Le blé est la seconde céréale la plus cultivée dans le monde et constitue un apport majeur de l’alimentation quotidienne. L’effort consenti à continuellement améliorer les qualités meunière et boulangère du blé tendre, s’est fait au détriment du caractère nutritionnel du grain. Ainsi la plupart des produits industriels dérivés des grains de blé sont produits à partir de farines blanches raffinées qui ne contiennent ni le germe ni les sons. Cependant, dans ces différents tissus qui sont éliminés et qui servent essentiellement à nourrir les animaux, se concentrent les principaux micronutriments tels que les vitamines, les minéraux, les fibres et des substances phytochimiques. Les différentes enquêtes épidémiologiques ont bien mis en évidence les conséquences négatives de la déplétion en micronutriments des produits céréaliers raffinés. Dans l’objectif d’une alimentation plus saine voir même préventive, la consommation d’aliments enrichis en micronutriments naturellement présents dans le grain de blé tendre semble être une démarche efficace. Dans cette optique, ce travail de thèse a permis de consolider et d’accroitre les connaissances concernant les voies d’amélioration des teneurs en vitamines des grains de blés tendres ainsi que des produits industriels qui en sont dérivés. En premier, nous nous sommes intéressés au développement d’une méthode simple et rapide basée sur la spectrométrie de masse couplée à la chromatographie liquide pour la détermination simultanée de sept vitamines hydrosolubles dans divers matériels végétaux. Les vitamines présentes dans les différents matériels végétaux furent séparées en moins de 15 min grâce à l’utilisation d’une colonne C18 en phase inverse, et analysées en mode ElectroSpray positif et MRM. La réponse pour toutes les vitamines a été linéaire sur l’ensemble des concentrations étudiées (0.05 to 9 μg/mL) avec des coefficients de corrélation compris entre 0.991 et 1. Les limites de quantification de la méthode analytique ont été évaluées entre 0.09 et 3.5 μg/g. Les précisions intra-journalière et inter-journalière étaient satisfaisantes. La deuxième partie de nos travaux a concerné l’impact des procédés de transformation du grain (production d’une nouvelle fraction de mouture et grillage) sur la teneur en vitamines. Afin de réaliser cette objectif, la méthode développée a été appliquée pour l’analyse simultanée des concentrations en vitamines hydrosolubles contenues dans différentes farines semi-complètes ainsi que dans les pâtons, pains et pains grillés qui en sont dérivés. En parallèle, les concentrations endogènes des vitamines E, de la Lutéine et du β-sitostérol ont également été évaluées dans le même matériel. Nous avons mis en évidence que les concentrations en acide nicotinique, pyridoxale, pyridoxine et acide pantothénique étaient significativement plus élevées dans les gros sons que dans les autres fractions de moutures, alors que les concentrations en β-sitostérol, lutéine, α-tocotriénol, α-tocophérol et thiamine (20.87 μg/g DM)étaient plus importantes dans la fraction de mouture enrichie. L’étape de grillage induit une augmentation significative en α-tocophérol (+216%), β-γ-tocophérol (+52%), α-tocotriénol (+83%), β-γ-tocotriénol (+32%), acide nicotinique (+55%), nicotinamide (+97%) et en pyridoxine (+77%). L’ensemble de ces résultats nous a permis de montrer qu’un enrichissement de farine blanche par la fraction de mouture dite enrichie pourrait potentiellement permettre d’accroître les produits qui en dérive en vitamine E. De plus le grillage pourrait libérer des composés bioactifs, augmentant ainsi leur biodisponibilité et la valeur nutritionnelle des pains. (...) / Wheat is the second largest crop cultivated around the world and constitutes a major part of the daily diet in Europe. During the course of improving the baking quality of wheat cultivar, most of the nutritional attributes have been underestimated. It is therefore unfortunate that most of wheat-based food products are mostly produced from refined white flour from which peripheral tissues (germ and envelopes) are removed. However, these tissues, which are eliminated and serve mainly for animal feeding, contain most of the vitamins, minerals, fiber and phytochemicals of the grain. It is becoming evident that many of the health benefits associated with the consumption of whole grain cereal products, relate to the enhanced intake of micronutrients, phytochemicals and dietary fiber. In the context of consuming wheat derived foods with enhanced nutritional value, as part of a healthy diet, this thesis provide results which strengthen the knowledge of vitamins accumulation in common wheat and in wheat-based food products. Firstly, we have developed a simple and rapid method based on liquid chromatography tandem mass spectrometry (LC-MS/MS) for the simultaneous screening of seven water soluble vitamins in various wheat-based food materials. The vitamins present in the test materials were separated in less than 15 min by using a reverse-phase C18 column, and analyzed by positive ion electrospray selected reaction monitoring MS/MS. The MS response for all the vitamins was linear over the working range (0.05 to 9 μg/mL) with correlation coefficients ranging between 0.991 and 1. Limits of quantification in the different food materials ranged from 0.09 to 3.5 μg/g. Intra-day and inter-day precision was found satisfactory. The second part of our research, have focused on monitoring the levels of vitamins upon the wheat-based foods processing operations, such as production of new wheat milling fraction (consisting in enriched fraction) and breadmaking toasted bread. In order to achieve this goal, the developed method was applied for the simultaneous analysis of the water-soluble vitamin natural content of different semi-coarse wheat flours and in their corresponding baking products. In addition the vitamin E, Lutein and β-sitosterol natural content was also measured in the same materials. It was shown that the concentration of nicotinic acid, pyridoxal, pyridoxine, pantothenic acid were significantly higher in the coarse bran than in the other milling fractions, while the concentration of β-sitosterol, lutein, α-tocotrienol, α-tocopherol and thiamin (20.87 μg/g DM) were the highest in the enriched fraction. The toasting step induced a significant increased of α-tocopherol (+216%), β-γ-tocopherol (+52%), α-tocotrienol (+83%), β-γ-tocotrienol (+32%), nicotinic acid (+55%), nicotinamide (+97%) and of pyridoxine (+77%). Furthermore, it was demonstrated that the enriched fraction could be a functional ingredient in order to enrich wheat-based products in fat soluble vitamins and that the toasting process could release bound bioactive compounds and led to enhance the nutritional quality of bread. (...)

