Dissertations / Theses on the topic 'Root meristems'

Continuing root growth is crucial for the ongoing survival of a plant and provides the structure basis for the acquisition of valuable resources such as water and nutrients required for growth and development. The root apical meristem, located at the root apex, contains a stem cell niche which is the source of root cell production and patterning. This project focuses on the influence of phytohormone signalling upon the maintenance of the root apical meristem (RAM) in Arabidopsis thaliana. Through a combination of physiological, genetic and molecular approaches, the project has uncovered evidence of the involvement of three plant hormones, auxin, abscisic acid (ABA) and ethylene, in regulating the differentiation of stem cells and their descendants in Arabidopsis root meristems. Key findings include: 1) exogenous application of auxin, ABA or 1-aminocyclopropane-1-carboxylic acid (ACC), which is an ethylene precursor, rescues the root meristem failure of a1f3-1 seedlings; 2) exogenous application of ABA promotes QC quiescence and suppresses stem cell differentiation in wild type Arabidopsis root meristems; 3) inhibition of ethylene biosynthesis and mutations that cause ethylene insensitivity induce differentiation of stem cells in root meristems and.i.on the other hand, exogenous application of ethylene precursor or mutations causes ethylene over-production suppress stem cell differentiation in Arabidopsis root meristems; 4) ABA and ethylene interact antagonistically with auxin in the regulation of both stem cell differentiation in Arabidopsis root meristem, and the expression of the CLE40 gene, which encodes a negative regulator of stem cell differentiation in root meristems; 5) ABA modulates the abundance of the LM6 arabinan cell wall epitope within at the root meristem; 6) ethylene suppresses the stem cell differentiation in Arabidopsis root meristems induced by nitrogen (N) and phosphorus (P) deficiencies. The results of the project demonstrate that stem cell regulation in Arabidopsis root meristems involves complex interactions of plant hormones and environmental signals.

La différentiation cellulaire, qui désigne la transition d’une cellule d’un état souche vers un état mature, est un processus morphogénétique : elle s’accompagne de changements phénotypiques cellulaires issus de modifications de l’expression des gènes. L’activation et la répression de l’expression des gènes résulte de l’activité conjointe de facteurs de transcription et de complexes régulateurs de la chromatine qui instruisent des états chromatiniens locaux via des modifications post-traductionnelles (PTM) des histones nucléosomales. Ces états peuvent faciliter ou empêcher la machinerie de transcription de se lier aux séquences promotrices et régulatrices de gènes. Le Complexe Répressif Polycomb 2 (PRC2) est un complexe régulateur de la chromatine spécialisé dans le dépôt de groupes tri-méthyl sur la lysine 27 de l’histone 3 (H3K27me3). H3K27me3 est en général associée à la répression transcriptionnelle. La perte d’activité de PRC2 désorganise les processus développementaux dans le temps et dans l’espace aux échelles cellulaire et tissulaire. Mon projet doctoral vise à étudier le rôle de PRC2 dans la régulation transcriptionnelle au cours de la différentiation cellulaire lors du développement végétatif de la racine d’Arabidopsis thaliana. En intégrant des données épigénomiques et transcriptomiques en cellule unique, publiées et originales, j'ai disséqué les variations d’expression des gènes ciblés par PRC2 au cours de la différentiation de plusieurs types cellulaires de la racine. Je montre d’abord que la régulation transcriptionnelle par PRC2 est essentiellement type cellulaire-spécifique. De fait, l’activité différentielle des gènes ciblés par PRC2 peut être considérée comme une signature de chaque type cellulaire. De plus, les changements d’activité transcriptionnelle au cours de la différentiation surviennent par vagues spécifiques de chaque type cellulaire et auxquelles contribuent significativement les gènes ciblés par PRC2. La seconde partie de ce projet vise à établir une relation de causalité entre l’activité chromatinienne de PRC2, la régulation transcriptionnelle découlant de l’activité de PRC2 et l’exécution correcte de la différentiation lors de la morphogenèse racinaire. Pour cela, une approche de génétique inverse consistant à implémenter chez A. thaliana un système inductible qui génère, dans des populations de cellules et à un stade développemental choisis, la perte de fonction du gène FIE codant pour une sous-unité essentielle de PRC2. D’après nos premières observations, la perte de FIE post-germination phénocopie des mutants constitutifs de PRC2, suggérant l’implication de PRC2 dans l’orchestration de la différentiation, le maintien des niches de cellules souches et la zonation fonctionnelle des méristèmes racinaires.Notre travail met en lumière l’interaction entre régulation chromatinienne par le dépôt d’une PTM d’histone spécifique, H3K27me3, et la régulation transcriptionnelle au cours de la différentiation cellulaire
Cell differentiation, the process that refers to the transition of stem cells to mature cells, is a morphogenetic process resulting in phenotypic changes at the cellular scale. It relies on a profound remodeling of cells transcriptome. Transcription activation and repression are the result of the intertwined activity of both transcription factors and chromatin-modifying complexes that define local chromatin states by depositing post-translational modifications on histone tails, thereby preventing or facilitating the transcription machinery to bind promoters and other regulatory elements. Polycomb Repressive Complex 2 (PRC2) is a chromatin-modifying complex that catalyses the tri-methylation of lysine 27 of histone 3 (H3K27me3) which deposition is associated with repressive chromatin and transcriptional silencing in eukaryotes. Loss of PRC2 activity deeply impacts developmental processes in plants and metazoans, impairing the orchestration of developmental programs in space and in time, at both cellular and tissular scales.My doctoral project aimed at deciphering the role of PRC2 in regulating transcription during the establishment of cell types during post-embryonic development, using the root of Arabidopsis thaliana as model.By integrating both publicly available and original epigenomic and transcriptomic data at the single cell resolution, I dissected the transcriptional response of PRC2-regulated genes all along the differentiation of several root cell types. These analyses first showed that the transcriptional regulation by PRC2 is for the most part cell type-specific and subsequently that the differential expression of PRC2 target genes is a signature of cell types. Moreover, we found that PRC2-regulated genes are dynamically expressed during cell differentiation and that transcriptional changes occur by waves at key stages in the differentiation of each cell type. The second part of this project seeked to establish a direct causal link between PRC2 activity, the resulting transcriptional regulations and the acquisition of cell identities in A. thaliana primary and lateral roots using a reverse genetics approach. We implemented an inducible gene editing system to knock-out FIE, a gene encoding for a core PRC2 subunit, in a cell type- and developmental stage-specific manner. Using this method, we provide the first evidence of causality between PRC2 activity and its involvement in the homeostasis of root cell differentiation during the post-embryonic development of A. thaliana. Preliminary results showed that FIE knock-out after germination phenocopies classical PRC2 mutants, highlighting the role of PRC2 in both guiding root differentiation and maintaining the indeterminacy and the longitudinal patterning of root meristems to support continuous root growth. Taken together, our results shed new lights into the role of chromatin regulation by PRC2 in the transcriptional control of cell differentiation

