Orientadores: Luciana Lasry Benchimol Reis, Luis Eduardo Aranha Camargo / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-23T04:26:18Z (GMT). No. of bitstreams: 1 Oblessuc_PaulaRodrigues_D.pdf: 15432495 bytes, checksum: 30c1cd638125be03e494a50fae4fe12b (MD5) Previous issue date: 2013 / Resumo: O feijão comum (Phaseolus vulgaris L.) é uma importante fonte de proteínas na dieta humana. A mancha angular (ALS), causada pelo fungo Pseudocercospora griseola (Sacc.) Crous & Braun, acarreta grandes prejuízos na produção do feijão. O melhoramento do feijoeiro busca ferramentas que agilizem a transferência de genes de resistência às doenças para cultivares em desenvolvimento. Assim, foi objetivo deste trabalho estudar os mecanismos genéticos e moleculares envolvidos na resposta do feijão à ALS, e com isso contribuir para o melhoramento dessa cultura. Primeiramente, QTLs (Quantitative Trait Locus) de resistência à ALS foram identificados utilizando a população de mapeamento UC (IAC-UNA x CAL 143) a partir do mapa genético previamente desenvolvido com marcadores microssatélites. O estudo quantitativo da severidade da ALS revelou distribuição normal e transgressiva na população UC, com resistência quantitativa observada em CAL 143. Ao todo foram mapeados sete QTLs em cinco diferentes grupos de ligação de feijão. Dentre estes, o loco ALS10.1 mostrou maior efeito (16% - 22%) e estabilidade nos três ambientes analisados: (1) condições naturais de infecção em época chuvosa de plantio; (2) condições naturais de infecção em época seca de plantio; e (3) condições controladas de infecção raça-específica em casa de vegetação. A região do loco ALS10.1 foi saturada com marcadores microssatélites, SCARs e Sequence-Tagged Site-DArTs (STS-DArTs); este último através da técnica de bulk segregant analysis (BSA). O intervalo de confiança foi reduzido de 13.4 cM para 3.0 cM após a saturação do loco, que teve seu número de marcadores aumentado de quatro para 10. O estudo do contexto genômico do ALS10.1 através do alinhamento dos marcadores com o rascunho do genoma do feijão possibilitou definir uma região core para o QTL na extremidade do cromossomo Pv10, com aproximadamente 5,3 Mb. Análise de Gene Onthology (GO) dos 323 genes preditos nesta região do genoma demonstrou que 61,6% destes genes estão envolvidos na resposta a estresse. Cluster de genes TIR-NB-ARC (domínios altamente conservado em genes (R) de Resistência) foi identificado cobrindo aproximadamente 849 Kb na região core de ALS10.1; além de esta região conter outros genes sabidamente relacionados à imunidade de plantas. Sete genes presentes na região core de ALS10.1 foram selecionados com base na função na resistência à patógenos dos respectivos ortólogos em Arabidopsis thaliana, e tiveram sua expressão gênica avaliada na resposta à P. griseola. Gene R TIR-NB-ARC (Phvul.010G025700) foi induzido em resposta compatível no genótipo IAC-UNA, com isso deve permitir a proliferação do patógeno, possivelmente através do reconhecimento do Avr (avirulência) do fungo, bloqueando a resposta de defesa. Além disso, genes putativos de regulação negativa da resposta imune pela inativação da via do ácido salicílico (SA) foram reprimidos durante resposta incompatível no genótipo CAL 143. O AS é um hormônio chave para resposta de defesa induzida por patógenos em plantas. Com isso, o reconhecimento do patógeno pelo feijão deve ocorrer através de genes R para sinalização downstream da resposta de defesa mediada por AS. Os resultados deste trabalho permitirão que o melhorista manipule a diversidade genética do feijão, seja pela introgressão e piramidação dos genes de resistência através de seleção assistida por marcadores ou transgenia; seja pela identificação de cultivares geneticamente resistentes pela análise de expressão gênica / Resumo: O feijão comum (Phaseolus vulgaris L.) é uma importante fonte de proteínas na dieta humana. A mancha angular (ALS), causada pelo fungo Pseudocercospora griseola (Sacc.) Crous & Braun, acarreta grandes prejuízos na produção do feijão. O melhoramento do feijoeiro busca ferramentas que agilizem a transferência de genes de resistência às doenças para cultivares em desenvolvimento. Assim, foi objetivo deste trabalho estudar os mecanismos genéticos e moleculares envolvidos na resposta do feijão à ALS, e com isso contribuir para o melhoramento dessa cultura. Primeiramente, QTLs (Quantitative Trait Locus) de resistência à ALS foram identificados utilizando a população de mapeamento UC (IAC-UNA x CAL 143) a partir do mapa genético previamente desenvolvido com marcadores microssatélites. O estudo quantitativo da severidade da ALS revelou distribuição normal e transgressiva na população UC, com resistência quantitativa observada em CAL 143. Ao todo foram mapeados sete QTLs em cinco diferentes grupos de ligação de feijão. Dentre estes, o loco ALS10.1 mostrou maior efeito (16% - 22%) e estabilidade nos três ambientes analisados: (1) condições naturais de infecção em época chuvosa de plantio; (2) condições naturais de infecção em época seca de plantio; e (3) condições controladas de infecção raça-específica em casa de vegetação. A região do loco ALS10.1 foi saturada com marcadores microssatélites, SCARs e Sequence-Tagged Site-DArTs (STS-DArTs); este último através