A estrutura populacional e o desequilíbrio de ligação são dois processos fundamentais para estudos evolutivos e de mapeamento associativo. Tradicionalmente, ambos têm sido investigados por meio de métodos clássicos comumente utilizados. Tais métodos certamente forneceram grandes avanços no entendimento dos processos evolutivos das espécies. No entanto, em geral, nenhum deles utiliza uma visão genealógica de forma a considerar eventos genéticos ocorridos no passado, dificultando a compreensão dos padrões de variação observados no presente. Uma abordagem que possibilita a investigação retrospectiva com base no atual polimorfismo observado é a teoria da coalescência. Assim, o objetivo deste trabalho foi analisar, com base na teoria da coalescência, a estrutura populacional e o desequilíbrio de ligação de um painel mundial de acessos de sorgo (Sorghum bicolor). Para tanto, análises de mutação, migração com fluxo gênico e recombinação foram realizadas para cinco regiões genômicas relacionadas à altura de plantas e maturidade (Dw1, Dw2, Dw4, Ma1 e Ma3) e sete populações previamente selecionadas. Em geral, elevado fluxo gênico médio (Μ = m/μ = 41,78 − 52,07) foi observado entre as populações considerando cada região genômica e todas elas simultaneamente. Os padrões sugeriram intenso intercâmbio de acessos e história evolutiva específica para cada região genômica, mostrando a importância da análise individual dos locos. A quantidade média de migrantes por geração (Μ) não foi simétrica entre pares recíprocos de populações, de acordo com a análise individual e simultânea das regiões. Isso sugere que a forma pela qual as populações se relacionaram e continuam interagindo evolutivamente não é igual, mostrando que os métodos clássicos utilizados para investigar estrutura populacional podem ser insatisfatórios. Baixas taxas médias de recombinação (ρL = 2Ner = 0,030 − 0,246) foram observadas utilizando o modelo de recombinação constante ao longo da região. Baixas e altas taxas médias de recombinação (ρr = 2Ner = 0,060 − 3,395) foram estimadas utilizando o modelo de recombinação variável ao longo da região. Os métodos tradicional (r2) e via coalescência (E[r2 rhomap]) utilizados para a estimação do desequilíbrio de ligação mostraram resultados próximos para algumas regiões genômicas e populações. No entanto, o r2 sugeriu padrões descontínuos de desequilíbrio em várias ocasiões, dificultando o entendimento e a caracterização de possíveis blocos de associação. O método via coalescência (E[r2 rhomap]) forneceu resultados que pareceram ter sido mais consistentes, podendo ser uma estratégia eventualmente importante para um refinamento dos padrões não-aleatórios de associação. Os resultados aqui encontrados sugerem que o mapeamento genético a partir de um único pool gênico pode ser insuficiente para detectar associações causais importantes para características quantitativas em sorgo. / Population structure and linkage disequilibrium are two fundamental processes for evolution and association mapping studies. Traditionally, both have been investigated using classical methods that are commonly used. These methods certainly provided important advances for the understanding of the evolution processes of the species. However, in general, none of them uses a genealogical view to consider genetic events occurred in the past, making difficult the understanding of the variation patterns observed in the present. An approach that enables the retrospective investigation based on the actual observed polymorphism is the coalescent theory. Here, we used the coalescent theory to analyze the population structure and linkage disequilibrium of a worldwide sorghum (Sorghum bicolor) accession panel. To reach this purpose, analyses of mutation, migration with gene flow and recombination were performed to five genomic regions related to plant height and maturity (Dw1, Dw2, Dw4, Ma1 e Ma3) and seven previously selected populations. In general, high average gene flow (Μ = m/μ = 41,78 − 52,07) was observed between populations considering each genomic region and all the regions simultaneously. The patterns suggested a high exchance of accessions between populations and a specific evolutionary history for each genomic region, showing that the individual analysis of each locus was important. The average number of migrants per generation (Μ) was not symmetric between reciprocal pairs of populations, according to the specific and simultaneous analyses of the regions. This result suggests that the historical and recent evolutionary relations between populations are not equal, showing that the classical methods to investigate population structure may be unsatisfactory. Low average recombination rates (ρL = 2Ner = 0,030 − 0,246) were observed using a constant recombination model along the region. Low and high average recombination rates (ρr = 2Ner = 0,060 − 3,395) were estimated using a variable recombination model along the region. Both traditional (r2) and coalescent (E[r2 rhomap]) methods for the estimation of linkage disequilibrium showed similar results for some genomic regions and populations. However, r2 suggested discontinuous patterns of linkage disequilibrium in several cases, making difficult the understanding and definition of the association blocks. The coalescent method (E[r2 rhomap]) provided results that seemed to be more consistent and could be an eventually important strategy to refine the non-random association patterns. The results detected here suggest that the genetic mapping from a unique gene pool may be insufficient to detect important causal associations for quantitative traits in sorghum.

