Plus de la moitié des pertes de bois dans les forêts européennes sont dues aux tempêtes. Une connaissance des mécanismes impliqués dans la stabilité mécanique des arbres est alors capitale. L’ancrage de l’arbre dans le sol constitue l’une des composantes principales du maintien mécanique de l’arbre. Il est principalement déterminé par l’architecture du système racinaire et son interaction mécanique avec le sol. Au cours de son développement, l’arbre modifie ses dimensions et se complexifie. Plus particulièrement, le système racinaire semble s’acclimater (ex : croissance en diamètre plus importante) aux déformations engendrées par le vent. L’ensemble de ces modifications conduit à une évolution des mécanismes à l’origine de l’ancrage au cours du développement de l’arbre. L’étude expérimentale de cette fonction est compliquée car les racines sont difficilement mesurables en continu dans le sol. Nous avons alors mis au point une approche numérique pour décrire la croissance du système racinaire et la distribution des déformations dues au vent. Une grande base de données structurée en chronoséquence de systèmes racinaires numérisés (Pinus pinaster) a été mobilisée. Comme l’étude de la structure et des fonctions des racines est plus efficiente quand la différentiation entre racines est prise en compte, nous avons d’abord formalisé les types racinaires du système racinaire du pin maritime à partir d’une technique de classification (« k-means clustering ») réalisée avec quatre variables. La classification des racines latérales du pin maritime nous a permis d’identifier 5 types racinaires au cours du développement du pin maritime. Ce regroupement explique 70% de la variabilité de notre base de données. Chaque système racinaire est caractérisé par trois grosses racines horizontales émises par la souche. Les racines montrent une forte différentiation pour leur tropisme, avec une direction de croissance soit horizontale soit verticale. La structure de la partie centrale du système racinaire est pratiquement complète dès l'âge de 4 ans. Sur la base des types racinaires identifiés, nous avons calibré un modèle architectural (RootTyp ; Pagès et al. 2004) pour le pin maritime. Treize paramètres pour chaque type racinaire ont été estimés par l’intermédiaire de la base de données, d’informations issues de la littérature et d’une procédure d'optimisation. Une modélisation réaliste du système racinaire jusqu'à 50 ans n’a pu être obtenue qu'en implémentant au modèle RootTyp de nouveaux processus biologiques : la diminution de la ramification avec la croissance de la racine et la diminution de la vigueur des racines avec l'ordre de ramification. Malgré ces améliorations, les systèmes racinaires de la base de données présentent des diamètres plus importants à proximité de la souche par rapport aux systèmes racinaires simulés. Ce biais systématique est principalement attribué à l’acclimatation des racines au vent dominant. Les altérations de croissance dues aux contraintes pédologiques ont également été implémentées grâce à l’amélioration du module de sol du modèle architectural.Enfin, pour comprendre les mécanismes à l’origine de l’acclimatation des racines nous avons combiné plusieurs modèles pour prédire la distribution spatiale des déformations dans des maquettes simplifiées de systèmes racinaires à 4, 6 et 13 ans, pour trois régimes de vent spécifiques à la région étudiée. D’après les simulations, les déformations des racines sous l'effet du vent diminuent avec l’âge, en raison de l’augmentation de la rigidité des racines. Cela suggère une plus forte réponse thigmomorphogénétique aux stades jeunes. Les modifications structurelles et anatomiques du système racinaire par acclimatation au vent s’expliquent principalement par les distributions des déformations et des contraintes dans les racines. / Storms cause more than 50% of the timber loss in European forests. However, forest tree anchorage mechanisms throughout their lifespan are not fully understood, especially the strong acclimation of root systems to common winds. This lack of knowledge is mainly due to technical difficulties: neither the root structure nor the mechanical contribution of the roots could be characterized continually. Thus we set up a numerical approach to model the development of the root system and to describe the strains resulting from common winds. This generic approach has been developed using Pinus pinaster grown in sandy soils as model species.Seven datasets of excavated root systems from 0 to 50 years were employed. The assessment of root structure and functions is more powerful if the differentiation of root system in several root types is considered. We first proposed an automatic classification of roots with the k-means clustering algorithm. Four root traits were chosen as classifiers, including three geometric architectural traits, which can be precisely assessed whatever the tree/root age. Clustering yielded similar five groups of laterals roots at all ages, explaining 70% of the variability. The three largest lateral roots per tree were all horizontal roots branching from stump and the other lateral roots show a large