da técnica de bulk segregant analysis (BSA). O intervalo de confiança foi reduzido de 13.4 cM para 3.0 cM após a saturação do loco, que teve seu número de marcadores aumentado de quatro para 10. O estudo do contexto genômico do ALS10.1 através do alinhamento dos marcadores com o rascunho do genoma do feijão possibilitou definir uma região core para o QTL na extremidade do cromossomo Pv10, com aproximadamente 5,3 Mb. Análise de Gene Onthology (GO) dos 323 genes preditos nesta região do genoma demonstrou que 61,6% destes genes estão envolvidos na resposta a estresse. Cluster de genes TIR-NB-ARC (domínios altamente conservado em genes (R) de Resistência) foi identificado cobrindo aproximadamente 849 Kb na região core de ALS10.1; além de esta região conter outros genes sabidamente relacionados à imunidade de plantas. Sete genes presentes na região core de ALS10.1 foram selecionados com base na função na resistência à patógenos dos respectivos ortólogos em Arabidopsis thaliana, e tiveram sua expressão gênica avaliada na resposta à P. griseola. Gene R TIR-NB-ARC (Phvul.010G025700) foi induzido em resposta compatível no genótipo IAC-UNA, com isso deve permitir a proliferação do patógeno, possivelmente através do reconhecimento do Avr (avirulência) do fungo, bloqueando a resposta de defesa. Além disso, genes putativos de regulação negativa da resposta imune pela inativação da via do ácido salicílico (SA) foram reprimidos durante resposta incompatível no genótipo CAL 143. O AS é um hormônio chave para resposta de defesa induzida por patógenos em plantas. Com isso, o reconhecimento do patógeno pelo feijão deve ocorrer através de genes R para sinalização downstream da resposta de defesa mediada por AS. Os resultados deste trabalho permitirão que o melhorista manipule a diversidade genética do feijão, seja pela introgressão e piramidação dos genes de resistência através de seleção assistida por marcadores ou transgenia; seja pela identificação de cultivares geneticamente resistentes pela análise de expressão gênica / Abstract: The common bean (Phaseolus vulgaris L.) is an important protein source in human diet. The angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola (Sacc.) Crous & Braun, leads to great common bean yield losses. The common bean breeding search for tools that improve the transferring of disease resistance genes to developing cultivars. Therefore, the objective of the present work was study the genetic and molecular mechanisms enrolled in the common bean responses to ALS, and with this contribute to this crop breeding. Initially, ALS resistance QTLs were identified using the UC (IAC-UNA x CAL 143) mapping population based on the genetic map previously developed with microsatellites markers. The quantitative study of the ALS disease severity reveals normal and transgressive distribution on the UC population, with quantitative resistance observed in CAL 143. Seven QTLs were mapped in five different common bean linkage groups. Of these, the ALS10.1 locus showed major effect (16% - 22%) and stability in all three environments analyzed: (1) natural infection conditions in the dry season; (2) natural infection conditions in wet season; and (3) race-specific controlled infection conditions in greenhouse. The ALS10.1 locos region was saturated with microsatellites, SCARs and Sequence-Tagged Site-DArTs (STS-DArTs) markers; the latter using the bulk segregant analysis (BSA). The confidence interval was reduced from 13.4 cM to 3.0 cM after the locus saturation, which had the markers number increased from four to 10. The study of the ALS10.1 genomic context through the alignment of the markers to the draft of the common bean genome enabled the identification of the QTL core at the end of the chromosome Pv10, with approximately 3.5 Mb. The Gene Ontology (GO) analyses of the 323 predicted genes for this genomic region demonstrated that 61.6% of the genes are involved in stress responses. A TIR-NB-ARC gene cluster (domains highly conserved in Resistance (R) genes), was observed covering approximately 849 Kb on the ALS10.1 core region; besides this region also presents other genes known to be related to plant immunity. Seven genes on ALS10.1 core region were selected based on the role in pathogen resistance of the respective Arabidopsis thaliana orthologs, and had their gene expression pattern evaluated in response to P. griseola. The R gene TIR-NB-ARC was induced during the compatible response of the genotype IAC-UNA; therewith it should enable the pathogen proliferation, probably through the fungus Avr recognition, blocking the defense response. In addition, putative negative regulator genes of immune response through the inactivation of salicylic acid (SA) via were repressed during the incompatible response of the CAL 143. The SA is a key hormone to pathogen induced plant defense response. Therefore, the common bean pathogen recognition should take place through the R genes to the downstream signaling of the SA-mediated defense response. The results of the present work will enable the manipulation of the bean genetic diversity by the breeder either by introgression and pyramiding of resistance genes through marker assisted selection or transgenesis; or by the identification of genetically resistant cultivars through gene expression analysis / Doutorado / Genetica Vegetal e Melhoramento / Doutora em Genética e Biologia Molecular

