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Self-incompatibility (SI) is present in around half of all species of flowering plants. SI limits endogamy and contributes to increased genetic diversity. SI is a very important trait in citrus because, when coupled with parthenocarpy, it allows seedless fruit production. Otherwise, SI is an impediment to genetic studies and breeding programs. Temperature stress, bud pollination and polyploidization can induce the breakdown of the SI mechanism in several species. In this work, we investigated how the SI mechanism can be broken down in two self-incompatible diploid citrus genotypes: ‘Fortune’ mandarin and ‘Clemenules’ clementine. The influence of temperature stress on the SI mechanism was assessed in self-pollinated flowers of ‘Fortune’ mandarins subjected to 2 temperature regimes (10 °C and 30 °C), whereas the bud pollination effect was investigated in the same genotype and in ‘Clemenules’ clementines cultivated under field conditions. The tetraploid ‘Clemenules’ clementine cultivated under field conditions was used to study if tetraploidization can bypass the SI reaction. Histological observations of pollen tube growth and seed production in self-pollinated flowers were used to evaluate the breakdown of SI, while the genetic analysis with SSR and SNP markers confirmed that all recovered plants were zygotic and had been originated by selfing. Our results confirm that the SI reaction can be surpassed by temperature stress, bud pollination and tetraploidy. To our knowledge, this is the first report in citrus in which the SI reaction breakdown by these three different strategies is demonstrated by molecular markers.

Temporal and spatial patterns in flowering phenology were assessed for eight tropical African tree species. Specifically, the frequency and seasonality of flowering at seven sites in central Africa were determined using field data, graphical analysis and circular statistics. Additionally, spatial variation in the timing of flowering across species range was investigated using herbarium data, analysing the relative influence of latitude, longitude and timing of the dry season with a Bayesian circular generalized linear model. Annual flowering was found for 20 out of the 25 populations studied. For 21 populations located at the north of the climatic hinge flowering was occurring during the dry season. The analysis of herbarium collections revealed a significant shift in the timing of flowering with latitude for E. suaveolens, and with the timing of the dry season for M. excelsa (and to a lesser extent L. alata), with the coexistence of two flowering peaks near the equator where the distribution of monthly rainfall is bimodal. For the other species, none of latitude, longitude or timing of the dry season had an effect on the timing of flowering. Our study highlights the need to identify the drivers of the flowering phenology of economically important African tree species., SCOPUS: ar.j, info:eu-repo/semantics/published

Flowering date is a trait of main interest in perennial fruit species including sweet cherry (Prunus avium L.). It is highly dependent on the environment and has a major impact on fruit formation: as already observed, a poor synchronization between flowering date and the environmental conditions can lead to significant economic losses. Understanding the genetic determinism of the flowering date is therefore essential to optimize selection strategies and create new varieties better adapted to future climatic conditions.The first objective of this thesis is to study the genotype-by-environment (G × E) and QTL-by-environment (QTL × E) interactions. To do this, an intra-specific population called 'Regina' × 'Lapins' (n = 122) was planted in five locations with contrasting climates distributed in four European countries. It was thus possible to identify two major QTLs. The first one, located on linkage group 4, is found in all environments except the site located in Murcia (Spain), characterized by the highest temperatures. In the latter environment, the major QTL is localized on linkage group 1. Highly significant G×E and QTL×E interactions were assessed using different statistical models.The second objective of this thesis is to fine-map the QTL on linkage group 4 using a second population, 'Regina' x 'Garnet' (n = 1386). This QTL, very stable across years, explains the most important part of the phenotypic variation in this plant material. This QTL was detected in a 68-kb interval, containing twelve candidate genes that were functionally characterized using the new cherry genome sequence of the cultivar 'Regina'. In addition, their expression was studied in 'Regina' and 'Garnet' cultivars during the period from dormancy to flowering, leading to the identification of a few promising candidates. Also, two KASP markers have been developed and validated on different genetic backgrounds and can be used in marker-assisted selection (MAS) for flowering date.In the long term, these results should help breeders to create new varieties that are well adapted to their planting site and to ensure the production of sweet cherries in geographical areas covering a wide range of climates., La date de floraison est un caractère d’intérêt majeur chez les espèces pérennes fruitières dont le cerisier (Prunus avium L.). Elle est très dépendante de l’environnement et a un impact majeur sur la formation des fruits : comme déjà observé, une mauvaise adéquation entre la date de floraison et les conditions environnementales peut entrainer d’importantes pertes économiques. La compréhension du déterminisme génétique de la date de floraison est donc primordiale pour optimiser les stratégies de sélection et créer de nouvelles variétés mieux adaptées aux conditions climatiques futures.Le premier objectif de cette thèse est d’étudier les interactions génotype x environnement (G × E) et QTL x environnement (QTL × E). Pour ce faire, une population intra-spécifique ‘Regina’ × ‘Lapins’ (n = 122) a été implantée dans cinq sites aux climats contrastés répartis dans quatre pays d’Europe. Il a ainsi été possible d’identifier deux QTL majeurs. Le premier, localisé sur le groupe de liaison 4, est trouvé dans tous les environnements sauf celui caractérisé par les températures les plus élevées (Murcie, en Espagne). Dans ce dernier environnement, le QTL majeur est localisé sur le groupe de liaison 1. Des interactions G × E et QTL × E fortement significatives ont été évaluées au moyen de différents modèles statistiques.Le second objectif de cette thèse est de cartographier finement le QTL du groupe de liaison 4 en utilisant une seconde population, ‘Regina’ x ‘Garnet’ (n = 1386). Ce QTL très stable, détecté durant toutes les années étudiées, explique la part la plus importante de la variance phénotypique dans ce matériel végétal. Ce QTL a pu être localisé dans un intervalle de 68kb, contenant douze gènes candidats caractérisés fonctionnellement en utilisant la nouvelle séquence du génome du cerisier issue du cultivar ‘Regina’. De plus, leur expression a été étudiée chez les cultivars ‘Regina’ et ‘Garnet’ au cours de la période allant de l’entrée en dormance jusqu’à la floraison, permettant d’identifier quelques candidats prometteurs. Aussi, deux marqueurs de type KASP ont été développés et validés sur différents fonds génétiques, et pourront être utilisés en sélection assistée par marqueurs (SAM) pour la date de floraison.A terme, l’ensemble de ces résultats devrait contribuer à accroître l’efficacité des programmes de sélection afin de créer de nouvelles variétés bien adaptées à leur site de plantation et d’assurer la production de cerises dans des zones géographiques couvrant une large gamme de climats.

