ABSTRACT: Formation of organ shape is an intriguing yet largely unanswered question in developmental biology. Shapes arise as a result of tightly controlled spatial variation in the rates and directions of tissue expansion over the course of development; therefore, quantifying these growth patterns could provide information about the underlying mechanisms of morphogenesis. Here we present a novel technique and computational tools for quantifying growth and shape changes in developing leaves, with a few unique capabilities. This includes the ability to compute growth from three-dimensional (3D) coordinates, which makes this the first method suitable for studying leaf growth in species or mutants with non-flat leaves, as well as small leaves at early stages of development, and allows us to simultaneously capture 3D shape changes. In the following, we apply these methods to study growth and shape changes in the first rosette leaf of Arabidopsis thaliana. Results reveal clear spatiotemporal patterns in growth rates and directionality, and tissue deformation maps illustrate an intricate balance involved in maintaining a relatively flat leaf surface in wild type leaves. Semi-automated tools presented make a high throughput of data possible with this method, and algorithms for generating mean maps of growth will make it possible to perform standardized comparative analyses of growth patterns between wild type and mutants and/or between species. The methods presented in this thesis will therefore be useful for studying leaf growth and shape, to further investigate the mechanisms of morphogenesis.   RÉSUMÉ: Comment un organe acquiert sa forme particulière au cours du développement est une question intéressante mais largement non résolue. La forme d’un organe résulte de la façon dont les taux et directions de croissance de ses tissues varient dans l’espace et dans le temps. Quantifier les motifs de croissance est donc nécessaire pout élucider les mécanismes sous-jacents de la morphogenèse. Nous présentons ici une nouvelle méthodologie pour quantifier la croissance et les changements de forme dans les feuilles en développement. Cette méthodologie s’appuie sur le développement de nouvelles techniques expérimentales et de programmes informatiques, et présente des avantages uniques : la croissance de la surface des feuilles et le changement de forme peuvent être analysés en trois dimensions (3D), pour une longue période et de large déformations. De plus l’analyse de multiples échantillons permet de générer une cartographie moyenne des motifs de croissance à la surface des feuilles au cours de leur développement, ainsi qu’une description quantitative de la déformation des tissus sous l’effet de leur croissance. Dans cette thèse, nous présentons les résultats de croissance et de changements de forme de la première feuille de rosette d'Arabidopsis thaliana au cours de son développement. Les cartes moyennes de croissance révèlent des motifs spatio-temporels évidents tant pour les taux que pour les directions de croissance. De plus, la description de la déformation des tissus démontre l'équilibre complexe impliqué dans le maintien d'une surface relativement plane dans les feuilles. La méthode proposée et les logiciels associés permettra d’effectuer des analyses comparative de la croissance entre feuilles de type sauvage et feuilles de mutants aux formes altérées, afin d’élucider les mécanismes de la morphogenèse foliaire.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The objectives of this thesis were (i) to identify the expanded leaves number (LNexp) and tips (LNtip) from which there is reduction in the contribution of culm reserves to leaf appearance rate in sugarcane and (ii) the effect of different densities of stem in leaf development in the culture of sugarcane. The experiments were conducted at the experimental area of the Departamento de Fitotecnia, Centro de Ciências Rurais, Universidade Federal de Santa Maria, during the 2012/2013 growing season. The sugarcane clone used was SP 711406, with intermediate developmental cycle and well adapted to this location. To achieve the first objective, described in Chapter 1, the experimental design was randomized with 32 replications. Treatments were culm cuttings with: twice the length of the internode, one internode, half the length of internodes, and no internode. Results indicated that the reserves of the culm cuttings of sugarcane have their maximum contribution to the emission of the first two expanded leaves and of the first five leaf tips, and the appearance rate of subsequent leaves decrease due to reduction in culm cuttings reserves. To achieve the second objective, described in Chapter 2, the experiment was conducted in plant cane cultivation system. In plants marked the variables expanded leaves number (LNexp) and tips leaves number (LNtip) in the main stem, linear dimensions of expanded leaves and later, at harvest were determined yield components (total stem length were measured, fresh biomass of commercial stem dry mass commercial stem, number of nodes, number of internodes, internode length, fresh weight and dry weight of internode). It was concluded that the change in rate of leaf emergence (phyllochron greater) from the 15th leaf on is caused by a change in microclimate in the canopy and the increase of the sink strength of photosynthates to stem growth; and yield components are affected negatively by lower densities than those recommended for the crop planting. / Os objetivos desta tese foram (i) identificar o número de folhas expandidas (NFE) e totais (NFT) a partir do qual ocorre redução da contribuição das reservas do tolete para a taxa de emissão de folhas em cana-de-açúcar e (ii) o efeito de diferentes densidades de colmos no desenvolvimento foliar na cultura da cana-de-açúcar. Os experimentos foram conduzidos na área experimental do Departamento de Fitotecnia, Centro de Ciências Rurais, da Universidade Federal de Santa Maria, na estação de 2012/2013. O clone de cana-de-açúcar utilizado nos experimentos foi SP 711406, por ser um clone de ciclo intermediário e bem adaptado ao local. Para alcançar o primeiro objetivo, descrito no Capítulo 1, o delineamento foi o Inteiramente Casualizado com 32 repetições. Foram testados quatro tratamentos: duas vezes o comprimento do entrenó, uma vez o comprimento do entrenó, metade do comprimento do entrenó e somente o nó. Os resultados indicaram que as reservas no tolete de cana-de-açúcar tem a contribuição máxima para a emissão das duas primeiras folhas expandidas e das cinco primeiras folhas totais e a taxa de emissão de folhas subsequentes decresce devido ao esgotamento das reservas do tolete. Para alcançar o segundo objetivo, descrito no Capítulo 2, o experimento foi conduzido em sistema de cultivo cana-planta. Nas plantas marcadas foram medidas as variáveis número de folhas expandidas (NFE) e número de folhas totais (NFT) no colmo principal, dimensões lineares das folhas expandidas e posteriormente, no momento da colheita, foram determinados os componentes do rendimento (comprimento total do colmo, fitomassa fresca de colmo comercial, fitomassa seca do colmo comercial, número de nós, número de entrenós, comprimento do entrenó, massa fresca do entrenó e massa seca do entrenó). Concluiu-se que a mudança na velocidade da emissão de folhas (filocrono maior) a partir da 15ª folha é causada por formação de microclima no dossel e devido ao aumento do dreno de fotoassimilados para crescimento dos colmos; e que os componentes do rendimento são afetados de forma negativa por densidades de plantio menores que as recomendadas para a cultura.