Plusieurs études ont montré que la productivité des forêts et des cultures décroît sur l’ensemble de la planète en réponse au changement climatique, et que les risques de mortalité liée à la sécheresse s’accroissent. Ces mortalités massives ont été observées dans tous les écosystèmes forestiers et seraient dues à un dysfonctionnement hydraulique des plantes, causé par de l’embolie xylémiène. Le spectre interspécifique de résistance à l'embolie a été largement étudiée, mais peu d'attention a été accordée à la variabilité intra-spécifique de ce trait. C’est pourquoi, l’objectif de ce travail de thèse était d’améliorer notre compréhension de la variabilité intra-spécifique de la résistance à l’embolie chez une espèce cultivée(Helianthus annuus L.) et chez un conifère (Pinus pinaster). Nous avons déterminé la vulnérabilité à l’embolie de quatre variétés de tournesol, présentant des différences significatives de P50 (pression induisant 50% de perte de conductivité hydraulique), allant de -2.67 à -3.22 MPa. Un compromis entre sécurité hydraulique et croissance a été observé mais pas entre la sécurité hydraulique et la capacité de transport de l'eau du xylème. Seuls quelques caractères anatomiques, tels que la densité des vaisseaux et la surface du lumen, présentent une corrélation avec la résistance à l’embolie. Dans un second temps, nous avons phénotypé pour la résistance à l’embolie et la densité du bois 477 génotypes de P. pinaster, issus d’une F2 de pleins-frères correspondant à la 3ème génération consanguine obtenue par auto-fécondation d’un hybride inter-provenance “Corse × Landes. La variabilité de la P50 au sein de l’espèce était extrêmement faible (CVP=5.6%). D’autre part, nous avons mis en évidence l’absence de compromis entre sécurité hydraulique et densité du bois. La part de variance du caractère P50 expliquée par QTLs (PEV)correspondait à 23.6% de la variance phénotypique totale mais aucun QTL commun n’a pu être détecté entre P50 et densité du bois, suggérant qu’au sein de cette famille, la plus forte résistance à l’embolie de certains génotypes n’est pas liée à un bois plus dense. Une analyse multi-caractère du fonctionnement de la feuille et du xylème a été réalisée via l’étude de la dynamique saisonnière de la fluorescence du photosystème II et des traits hydrauliques de la tige, sur une famille de pleins-frères d’un hybride interprovenance “Maroc × Landes” de P. pinaster ; en réponse à une diminution du potentiel hydrique,l’efficience du photosystème II et la conductance stomatique ont tous deux diminué, induisant une décroissance rapide du taux d’assimilation. La résistance à l’embolie du xylème n’a pas montré de relation significative avec les traits foliaires. L’absence de compromis entre ces caractères permet donc d’envisager la sélection génétique de génotypes à la fois efficients et résistants. / As a consequence of current global climate change, forest and crop ecosystems are decreasing inproductivity worldwide and are under increased threat of widespread drought-induced mortality due tohydraulic failure caused by xylem embolism. The range of embolism resistance across species has been intensively studied but little attention has been paid to intraspecific variability. This thesis aimed thereforeat improving our understanding of the intraspecific variation in embolism resistance in one crop species(Helianthus annuus L.) and one conifer species (Pinus pinaster). In the first place, vulnerability to embolism was determined across four sunflower accessions with significant variations in P50 (pressure inducing 50% loss of hydraulic conductivity) ranging between -2.67 and -3.22 MPa. A trade-off between hydraulic safety and growth was observed but not between hydraulic safety and efficiency. Only few anatomical traits, such as vessel density and vessel lumen area, were found related to embolism resistance.Secondly, we phenotyped 477 P. pinaster full-sib F2 genotypes corresponding to a three-generation inbred pedigree obtained by the self-pollination of an inter “Corsica × Landes” provenance hybrid, for embolismresistance and wood density. The variability for P50 within species was remarkably low (CVP=5.6%). Wealso found a lack of trade-off between hydraulic safety and wood density. The phenotypic variance explained by QTLs (PEV) detected for P50 accounted for 23.6% of the phenotypic variation but no QTL collocated between P50 and wood density, suggesting that embolism resistant genotypes in this family are not dependent on denser wood. A multi-trait analysis of leaf and xylem functioning was performed through seasonal measurements of photosystem II fluorescence and stem hydraulic traits on a full-sib family of aninter “Morocco × Landes” provenance hybrid of P. pinaster; it revealed that with decreasing water potential, the efficiency of both photosystem II and stomatal conductance decreased which resulted in rapid decrease in assimilation rate. Xylem resistance to embolism was found having no relationship with leaf functioning traits. The absence of trade-off between these traits makes it possible to consider selection for both efficient and resistant genotypes.