differentiation for tropism: nearly all the roots were horizontal or vertical roots. The framework of the central part of the root system can be almost completed in 4-year-old trees (3.5 cm collar diameter). We then calibrated the existing RootTyp (Pagès et al. 2004) architectural model for P. pinaster for each of the root types defined by the cluster analysis. We used the database combined with a literature review and an optimization method to get accurate values for 13 parameters by root types. We devoted effort to validate our model calibration. In order to model architecture of the root system, damping properties had to be implemented to yield realistic outputs up to the mature stage. Branching varied as a function of distance from the root base, and growth capacity decreased with branching order. Nevertheless, the root diameters of simulated root systems were generally underestimated. This was certainly due to root growth plasticity to the prevailing wind, an acclimation facet not taken into account at this calibration step. Growth alterations due to a cemented horizon were reproduced using the new calibrated soil module. Then, the wind acclimation of roots was numerically investigated by examining the root mechanical stimuli due to wind. A chain of biomechanical models was used to predict the spatial distribution of stress and strain in simplified root systems at 4, 6 and 13-year-old as a result of three levels of usual winds. According to simulations, the strain amplitude decreased with tree growth due to the increasing root system stiffness. This suggests larger thigmomorphogenetic responses at young stages. The modifications of the structural and wood root properties related to wind acclimation were largely explained by the stress and strain distribution in the root system.

Development Related Termination of the Root Apical Meristem Activity Abstract Root system architecture is modulated through growth and branching of individual roots, while the growth is strictly regulated via long term apical meristem (RAM) maintenance and cell elongation. RAM activity is not consistent during root on- togeny, which was shown in several dicotyledonous species as change in root meristem structure and decline in root growth rate during individual root development. This thesis is focused on changes in extent and arrangement of meristematic tissues and their derivatives within adventitious roots of Acorus calamus and Oryza sativa during long term cultivation. Changes in meristem and elongation zone length, the root cap length, radial tissue complexity, as well as the changes in root hair emergence, etc., are put into relation with quantified expression level of selected important regulatory elements taking part in RAM maintenance (WOX and SCR family transcription factors). Methodology and approach for future research in this field are outlined. Keywords: Root, Apical Meristem, Root System Architecture, RAM Termination

Increasing salinity is a worldwide problem, but the knowledge on how salt enters the roots of plants remains largely unknown. Non-selective cation channels (NSCCs) have been suggested to be the major pathway for the entry of sodium ions (Na+) in several species. The hypothesis tested in this research is that PQ loop (PQL) proteins could form NSCCs, mediate some of the Na+ influx into the root and contribute to ion accumulation and the inhibition of growth in saline conditions. This is based on previous preliminary evidence indicating similarities in the properties of NSCC currents and currents mediated by PQL proteins, such as the inhibition of an inward cation current mediated by PQL proteins by high external calcium and pH acidification. PQL family members belonging to clade one in Arabidopsis and barley were characterized using a reverse genetics approach, electrophysiology and high-throughput phenotyping. Expression of AtPQL1a and HvPQL1 in HEK293 cells increased Na+ and K+ inward currents in whole cell membranes. However, when GFP-tagged PQL proteins were transiently overexpressed in tobacco leaf cells, the proteins appeared to localize to intracellular membrane structures. Based on q-RT-PCR, the levels of mRNA of AtPQL1a, AtPQL1b and AtPQL1c is higher in salt stressed plants compared to control plants in the shoot tissue, while the mRNA levels in the root tissue did not change in response to stress. Salt stress responses of lines with altered expression of AtPQL1a, AtPQL1b and AtPQL1c were examined using RGB and chlorophyll fluorescence imaging of plants growing in soil in a controlled environment chamber. Decreases in the levels of expression of AtPQL1a, AtPQL1b and AtPQL1c resulted in larger rosettes, when measured seven days after salt stress imposition. Interestingly, overexpression of AtPQL1a also resulted in plants having larger rosettes in salt stress conditions. Differences between the mutants and the wild-type plants were not observed at earlier stages, suggesting that PQLs might be involved in long-term responses to salt stress. These results contribute towards a better understanding of the role of PQLs in salinity tolerance and provide new targets for crop improvement.

