<p>Wheat is a major source of calories and protein for humans worldwide. Wheat is the most widely grown crop, with cultivation areas and production systems on every continent. The cultivated land area is vast because of its importance and adaptability to various environmental conditions. Global wheat production has not kept up with the growing population, provoking the need to develop new methods and techniques to increase genetic gains. The first research chapter of this Ph.D. dissertation involves performing genome-wide association studies (GWAS) to identify and examine transferability of marker-trait associations (MTAs) across environments. I evaluated yield and yield components traits among 270 soft red winter (SRW) wheat varieties. The population consists of experimental breeding lines adapted to the Midwestern and eastern United States and developed by public university breeding programs. Phenotypic data from a two-year field study and a 45K-SNP marker dataset were analyzed by FarmCPU model to identify MTAs for yield related traits. Grain yield was positively correlated with thousand kernel weight, biomass, and grain weight per spike while negatively correlated with days to heading and maturity. Sixty-one independent loci were identified for agronomic traits, including a region that with <i>–logP</i> of 16.35, which explained 18% of the variation in grain yield. Using 12 existing datasets from other states and seasons, in addition to my own data, I examined the transferability of significant MTAs for grain yield and days to heading across homogenous environments. For grain yield and days to heading, I only observed 6 out of 28 MTAs to hold up across homogenous environments. I concluded that not all marker-trait associations can be detected in other environments.</p><p>In the second research chapter of this Ph.D. dissertation, I dissected yield component traits under contrasting nitrogen environments by using field-based low-throughput phenotyping. I characterized grain yield formation and quality attributes in soft red winter wheat. Using a split-block design, I studied responses of 30 experimental lines, as sub-plot, to high nitrogen and low nitrogen environment, as main-plot, for two years. Differential N environments were imposed by the application, or lack thereof, of spring nitrogen application in a field, following a previous corn harvest. In this study, I measured agronomic traits, in-tissue nitrogen concentrations, nitrogen use efficiency, nitrogen harvest index and end-use quality traits on either all or subset of the germplasm. My data showed that biomass, number of spikes and total grain numbers per unit area were most sensitive to low nitrogen while kernel weight remained stable across environments. Significant genotype x N-environment interaction allowed me to select N-efficient germplasm, that can be used as founding parents for a potential breeding population specifically for low-N environments. I did this selection on the basis of superior agronomic traits and the presence of the desirable gluten quality alleles such as <i>Glu-A1b </i>(<i>2*</i>) and <i>Glu-D1d </i>(<i>5+10</i>).</p>

<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>

<div>The biological underpinnings that control iris pigmentation and facial morphology are two areas of research that over the last decade are becoming more thoroughly investigated due to the increased affordability of genotyping and advances in technology allowing for more advanced analysis techniques. Despite the ease of access to the data and the tools required to perform iris pigmentation and facial morphological studies, there are still numerous challenges researchers must overcome when exploring the genetics of these complex phenotypes. Some of these challenges include difficulty in working with the bioinformatic programs designed to analyze genetic associations, the inability to define a phenotype that captures the true nature of these traits, and analysis techniques that fail to model complex gene-gene interactions and their effect on a phenotype or phenotypes of interest.</div><div><br></div><div>In this body of work, I attempted to address these challenges by designing a bioinformatic pipeline, Odyssey, that bridges the communication gaps between various data preparation programs and the programs that analyze genomic data. With this program, genome-wide association studies (GWAS) could be conducted in a quicker, more efficient, and easier manner. I also redefined iris color as a quantitative measurement of pre-defined color classes. In this way it is possible to define and quantify the unique and intricate mixtures of color, which allows for the identification of known and novel variants that affect individual iris color. I also improved upon current prediction models by developing a neural network model capable of predicting a quantitative output to four pre-defined classes; blue/grey, light brown (hazel), perceived green, and dark brown. I examined the effects of defining a simple facial morphology phenotype that more accurately captures the lower face and jaw shape. I then analyzed this phenotype via a GWAS and found several novel variants that may be associated with a square and diamond shaped face. Lastly, I demonstrated that structural equation modeling can be used in combination with traditional GWAS to examine interactions amongst associated variants, which unearths potential biological relationships that impact the multifaceted phenotype of facial morphology.</div>