A caracterização e o entendimento das variações genômicas e morfológicas, bem como a estrutura genética de variedades locais armazenadas em bancos de germoplasma é importante para sua efetiva utilização em programas de melhoramento visando tolerância a estresses. Neste trabalho um conjunto de 192 variedades oriundas de diferentes regiões geoclimáticas do Japão foram testadas quanto à suas características morfológicas e produtivas, utilizando ensaios de campo e metodogias de fenotipagem de alto desempenho. A fenotipagem por meio da metodologia de camadas de herbicida (Aminotriazol+Diuron+2,4D, 100mg/plant) alocado a 30 centímetros de profundidade foi possível detectar variação entre as variedades para comprimento de raiz e velocidade de emissão de raiz sendo possível a distinção de variedades com sistema radicular profundo e sistema radicular superficial baseando-se na sua pontuação no ensaio de herbicida, destacando-se 20 genótipos como possíveis doadores de genes para comprimento, densidade e velocidade de emissão de raízes. Ensaios a campo foram conduzidos em 4 localidades expondo as variedades as mais distintas condições climáticas, buscando analisar a diversidade fenotípica para caracteres agromorfológicos. Os dados fenotípicos obtidos pelos marcadores morfológicos geraram um total de 15 grupos de acessos quando utilizados os 13 caracteres avaliados. A média do índice de sensibilidade a seca foi de 0,99 havendo materiais tolerantes com índices próximos a 0,6 e materiais sensíveis com índice próximos a 1,12. Os 384 marcadores SNP detectaram um total de 73728 alelos indicando alta porcentagem de A (40,8%) e G (34,6%) comparado com C (15,6%) e T (3,6%). Quanto aos heterozigotos, a maior porcentagem foi observada de A/G (0,54%) e a menor porcentagem de A/T (0,04%), sendo a maior parte dos heterozigotos observados nos cromossomos 3 e 8 comparado com outros cromossomos. As análises caracterizaram os acessos japoneses como 98,4% pertencentes à subespécie Japônica. Para associação entre marcadores e fenótipos, foi utilizada a abordagem de modelo linear misto (MLM), o qual incorpora informações de estrutura populacional e parentesco. Os resultados obtidos deverão ser investigados futuramente a fim de confirmar as associações em diferentes populações. O aumento do estresse hídrico teve efeito significativo no desempenho dos acessos, e a interação genótipo e estresse hídrico foi significativa para rendimento final e tamanho de panícula. Entre os acessos estudados foi observada variação genética para as características relacionadas com a tolerância a estresse hídrico e encontraram-se acessos com reduções no rendimento devido ao déficit hídrico comparáveis com o das testemunhas, embora com tamanho de panícula menor, inclusive em condições ótimas. Dos 384 marcadores utilizados, 10 foram responsáveis por associações significativas com o índice de sensibilidade a seca, com base nos diferentes métodos de correção para múltiplos testes. Estas associações foram selecionadas para verificar o efeito alélico sobre o genótipo observado, gerando informações preliminares para a aplicação futura de seleção assistida por marcadores (SAM). O tamanho dos blocos de ligação foram estimados em ~100 kb (r < 0,05) e ~75kb (r < 0,1). / Germplasm characterization and the knowledge of its diversity and population structure are important to effective utilization of genetic resources in breeding programs specially drought breeding program. In this work 192 landraces from all over Japan were evaluate for their morphological and productive characteristics, using field trials and high throughput screening methods. The screening using herbicide barrier approach at 30 cm depth was able to detect genetic diversity between the landraces for root length and clearly distinguish between deep root landraces and shallow root landraces. With this approach was possible to select 20 landraces with deep root system as possible donor of drought tolerance genes. Aiming characterize the landraces to agromorphological characteristics field trials were carried in 4 different locations exposing the landraces for a diversity environment effect. Using 13 traits phenotypically data generate a total of 15 groups during cluster analysis. The average result for drought sensitive index was 0.99, however this results presents a huge variability having landraces with scores about 0.6 to landraces with score up to 1.12. Drought effect was huge and statistically significant affecting directly yield and panicle size. The landraces presented genetic variability for drought tolerance and some landraces presenting yield and panicle size reductions due to drought comparable with drought-tolerant controls were detected. A total of 73728 alleles were detected by the SNP markers, indicated a high percentage of A (40,8%) and G (34,6%) alleles compared to C(15,6%) and T (3.6%). Heterozygocity of A/G was highest (0,54%) and lowest in A/T (0.04%). Of 3 chromosomes of rice, chromosome 8 produced highest percentage of heterozygocity compared to other chromosomes. Accessions were classified as 98.4% belonging to japônica subspecies. Association between markers and phenotypes was performed using a mixed linear approach (MLM), which incorporates information regarding population structure and kinship. Among the 384 markers used, 10 were responsible for significant associations with drought sensibility index, based on different criteria to correct for multiple tests.These associations were selected to determine the allelic effects over the traits, in order to generate preliminary data for marker assisted selections (MAS). Estimated size of haplotype blocks were ~100 kb (r <0.05) and ~75 kb (r <0.1). Future studies should confirm marker trait associations here found using different populations.