Monitoring, tracking, and analyzing the dynamic growth of a living organism is essential to understanding its response to changes in its surrounding environment. Imaging tools to study these dynamics at spatial and temporal scales with optimal resolution rely on high-performance instrumentations. These systems are generally costly, stationary, and not flexible. In addition, performing non-destructive high-throughput phenotyping to extract roots' structural and morphological features remains challenging. We developed the MultipleXLab: a modular, mobile, and cost-effective robotic root imager to tackle these limitations. Among its advantages associated with a large field-of-view, integrated programmable plant-growth lighting, and high magnification with a high resolving power, the system is useful for a wide range of biological applications. We have also created the MultipleXLab Advanced; this configuration turns the system into a mobile environmental chamber by also featuring temperature control and automated irrigation. Another system we developed was the MultipleXLab Advanced Fluorescence to allow fluorescence imaging with a resolution that competes with a fluorescence binocular or even a fluorescence microscope. Furthermore, we have implemented various technologies and techniques to facilitate 3D imaging and quantification, ranging from X-ray micro-Computed Tomography to 3D segmentation of tissues, cells, and cellular compartments within the cell imaged using Confocal Laser Scanning Microscopy. For future research, we have conceptualized an upscaled system named MultipleXLabXL. This larger system will allow tracking, monitoring, and quantifying root growth of a much higher number of seedlings for more extended periods.

Crop yields are expected to face more threatening circumstances due to ongoing climatic and environmental change. The continued sustainability of crop production will depend on genetic capacity of crops to adapt to increased biotic and abiotic barriers induced by climate change. Historically, shoot-based traits were breeding targets for overcoming yield gaps between developed and undeveloped nations. However, the rate of genetic gain has stabilized with conventional breeding targets for indirect yield improvement. As the availability of mineral fertilizers is steadily declining and the occurrence of low-fertility soils has increased, reoccurring yield disparities worldwide are propelling us to evaluate new breeding targets. There is potential for plant breeders to shift their focus to the root system architecture (RSA) as a new target for indirect selection, enabled by the phenotypic plasticity of winter wheat (Triticum sp.), one of the main staple agronomic crops. Our current limited understanding of the dynamic nature of the root system architecture is due to the difficulties associated with in situ phenotyping and characterization of anatomical traits. The objectives of this thesis were to 1) review advancements in root phenotyping methodologies and past, present, and future predictions; 2) evaluate differences in root biomass accumulation and remobilization among 22 Virginia Tech-developed elite germplasm; 3) evaluate potential genetic variability for root biomass accumulation across breeding lines. Minimal genetic variation was observed for root biomass accumulation through time. Soil coring proved not to be a very effective method for capturing genetic variability of root biomass accumulation from a soil depth of 10 cm. However, a low genetic signal was also observed for shoot biomass, even though the entire field plot for each genotype was sampled. Yet, a considerably higher genetic signal was observed for plant height. These results suggest that both root and shoot biomass are complex, polygenic traits that require significantly more attention to evaluate genetic differences. / Master of Science / Climate change induces numerous abiotic and biotic barriers to our global cropping systems. Mineral fertilizer reserves are expected to deplete within the next 80 years while our agricultural lands continue losing fertility. This translates into increased yield discrepancies among the most prominent staple agronomic crops. Historically, crop improvement has been performed through indirect selection upon shoot-based traits for yield improvement. However, the capacity of genetic gain from these conventional selection criteria is projected to stabilize. Therefore, it would be beneficial for future global crop production if the initiative was taken to identify a new breeding target that can ensure climate resiliency in staple crops, such as winter wheat (Triticum). Root system architecture (RSA) is defined as the spatial distribution of embryonic and post-embryonic roots throughout a growth medium. This has the potential to become a new breeding target. However, there are numerous difficulties to overcome when evaluating roots in situ. In addition, there is no standardized root phenotyping method that can be implemented nationwide due to the variability in phenotypic response in various growing environments. The objectives of this thesis are to 1) reveal the advancements in root phenotyping and its legitimacy for standardization, 2) explore the genetic architecture of root system architecture, and 3) evaluate the genetic variability of root biomass accumulation for climate resiliency. Minimal genetic variation was observed for root biomass accumulation through time. Soil coring proved not to be a very effective method for capturing genetic variability of root biomass accumulation from a soil depth of 10 cm. However, a low genetic signal was also observed for shoot biomass, even though the entire field plot for each genotype was sampled. Yet, a considerably higher genetic signal was observed for plant height. These results suggest that both root and shoot biomass are complex, polygenic traits that require significantly more attention to evaluate genetic differences.