Durante esse trabalho de pesquisa verificou-se que a aquisição de competência para conversão de ápices radiculares de Catasetum fimbriatum em gemas caulinares aumentava à medida que as plantas envelheciam. Esse processo esteve relacionado ao estabelecimento do crescimento determinado das raízes e com a parada da atividade e re-organização estrutural do meristema apical radicular (MAR). Este, quando ainda jovem e destituído de competência para a conversão em gemas, apresentava uma organização do tipo fechada, ao passo que em estágios avançados do envelhecimento este padrão transformou-se em um tipo aberto, marcado pela diferenciação e predominância de células parenquimáticas. Tais alterações, aparentemente, ocorreram com a concomitante perda das características e funções do centro de quiescente (CQ). De maneira complementar, constatou-se que a aquisição de competência do MAR para conversão em gemas estava correlacionada a uma série de alterações metabólicas, as quais, supostamente, participaram de uma condição fisiológica favorável a esse processo. Com base no conjunto de dados obtidos, pode-se observar que os teores endógenos de importantes participantes na progressão de divisões celulares, tais como auxinas, citocininas e formas reduzidas de ascorbato e glutationa tenderam a diminuir durante o envelhecimento das raízes. Por outro lado, durante esse mesmo período, o conteúdo de alguns hormônios envolvidos na sinalização de condições de estresse ou diferenciação celular, tais como etileno, ácido abscísico e giberelinas tenderam a aumentar. As concentrações relativas de importantes sinalizadores secundários, tais como óxido nítrico e cálcio citossólico também apresentaram aumento conspícuo na região do MAR durante o envelhecimento. Agregando elementos a estas constatações, verificou-se que o transporte polar de auxina seria um importante sinal posicional para a manutenção das características e função do MAR, uma vez que o seu bloqueio em plantas jovens foi suficiente para causar a aquisição da competência do MAR, no entanto, o processo de conversão não era consolidado enquanto os ápices radiculares permaneceram ligados às plantas. A aplicação de etileno em plantas jovens, por sua vez, desencadeou efeitos similares; no entanto, além de induzir a competência, esse hormônio também proporcionou a conversão dos MARs em gemas via aumento nos teores endógenos de citocininas. O tratamento de ápices radiculares jovens com diferentes tipos de citocininas revelaram que citocininas do tipo isopenteniladenina (iP e iPR) mostraram-se mais de perto relacionadas à retenção de características radiculares, ao passo que as do tipo zeatina (Z e ZR) apresentou maior influência e presença em condições em que as características radiculares foram perdidas. Por outro lado, a aplicação de substâncias moduladoras do balanço redox em ápices radiculares jovens mostrou que o estresse oxidativo proporcionou a aquisição de competência do MAR para conversão em gemas. Essa mesma tendência foi observada com a aplicação de concentrações relativamente elevadas de substâncias indutoras da elevação dos teores de óxido nítrico e cálcio citossólico nos tecidos. Os ápices radiculares com competência parcialmente estabelecida, analisados logo nas primeiras horas após o isolamento, revelaram que sua separação da planta-mãe acelerava as mudanças morfológicas que naturalmente ocorrem no MAR em estágios avançados do envelhecimento. Durante esse mesmo período, verificou-se uma queda rápida nos teores endógenos de citocininas (principalmente do tipo iP), proporcionando a predominância de citocininas do tipo Z durante a maior parte do primeiro dia de isolamento dos explantes, a qual coincidiu com a mudança no padrão de organização do MAR do tipo intermediário-aberto para o totalmente aberto. O avanço das modificações no ápice radicular após esse período desencadeou o estabelecimento do meristema caulinar, cujo evento esteve relacionado a uma tendência de aumento nos teores de citocininas e de ascorbato após o primeiro dia de isolamento. Dessa forma, os estágios mais avançados do envelhecimento radicular, bem como a separação de ápices radiculares com competência parcialmente estabelecida, parecem desencadear e aumentar a competência do MAR para conversão por meio de modificações morfológicas e fisiológicas muito similares nos ápices radiculares. Essas alterações envolveram a perda das características radiculares, a qual parece depender de alterações no controle exercido pelo CQ sobre o desenvolvimento das demais células no MAR. Esses eventos na região do CQ se revelaram condição sine qua non para a complementação da aquisição de competência do MAR, sendo esta dependente da intensidade das perturbações sobre o controle da organização do MAR. Dessa forma, a conversão do meristema apical radicular de C. fimbriatum em gemas caulinares parece decorrer da formação de um novo grupo de células na antiga região do CQ do MAR alterado. Essas células pareceram competentes para responder a diferentes estímulos que as direcionariam a uma nova rota do desenvolvimento que, nesse caso, seria o estabelecimento de um meristema caulinar com conseqüente desenvolvimento de uma gema vegetativa.
During this research work, it was noticed that competence acquisition for the conversion of Catasetum fimbriatum root tips into buds was related to the plant ageing. This process seems to be coupled with the establishment of the determinate root growth and with the cessation in the activity and structural re-organization of the root apical meristem (RAM). Young and non-competent root tips showed a closed RAM architecture, and the ageing process stimulated the establishment of an open organization in the RAM, as indicated by a higher level of differentiation and a predominance of parenchymatic cells in the old root apices. These alterations were concomitant with the modifications on the characteristics and functions of quiescent center (QC). In agreement with these observations, the competence acquisition to the conversion of the MAR into buds was linked to a series of metabolic alterations, which probably play a role in this process. Based on the data obtained, it was observed that the endogenous levels of important components of the cell division progression, such as auxins, cytokinins and the reduced forms of ascorbate and glutathione showed a tendency of decrease during the root ageing. On the other hand, during this same period, the content of some hormones involved in signalling events of stress conditions or cellular differentiation, such as ethylene, abscisic acid and gibberellins exhibited a pattern of increase. The relative concentrations of important second messengers, such as nitric oxide and cytosolic calcium also displayed a marked increased in the RAM region during the ageing. Additionally, it was noticed that the auxin polar transport represents an important positional signal for the maintenance of the RAM characteristics and functions, once treatments that blocked the transport of this hormone promoted the MAR competence acquisition even in young plants, although, the conversion process did not complete while the root tips were maintained attached to the plants. The treatment of young plants with ethylene, on the contrary, caused similar effects; however, besides inducing the competence, this hormone also promoted the RAM conversion into buds via the elevation in the endogenous levels of cytokinins. The treatment of young root tips with different types of cytokinins indicated that iP-type cytokinins (iP and iPR) were more closely associated to the preservation of the root characteristics, while the Z-type cytokinins (Z and ZR) showed a higher importance when the root characteristics were lost. Furthermore, the treatment of young root apices with compounds that cause alterations in the cellular redox status indicated that the oxidative stress stimulated the competence acquisition for the RAM conversion into buds. This same tendency was observed with the application of relatively high concentrations of compounds that induce elevations in the levels of nitric oxide and cytosolic calcium in the tissues. The analyses carried out during the first hours after the isolation of partially competent root apices indicated that the detachment of the root tips from the original plants accelerated the morphological modifications that naturally occur at advanced stages of ageing. During this same period, it was observed a rapid decrease in the endogenous levels of cytokinins (specially of the iP-type), leading to a predominance of the Z-type cytokinins during the first day after the isolation of the explants, which coincided with the alteration of the RAM architecture from the intermediate-open type to the completely open type. After the first day of isolation, the progress in the root apices modifications resulted in the establishment of the shoot meristem, which was accompanied by an elevation in the endogenous levels of cytokinins and ascorbate. Therefore, advanced stages of root ageing, as well the isolation of the partially competent root apices, seem to increase the competence for the RAM conversion into buds via similar morphological and physiological changes in the root apices. These alterations involved the loss of the root characteristics, which possibly resulted from modifications in the control of the QC on the development of the other cells in the RAM. These events in the QC represent a sine qua non condition for the completion of the MAR competence acquisition, which is affected by the intensity of the perturbations on the control of the RAM organization. Therefore, the conversion of root apical meristem of C. fimbriatum into buds probably results from the formation of a new group of cells in the region of the QC of the altered RAM. These cells seem to be competent to respond to different stimulus that would directionate them to a new developmental route that, in this case, consists in the establishment of a shoot meristem.

