Orientador: Eliana Regina Forni-Martins / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-13T10:03:06Z (GMT). No. of bitstreams: 1 Costa_ItayguaraRibeiro_D.pdf: 2898374 bytes, checksum: 078db4f644b0fd0bf359c0dfc61360eb (MD5) Previous issue date: 2009 / Resumo: Myrtaceae é considerada uma das mais importantes famílias em diversidade de espécies nos neotrópicos, principalmente ao longo da Mata Atlântica e do Cerrado, representando de 10 a 15% da diversidade destes biomas. Myrteae é a mais diversificada tribo (73 gêneros e 2375 espécies) da família. Em termos gerais, os representantes sul-americanos de Myrtaceae são considerados táxons complexos e estudos biossistemáticos são fundamentais para uma melhor delimitação taxonômica de suas espécies. Provavelmente, a dificuldade de identificação das mirtáceas brasileiras possa ser atribuída à especiação decorrente de hibridação e poliploidia, com aparecimento de tipos recombinantes com características intermediárias entre os taxa originais, sendo o fluxo gênico interrompido por diferenciação cromossômica, especialmente pela duplicação do número cromossômico. Este trabalho teve como objetivos principais contribuir para o conhecimento citotaxonômico / citogenético da família, bem como aprimorar a filogenia da tribo Myrteae, onde as relações entre os gêneros ainda são incertas, enfatizando Psidium e gêneros relacionados (grupo Pimenta). Em termos gerais, a poliploidia surgiu de maneira independente ao longo da diversificação das diferentes linhagens na família, ocorrendo em 16% das espécies com número cromossômico conhecido, além de ser observada uma redução drástica de números cromossômicos em relação à x = 11, chegando a x = 5 e x = 6 na tribo Chamelaucieae, clado que concentra metade dos registros poliplóides. Na tribo Myrteae, a ocorrência do número cromossômico x = 11 é quase constante, com exceção de 26% das espécies analisadas que são poliplóides. Eugenia e Psidium, dois dos principais gêneros de Myrteae nos neotrópicos e Decaspermum, essencialmente australasiano, registram a maioria das variações poliplóides da tribo, o que possivelmente tenha favorecido a colonização de novos habitats e ampliado a distribuição geográfica em relação aos demais gêneros da tribo. Do ponto de vista cariotípico, os cromossomos em Myrteae são pequenos (<2mm), porém é observado certo grau de assimetria nos cariótipos de espécies com de frutos carnosos quando comparadas com as de frutos secos, nas quais os cariótipos são altamente simétricos. Do ponto de vista molecular, a variação no número de sítios DNAr 45S forneceu subsídios para a diferenciação de espécies em alguns complexos de Psidium, bem como indicou a possível origem alopoliplóide em um par de citótipos de P. cattleianum, sendo este o primeiro trabalho desta natureza em Myrtaceae. O tamanho do genoma em Myrteae é pequeno e correspondeu diretamente ao nível de ploidia das espécies. Em Psidium, esta variação foi da ordem de 9x e os resultados obtidos para espécies do complexo P. grandifolium podem ser utilizados em discussões taxonômicas, além de fornecer indícios adicionais sobre a evolução alopoliplóide entre algumas populações de P. cattleianum. Estas abordagens são inéditas para representantes de Myrteae. A análise filogenética (94 espécies de 38 gêneros) confirmou o monofiletismo de Myrteae, bem como do gênero Psidium e suas relações de parentesco dentro do grupo Pimenta. O gênero-irmão de Psidium é Myrrhinium. São reconhecidos sete grupos informais: grupo Eugenia, grupo Myrceugenia, grupo Myrcia, grupo Myrteola, grupo Pimenta, grupo Plinia e grupo Australasiano. Futuramente, serão explorados os caracteres macromorfológicos e biogeográficos que sustentem uma nova proposta de classificação para os gêneros de Myrteae. / Abstract: Myrtaceae is one of the most diverse families in Neotropical region; principally belong to Mata Atlântica and Cerrado, reaching 10 to 15% of biodiversity of these biomes. Myrteae is the most generically tribe (73 genera and 2375 species) in this family. Generally, South-American taxa are considered a complex group and biosystematic studies are necessary to understand the taxonomic delimitation of their species. Probably, the identification difficulties of Brazilian Myrtaceae would be due to speciation by hybridization and polyploidy, appearing species with intermediate characters between parental taxa and the genetic flow blocked by chromosomal differentiation, principally by chromosome duplication. This work aims to contribute to Cytotaxonomical/Cytogenetical knowledge in Myrtaceae and to update the Myrteae phylogeny, where the relationships between some genera are unclear, emphasizing Psidium and related genera (Pimenta group). Polyploidy evolves independently belong to diverse lineages belong Myrtaceae, reaching 16% of species that the chromosome numbers are know, besides is observed a drastic reduction of chromosome numbers in relation to x = 11, reaching to x = 5 or x = 6 in the Chamelaucieae tribe, this tribe concentrates half of polyploid records in Myrtaceae. In Myrteae, the occurrence of chromosome number x = 11 is practically constant, exception to 26% of polyploid species. Eugenia and Psidium are two of the principal Neotropical genera of Myrteae and Decaspermum, an Australasian genus, presents the majority of polyploidy variations in Myrteae, that would explicate the widespread distribution and the new habitat colonization in relation to the others genera in Myrteae. The chromosome length are small (<2mm), wherever was observed asymmetric karyotypes in fleshy-fruited taxa against dry-fruited