Dans de nombreux projets de végétalisation, le sol est la principale entrave à l’implantation des végétaux. Il est donc fondamental de connaitre la manière dont les systèmes racinaires se mettent en place dans le sol. La mise en place du système racinaire dans le milieu souterrain correspond à l’expression du patrimoine génétique guidé par les contraintes du sol. A travers ce document nous avons tout d’abord présenté la mise en place des systèmes racinaires des espèces herbacées résultant du patrimoine génétique puis nous avons présenté sa plasticité face à certaines contraintes du sol. Les espèces ne possèdent pas forcément un simple système racinaire mais une combinaison de systèmes racinaires qui se met progressivement en place. Nous présentons dans ce document une typologie et une classification de ces systèmes racinaires selon leur localisation et l’implication de l’organe-support dans la multiplication de l’espèce. Nous nous intéressons aussi à l’effet des contraintes du sol sur la mise en place de l’architecture racinaire : la résistance à la pénétration qui est une contrainte récurrente même dans les terres cultivées et la porosité grossière qui est une contrainte présente dans les sols remaniés. Des expérimentations ont été menées sur une diversité d’espèces herbacées afin de comparer leur architecture racinaire en présence ou non une zone de contrainte. Concernant la résistance à la pénétration, nous retrouvons et généralisons les résultats obtenus par d’autres chercheurs sur d’autres espèces herbacées tels que la diminution du taux de croissance ou l’augmentation du diamètre des racines au niveau de la contrainte. De même, nous retrouvons des traits prédictifs de capacité de pénétration tels que le diamètre apical racinaire et le taux de croissance racinaire et nous mettons en avant la teneur en matière sèche du système racinaire avec une corrélation négative. Concernant la porosité grossière, nous observons un effet sur la croissance racinaire, le diamètre apical racinaire et le développement de primordia lorsque la porosité est très grossière / In many revegetation projects, the soil is the main obstacle to the establishment of plants. It is therefore essential to know how the root systems are set up in the ground. The root systems establishment is the expression of the genetic heritage guided by the constraints of the environment. In this document we first presented the root systems development of herbaceous species resulting from genetic and then we presented its plasticity face to soil constraints. The species do not have a single root system, but a combination of root systems that are implemented gradually. We present here a typology and classification of root systems depending on their location and on the bearing-organ involvement in the vegetative multiplication of the species. We are also interested in the effect of soil constraints on the development of root architecture: the penetration resistance is a recurring stress even in cultivated land and the gross porosity is a stress present in soils reworked. Experiments were conducted on a variety of herbaceous species to compare their root architecture with or without a stress zone. Regarding the penetration resistance, we find and generalize the results obtained by other researchers on other herbaceous species such as the decreasing root growth rate or the increasing root diameter at the level of the stress. Similarly, we find the traits predicting the penetration such as root apical diameter and root growth rates and we highlight the root dry matter content with a negative correlation. Regarding the gross porosity, we observe an effect on root growth rate, root apical diameter and primordia development when the porosity is very gross