Setaria viridis é uma espécie de gramínea muito relevante em estudos de desenvolvimento vegetal, por determinadas características que a fazem uma excelente proposta de organismo modelo para plantas monocotiledôneas de metabolismo C4. Para que a espécie seja utilizada amplamente em estudos que visem compreender o funcionamento e desenvolvimento vegetal, bem como os mecanismos moleculares que o modulam, é essencial que aspectos de seu desenvolvimento sejam desvendados. Nesse contexto, a caracterização do meristema radicular e das estruturas presentes nos estágios iniciais da germinação é importante para se compreender como ocorre, em gramíneas, o surgimento de tipos de raízes diferentes, além de correlacionar quais fatores ambientais e endógenos estão envolvidos na escolha de diferentes arquiteturas de sistemas radiculares em gramíneas. Além disso,a caracterização do desenvolvimento de estruturas florais em Setaria viridis é importante, uma vez que traz informações que podem contribuir com um aumento na eficiência de metodologias de transformação genética para a espécie, via \"spike dip\". O presente trabalho caracterizou morfoanatomicamente o desenvolvimento radicular desde os estágios iniciais da germinação e o desenvolvimento floral em Setaria viridis. Além disso, buscou estabelecer relação entre o surgimento de diferentes tipos de raízes (primárias e as adventícias) com diferentes condições de luminosidade em cultivos in vitro
Setaria viridis is a very important grass in studies of plant development, due to some characteristics that make it an excellent proposed model organism for monocotyledonous plants with C4 metabolism. To be widely used in studies that aim to understand plant functioning and development, as well as the molecular mechanisms that modulate it, it is essential that aspects of its development be unraveled. In this context, the characterization of the root meristem and structures present in the early stages of germination is also important to understand how the emergence of different root types occurs in grasses. Moreover, to correlate the environmental and endogenous factors involved in the choice of different architectures of root systems in grasses. Furthermore, the characterization of the development of floral structures in Setaria viridis is important, since it brings information that can contribute to the efficiency of methodologies of genetic transformation for the species. The present work characterized morphologically the root development during the initial stages of germination and the floral development of Setaria. In addition, it sought to establish a relationship between the emergences of different types of roots (primary and adventitious) with different light conditions in in vitro cultures

Dans l’optique d’une seconde Révolution Verte, visant, à la différence de la première, à accroître les rendements des cultures dans un contexte de faible fertilité, les stratégies mises en place par les plantes pour une assimilation optimale des nutriments du sol se trouvent au cœur du problème. Afin de le résoudre et d’identifier les variétés idéales parmi la diversité génétique des plantes cultivées, les systèmes racinaires, leur développement et leur architecture, sont appelés à jouer le premier rôle. La variabilité au sein des racines latérales semble s’avérer une caractéristique cruciale pour l’optimisation de l’exploration du sol et de l’acquisition de ses ressources mobiles et immobiles, mais ce phénomène est encore mal appréhendé.Le travail présenté dans cette thèse se concentre sur les racines latérales du maïs (Zea mays L.) dans un effort pour révéler les processus à l’origine des variations intrinsèques dans le développement racinaire. Il s’appuie en particulier sur le phénotypage des racines latérales à une échelle sans précédent, suivant la croissance journalière de milliers d’entre elles à haute résolution spatiale, pour caractériser précisément les variations spatio-temporelles entre et au sein des individus racinaires. Les profils individuels de vitesse de croissance ont été analysés à l’aide d’un modèle statistique qui a identifié trois principales tendances temporelles dans les vitesses de croissance menant à la définition de trois classes de racines latérales avec une vitesse et durée de croissance distinctes. Des différences de diamètre à l’émergence de ces racines (dont l’origine remonte au stade du primordium) conditionnent probablement la tendance ultérieur de croissance mais ne suffisent pas à déterminer le destin de la racine. Finalement, ces classes racinaires sont distribuées aléatoirement le long de la racine primaire, ce qui suggère qu’aucune stimulation ou inhibition locale n’existe entre racines voisines.Pour expliquer l’origine des variations observées dans la croissance, ce travail a été complété par une caractérisation multi-échelle de groupes de racines latérales présentant une croissance distincte, à un niveau cellulaire, anatomique et moléculaire. Un effort particulier a été dirigé à l’analyse des profils de longueur de cellules dans des apex racinaires pour lequel nous avons introduit un modèle de segmentation pour identifier des zones développementales. Grâce à cette méthode, une forte modulation dans la longueur des zones de division et d’élongation a été mise en évidence, en lien avec les variations de la croissance des racines latérales. Le rôle régulateur de l’auxine sur l'équilibre entre les processus de prolifération et d’élongation cellulaire a été montré avec l’utilisation de lignées mutantes. En fin de compte, les variations de la croissance entre racines latérales sont remontées jusqu’à l’allocation d’assimilats carbonés et la capacité de transport de la racine, ce qui suggère l’existence d’un mécanisme de rétroaction qui pourrait jouer un rôle déterminant dans la mise en place de tendances contrastées dans la croissance des racines latérales
In the perspective of a second Green Revolution, aiming, unlike the first one, to enhance yields of crops in a low fertility context, the strategies used by plants for an optimal uptake of soil nutrients are at the core of the problem. To solve it and identify ideal breeds among the genetic diversity of crops, plant root systems, their development and their architecture, are called upon to play the leading role. The variability among secondary roots appears as a crucial feature for the optimality of soil exploration and acquisition of mobile and immobile resources, but this phenomenon remains poorly understood. The work presented in this thesis focuses on the lateral roots of maize (Zea mays L.) and attempts to unravel the processes at the origin of intrinsic variations in lateral root development. It relies notably on the phenotyping of individual lateral roots at an unprecedented scale, tracking the daily growth of thousands of them at a high spatial resolution, in order to characterize precisely the spatio-temporal variations existing both between and within root individuals. Individual growth rate profiles were analyzed with a statistical model that identified three main temporal trends in growth rates leading to the definition of three lateral root classes with contrasted growth rates and growth duration. Differences in lateral root diameter at root emergence (originating at the primordium stage) were likely to condition the followed growth trend but did not seem enough to entirely determine lateral root fate. Lastly, these lateral root classes were randomly distributed along the primary root, suggesting that there is no local inhibition or stimulation between neighbouring lateral roots. In order to explain the origin of the observed differences in growth behaviour, we complemented our study with a multi-scale characterization of groups of lateral roots with contrasted growth at a cellular, anatomical and molecular level. A particular focus is set on the analysis of cell length profiles in lateral root apices for which we introduced a segmentation model to identify developmental zones. Using this method, we evidenced strong modulations in the length of the division and elongation zones that could be closely related to variations in lateral root growth. The regulatory role of auxin on the balance between cellular proliferation and elongation processes is demonstrated through the analysis of mutant lines. Ultimately, variations in lateral root growth are traced back to the allocation of carbon assimilates and the transport capacity of the root, suggesting that a feedback control loop mechanism could play a determinant role in the setting out of contrasted lateral root growth trends