The C₄ photosynthetic pathway acts to concentrate CO₂ around the enzyme Ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), ensuring that it catalyses a carboxylation rather than oxygenation reaction, which in turn suppresses photorespiration. In nearly all cases C₄ photosynthesis is underpinned by characteristic Kranz anatomy, with concentric wreaths of bundle sheath (BS) and mesophyll (M) cells surrounding closely spaced veins. The increased yields associated with the C₄ pathway have lead to the suggestion that C₃ crops such as rice should be engineered to undertake C₄ photosynthesis, however, this goal is currently held back by a lack of understanding about how the development of Kranz anatomy is regulated. Recently, a number of candidate Kranz regulators have been identified in an RNA-seq study that compared leaf development in maize foliar (Kranz) and husk (non-Kranz) leaves. However, this study did not consider the impact of a recent whole genome duplication in the maize lineage on the gene expression patterns analysed. Therefore, in this thesis maize homeolog gene-pair divergence during early leaf development was assessed. This revealed that expression divergence of homeolog gene-pairs is a significant evolutionary phenomenon. Functional validation of a subset of Kranz candidates revealed that a Zmscr1-1; Zmscr1h-1 double mutant exhibited defects in Kranz patterning, including increased formation of extra BS cells and veins with no separating M cells. Furthermore, Zmnkd1; Zmnkd2 double mutants exhibited a subtle increase in extra BS cell formation. Taken together, this indicates that both ZmSCR1/ZmSCR1h and ZmNKD1/ZmNKD2 function redundantly during Kranz development. No evidence was obtained that two additional genes, ZmSHR2 and ZmRVN1, play a role in Kranz development, and expression of candidate Kranz regulators in rice did not alter leaf anatomy. Together, this work has confirmed roles for a number of genes in Kranz regulation, and has provided insight into the complex regulation underpinning Kranz development in maize.