Background and Aims Daylength determines flowering dates. However, questions remain regarding flowering dates in the natural environment, such as the synchronous flowering of plants sown simultaneously at highly contrasting latitudes. The daily change in sunrise and sunset times is the cue for the flowering of trees and for the synchronization of moulting in birds at the equator. Sunrise and sunset also synchronize the cell circadian clock, which is involved in the regulation of flowering. The goal of this study was to update the photoperiodism model with knowledge acquired since its conception. Methods A large dataset was gathered, including four 2-year series of monthly sowings of 28 sorghum varieties in Mali and two 1-year series of monthly sowings of eight rice varieties in the Philippines to compare with previously published monthly sowings in Japan and Malaysia, and data from sorghum breeders in France, Nicaragua and Colombia. An additive linear model of the duration in days to panicle initiation (PI) and flowering time using daylength and daily changes in sunrise and sunset times was implemented. Key Results Simultaneous with the phyllochron, the duration to PI of field crops acclimated to the mean temperature at seedling emergence within the usual range of mean cropping temperatures. A unique additive linear model combining daylength and daily changes in sunrise and sunset hours was accurately fitted for any type of response in the duration to PI to the sowing date without any temperature input. Once calibrated on a complete and an incomplete monthly sowing series at two tropical latitudes, the model accurately predicted the duration to PI of the concerned varieties from the equatorial to the temperate zone. Conclusions Including the daily changes in sunrise and sunset times in the updated photoperiodism model largely improved its accuracy at the latitude of each experiment. More research is needed to ascertain its multi-latitudinal accuracy, especially at latitudes close to the equator.

