least squares (PLS) regression method to comprehensively quantify the effects of thirty-five phenological related factors and six meteorological factors on the infection level of powdery mildew of rubber trees over 9-year records (2003–2011). The relative contributions of significant factors were further investigated by the variation partition analysis. We found that the most influential variables were the mean temperature during winter and the duration of leaf development to maturation which explained 32 and 26% of the variations in the infection level. We found the controlling role of winter mean temperature, for the first time, on the infection level of powdery mildew. The controlling role of winter temperature may have directly increase the infection level when winter temperature is high and indirectly increase the infection level through prolonging the duration of leaf development to maturation, although the duration itself had smaller influences. We detected a warming trend of the winter temperatures from 2003 to 2011, which indicates that the infection level of powdery mildew will be increased if the winter warming continues.

The quinoa pest Copitarsia incommoda (Walker, Lepidoptera: Noctuidae) is a cause of significant damage, and it is thus critical for Andean countries to have access to phenological models to maintain production and food safety. These models are key components in pest control strategies in the context of global warming and in the development of sustainable production integrating agroecological concepts. Phenological models are mainly based on outlining the relationship between temperature and development rate. In this study, we investigated the combined effect of protein content within the diet (artificial diet; artificial diet with −20% protein; artificial diet with +20% protein; natural quinoa diet) and temperature (12, 16.9, 19.5, 22.7, 24.6°C) as drivers of the development rate. Our study supports the literature, since temperature was found to be the main driver of the development rate. It highlights the significant role played by protein content and its interaction with temperature (significant effects of temperature, diet, and diet:temperature on development time using GLMs for all foraging life stages). We discuss the implications of such drivers of the development rate for implementing and applying phenological models that may benefit from including factors other than temperature. While performance curves such as development rate curves obtained from laboratory experiments are still a useful basis for phenological development, we also discuss the need to take into account the heterogeneity of the insect response to environmental factors. This is critical if pest control practices are to be deployed at the optimal time.

International audience; Phenology—the timing of life-history events—is a key trait for understanding responses of organisms to climate. The digitization and online mobilization of herbarium specimens is rapidly advancing our understanding of plant phenological response to climate and climatic change. The current practice of manually harvesting data from individual specimens, however, greatly restricts our ability to scale-up data collection. Recent investigations have demonstrated that machine-learning approaches can facilitate this effort. However, present attempts have focused largely on simplistic binary coding of reproductive phenology (e.g., presence/absence of flowers). Here, we use crowd-sourced phenological data of buds, flowers, and fruits from >3,000 specimens of six common wildflower species of the eastern United States (Anemone canadensis L., A. hepatica L., A. quinquefolia L., Trillium erectum L., T. grandiflorum (Michx.) Salisb., and T. undulatum Wild.) to train models using Mask R-CNN to segment and count phenological features. A single global model was able to automate the binary coding of each of the three reproductive stages with >87% accuracy. We also successfully estimated the relative abundance of each reproductive structure on a specimen with ≥90% accuracy. Precise counting of features was also successful, but accuracy varied with phenological stage and taxon. Specifically, counting flowers was significantly less accurate than buds or fruits likely due to their morphological variability on pressed specimens. Moreover, our Mask R-CNN model provided more reliable data than non-expert crowd-sourcers but not botanical experts, highlighting the importance of high-quality human training data. Finally, we also demonstrated the transferability of our model to automated phenophase detection and counting of the three Trillium species, which have large and conspicuously-shaped reproductive organs. These results highlight the promise of our two-phase crowd-sourcing and machine-learning pipeline to segment and count reproductive features of herbarium specimens, thus providing high-quality data with which to investigate plant responses to ongoing climatic change.

International audience; Herbarium specimens represent an outstanding source of material with which to study plant phenological changes in response to climate change. The fine‐scale phenological annotation of such specimens is nevertheless highly time consuming and requires substantial human investment and expertise, which are difficult to rapidly mobilize.Methods: We trained and evaluated new deep learning models to automate the detection, segmentation, and classification of four reproductive structures of Streptanthus tortuosus (flower buds, flowers, immature fruits, and mature fruits). We used a training data set of 21 digitized herbarium sheets for which the position and outlines of 1036 reproductive structures were annotated manually. We adjusted the hyperparameters of a mask R‐CNN (regional convolutional neural network) to this specific task and evaluated the resulting trained models for their ability to count reproductive structures and estimate their size.Results: The main outcome of our study is that the performance of detection and segmentation can vary significantly with: (i) the type of annotations used for training, (ii) the type of reproductive structures, and (iii) the size of the reproductive structures. In the case of Streptanthus tortuosus , the method can provide quite accurate estimates (77.9% of cases) of the number of reproductive structures, which is better estimated for flowers than for immature fruits and buds. The size estimation results are also encouraging, showing a difference of only a few millimeters between the predicted and actual sizes of buds and flowers.Discussion: This method has great potential for automating the analysis of reproductive structures in high‐resolution images of herbarium sheets. Deeper investigations regarding the taxonomic scalability of this approach and its potential improvement will be conducted in future work.

International audience; Highlights:• The most diversified groups of predatory ants had a significant negative top down effect on CBB infestation.• Higher % of shade favours CBB infestation.• Regulation of CBB depends on the balance between the effects of local (in plot) and global (farm level) variables.• Farmers practices could be efficient to manage CBB and to reduce related damage.• Holistic approach is required to characterize more precisely regulating network in agroforestry systems.Abstract:Pest regulation in agroforestry systems (AFS) is beginning to be well-recognized, but the mechanisms implied in the interaction network between the environment, pests and predators in AFS are still not well-described. The aim of this work is to understand how plant diversity associated with AFS regulates the coffee berry borer (CBB) taking into account a tripartite interaction network: pest–predator–environment. It further seeks to understand how farmers' management practices can modify the regulating network. Using field data from coffee-based AFS and structural equation modeling, we assessed the effects of environmental conditions (% shade cover, tree area surface, coffee density) and farm management (conventional, integrated, organic) on (1) ant predatory groups, (2) the abundance and the damage from CBB and (3) their interactions. Percentage of shade cover was positively correlated to CBB initial infestation (through direct effect) and negatively through its effect on coffee phenology. A higher percentage of shade is also negatively related to damage intensity. Farmers’ practices significantly reduced the CBB population without considerable side effects on the ant predatory group, probably due to the high plant diversity within these farms. The abundance of the most diversified ant predatory group has a top-down effect on the peak of the CBB infestation rate. Our approach appears promising for a better understanding of the complex regulating network in coffee AFS and confirms the importance of an integrated management strategy to reduce CBB damage.