Dans un contexte d’agriculture durable, la création de variétés combinant des facteurs génétiques de résistance et d’architecture de la plante présente un intérêt majeur pour limiter le développement des maladies. La thèse a visé à analyser l’interdépendance des déterminants génétiques de l’architecture racinaire et de la résistance à A. euteiches, agent pathogène tellurique majeur du pois. Une analyse de génétique d’association conduite sur tout le génome, à partir d’une collection de 266 lignées de pois, a permis d’identifier 150 locus de résistance et d’architecture et de les comparer aux QTL précédemment étudiés. Une région commune à effet majeur a été associée à la résistance et à un caractère de développement racinaire intrinsèque. Plusieurs régions ont été détectées à la fois pour la résistance et des caractères de vigueur racinaire en réponse à l’infection.La combinaison de la résistance et de caractères d’architecture dans une sélection de lignées a été associée à une réduction des pertes de rendement au champ. Les résultats ont permis d’apporter des connaissances originales sur la génétique comparative de la résistance aux maladies et de l’architecture des plantes au niveau racinaire. Ils fournissent des outils, géniteurs et éléments de choix de QTL de résistance et d’architecture racinaire à combiner pour la sélection de futures variétés de pois résistantes à A. euteiches. / In a sustainable agriculture context, breeding for varieties combining genetic resistance and plant architecture is of major interest to limit diseases impacts in crops. The aim of this thesis was to analyze the interpendance of the genetic determinants of root architecture and resistance to Aphanomyces euteiches, a major soil born pathogen of peas. A genome wide association analysis among a 266-pea-line collection enabled us to pinpoint a total of 150 loci associated with resistance and plant architecture, and to compare them with QTL detected in previous studies. A common major locus was associated with resistance and an intrinsic root architecture trait.Several loci were detected for both resistance and disease-induced architecture. The combination of resistance and some architecture traits in selected pea lines was associated with reduced yield losses in infested fields. Results provide original knowledge on comparative genetics of disease resistance and plant architecture for root rot diseases. They provide tools (SNPs and marker haplotypes), parental lines and information for the choice of resistance and architecture QTL to combine in breeding strategies to improve resistance to A. euteiches in future pea varieties.

Abstract Plants and animals colonized Northern Europe after the last Ice Age from different refugia, not covered by the ice sheet. Many plants, such as the northern rock cress (Arabidopsis lyrata ssp. petraea) adapted to the short growing season in the North. We thus expect that colonization of the new environment was accompanied by directional selection for traits conferring this adaptation. In this thesis I studied whether recent directional selection can be detected in two important genes, PHYTOCHROME A (PHYA) and FLOWERING LOCUS C1 (FLC1), related to the flowering time pathway. To detect directional selection, I compared DNA sequence variation from the samples of a southern (Plech, Germany) and a northern (Spiterstulen, Norway) population. I also studied the current response potential to changing conditions in the marginal Spiterstulen population. Adaptation potential was characterized by assessing plasticity and amount of additive genetic variation, focusing on flowering traits. In addition, associations of 21 flowering time candidate genes for phenological and fitness traits were studied. There were several lines of evidence for recent directional selection in both candidate genes, PHYA and FLC1, in the northern Spiterstulen population Variation was strongly reduced around both genes and in addition they were highly differentiated between populations. In the Spiterstulen population there was a remarkable reduction in additive genetic variation for flowering traits, for instance when compared with morphological traits. On the other hand, phenological traits showed high plasticity. Some of the photoperiodic pathway genes showed association to flowering or reproductive fitness. The results suggest that directional selection during the colonization of the northern areas has impacted the two studied genes. Genetic changes were likely involved in altered photoperiodic and vernalization responses which might be adaptive for a short growing season. Further, directional selection was probably responsible for reducing additive genetic variation in flowering traits. Because there was only little genetic variation, adaptation to future environmental change of the marginal Spiterstulen population is likely to rely largely on plastic reactions to environmental signals, or tracking the environment by dispersal. / Tiivistelmä Kasvit ja eläimet levittäytyivät Pohjois-Eurooppaan viimeisen jääkauden jälkeen mannerjäätikön ulkopuolella jääneistä refugioista. Useat kasvit, kuten idänpitkäpalko (Arabidopsis lyrata ssp. petraea) sopeutuivat