Eragrostis curvula es una gramínea estudiada por su tolerancia al estrés por sequía y por tener la capacidad de reproducirse por apomixis, la cual es definida como un mecanismo que permite la clonación natural por medio de semillas resultando la descendencia genéticamente idéntica a la planta madre. E. curvula tiene un número básico de cromosomas de 10 y contiene genotipos con distintos niveles de ploidias. Una de las características la especie es que los genotipos diploides son siempre sexuales mientras que los poliploides son generalmente apomícticos aunque existen tetraploides sexuales. Desde hace décadas la apomixis ha sido estudiada con el fin de identificar las bases moleculares y genéticas para ser transferidas a otros cultivos de importancia económica. Las técnicas de secuenciación de ADN son una herramienta sumamente útil para descubrir genes y regiones asociadas a distintos caracteres biológicos, así como para realizar análisis filogenéticos y de sintenia entre especies. En el trabajo de esta tesis se propuso obtener secuencias genómicas de E. curvula utilizando tecnologías de última generación con el fin de identificar los genes relacionados a la apomixis y otros genes de interés como los de la tolerancia al estrés por sequía y la calidad forrajera. El primer genoma de la especie secuenciado fue el genotipo diploide sexual Victoria que fue originado del tetraploide apomíctico Tanganyika INTA. Las plataformas utilizadas para su secuenciación fueron PacBio, Chicago y Hi-C y fue ensamblado a través del software FALCON con el que se obtuvo un N50 de ~43 mega pares de bases (Mb) y 1.143 contigs. Los genes anotados fueron 56.469 los cuales fueron utilizados para determinar la historia evolutiva de la especie. Además se caracterizaron las secuencias de los genes de las vías de la lignina relacionados con la calidad forrajera y los genes de la familia WRKY, vinculados a la tolerancia al estrés por sequía. Por otro lado se encontraron genes de E. curvula ortólogos a los expresados en etapas específicas de la vía sexual de Oryza sativa. Los genomas tetraploides apomícticos secuenciados fueron el del cultivar Tanganyika INTA obtenido mediante la plataforma Illumina y el de Don Walter combinando las tecnologías Chromium 10X y Oxford Nanopore. El ensamblado de Tanganyika INTA con el software Masurca resultó en un N50 de 4.715 pb y 293.300 contigs, mientras que en el genoma de Don Walter ensamblado con Supernova+DBG2OLC se obtuvo un N50 de 224.390 pb y 7.542 contigs. Por medio de un análisis comparativo se pudo identificar la región vinculada la apomixis en todos los genomas en la cual se encontraron genes que podrían tener un rol activo en la regulación del modo reproductivo de acuerdo con la literatura. A través de esta tesis se pudieron secuenciar, ensamblar y anotar tres genomas de E. curvula lo cual representa un avance significativo en la caracterización de la especie. La identificación de regiones asociadas a la apomixis y sus posibilidades de expresión y regulación permitirá, en una instancia futura, manipular el carácter e intentar la introgresión del mismo en especies sexuales de interés agrícola por medio de ingeniería genética. / Eragrostis curvula is forage grass studied for its tolerance to draught stress and because its characteristic reproductive pathway, the apomixis. Apomixis is an asexual way of reproduction by seeds in which the progeny result genetically identical to the mother plant. The basic number of chromosomes of E. curvula is 10 and has different ploidy levels being the diploids always sexual while the polyploids are mainly apomictic despite there are fully sexual tetraploids. Apomixis has been studied in order to identify its molecular and genetic basis to transfer this trait to economically import crops. The DNA sequencing is a powerful tool to detect genes and/or regions associated to different traits and disclose the evolutionary history of the species. In this Thesis the latest generation technologies have been used to sequencing and assembly the E. curvula genome to identify the genes related to apomixis and other interesting traits like draught tolerance and forage quality. The first sequenced genome of the species was the diploid sexual genotype Victoria originated from the apomictic tetraploid Tanganyika INTA. The technologies used for the sequencing were a combination of PacBio, Chicago and Hi-C and the assembler with best performance was FALCON. The final N50 obtained here was ~43 Mb and the number of contigs was 1,143. The 56,469 genes annotated in this genome were used to unravel the evolutionary history of E. curvula. Furthermore we identify genes in the lignin pathway associated to the forage quality and genes of the WRKY family which are related to al multiple abiotic stress like drought stress. The genes related to the sexual pathway were evaluated through a comparative analysis with specific development stages in Oryza sativa. The tetraploids genomes of E. curvula sequenced here were derived from Tanganyika INTA, sequenced with Illumina, and Don Walter using a combination of Chromium 10x and Oxford Nanopore. The Tanganyika INTA assembly was performed with Masurca software obtaining an N50 of 4,715 bp and 293,000 contigs, while Don Walter was assembled with Supernova+DBG2OLC rendering an N50 of 224,390 bp and 7,542 contigs. Interestingly a region linked to apomixis was found through a comparative analysis between the genomes of E. curvula that could have an active role in the regulation of the reproductive pathway based on the literature. In this Thesis were sequenced, assembled and annotated three genomes of E. curvula representing a significant step forward in terms of characterisation of the species. The identification of the regions linked to apomixis, its expression and regulation could allow handling the trait and, in future instances, to introduce apomixis to sexual economically important crops.