Background and AimsLike other clades, the Coffea genus is highly diversified on the island of Madagascar. The 66 endemic species have colonized various environments and consequently exhibit a wide diversity of morphological, functional and phenological features and reproductive strategies. The trends of interspecific trait variation, which stems from interactions between genetically defined species and their environment, still needed to be addressed for Malagasy coffee trees.MethodsData acquisition was done in the most comprehensive ex situ collection of Madagascan wild Coffea. The structure of endemic wild coffees maintained in an ex situ collection was explored in terms of morphological, phenological and functional traits. The environmental (natural habitat) effect was assessed on traits in species from distinct natural habitats. Phylogenetic signal (Pagel’s λ, Blomberg’s K) was used to quantify trait proximities among species according to their phylogenetic relatedness.Key ResultsDespite the lack of environmental difference in the ex situ collection, widely diverging phenotypes were observed. Phylogenetic signal was found to vary greatly across and even within trait categories. The highest values were exhibited by the ratio of internode mass to leaf mass, the length of the maturation phase and leaf dry matter content (ratio of dry leaf mass to fresh leaf mass). By contrast, traits weakly linked to phylogeny were either constrained by the original natural environment (leaf size) or under selective pressures (phenological traits).ConclusionsThis study gives insight into complex patterns of trait variability found in an ex situ collection, and underlines the opportunities offered by living ex situ collections for research characterizing phenotypic variation.

International audience; Understanding the processes driving plant phenology is crucial for assessing how shifts in climate affect plant productivity and species’ distribution. Despite the key role of fine roots in carbon and nutrient cycling, root phenology is less well characterized than shoot phenology, due largely to methodological problems when measuring root systems at depths > 1.0 m. Fine root demography is also poorly related to the better established patterns of aboveground primary and secondary growth. We examined the influence of climatic factors on the dynamics of fine root elongation rate (RER), to a depth of 4.7 m, and assessed relationships with shoot phenology of walnut trees (Juglans nigra × J. regia) in a Mediterranean agroforestry system. Rhizotrons and minirhizotrons were installed for 21 months to monitor RER. Dendrometers were used to measure trunk and lateral root radial growth during the same period. Results showed that RER was not synchronous with budbreak and leaf unfolding (occurring from April to May) at any soil depth. However, during phase 2 of the growing season (June–November), daily RER in the upper soil (0.00–1.70 m) was synchronous with both trunk and lateral root radial growth, which were themselves positively correlated with the mean monthly soil and air temperatures and the mean monthly solar irradiance. Mean daily RER was not correlated to mean monthly soil and air temperatures at any soil depth during phase 2 of the growing season. However, during this period, mean daily RER of very shallow roots (0.00–0.85 m) was significantly and positively correlated with both mean monthly soil water content and solar irradiance. Maximal daily RER occurred during phase 2 of the growing season for the three upper soil layers (June–October), but peaked during the aerial dormant season (December) in the deepest soil layer (4.00–4.70 m). We conclude that drivers of phenology for different tree organs and between shallow and deep roots are not the same. This spatial plasticity in growth throughout a tree enables it to maximize resource uptake, even throughout the winter months, and thus is a highly useful mechanism for increasing tree resistance to abiotic stresses.

International audience; Rubber powdery mildew caused by the foliar fungiOidium heveaeis one of the main diseases affecting rubber plantations (Hevea brasiliensis) worldwide. It is particularly serious in sub-optimal growing areas, such as Xishuangbanna in SW China. To prevent and control this disease, fungicides causing serious environmental problems are widely used. Strong correlations between the infection level and the temperature variables were reported previously, but they were related to monthly data that did not allow unraveling the patterns during the entire sensitive period. We correlated the infection level of powdery mildew of rubber trees recorded over 2003-2011 with antecedent 365 days daily temperature variables using partial least squares (PLS) regression. Our PLS regression results showed that the infection level of powdery mildew responded differently to the temperature variables of the defoliation and refoliation periods. Further analysis with Kriging interpolation showed that the infection level increased by 20% and 11%, respectively, per 1 degrees C rise of the daily maximum and mean temperature in the defoliation season, while it decreased by 8% and 10%, respectively, per 1 degrees C rise of the daily maximum and temperature difference in the refoliation season. This pattern was likely linked to the effects of temperature on leaf phenology. It seems highly possible that the infection level of powdery mildew increases, as increasing trends of maximum temperature and mean temperature during the defoliation continue.

AGAP; International audience; In West Africa Sudano-Sahelian zone, sorghum sensitivity to photoperiod is a major trait for flowering adjustment toward the end of the rainy season. This trait ensures that conditions for crop development are optimal. Improving the understanding of the genetic control of flowering time in sorghum is thus an important step toward breeding climate resilient varieties for meeting the challenge of climate smart agriculture. In the wake of green revolution, most sorghum breeders eliminated photoperiod sensitivity to develop early maturing varieties. The evidence is now that simultaneous improvement of production, yield stability and grain quality requires the development of photoperiod-sensitive varieties. A segregating sorghum population derived from a cross between two photoperiod sensitive elite parents was evaluated in three different locations and five environments. CERES crop model was applied to decompose the flowering time of each genotype into basic vegetative phase, critical photoperiod and photoperiod sensitivity. Phenology and model derived variables were used for genetic analysis. The three model parameters were controlled by specific genomic regions. A major QTL affecting critical photoperiod was identified, whereas only independent minor QTLs were found for basic vegetative phase and photoperiod sensitivity. Candidate gene analysis in the major QTL region allowed us to propose a candidate gene (ELF3) involved in the circadian clock as a key regulator of flowering time in photoperiod-sensitive sorghum. Our findings provide critical information supporting the development of photoperiod-sensitive genotypes specifically adapted to climate variability encountered in Sudano-Sahelian zone.

A quantitative method was tested to describe crown phenophases in relation to water content and to secondary growth in ring-porous species, based on the hypothesis that new shoots require hydrated tissues to maintain the necessary turgor for extension, leading to a reduction in dry matter content (DMC). We collected a three-year-old branch from 11 Quercus pyrenaica Willd. trees at 10-day intervals to estimate DMC of newly developing buds, leaves, and twigs, and processed two opposite stem microcores for xylogenesis. Branch phenophases and shoot length were recorded in the field. The DMC of all organs decreased during crown development, with a minimum in early June, followed by a gradual increase up to initial values in late September. The shoot extension period concurred with the lowest DMC, but also with the beginning of earlywood maturation in the main stem, suggesting a high tissue hydration only when earlywood vessels become functional to fulfill enough water requirements for shoot and leaf extension. These results confirm the usefulness of DMC to accurately quantify the phenology of primary growth from bud swelling up to full leaf extension, as a complement to qualitative methods. This variation in DMC appears to be linked to secondary growth as a result of earlywood vessel development.