La luzerne est une légumineuse fourragère pérenne qui présente de nombreux avantages agronomiques et environnementaux. La performance des associations luzerne - graminées est conditionnée par la production de biomasse et la teneur en protéines de chaque espèce et sa survie. L’effet de la variabilité génétique de la luzerne sur les composantes du rendement dans les associations est mal connu. Dans ce contexte, cette thèse a deux objectifs : i) caractériser la diversité génétique pour les caractères liés à la production et à la qualité de la luzerne dans l’association ii) analyser le contrôle génétique de ces caractères. Deux dispositifs comprenant trois traitements (mélange luzerne-fétuque, monoculture et isolé) ont été mis en place. Le premier comprenant 46 génotypes contrastés de luzerne a été phénotypé sur deux ans pour l’architecture, la biomasse et la concentration en protéines. Le deuxième composé d’une population F1 de 198 individus, a été phénotypé sur une année. Cette population F1 a été génotypée avec des marqueurs SSR et DArT pour établir une carte génétique. Une large variation génétique entre les génotypes de luzerne a été montrée. Cette variation affecte la hauteur et la teneur en protéines de la fétuque associée. On a observé que les caractères mesurés en isolé ou en monoculture sont relativement prédictifs des mêmes caractères en mélange, mais une évaluation des génotypes en mélange reste indispensable. La détection de QTL montre que certains QTL sont communs aux différents traitements. Chaque QTL explique de 6 à 23% de la variation observée pour la hauteur et la biomasse. Des pistes méthodologiques pour la sélection sont envisagées. / Alfalfa is a perennial forage legume that has many agronomic and environmental benefits. The performance of alfalfa - grass mixtures depends on biomass production and protein content of each species and its survival. The effect of genetic variation on alfalfa yield components in mixtures is little described. In this context, this thesis has two objectives: i) to characterize the genetic diversity for traits related to alfalfa production and quality in mixture ii) to analyze the genetic control of these traits. Two designs that included three treatments (alfalfa - fescue mixture, monoculture and spaced plants) were established. The first design comprised 46 contrasting alfalfa genotypes which were phenotyped over two years for architecture, biomass and protein concentration. The second design comprised an F1 population of 198 individuals being phenotyped over one year. The F1 population was genotyped with SSR and DArT markers to construct a genetic map. A wide genetic variation among alfalfa genotypes was shown. This variation affected the height and protein content of associated fescue. It was observed that the measured traits of spaced plants or in monoculture are relatively predictive of the same traits in the mixture, but genotype evaluation in mixture is required. QTL detection shows that some QTL were common to different treatments. Each QTL explained 6-23 % of the variation for height and biomass. Some methodologies for selection are proposed.

La connaissance des effets et modes d’action des QTL (Quantitative Trait Loci) de résistance des plantes aux maladies est un enjeu majeur pour l’exploitation durable des résistances génétiques en agriculture. Dans le pathosystème pois/Aphanomyces euteiches, présentant une importance économique majeure, l’objectif de la thèse a consisté à valider les effets de QTL de résistance, seuls ou en combinaison, et à connaitre leurs modes d’action sur les étapes du cycle de l’agent pathogène. Un total de 157 NILs (Near Isogenic Lines) de pois issues d’un programme de Back-cross Assisté par Marqueurs, porteuses d’aucun, un, deux ou trois des sept principaux QTL de résistance préalablement identifiés, a été génotypé à l’aide d’une puce 15K SNPs et évalué pour la résistance. Les NILs porteuses de QTL à effets majeurs, seuls ou en combinaison avec des QTL à effets mineurs,ont présenté des niveaux accrus de résistance partielle en conditions contrôlées et au champ par rapport aux NILs dépourvues de QTL, dans différents fonds génétiques. Certaines NILs comportant des QTL individuels ou combinés à effets mineurs ont également montré un niveau réduit de sévérité de la maladie dans l’une ou les deux conditions de test. La plupart des QTL a présenté des effets significatifs sur le ralentissement de l’infection et/ou de la quantité d’ADN pathogène ayant colonisé la racine pendant sept jours après inoculation. Cette thèse fournit des outils et éléments de choix de QTL à combiner en sélection pour augmenter l’efficacité de la résistance partielle à A. euteiches dans les futures variétés de pois / Knowledge of the effects and action modes of resistance QTL to plant diseases is a major challenge for the durable use of genetic resistances in agriculture. In the pea/Aphanomyces euteiches pathosystem, which has a major economic importance, the aim of this study was to validate the single or combined effects of main resistance QTL, and study their action modes on steps of the pathogen life cycle. A total of 157 pea NILs (Near Isogenic Lines) created by Marker-Assisted Back-crossing and carrying no, one, two or three of the seven main resistance QTL previously identified, was genotyped using a 15K SNPs array and evaluated for resistance. The NILs carrying major-effect QTL, individually or in combination with minor-effect QTL, had increased levels of partial resistance in controlledconditions and in the field compared to NILs without QTL, in different genetic backgrounds. Several NILs carrying single or multiple minor-effect QTL also showed reduced levels of disease severity in one or the two test conditions. Most of the QTL had significant effects on slowing down infection and/or pathogen DNA quantity which had colonized the root for seven days after inoculation. This study gives tools and information for the choice of resistance QTL to use in pyramiding breeding strategies for increasing partial levels of resistance to A. euteiches in future pea varieties.