taxa whit higher symmetric karyotypes. The variation of DNAr 45S loci supplied additional parameters to species differentiation in some Psidium complexes and supplied indications about the possible allopolyploid origin in cytotypes of P. cattleianum, being this the first approach with molecular cytogenetic in Myrtaceae. The species of Myrteae presents a very small genome, and was observed a positive correlation with ploidy levels. In Psidium, the variation of genome size was 9x and the obtained results for P. grandifolium complex would be useful in taxonomic discussions besides supply additional characters about the allopolyploid origin in some populations of P. cattleainum. This approach also represents new records in Myrteae. The phylogenetic study (94 species and 38 genera) confirm that the tribe Myrteae and the genus Psidium are monophyletic. The sister group of Psidium is Myrrhinium. Seven informal clades are recognized: Eugenia group, Myrceugenia group, Myrcia group, Myrteola group, Pimenta group, Plinia group e Australasian group. In the future, we will to explore morphological and biogeographical characters that would be support a new classification of Myrteae. / Doutorado / Doutor em Biologia Vegetal

Orientadores: João Semir, Lucia Garcez Lohmann / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-15T14:46:18Z (GMT). No. of bitstreams: 1 Firetti-Leggieri_Fabiana_D.pdf: 148843515 bytes, checksum: bfb6fa893bb9997ed92b1d321acb5e7a (MD5) Previous issue date: 2009 / Resumo: O complexo Anemopaegma arvense é constituído por espécies e variedades de difícil delimitação. As opiniões dos taxonomistas, baseadas em caracteres morfológicos, são controversas em considerálas uma única espécie altamente polimórfica ou separá-las. Com o intuito de auxiliar na circunscrição de tais táxons, realizou-se um estudo biossistemático que englobou os seguintes assuntos: morfologia e morfometria de caracteres vegetativos e reprodutivos, anatomia da lâmina foliolar, contagem cromossômica, aplicação de marcadores AFLP para a delimitação genética, fenologia, biologia floral e polinização, sistema reprodutivo e hibridação e, poliembrionia em espécies do gênero com distintos níveis de ploidia. As morfoespécies do complexo diferem principalmente na morfologia foliar, sendo os táxons de Anemopaegma acutifolium caracterizados por folíolos elípticos a estreitamente oblanceolados com razão comprimento/largura do folíolo 3,5 a 18,5, os de A. arvense por folíolos lineares a estreitamente oblanceolados (razão 22,2 a 45,5) e, A. glaucum por folíolos largamente oblanceolados, oblongos a obovados (razão entre 1,69 e 3,9). A partir de caracteres morfológicos, como crescimento indeterminado dos ramos, exclui-se A. scabriusculum do complexo. O estudo morfométrico de caracteres foliares se mostrou útil para a separação das espécies. Já a morfometria de caracteres reprodutivos não foi informativa para a delimitação de tais táxons. Anatomicamente, as espécies e morfoespécies do complexo diferem quanto à disposição dos estômatos, tipo de epiderme constituição do sistema vascular da nervura mediana e composição da bainha dos feixes vasculares das nervuras laterais. Dentre as morfoespécies de A. acutifolium, A. acutifolium "típica" difere das demais por possuir folíolos anfiestomáticos e A. acutifolium "sarmentosa" por apresentar epiderme da face adaxial com desdobramentos pontuais. Já A. arvense é caracterizada pela ausência de cordões floemáticos no sistema vascular da nervura mediana e por possuir a margem destituída de parênquima fundamental subepidérmico. As morfoespécies de A. glaucum, "típica" da Bahia e "não glauca", são diferenciadas das demais pela ausência de calotas de fibras sobre o xilema nas nervuras laterais de grande e médio calibre. A. scabriusculum difere das outras espécies por possuir extensão de bainha nos feixes vasculares de grande e médio calibre e estômatos agrupados nas regiões internervurais com câmaras subestomáticas unidas. A contagem cromossômica revelou a condição poliplóide das espécies e morfoespécies do complexo, tendo estas 2n = 80. Os marcadores AFLP, apesar de serem bastante utilizados para a separação de táxons em nível infra-específico, não se mostraram eficientes para a delimitação das espécies do complexo Anemopaegma arvense. Quanto ao comportamento fenológico, A. acutifolium, A. arvense e A. glaucum apresentaram eventos anuais de brotamento, floração e frutificação. Já os indivíduos de A. scabriusculum têm dois a três eventos de floração e frutificação por ano. As flores das espécies são bastante semelhantes quanto à morfologia e recursos produzidos e são polinizadas pelas mesmas espécies de abelhas. Através de polinizações controladas constatou-se que tais espécies são auto-compatíveis e interférteis, havendo, portanto, alta probabilidade de formação de híbridos em populações simpátricas destas espécies. Notou-se uma relação positiva entre poliploidia e poliembrionia nas espécies do gênero aqui abordadas, tendo as sementes das espécies poliplóides mais de um embrião e as da espécie diplóide, A. album, somente um embrião. / Abstract: Anemopaegma arvense complex is constituted by species and varieties of difficult delimiting. Taxonomists opinions based upon morphologic features are controversial as to considering them either an only highly polymorphic species or separating them into different taxa. In order to help with the circumscription of such taxa, a biosystematic study was conducted which included the following subjects: morphology and morphometry of vegetative and reproductive features, leaflet blade anatomy, chromosome