Agroforestry systems structured around fruit trees to produce fresh fruit is still under-developed in temperate zones. This study is based on the idea that the fruit tree can be integrated into multi-strata agroforestry systems where it would be grown with timber trees occupying the upper stratum and shrubs and/or herbaceous plants in the lower stratum. In addition to the production of fresh fruit, such systems would then combine different agro-ecosystemic services. The study focuses on a major temperate fruit species at the national and global levels, the apple tree. The general objective is to acquire a detailed knowledge of the tree's architectural development, its flowering and the quality of its fruiting, along these competition gradients. The work focuses on three actions: (i) defining an indicator to characterize each apple tree environment in this complex agrosystem, (ii) analyse at the tree scale the impact of agroforestry on morphological, phenological and architectural traits, and (iii) analysing the daily and annual sap flow regarding environmental variables and in relation to the aforementioned architectural traits. Using the light as a variable to analyse our architectural data, we have shown that apple trees did express shade avoidance traits affecting morphology (decreased taper and increased slenderness and specific leaf area), architecture (fewer growing shoots and proportion of flower clusters) and phenology (reduced number of days at full bloom). Finally, we have shown that sap flow and transpiration per unit of leaf area was affected by environmental variables (vapour pressure deficit and reference evapotranspiration). Shade did not change apple trees sap flow daily dynamics and reduced water and transpiration per unit of leaf area mainly because of morphological and architectural adaptation to shade in our experimental conditions. An increase of leaf area or a complexification of the apple tree architecture (i.e. the number of ramifications) increased transpiration per unit of leaf area during the summer. 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.; Les systèmes agroforestiers structurés autour des arbres fruitiers pour la production de fruits frais sont encore peu développés dans les zones tempérées. Cette étude est basée sur l'idée que l'arbre fruitier peut être intégré dans des systèmes agroforestiers multi-strates où il serait cultivé avec des arbres à bois occupant la strate supérieure et des arbustes et/ou des plantes herbacées dans la strate inférieure. Outre la production de fruits frais, ces systèmes combineraient alors différents services agro-écosystémiques. L'étude se concentre sur une espèce fruitière tempérée majeure aux niveaux national et mondial, le pommier. L'objectif général est d'acquérir une connaissance détaillée de l’établissement architectural de l'arbre, de sa floraison et de sa nouaison, le long de ces gradients de compétition. Le travail se concentre sur trois actions : (i) définir un indicateur pour caractériser l’environnement du pommier dans cet agrosystème complexe, (ii) analyser à l'échelle de l'arbre l'impact de l'agroforesterie sur les caractéristiques morphologiques, phénologiques et architecturales, et (iii) analyser la dynamique de flux de sève journalière et le cumul annuel en fonction des variables environnementales et en relation avec les caractéristiques architecturales susmentionnées. En utilisant la quantité de lumière comme variable pour analyser nos données architecturales, nous avons montré que les pommiers exprimaient des traits d’adaptation à l'ombre affectant la morphologie (diminution de la conicité et augmentation de l'élancement et la surface foliaire spécifique), l'architecture (moins de pousses en croissance et d’inflorescences) et la phénologie (réduction de la pèriode de pleine floraison). Enfin, nous avons montré que la densité de flux de sève n’était pas affecté par nos variaibles envionnementales (déficit de pression de vapeur et évapotranspiration de référence) contrairement à la transpiration par unité de surface foliaire. Dans nos conditions expérimentales, l'ombre n'a pas modifié la dynamique quotidienne du flux de sève des pommiers et a réduit la transpiration par unité de surface foliaire, principalement en raison d’adaptation morphologique et architecturale. Une augmentation de la surface foliaire ou une complexification de l'architecture du pommier (c'est-à-dire le nombre de ramifications) a augmenté la transpiration par unité de surface foliaire pendant l'été. Nos résultats suggèrent que si l'architecture des pommiers est modifiée par une réduction de l'intensité lumineuse, ce n'est qu'à partir d'une réduction de 65% que la capacité à produire des fruits est entravée.

International audience; Ces dernières années, les phénomènes de dépérissement de la végétation méditerranéenne se sont multipliés en lien avec l’augmentation des sécheresses estivales. En parallèle, une diminution des floraisons et une chute de la quantité et diversité des pollinisateurs ont pu être observés. C’est le cas dans les garrigues à romarin sur le massif de la Côte Bleue, occasionnant des problèmes de compétition entre abeilles domestiques et sauvages, et des baisses de production de miel. Afin de tester si une gestion adaptée de la végétation pourrait améliorer la croissance, la santé et le niveau de floraison des romarins, un dispositif expérimental de 18 placettes a été mis en place selon 3 modalités de traitement (taille haute à 70% de la hauteur totale du romarin, taille basse à 50%, témoin) et 2 niveaux de fertilitédu sol (fertile et mauvais). A l’issue de la première saison de végétation, la santé des romarins taillés ne s’est pas améliorée, et logiquement, la coupe qui élimine de nombreux rameaux a drastiquement réduit la floraison. Mais dès la deuxième année, la taille en position haute a nettement amélioré leur santé sur les sols fertiles avec une reprise des floraisons ; cet effet positif est encore observable après 5 ans de suivi, date à laquelle ils ont presque retrouvé leur hauteur initiale. Cependant, la coupe augmente aussi le risque de mortalité des pieds (notamment en taille basse), a un impact moins visible en conditions peu fertiles. L’effet de la coupe sur la floraison dépend aussi beaucoup des années, les fortes sécheresses la réduisant fortement dans tous les cas. Cet effet positif de la gestion des romarins comportedonc des précautions dans la hauteur de la coupe et doit être confirmé par un suivi à plus long terme.In recent years, the occurence of dieback events in Mediterranean vegetation has risen due to the increase in summer drought. In parallel, a decrease both in flowering and in the quantity and diversity of pollinators has been observed. This is the case, too, for the rosemary scrublands on the “Côte Bleue” massif, in southern France, which has caused problems of competition between domestic and wild bees and a drop in honey production. In order to test whether well-adapted vegetation management could improve the growth, health and flowering level of rosemary, an experimental trial of 18 plots was set up with 3 treatment protocols (high pruning, at 70% of the total height of the rosemary; low pruning, at 50% of height; and a control) and 2 levels of soil fertility (fertile and poor). At the end of the first growing season, the health of the pruned rosemary plants had not improved and, logically,flowering was reduced in proportion to the number of branches eliminated. But from the second year onwards, high-position pruning clearly improved the bushes’ health on fertile soils with a resumption of flowering; this positive effect is still observable after 5 years of monitoring, by which time they have almost regained their initial height. However, pruning has also increased the risk of plant mortality (especially when done at 50% of their height), and has a less visible impact in low fertility conditions. The effect of pruning on flowering is also highly dependent on the year, with significant reductions during severe droughts. To sum up: the positive effect of rosemary management requires caution in the height of the cut and must be confirmed by longer-term monitoring.