The ultimate goal of my thesis is to develop a better understanding of the contribution of indirect benefits (i.e. good genes) to the evolution of female mate preferences. It is genetic variance in, and genetic correlations (covariances) among, male sexual displays, female preferences for them, and fitness that in part determine the degree to which females preferring certain male displays over others will gain an indirect benefit by having higher fitness offspring. Recent advances in quantitative genetic theory provide the mathematical means for quantifying the strength of indirect selection for female mate preferences (Kirkpatrick and Hall 2004), at least under certain conditions, but there are few empirical systems for which such data exist (Brooks and Endler 2001; Qvarnström et al. 2006). I have undertaken a classic half-sibling breeding design with the ultimate goal of estimating the specific parameters of this model in a population of the Australian fruit fly Drosophila serrata. The breeding design was performed across two environments - one to which the population was well adapted and a novel environment to which it was not - thereby also providing insight into genotype-by-environment interactions for this suite of traits and their effects on good genes indirect benefits in a novel environment. General insight is also gained into the genetic covariance of male and female fitness and the prevalence of intralocus sexual conflict, the quantitative genetic basis of female mate preferences for multiple male traits, the condition-dependence of these traits, and the genetic association between sexual displays and fitness when mutation-selection balance is inferred. My results advocate caution in the application of existing theory to quantify the strength of indirect selection, suggesting that a good genes process may be fundamentally different when the exaggeration of sexual displays is eventually halted and an equilibrium is reached between opposing selection.

Le comportement humain est à la fois singulier et universel. La singularité serait principalement due aux trajectoires de vie propre à chaque individu (variant entre autres selon leur culture) alors que l’universalité émanerait d’une nature universelle ancrée dans un génome universel. Démêler les influences de la nature et de la culture sur le comportement humain est le Saint Graal de l’anthropologie biologique. J’aborde cette question en explorant les effets génétiques et environnementaux sur les bases psychiques du comportement. Plus particulièrement, je teste l’hypothèse que la singularité et l’universalité comportementales humaines s’observent au plan psychique par l’exploration de leur substrat neurobiologique, et que ce substrat possède à la fois un ancrage génétique et environnemental. À l’aide de données d’imagerie par résonance magnétique fonctionnelle (IRMf) recueillies auprès de 862 participants du Human Connectome Project (HCP), j’analyse les activations cérébrales liées à sept tâches socio-cognitives qui recoupent diverses facultés, dont le langage, la mémoire, la prise de risque, la logique, les émotions, la motricité et le raisonnement social. Après avoir groupé les sujets selon la similarité de leurs patrons d’activation cérébrale (c.-à-d. leurs sous-types neurobiologiques), j’estime l’influence génétique et environnementale sur la variabilité interindividuelle de ces divers sous-types. Les résultats démontrent bel et bien l’existence d’un regroupement des sujets selon la similarité de leurs cartes d’activation cérébrale lors d’une même tâche socio-cognitive, ce qui reflète à la fois le caractère singulier et universel des corrélats neuronaux d’un comportement observable. La variabilité interindividuelle constatée dans ces regroupements cérébraux témoigne quant à elle d’effets génétiques (héritabilité) ainsi qu’environnementaux (environnementalité), dont les ampleurs respectives varient selon la nature de la tâche effectuée. De plus, les sous-types cérébraux mis à jour révèlent une association avec les mesures comportementales et de performance effectuées lors des diverses tâches à l’étude. Enfin, les sous-types neurobiologiques résultant des diverses tâches partagent certaines bases génétiques. Dans leur ensemble, ces résultats appuient la notion que le comportement humain, ainsi que les processus neurobiologiques le sous-tendant, sont des phénotypes au même titre qu’un caractère morphologique ou physiologique, c’est-à-dire qu’ils sont le résultat de l’expression conjointe de bases génétiques (nature) et environnementales (culture). / Human behaviour is both singular and universal. Singularity is believed to be mainly due to life trajectories unique to each individual (influenced among others by culture), whereas universality would stem from a universal nature resulting from a panhuman genome. Unravelling the influences of nature and nurture on human behaviour is the Holy Grail of biological anthropology. I approach this issue by exploring genetic and environmental influences on the neuropsychological underpinnings of behaviour. In particular, I test the hypothesis that the singularity and universality of human behaviour are also observed at the psychological level through the exploration of the neurobiological basis of behaviour, and that these bases have both genetic and environmental sources. Using Functional Magnetic Resonance Imaging (fMRI) data of 862 participants from the Human Connectome Project (HCP), I analyze brain activation related to 7 socio-cognitive tasks covering language, memory, risk taking, logic, emotions, motor skills, and social reasoning. After grouping subjects according to the similarity of their brain activation patterns (neurobiological subtypes), I estimate the genetic and environmental influences on the variation between participants on these subtypes. The inter-individual variability in cerebral groupings appears to have both genetic (heritability) and environmental (environmentality) sources that vary according to the particular psychological task involved. Moreover, these neurobiological subtypes show an association with behavioural and performance measures assessed by the socio-cognitive tasks. Finally, the neurobiological subtypes across the 7 tasks share common genetic links. Overall, the results support the notion that human behaviour, as well as its underlying neurobiological processes, are phenotypes in the same way as morphology or physiology, i.e., are the results of the integrated expression of a genetic basis (nature) and environmental influences (nurture).