pohjoisen lyhyeen kasvukauteen. On syytä olettaa, että suuntaava valinta vaikutti sopeutumisessa tärkeisiin ominaisuuksiin. Tässä väitöskirjassa tutkin voidaanko suuntaavan valinnan aiheuttamia jalanjälkiä löytää kahdesta tärkeästä kukkimisaikageenistä, FYTOKROMI A (PHYA) ja FLOWERING LOCUS C1 (FLC1) geeneistä. Tätä varten vertasin DNA sekvenssimuuntelua pohjoisessa (Norja) ja eteläisessä (Saksa) populaatiossa, kiinnittäen erityisesti huomiota geneettisen muuntelun määrään ja erilaistumiseen. Lisäksi tutkin miten Spiterstulenin reunapopulaatio voi vastata tulevaisuudessa muuttuvaan ympäristöön. Sopeutumispotentiaalia arvioitiin sekä fenotyyppisen plastisuuden että additiivisen geneettisen muuntelun määrällä. Lisäksi tutkin miten vaihtelu 21 kukkimisaikageenissä liittyy fenologisiin ja kelpoisuusominaisuuksiin. Useat merkit viittasivat siihen, että suuntaava valinta oli vaikuttanut kummassakin tutkitussa geenissä. Muuntelu oli vähentynyt voimakkaasti kumpaakin geeniä ympäröiviltä kromosomialueilta, jotka olivat myös selkeästi erilaistuneet. Additiivinen geneettinen muuntelu oli selvästi vähentynyt kukkimisominaisuuksissa verrattuna morfologisiin ominaisuuksiin, mahdollisesti suuntaavan valinnan johdosta. Kukkimisominaisuudet olivat kuitenkin plastisia. Jotkin valojaksoreitin geenit vaikuttivat sekä kukkimiseen että lisääntymiskykyyn. Nämä tulokset osoittavat että suuntaava valinta vaikutti kahteen tutkittuun geeniin pohjoiseen levittäytymisen aikana. Geneettiset muutokset liittyivät todennäköisesti muuttuneisiin valojakso-, ja vernalisaatiovasteisiin, jotka saattoivat edistää sopeutumista lyhyeen kasvukauteen. Koska geneettistä muuntelua oli vain hyvin vähän, fenotyyppisellä plastisuudella on todennäköisesti tärkeä rooli sopeutumisessa muuttuvaan ympäristöön Spiterstulenin reunapopulaatiossa.

Chez la tomate, l'amélioration pour la qualité du fruit est rendue difficile par la multiplicité et la complexité des caractères. La cartographie de QTL a permis la caractérisation génétique de ces caractères. L'objectif est maintenant d'identifier les gènes sous-jacents aux QTL. Nous avons utilisé la cartographie par déséquilibre de liaison (DL) dans ce but. Pour éviter les fausses associations entre caractères et polymorphismes moléculaires, la structure génétique a été prise en compte dans l'analyse. La tomate cultivée montre un faible niveau de diversité génétique, ce qui réduit la résolution de cartographie. Le génome de la tomate de type cerise est décrit comme une mosaïque entre celui de la tomate cultivée et de l'ancêtre sauvage. Ce mélange devrait augmenter la résolution des études d'association. Nous avons utilisé une « core collection » focalisée sur des accessions de type cerise pour valider la région génomique contenant un QTL pour le nombre de loges. Deux mutations sont associées avec le caractère. Ces deux SNP ont évolué différemment du reste du chromosome 2, en subissant une sélection balancée qui témoigne de l'augmentation de la diversité morphologique lors de la domestication. L'étude, focalisée sur le chromosome 2, a permis d'analyser l'étendue du DL en fonction de la distance génétique et physique. Des associations, entre polymorphismes et phénotypes étudiés, ont été détectés avec des méthodes prenant en compte la structure génétique. Nous avons montré l'intérêt d'utiliser la structure en mosaïque du génome des accessions de type cerise pour surmonter les limitations de résolution dans les analyses d'associations chez une espèce cultivée autogame. / In Tomato (Solanum lycopersicum), breeding for fruit quality is difficult due to the multiplicity and complexity of the traits. QTL mapping has allowed the genetic characterization of these traits. One of the challenges is now to identify the genes underlying these QTLs. Following this aim, we used linkage-disequilibrium (LD) mapping. To avoid hazardous associations between traits and polymorphisms, the genetic structure has to be taken into account for LD mapping. Cultivated tomato showed low genetic diversity reducing mapping resolution. Cherry type tomato genome is described to be admixture between cultivated tomato and its wild ancestor. Such admixture may increase resolution of association mapping. We used a core collection focused on cherry type accessions to validate a candidate gene for a fruit locule-number QTL. We found that two single nucleotide polymorphisms (SNP) were highly associated with the trait. These two SNP evolved differently from the rest of the chromosome 2. They underwent a balanced selection which testifies a selection for fruit morphology diversity by human. Association mapping, focused on whole chromosome 2, allowed us to assess the extent of linkage disequilibrium over genetic and physical distances. Associations of polymorphisms with phenotypes were detected with structured association methods. We thus showed efficiency of genome admixture to overcome the low-resolution limitation of association mapping for an inbred crop. We validated previously identified QTLs and found associations with new QTLs and new candidate genes. An evolutionary model including bottleneck and gene flow between wild and domesticated forms is also presented.