The physiological stage of mango maturity at harvest affects fruit quality at the time it is commercialized. The objective assessment of the mango maturity stage at harvest remains a challenge because of the multiple interactions between the visual aspect, the physicochemical composition, and the morphology of the fruit. This study aims to quantify the optimal harvest date to guarantee the maturity and quality of mango cv. ‘Kent’. In this study, which took place in Korhogo in northern Côte d’Ivoire, the maturity stage and the quality of fruits were measured on 240 Kent mangoes harvested at four different harvest dates (90, 95, 100, and 105 days after flowering). A morphological, physical, and chemical characterization (length, width, mass, soluble sugar content, dry matter, skin appearance, and mass loss) was carried out at each date on 30 fruits at harvest and 30 fruits after ripening at room temperature. The number of days necessary for ripening was quantified. The results showed that the optimal harvest date is 100 days after flowering for Kent mangoes in Côte d’Ivoire. Mangoes harvested at this date developed better organoleptic characteristics (less wrinkled skin, lower mass losses, and a shorter ripening time). Assessment of the harvest date, guaranteeing better ripening of the fruit, is of utmost importance for organizing harvests in the mango sectors in West Africa, and especially in Côte d’Ivoire.

Climate change is placing increasing pressure on forests around the world, and its potential impacts on the reproductive capacity of individuals are yet poorly understood. Many forest tree species reproduce following so-called masting patterns, in which seed production is intermittent and synchronized among individuals, whose drivers need to be identified in order to better understand the impact of climate on the fecundity of forest trees. The general objective of this thesis is to deepen our knowledge of the environmental drivers of the fecundity of forest trees and their interactions, by focusing on the holm oak, a widespread species in the Mediterranean basin. It also aimed to determine how fecundity could be impacted by climate change, and to develop a process-based model capable of predicting this impact. This thesis work combines analyses of long-term monitoring in a holm oak forest exposed to a rainfall exclusion experiment, experimental manipulations of source-sink interactions involved in the resource allocation to reproduction, and modelling. I have shown that reproduction was strongly regulated by weather conditions during the reproductive cycle and in particular by the water availability in summer-autumn, and to a lesser extent by the availability of carbon and nutrients, as well as by competition between fruits and new buds. My experimental results show that the allocation of resources to reproduction could be modified in case of resource limitation due to defoliation; and that developing fruits have a negative impact on the dynamics of nitrogen and zinc reserves in branches, as well as on the production of female flowers the following year. Long-term observations show that multi-year rainfall reduction induce a decrease in the number of fruits produced which is additional to the interannual variability and that tree reproduction does not acclimate to drought. Finally, within the PHENOFIT model, I have developed a fecundity model based on the assumptions and results from my work and from the literature.; Le changement climatique exerce une pression croissante sur les forêts du monde entier, et ses impacts potentiels sur la fécondité des arbres sont encore mal compris. De nombreuses espèces d’arbres forestiers se reproduisent suivant des patrons de fructification intermittente et synchronisée entre les individus, dits de masting, dont les déterminants complexes doivent être identifiés pour comprendre l’effet du climat sur la fécondité des arbres forestiers. Cette thèse a comme objectif général d’approfondir notre connaissance des déterminants environnementaux de la fécondité des arbres forestiers et de leurs interactions, en se focalisant sur le chêne vert, une espèce très répandue en milieu méditerranéen. Elle a aussi pour objectif de déterminer comment la fécondité du chêne vert pourrait être affectée par le changement climatique, et de développer un modèle basé sur les processus capable de prédire cet impact. Ce travail de thèse a donc combiné des analyses de suivis à long terme dans une forêt de chêne vert soumise à une manipulation des précipitations, des expérimentations de manipulation des relations sources-puits pour l’allocation des ressources à la reproduction à l’échelle individuelle, et de la modélisation. J’ai montré que la reproduction était fortement régulée par les conditions météorologiques durant le cycle reproducteur, et en particulier par la disponibilité en eau en été-automne, et dans une moindre mesure par la disponibilité en carbone et nutriments ainsi que par la compétition entre fruits et nouveaux bourgeons. Mes résultats expérimentaux montrent que l’allocation de ressources à la reproduction peut être modifiée en cas de limitation des ressources par une défoliation ; et que les fruits en développement ont un impact négatif sur les dynamiques des réserves en azote et en zinc dans les branches ainsi que sur la production des fleurs femelles l’année suivante. Les observations en forêt indiquent qu’une réduction continue des précipitations sur plusieurs années induit une diminution du nombre de fruits produits, indépendamment des effets de la variabilité interannuelle et sans que les arbres semblent être capables de s’y acclimater. Enfin, j’ai développé, au sein du modèle de fonctionnement de l’arbre PHENOFIT, un modèle de fécondité se basant sur les hypothèses et résultats issus de mes travaux et de la littérature.