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Conselho Nacional de Desenvolvimento Científico e Tecnológico
A organogênese de brotos a partir de raízes (rootsuckers) permite a propagação vegetativa daArabidopsis lyrata, o parente mais próximo daArabidopsis thaliana. Utilizando um sistema in vitro, o presente estudo objetivou compreender melhor a propagação vegetativa nessa espécie modelo A. lyrata, no que se refere ao desenvolvimento morfológico de suckers, à capacidade de propagação vegetativa em diferentes condições de crescimento in vitro e à identificação de genes potencialmente envolvidos na formação do meristema apical dos brotos.O surgimentodos suckers ocorreu após 30 dias, mais freqüentemente na região axilar das raízes laterais. Os cortes transversais das raízes mostraram uma estrutura primária típica diarca e após cerca de 25 dias, pode-se observar o crescimento secundário da raiz, como indicado pela formação do câmbio. Conclui-se que a emergência do sucker assemelha-se à iniciação das raízes laterais a partir do periciclo, tecido que dá origem ao câmbio vascular durante o crescimento secundário. Em relação às condições de crescimento in vitro, a força total no meio MS induziu o maior número de suckers por planta, seguido por alta concentração de sacarose (3%).Exposição à luz e privação de sacarose não são estritamente necessários para a formação de suckers. Nossos dados também revelaram que a auxina promove a formação dos brotos. Máximas de auxina vascular são necessários para desencadear a iniciação da raiz lateral, sugerindo que a formação de suckers promovida por auxina ocorre provavelmente por mecanismos semelhantes. A avaliação de diferentes genes relacionados a meristema apical, demonstram que o gene STM pode ser um marcador para distinguir as células responsáveis pela formação de suckers. Arabidopsis lyrata provou ser um excelente modelo para estudos de organogênese em raíz e posteriores estudos usando esse sistema de reproduçãopara detectar marcadores epigenéticos através das várias gerações de propagação clonal.
Shoot organogenesis from roots (root suckers) allows vegetative propagation of Arabidopsis lyrata, the closest relative of Arabidopsis thaliana, in addition to sexual propagation and is an important trait associated with the root system. Using an in vitro system, we aimed to better understand the vegetative propagation in the model species A. lyrata, in what regards the morphological development of root suckers, the ability of vegetative propagation in different in vitro growth conditions, and identifying genes potentially involved in the formation of the new shoot apical meristem.Root sucker appearanceoccurred after30 days,most frequently in the axils of lateral roots. Root cross-sections showed a typical diarch primary structure and after 25 days, secondary root growth could be observed, as indicated by formation of the cambium. According to our data,root sucker emergence resembles the initiation of lateral roots from the pericycle, the tissue that gives rise to the vascular cambium during secondary growth. Regarding the in vitro growth conditions, full strength of MS induced the highest number of root suckers per plant, followed 3% of sucrose. However, light exposure and sucrose deprivation are not strictly required for sucker formation. Our data also revealed that auxin promotes root suckering. Vascular auxin response maxima are required to trigger lateral root initiation, suggesting that auxin- promoted sucker formation likely occurs by similar mechanisms. The evaluation of different shoot apical meristem related genes, suggests that the STM gene can be a potential marker to identify cells responsible in driving sucker formation. Arabidopsis lyrata proved to be an excellent model for further studies using root suckers, for example to study epigenetic marks throughout generations of clonal propagation.

L'auxine régule la croissance et le développement des plantes grâce aux facteurs de transcription de la famille des "AUXIN RESPONSE FACTOR" (ARF). Chez Arabidopsis thaliana en particulier, ARF5, 6, 7, 8 et 19 activent l'expression de gènes cibles en réponse à l'auxine. Ces cinq ARF activateurs contrôlent de façon plus ou moins redondante des processus divers au cours du développement de la plante, notamment la régulation des croissances au niveau des méristèmes racinaires et aériens ainsi que la formation des racines latérales ou des méristèmes axillaires.Chacun de ces cinq ARF activateurs présente des patrons d'expression uniques dans chacun des tissus racinaires et aériens, en association avec leurs fonctions particulières. Il est probable que cette expression tissu-spécifique trouve son origine dans un contrôle différencié de leur transcription. Dans cette étude, des régulateurs amonts de la transcription de ARF5, 6, 7, 8 et 19 ont été identifiés par une méthode haut-débit de crible simple hybride en levure (Y1H). Une procédure d'expression transitoire en protoplastes a permis de confirmer que l'expression de chaque ARF activateur est contrôlée par des régulateurs spécifiques, dont la majorité se comportent comme des répresseurs de la transcription des ARF in planta. Parmi les régulateurs identifiés, les facteurs de transcription ont été étudiés grâce à des mutants pour préciser les interactions in planta. Ces mutants montrent des phénotypes développementaux typiques de perturbations de l'auxine dans les racines et les tiges : altérations des cinétiques de croissance, de l'émergence des organes latéraux ou de réponses à l'auxine et modification de l'expression des ARF activateurs.Par ailleurs, ce travail aborde également les dialogues entre les voies de signalisation de l'auxine et des cytokinines, et en particulier le rôle de ces interactions dans le développement des racines et des tiges. Une des interactions identifiées dans le crible Y1H est la répression de ARF7 par CRF10, un gène membre de la famille des "Cytokinin Response Factors". Nous avons mis en évidence l'importance de cette interaction pour le maintien de l'architecture du méristème apical racinaire, pour la sénescence des feuille et pour la réponse phototropique à la lumière bleue dans les hypocotyles
Auxin regulates plant growth and development through the transcription factors of the AUXIN RESPONSE FACTOR (ARF) gene family. Most notably in Arabidopsis thaliana ARF5, 6, 7, 8 and 19 activate expression of target genes in response to auxin. These five ARF activators control both variable and overlapping processes during plant development including regulation of growth at the root and the shoot apical meristems, lateral root and axillary shoot formation. Each of the five ARF activators shows unique tissue-specific expression patterns in the root and the shoot associated with their distinct functions. This tissue-specific expression is likely derived from the differences in the control of ARF activator transcription. In this study the upstream regulators of ARF5, 6, 7, 8 and 19 transcription were identified. This was achieved by utilizing a high-throughput yeast one-hybrid (Y1H) method. The transient protoplast assay revealed that each ARF activator is controlled by specific transcriptional regulators and that the majority of these regulators are repressors of ARF transcription in planta. Mutants of the regulatory transcription factors were utilized to additionally investigate the interactions in planta. These mutants display auxin-related developmental phenotypes in the root and the shoot including alternations in growth kinetics, emergence of lateral organs, responses to auxin and altered expression of ARF activators. Furthermore, this study additionally focuses on cross-talk between the auxin and cytokinin signaling pathways and its role in root and shoot development. One of the interactions identified in the Y1H screen is a repression of ARF7 by CRF10, a member of the Cytokinin Response Factors gene family. The importance of this interaction in maintaining architecture of the root apical meristem, in leaf senescence and in the phototropic response to blue light in hypocotyls is studied