ABSTRACT: Formation of organ shape is an intriguing yet largely unanswered question in developmental biology. Shapes arise as a result of tightly controlled spatial variation in the rates and directions of tissue expansion over the course of development; therefore, quantifying these growth patterns could provide information about the underlying mechanisms of morphogenesis. Here we present a novel technique and computational tools for quantifying growth and shape changes in developing leaves, with a few unique capabilities. This includes the ability to compute growth from three-dimensional (3D) coordinates, which makes this the first method suitable for studying leaf growth in species or mutants with non-flat leaves, as well as small leaves at early stages of development, and allows us to simultaneously capture 3D shape changes. In the following, we apply these methods to study growth and shape changes in the first rosette leaf of Arabidopsis thaliana. Results reveal clear spatiotemporal patterns in growth rates and directionality, and tissue deformation maps illustrate an intricate balance involved in maintaining a relatively flat leaf surface in wild type leaves. Semi-automated tools presented make a high throughput of data possible with this method, and algorithms for generating mean maps of growth will make it possible to perform standardized comparative analyses of growth patterns between wild type and mutants and/or between species. The methods presented in this thesis will therefore be useful for studying leaf growth and shape, to further investigate the mechanisms of morphogenesis.   RÉSUMÉ: Comment un organe acquiert sa forme particulière au cours du développement est une question intéressante mais largement non résolue. La forme d’un organe résulte de la façon dont les taux et directions de croissance de ses tissues varient dans l’espace et dans le temps. Quantifier les motifs de croissance est donc nécessaire pout élucider les mécanismes sous-jacents de la morphogenèse. Nous présentons ici une nouvelle méthodologie pour quantifier la croissance et les changements de forme dans les feuilles en développement. Cette méthodologie s’appuie sur le développement de nouvelles techniques expérimentales et de programmes informatiques, et présente des avantages uniques : la croissance de la surface des feuilles et le changement de forme peuvent être analysés en trois dimensions (3D), pour une longue période et de large déformations. De plus l’analyse de multiples échantillons permet de générer une cartographie moyenne des motifs de croissance à la surface des feuilles au cours de leur développement, ainsi qu’une description quantitative de la déformation des tissus sous l’effet de leur croissance. Dans cette thèse, nous présentons les résultats de croissance et de changements de forme de la première feuille de rosette d'Arabidopsis thaliana au cours de son développement. Les cartes moyennes de croissance révèlent des motifs spatio-temporels évidents tant pour les taux que pour les directions de croissance. De plus, la description de la déformation des tissus démontre l'équilibre complexe impliqué dans le maintien d'une surface relativement plane dans les feuilles. La méthode proposée et les logiciels associés permettra d’effectuer des analyses comparative de la croissance entre feuilles de type sauvage et feuilles de mutants aux formes altérées, afin d’élucider les mécanismes de la morphogenèse foliaire.

For optimal growth, plants have evolved strategies to integrate environmental signals to coordinate complex developmental and defensive processes to cope with the changing surroundings. Under challenges, plants prioritize their defense over growth. This trade-off involves complex interactions between multiple hormonal pathways and developmental networks. We discovered that JACKDAW (JKD), the core component of the SHORTROOT (SHR)-SCARECROW (SCR)- JKD plant developmental regulatory network is linking defense responses to the developmental programming. Unlike the well-studied function of JKD in root development, its function in leaves is yet to be understood. We found that JKD is expressed on the abaxial side of the leaf ground tissue. It has conserved functions in promoting SHR nuclear retention and restricting cyclinD6 expression in the leaf. Additionally, JKD has a function in leaf internal architecture establishment, including suppression of the bundle sheath cell division and shaping of the leaf ground tissue. We also found that SHR is a universal asymmetric cell division (ACD) activator, as ectopic SHR expression in the leaf ground tissue promotes stomata development via promoting the ACD to produce more stomata precursor cells. We showed that the knockout mutant of JKD has larger rosettes and better photosynthesis capacity, while the basal defense level and resistance to Botrytis cinerea, a necrotrophic pathogen, are enhanced. Our transcriptome and transcription studies revealed that JKD suppresses the expression of the plant defense hormone Jasmonic acid (JA) response genes and is itself downregulated by JA. This suggests that JKD is involved in the JA signaling, which mediates defense responses for wounding and herbivore attacks. Together, our study indicates that the loss of JKD uncoupled the plant growth-defense trade-off. JKD is a new link between plant development and defense. To verify whether this function of JKD is conserved in crops, JKD orthologues in tomatoes are identified, CRISPR-Cas9 and TILLING mutants are created and analyzed. The results showed that the functions of JKD in root development and resistance to botrytis are conserved. The broad presence of JKD orthologs makes them a great target for molecular breeding to generate crops that do not have to sacrifice their normal growth to defense response.

No description available.

No description available.