Please read the abstract in the section 10back of this document / Dissertation (MSc)--University of Pretoria, 2009. / Plant Science / unrestricted

This thesis examines the hypothesis that, in southern New South Wales and northeast Victoria, Australia, palatable taxa of E. curvula offer advantages that complement those of the species that are traditionally sown in temperate pastures in a landscape context.This hypothesis was based on a review of literature showing that, prior to European settlement, the vegetation, the landscape and the climate were broadly in balance, and the wateruse pattern of the vegetation of southeastern Australia resulted in water being used more-or-less completely by the end of summer. This maximised the capacity of the soil to take up and store water during autumn and winter.Three grazing experiments and one spaced-plant species evaluation study were used to assess the role of summer-growing, C4 Eragrostis curvula in pastures in the temperate zone of southeastern Australia.Issues relating to pasture production and the productivity of wool-growing sheep were investigated. Factors affecting the sustainability of the pastures and their potential on and off site impacts were emphasised.Modelling was used to explore issues of water use, arising from the grazing experiments. It is concluded that the persistence, production, water use patterns, and the adaptability of palatable varieties of E. curvula make it a useful and complementary addition to the range of species that are currently available for use as sown pastures in southern Australia. / Doctor of Philosophy (PhD)

Les pelouses alpines à Carex curvula (laîche courbée) constituent l'une des formations les plus emblématiques de l'étage alpin des montagnes européennes. Cette thèse se présente comme une contribution à l'étude des patrons de la diversité génétique de Carex curvula et des patrons de la diversité floristique des pelouses alpines à Carex curvula en Europe.<br /> Dans un premier temps, ce travail examine la variabilité floristique des pelouses dominées par C. curvula et tente d'identifier les forces qui ont joué le rôle le plus important dans la structuration des espèces de l'étage alpin acidiphile européen. Les résultats des analyses montrent qu'il existe une variabilité importante pour la distribution de la diversité interspécifique et seulement une correspondance partielle entre la position des barrières biogéographiques de l'étage alpin et les grandes distances géographiques qui séparent les massifs montagnards. Il ressort nettement que les forces qui ont joué le rôle le plus important dans la structuration floristique de l'étage alpin acidiphile européen sont de nature historique et dans une moindre mesure de nature écologique.<br /> Ensuite, nous explorons la distribution de la diversité génétique dans les populations de C. curvula dans un contexte phylogéographique. L'impact des glaciations quaternaires correspond à deux histoires différentes pour les flores alpines dans les montagnes de l'ouest et de l'est du continent européen. Chez C. curvula, les mécanismes de recolonisations postglaciaires auraient impliqué un large vague de migration est-ouest dans les Alpes et une migration verticale beaucoup plus locale dans les Carpates. Les Pyrénées auraient été colonisé plus récemment, à partir d'un refuge secondaire localisé dans les Alpes du Sud-Ouest.<br /> Enfin, dans un troisième temps, nous nous intéressons au problème des relations entre la diversité génétique et floristique, en analysant la diversité locale des espèces dans les pelouses à C. curvula et la diversité génétique de l'espèce dominante. Le manque de corrélation positive entre les deux niveaux de la diversité est expliqué par des réponses différentes des gènes et des espèces aux grands changements climatiques qui sont intervenus au cours du Quaternaire.<br /> Nous concluons sur les perspectives de biogéographie comparative ouvertes par ce travail, en particulier sur l'articulation souhaitée entre les efforts de modélisation de la distribution biologique, la phylogéographie et l'écologie évolutive.

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2014-09-24T12:10:01Z No. of bitstreams: 2 Bergamini, Leonardo Lima.pdf: 1174414 bytes, checksum: 8ab040a0c96a503f2c2dab35be6be5ea (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2014-09-24T15:37:12Z (GMT) No. of bitstreams: 2 Bergamini, Leonardo Lima.pdf: 1174414 bytes, checksum: 8ab040a0c96a503f2c2dab35be6be5ea (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-09-24T15:37:12Z (GMT). No. of bitstreams: 2 Bergamini, Leonardo Lima.pdf: 1174414 bytes, checksum: 8ab040a0c96a503f2c2dab35be6be5ea (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2013-06-02 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The process of host-plant selection is the main interface in the herbivore-plant interactions, with deep consequences for the ecology and evolution of those groups. In this work, we investigate some steps of the host-plant selection in two congeneric species of seed beetles. In the first chapter, we assess the oviposition pattern and larval survival in the seed-beetle G. cavillator to evaluate whether oviposition site choices maximize offspring survival, accounting for the spatially hierarchic structure of the system. In the second chapter, we analyze the fine-scale positioning of G. speculifer eggs, and explore the role of geometric constraints in the egg distribution patterns. Altogether our results exemplify how small differences in key traits of the host-plant selection can lead to significant differences in the interaction between herbivore insects and their host plants. / O processo de seleção de plantas hospedeiras é a principal interface nas interações herbívoro-planta, com profundas consequências para a ecologia e evolução destes grupos. Neste trabalho investigamos algumas etapas da seleção de hospedeiras em duas espécies co-genéricas de besouros bruquíneos. No primeiro capítulo avaliamos o padrão de oviposição e de sobrevivência das larvas de G. cavillatorpara testar se as escolhas das fêmeas estão de acordo com as expectativas da teoria de oviposição ótima, considerando a estrutura espacialmente hierárquica do sistema. No segundo capítulo analisamos a seleção em fina-escala da posição dos ovos nas vagens pelas fêmeas de G. speculifer, e exploramos o papel da restrição geométrica da vagem em definir o padrão de distribuição dos ovos. Tomados em conjunto, os resultados dos dois capítulos exemplificam como pequenas diferenças em atributos-chave do processo de seleção de hospedeiras podem levar a importantes diferenças na interação entre insetos herbívoros e suas plantas hospedeiras.