La paroi des cellules végétales subit des modifications afin de s'assouplir ou de se rigidifier selon les besoins de la plante. Cette paroi est une structure complexe, composée de cellulose, d'hémicellulose et de pectines. Les modifications subies par les pectines au cours de l'élongation cellulaire sont encore assez peu caractérisées. Dans ce contexte, le but de ce projet est d'étudier le rôle de deux polygalacturonases (PG) dans le développement racinaire de la plante modèle A. thaliana. Les PG sont des enzymes de dégradation des homogalacturonanes (HG), le composant pectique majoritaire de la paroi primaire. Notrehypothèse est que les PG dégradent partiellement les HG des parois longitudinales des cellules racinaires en élongation. Cette dégradation engendrerait un assouplissement pariétal localisé, permettant la croissance anisotropique des cellules. Nos résultats indiquent que les gènes des deux PG étudiées, nommés PG ROOT APICAL MERISTEM (PG RAM) et PG ROOT (PG R) sontexprimés de façon complémentaire dans la racine, l'un dans le méristème racinaire (PG RAM), et l'autre dans la zone d'élongation et de différenciation (PG R). De plus, la sur-expression de la protéine PG R entraine une augmentation de l’élongation des hypocotyles étiolés, ainsi qu'une augmentation de la densité de racines latérales par rapport au sauvage, démontrant son rôle dans le développement racinaire et dans l'allongement cellulaire. Enfin, nous avons démontré que l'expression des gènes de ces PG était contrôlée de façon différentielle par les facteurs de transcription de la famille PLETHORA (PLT)
Plant cell wall structure is modified to control its stiffness or flexibility according to plant’s requirements. The cell wall is a complex structure, composed of cellulose, hemicelluloses and pectins. Pectin modifications during cellular elongation are not very well characterized. In this context, the aim of this project is to study the roles of two polygalacturonases (PG) in the root development on the model plant A. thaliana. PG are homogalacturonans (HG) degradation enzymes, HG being the major pectic component of the primary cell wall. This degradation would lead to a local parietal relaxation, allowing anisotropic growth of the cells. Our results show that the two studied PG, named PG ROOT APICAL MERISTEM (PG RAM) and PG ROOT (PG R), are expressed in complementary areas of the root, either in the root apical meristem (PG RAM) or in the elongated and differenciated root tissues (PG R). Furthermore, the over-expression of PG R results in longer etiolated hypocotyls and increases root density when compared to wild-type, demonstrating its function in root development and in cell elongation. Finally, we demonstrated that expression of these two PG genes is under the control of PLETHORA (PLT) family transcription factors, by differentially ways

Plant growth and development depends on controlled cell expansion. This, in itself, is determined by the plant cell wall, a structural matrix of polysaccharides encasing the plant cell. One line of investigation that has proven particularly successful in elucidating the components of the plant cell wall machinery has been the forward genetic screens of cell wall mutants. In this study, the molecular and cellular characterisation of sloughy, a cell separation mutant in Arabidopsis thaliana, was commenced. This mutant has a striking phenotype, with files of elongating epidermal cells snaking away from the adjacent epidermal cells and from the underlying cortex, loosing contact from the side walls while remaining attached at the cell ends, in a manner reminiscent of border-like cells in the root cap of arabidopsis. The sloughy mutation was fine mapped to a short region on chromosome I using high resolution melt point analysis. On sequencing all five genes in this region, a single nucleotide mutation, introducing a stop codon, was detected in exon 2 in the previously-described heat shock transcription factor SCHIZORIZA that results in a truncated protein missing several conserved domains essential for activity. SCHIZORIZA acts as a cell fate determinate in the root meristem to promote cortex fate, while suppressing epidermal and root cap fate in the mature ground tissue. Although the literature on schizoriza mutants has focused on the developing root meristem, with little documentation on the cell separation phenotype further up in the roots, the investigation of a collection of schizoriza TILLING mutants revealed that aberrant cell separation was ubiquitous to schizoriza mutants with a severely truncated protein. To investigate cell identity in the mature roots, sloughy was crossed to GAL4-GFP enhancer trap lines that act as cell-specific markers. Epidermal identity lines revealed that sloughy possessed a supernumerary ground tissue layer with epidermal identity. A cortex and endodermal line revealed that these two identities are restricted to the endodermal layer and the next ground tissue layer out. There was no indication of root cap identity in the mature root with any of the root cap lines used, although partial lateral root cap identity has been previously described in the epidermal and subepidermal cell layers in the meristem of schizoriza mutants expressing SOMBRERO-GFP, a lateral root cap-specific transcription factor. Immunolabelling of cell wall epitopes revealed that the JIM13 antibody, which specifically labels arabinogalactan-proteins in wild-type root caps, often labelled the epidermal cells and surrounding mucilage further up the in the roots of sloughy. The aberrant cell separation present in sloughy is thought to be a consequence of epidermal cells possessing partial lateral root cap identity. The data on sloughy/schizoriza is sufficient to generate a model on how a meristem developmental gene can generate a cell separation phenotype in the mature roots. Loss of SCHIZORIZA causes confused cell identity in the root meristem that results in an epidermal and subepidermal layer possessing mixed epidermal and lateral root cap identity. The distinctive properties of border-like cells in the root cap of arabidopsis have been linked to unique cell wall maturation and developmental processes, implicating the cellulases CEL3 and CEL5, the pectin glycosyltransferase QUA1, the pectin methyltransferase QUA2 and other pectolytic enzymes. The ectopic expression of these cell wall enzymes in the epidermal and subepidermal layers of sloughy roots result in reduced adhesion along the sides of the cell, while the ends remain attached, causing the observed cell separation phenotype.