La sélection des nouveaux porte-greffes du genre Prunus a pour principal objectif d’utiliser lavariabilité génétique existant au sein des différentes espèces de Prunus afin de créer un matérielvégétal innovant, performant au plan agronomique et résistant à différentes contraintes biotiques etabiotiques. L’exploitation de la variabilité génétique s'appuie sur le phénotypage des différentsindividus présents dans les collections de ressources génétiques pour les caractères recherchés. Celapermet de sélectionner des génotypes spécifiques pour améliorer un trait donné.Dans cette étude constituée de deux parties, nous avons exploré la diversité génétique au seindu genre Prunus pour ce qui concerne deux traits importants : l’aptitude au bouturage et les réponsesde certains porte-greffes à la contrainte hydrique.Dans la première partie l’aptitude au bouturage ligneux a été explorée dans une collectiongénétique de 222 génotypes. Les résultats obtenus montrent une variabilité considérable entre les sousgenresAmygdalus et Prunophora et également une variabilité interspécifique au sein de chaque sousgenre.La réussite au bouturage est nettement améliorée chez les hybrides interspécifiques dont un desparents appartient à l’espèce P cerasifera.Dans la deuxième partie nous avons étudié les réponses à la contrainte hydrique chez neufgénotypes couramment utilisés comme porte-greffes. Nous avons comparé trois régimes hydriquesdifférents : témoins, stressés et recouvrés. L’humidité du substrat est maintenue à la capacité au champtout au long de l’expérience pour les plants témoins, par contre l’arrosage a été arrêté pendant 14 jourspour les plants stressés, puis il a été repris pendant 10 jours pour les plants recouvrés. Durant cetteexpérience, nous avons effectué des mesures morphologiques et physiologiques sur la partie aérienneainsi que des excavations à la fin de chaque phase pour examiner les modifications au niveau dusystème racinaire. Sur la partie aérienne, la contrainte hydrique a provoqué une diminutionsignificative de la photosynthèse nette, de la transpiration totale, de la conductance stomatique, et del’expansion des feuilles.Le système racinaire a répondu à cette contrainte par plusieurs modifications. D’abord, le ratio racines/pousses a augmenté pour 4 génotypes (GF305, GF677, Montclar et Myrobolan1254). Ensuite, lesdifférents traits de l’architecture racinaire ont montré des modifications sous l’effet de la contraintehydrique : la longueur de la zone apicale non ramifiée (LZANR) qui traduit l’élongation racinaire,ainsi que les diamètres apicaux des racines ont diminué chez tous les génotypes. Par conséquent lesracines se sont affinées et ont réduit leur croissance en longueur. Produire des racines plus finesaugmente la surface de contact entre les racines et le sol et améliore la capacité d’absorption. Unediminution de la distance inter-ramification a été observée chez les plants stressés. Cette modificationpourrait s’expliquer par le fait que les plantes produisent plus de racines latérales en profondeur oùl’eau est souvent plus disponible. De plus, les racines latérales produites étaient également plus fines.Au plan qualitatif, les génotypes ont eu des réponses semblables, mais l’intensité de la réponse a variéselon les génotypes. / In breeding programs of Prunus rootstocks the aim is to use the existing genetic variabilitywithin Prunus species in order to create new rootstock genotypes with excellent agronomic traits, andimproved resistance to biotic and abiotic stresses.Exploitation of the genetic variability is based on the evaluation of phenotypic variation amongindividuals within genetic collections for desirable traits. This make possible to select specificgenotypes to improve a given trait.This study consists of two parts; we explored the genetic diversity within the genus Prunusregarding two important characteristics: rooting ability of hardwood cuttings and responses of somerootstocks to water stress.In the first part, rooting ability of hardwood cuttings was evaluated among 222 genotypespreserved in genetic collection. The results show considerable variability among the sub genusAmygdalus, Prunophora, and also an interspecific variability within each of them. Rooting ability byhardwood cutting was significantly improved in interspecific hybrids if one parent belongs to Pcerasifera species.In the second part of this study we studied the responses of nine genotypes, commonly usedrootstocks, to water stress. We applied three treatments: control, water stress and recovering.Soil moisture was maintained at field capacity through all stages of the experiment for the controlplants. On the contrary we stopped watering during 14 days for the stressed plants, and then we rewateredthe recovered plants for 10 days.During this experience, we performed morphological and physiological measurements on the aboveground parts of plants and we excavated plants at the end of