Die vorliegende Dissertation verbindet Ergebnisse aus neuroethologischen, verhaltensbiologischen, quantitativ genetischen und genomischen Ansätzen bei Feldgrillen (Gryllus), um neue Erkenntnisse über die Rolle von sexueller Selektion bei Artbildung zu erlangen. Es wird gezeigt dass multivariate Gesangspräferenzen von Grillenweibchen von wenigen Merkmalen abhängen und zwischen Arten ähnlich sind, während sich Männchengesänge in allen Merkmalen unterschieden. Verschiedene Ebenen der Gesangserkennung sind durch unterschiedliche Präferenzfunktionen charakterisiert. Multivariate Präferenzen können also gleichzeitig verschiedene Indikatoren für Paarungspartnerqualität aus den Gesangsmerkmalen erkennen. Eine polygene genetische Architektur der Gesangsmerkmale und der Präferenz wurde beobachtet und weist auf eine eher langsamere Divergenz hin, obwohl gonosomale Vererbung mehrerer Gesangsmerkmale höhere Evolutionsraten zulässt. Starke Kovarianz zwischen den Merkmalen die direkt sexueller Selektion unterliegen und Merkmale, die nicht direkt von Weibchen gewählt werden, zeigen, dass indirekte Selektion teilweise für die markante Divergenz der Gesänge verantwortlich sein könnte, trotz begrenzter Divergenz der Präferenzen. Ferner zeigte ein Artvergleich der multivariaten Gesangsmerkmale, dass die Form der Präferenzfunktion die Ausrichtung der Kovarianzen und damit die erwartete Selektionsantwort der männlichen Gesänge beeinflussen kann. Simulationen ergaben starke Hinweise auf Genfluss zwischen zwei nahverwandten Arten über einen langen Zeitraum . Nur wenige Contigs zeigten hohe genetische Divergenz und hohe Raten nicht-synonymer Polymorphismen. Diese stimmten aber mit Genen überein, die experimentell nachgewiesene Funktionen in neuromuskulärer Entwicklung und im Paarungsverhalten haben. Zusammen zeigen die Ergebnisse das Potential von sexueller Selektion bei der Entstehung und Aufrechterhaltung von reproduktiver Isolation zwischen Arten. / This thesis integrates insights from neuro-ethological, behavioural, quantitative genetics, and genomic approaches in field crickets to provide novel insights in the role of sexual selection in speciation, in particular focusing on speciation with gene flow. It was shown that song preferences depend on few traits and are similar across species while the male song has diverged strongly in all traits. Because the different levels of song recognition are characterized by different types of preference functions, it is conceivable that multivariate preferences can extract various cues for mate quality from different traits simultaneously. A polygenic genetic architecture was found for song traits and preferences, probably limiting divergence rates. However, sex-chromosomal inheritance of some song traits may have allowed for somewhat higher rates. Strong covariance was found between traits that are under sexual selection and traits that are not directly selected by females. This indicates that indirect selection may be responsible in part for striking multivariate divergence in the male calling song despite limited divergence in female preferences. Furthermore, comparing multivariate song traits among species showed that the shape of the preference function can affect the orientation of trait covariance and thereby the selection responses of the male song. Coalescent simulations revealed evidence for a long history of gene flow between two closely related cricket species. Only few contigs with high genetic divergence and high rates of non-synonymous SNPs were found, but many of those that were highly diverged matched genes with experimentally proven functions in neuromuscular development and courtship behavior. Together, these findings underline the potential for sexual selection to drive reproductive isolation.