counting, AFLP markers application for genetic delimitation, phenology , floral biology and pollination, reproductive system and hybridization and polyembryony of the genus species with different ploidy levels .The morphs of the complex differ mainly in leaf morphology where the Anemopaegma acutifolium taxa are characterized by elliptical leaflets with the lengh / width ratio of leaflet falling within the range 3,5 to 18,5; A. arvense characterized by linear leaflets to narrowly oblanceolate (ratio between 22,2 and 45,5) and, A. glaucum by leaflets broadly oblanceolate, from oblong to obovate (ratio between 1,69 and 3,9).Taking into account morphologic features such as undetermined growth of the branches, A. scabriusculum may be excluded off the complex. The morphometric study of the leaf features has been found useful for species separation. However, the morphometry of reproductive features were not informative enough for the delimitation of such taxa. Anatomically, the species and morphs of the complex differ from one another as to the stomata disposition, epidermis type, vascular system constitution of the midrib and, composition of the vascular bundle of the lateral veins. Among the A. acutifolium morphs, A. acutifolium "típica" differs from the others for possessing anphistomatic leaflets and, A. acutifolium "sarmentosa" for presenting the adaxial face epidermis with punctual unfoldings. As for A. arvense, it is characterized by the absence of phloematic strings in the midrib vascular system and parenchyma absent in the marginal region. As for the two morphs, A. glaucum "típica" of Bahia and "não glauca", they are differentiated from the others by the absence of fibers caps on the xilem on the lateral ribs of large and medium caliber. A. scabriusculum differs from the other species for possessing extension sheath in the vascular bundles of large and medium caliber and, stomata grouped between vascular bundles presenting substomatic cameras linked to one another. The chromosome counting revealed polyploidy condition of the species and the morphs of the complex, those presenting 2n = 80. The AFLP markers, in spite of being quite utilized for taxa separation in an infraspecific level, were not found efficient for the species delimitation of Anemopaegma arvense complex. With relation to the phenologic behavior, A. acutifolium, A. arvense and A. glaucum presented annual events of sprouting, blooming and fructification. However, A. scabriusculumindividuals presented two to three blooming and fructification events a year. The flowers of the species are very similar to one another as to their morphology and to the resources provided by them and are pollinated by the same species of bees. Through controlled pollinations, it could be verified, that such species are self- ompatible and inter fertile, bearing, therefore, high probability of hybrid formation in sympatric populations of those species. A positive relationship between polyploidy and polyembryony in the species of the genus studied here was observed, as well as the fact that more than one embryo were found for polyploidy species seeds whereas for diploid species, A. album, only one embryo has been registered. / Doutorado / Doutor em Biologia Vegetal

Orientadores: Eliana Regina Forni Martins, Vidal de Freitas Mansano / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T00:22:48Z (GMT). No. of bitstreams: 1 Pinto_RafaelBarbosa_M.pdf: 4856945 bytes, checksum: 7af922214bf499ea2e8fe2cfb2e9e2f4 (MD5) Previous issue date: 2013 / Resumo: Swarzia é um gênero basal da subfamília Papilionoideae (Leguminosae). Apesar do seu posicionamento ter gerado debate entre muitos autores no passado, estudos sistemáticos recentes confirmam a monofilia de Swartzia, compondo o clado swartzióide juntamente com mais sete gêneros. A diversidade morfológica e a ampla distribuição geográfica na região neotropical tornam o gênero um interessante objeto de estudos taxonômicos e sistemáticos. Embora Swartzia apresente centro de diversidade amazônico, também possui alta riqueza de espécies na região extra-amazônica, apresentando complexos de espécies, com difícil delimitação morfológica de alguns táxons, necessitando de ferramentas adicionais para uma melhor compreensão da evolução no grupo. A citogenética, mediante estudos cromossômicos, fornece informações importantes na elucidação de relações supra e infra genéricas e, através de uma abordagem citotaxonômica, pode contribuir para o esclarecimento de problemas sistemáticos e taxonômicos. O presente trabalho visa ampliar os estudos do gênero, contribuindo com um inédito estudo citogenético e ampliando estudos taxonômicos das Swartzia na região extra-amazônica brasileira. Para o capítulo 1 foram coletadas sementes de 18 espécies distribuídas no território brasileiro para análise cromossômica e no capítulo 2 é apresentado um estudo taxonômico de Swartzia na região extra-amazônica brasileira, com chave de identificação. Swartzia apresentou número cromossômico constante entre as espécies analisadas (2n=2x=26). Entretanto, S. leptopetala demonstrou potencial de autopoliploidização ao apresentar sementes 2n=2x=26 e 2n=4x=52 numa mesma árvore, configurando processos de poliploidização em meristemas isolados. O tamanho dos cromossomos (tamanho relativo dos cromossomos e comprimento total de cromatina - TCL) foi medido para todas as 18 espécies coletadas. No geral, os cromossomos são pequenos, sendo o menor cromossomo encontrado em S. acuminata (0.25?m), enquanto o maior foi encontrado em S. euxylophora (1.41?m). Os números de bandas CMA+/DAPI- (2) e