Apple tree bloom onset in Germany has advanced by 2 days/decade in 1951-2014 and by 3 days/decade in 1988-2014, behaving similarly in respect to its evolution since 1951 and its sensitivity to temperature to other species’ phenological spring phases. The evolution however was not linear; by conducting a split moving-window dissimilarity analysis (SMWDA) we were able to detect the “break-period” 1987-1989 which coincides with a breakpoint that has been identified in the phases of the North Atlantic Oscillation (NAO). We observed distinct spatial patterns with apple bloom advancing from southwest to northeast and, most interestingly, a longitudinal gradient in the trend of apple bloom onset revealed by a probabilistic principal components analysis (PPCA). In the period of 1951-2014, plants located in the east displayed a much stronger trend (‑16.53 days on average) than those in the western part of the country (‑6.74 days on average). This pattern seems to be linked to patterns in temperature which is highly correlated to apple bloom onset (best one predictor model: mean temperature March to May, R² = 0.82, ‑6 days/°C): the coldest regions exhibit the strongest warming trends and the greatest advances in apple bloom onset., Les dates de floraison des pommiers en Allemagne ont en moyenne avancé de 2 jours/décade de 1951 à 2014 et de 3 jours/décade de 1988 à 2014, en accord avec l’évolution des phases phénologiques d’autres espèces. Cependant, cette évolution n’a pas été linéaire : en réalisant une analyse de dissimilarité d’une fenêtre glissante fractionnée (SMWDA), nous avons détecté une période de rupture entre 1987 et 1989 qui coïncide avec un point de rupture qui a été identifié dans les phases de l’oscillation nord-atlantique (ONA). Nous avons également pu constater une structuration spatiale : la floraison des pommiers progresse du sud-ouest du pays au nord-est ; en termes de variabilité interannuelle des dates de floraison, il existe, superposé à un mode principal commun à l’ensemble du pays, un gradient longitudinal qui a été révélé par une analyse probabiliste en composantes principales (PPCA). Entre 1951 et 2014, la tendance à la précocité est plus marquée à l’est du pays (en moyenne ‑16,53 jours) qu’à l’ouest (en moyenne ‑6,74 jours) et la floraison des pommiers est très étroitement liée à la variabilité des températures moyennes de mars à mai (R² = 0,82 ; ‑6 jours/°C). Les régions les plus froides montrent les tendances les plus importantes au réchauffement et à la précocité de la floraison.

International audience; In the Toba Highlands of North Sumatra (Indonesia), coffee production (Coffea arabica L. var. Sigarar Utang) is an important outcome for smallholders; however, the attack of the coffee berry borer (CBB) Hypothenemus hampei, is an obstacle for the development of coffee cultivation in this area. This pest causes great economic losses produced by the development of its offspring inside the coffee berries, making it difficult to control. This concerning situation has led us to consider the development of a CBB control strategy, but beforehand, it was necessary to acquire key information on the phenology of the coffee tree and its implication on the bioecology of the pest. Thus, two study designs were set up, one comprising six plots with two different age classes and the other corresponding to a single plot dedicated only to the study of short distance dispersal of CBB. Part of this study focused on the phenology of the coffee trees and showed that berry production mainly takes place in the upper parts of the trees and significantly decreases with tree age. Due to the equatorial climate, berries were practically always present. Berries were produced following two major flowering periods and some minor ones distributed over the year, and harvested at regular intervals. Berry distribution on the branches varied over time. Dynamics of infestations by CBB showed that ripe berries were more infested than unripe berries because they had been exposed longer to CBB attacks, that older trees were more exposed than younger trees and that infestation was evenly distributed along branches. In addition, internode pedestrian dispersal of CBBs was shown to occur, but considerably less frequently than airborne dispersal. In conclusion, it appears that in the agro-climatic context of the Toba region, the virtual year-round presence of berries - which fosters CBB infestations and CBB short-distance dispersal - is a constraint that must be taken into consideration for designing future pest management measures. To this end, it will be necessary in particular to evaluate the potential of trapping mainly used in tropical areas and to put into practice the sanitation harvesting applied in other countries.

Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology. The objectives were to improve the RIDEV model of rice thermal sterility, to estimate response traits by fitting model parameters, and to link the response traits to genomic regions through genome-wide association studies (GWAS). RIDEV captured 64% of variation of sterility when cold acclimation during vegetative stage was simulated, but only 38% when it was not. The RIDEV parameters gave more and stronger quantitative trait loci (QTLs) than index variables derived more directly from observation. The 15 QTLs identified at P

Phenology and time of flowering are crucial determinants of rice adaptation to climate variation. A previous study characterized flowering responses of 203 diverse indica rices (the ORYTAGE panel) to ten environments in Senegal (six sowing dates) and Madagascar (two years and two altitudes) under irrigation in the field. This study used the physiological phenology model RIDEV V2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (Tbase) and optimum temperature), basic vegetative phase, photoperiod sensitivity and cold acclimation, and to conduct a genome-wide association study for these traits using 16 232 anonymous single-nucleotide polymorphism (SNP) markers. The RIDEV model after genotypic parameter optimization explained 96% of variation in time to flowering for Senegal alone and 91% for Senegal and Madagascar combined. The latter was improved to 94% by including an acclimation parameter reducing Tbase when the crop experienced low temperatures during early vegetative development. Eighteen significant (P

Background and Aims Mango (Mangifera indica L.) is the fifth most widely produced fruit in the world. Its cultivation, mainly in tropical and sub-tropical regions, raises a number of issues such as the irregular fruit production across years, phenological asynchronisms that lead to long periods of pest and disease susceptibility, and the heterogeneity of fruit quality and maturity at harvest. To address these issues, we developed an integrative functional–structural plant model that synthesizes knowledge about the vegetative and reproductive development of the mango tree and opens up the possible simulation of cultivation practices. Methods We designed a model of architectural development in order to precisely characterize the intricate developmental processes of the mango tree. The appearance of botanical entities was decomposed into elementary stochastic events describing occurrence, intensity and timing of development. These events were determined by structural (position and fate of botanical entities) and temporal (appearance dates) factors. Daily growth and development of growth units and inflorescences were modelled using empirical distributions and thermal time. Fruit growth was determined using an ecophysiological model that simulated carbon- and water-related processes at the fruiting branch scale. Key Results The model simulates the dynamics of the population of growth units, inflorescences and fruits at the tree scale during a growing cycle. Modelling the effects of structural and temporal factors makes it possible to simulate satisfactorily the complex interplays between vegetative and reproductive development. The model allowed the characterization of the susceptibility of mango tree to pests and the investigatation of the influence of tree architecture on fruit growth. Conclusions This integrative functional–structural model simulates mango tree vegetative and reproductive development over successive growing cycles, allowing a precise characterization of tree phenology and fruit growth and production. The next step is to integrate the effects of cultivation practices, such as pruning, into the model.

Premise of the Study: Phenological annotation models computed on large‐scale herbarium data sets were developed and tested in this study. Methods: Herbarium specimens represent a significant resource with which to study plant phenology. Nevertheless, phenological annotation of herbarium specimens is time‐consuming, requires substantial human investment, and is difficult to mobilize at large taxonomic scales. We created and evaluated new methods based on deep learning techniques to automate annotation of phenological stages and tested these methods on four herbarium data sets representing temperate, tropical, and equatorial American floras. Results: Deep learning allowed correct detection of fertile material with an accuracy of 96.3%. Accuracy was slightly decreased for finer‐scale information (84.3% for flower and 80.5% for fruit detection). Discussion: The method described has the potential to allow fine‐grained phenological annotation of herbarium specimens at large ecological scales. Deeper investigation regarding the taxonomic scalability of this approach is needed.

International audience; Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.