Sexually selected ornaments are among the most spectacular traits in nature. Indeed, the extreme costs associated with producing sexual traits seem to play a crucial role in their evolution by enforcing honest levels of advertisement: only males with high levels of acquired resources (or high ‘condition’, as it is known in the literature) can afford to produce extravagant signals, a phenomenon which maintains signal reliability in a constant environment. In my thesis I examine many implications of this condition-dependent model of ornament and preference evolution for variation in age-dependent allocation to sexual signals and other life history traits. In Chapter 1, I review theoretical implications of condition-dependent signalling for life history and sexual selection theory. I note that a universal cost of expenditure in sexual advertisement is metabolic in nature: metabolites used to fund ornament expression are by definition unavailable to other life history traits that compete for a limited resource pool. This universal constraint on expenditure does more than maintain honesty (as noted above), however: the reliance of sexual displays on high levels of nutrient acquisition may help maintain genetic variation in sexual signals that would otherwise be eroded by strong mate choice, and without which the selective basis for good-genes choice would disappear. Three mechanisms in particular probably help to maintain genetic variation in acquisition. 1) Because acquiring resources and converting them efficiently to useful forms depends on the high function of many biochemical pathways, condition is undoubtedly highly polygenic, which slows the erosion of genetic variation under strong directional selection by females (especially in the presence of epistatic interactions). 2) The highly polygenic nature of condition also presents a large target for mutation, which continually restores variation at the loci under selection. 3) The many loci underlying condition may also be particularly sensitive to environmental heterogeneity in time or space. By favouring the most ornate males, females acquire high performing genes for their offspring, regardless of the precise allele combinations that have conferred the ability to acquire resources. Selection on specific alleles is liable to fluctuate over time or space whenever allelic performance is strongly context-specific. I close by noting the considerable challenges in advancing research on sexual selection and life history allocation, including the fact that two key processes central to life history (acquisition and allocation) are latent variables that interact in complexways and are intrinsically difficult to measure empirically. In the remainder of my thesis I conduct a series of experiments involving decorated crickets, Gryllodes sigillatus, which are useful models for studying life history because they enable precise measurement of male reproductive effort. Male G. sigillatus face important allocation decisions owing to the highly polyandrous nature of females, and the substantial costs involved in signalling and mating. Chapter 2 examines sex differences in age-dependent reproductive effort as a function of diet and development stage. I reared outbred crickets using four combinations of diet nutritional quality, and studied the effects of these combinations on male and female reproductive effort (calling effort in males and fecundity in females) and longevity. While I expected males to be more sensitive than females to variation in diet and developmental changes in its quality, I actually observed the opposite: males in all treatments increased calling effort over time, exhibiting consistently positive covariance between calling effort and longevity across treatments. By contrast, the relationships between female reproductive effort and longevity changed dramatically across treatments, and females who lived to intermediate ages had the highest fecundity. Although my results support sex-specific selection on life history allocation over time, a compelling additional explanation for my findings relates to the strategic role of calling for achieving male fitness. In the absence of positive feedback from potential mates, perhaps male allocation to sexual advertisement is careful and only increases gradually as a function of accumulating metabolic resources and increasing risk of intrinsic mortality. Alleles underlying condition are expected to be particularly sensitive to environmental heterogeneity. While this sensitivity may help maintain additive variation in male quality (which is essential for the sustenance of adaptive good-genes mate choice, as noted in Chapter 1), too much environmental sensitivity could also underiii mine the signal value of the male trait. For example, if there are strong genotypeby- environment interactions (GEIs) for sexual advertisement, in a rapidly changing environment females risk favouring a male whose alleles are no longer best suited to current conditions. This problem is particularly pressing for animals like crickets where males exhibit a