sítios de rDNA 45S (2) e 5S (2) também não apresentaram variação interespecífica. Swartzia euxylophora, cuja inclusão no gênero havia sido anteriormente questionada, apresentou as características citogenéticas semelhantes às demais Swartzia e, somadas à morfologia observada em campo, sustentam o posicionamento do táxon dentro do gênero. Os dados cariotípicos (número e tamanho cromossômicos, e número de bandas CMA/DAPI e de genes ribossomais) não permitem a diferenciação das espécies em nível de sessão. Até o momento são disponibilizadas informações cromossômicas para cerca de 10% das Swarztia, não sendo possível sugerir mecanismos de evolução cariotípica no gênero. Mediante a análise dos dados citogenéticos fornecidos neste trabalho e disponíveis na literatura é possível afirmar que os gêneros do clado swartzióide apresentam números cromossômicos diferentes, sendo este um caráter diagnóstico. No capítulo 2, os estudos taxonômicos para as Swartzia extra-amazônicas resultaram na descrição de cinco novas espécies e na elaboração de uma chave de identificação para táxons da região. Quatro delas, S. alagoensis, S. arenophila, S. revoluta e S. submontana, pertencem à seção Acutifoliae que se destaca por possuir alta diversidade e por ser exclusivamente brasileira. Swartzia thomasii pertence à seção Glabriplantae, anteriormente uma seção exclusivamente amazônica / Abstract: Swartzia is a basal genus of subfamily Papilionoideae (Leguminosae). Although the positioning of the genus has been a controversial issue among some authors in the past, recent systematic studies confirm the monophily of Swartzia as being part of a swartzioid clade with other seven genera. The morphological diversity and the widespread geographical distribution at the Neotropical region, make the genus an interesting object of taxonomic and systematic studies. Although Swartzia present an amazonian diversity center, it also has high species richness at extra-amazonian region, presenting species complex, with hard morphological delimitation of some taxa, requiring additional tools for a better comprehension of evolution within the group. Cytogenetics, by studying chromosomes, provides important informations for elucidating supra- and infrageneric relations and, by a citotaxonomic approach, it can contribute to solve systematic and taxonomic problems. The present study aims to increase the studies of the genus, contributing with an inedit cytogentic study and extending taxonomic studies of Brazilian extra-amazonian Swartzia. For chapter 1, there were collected 18 species distributed through Brazilian territory for chromosomal analyses and in chapter 2 we presenting a taxonomic study of Swartzia in extra-Amazonian region of Brazil with a description key. Swartzia presented a conservated chromosome number among species (2n=2x=26). However, S. leptopetala demonstrated an autopolyploidization potential, presenting seeds with 2n=2x=26 and 2n=4x=52 in the same tree, being a polyploidization process in isolated meristems. Chromosome length (relative chromosome length and total chromatin length - TCL) were measured for all 18 species collected. In general, Swartzia chromosomes are small, being the shortest chromosome found in S. acuminata (0.25?m) and the longest in S. euxylophora (1.41?m). The number of CMA+/DAPI- bands (2) and rDNA sites 45S (2) and 5S (2) did not present interspecific variation too. Swartzia euxylophora, which the inclusion in the genus was questioned, presented all cytogentics characteristics similar to all other analyzed Swartzia and together with morphological features observed in the field, it supports the taxon as belonging to the genus. The karyotypic data (number and size of chromosomes, and number of CMA/DAPI and ribosomal genes) do not allow the differentiation of species at section level. Until now, there is chromosomal information for about 10% of Swartzia species available, not being possible suggest karyotypic evolution mechanisms in the genus. By analyzing cytogentic data provided by this study and available in the literature, it is possible to say that genera in swartzioid clade have different chromosome number, being a diagnostic character. In chapter 2, the taxonomic studies of extra-Amazonian Swartzia resulted in a description of five new species and the elaboration of a regional key for the regional taxa. Four of them, S. alagoensis, S. arenophila, S. revoluta and S. submontana, belong to section Acutifoliae, which stands out for having high diversity and for be exclusively Brazilian. Swartzia thomasii belongs to section Glabriplantae, otherwise an exclusively Amazonianian section / Mestrado / Taxonomia Vegetal / Mestre em Biologia Vegetal

La polyploïdie se caractérise par une duplication du génome entier. Elle inhibe efficacement la prolifération cellulaire et joue pourtant un rôle clé dans les étapes précoces de la tumorigénèse. Comment est-elle capable de promouvoir une instabilité génétique dans les cellules cancéreuses est une question en suspens. J'ai établi un système modèle affectant la cytocinèse pour étudier les conséquences de la polyploïdie dans les cellules souches neuronales (CSN) et dans le disque imaginal de l'aile de drosophile. Les cellules polyploïdes du disque sont rapidement éliminées, les CSN polyploïdes continuent de proliférer. Les CSN polyploïdes sont caractérisées par une instabilité génétique précoce et deux facteurs en sont responsables: les erreurs mitotiques et des dommages à l'ADN. Ces dommages sont issus en partie de l'incapacité des cellules à restreindre leur progression dans le cycle