International audience; Floral induction (FI) in shoot apical meristems (SAM) is assumed to be triggered by antagonistic endogenous signals. In fruit trees, FI occurs in some SAM only and is determined by activating and inhibiting signals originating from leaves and fruit, respectively. We developed a model (SigFlow) to quantify on 3D structures the combined impact of such signals and distances at which they act on SAM. Signal transport was simulated considering a signal ‘attenuation’ parameter, whereas SAM fate was determined by probability functions depending on signal quantities. Model behaviour was assessed on simple structures before being calibrated and validated on a unique experimental dataset of 3D digitized apple trees with contrasted crop loads and subjected to leaf and fruit removal at different scales of tree organization. Model parameter estimations and comparisons of two signal combination functions led us to formulate new assumptions on the mechanisms involved: (i) the activating signal could be transported at shorter distances than the inhibiting one (roughly 50 cm vs 1 m) (ii) both signals jointly act to determine FI with SAM being more sensitive to inhibiting signal than activating one. Finally, the genericity of the model is promising to further understand the physiological and architectural determinisms of FI in plants.

Expansion of the maize growing area was central for food security in temperate regions. In addition to the suppression of the short-day requirement for floral induction, it required breeding for a large range of flowering time that compensates the effect of South-North gradients of temperatures. Here we show the role of a novel florigen gene, ZCN12, in the latter adaptation in cooperation with ZCN8. Strong eQTLs of ZCN8 and ZCN12, measured in 327 maize lines, accounted for most of the genetic variance of flowering time in platform and field experiments. ZCN12 had a strong effect on flowering time of transgenic Arabidopsis thaliana plants; a path analysis showed that it directly affected maize flowering time together with ZCN8. The allelic composition at ZCN QTLs showed clear signs of selection by breeders. This suggests that florigens played a central role in ensuring a large range of flowering time, necessary for adaptation to temperate areas., Author summary The cultivation of maize in temperate climates required the suppression of photoperiod sensitivity and the selection of a wide range of flowering time for the adaptation to local environmental constraints. Photoperiodic flowering requires the production of a systemic protein signal referred to as the florigen, which is transcriptionally activated in leaves. A key question is to what extent the expression of the florigen gene can explain flowering time variability of temperate maize, where photoperiod sensitivity has been eliminated by artificial selection. Our results reveal large variability in two related florigen genes which is strongly correlated with variability in flowering time. Using association genetics approaches we could detect genomic regions responsible for the expression of the two florigens that precisely co-localise with flowering time-related regions, thereby supporting the significance of quantitative changes in florigen levels in driving flowering time variability. Markers associated with florigen expression/flowering time display significant signatures of selection indicating that variable patterns of florigen accumulation underpin the adaptation of temperate maize flowering.

Ethylene regulates many aspects of plant growth and development. It is perceived by a family of ethylene receptors (ETRs) that have been well described. However, a full understanding of ETR function is complicated by functional redundancy between the receptor isoforms. Here, we characterize a new ETR, SlETR7, that was revealed by tomato genome sequencing. SlETR7 expression in tomato fruit pericarp increases when the fruit ripens and its expression is synchronized with the expression of SlETR1, SlETR2, and SlETR5 which occurs later in the ripening phase than the increase observed for SlETR3, SlETR4, and SlETR6. We uncovered an error in the SlETR7 sequence as documented in the ITAG 3 versions of the tomato genome which has now been corrected in ITAG 4, and we showed that it belongs to sub-family II. We also showed that SlETR7 specifically binds ethylene. Overexpression (OE) of SlETR7 resulted in earlier flowering, shorter plants, and smaller fruit than wild type. Knock-out (KO) mutants of SlETR7 produced more ethylene at breaker (Br) and Br + 2 days stages compared to wild type (WT), but there were no other obvious changes in the plant and fruit in these mutant lines. We observed that expression of the other SlETRs is upregulated in fruit of SlETR7 KO mutants, which may explain the absence of obvious ripening phenotypes. Globally, these results show that SlETR7 is a functional ethylene receptor. More work is needed to better understand its specific roles related to the six other tomato ETRs.

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.

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

The article reports the growth stop phenomenon, which was documented only for baobabs, i.e. for trees belonging to the Adansonia genus. The identification of growth stop was enabled by radiocarbon dating, which allows a complex investigation of samples collected from the trunk/stems of baobabs. In several cases, the outermost rings of baobabs, which were close to the bark, were found to be old, with ages of several hundreds of years, instead of being very young. Dating results of samples collected from six baobabs are presented. For multistemmed baobabs, the growth stop may occur only for one or several stems. We identified four factors that may induce the growth stop: (i) stress determined by severe climate conditions, (ii) old age, (iii) the need to keep a stable internal architecture, and (iv) the collapse of stems that survive this trauma. Baobabs and their stems affected by growth stop may survive for several centuries, by continuing to produce leaves, flowers, and fruits. This phenomenon was associated with the capacity of baobabs to store large amounts of water in their trunks/stems in the rainy season. This reservoir of water is used during the dry season and allows the trees to survive prolonged drought periods.