behaviourally plastic sexual display (such as calling), and so may dynamically adjust signalling effort over time. In Chapter 3, I used inbred lines of decorated crickets to quantify age and diet dependent genetic variation in male signalling. I demonstrate that while genetic correlations across diets were quite strong for morphological traits, correlations between measures of the male sexual trait rapidly approached zero as I increased the distance in time (i.e., across widely spaced ages) or diet (i.e., comparing more dissimilar dietary histories) between samples. While extrapolating from my laboratory experiments to nature is difficult, my findings nevertheless cast doubt on the value of behaviourally dynamic signals (such as cricket calls) for reliably indicating genetic quality in realistically complex environments. In Chapter 4 I used physiological assays to evaluate factors affecting metabolite storage and use over time in decorated crickets. I manipulated the acquisition ability of all males using artificial diets that varied linearly in nutrient quality, and manipulated access to female mates over the course of the second week of adult life. By sacrificing crickets at key stages before and after manipulating the diet and social environment, I was able to estimate changes in stored metabolites, and relate these changes to calling effort and longevity. During the first week of adulthood (in the absence of females), higher diet quality significantly increased calling effort and storage of lipid, glycogen, and carbohydrate (but not protein). The presence of females increased both the probability of calling and the amount of calling during the second week, whereas diet quality only improved calling effort. By the end of the second week, calling effort had decreased, even by high quality males in the presence of females, suggesting a depletion of resources. Furthermore, the loss of condition during week 2 covaried with calling effort during the previous week irrespective of diet. Males who started the second week in high condition lost more glycogen and carbohydrate than rivals; meanwhile, lipid accumulation covaried positively with calling effort during week 2. The contrasting patterns of storage and use for lipids compared to the ‘quick-release’ metabolites (glycogen and carbohydrates) affirms starkly distinct functions for the different storage components, and underlines the importance of specific physiological measures in life history research. Finally, in the general discussion, I attempt to synthesise my thesis’s contributions to the study of life history trade-offs involving behavioural sexual displays.

Des génotypes adaptés à des environnements contrastés ont de grandes chances de se comporter différemment lorsqu’ils sont placés dans des conditions similaires et contrôlées, notamment si leur sensibilité aux signaux environnementaux et/ou leur croissance intrinsèque sont limitées à différents niveaux. De ce fait, la variabilité observée dans les populations naturelles peut être utilisée comme une source illimitée de nouveaux allèles ou gènes pour l’étude des bases génétiques de la variation des traits quantitatifs. Mon travail de doctorat a consisté en l’analyse de la variabilité naturelle pour la croissance et la réponse à l’environnement chez Arabidopsis thaliana. Le but des approches de génétique quantitative est de comprendre comment la diversité génétique et épigénétique contrôle la variabilité phénotypique observée dans les populations à différentes échelles, au cours du développement et sous différentes contraintes environnementales. De plus, ces analyses ont pour objectif de comprendre comment les processus adaptatifs et démographiques influencent la fréquence de ces variants dans les populations en fonction de leur environnement local. Ainsi, l’étude de la variabilité naturelle peut être appréhendée en utilisant diverses approches, de la génétique et des méthodes de biologie moléculaire aux études écologiques et évolutives. Au cours de mon doctorat, j’ai eu la chance de travailler sur plusieurs de ces aspects au travers de trois projets indépendants qui exploitent tous la variabilité naturelle d’A. thaliana.Le premier projet a consisté en l’analyse du pattern de polymorphisme observé dans des populations d’A. thaliana au gène MOT1 qui code pour un transporteur de molybdate (la forme assimilable du molybdène (Mo), un micro-élément essentiel) et qui est responsable d’une partie des variations de croissance et de fitness observées à l’échelle de l’espèce en fonction de la disponibilité en Mo des sols. J’ai montré à différentes échelles géographiques que le pattern de polymorphisme à MOT1 ne reflète pas une évolution neutre mais présente plutôt des traces de sélection diversifiante. Ce travail a contribué à renforcer l’hypothèse selon laquelle des mutations au niveau du gène MOT1 pourraient avoir été sélectionnées dans certaines populations pour faire face aux niveaux élevés de Mo observés dans certains sols et potentiellement délétères malgré leur effet négatif sur des milieux pauvres en Mo.Le deuxième projet