cellulaire après une réplication incomplète de l'ADN. J'ai trouvé que de multiples domaines nucléaires au sein de la même CSN polyploïde pouvaient présenter une asynchronie de leur progression dans le cycle cellulaire. Les domaines nucléaires en retard dans leur progression sont les cibles des lésions à l'ADN au moment de l'entrée en mitose. Les lésions sont réduites après surexpression de Chk1, une kinase de la voie ATR de réponse aux dommages à l'ADN. De plus, la prolifération incontrôlée des CSN polyploïdes génétiquement instables est responsable de leur potentiel tumorigénique dans les essais de transplantation. Mes résultats montrent que la tolérance à la polyploïdie dépend du tissu et qu'une série d'événements contribue à l'instabilité génétique dans les CSN polyploïdes. / Polyploidy, which derives from whole-genome duplication events, is normally a potent inhibitor of cell proliferation, but plays important roles during the early steps of tumorigenesis. However, how the gain of multiple sets of chromosomes promotes the generation of unbalanced karyotypes typical of cancer cells remains to be investigated. Using a number of conditions that affect cytokinesis, I established a model system to study the consequences of polyploidy in the neural stem cells (NSCs) of Drosophila and in the wing disc (WD). Importantly, while polyploidy is rapidly eliminated from the WD, polyploid NSCs continue to proliferate. Polyploid NSCs are characterized by early-onset genetic instability and two sources account for the generation of unstable karyotypes: mitotic errors and high-levels of DNA damage. DNA damage in polyploid NSCs arises, at least in part, from the inability of polyploid cells to restrain cell cycle progression in response to incomplete DNA replication. Surprisingly, I found that multiple nuclear domains in the same polyploid NSC can exhibit asynchrony in cell cycle progression, with delayed nuclear domains experiencing acute DNA damage at mitotic entry. I show that DNA damage in polyploid NSCs can be reduced over-expressing Chk1, the main downstream kinase engaged by ATR in the DNA damage response. I also show that uncontrolled proliferation of genetically unstable polyploid NSCs holds tumorigenic potential in transplantation assays. Overall, my results show that the tolerance to polyploidy is tissue dependent and that a complex network of events contributes to the generation of unbalanced karyotypes in polyploid NSCs.

Nous avons étudié les phénomènes de polyploïdisation chez l'igname Dioscorea alata qui comprend trois cytotypes diploïde (2n=40), triploïde (2n=60) et tétraploïde (2n=80) en vue d'optimiser les stratégies de production d'hybrides polyploïdes. Chez ce complexe polyploïde l'augmentation de la ploïdie est corrélée avec une augmentation de la vigueur et des rendements plus élevés et plus stables. Dans un premier temps nous avons démontré l'autotétraploïdie des variétés tétraploïdes à l'aide de trois approches différentes: des analyses d'hérédité de marqueurs microsatellites, l'observation de phénomènes de double réduction et l'étude des méioses des cellules mères de pollen. Nous avons ensuite déterminé quels sont les mécanismes les plus probables à l'origine des polyploïdes naturels via l'étude de la transmission de l'hétérozygotie parentale à l'aide de microsatellites et par l'étude des incompatibilités au niveau de l'albumen lors de différents croisements intracytotypes et intercytotypes en utilisant la cytométrie en flux. Les résultats obtenus montrent que les polyploïdes de D. alata seraient apparus via la formation de gamètes non réduits de clones diploïdes. Le pool triploïde se serait édifié et diversifié uniquement par voie femelle, du fait de la non viabilité des croisements intercytotypes et de la stérilité des femelles et mâles triploïdes. Le pool tétraploïde serait apparu par union de deux gamètes non réduits de clones diploïdes (polyploidisation sexuelle bilatérale). Par la suite ce pool aurait été diversifié via des croisements intercy / We studied polyploidisation phenomena in the yam Dioscorea alata that includes three cytotypes -diploid (2n=40), triploid (2n=60) and tetraploid (2n=80) -in order to optimise polyploid hybrid production strategies. In this complex polyploid, the increase in ploidy is correlated with an increase in vigour and higher and more stable yields. We first showed the autotetraploidy of tetraploid varieties using three different approaches: heredity analyses of microsatellite markers, the observation of double reduction phenomena, and the study of meiosis of pollen mother cells. We then determined the mechanisms most likely to be at the origin of natural polyploids through the study of the transmission of parental heterozygoty using microsatellites and the study of incompatibilities at the endosperm level at the time of different intracytotypic and intercytotypic crosses using flow cytometry. The results obtained reveal that the polyploids of D. alata probably appeared through the formation of non-reduced gametes of diploid clones. The triploid pool would then have been constituted and diversified through the female pathway as a result of the non-viability of intercytotypic crosses and the sterility of female and male triploids. The tetraploid pool would have appeared as a result of the union of two non-reduced gametes of diploid clones (bilateral sexual polyploidisation). This pool would then have diversified through intercytotypic crosses with the formation of 2n gamètes through both the female and the male pathway, as well as by intracytotypic crosses within the 4X pool.