This study focused on leaf and root density dynamics of the most dominant tree species (Vitellaria paradoxa) of West African savannas in two land use types (farmed land and forest). Ten trees located at least 100 m from each other were selected, with five trees each located in the field and in the forest. Five of the trees were of small-diameter [two in the fields (diameter at breast height or DBH 20.1–20.7 cm) and three in the forest (DBH 7.0–8.0–10.8 cm)] and five others were of large-diameter [three in the fields (DBH 38.2–81.8–81.9 cm) and two in the forest (DBH 20.1–20.7 cm)]. One near-vertical rhizotron was installed under each tree to evaluate root density while canopy openness, diffuse and directly transmitted light were monitored by taking hemispheric photograph monthly. After a two-year period of monitoring, the results revealed a strong seasonality in root density with peak root density observed during the rainy season in August and the lowest production during the dry season in April. Significant lowest canopy openness was observed from August to September while the highest occurred from March to May, which was found to be synchronous with fine root dynamics. The light interception followed the same trends as the leaf production. Furthermore, both mature and young trees showed significant higher root density in the fields compared to the forest while the mean values of all the parameters of canopy openness and light transmittance were higher in the forest than the fields.

International audience; Temperate plants are at risk of being exposed to late spring freezes. These freeze events—often called false springs—are one of the strongest factors determining temperate plants species range limits and can impose high ecological and economic damage. As climate change may alter the prevalence and severity of false springs, our ability to forecast such events has become more critical, and it has led to a growing body of research. Many false spring studies largely simplify the myriad complexities involved in assessing false spring risks and damage. While these studies have helped advance the field and may provide useful estimates at large scales, studies at the individual to community levels must integrate more complexity for accurate predictions of plant damage from late spring freezes. Here we review current metrics of false spring, and how, when and where plants are most at risk of freeze damage. We highlight how life stage, functional group, species differences in morphology and phenology, and regional climatic differences contribute to the damage potential of false springs. More studies aimed at understanding relationships among species tolerance and avoidance strategies, climatic regimes, and the environmental cues that underlie spring phenology would improve predictions at all biological levels. An integrated approach to assessing past and future spring freeze damage would provide novel insights into fundamental plant biology, and offer more robust predictions as climate change progresses, which is essential for mitigating the adverse ecological and economic effects of false springs.

International audience; Aim: The success of inflorescence primordia initiation and differentiation within latent buds (i.e. bud fruitfulness) is a critical issue for grapevine yield sustainability under climate change. The aim of the present study was to track the timing and rate of inflorescence development in latent buds along the cane and to quantify their responses to elevated day/night (D/N) temperatures. Methods and Results: The experiments were conducted under controlled conditions, using the microvine model, which is suitable for establishment in small areas. Two imagery methods for analyzing bud anatomy were assessed: light microscopy and x-ray microtomography. Light microscopy was laborious, but it was the most accurate method for investigating organogenesis in the primordial shoot of the latent bud. In plants grown in a greenhouse (D/N, 25°C/15°C), the number of phytomer primordia in latent buds increased linearly from the apical to the basal buds on the cane. A maximum of six phytomers and two inflorescence primordia were observed beneath the 20th bud position that is, slightly fewer than usually reported with macrovines. The first and second inflorescences started to differentiate at the 14th and 18th bud position, respectively. Temperature increases in the growth chamber (D/N, 20–30°C/15–25°C) only slightly changed the final number of preformed phytomers and the probability of inflorescence primordia differentiation per bud. However, elevated temperature sharply accelerated and thereby shortened development of the latent bud primordial shoot, resulting in differentiation of the first inflorescence primordia straight from the fifth bud position. Based on the spatiotemporal conversion of bud position into thermal time, the first inflorescence started to differentiate 332 growing degree days (°Cd) (or 41 days) after bud emergence at D/N 20°C/15°C, and only 98°Cd (or 5 days) after bud emergence at D/N 35°C/25°C. Finally, the number of preformed phytomers was shown to correlate with primary bud length and cane diameter, independent of temperature. These easily measured variables may be used as indicators of bud developmental stage and potential bud fruitfulness in further studies using the microvine. Conclusions: The microvine appears to be suitable for parameterizing a developmental model of grapevine latent buds under controlled environmental conditions and when evaluating the response to elevated D/N temperatures. Significance and impact of the study: The precise description of the timing and rate of differentiation of phytomers and inflorescences opens new perspectives for understanding the molecular processes underlying the response of bud fruitfulness to environmental constraints.

International audience; The diversity of herbivorous insects may arise from colonization and subsequent specialization on different host plants. Such specialization requires changes in several insect traits, which may lead to host race formation if they reduce gene flow among populations that feed on different plants. Behavioural changes may play a relevant role in host race formation, for example if different races evolve distinct sexual communication signals or adult phenology. Previous research has revealed differences in larval phenology in different host-associated populations of the browntail moth, Euproctis chrysorrhoea (Lepidoptera: Erebidae). Here, sex pheromones among populations of this species are compared, and pheromone trapping data obtained is used in the field to build a phenological model that tests whether populations that feed on different plants differ in their adult flight period. The chemical and electrophysiological analyses revealed that two E. chrysorrhoea populations (on Prunus and on Arbutus unedo) use the same sex pheromone component for mate finding. Our trapping data, however, showed that males fly on average 25 days earlier in populations whose larvae feed on A. unedo compared to those whose larvae feed on Quercus species. Although the shifted phenology described here may underlie host-plant specialization in E. chrysorrhoea, and adults of this species are short-lived, the use of a common sexual pheromone and a large overlap in flight periods suggest that host race formation via allochronic isolation is unlikely in this moth.

International audience; center dot Key message Spring temperature increase is the main driver of larch tree wood formation onset along a 1000-m elevation gradient in the Southern Alps, while its cessation is more probably controlled by water stress at the lowest elevation and photoperiod at higher ones. center dot Context The survival of perennial plants depends on their adaptation to changing environment and specially temperature, which in trees is notably implemented through wood formation process. center dot Aims Our main objective is to understand how the phenology of wood formation is related to environmental factors and to temperature in particular. center dot Methods We monitored the xylogenesis of 60 larch trees, distributed in four stands along an elevation gradient of 1000 m in the French Southern Alps. center dot Results Cambial activity started around mid-May at the lowest site (1350 m) and around mid-June at the highest one (2300 m), showing a delay of 5.4 days per degrees C. The onset of wall-thickening and mature phenophases followed the same linear trend with a delay of 5.2 and 3 days per degrees C, respectively. Phenophase cessations followed a parabolic trend with trees from the lowest site finishing their growth the first, while those from 1700 m finished the last. Our results show that the onset of xylem formation is mainly driven by spring temperature increase, while its cessation is more related to photoperiod, with water shortage being able to hasten it. center dot Conclusion Future climatic changes will most probably increase growing season length (but not necessarily wood production) and shift upwards the optimal elevation for larch growth in the Southern Alps.