La fusariose de l’épi est une maladie fongique qui touche toutes les cultures de céréales à paille à travers le monde entrainant des baisses de rendements et de la qualité des grains. La fusariose pose également un problème pour la sécurité alimentaire lié à la contamination des grains infectés par des mycotoxines. Le développement de variétés résistantes est considéré comme la méthode la plus efficace et la plus durable pour réduire les dommages causés par la maladie et pour limiter la contamination par les mycotoxines. L’amélioration de la résistance à la fusariose chez le blé dur (Triticum durum Desf.) demeure un défi du fait de son extrême sensibilité à la maladie et de la faible variabilité génétique disponible pour ce caractère. L’objectif principal de cette thèse a été d’évaluer l’effet de Fhb1, le QTL majeur de résistance à la fusariose chez le blé tendre (Triticum aestivumL.), au sein de fonds génétiques de blé dur élite. Pour cela, trois populations de cartographie, comprenant chacune environ 100 F7-RIL (lignées pures recombinantes ou « recombinant inbred lines »), ont été développées à partir de croisements entre la lignée expérimentale de blé dur DBC-480, portant une introgression de Fhb1, et les cultivars de blé dur Karur, Durobonus et SZD1029K. Les lignées ont été évaluées au champ, sur trois saisons, pour leur résistance globale à la fusariose après inoculation en spray de Fusarium culmorum. Des notations morphologiques (date de floraison, hauteur des plantes) ont également été réalisées afin d'évaluer leur influence sur l'infestation. Les lignées ont été génotypées à l’aide de marqueurs SSR et de marqueurs GBS (génotypage par séquençage ou « genotyping-by-sequencing ») développés par DArTseq. L’analyse de liaison a permis d’identifier des QTL de résistance sur les bras des chromosomes 2BL, 3BS, 4AL, 4BS, 5AL et 6AS. DBC-480 contribuait à l’allèle de résistance à tous ces loci. Le QTL sur 3BS a été détecté au sein des trois populations centré sur l’intervalle de Fhb1, confirmant, pour la première fois, son introgression dans le blé dur. L’évaluation de la résistance à la propagation après inoculation ponctuelle, réalisé au sein d’une des trois populations, a également permis de valider l’effet de Fhb1 sur la résistance de type 2 chez le blé dur. La hauteur des plantes influe fortement sur la résistance globale à la fusariose et, en particulier, l’allèle de nanisme Rht-B1b est associé à une plus grande sensibilité à la maladie dans les trois populations. Cependant, l’effet négatif de Rht-B1b sur la résistance est largement compensé dans les lignées possédant Fhb1. Des lignées semi-naines avec un meilleur niveau de résistance ont été sélectionnées et favoriseront le développement de cultivars de blé dur résistants à la fusariose. / Fusarium head blight (FHB) is a devastating disease affecting small-grain cereals worldwide causing yield and quality losses. FHB affects food safety due to the contamination of infected grains by mycotoxins. Host plant resistance is considered the most efficient and sustainable approach to contain FHB and mycotoxin contaminations. In durum wheat (Triticum durum Desf.) breeding for FHB resistance remains a challenge due to its extreme susceptibility and to lack of genetic variation available in the primary durum wheat gene pool. The primary goal of this thesis was to evaluate the effect of Fhb1, the major common wheat (Triticum aestivum L.) FHB resistance QTL, in elite durum wheat background. Three F7-RIL (recombinant inbred lines) mapping populations of about 100 lines were developed from crosses between the durum wheat experimental line DBC-480, harboring Fhb1, and the durum wheat cultivars Karur, Durobonus and SZD1029K. The RILs were tested under field conditions by artificial spray inoculation with Fusarium culmorum in three seasons. Morphological traits (flowering date, height) were also recorded to assess their influence on FHB infestation. Genotyping of the lines was performed with SSR and genotyping-by-sequencing (GBS) DArTseq markers. QTL analysis identified genomic regions associated with FHB resistance on chromosome arms 2BL, 3BS, 4AL, 4BS, 5AL and 6AS. DBC-480 contributed the resistant allele at all loci. Fhb1 was detected in all three populations, demonstrating for the first time its successful deployment in durum wheat. The effect of Fhb1 on FHB resistance in durum wheat was further verified by evaluating type 2 resistance in one of the three populations. Plant height had a strong influence in modulating FHB severity. Although the semi-dwarf allele Rht-B1b was associated with increased FHB susceptibility, its negative effect was efficiently counterbalanced in lines carrying Fhb1. Semi-dwarf lines with enhanced levels of resistance were selected and will assist the development of FHB resistant cultivars.

La filière « poule pondeuse » représente un marché en pleine expansion. L’amélioration des caractères est essentielle pour satisfaire les attentes des consommateurs et des industriels. Cette amélioration est réalisée via la sélection. Actuellement, les candidats à la sélection sont évalués à partir de leur valeur génétique estimée (Estimated Breeding Value, EBV) en appliquant un modèle statistique prenant en compte l’ensemble des phénotypes disponibles sur leurs apparentés (BLUP). L’essor de nouvelle technologie permettant le génotypage à moindre coût de nombreux individus, permet d’envisager la mise en place d’une sélection génomique dans cette filière. La valeur génomique estimée (Genomic Estimated Breeding Value, GEBV) serait potentiellement plus précise que l’EBV, disponible dès la naissance de l’individu et sûrement pour un plus grand nombre de candidats, engendrant ainsi un gain de progrès génétique.Par ailleurs, un même type génétique de poule pondeuse étant largement diffusé à travers le monde, les animaux produisent dans des environnements différents (alimentation, température…). Des interactions génotype – environnement pourraient donc affecter l’estimation des valeurs génétiques des candidats à la sélection. L’objectif premier de ce travail est de préciser l’impact de celles-ci sur un panel large de caractères de production et de qualité des œufs aussi bien au niveau de leur architecture génétique qu’au niveau des évaluations. De plus, les conséquences de l’architecture génétique des caractères sur l’estimation des valeurs génétiques également ont été étudiées. / The laying hens farming represents a growing market. The improvement of traits is needed to satisfy the willing of customers and industrials. This improvement is done with selection. Actually, (candidates for selection are evaluated according to their Estimated Breeding Value (EBV), which is estimated, using a statistic model which considers all the available phenotypes of their relative BLUP). The development of new technologies which allow the genotyping at a lower cost of numerous individuals, could allow the development of genomic selection in this farming. The Genomic Estimated Breeding Value (GEBV) could be potentially more accurate than the EBV, available at the birth of the individual and for probably a larger number of candidates, increasing the rates of genetic progress.Besides, a same genetic type of laying hens is widely distributed around the world, so animals produce in various environments ((alimentation, temperature, hygiene standards…). So, genotype – environment interactions could affect the estimation of breeding values of the candidates for selection. The first objective of this work is to determine of the impact of these interactions on a large panel of egg production and egg quality traits, as well at the genetic architecture level than at the evaluations level. Moreover, the consequences of genetic architecture of these traits on breeding value estimation have been studied.