La fusariose des épis des céréales est due à un champignon pathogène (Fusarium spp.) qui entraine non seulement une perte directe de rendement en interrompant le remplissage des grains, mais également une perte indirecte par la production de mycotoxines, responsables de perturbations de procédés industriels et d'intoxications alimentaires. Parmi les différents moyens de lutte, la création de variétés résistantes semble la stratégie la plus efficace et la plus durable. Plusieurs variétés exotiques ont ainsi été identifiées comme résistantes mais présentent la particularité d'être difficilement cultivables sous nos latitudes. L'obtention de variétés résistantes adaptées à nos climats passe donc par une meilleure connaissance des mécanismes de résistance disponibles. La détection de QTL (Quantitative Trait Loci) chez le blé tendre a déjà permis de localiser certains des facteurs génétiques impliqués dans des mécanismes de résistance. Cependant l'utilisation de ces résultats en amélioration des plantes se heurte à deux contraintes majeures : la position des QTL reste le plus souvent imprécise et ces QTL, dérivant de populations biparentales, ne représentent qu'une fraction de la diversité génétique potentiellement intéressante pour ce caractère. L'objectif de la thèse était d'étudier la résistance du blé à la fusariose en réalisant une approche de génétique d'association. L'utilisation de génotypes faiblement apparentés et d'une densité élevée de marqueurs a permis de détecter des associations entre le polymorphisme génétique et des variations phénotypiques. Après avoir réalisé une synthèse sur le pathogène et sur l'approche par génétique d'association, le premier travail a été de réaliser une carte génétique fiable afin de pouvoir localiser les associations mises en évidence. Un panel de 195 variétés de blé tendre élites a été évalué pour leur résistance globale à la fusariose, pour leur résistance à la progression des symptômes et pour leur résistance à l'accumulation des mycotoxines. Des notations morphologiques (précocité, taille, aristation, nombre d'épillets par épi et extrusion des anthères) ont également été réalisées afin d'évaluer leur influence dans l'infestation. Ces variétés ont été génotypées avec 3016 marqueurs SNP, 200 marqueurs SSR et 1400 marqueurs DArT. Préalablement à la réalisation des tests d'association, l'étude de la structure a mis en évidence trois origines géographiques (française, anglaise et allemande) des variétés du panel. De même, l'étude du déséquilibre de liaison a montré que celui-ci était conservé sur une distance comprise entre 2 et 6 cM. L'étude d'association réalisée sur les notations d'infestation a permis d'identifier plusieurs zones associées, dont plusieurs sont colocalisées avec des Meta-QTL et/ou avec des zones identifiées avec les notations morphologiques. La densification en marqueurs de 6 zones associées avec les différentes notations d'infestation, localisées sur les chromosomes 1A, 1D, 2A, 2B, 5A et 7A, ont permis de confirmer ces régions, de restreindre fortement l'intervalle d'intérêt et de mettre en évidence de potentiels gènes candidats. Cette analyse a ainsi permis de mieux comprendre les mécanismes génétiques et morphologiques impliqués dans la résistance à la fusariose des épis. La décomposition en trois partie de cette résistance (résistance globale, résistance à la progression des symptômes, et résistance à l'accumulation des mycotoxines) montre l'existence de mécanismes génétiques indépendants et donc complémentaire à prendre en compte dans une stratégie de création de variétés résistantes à la fusariose des épis. / Fusarium head blight (FHB), caused by the fungal pathogen Fusarium spp., is a major cereals disease that not only cause direct yield losses, by interrupting grain filling, but also indirect quality losses by the production of mycotoxins, responsible of industrial processes disturbance and food poisoning. Most wheat breeding programs in FHB-affected areas of the world have been screening germplasm to identify sources of improved tolerance. Unfortunately, these sources of genetic resistance are often of exotic origin and not adapted to West European growing conditions. The selection of adapted varieties with improved tolerance therefore needs a better characterization of resistance mechanisms. Several QTL for FHB resistance in wheat have been identified in European germplasm, but the use of these information in marker-assisted selection is constrained by the precision of the QTL and the low diversity tested by using biparental population.The aim of the present study is to use association mapping, also called linkage disequilibrium mapping, to identify loci involved in the resistance to FHB. This method refers to the analysis of statistical associations between genotypes determined in a collection of individuals, and the phenotypes of the same individuals. A dense genetic map was compiled to localize precisely the association results. Resistance to F. graminearum was studied in a panel of 195 elite wheat varieties by the evaluation of three components: resistance to global infection, resistance to symptom progression and resistance to accumulation of mycotoxins. Morphological factors (plant height, heading date, awnedness, spikelets per ears, anther extrusion), known to influence resistance to FHB, were also recorded. All the varieties have been genotyped with around 3300 SNP markers, 200 SSR markers and 1400 DArT markers. We first investigated the structure of the panel, which could generate bias in the estimate of allele effects, if not included explicitly in the association models. We showed that the structure is based on geographical origin (French, German and UK). Study of the linkage disequilibrium (LD) showed an extent of LD between 2 and 6 cM. Results of association studies permitted to identify several loci for each of the evaluated components of resistance. Some of these loci colocalized with the results of the MetaQTL analysis and/or with loci associated with morphological traits. We selected more specifically 6 loci, located on chromosome 1A, 1D, 2A, 2B, 5A and 7A. Marker saturation of the regions, allowed to confirm the genome wide association results and to increase the accuracy of the loci of interest. This analysis allowed to better understand the many factors that influenced FHB resistance, whether genetic or morphological. Results show that the genetic mechanisms are independent between the three components and therefore, information obtained for each component are to be used complementary to create varieties with increased resistance to FHB.