Dans le but d’obtenir des éléments de compréhension de la croissance des arbres en milieu urbain, des micro-dendromètres PépiPIAF permettant le suivi en continu des variations de diamètre de charpentières ont été installés dans la ville de Paris sur des Marronniers blancs (Aseculus hippocastanum L.). Cette essence, très répandue en milieu urbain et fortement appréciée pour sa longue floraison printanière, est souvent menacés par un insecte (Cameraria Ohridella), dont les larves creusent des tunnels appelés « mines », provoquant le dessèchement des feuilles et leurs chutes précoces en plein été. Nos résultats montent que le suivi en continu de la croissance diamétrale permet de visualiser le débourrement des marronniers et l’intensité variable de leur floraison selon les individus. Ces mesures nous conduisent à faire des hypothèses sur l’utilisation et la localisation des réserves carbonées durant cette phase phénologique que représente la floraison et sur le coût carboné selon l’intensité de cette dernière. Les mêmes mesures nous indiquent clairement et précocement (15 jours à un mois avant la détection visuelle) le développement de l’infection par la mineuse des feuilles des Marronniers et les conséquences sur la croissance en diamètre des branches instrumentées.

Depuis 2001, je développe des travaux sur l’étude du déterminisme génétique de caractères d’intérêt chez le rosier. Ces travaux ont été menés sur des populations issues de croisements et à partir desquels plusieurs cartes génétiques (marqueurs AFLP, microsatellites et SNP) ont été construites. Plusieurs caractères ont été étudiés : remontée de floraison, nombre de pétales, date de floraison, composants architecturaux, composants du parfum et plus récemment résistance à la maladie de la tâche noire et nombre d’épines. Ces deux derniers caractères font l’objet de deux sujets de thèse que je co-encadre. Pour l’ensemble de ces caractères, des gènes majeurs et/ou QTLs ont été identifiés sur les groupes de liaison des différentes cartes génétiques. La carte génétique haute densité de la population OW a été utilisée pour l’ancrage du génome du rosier et a permis d’obtenir un génome de bonne qualité comprenant 196 contigs assignés sur les 7 pseudo molécules du génome. En parallèle, j’ai participé à l’établissement d’un protocole de transformation génétique du rosier pour étudier par validation fonctionnelle des gènes candidats dans la mise en place des caractères étudiés. Nous possédons un système fonctionnel bien qu’encore long et peu efficace. et dont l’efficacité doit être amélioréeDans le cadre de collaboration avec des partenaires privés, j’ai développé et dirigé plusieurs projets sur l’étude de maladies foliaires du rosier et notamment sur la maladie des tâches noires. Ces travaux nous ont permis de développer une collection de souches de champignons et de montrer que les souches isolées sur rosier sauvage se différenciaient des souches isolées sur rosier moderne. Un test sur boutures en conditions contrôlées a été développé pour étudier la virulence et l’agressivité de ces souches. Ces travaux ont été en grande partie menés dans le cadre d’encadrement ou co-encadrement de stagiaires, étudiants, CDD et personnels permanents.Comme Anne Sylvestre, j'aime les gens qui doutent

Histone methylation catalyzed by histone methyltransferase is essential in transcriptional regulation of gene expression. Histone methyltransferases are known to play crucial roles in multiple cellular processes in plants. My PhD work investigated the biological function of two histone methyltransferases in controlling plant responses to various environmental stimuli in Arabidopsis thaliana. In the first part, my results demonstrated that the H3K36-methyltransferase SDG8 transcriptionally regulates NPR1, a central player in salicylic acid-mediated immunity and co-acts with the RNAPII to enable the efficient transcriptional induction of several defense genes upon stimulation. In the second part, my work unraveled that SDG26, another ortholog of the animal H3K36-methyltransferase, plays an important role in plant response to abiotic stresses. By focusing on cold stress, SDG26 was shown to regulate the cold stress response by directly activating the transcription of SOC1 and CBF genes through binding their chromatin and depositing H3K36me3. Interestingly, SDG26 mastered the accumulation of ABA by regulating the expression of ABA homeostasis-related genes, suggesting an involvement of ABA pathway in the cold response. In the last part, using a genetic approach my work established SDG26 as an autonomous flowering pathway component. Accordingly, SDG26 was found in a multiple-protein complex comprising the histone demethylase FLD, the homeobox-domain transcription factor LD, as well as a putative COMPASS component APRF1. This multiple-protein complex was found in controlling the repression of the major flowering repressor FLC as well as the activation of the flowering activator SOC1 to precisely regulate the floral transition.; La méthylation des histones par des histone-méthyltransférases est essentielle à la régulation de la transcription. Chez les végétaux, plusieurs méthyltransférases jouent un rôle central dans différents processus cellulaires. Lors de ma thèse, j'ai étudié la fonction biologique de deux d’entre elles dans le contrôle des réponses à plusieurs stimuli chez Arabidopsis thaliana. Premièrement, mes résultats ont permis de démontrer que SDG8, une méthyltransférase spécifique de H3K36, contrôlait la transcription de NPR1, un acteur central de l’immunité induite par l’acide salicylique, et en lien avec la RNAPII permettait l’induction transcriptionnelle efficace de plusieurs gènes de défense suite à leur stimulation. Deuxièmement, j'ai démontré que SDG26, une méthyltransférase proche de SDG8, jouait un rôle important dans la réponse aux stress abiotiques. J'ai découvert ainsi que SDG26 régulait la réponse au froid en activant directement la transcription des gènes SOC1 et CBF en se liant à leur chromatine et en déposant H3K36me3. Sachant que l’acide abscissique (ABA) joue un rôle important dans la réponse aux stress abiotiques, j'ai pu constater que SDG26 contrôlait l'accumulation d'ABA en régulant l'expression de gènes liés à son homéostasie. Enfin, j'ai confirmé par une approche génétique que SDG26 était un élément appartenant à la voie de floraison dite autonome. Au sein d'un complexe multi-protéique comprenant l'histone déméthylase FLD, le facteur de transcription homéobox LD, ainsi qu'un composant de COMPASS, APRF1, SDG26 semble contrôler la transcription du répresseur de floraison, FLC, ainsi que de sa cible, l'activateur de floraison SOC1, afin de réguler précisément la transition florale.