La verticilliose est une maladie vasculaire des plantes dont les symptômes typiques sont un flétrissement des parties aériennes, des feuilles chlorosées puis séchées, et dans les cas de maladie grave la mort de la plante. Au niveau des racines on observe une coloration brune du tissu conducteur. Cette maladie est causée par un champignon du sol du genre Verticillium. Les espèces majeures V. dahliae et V. albo-atrum sont responsables de pertes importantes de rendement sur de nombreuses cultures. Le champignon entre dans la racine par des blessures ou par des fissures au niveau de sites d’émergence de racines latérales, puis il avance vers le cylindre central et envahit les vaisseaux du xylème. Sa croissance reste pendant longtemps limitée aux vaisseaux qu’il colonise en avançant vers les parties aériennes de la plante. Aux stades tardifs, le champignon sort du cylindre central et colonise les autres tissus. En Europe, V. albo-atrum constitue l’une des principales causes de maladies chez la luzerne pérenne et est à l’origine de pertes économiques très importantes. La capacité de V. albo-atrum de survivre dans le sol ainsi que sa localisation protégée dans le cylindre centrale des plantes infectées en font un pathogène difficile à combattre, la lutte génétique par sélection de variétés tolérantes apparaissant comme une approche prometteuse. Cependant, la capacité des microorganismes pathogènes de s’adapter rapidement à des nouvelles plantes hôtes est une menace bien connue de la durabilité des variétés résistantes. Au laboratoire, des travaux ultérieurs ont établi que la plante modèle des légumineuses Medicago truncatula, une espèce sauvage proche de la luzerne cultivée, peut être utilisée pour étudier les mécanismes de résistance et sensibilité vis-à-vis de V. alboatrum. Une lignée résistant et une lignée sensible ont été identifiées et l’étude de la descendance d’un croisement entre ces deux lignées a permis d’identifier un locus majeur (Quantitative trait locus, QTL) contrôlant la résistance à une souche de V. albo-atrum isolée de la Luzerne (Ben et al., 2013 ; Negahi en 6e co-auteur). Ce travail a également montré qu’il existait une grande biodiversité au sein de l’espèce M. truncatula par rapport à la réponse à cette souche de V. albo-atrum. / Verticillium wilt, caused by Verticillium albo-atrum (Vaa) and Verticillium dahliae (Vd), is responsible for yield losses in many economically important crops. The capacity of pathogenic fungi to adapt to new hosts is a well-known threat to the durability of resistant crop varieties. Medicago truncatula is a good model for studying resistance and susceptibility to Verticillium wilt in legume plants. Phenotyping a population of inbred lines from a cross between resistant parent line A17 and susceptible parent F83005.5 contributed to the identification of a first QTL controlling resistance to an alfalfa strain of Vaa in M. truncatula. Then, 25 M. truncatula genotypes from a core collection and six Vaa and Vd strains were used to study the potential of non-host Verticillium strains isolated from different plant species to infect this legume plant, and the plant’s susceptibility to the pathogens. The experiment was arranged as factorial based on a randomized complete block design with three replications. The wilt symptoms caused by Vaa and Vd were scored on a disease index scale from 0 to 4, during 30 days after inoculation of ten day-old plantlets. Disease severity was quantified by the parameters Maximum Symptom Scores (MSS) and Areas Under the Disease Progress Curves (AUDPC). Highly significant differences were observed among plant genotypes and fungal strains, and their interaction was also significant. The correlation between MSS and AUDPC was 0.86 and highly significant. The most severe symptoms were caused by the alfalfa strain Vaa-V31-2 and the least severe by Vd-JR2, as shown by mean values obtained on the 25 genotypes. M. truncatula genotype TN8.3 was identified as the most susceptible genotype by mean values obtained with the 6 fungal strains, whereas F11013-3, F83005.9 and DZA45.6 were highly resistant to all strains studied. The results were used to choose parents for studying the genetics of resistance in M. truncatula to a nonalfalfa Verticillium strain. So, in the second part of this work, genotype A17 which was susceptible and genotype F83005.5 which was resistant to the potato strain Vaa-LPP0323 and recombinant inbred lines (RILs) from a cross between these genotypes were selected in order to study the genetic control of resistance to this strain of the pathogen. Our experimental design was a randomized complete blocks with 116 RILs and three replications. High genetic variability and transgressive segregation for resistance to Vaa-LPP0323 were observed among RILs. A total of four QTLs controlling resistance to Vaa-LPP0323 were detected for the parameters MSS and AUDPC. The phenotypic variance explained by each QTL (R2) was moderate, ranging from 3 to 21%. A negative sign of additive gene effects showed that favourable alleles for resistance come from the resistant parent.