Les plantes de la famille des légumineuses ont la particularité d’héberger intracellulairement des bactéries du sol communément appelées rhizobia. Cette interaction symbiotique se déroule au sein de la nodosité, un organe formé de-novo au niveau racinaire. L’activité nitrogénase bactérienne y permet la réduction de l’azote atmosphérique en NH3 assimilable par la plante. Si les mécanismes moléculaires gouvernant la reconnaissance entre les deux partenaires, l’infection intracellulaire et l’organogénèse des nodosités ont été particulièrement bien décrits au cours des dernières décennies ; peu d’informations sont quant à elles disponibles sur l’origine de ce programme morphogénétique nouveau chez les Angiospermes. Les nodosités des deux légumineuses modèles Medicago truncatula et Pisum sativum sont qualifiées d’indéterminées en raison de la persistance d’un méristème en position apicale. Les nodosités des mutants noot (nodule-root) chez M. truncatula et coch (cochleata) chez le pois développent des racines ectopiques à partir des tissus vasculaires des nodosités, montrant ainsi que les nodosités et racines sont plus apparentées que leur simple comparaison anatomique ne pouvait le suggérer. En outre, l‘activité mérsitématique des nodosités est fortement perturbée chez ces deux mutants qui présentent des nodosités multilobées et élargies. Nous avons montré que les gènes MtNOOT et PsCOCHLEATA étaient orthologues aux gènes AtBLADE-ON-PETIOLE1 et 2 qui codent deux activateurs transcriptionels redondants et cruciaux pour la régulation de nombreux processus développementaux chez Arabidopsis thaliana. En raison de la forte conservation des fonctions biologiques des protéines NOOT, BOPs et COCH, notamment pour la régulation de la morphologie foliaire et florale, de l’architecture de l’inflorescence et de la formation des zones d’abscission, nous proposons que ces fonctions représentent les fonctions ancestrales de la famille des gènes NBCL (NOOT BOP COCH LIKE). L’étude de déterminants hormonaux et génétiques du méristème racinaire dans les nodosités sauvages et mutantes noot ainsi que la caractérisation de l’homéose nodule/racine nous ont permis de dégager des parallèles importants entre les tissus périphériques de la nodosité et ceux de la racine. Nous proposons donc un modèle de développement des tissus vasculaires de la nodosité par co-option du programme racinaire dont la répression est en partie assurée par NOOT
Legume plants are able to house intracellularly soil bacteria collectively called rhizobia. This symbiotic process takes place in a new organ generally formed on the host roots, the nodule. This interaction allows atmospheric nitrogen fixation to the benefit of the plant by using the bacterial nitrogenase activity. Despite an exhaustive description of molecular determinants of this interaction allowing partners recognition, intracellular accommodation and early nodule organogenesis, less is known about cell lineage and identity of the nodule morphogenetic pathway which is thought to represent a recent acquisition during Angiosperms evolution. Nodules from model legumes such as Medicago truncatula or Pisum sativum are described as indeterminate because of the persistence of a distal meristem. The noot (nodule-root) and coch (coch) mutants, in M. truncatula and P. sativum respectively, develop ectopic roots from the nodule vasculature, suggesting that roots and symbiotic nodules are more closely related than previously admitted based on their anatomical comparison. Moreover, the meristematic activity is strongly modified in noot and coch nodules that harbor numerous and enlarged lobes. We showed that NOOT and COCH are orthologs to AtBLADE-ON-PETIOLE1 and 2 redundant transcriptional activators that represent key regulators of versatile plant developmental processes in Arabidopsis thaliana. Because of the conservation of biological functions controlled by NOOT, BOPs and COCH proteins, in particular the regulation of leaf and floral morphologies, abscission zones formation and inflorescence architecture, we proposed that such functions are inherited from a NBCLs (NOOT BOP COCH LIKE) ancestral gene. Our studies of hormonal and genetic determinants of the root meristem in noot and wild-type nodules as well as the characterization of nodule-to-root homeosis have highlighted important parallels between nodule peripheral tissues and roots. We thus propose a model of nodule vascular unit maintenance by the NOOT-dependent repression of a co-opted root morphogenetic program