portait sur la caractérisation et l’analyse fonctionnelle de deux récepteur-kinase putatifs (RLK) identifiés de part leurs effets sur la croissance foliaire spécifiquement en réponse à un stress induit par du mannitol mais pas sous d’autres contraintes osmotiques. La fonction de ces récepteurs chez A. thaliana -qui n’est pas connu pour produire du mannitol- peut paraître intrigante. Les différentes expériences réalisées au cours de cette thèse nous ont cependant permis de construire un modèle selon lequel ces récepteurs pourraient être activés par le mannitol produit par certains pathogènes tel que les champignons et participer aux réponses de défense de la plante.Le troisième projet a été réalisé en collaboration avec l’équipe de Michel Vincentz (CBMEG, Brésil) et de Vincent Colot (IBENS, Paris) et consiste en l’analyse de l’occurrence de variants épigénétiques naturels au gène QQS dans différentes populations d’Asie Centrale et de leurs possibles conséquences phénotypique et adaptative.En conclusion, l’analyse des variants génétiques et épigénétiques naturels à l’origine des variations de biomasse en interaction avec l’environnement permet de comprendre comment l’évolution façonne la variabilité naturelle. / Genotypes adapted to contrasting environments are expected to behave differently when placed in common controlled conditions, if their sensitivity to environmental cues or intrinsic growth behaviour are set to different thresholds, or are limited at distinct levels. This allows natural variation to be exploited as an unlimited source of new alleles or genes for the study of the genetic basis of quantitative trait variation. My doctoral work focuses on analysing natural variation for shoot growth and response to the environment in A. thaliana. Natural variation analyses aim at understanding how molecular genetic or epigenetic diversity controls phenotypic variation at different scales and times of plant development and under different environmental conditions, and how selection or demographic processes influence the frequency of those molecular variants in populations for them to get adapted to their local environment. As such, the analysis of A. thaliana natural variation can be addressed using a variety of approaches, from genetics and molecular methods to ecology and evolutionary questions. During my PhD, I got the chance to tackle several of those aspects through my contributions to three independent projects which have in common to exploit A. thaliana natural variation. The first one is the analysis of the pattern of polymorphism from a set of 102 A. thaliana accessions at the MOT1 gene coding for a molybdate transporter (an essential micronutrient) and responsible for contrasted growth and fitness among accessions in response to Mo availability in the soil. I showed at different geographical scales that MOT1 pattern of polymorphisms is not consistent with neutral evolution and shows signs of diversifying selection. This work helped reinforce the hypothesis that in some populations, mutations in MOT1 have been selected to face soils rich in Mo and potentially deleterious despite their negative effect on Mo-limiting soils. The second project consists in the characterisation and functional analysis of two putative receptor-like kinases (RLKs) identified from their effect on shoot growth specifically under mannitol-supplemented media and not in response to other osmotic constraints. The function of such RLKs in A. thaliana, which is not known to synthesize mannitol was intriguing at first but, through different experiments, we built the hypothesis that those RLKs could be activated by the mannitol produced by some pathogens such as fungi and participate to plant defensive response. The third project, in collaboration with Michel Vincentz’s team from CBMEG (Brasil) and Vincent Colot (IBENS, Paris), consists in the analysis of the occurrence of natural epigenetic variants of the QQS gene in different populations from Central Asia and their possible phenotypic and adaptive consequences. Overall, these analyses of the genetic and epigenetic molecular variation leading to the biomass phenotype(s) in interaction with the environment provide clues as to how and where in the pathways adaptation is shaping natural variation.

Na última década, a podridão vermelha das raízes da soja (PVR), ou síndrome da morte súbita, causada pelo fungo Fusarium solani f.sp. glycines, tornou-se uma doença que é motivo de preocupação para os sojicultores, técnicos e pesquisadores nas regiões onde esta doença já foi constatada, sendo a única estratégia de controle viável a utilização de cultivares resistentes. Diante disto, o principal objetivo do presente trabalho foi o estudo do controle genético da reação da soja a PVR por meio de técnicas de genética clássica e molecular. Foi utilizada a geração F2 de um dialelo 5x5, sem os recíprocos, envolvendo cinco cultivares: Forrest, MG/BR-46 (Conquista), IAC-4, FT-Cristalina e FT-Estrela, sendo as duas primeiras mais resistentes a PVR que IAC-4, considerada moderadamente resistente e, as duas