Rubber ( Hevea brasiliensis ) growing in Latin America is severely limited by South American Leaf Blight, a disease caused by the Ascomycete fungus Microcyclus ulei , recently renamed Pseudocercospora ulei . Sustainable ways of controlling it may be genetic, using resistant cultivars, or may consist in seeking so-called “escape zones”, where disease incidence is low thanks to climatic conditions unsuitable for the fungus. After identifying one such zone on the Pacific coast of Ecuador, between 2006 and 2014 we used an 8.2 ha trial to compare the agronomic performance of ten rubber clones originating from Asia and Africa. The study focused on tree growth, susceptibility to the disease and clone phenology. For most of the assessed clones, the results obtained over 8 months showed good adaptability and a good agronomic performance during the immature period, so that tapping could begin on the earliest trees at 6½ years. An examination of the monthly values for climatic factors such as rainfall, relative humidity, minimum temperature and dew point temperature, showed that conditions during the dry season, which lasted 5 months, were detrimental to P. ulei fungus development, even though the mean relative humidity of the driest months did not fall below 75%. In addition, between September and December, the minimum temperature remained above the dew point temperature, preventing dew formation on the leaf surface. These conditions enabled the trees to complete their natural refoliation without any risk of parasite pressure, and to conserve a foliar density over 90% up to natural defoliation the following year. The results obtained during the early growing phase, i.e. the immature phase, confirmed the suitability of this zone for rubber growing, especially for materials with a high yield potential, despite their known susceptibility to the disease. These escape zones consequently offer an undeniable alternative for developing rubber, due to a low phytosanitary risk arising from P. ulei .

Recent outbreaks of highly pathogenic avian influenza virus (AIV) in birds, humans and other mammalian species calls for a better understanding of virus dynamics in wild bird species and populations that act as maintenance hosts. Host ecology influences the transmission of pathogens and can be used to explore and infer pathogen dynamics. Most of the ecological processes proposed to explain AIV transmission in wild birds have been derived from studies conducted in the temperate and boreal regions of the northern hemisphere. We evaluate the role of two key drivers of AIV dynamics in a waterfowl community in Zimbabwe (southern Africa): (1) the recruitment of young birds and (2) the seasonal aggregation of birds. We analyse the seasonal variation of AIV prevalence in waterfowl and overlay these data with the phenology of reproduction and the seasonal variation in the local abundance of these species. We find that the breeding period of southern Afrotropical waterfowl species is more extended and somewhat less synchronized among species in the community than is the case in temperate and boreal waterfowl communities. Young birds are recorded at most times of the year, and these immunologically naive individuals can therefore act as new hosts for AIV throughout the year within the wild bird population. Although host aggregation peaks in the cold-dry to hot-dry season, birds still aggregate throughout the year and this potentially spreads the opportunities for first infection of juveniles and other naive birds temporally. We did not find a relationship between season, AIV prevalence in waterfowl, the influx of juveniles or the gradual aggregation of birds during the dry season. Therefore, the main drivers of AIV dynamics (juvenile influx and host abundance/aggregation), although present in Afrotropical regions, could not explain the AIV seasonal patterns in our study in contrast to results reported from temperate and boreal regions. These differences imply variation in the risk of AIV circulation in waterfowl and in the risk of spread to poultry, other animals or humans. (Resume d'auteur)

High-yielding rice varieties (HYV) show strong compensation among sequentially developed yield components (YC). This phenotypic plasticity has adaptive value but for crop improvement, more information is needed on its effects on yield. SAMARA, a deterministic crop model predicting trait-trait and trait-environment interactions by simulating morphogenetic processes and competition among sinks for assimilates, was developed to study crop phenotypic plasticity. Dynamics of YC and morphology were observed on the HYV IR72 planted at standard and 4-fold greater density in 4 environments in the Philippines in 2012/13. Data for other years/seasons were obtained for model validation. Sequential path analysis was used to determine the phenotypic plasticity of traits consecutively contributing to yield. Tiller number at flowering (R2 = 0.94) and maturity (R2 = 0.84) and grain yield (R2 = 0.77) were predicted accurately for independent datasets. The model also predicted accurately density effects on aboveground dry weight (agdw), plant height, leaf size, spikelet number per panicle and filling percentage. Tiller and leaf mortality were over-estimated under high density. Overall, the model predicted satisfactorily the sequential compensation processes among YCs. They led to stable grain yield despite large morphological differences among density treatments and environments. Sensitivity analysis of simulation outcomes vs. variation in crop parameters indicated that modified genotypic tillering ability, phyllochron or leaf size had little effect on final grain yield because of compensations by other traits, although IR72 appeared to have an optimal combination of parameter values. Larger effects on grain yield were predicted for variation of parameters affecting the sensitivity of leaf and tiller mortality to assimilate resources and the ability to mobilize stem non-structural carbohydrates during grain filling. The model will be used next to perform physiological trait dissection and plasticity analyses for diverse genotypes.

The combined production of grain and sugar by sorghum requires efficient leaf C acquisition (source) and allocation to productive sinks, namely the stem and the panicle. Photoperiod sensitivity, which regulates plant phenology and growth, is also likely to be a key regulator of such C source-sink relationships, while it is crucial to drought adaptation. This study set out to evaluate the contribution of plant leaf area and stem growth to the production of grain and sugar by sweet, photoperiodic sorghum depending on the sowing date and post-flowering water availability. Twelve West African accessions were studied in the field in Senegal during two consecutive rainy seasons, comparing two sowing dates and post-anthesis water regimes (irrigated, or not). Plant growth and development were monitored weekly up to flowering. Organ size and biomass, stem juiciness and sweetness were characterized at flowering and maturity. At flowering, early sowing enhanced plant leaf area, stem dry weight and sugar production, and plant leaf area expressed per unit of stem dry weight was positively correlated to stem sweetness, suggesting that a high pre-flowering source-to-sink ratio favors early sugar accumulation. Overall, a late sowing date reduced sugar and grain production more than post-anthesis drought, whereas early sowing enhanced both types of production. No post-anthesis competition was found between grain filling and stem sugar accumulation. However, under drought conditions, the maintenance of combined production was better for the most leaf stay-green accessions. It is suggested that the combined production of sugar and grain by sweet, photoperiodic sorghum in response to the sowing date and post-anthesis drought is firstly sink-driven but that source (plant leaf area) dynamics can enhance stem sugar accumulation and its maintenance under drought conditions. These results provide further insight into the traits to be combined in dual-purpose ideotypes dedicated to drought-prone environments.

Ecuador has an outstanding diversity of palm species, some of which have been well studied, certain others remain an enigma, however. A particular case is the American oil palm, Elaeis oleifera (Kunth) Cortés, first recorded in Ecuador in 1986. The genus Elaeis has a trans-Atlantic (Africa-America) distribution, with E. oleifera from the Neotropics, and E. guineensis Jacq. from Africa. It has been hypothesized that E. oleifera derives from populations of E. guineensis, which diverged 15 million years ago. At the local level, the populations of E. oleifera have a disjunct distribution, with isolated populations in Central America, the Amazonia basin, the Guianas, Chocó and the Caribbean Cost of Colombia and Venezuela, frequently associated with human or archaeological settlements. Despite the spatial and historical separation between the two species, there are no reproductive barriers to the generation of fertile hybrids. This important reproductive characteristic has allowed E. oleifera to become a major source of genetic variation for the improvement and adaptability of commercial populations of E. guineensis throughout the tropics. The Ecuadorian populations of E. oleifera from Taisha, with morphological, reproductive and agronomically important biochemical characteristics, have been used for the creation of commercial hybrids, which today are planted in many tropical regions.