L'épistasie a longtemps été négligée, mais aujourd'hui elle connait un regain d'intérêt avec le développement du séquençage haut-débit et des études d'association pangénomique (GWAS). Elle est quasi-omniprésente, ayant été détectée sur de nombreux traits et chez de nombreuses espèces. Elle joue un rôle important d'un point de vue évolutif, puisqu'elle est à l'origine d'incompatibilités de Dobzhansky-Müller, expliquant l'isolement reproductif entre lignées apparentées. Par ailleurs, chez les polyploïdes à héritabilité disomique (essentiellement des allopolyploïdes), elle peut permettre de fixer l'hétérosis. L'objectif de cette thèse a été d'étudier l'épistasie dans ce contexte évolutif. Le matériel d'étude a été une population à base génétique large d'une espèce autogame allopolyploïde, le blé dur (Triticum turgidum), possédant deux génomes : le génome A et le génome B. Cette population a été constituée à partir de différents taxons : blé dur (T. t. durum), amidonnier domestique (T. t. dicoccum) et amidonnier sauvage (T. t. dicoccoides). Il est donc possible qu'elle présente des combinaisons de gènes coadaptées, et donc de l'épistasie générant des incompatibilités de Dobzhansky-Müller.Une première partie présente différents modèles permettant d'estimer l'épistasie. Ces modèles ont des inconvénients et des avantages, qui dépendent de l'objectif que l'on s'est fixé. Dans une deuxième partie, nous avons utilisé l'un de ces modèles sur des données de RNA-seq (données d'expression et de génotypage) de la population de blé dur, afin de détecter des effets régulateurs de l'expression, et notamment de l'épistasie entre gènes homéologues. Cette analyse est une première pour le blé dur et probablement pour les espèces polyploïdes. Nous n'avons presque pas détecté d'épistasie de premier ordre, mais des interactions avec le fond génétique ont été observées. Nous avons trouvé plus d'eQTL sur le génome B que sur le génome A, ce qui est peut-être dû au fait que les ancêtres diploïdes du blé dur n'avaient pas le même régime de reproduction. Par ailleurs, nous avons montré que les niveaux d'expression des gènes homéologues étaient très fréquemment (80%) corrélés de manière positive, ce qui indique que les gènes homéologues appartiennent fréquemment aux mêmes complexes de gènes corégulés. Enfin, les régulations trans sont plus fréquentes au sein des paires de gènes d'homéologues, ce qui corrobore également l'idée que les gènes homéologues appartiennent aux mêmes réseaux de gènes. Dans une troisième partie, le rôle évolutif de l'épistasie a été examiné. D'abord, nous avons montré comment l'épistasie influençait la covariance parents-enfants, et donc l'évolution à courts termes d'une population. Ensuite, nous avons étudié l'impact d'un type particulier d'épistasie (celui à l'origine des d'incompatibilités de Dobzhansky-Müller, présentant des combinaisons de gènes coadaptés) sur l'évolution d'une population soumise à de la sélection par troncation (comme dans les populations de pre-breeding), à l'aide d'un modèle haploïde bilocus, en fonction du taux de recombinaison et de l'intensité de la sélection. Nous avons montré que si le génotype optimal n'est pas présent dans la population initiale, un fort taux de recombinaison risque de mener à la fixation du génotype sous-optimal. Néanmoins, un peu de recombinaison est nécessaire pour créer ce génotype optimal et le fixer.En perspectives, nous proposons d'adopter une méthode basée sur les réseaux de gènes pour approfondir les mécanismes de la régulation de l'expression chez le blé dur. Nous proposons également de complexifier le modèle permettant d'étudier l'effet de la recombinaison sur l'évolution d'un trait épistatique, sélectionné par troncation, et de compléter ces travaux de modélisation par des études expérimentales. / Epistasis has long been neglected, but it is currently subject to a renewed interest with the development of high-throughput sequencing technologies and of genome-wide association studies (GWAS). It is virtually ubiquitous, having been detected on many traits and in many species. It plays an important evolutionary role, since it is one of the sources of Dobzhansky-Muller incompatibilities, explaining reproductive isolation between related lineages. Moreover, it can enable to fix heterosis in disomic polyploids (mostly allopolyploids). The objective of this thesis was to study epistasis in this evolutionary context. The study material was a broad genetic basis population of a self-pollinating allopolyploid species, durum wheat (Triticum turgidum), having two genomes: A and B genomes. This population was composed from different taxa: durum wheat (T. t. durum), domestic emmer (T. t. dicoccum) and wild emmer (T. t. dicoccoides). Therefore, there are probably combinations of coadapted genes in this population, and thus epistasis generating Dobzhansky-Muller incompatibilities.The first part presents different models to estimate epistasis. These models have advantages and drawbacks, depending on the overall objective. In a second part, we used one of these models on RNA-seq data (expression and genotyping data) of the population of durum wheat to detect regulatory effects of expression, including epistasis between homoelogous genes. This analysis is unique in durum wheat, and probably in polyploid species. We did not detect first-order epistasis, but interactions with genetic background were observed. We found more eQTL on the B genome than on the A genome, which may be due to the fact that the diploid progenitors of durum wheat did not have the same mating system. Furthermore, we showed that the expression levels of homoelogous genes were frequently (80%) positively correlated, indicating that homoelogous genes often belong to the same complex of coregulated genes. Finally, trans regulations are more common among pairs of homoelogous genes, which also supports the idea that homoelogous genes belong to the same gene networks. In the third part, the evolving role of epistasis was examined. First, we showed how epistasis influences the parent-offspring covariance, and thus the short-term evolution of a population. Then we studied the impact of a particular type of epistasis (the one which can generate Dobzhansky-Muller incompatibilities, with combinations of co-adapted genes) on the evolution of a population subjected to truncation selection (as in pre-breeding populations), using a haploid bilocus model, based on the recombination rate and selection intensity. We have shown that if the optimal genotype is not present in the initial population, a high rate of recombination may lead to the fixation of the sub-optimal genotype. However, some recombination is needed to create this optimal genotype and fix it.In perspective, we propose to adopt a network-based method to further the regulation mechanisms of expression in durum wheat. We also propose to make the model more complex, in order to study the effect of recombination on the evolution of an epistatic trait selected by truncation, and complete these modelling works by experimental studies.