Low temperatures are required to regulate the transition from vegetative to reproductive growth via a pathway called vernalization. In wheat, vernalization predominantly involves the cold upregulation of the floral activator VERNALIZATION1 (VRN1). Here, we have used an extreme vernalization response, identified through studying ambient temperature responses, to reveal the complexity of temperature inputs into VRN-A1, with allelic inter-copy variation at a gene expansion of VRN-A1 modulating these effects. We find that the repressors of the reproductive transition, VERNALIZATION2 (VRN2) and ODDSOC2, are re-activated when plants experience high temperatures during and after vernalization. In addition, this re-activation is regulated by photoperiod for VRN2 but was independent of photoperiod for ODDSOC2. We also find this warm temperature interruption affects flowering time and floret number and is stage specific. This research highlights the important balance between floral activators and repressors in coordinating the response of a plant to temperature, and that the absence of warmth is essential for the completion of vernalization. This knowledge can be used to develop agricultural germplasm with more predictable vernalization responses that will be more resilient to variable growth temperatures., Highlighted Article: Analysis of the flowering and growth responses of a range of Triticum aestivum cultivars to warmer growth temperatures reveals an additional layer of temperature regulation in the vernalization response pathway.

RATIONALE Flowering is a particularly important trait in coffee (Cofjea arabica L.). It determines the coffee yield, quality and production costs. It defines the critical period of highest demand for nutrients, water and pest and disease control. During this development phase, the plant is most susceptible to extreme climatic conditions. Factors such as temperature, light, soil and air water availability, carbon-to-nitrogen ratio, crop load and genotype can affect flowering. Recent advances in understanding the physiological mechanisms of the coffee plant, including the effects of elevated atmospheric [C02], have greatly improved our abilities to predict possible impacts of climate change on coffee's photosynthetic capacity and allocation of photoassimilates. Yet, we know very little regarding the effects of climate change on reproductive processes and hence final crop yield. The question arises thus, whether flowering might constitute the process most affected by increasing temperature and changes in rainfall pattern and intensity, even though the coffee's physiology might be able to partially adapt. This study reviews current knowledge on coffee flowering and its possible response to climate change. We use a simulation model to evaluate the impact of possible changes in climate on flowering success. METHODS We use a process-based coffee model with a detailed flowering module representing different assumptions regarding flowering initiation, intensity, and success, accounting for multiple flowering events. The flowering module was implemented using an age-structured matrix population model that classifies the flowering process into five development stages: Nodes, floral initiation, ready to flower, pinhead stage, and bean maturation. The model is compared to observation data registered in Cajibio, Cauca, Colombia and climate change scenarios are explored using different assumptions. RESULTS We highlight important knowledge gaps related to coffee flowering success. The key question will be whether floral initiation, abnormal flowering, and flower abortion are caused by heat and water stress independent of carbohydrate supply and hence unaffected by elevated atmospheric [C02]. Heat sterility reduces bean yield independent of atmospheric [C02], yet we know little about these temperature thresholds, nor whether differences exist among coffee varieties. We show how climate variability (e.g. El Nino-Southern Oscillation[ENSO]) affects flowering and biennual bearing in different climatic conditions, requiring careful adaptation of agronomic management depending on ENSO year. CONCLUSIONS & PERSPECTIVES By combining field observations and simulation models we can test different assumptions on how climate affects coffee flowering (number of events, intensity and survival) and hence agronomic management needs, labour demand, bean yield, and profitability. Closing the knowledge gaps of the mechanisms of flowering success as affected by temperature, rainfall, and light will require detailed flowering data sets distributed across the coffee growing regions to test our current assumptions. Consequently, we would like to take this opportunity to develop a network to share data between instiutions and researchers on this strategic issue.