We present the first cross continental comparison of the flowering and fruiting phenology of tropical forests across Africa. Flowering events of 5,446 trees from 196 species across 12 sites, and fruiting events of 4,595 trees from 191 species, across 11 sites were monitored over periods of 6 to 29 years, and analysed to describe phenology at the continental level. To study phenology we used Fourier analysis to identify the dominant cycles of flowering and fruiting for each individual tree and we identified the time of year African trees bloom and bear fruit and their relationship to local seasonality. Reproductive strategies were diverse and no single regular cycle was found in >50% of individuals across all 12 sites. Additionally, we found annual flowering and fruiting cycles to be the most common. Sub-annual cycles were the next most common for flowering whereas supra-annual patterns were the next most common for fruiting. We also identify variation in different subsets of species, with species exhibiting mainly annual cycles most common in West and West-Central African tropical forests, while more species at sites in East-Central and Eastern African forests showed cycles ranging from sub-annual to supra-annual. Despite many trees showing strong seasonality, at most sites some flowering and fruiting occurred all year round. Environmental factors with annual cycles are likely to be important drivers of seasonal periodicity in trees across Africa, but proximate triggers are unlikely to be constant across the continent

International audience; In rhythmic tree growth, the alternation between growth and resting phases can be either periodic or irregular, depending on climatic and endogenous factors. The aim of this study was to analyze the growth pattern of yerba-mate, a subtropical South American tree with monopodial and rhythmic growth, over a two-year period. Metamer emission rate of selected axes was followed during two years after a severe pruning in two cultivation systems contrasting for light conditions, agroforestry system and monoculture. A new longitudinal data modeling approach relying on hidden semi Markov chains to identify growth and resting phases and multiple change-point models to relate these phases to climatic factors was used. Despite large variability among individuals, two growth phases separated by a resting phase were most often identified within each year. Contrasting situations regarding the modulation of the polycyclism were observed between the two years and cultivated systems: in the first year of growth, the pattern consisted of a single long growth phase in vigorous individuals and the cultivation system had a major effect, likely due to the induced light environment; in the second year, some individuals did not grow during the second autumn phase likely due to the drought during the warm season. The observed differences in growth patterns between years and cultivation systems were interpreted with respect to ontogenetic and climatic effects, in interaction with endogenous factors resulting from plant reproductive phenology. This study introduces a new longitudinal data analysis approach for investigating the phenology of perennial plants over long follow-up periods, at time scale intermediate between days and years.

UMR SYSTEM : équipe SYME; Background and aims :Plant phenology is a sensitive indicator of plant response to climate change. Observations of phenological events belowground for most ecosystems are difficult to obtain and very little is known about the relationship between tree shoot and root phenology. We examined the influence of environmental factors on fine root production and mortality in relation with shoot phenology in hybrid walnut trees (Juglans sp.) growing in three different climates (oceanic, continental and Mediterranean) along a latitudinal gradient in France.Methods : Eight rhizotrons were installed at each site for 21 months to monitor tree root dynamics. Root elongation rate (RER), root initiation quantity (RIQ) and root mortality quantity (RMQ) were recorded frequently using a scanner and time-lapse camera. Leaf phenology and stem radial growth were also measured. Fine roots were classified by topological order and 0–1 mm, 1–2 mm and 2–5 mm diameter classes and fine root longevity and risk of mortality were calculated during different periods over the year.Results :Root growth was not synchronous with leaf phenology in any climate or either year, but was synchronous with stem growth during the late growing season. A distinct bimodal pattern of root growth was observed during the aerial growing season. Mean RER was driven by soil temperature measured in the month preceding root growth in the oceanic climate site only. However, mean RER was significantly correlated with mean soil water potential measured in the month preceding root growth at both Mediterranean (positive relationship) and oceanic (negative relationship) sites. Mean RIQ was significantly higher at both continental and Mediterranean sites compared to the oceanic site. Soil temperature was a driver of mean RIQ during the late growing season at continental and Mediterranean sites only. Mean RMQ increased significantly with decreasing soil water potential during the late aerial growing season at the continental site only. Mean root longevity at the continental site was significantly greater than for roots at the oceanic and Mediterranean sites. Roots in the 0–1 mm and 1–2 mm diameter classes lived for significantly shorter periods compared to those in the 2–5 mm diameter class. First order roots (i.e. the primary or parents roots) lived longer than lateral branch roots at the Mediterranean site only and first order roots in the 0–1 mm diameter class had 44.5% less risk of mortality than that of lateral roots for the same class of diameter.Conclusions :We conclude that factors driving root RER were not the same between climates. Soil temperature was the best predictor of root initiation at continental and Mediterranean sites only, but drivers of root mortality remained largely undetermined.

Background and Aims Fine roots play a major role in the global carbon cycle through respiration, exudation and decomposition processes, but their dynamics are poorly understood. Current estimates of root dynamics have principally been observed in shallow soil horizons (2.5 m) root growth occurred at two distinct periods, at bud break in spring and throughout the winter i.e., after leaf fall. In contrast, shallow roots grew mainly during the spring-summer period. Maximum root elongation rates ranged from 1 to 2 cm day−1 depending on soil depth. Most root mortality occurred in upper soil layers whereas only 10 % of fine roots below 4 m died over the study period. Fine root lifespan was longer in thicker and in deeper roots with the lifespan of the thinnest roots (0.0–0.5 mm) increasing from 129 days in the topsoil to 190 at depths > 2.5 m. Conclusions The unexpected growth of very deep fine roots during the winter months, which is unusual for a deciduous tree species, suggests that deep and shallow roots share different physiological strategies and that current estimates based on the shortest root growth periods (i.e., during spring and summer) may be underestimating root production. Although high fine root turnover rates might partially result from the minirhizotron approach used, our results help gain insight into some of the factors driving soil organic carbon content.

In order to quantify the effects of forests to oil palm conversion occurring in the tropics on land–atmosphere carbon, water and energy fluxes, we develop a new perennial crop sub-model CLM-Palm for simulating a palm plant functional type (PFT) within the framework of the Community Land Model (CLM4.5). CLM-Palm is tested here on oil palm only but is meant of generic interest for other palm crops (e.g., coconut). The oil palm has monopodial morphology and sequential phenology of around 40 stacked phytomers, each carrying a large leaf and a fruit bunch, forming a multilayer canopy. A sub-canopy phenological and physiological parameterization is thus introduced so that each phytomer has its own prognostic leaf growth and fruit yield capacity but with shared stem and root components. Phenology and carbon and nitrogen allocation operate on the different phytomers in parallel but at unsynchronized steps, separated by a thermal period. An important phenological phase is identified for the oil palm – the storage growth period of bud and "spear" leaves which are photosynthetically inactive before expansion. Agricultural practices such as transplanting, fertilization and leaf pruning are represented. Parameters introduced for the oil palm were calibrated and validated with field measurements of leaf area index (LAI), yield and net primary production (NPP) from Sumatra, Indonesia. In calibration with a mature oil palm plantation, the cumulative yields from 2005 to 2014 matched notably well between simulation and observation (mean percentage error = 3 %). Simulated inter-annual dynamics of PFT-level and phytomer-level LAI were both within the range of field measurements. Validation from eight independent oil palm sites shows the ability of the model to adequately predict the average leaf growth and fruit yield across sites and sufficiently represent the significant nitrogen- and age-related site-to-site variability in NPP and yield. Results also indicate that seasonal dynamics of yield and remaining small-scale site-to-site variability of NPP are driven by processes not yet implemented in the model or reflected in the input data. The new sub-canopy structure and phenology and allocation functions in CLM-Palm allow exploring the effects of tropical land-use change, from natural ecosystems to oil palm plantations, on carbon, water and energy cycles and regional climate. Open-Access Publikationsfonds 2015 peerReviewed