Trabalhos recentes vêm tentando resolver as relações filogenéticas na subordem Portulacineae. A família Portulacaceae, como tradicionalmente circunscrita, não constituía um grupo monofilético e recentemente foi desmembrada em diversas famílias menores. Algumas destas famílias, juntamente à família Cactaceae, formam o clado ACPT (Anacampsetotaceae, Cactaceae, Portulacaceae e Talinaceae), sustentado principalmente por dados moleculares, sendo poucos os caracteres morfológicos e anatômicos reconhecidos como sinapomorfias. A presente dissertação teve como objetivo documentar a anatomia e o desenvolvimento de folhas e da região da axila foliar em espécies de Portulacaceae e Talinaceae, discutindo os resultados com a literatura existente para outros grupos do clado ACPT. Técnicas usuais em anatomia vegetal foram usadas para analisar folhas e regiões nodais do ápice e base do caule. Como principais resultados, pudemos observar diversos caracteres presentes na região da axila foliar que representam homologias primárias dentro do clado ACPT. Além disso, descrevemos diferentes padrões de desenvolvimento foliar, relacionados especialmente com a atividade do meristema marginal, levando a diferentes morfologias foliares. Acreditamos que os dados aqui obtidos sejam relevantes para uma melhor compreensão da evolução das diferentes linhagens do clado ACPT, e que futuros estudos, abordando outros grupos com maiores detalhes, poderão testar estas hipóteses de homologias primárias aqui propostas. / Recent works attempt to resolve the phylogenetic relationships within suborder Portulacineae. The family Portulacaceae, as traditionally circunscribed, is not monophyletic, and was recently split into several smaller families. Some of these families, along with Cactaceae, form the ACPT clade (Anacampsetotaceae, Cactaceae, Portulacaceae and Talinaceae), sustained mainly by molecular data. Few morphological and anatomical synapomorphies are known for the group. This dissertation aims to investigate the anatomy and development of leaves and leaf axils in species of Portulacaceae and Talinaceae, discussing the results with existing literature for other groups of the ACPT clade. Usual techniques of plant anatomy were used to examine leaves and nodal regions of apical and basal portions of stems. As main results, we observed several characters present in the region of leaf axil that represent primary homologies within ACPT clade. In addition, we describe different patterns of leaf development, especially related to the activity of the marginal meristem leading to different leaf morphologies. We believe that these data are relevant to a better understanding of the evolution in different lineages of the ACPT clade. Future studies, addressing other groups in greater detail, will be able to test these hypotheses of primary homologies proposed here.

No description available.

Le colza est une culture oléagineuse très exigeante en intrants azotés associée à une faible efficience d’usage de l’azote (EUA). Le défi majeur vise à améliorer le bilan agroenvironnemental du colza par une optimisation de l’EUA, notamment en condition où l’azote est limitant dans le sol. L’EUA est limitée par une faible efficience de remobilisation de l’azote (ERA) lors de la sénescence des feuilles. L’objectif de ce travail de thèse a consisté à rechercher, chez le colza, la topologie et l’orientation des attributs métaboliques associées à l’ERA pendant la sénescence foliaire.Les résultats montrent que le métabolome des feuilles évolue tout au long de leur développement végétatif, de leur croissance à leur chute. Il est spécifique à chaque étage foliaire et traduit des relations trophiques et environnementales particulières liées au positionnement des feuilles dans le couvert végétal. Ces spécificités sont associées à des variations de teneurs en glucides, d’acides aminés,de glucosinolates et de coumarines en lien étroit avec la régulation phytohormonale du développement foliaire et avec leur translocation dans le phloème. Le cas de la Proline a été plus particulièrement approfondi et l’activation de son catabolisme sous régulation circadienne dans les tissus sénescents a été mise en évidence. Une approche combinée de transcriptomique et de métabolomique a permis de démontrer une variabilité génotypique importante dans les processus de dégradation et de transport des protéines, glucides et acides aminés entre deux génotypes à forte ERA. De la même manière, des relati / Oilseed rape is a very demanding oleaginous crop for nitrogen inputs associated with a low nitrogen use efficiency (NUE). The main challenge to improve the agri-environmental balance of oilseed rape is to optimize the NUE, especially under nitrogen deprivation. The NUE is limited by a low nitrogen remobilization efficiency (NRE) during leaf senescence. The aim of this thesis was to define the metabolome topology and orientation associated with NRE during leaf senescence in oilseed rape.The results show that leaf metabolome dynamically evolves throughout their vegetative growth, until their fall. Metabolome was found specific to each leaf rank, reflecting the trophic and environmental relationships related to the leaf positioning in the canopy. These specificities are associated with variations in carbohydrates, amino acids, glucosinolates and coumarins contents in close connection with the phytohormonal regulation of leaf development and with their translocation in the phloem.In particular, the activation of Proline circadian-controlled catabolism in senescent tissues was demonstrated. Finally, significant variations in the degradation and transport of proteins, carbohydrates and amino acids between two highly efficient NRE genotypes were highlighted using a combined transcriptomic and metabolomic approach. Similarly, a close relationship has been described between the genes expression levels and the metabolic content involved to increase NRE under low nitrogen input.The results are discussed regarding nitrogen remobilization improvement and more generally nutrients i