Les nouvelles technologies de séquençage (NTS) offrent de nouvelles opportunités d'explorer les génomes et transcriptomes d'espèces polyploïdes. L'assemblage de transcriptomes et l'identification des copies de gènes dupliqués par allopolyploïdisation (homéologues) constituent cependant un véritable défi C ‘est plus particulièrement le cas dans un contexte de superposition de plusieurs évènements de polyploïdie et en l'absence de génome de référence diploïde. Les Spartines (Poaceae, Chloridoideae) représentent un excellent système pour étudier les conséquences à court terme des évènements d'hybridation et de polyploïdisation. En effet, S. maritima (hexaploïde) s'est hybridée à deux reprises avec S. alterniflora (hexaploïde) suite à son introduction récente en Europe, formant deux hybrides homoploïdes (S. x townsendii et S. x neyrautii). La duplication du génome de S. x townsendii a formé une nouvelle espèce allododécaploïde S. anglica (à la fin du XIXème siècle) qui a depuis envahi les marais salés de plusieurs continents. L'identification des gènes dupliqués au sein de S. anglica et de ses parents est importante pour la compréhension de son succès évolutif. Cependant, leurs niveaux de ploïdie, et l'absence d'espèce diploïde de référence chez les spartines nécessitent le développement d'outils adaptés. Dans ce contexte, nous avons développé et validé différents outils bioinformatiques permettant de détecter des polymorphismes afin d'identifier les différents haplotypes au sein de jeux de données NTS. Ces approches nous ont permis d'étudier l'hétérogénéité des domaines de l'ADN ribosomique 45S de S. maritima. Nous avons mis en évidence la perte de copies homéologues en conséquence de la diploïdisation en cours. Afin de développer les ressources transcriptomiques de ces espèces, cinq nouveaux transcriptomes de référence (110 423 contigs annotés pour les 5 espèces dont 37 867 contigs non-redondants) ont été assemblés et annotés. Les co-alignements des haplotypes parentaux et hybrides/allopolyploïdes nous ont permis d'identifier les homéo-SNPs discriminant les séquences homéologues. De plus, nous avons évalué la divergence entre les copies de gènes, identifié et confirmé les évènements de duplications récents au sein des Spartines. Au cours de cette thèse, nous avons également initié des approches de phylogénomique des spartines, qui permettront de préciser l'origine évolutive des copies dupliquées. / Next generation sequencing (NGS) technologies offer new opportunities to explore polyploid genomes and their corresponding transcriptomes. However, transcriptome assemblies and identification of homoeologous gene copies (duplicated by polyploidy) remain challenging, particularly in the context of recurrent polyploidy and the absence of diploid reference parents. Spartina species (Poaceae, Chloridoideae) represent an excellent system to study the short term consequences of hybridization and polyploidization in natural populations. The European S. maritima (hexaploid) hybridized twice with the American S. alterniflora (hexaploid) following its recent introduction to Europe, which resulted in the formation of two homoploid hybrids (S. x townsendii and S. x neyrautii). Whole genome duplication of S. x townsendii resulted in the fertile new allododecaploid S. anglica species (during the 19th century) that has now invaded saltmarshes on several continents. Identification of duplicated genes in S. anglica and its parental species is critical to understand its evolutionary success but their high ploidy levels require the development of adapted tools. In this context, we developed and validated different bioinformatics tools to detect polymorphisms and identify the different haplotypes from NGS datasets. These approaches enabled the study of the heterogeneity of the highly repeated 45S rDNA in S. maritima. In order to develop transcriptomic resources for these species, 5 new reference transcriptomes (110 423 annotated contigs for the 5 species with 37 867 non-redundant contigs) were assembled and annotated. Co-alignments of parental and hybrid/allopolyploid haplotypes allowed the identification of homoeoSNPs discriminating homoelogs. The divergence between duplicated genes was used to identify and confirm the recent duplication events in Spartina. Phylogenomic approaches on Spartina were also initiated in this thesis in the perspective of exploring the evolutionary history of the duplicated copies.