Wheat and rice are the most important food crops in agriculture providing around 50% of all calories consumed in the human diet. While both are C3 species, the evolution and domestication of wheat and rice occurred in very different environments, resulting in diverse anatomical and metabolic adaptation. This review focuses on the current understanding of their adaptation in an agronomic context. The similarities and differences between wheat and rice are discussed, focusing on traits related to phenology, photosynthesis, assimilate partitioning, and lodging resistance, these being the main abiotic drivers of yield expression in most agro-ecosystems. Currently, there are significant knowledge gaps in the major biological processes that account not only for differential adaption among cultivars within each species, but even between the two species. By addressing what is known as well as where gaps exist in a comparative context, this review aims to highlight translational research approaches that could provide insights into the genetic improvement of both crops. (Resume d'auteur)

Sweet sorghum is highly coveted to contribute and take up food and energy challenges. A collection of 84 West Africa landraces mostly from Senegal and four control cultivars were screened to identify relevant accessions and trait combination for multi-purpose (sugar/grain/biomass). The implication of photoperiod sensitivity was particularly addressed. A total of 20 traits related to phenology, morphology, grain and sugar production were assessed in two sowing dates (July and August) at CNRA Bambey in Senegal. Late sowing resulted in shortened vegetative phase and a significant decrease in traits related to plant size, stem sugar, biomass and grain productions. Broad-sense heritability was moderate to high for most of the phenology, morphology, grain and sugar-related traits, suggesting their interest for breeding. All the traits related to plant size were positively correlated with plant sugar production except plant height. A cluster analysis identified three groups contrasting in their ability to combine sugar, grain or fodder production based on 18 traits measured for the early sowing. Clusters I and III were suitable for one purpose: grain and sugar, respectively. Cluster II was the most suitable for multi-purpose, showing the best trade-off among grain, sugar and vegetative biomass production. The best accessions for stem sugar yield belonged to durra, caudatum and their intermediate types. The relationship between internode size and sweetness should be further studied, in particular exploring their relationship with internode tissue anatomy. Further studies are also needed to evaluate the role that stay-green can play in sugar yield maintenance under post-flowering drought. (Resume d'auteur)

It is crucial to understand the adaptive mechanisms of woody plants facing periodic drought to assess their vulnerability to the increasing climate variability predicted in the Sahel. Guiera senegalensis J.F.Gmel is a semi-evergreen Combretaceae commonly found in Sahelian rangelands, fallows and crop fields because of its value as an agroforestry species. We compared canopy leafing, and allometric measurements of leaf area, stem area and stem length and their relationships with leaf water potential, stomatal conductance (gs) and soil-to-leaf hydraulic conductance (KS-L), in mature and current-year resprouts of G. senegalensis in Sahelian Niger. In mature shrubs, seasonal drought reduced the ratio of leaf area to cross-sectional stem area (AL : AS), mainly due to leaf shedding. The canopy of the current-year resprouts remained permanently leafed as the shrubs produced leaves and stems continuously, and their AL : AS ratio increased throughout the dry season. Their KS–L increased, whereas gs decreased. West, Brown and Enquist's (WBE) model can thus describe allometric trends in the seasonal life cycle of undisturbed mature shrubs, but not that of resprouts. Annual clear cutting drives allometric scaling relationships away from theoretical WBE predictions in the current-year resprouts, with scaling exponents 2.5 times greater than those of mature shrubs. High KS-L (twice that of mature shrubs) supports this intensive regeneration process. The adaptive strategy described here is probably common to many woody species that have to cope with both severe seasonal drought and regular disturbance over the long term.

Night temperature (NT) increases faster than day temperature with global warming and this may have strong implications for crop yield. One of the assumptions is the increase in night respiration and thus the increase in carbon losses over time. Some rice cultivars (indica, aus and japonica types) were grown in the field in the Philippines and in heated greenhouses in Montpellier, France, to quantify the response of respiration to increased NT and its implication at crop level. Increased NT by 3.8 and 5.4 °C over the whole crop cycle in two greenhouse experiments and by 1.9 °C in the field from 33 days after transplanting up to maturity using a free-air-controlled enhancement increased night respiration rate significantly. Overall, the cost in CH 2 O of night respiration over crop duration was 17 to 20% (field) and 8 to 18% (greenhouse) of the potential shoot dry matter (including that lost by respiration). Additional respiratory burden due to increased NT was only 1 to 7% of the potential shoot dry matter at maturity, and was not associated with significant loss in additional dry matter. The absence of any dry matter reduction with increased NT within indica cultivars questions the assumptions of recent papers.

The ecotypic diversity of perennial ryegrass (Lolium perenne L.) is a major genetic resource for breeding programs. In three replicated micro-sward trials in France, Belgium and Germany, we measured spring growth and recorded heading date of round 400 genebank accessions from the natural diversity of L. perenne that were selected as to represent the wide range of variability in this species. We observed marked differences between trial locations as well as interaction between accessions and locations in the timing of spring growth rates along growing-degree-days (GDDs). These preliminary results are part of a wider project aiming to investigate the natural adaptation of perennial ryegrass to various regional climates across its spontaneous area of presence in Europe.

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; International audience; In plants, carbon source–sink relationships are assumed to affect their reproductive effort. In fruit trees, carbon source–sink relationships are likely to be involved in their fruiting behavior. In apple, a large variability in fruiting behaviors exists, from regular to biennial, which has been related to the within-tree synchronization vs desynchronization of floral induction in buds. In this study, we analyzed if carbon assimilation, availability and fluxes as well as shoot growth differ in apple genotypes with contrasted behaviors. Another aim was to determine the scale of plant organization at which growth and carbon balance are regulated. The study was carried out on 16 genotypes belonging to three classes: (i) biennial, (ii) regular with a high production of floral buds every year and (iii) regular, displaying desynchronized bud fates in each year. Three shoot categories, vegetative and reproductive shoots with or without fruits, were included. This study shows that shoot growth and carbon balance are differentially regulated by tree and shoot fruiting contexts. Shoot growth was determined by the shoot fruiting context, or by the type of shoot itself, since vegetative shoots were always longer than reproductive shoots whatever the tree crop load. Leaf photosynthesis depended on the tree crop load only, irrespective of the shoot category or the genotypic class. Starch content was also strongly affected by the tree crop load with some adjustments of the carbon balance among shoots since starch content was lower, at least at some dates, in shoots with fruits compared with the shoots without fruits within the same trees. Finally, the genotypic differences in terms of shoot carbon balance partly matched with genotypic bearing patterns. Nevertheless, carbon content in buds and the role of gibberellins produced by seeds as well as the distances at which they could affect floral induction should be further analyzed.