Con el propósito de simular la fenología y el comportamiento de la curva de floración de plantaciones comerciales de banano (Musa AAA, Cavendish, cv. 'Grande Naine') bajo condiciones de la Vertiente Caribe de Costa Rica, se calibró y optimizó un modelo alternativo (SIMBA-CR), a partir del modelo SIMBA-POP desarrollado en las islas de Martinica y La Guadalupe para este cultivo. Los registros de 48 áreas de plantación o “cables” provenientes de tres plantaciones de banano fueron usados. El modelo SIMBA-CR se adaptó para simular el desarrollo de las plantas individuales de banano desde la siembra, considerando la temperatura ambiental, por medio de los Grados-Día Acumulados (GDA), como la principal variable climática que determina el desarrollo de la planta. Bajo las condiciones en que se desarrolló este estudio, el modelo SIMBA-CR es una buena herramienta, con la que los productores de banano pueden estimar con mayor precisión la curva de floración del cultivo, con respecto a la metodología tradicional empleada en las fincas.

International audience

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.

Natural selection driven by water availability has resulted in considerable variation for traits associated with drought tolerance and leaf‐level water‐use efficiency (WUE). In Arabidopsis, little is known about the variation of whole‐plant water use (PWU) and whole‐plant WUE (transpiration efficiency). To investigate the genetic basis of PWU, we developed a novel proxy trait by combining flowering time and rosette water use to estimate lifetime PWU. We validated its usefulness for large‐scale screening of mapping populations in a subset of ecotypes. This parameter subsequently facilitated the screening of water use and drought tolerance traits in a recombinant inbred line population derived from two Arabidopsis accessions with distinct water‐use strategies, namely, C24 (low PWU) and Col‐0 (high PWU). Subsequent quantitative trait loci mapping and validation through near‐isogenic lines identified two causal quantitative trait loci, which showed that a combination of weak and nonfunctional alleles of the FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) genes substantially reduced plant water use due to their control of flowering time. Crucially, we observed that reducing flowering time and consequently water use did not penalize reproductive performance, as such water productivity (seed produced per unit of water transpired) improved. Natural polymorphisms of FRI and FLC have previously been elucidated as key determinants of natural variation in intrinsic WUE (δ13C). However, in the genetic backgrounds tested here, drought tolerance traits, stomatal conductance, δ13C. and rosette water use were independent of allelic variation at FRI and FLC, suggesting that flowering is critical in determining lifetime PWU but not always leaf‐level traits., Accelerated flowering time achieved through nonfunctional and weak alleles of flowering time genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC) reduce water use in Arabidopsis thaliana without detrimentally impacting reproductive output.

This chapter concerns the use of flowering plants in organic agroecosystems. First, a review of the available literature explores the use of flower strips in controlling pest populations as part of conservation biological control. The positive effects of flower strips on beneficial insects are then explored and potential candidates for flower strips proposed. Finally, practical recommendations for installing flower strips are given. Secondly, a case study is presented: The use of flowering plants in organic mango orchards in Reunion. We study the interactions between selected flowering plants and beneficial and pest arthropods. We initially focus on all arthropods and we characterize the insect fauna present on three selected plants. We then focus on the entomological group Parasitica (Hymenoptera), many of which are parasitoids of other insects, including pests. The plant with the greatest abundance and diversity of Parasitica is Lobularia maritima (Brassicaceae). In 2013, we used malaise traps to ascertain that an orchard containing flower strips harbors 10 times more parasitoids than a bare orchard. These results confirm the value of using flowering plants as a conservation biological control tool to encourage pest parasitoids in organic farming.

Highlight In perpetual flowering genotypes of strawberry, there are four phases of flowering of which the intensity of the last one is controlled by a newly identified locus., The genetic control of the switch between seasonal and perpetual flowering has been deciphered in various perennial species. However, little is known about the genetic control of the dynamics of perpetual flowering, which changes abruptly at well-defined time instants during the growing season. Here, we characterize the perpetual flowering pattern and identify new genetic controls of this pattern in the cultivated strawberry. Twenty-one perpetual flowering strawberry genotypes were phenotyped at the macroscopic scale for their course of emergence of inflorescences and stolons during the growing season. A longitudinal analysis based on the segmentation of flowering rate profiles using multiple change-point models was conducted. The flowering pattern of perpetual flowering genotypes takes the form of three or four successive phases: an autumn-initiated flowering phase, a flowering pause, and a single stationary perpetual flowering phase or two perpetual flowering phases, the second one being more intense. The genetic control of flowering was analysed by quantitative trait locus mapping of flowering traits based on these flowering phases. We showed that the occurrence of a fourth phase of intense flowering is controlled by a newly identified locus, different from the locus FaPFRU, controlling the switch between seasonal and perpetual flowering behaviour. The role of this locus was validated by the analysis of data obtained previously during six consecutive years.

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