Les racines ont deux grands rôles. Le premier est le prélèvement de l’eau et des éléments nutritifs et le second est l’ancrage dans le sol. Identifier les gènes responsables de la mise en place des tissus et de l'architecture du système racinaire est donc essentiel pour pouvoir améliorer les variétés de riz soumises à des stress abiotiques de plus en plus fréquents et nombreux du fait du changement climatique. Au cours de cette thèse, j'ai réalisé une analyse fonctionnelle du gène DEFECTIVE IN OUTER CELL LAYER SPECIFICATION (DOCS1) qui appartient à la famille des récepteurs kinases à répétitions riches en leucine (LRR-RLK). Ces protéines sont composées de deux domaines principaux: un domaine extra-cytoplasmique composé de répétitions LRR et un domaine kinase intra-cytoplasmique. Un mutant de ce gène, nommé c68, possède une mutation non-sens dans le domaine kinase. Les plantes mutantes c68 présentent plusieurs phénotypes: une sensibilité accrue à l'aluminium, une réduction du nombre et de la taille des poils absorbants dans les racines, et des couches d’exoderme/épiderme d’identité mêlée. Le premier chapitre de la thèse porte sur l’étude conjointe de lignées knock-out CRISPRs du gène DOCS1 et de c68. Nos résultats ont montré que les mutants c68 et CRISPRs présentaient les mêmes phénotypes : sensibilité à l’aluminium, défauts des poils absorbants et tissus externes d’identité mixte. Ces résultats suggéraient que chez le mutant c68, soit la protéine DOCS1 n'était pas fonctionnelle, soit elle n'était pas traduite. Nos analyses phénotypiques ont aussi révélé que tous les mutants présentaient des défauts de réponse à la gravité à différents stades de développement. A 3 jours, un retard de réponse à la gravité était observé pendant la première heure après gravistimulation. Les plantules mutantes présentaient aussi des défauts de localisation d’un transporteur d’auxine. A 40 jours, nous avons observé que l'angle du cône racinaire des plantes mutantes était plus ouvert que celui des plantes sauvages. Deux gènes liés à l’auxine et plusieurs QTLs ont déjà été identifiés comme participant à ce phénotype chez le riz. Dans la suite de notre étude, nous avons donc cherché à identifier de nouveaux QTLs et gènes impliqués dans ce phénotype morphologique par étude d'association pan-génomique dans deux panels Indica et Japonica. Toutes les accessions de l'écotype bulu d'Indonésie et trois japonicas tempérés d'Asie du Sud présentaient un angle du cône racinaire très ouvert. En utilisant un modèle mixte associé à une technique de ré-échantillonnage, 55 QTLs ont été détectés. L'analyse des gènes sous-jacents ou voisin (+/- 50kb) a identifié 539 gènes, dont 6 LRR-RLK, 5 gènes liés à l’auxine et 5 gènes avec une fonction validée dans le développement ou l'architecture racinaire. Une approche complémentaire par cartographie génétique classique est proposée pour identifier les gènes en cause dans la ou les mutations à angle du cône racinaire très ouvert. Des perspectives de poursuite du travail effectué sont aussi présentées afin de déterminer si le phénotype affectant l'angle du cône racinaire induit par les mutations du gène DOCS1 ou des nouveaux gènes identifiés est lié à des perturbations des flux d’auxine
Roots have two major roles. The first one is to uptake water and nutrients and the second one is to anchor plants into the ground. Identifying the genes responsible for the establishment of tissues and architecture of the root system is essential to improve rice varieties subject to increasingly frequent and numerous abiotic stresses due to climate change. During my PhD, I undertook a functional analysis of the DEFECTIVE IN OUTER CELL LAYER SPECIFICATION (DOCS1) gene which belongs to the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family. These proteins are composed of two main domains: an extra-cytoplasmic domain containing LRR repeats and a cytoplasmic kinase domain. A mutant of this gene, named c68, carries a nonsense mutation in the kinase domain. The c68 mutant plants show several phenotypes: increased sensitivity to aluminum, reduced number and size of root hairs, and layers of external tissues with exodermis/epidermis mixed identity. The first chapter of the thesis focuses on the joint study of knockout CRISPRs lines of the DOCS1 gene and c68. Our results showed that the c68 and CRISPRs mutants displayed the same phenotypes: sensitivity to aluminum, defects in root hairs and mixed identity of external tissues. These results suggested that in the c68 mutant, either the DOCS1 protein was not functional, or the protein was not translated. Our phenotypic analyses also showed that all mutants exhibited impaired gravity responses at different development stages. At 3 days, a delay of response to gravity was observed during the first hour after gravistimulation. Mutant seedlings also had defects in an auxin transporter localization. At 40 days, we observed that the root cone angle of mutant plants was more open than that of wild-type plants. Two genes associated with auxin and several QTLs have been identified as contributing to this phenotype in rice. In the rest of our study, we therefore tried to identify new QTLs and genes involved in this morphological phenotype by a genome-wide association study in two Indica and Japonica panels. All accessions of the bulu ecotype from Indonesia and three South Asian temperate japonica had a very open root cone angle. Using a mixed model associated with a resampling technique, 55 QTLs were detected. The analysis of the underlying or neighbor (+/- 50kb) genes identified 539 genes, including 6 LRR-RLK, 5 genes related to auxin and 5 genes with a function validated in root development or architecture. A complementary approach by classical genetic mapping is proposed to identify genes involved in the mutation(s) involved in very open root cone angle. Prospective research lines are also presented to determine if the root cone angle phenotype , induced by DOCS1 or by newly identified genes, is linked with disruption of auxin fluxes

La capacité d’une plante à réguler sa croissance racinaire est une composante importante de l’acclimatation aux stress environnementaux. A l’échelle cellulaire, cette régulation est effectuée via le contrôle de la division et de l’élongation des cellules mais les rôles respectifs de chaque processus et leurs interactions sont peu connus. Notamment, l’activité de production de cellules du méristème apical racinaire (RAM) est trop souvent négligée. Dans cette thèse, l’analyse spatiale de la croissance le long de l’apex racinaire et l’analyse temporelle des trajectoires de croissance des cellules ont été couplées pour comprendre les liens existants entre division et élongation cellulaire. Pour cela, j’ai développé un système de phénotypage de la croissance à haute résolution spatio-temporelle qui a été appliqué à l’étude de racines d’un peuplier euraméricain (Populus deltoides × Populus nigra) en réponse à différents stress (stress osmotique, impédance mécanique). Une forte variabilité du taux de croissance racinaire entre individus ainsi que des variations individuelles cycliques de la croissance ont été observées malgré des conditions environnementales contrôlées. L’utilisation de cette variabilité couplée à la quantification de l’activité du RAM a mis en évidence l’importance du taux de production de cellules pour soutenir la croissance racinaire. Ces travaux analysent une nouvelle échelle de variations spatiales et temporelles de la croissance peu prise en compte jusqu’à présent. Hautement applicable à d’autres questions scientifiques, l’analyse du devenir des cellules une fois sortie du RAM est également discutée pour des conditions de croissance non stables
Regulation of root growth is a crucial capacity of plants for acclimatization to environmental stresses. At cell scale, this regulation is controlled through cell division and cell elongation but respective importance of these processes and interactions between them are still poorly known. Notably, the cell production activity of the root apical meristem (RAM) is often excluded. During this thesis, spatial analyses of growth along the root apex were coupled with temporal analyses of cell trajectories in order to decipher the links between cell division and cell elongation. This required the setup of a system for phenotyping root growth at a high spatiotemporal resolution which was applied to study the growth of roots from an euramerican poplar (Populus deltoides × Populus nigra) in response to different environmental stresses (osmotic stress or mechanical impedance). An important variability of root growth rate between individuals as well as individual cyclic variations of growth along time were observed despite tightly controlled environmental conditions. Use of this variability coupled with quantification of the RAM activity led us to a better understanding of the importance of the cell production rate for sustaining root growth. This work analyses a new spatiotemporal scale of growth variability poorly considered. Widely applicable to others scientific questioning, temporal analyses of cell fate once produced in the RAM is also discussed for non-steady growth conditions