Four tree species in the Kostelec n. C. l. arboretum (Czech Republic) have been repeatedly damaged by Dendrocopos medius. The unique aspect of this otherwise common behavior called girdling consists in regularly visiting the same trees every spring, although there are more than 1.200 tree species within the arboretum. We monitored transpiration, leaf phenology and the chemical composition of the xylem sap of girdled and nongirdled trees. Spectral analysis revealed slightly higher amounts of sugars, especially saccharose, in Cladrastis Raf. as the most regularly girdled tree among other conditions, comparing girdled to non-girdled trees. Higher transpiration rates were not confirmed in connection with girdling—quite the opposite—Cladrastis Raf. as the most highly favored tree for girdling showed the lowest transpiration rates (in average 6 kg water per day within spring months) compared to other non-girdled trees. We presume that the birds do not choose a particular tree on the basis of any visible or chemical traits but they examine many trees within their territory. Afterwards they probably remember the position of trees whose xylem sap starts to flow early in the spring compared to other trees, as their transpiration stream is enriched with sweet organic substances that represent an advantage for the forthcoming nesting period.

UMR AGAP - équipe AFEF - Architecture et fonctionnement des espèces fruitières; This study presents the first evaluation of apple flowering phenology models using data from 14 sites across the globe. The dataset includes large variability in growing climates, a prerequisite to investigate phenology models for use in climate change applications. Two flowering stages, early and full, were investigated allowing for unique model evaluation based on both statistical performance and biological assumptions. Two overarching phenology models (Sequential and Chill Overlap) and two sub-models of chill (Dynamic and Triangular) and heat (GDH and Sigmoidal) were tested. Flowering times from the different sites illustrated the differing effects of contrasting winter and spring temperatures. Sites with similar springtime temperatures, but different winter temperatures, had different flowering patterns (warmer winter sites flowered later). Across all analyses, results from the Chill Overlap model were better than those from the Sequential model. Of the Chill Overlap models, those fitted with the Triangular or Dynamic chill model and the GDH heat sub-model performed well statistically and met the assumptions of the model across both flowering stages. The mild sites in the analysis were least well represented, regardless of model selection. This global evaluation demonstrated that flowering modelling in temperate fruit trees would progress through appropriate choices of overarching model, sub-models and parameters.

Key message: The chronology of periods of organogenesis and elongation is highlighted in Pinus halepensis.The two first growth units of an annual shoot are preformed inside the bud during the previous year. The following growth units are formed during the spring or summer of the current year. Context: Analysis of annual shoot length growth phenology is crucial to assess the impact of climate change on tree production. Little is known about the basic growth characteristics and the phenology of pines. Aims: The present study disentangles the roles of shoot organogenesis vs elongation in the annual growth cycle of the polycyclic Aleppo pine. Methods: Growth of young Pinus halepensis trees was monitored monthly for 1 year. At each monitoring date, the bud content and meristem dimensions of the main stem shoots apices were analyzed. Results: The two first growth units of an annual shoot are preformed inside the bud during the previous year. The following growth units are formed during the spring or summer of the current year. The gap between a shoot organogenesis and its elongation may vary from 1 month, for the last growth unit, to half a year, for the first growth units. Conclusion: Our results underline the importance of taking seasonal environmental conditions from both the previous and the current year into account, in order to study the plasticity of annual shoot growth and its response to climate change and variability.

Better defining niches for the photoperiod sensitive sorghum (Sorghum bicolor L. Moench) varieties of West Africa into the local cropping system might help to improve the resilience of food production in the region. In particular, crop models are key tools to assess the growth and development of such varieties against climate and soil variability. In this study, we compared the performance of three process-based crop models (APSIM, DSSAT and Samara) for prediction of diverse sorghum germplasm having widely varying photoperiod sensitivity (PPS) using detailed growth and development observations from field trials conducted in West Africa semi-arid region. Our results confirmed the capability of each selected model to reproduce growth and development for varieties of diverse sensitivities to photoperiod. Simulated phenology and morphology organs during calibration and validation were within the closet range of measured values with the evaluation of model error statistics (RMSE and R2). With the exception of highly sensitive variety (IS15401), APSIM and Samara estimates indicate the lowest value of RMSE (

The timing of leaf phenophases greatly influences the functioning of trees. Phenological traits are thus considered major components of tree fitness, and are expected to be strongly selected under environmental or biotic pressures. To date, most phenological studies have been conducted at the population scale, with comparatively very few works at the scale of individuals. We take advantage of a unique phenological database, consisting of leaf unfolding (LU) and leaf senescence (LS) observations done at the individual scale for 5 years over 35 populations, representing >1200 dominant and co-dominant trees of three species (Quercus robur, Quercus petraea and Fagus sylvatica), to document the within-population variability of phenological traits in temperate deciduous forest trees. We show that individual phenological ranks mostly repeat from year to year among trees of a given population, though LU ranks tend to repeat more than LS ranks. Using simulated dynamics of soil water content, we suggest that inter-individual differences in the access to soil water may play a role in determining tree phenological ranks. The timing of leaf phenology is further correlated with individual growth in a given tree population. In Beech populations, early-leafers tend to grow more. On the other hand, Oak trees entering senescence later tend to grow more. The growth of Oak trees, being more prone to spring pathogenic attacks than Beech, may benefit less from a spring extension of leaf display.

The intrinsic quality of a wine is strongly linked with its volatile compound composition involved in the complexity of wine’s subtle flavor nuances. Those reminiscent of green pepper, herbaceous, blackcurrant, blackberry, figs or prunes are strongly linked with the maturity of the grapes. Nowadays it is well accepted that macroscopic effects of climate change modify the environmental conditions of grape growing at local scale in all the vineyards across the world. The expected effects on grape and wine production can be positive when they increase the maturity of the grapes, but when the conditions are too warm and too dry they induce opposite effects producing grapes and wines with a lower intrinsic quality. These effects were perceived in young wines but also in older wines kept several years in bottle.In this article, we provide some examples of effects of climate change and growing conditions on grapevine and wine quality expressed as flavors and antioxidant composition. We also report some results associated with the incidence of grape growing conditions on white and red wine aging potential and on the composition of old wines.Finally, we discuss the opportunities for vine growers and winemakers to manage the quality of their grapes and wines in this climate change context.

Context[br/] Parasites can induce strong effects on their host’s growth, not only as a result of host resource exploitation (growth loss) but also with a potential adaptive value for host (tolerance response) and themselves (increased transmission).[br/] [br/] Aims[br/] We assessed these three types of phenotypic changes in oak seedlings infected by powdery mildew.[br/] [br/] Methods[br/] A manipulative field experiment with three levels of parasite inoculum was designed in order to tease apart infection from genetic effects on oak growth. Seedlings were monitored during 3 years for height growth, phenology and infection.[br/] [br/] Results[br/] Powdery mildew infection induced both significant growth loss and qualitative changes in plant architecture. The most striking and unexpected change was increased growth polycyclism in infected seedlings. This benefitted both the host as a form of compensation for infection-caused height loss, and the pathogen, by increasing sporulation.[br/] [br/] Conclusion[br/] The study highlights the effect of parasites in the expression of plant phenotypic traits, such as phenology and ultimately tree architecture. Both host tolerance and parasitic manipulation may be involved in the observed changes in growth patterns. These results suggest a complex interplay between development and defence in trees and emphasize the need to better assess tolerance mechanisms when considering the defence strategies of trees against pathogens.