Depuis le Néolithique, les activités anthropiques ont fortement impacté la persistance et l’évolution des espèces méditerranéennes, avec des effets variés sur la biodiversité, notamment son érosion et son homogénéisation. Composé seulement de trois à cinq espèces, le genre méditerranéen et Sud-asiatique Arundo L. (Poaceae) illustre bien les interactions Homme-Biodiversité. Tout d’abord, l’imprécision des statuts taxonomiques pour la plupart de ces espèces dessert autant la conservation des populations françaises protégées d’A. plinii Turra s.l. que la lutte contre l’invasive mondiale A. donax L. Suite à la révision systématique du complexe circumméditerranéen A. plinii Turra s.l., trois taxons ont été distingués, élevant les populations françaises au rang d’endémique ligure, A. donaciformis (Loisel.) Hardion et al. Cette dernière s’est différenciée en marge de son espèce-sœur, l’Italo- Balkanique A. plinii s.s., sous les effets conjugués de la polyploïdie et des oscillations climatiques du Pléistocène. La forte clonalité du genre et la formation récente d’A. donaciformis ont réduit son potentiel adaptatif. Malgré une persistance ancienne au sein d’un paysage agricole, son actuelle position urbaine sur la Côte d’Azur la menace fortement. Enfin, l’origine perse d’A. donax et l’hypothèse de son statut d’archéophyte en Méditerranée illustre l’intérêt primordial de ce genre lors du développement des civilisations antiques. / Human activities have scrambled biodiversity persistence and evolution of Mediterranean species since the Neolithic, inducing various impacts on biodiversity, from reduction to homogenisation. With only three to five species, the Mediterranean and South- Asian genus Arundo L. (Poaceae) well illustrate these Human-Biodiversity interactions. First, the taxonomic mess for almost all Arundo taxa harms the conservation of protected French populations of A. plinii Turra s.l. as much as the biological control of the worldwide invasive A. donax L. The systematic revision of the circum-Mediterranean A. plinii complex in three distinct taxa has distinguished French populations as a Ligurian endemic species, A. donaciformis (Loisel.) Hardion et al. This species was differentiated from its nearest relative, the italo-balkan A. plinii s.s., under the coupled effects of polyploidy and Pleistocene climatic variations. The dominating clonality of the genus and the recent speciation of A. donaciformis have reduced its adaptive potential. Despite its ancient persistence under farmlands, its current urban position on the French Riviera threatens this protected species. Finally, the Persian origin of A. donax and its hypothetic status of archeophyte in the Mediterranean show the essential usefulness of this genus during the development of antic civilisations.

No description available.

La recombinaison méiotique produite par les Crossing Overs (COs) est un facteur limitant pour l’efficacité de la sélection variétale. Une possibilité pour produire des plantes hyper-recombinantes serait d’exploiter la variabilité intraspécifique pour les fréquences de recombinaison. L’identification des polymorphismes causaux, liés à la séquence ou l’expression, représente un travail de longue haleine. Une approche alternative serait de produire des mutants pour des régulateurs négatifs des fréquences de recombinaison. Chez le colza, jeune allotétraploïde (AACC, 2n=38), il est possible de jouer sur ces 2 approches. Dans un premier temps j’ai cherché à vérifier dans quelle mesure pouvait varier le transcriptome méiotique entre 2 variétés ayant servi à cartographier un QTL pour le contrôle de la recombinaison entre chromosome homoéologues (hérités des génomes parentaux). Ce transcriptome méiotique s’est révélé de façon inattendue très variable ; les principales sources de cette variation étant notamment la nature du génome (A ou C) ainsi que l’effet variété. J’ai montré que les HEs (le remplacement d’une région chromosomique par la duplication de la région homoéologue) contribuent de façon importante aux différences d’expression observées à la fois entre variétés ou au sein d’un même génotype. Dans un second temps, j’ai vérifié que FANCM décrit chez Arabidopis thaliana comme un régulateur négatif pour les fréquences de recombinaison avait bien la même fonction chez les Brassica. Chez Brassica rapa j’ai vérifié qu’un mutant fancm complémente comme attendu un mutant déficient pour la voie majoritaire de formation des COs. Chez Brassica napus j’ai observé une faible augmentation à la fois des fréquences de recombinaison entre chromosomes homologues et homoéologues. Ce travail souligne l’importance de la caractérisation des HEs chez les allopolyploïdes. Au-delà de leurs impacts sur le contenu et l’expression génique, les HEs ont très certainement des conséquences phénotypiques. Cette étude présente aussi un exemple de biologie translationnelle pour un trait important en amélioration des plantes. / Meiotic recombination driven by Crossing-Over (CO) is a limiting factor for the efficiency of plant breeding. One way to produce hyper-recombinant plants is to use the existing interspecific variability for recombination frequencies. Identification of the causal polymorphisms, either link to gene sequence or expression, represents a long-term endeavour. Another possibility is to mutate anti-meiotic CO genes. In rapeseed, a young allotetraploid species (AACC, 2n=38), both of these approaches are possible. First I wanted to check how much varies the meiotic transcriptome between 2 varieties that differ in term of recombination between homoeologous chromosomes (inherited from parental genomes). Unexpectedly, the meiotic transcriptome turned out to be very variable, the main source of this variation being notably the origin of the genome (A or C) and the variety. I also showed that homoeologous exchanges (HEs; the replacement of one chromosomal region with a duplicate of the homeologous region) contributed to this variation and led to large changes in expression both between and within varieties. Then I assessed whether FANCM, an anti-CO protein identified in Arabidopis thaliana had the same function in the Brassica genus. In Brassica rapa, a fancm mutant complements as expected a meiosis mutant defective in the main formation pathway for the formation of meiotic COs. In Brassica napus, I observed a slight increase in both homologous and homoeologous recombination frequencies. This work emphasizes the importance of characterizing HEs in allopolyploids species. Beyond their impact on gene content and expression, HEs most have likely phenotypic consequences. This study also presents an example of translational biology for an important trait in crop breeding.