Common bean is a major dietary component in several countries, but its productivity is negatively affected by abiotic stresses. Dissecting candidate genes involved in abiotic stress tolerance is a paramount step toward the improvement of common bean performance under such constraints. Thereby, this thesis presents a systematic analysis of the DEHYDRATION RESPONSIVE ELEMENT-BINDING (DREB) gene subfamily, which encompasses genes that regulate several processes during stress responses, but with limited information for common bean. First, a series of in silico analyses with sequences retrieved from the P. vulgaris genome on Phytozome supported the categorization of 54 putative PvDREB genes distributed within six phylogenetic subgroups (A-1 to A-6), along the 11 chromosomes. Second, we cloned four novel PvDREB genes and determined their inducibility-factors, including the dehydration-, salinity- and cold-inducible genes PvDREB1F and PvDREB5A, and the dehydration- and cold-inducible genes PvDREB2A and PvDREB6B. Afterwards, nucleotide polymorphisms were searched through Sanger sequencing along those genes, revealing a high number of single nucleotide polymorphisms within PvDREB6B by the comparison of Mesoamerican and Andean genotypes. The nomenclature of PvDREB6B is discussed in details. Furthermore, we used the BARCBean6K_3 SNP platform to identify and genotype the closest SNP to each one of the 54 PvDREB genes. We selected PvDREB6B for a broader study encompassing a collection of wild common bean accessions of Mesoamerican origin. The population structure of the wild beans was accessed using sequence polymorphisms of PvDREB6B. The genetic clusters were partially associated with variation in latitude, altitude, precipitation and temperature throughout the areas such beans are distributed. With an emphasis on drought stress, an adapted tube-screening method in greenhouse conditions enabled the phenotyping of several drought-related traits in the wild collection. Interestingly, our data revealed a correlation between root depth, plant height and biomass and the environmental data of the location of the accessions. Correlation was also observed between the population structure determined through PvDREB6B and the environmental data. An association study combining data from the SNP array and DREB polymorphisms enabled the detection of SNP associated with drought-related traits through a compressed mixed linear model (CMLM) analysis. This thesis highlighted important features of DREB genes in common bean, revealing candidates for further strategies aimed at improvement of abiotic stress tolerance, with emphasis on drought tolerance / O feijoeiro é um componente essencial na dieta em diversos países, no entanto, sua produção é afetada negativamente por estresses abióticos. O estudo de genes candidatos envolvidos na adaptação aos estresses é uma etapa fundamental para o melhoramento da performance do feijoeiro sob tais estresses. Desse modo, esta tese apresenta uma análise sistemática da subfamília de genes DEHYDRATION RESPONSIVE ELEMENT-BINDING (DREB), que reúne genes envolvidos em diversos processos em resposta a estresses, mas pouco estudados no feijoeiro. Primeiramente, uma série de análises in silico com sequências de feijoeiro obtidas da plataforma Phytozome possibilitaram a categorização de 54 genes PvDREB putativos, distribuídos em seis subgrupos (A-1 até A-6) nos 11 cromossomos da espécie. Posteriormente, quatro novos genes PvDREB foram clonados e seus padrões de inducibilidade foram determinados. PvDREB1F e PvDREB5A foram induzidos por desidratação, baixa temperatura e salinidade, enquanto PvDREB2A e PvDREB6B foram predominantemente induzidos por desidratação e baixa temperatura. Polimorfismos de nucleotídeos foram buscados através de sequenciamento por método derivado de Sanger, revelando elevado número de SNP no gene PvDREB6B. A nomenclatura desse gene foi discutida detalhadamente ao longo da tese. A plataforma de marcadores SNP BARCBean6K_3 foi acessada para identificar o SNP mais próximo de cada um dos 54 PvDREB. O gene PvDREB6B foi selecionado para um estudo mais amplo, envolvendo uma coleção de acessos selvagens de origem Mesoamericana. A estrutura populacional destes genótipos foi analisada a partir de polimorfismos na sequência de PvDREB6B. Os grupos genéticos apresentaram associação parcial com variação da latitude, altitude, precipitação e temperatura das áreas em que os acessos naturalmente ocorrem. Com ênfase no estudo do déficit hídrico, uma plataforma de fenotipagem destes acessos em casa de vegetação, utilizando um sistema de tubos plásticos, foi elaborada para a análise de diversos parâmetros relacionados ao estresse por déficit hídrico. Os dados revelaram correlação entre profundidade de raízes, altura das plantas e a biomassa e as variáveis ambientais de cada local. A correlação também foi detectada entre a estrutura populacional estudada por PvDREB6B e os dados ambientais. Finalmente, um estudo de associação genética foi realizado entre os SNP da plataforma e ligados a DREB e os parâmetros fenotípicos, permitindo a identificação de marcadores SNP associados a caracteres específicos, usando um modelo linear misto (CMLM). Esta tese apresentou importantes aspectos sobre os genes DREB em feijoeiro, revelando candidatos para seu uso em estratégias de melhoramento para tolerância a estresses abióticos, com ênfase em déficit hídrico