Les différents scénarios sur l'évolution du climat prévoient une augmentation de la fréquence et de l'intensité des sécheresses. La croissance des arbres forestiers étant fortement conditionnée par la disponibilité en eau, ces changements devraient impacter de manière significative la productivité des forêts plantées. La compréhension de l'impact des facteurs génétiques et environnementaux sur la dynamique de croissance est donc un enjeu majeur pour assurer les niveaux de production des plantations de demain. L'Eucalyptus, grâce à sa croissance rapide et à la disponibilité de ressources génétiques et génomiques, est un modèle biologique idéal pour mener ces recherches.L'objectif de cette thèse est de caractériser l'architecture génétique de la dynamique de croissance à différentes échelles de temps chez l'eucalyptus en relation avec : (i) les variations environnementales, et notamment l'évolution de la disponibilité en eau, et (ii) la composition isotopique du carbone de l'arbre (delta 13C), un caractère lié à l'efficience d'utilisation de l'eau. Pour répondre à cet objectif, un croisement interspécifique Eucalyptus urophylla x E. grandis a été étudié dans quatre dispositifs expérimentaux en République du Congo. Notre approche se base sur la cartographie des loci à effet quantitatif (QTL) et combine : (i) un génotypage haut débit, (ii) une caractérisation inter et intra-annuelle de la croissance et du delta 13C, ainsi qu'un suivi en continu des micro-variations du rayon et (iii) une caractérisation en continu des facteurs environnementaux.Ces travaux ont tout d'abord conduit à la construction des premières cartes génétiques à haute résolution chez l'Eucalyptus. L'analyse de l'architecture génétique du delta 13C a ensuite permis de mettre en évidence des gènes candidats positionnels, potentiellement impliqués dans la variation de ce caractère. Enfin, la caractérisation inter et intra-annuelle de la dynamique de croissance a permis de montrer que l'architecture génétique de la croissance, au stade adulte, est structurée par les réponses à l'environnement au stade juvénile. Ces réponses ont ensuite été analysées grâce aux profils de micro-variations du rayon, permettant ainsi de préciser leurs déterminants génétiques Nos résultats soulignent l'importance de considérer la croissance comme un caractère dynamique, non seulement pour la compréhension de ses bases génétiques, mais également à des fins de sélection de variétés adaptées à un environnement changeant. / Scenarios of climate changes forecast an increase in frequency and intensity of droughts, related to an increase of global temperatures and changes in rainfall distribution. Growth of forest trees highly depends on water availability and will be significantly impacted by these changes. The understanding of the impact of genetic and environmental factors on the growth dynamics is a major challenge to ensure production levels of future planted forests. Eucalyptus, thanks to its rapid growth and the availability of genetic and genomic resources, is a perfect model to conduct this research.The objective of this thesis is to characterize the genetic architecture of growth dynamics in Eucalyptus at different time scales, in relation with: (i) environmental changes, including changes in water availability, and (ii) isotopic composition of carbon (delta 13C), a character associated with water-use efficiency. To this end, an interspecific cross between E. urophylla x E. grandis was studied in four experimental trials in the Republic of Congo. Our approach, based on mapping of quantitative trait loci (QTL), combines (i) a high-throughput genotyping, (ii) a characterization of inter and intra-annual growth dynamics and delta 13C, as well as a continual measurement of stem radial micro-variations and (iii) a continual characterization of environmental factors.First of all, this work led to the construction of the first high-resolution genetic maps in Eucalyptus, improving the sequence of the reference genome. Then, the analysis of genetic architecture of delta 13C enabled the identification of positional candidate genes which might be involved in the variation of this trait. Finally, inter and intra-annual characterization of growth dynamics highlight that genetic architecture of adult growth is structured by responses to the environment at the juvenile stage. These responses were then analyzed using daily profiles of stem radial micro-variations, which enabled the characterization of the genetic determinants of response to the environmental factors at the juvenile stage.Our results highlight the importance of considering growth as a dynamic trait, not only to understand its genetic basis, but also to select in a changing environment.