each phase to observe root systemmodifications.Aboveground parts of plant responded to water stress by a significant decrease in net photosynthesis,total transpiration, stomatal conductance and leaf expansion.Root system responded to water stress by several modifications:Four genotypes (GF305, Montclar, GF677 and Myrobolan) showed a significant increase in root toshoot ratio under drought conditions. We also detected morphological modifications on the differenttraits of root architecture in response to water stress.The length of the apical unbranched zone LAUZ and the apical diameter were decreased forall genotypes, consequently, roots became finer and reduced their rate of elongation. Fine rootsenhance the surface of contact between roots and soil which in turn improve the acquisition of waterunder drought condition.The inter-branch distance also responded, and it tended to decrease under the water stress treatment.The decrease in inter-branch distance can be explained by a production of more lateral roots in deeplayers, where water was more available, moreover these new laterals roots were also finer.Qualitatively, a common response to water stress was observed on the different traits of the rootsystem architecture, but we showed a genotypic effect determining the level of the response.

Les tempêtes hivernales causent des pertes en bois qui s’élèvent à 50% du volume des dégâts dans les forêts européennes. Les phénomènes de déracinement des arbres (chablis) sont les plus fréquents or ils sont encore mal compris. Cette thèse vise à mieux comprendre le processus de déracinement de l’arbre et à identifier les traits structuraux et matériels (racines, sol) ayant un effet du premier ordre sur l’ancrage racinaire dans le cas du Pinus pinaster. Un modèle d’éléments finis a été développé et permis de simuler et suivre la chronologie des ruptures successives au cours du déracinement. Un seuil de rupture globale de l’ancrage est ainsi défini comme une résultante de l’architecture et de la résistance des matériaux en jeu (racines, sol). Cela devrait permettre à terme d’améliorer les modèles de risque au vent qui actuellement n’incluent pas de relation mécaniste pour le chablis. Dans la même logique, nous nous sommes appuyés sur les données expérimentales pour construire une architecture simplifiée du système racinaire du P. pinaster. L’importance des différentes composantes sur le mécanisme d’ancrage a été étudiée et le rôle essentiel joué par le pivot et les racines traçantes montré. Ce résultat confirme de nombreuses études expérimentales et théoriques et pour la première fois permet de quantifier ces effets. Le nombre de paramètres pertinents pourra ainsi être réduit pour exprimer l’ancrage. Cela ouvre des perspectives intéressantes pour simplifier l’utilisation du modèle pour l’appliquer à d’autres espèces, d’autres conditions de sol et différentes pratiques sylvicoles. / Winter storms cause 50% of wood damage by volume to European forests. Tree uprooting isthe most frequent phenomenon during storms ; however the mechanism is not well understood.This thesis aims to better understand the tree uprooting process and to identify both rootstructural features and material properties which have first-order effects on tree anchoragestrength for the case ofPinus pinaster. A Finite Element Model has been developed and allowedsimulating and tracking the sequential root breakage during the course of tree overturning. Anoverall tree anchorage strength is thus defined as the resultant of contribution of root systemarchitecture and material strength (roots, soil). This would allow improving the risk modelswhich currently don’t include any mechanistic relationships to describe tree uprooting. In thesame spirit, we have relied on root architectural data to build a simplified root system patternwith features ofP. pinaster. Importance of different root components has been studied andthe essential role of the taproot and shallow roots demonstrated. This result has confirmednumerous experimental and theoretical studies and for the first time quantified these impacts.Therefore the number of relevant parameters can be reduced to express overall root anchorage.This opens new prospects to simplify the model in order to apply to other species under othersoil conditions and considering different silvicultural practices