Les téosintes Zea mays ssp. parviglumis et ssp. mexicana sont les apparentés sauvages les plus proches du maïs cultivé. Elles occupent au Mexique des niches écologiques distinctes bien délimitées par l’altitude. Zea mays ssp. parviglumis pousse dans des environnements chauds et humides situés à moins de 1800m d’altitude, tandis que Zea mays ssp mexicana pousse dans des environnements plus secs et froids (au-dessus de 1800m). Nous nous sommes intéressés aux bases génétiques de l’adaptation locale des téosintes à l’altitude. Dans ce but, 37 populations ont été échantillonnées le long de deux gradients altitudinaux, utilisés comme réplicats biologiques. Deux populations extrêmes de chaque gradient ainsi que deux populations de moyenne altitude de chaque sous-espèce du gradient 1 ont été séquencées à faible profondeur afin de découvrir des polymorphismes dont les fréquences alléliques sont contrastées entre les extrêmes tout en contrôlant pour la différenciation entre les sous-espèces. A partir de méthodes de détection de la sélection intra- et inter-populationnelle, des locus candidats ont été détectés. Une revue bibliographique a permis d’établir des correspondances entre nos candidats et des régions précédemment décrites pour leurs effets phénotypiques sur des caractères adaptatifs. Nous montrons ainsi un rôle important des interactions sol-plante et de la pilosité des feuilles dans l’adaptation à l’altitude. Pour valider certains de nos candidats, 270 polymorphismes ont été génotypés sur les 37 populations afin de réaliser des études de clines de fréquence. Parallèlement, nous avons mis en œuvre un dispositif de caractérisation phénotypique (2 lieux x 2 années) afin de tester l’association entre ces polymorphismes et 18 caractères mesurés en champ. Nous discutons des apports méthodologiques de notre étude aussi bien du point de vue des technologies haut débit que de la détection de la sélection. Notre dispositif devra être pleinement exploité pour valider nos candidats. Les perspectives incluent la poursuite de l’étude sur d’autres types de polymorphismes ainsi qu’un suivi temporel des populations. / Teosintes Zea mays ssp parviglumis (parviglumis) and Zea mays ssp mexicana (mexicana) are the closest wild relatives of cultivated maize. They occupy distinct ecological niches in Mexico, well separated by altitude. Zea mays ssp. parviglumis encountered below 1800m grows in wet and warm conditions, while mexicana grows in drier and colder climates (above 1800m). In order to investigate the genetic bases of local adaptation to altitude, we sampled 37 populations along two altitudinal gradients. We sequenced the two most extreme populations of each gradient as well as two intermediate populations - one from each subspecies along gradient 1. We searched for polymorphisms with contrasted allele frequencies between the extremes while accounting for subspecies differentiation. Using both inter- and intra- population methods we identified several candidate loci. Based on a literature review, we confronted them with regions previously described as involved in phenotypic variation of adaptive traits. Our results highlight the role of plant-soil interactions and leaves hairiness in the adaptation to altitude. To validate further a subset of 270 polymorphisms chosen among our best candidates, we genotyped them on the 37 populations with the aim of performing clinal analyzes of allele frequencies. In parallel, we undertook phenotypic evaluation trials (2 locations x 2 years) to test the association of these polymorphisms with 18 traits measured in the field. We discuss the methodological contributions of our study both from the standpoint of high throughput technologies and detection of selective footprints. Our setting will be fully exploited to validate our candidates. Perspectives include the discovery and assessment of the contribution of other types of polymorphisms and the temporal follow-up of populations.

<p></p>Comprehensive information of breeding germplasm is a necessity to develop effective strategies for accelerated breeding. I characterized Purdue University soft red winter wheat breeding population that was subjectof intensive germplasm introduction and introgression from exotic germplasm. Using genotyping-by-sequences (GBS) approach, I developed ~15,000 single nucleotide polymorphisms (SNPs) and studied extent of linkage disequilibrium (LD)and hidden population structure in the population.The extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LDandslow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for signatures of selection using FSTand hapFLK identified 13 genomic regions under selection, of which six loci (<i>LT, Ppd-B1, Fr-A2, Vrn-A1, Vrn-B1, Vrn3</i>) were associated with environmental adaptation and two loci were associated with disease resistance genes (<i>Sr36 </i>and <i>Fhb1</i>).<br><p></p><div><br></div><div>The population was evaluated for agronomic performance in field conditions across two years in two locations. Genome-wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, large effects loci were identified on chromosome 6A and 7B. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for grain yield<i> per se</i>, no major loci were detected. A combination of selection for other large effect loci for yield components and genomic prediction could be a promising approach for yield improvement.<br></div><div><br></div><div>In addition, the population was evaluated for FHB resistance under misted FHB nurseries inoculated with scabby corn across 2017-18 (Y1) and 2018-19 (Y2) seasons at Purdue Agronomy Farm, West Lafayette,in randomized incomplete block designs. Phenotypic data included disease incidence (INC), disease severity (SEV), <i>Fusarium</i> damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Twenty-five loci were identified at -<i>log</i>P ≥ 4.0 to be associated with five FHB-related traits. Of these 25, eighteen explained more than 1% of the phenotypic variations. A major QTL on chromosome 2Bi.e., Q2B.1 that explained 36% of variation in FDK was also associated with INC, FHBdx, and DON. The marker-trait associations that explained more than 5% phenotypic variation were identified on chromosomes 1A, 2B, 3B, 5A, 7A, 7B,and 7D. To investigate the applicability of other QTL with less signal intensity, the threshold criterion was lowered to -<i>log</i>P ≥ 3.0, which resulted in the identification of 67 unique regions for all traits. This study showed that the FHB-related traits have significant correlations with the number of favorable alleles at these loci, suggesting their utility in improving FHB resistance in this population by marker-assisted selection.The genotype and phenotype data produced in this study will be valuable to train genomic prediction models and study the optimal design of genomic selection training sets. This study laid foundation for the design and breeding decisions to increase the efficiency of pyramiding strategies and achieving transgressive segregation for economically important traits such as yield and FHB resistance.<br></div>