Orientadores: Anete Pereira de Souza, Marcelo Mollinari / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-27T05:08:40Z (GMT). No. of bitstreams: 1 Costa_EstelaAraujo_D.pdf: 11739408 bytes, checksum: 278f864d2e779d0170b184a660242954 (MD5) Previous issue date: 2015 / Resumo: A grande importância da cana-de-açúcar e seus derivados tem resultado em grande investimento financeiro e científico. Esse fato se deve, principalmente, à complexidade do genoma da cana e às dificuldades encontradas na obtenção de novas cultivares mais produtivas, através dos métodos tradicionais de seleção. A construção de mapas genéticos de ligação permite associar locos mapeados com características de interesse econômico, podendo acelerar o processo de melhoramento da espécie. Logo, a utilização dos marcadores em estudos de mapeamento genético e de QTL¿s (Quantitative Trait Loci) tem proporcionado um importante progresso no conhecimento da estrutura genética e genômica da cana-de-açúcar. Utilizando uma população segregante derivada do cruzamento entre as variedades comerciais IACSP95-3018 e IACSP93-3046, contendo 187 indivíduos F1, esta tese teve como objetivo realizar o mapeamento genético funcional e o mapeamento de QTLs de características de importância econômica. Para tanto, as características avaliadas foram diâmetro, peso, altura, porcentagem de fibra, conteúdo de sacarose (Pol) e conteúdo de sólido solúvel (Brix), em dois locais, por três anos (2012, 2013 e 2014) que se juntaram a dois outros anos, previamente coletados. O mapa se originou de 421 marcas (SSRs, AFLP e SNPs em dose única) ligadas, e resultou em 118 grupos de ligação e 16 grupos de homologia, com cobertura de 4512,6 cM. Utilizando mapeamento por intervalo composto (CIM), os QTLs foram mapeados, gerando um total de 25 QTLs, sendo seis QTLs para diâmetro, cinco para peso, quatro para altura, cinco para fibra, dois para Pol e três para Brix. A proporção da variação fenotípica explicada por QTL variou de 0,069% a 3,87%. Em paralelo, realizou-se o desenvolvimento de marcadores SNPs (Single Nucleotide Polymorphism) em genes envolvidos em duas vias metabólicas de extrema importância para a cana-de-açúcar, a via de Fotossintética C4 e a via de Metabolismo de Sacarose. No total, 130 locos SNPs foram desenvolvidos, analisados e caracterizados pelo programa SuperMASSA. Estimando a ploidia e a dosagem alélica de cada loco SNP, um alto número de locos SNPs com ploidias elevadas foi detectada, resultando na identificação de aproximadamente 80% dos locos estudados com evidências de, ao menos, duplicação no genoma de parentes próximos a cana-de-açúcar (sorgo, milho ou arroz). Os resultados desta tese podem auxiliar programas de melhoramento da espécie pela identificação de marcadores SNPs em genes relacionados a características de interesse econômico e o mapeamento de QTLs para também características de mesmo interesse / Abstract: The importance of sugarcane crop has resulting in a high financial and cientific support. Because, mainly, the genetic complexity of sugarcane genome and the difficult to create new varieties, using traditional breeding methods.The genetic linkage map allow find molecular markers associated with important economic traits, helping to accelerate the breeding process. In this way, molecular markers associated with genetic mapping and QTLs (Quantitative Trait Loci) mapping are important tools to improve the knowledge about the genetic and genomic organization of sugarcane genome. The segregating population of sugarcane consisted of 187 F1 individuals derived from a cross between IACSP95-3018 and IACSP93-3046, this thesis aimed perform a functional genetic mapping and QTLs mapping of economic importance. Thus, yield components evaluated were stalk diameter (SD), stalk weight (SW), stalk height (SH), stalk number (SN), fiber percentage (Fiber), sucrose content (Pol), and soluble solid content (Brix) in two places for three harvest years (2012, 2013 and 2014), adding with two previously collected. The genetic linkage map had a total of 421 markers (SSRs, AFLP and SNPs in single dose) linked, resulting in 118 linkage groups and 16 putative homology groups, with a total length of 4512,6 cM. Using Composite Interval Mapping (CIM), a total of 25 QTL were detected for SD (six QTLs), SW (five QTLs), SH (four QTLs), Fiber (five QTLs), Pol (two QTLs) and Brix (three QTLs). The proportion of phenotypic variation explained by each QTL ranged from 0.069% to 3.87%. Adding this thesis, the development of SNPs (Single Nucleotide Polymorphism) markers was performed, using genes involved in two important metabolic pathways for sugarcane, the C4 Photosynthesis and the Sucrose Metabolism, in total 130 locus SNPs were developed, analyzed and characterized using SuperMASSA software. Ploidy level and allelic dosage were estimated in each SNP loco and a high number of high ploidy level was detected, this result induced to search for evidence for gene duplication on the sugarcane genome, resulting in 80% of studied loci showing duplication regions in at least one relative genome from sugarcane (sorghum, maize or rice). Our results can help sugarcane breeding programs, by SNPs markers identification in genes of economic interesting traits and the QTL mapping for also interesting economic traits / Doutorado / Genetica Vegetal e Melhoramento / Doutora em Genética e Biologia Molecular

This MSc. thesis deals with dissecting the link between memory, genetics, and metabolic syndrome. Memory is a very complex behavioral trait, probably influenced by innumerable factors. For this experiment HXB/BXH rat recombinant inbred lines (n= 30) and their parental strains (n=2) were used to be trained in the hippocampus dependant spatial learning task called Allothetic Active Place Avoidance. Rats were to memorize sector of a rotating circular arena, which they were to avoid, being motivated by receiving an electric shock upon entering the forbidden sector (4 training sessions; shock sector on the North, 1 retrieval session (no shock), and 3 reversal sessions, to-be-avoided sector facing South; each session 20-min long, retrieval 10-min). Control experiments to exclude impact of motor or sensory abnormalities were run in a form of open-field test and beam-walking test. Correlation with metabolic phenotypes was conducted in an online database of known HXB/BXH phenotypes (GeneNetwork.org). The results showed that differences in learning were significant between the groups (p<0.05); correlation analysis indicated no putative link between selected traits related to metabolic syndrome and memory in rats. The genetic analysis showed a suggestive locus on chromosome 20 for a learning parameter, and...