Les cellules végétales détectent et répondent à divers stimuli mécaniques externes comme le toucher ou le vent, et internes comme la pression osmotique et la tension des parois cellulaires. Dans cette étude, j'ai démontré que la forme et la rigidité du noyau sont affectées de manière réversible en condition de stress hyperosmotique et sont corrélées à l’expression de gènes. Afin d'identifier les bases moléculaires de cette réponse, nous avons étudié différents mutants. En particulier, les protéines GIP lient cytosquelette, enveloppe nucléaire et chromatine ; nous avons observé que le mutant gip1gip2 présente une réponse nucléaire de type hyperosmotique constitutive et acquiert même une résistance physiologique au stress hyperosmotique. De façon plus exploratoire, j’ai commencé à analyser l’impact du nucléosquelette (mutant crwn1) et de la paroi (mutant eli1) sur la forme des noyaux et leurs réponses au stress hyperosmotique. Notre étude ouvre le champ de la mécanotransduction nucléaire chez les plantes, et offre de nombreuses perspectives
Plant cells sense and respond to external mechanical stimuli such as touch or wind, and to internal mechanical stimuli, such as turgor pressure and cell wall tension. In this study I have demonstrated that the nuclear shape and mechanics are impacted upon hyperosmotic stress in a reversible manner and are correlated with gene expression. To identify the molecular bases of this response, we have investigated different mutants. First the GIP proteins are at the nexus between cytoskeleton, nuclear envelope, and chromatin. We found that the gip1gip2 mutant defects exhibits a constitutive hyperosmotic nuclear response and is already primed to resist hyperosmotic stress. As a more exploratory work, I also analysed the contribution of the nucleoskeleton (crwn1 mutant) and cell wall (eli1 mutant) on nucleus behaviour in response to hyperosmotic stress. Our study opens the path to nuclear mechanotransduction in plants, while also offering several prospects for future research in this area

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

La crescita della radice in Arabidopsis thaliana si basa sull'attività della zona meristematica. La dimensione del meristema della radice è regolato dai fitoormoni auxina, citochinine e gibberelline, che controllano un circuito di espressione genica che converge sul gene SHY2. Regolando SHY2, gli ormoni vegetali controllano il rapporto tra la divisione cellulare e il differnziamento cellulare. In un lavoro precedente abbiamo riportato che l'allungamento della radice di Arabidopsis è promosso da concentrazioni micromolari di prolina esogena. Al fine di verificare se un mutante con deficit di prolina è caratterizzato da un problema nella crescita delle radici, abbiamo analizzato la lunghezza, rispetto al wild type , delle radici nel mutante p5cs1 p5cs2 / P5CS2. Le nostre analisi mostrano che piante con genotipo p5cs1 p5cs2 / P5CS2 sono caratterizzate da radici più brevi, e meristemi più piccole rispetto al wild type. Questi dati preliminari suggeriscono che la prolina in grado di modulare le dimensioni del meristema radicale e, a sua volta, la crescita delle radici. Per valutare questa ipotesi abbiamo usato una combinazione di analisi genetiche, farmacologiche e molecolari, e dimostrato che prolina colpisce specificamente crescita delle radici modulandone la dimensione del meristema . Gli effetti della prolina sulla dimensione del meristema sono paralleli e indipendenti dalle vie ormonali, e non comportano l'espressione di geni che controllano il differenziamento cellulare in corrispondenza della zona di transizione (SHY2). Al contrario, la prolina sembra controllare la divisione cellulare nelle prime fasi postembrionali di sviluppo delle radici, come indicato dall'espressione del gene CYCLINB1 che conrolla la transizione tra le fasi G2 / M. I dati complessivi indicano che la prolina può modulare la dimensione della zona meristematica della radice, probabilmente controllando la divisione cellulare.
The Arabidopsis thaliana root growt relies on the activity of the root meristematic zone . The size of root meristem is regulated by the plant hormones auxin, cytokinin and gibberellin, which control a short regulatory circuit converging on the gene SHY2. By regulating SHY2, plant hormones control the ratio between cell division and cell differentiation. In a previus work we reported that root elongation in Arabidopsis is promoted by micromolar concentrations of exogenous proline. In order to verify whether a proline-deficient mutant is hampered in root growth, we analyzed the length, relative to wild type, of roots from the proline-deficient mutant p5cs1 p5cs2/P5CS2. Our analyses display that the p5cs1 p5cs2/P5CS2 mutant is characterized by shorter roots, and smaller meristems than wild type. These preliminary data suggest that proline can modulate root meristem size and, in turn, root growth. To evaluate this hypothesis we used a combination of genetic, pharmacological and molecular analyses, and showed that proline specifically affects root growth by modulating the size of the root meristem. The effects of proline on meristem size are parallel to, and independent from, hormonal pathways, and do not involve the expression of genes controlling cell differentiation at the transition zone (SHY2). On the contrary, proline appears to control cell division in early stages of postembryonic root development, as shown by the expression of the G2/M-specific CYCLINB1;1 gene and the G1/S-specific CYCLIND3;1 gene The overall data suggest that proline can modulate the size of root meristematic zone in Arabidopsis likely controlling cell division and, in turn, the ratio between cell division and cell differentiation.

The Arabidopsis root apical meristem (RAM) is a complex tissue capable of generating all the cell types that ultimately make up the root. The work presented in this thesis takes advantage of the versatility of high-throughput sequencing to address two independent questions about the root meristem. Although a lot of information is known regarding the cell fate decisions that occur at the RAM, cortex specification and differentiation remain poorly understood. In the first part of this thesis, I used an ethylmethanesulfonate (EMS) mutagenized marker line to perform a forward genetics screen. The goal of this screen was to identify novel genes involved in the specification and differentiation of the cortex tissue. Mapping analysis from the results obtained in this screen revealed a new allele of BRASSINOSTEROID4 with abnormal marker expression in the cortex tissue. Although this allele proved to be non-cortex specific, this project highlights new technology that allows mapping of EMS-generated mutations without the need to map-cross or back-cross. In the second part of this thesis, using fluorescence activated cell sorting (FACS) coupled with high throughput sequencing, my collaborators and I generated single-base resolution whole genome DNA methylomes, mRNA transcriptomes, and smallRNA transcriptomes for six different populations of cell types in the Arabidopsis root meristem. We were able to discover that the columella is hypermethylated in the CHH context within transposable elements. This hypermethylation is accompanied by upregulation of the RNA-dependent DNA methylation pathway (RdDM), including higher levels of 24-nt silencing RNAs (siRNAs). In summary, our studies demonstrate the versatility of high-throughput sequencing as a method for identifying single mutations or to perform complex comparative genomic analyses.

Dissertation

Plant root architecture is regulated by the formation and function of meristems at the sites of root organogenesis. Meristem formation requires the generation of stem cell niches which produce the new cells of the growing organ. microRNAs (miRNAs) have emerged as regulators of many key biological functions in plants including root organogenesis. To identify key miRNAs involved in root meristem formation in M. truncatula, deep sequencing was used to compare the miRNA populations between root tip (RT), containing root apical meristem, and elongation zone (EZ) tissue plus root forming callus (RFC) and non-root forming callus (NRFC). We identified 83 previously reported miRNAs, 24 new to M. truncatula, in 44 families. Functional analysis was performed on two of these predicted miRNAs, miRN304 and miR166g-5p. Over-expression of novel miRNA, miRN304, produces severe root abnormalities including stunted growth, loss of meristem structure and a poorly formed vasculature. mtr-miR166a-5p corresponds to the passenger strand of miR166a-3p, a miRNA previously shown to negatively regulate lateral root and nodule numbers. miR166a-5p over-expression results in increased nodule numbers and acts independently of miR166a-3p and may be a previously un-identified.