últimas, altamente suscetíveis. Além de testes de inoculação com as cultivares, foram conduzidos três experimentos com a geração F2: um em telado (semeadura em julho de 2001) e dois em casa de vegetação (semeadura em setembro de 2001 e julho de 2002), sendo os dois primeiros em blocos ao acaso e o terceiro no delineamento inteiramente casualizado. O patógeno foi inoculado com grãos de sorgo colonizados, colocando-se três grãos no fundo de cada cova, no momento da semeadura, fazendo-se cinco covas por vaso, cada qual constituindo uma parcela com cinco plantas. Em cada experimento, foram avaliadas individualmente 50 plantas de cada genitor e 150 plantas de cada cruzamento F2, entre os 30 e 40 dias após a emergência, utilizando-se uma escala de notas de 1 a 5 para a severidade dos sintomas foliares da PVR. A porcentagem de incidência da doença em cada parcela e um índice de doença também foram calculados. Nas análises de variância com os dados de médias de parcelas, observaram-se diferenças altamente significativas entre os genitores e entre populações F2 para a severidade e índice de doença dos sintomas foliares, na maioria dos casos, embora os genitores resistentes e suscetíveis não foram muito contrastantes. As cultivares Forrest e Conquista comportaram-se sempre como resistentes, e Cristalina e Estrela como suscetíveis, enquanto que IAC-4 apresentou comportamento instável. Pela análise dialélica de Jinks-Hayman reafirmou-se a influência do ambiente sobre o controle da resistência à manifestação dos sintomas foliares da PVR, a qual foi controlada quantitativamente. Nos experimentos de 2001, constatou-se apenas a ação de efeitos gênicos aditivos. Porém, no experimento conduzido em telado, a resistência demonstrou controle por genes recessivos, enquanto que na casa de vegetação, na maior parte, por genes dominantes. No experimento de 2002 constatou-se a presença de efeitos gênicos aditivos e de dominância, predominando o efeito destes últimos. Assim, com base no experimento de 2002, para o grupo de cultivares estudado, os parâmetros genéticos calculados permitiram verificar que: o grau médio de dominância indicou a presença de sobredominância; predominaram genes recessivos no grupo dos genitores; pelo menos três locos ou blocos gênicos que exibiram dominância foram responsáveis pelo controle da resistência a PVR; as herdabilidades estimadas no sentido restrito foram médias (0,33 a 0,62) e, no sentido amplo, altas (0,90 a 0,96), confirmando a presença de dominância; a resistência foi controlada, na maior parte, por genes dominantes e a ordem decrescente de dominância das cultivares foi a seguinte: 'Conquista', 'Cristalina', 'Forrest', 'Estrela' e 'IAC-4'; a exclusão de 'Cristalina', por suspeita de apresentar distribuição de genes correlacionada com 'Conquista' e 'Estrela', melhorou a adequação dos dados de índice de doença ao modelo genético aditivo-dominante de Jinks-Hayman. A utilização de cinco marcadores moleculares microssatélites (Satt163, Satt309, Satt354, Satt371 e Satt570), relatados como ligados a cinco QRLs da PVR, indicou a provável presença de multialelismo nestes locos, o que não invalidou a adequação dos dados ao modelo de Jinks-Hayman. Pela análise de ligação entre 126 indivíduos F2 do cruzamento 'Conquista' x 'Estrela' com os marcadores Satt163 e Satt354, no experimento conduzido em telado, houve ligação fraca (P<0,10) entre estes locos e os respectivos QRLs, havendo tendência dos alelos recessivos serem os responsáveis pelo controle da resistência nestes dois locos, concordando com os resultados da análise dialélica para este experimento. / In order to study the genetic control of soybean resistance to sudden death syndrome (SDS) by classical and molecular genetic techniques a 5x5 diallel with the F2 generation, without the reciprocals, was carried out. The following parents were used: 'Forrest', 'MG/BR-46 (Conquista)', 'IAC-4', 'FT-Cristalina' and 'FT-Estrela'. The first two cultivars are more resistant to SDS than 'IAC-4', that is considered to be moderately resistant to SDS, and the last two cultivars are highly susceptible. Tests of inoculation were done with the cultivars and three experiments with the F2 generation (two in 2001 and one in 2002) were carried out, all of them in greenhouses. The fungus was inoculated by three colonized sorghum grains placed at the bottom of the holes at the planting. It was used five-holes/clay pot, which one was considered a plot with five plants. In each experiment with the F2 generation 50 single plants of each parent and 150 single plants of each F2 population were evaluated between 30 and 40 days after emergency by using a scale (1 to 5) based on foliar severity symptoms. The disease incidence and a disease index also were calculated for each plot. In the ANOVAs with data plot average for severity and disease index highly significant differences were detected among the treatments in almost all cases, although the resistant and the susceptible parents did not differ too much. The parents 'Forrest' and 'Conquista' were always more resistant than the others. 'Cristalina' and 'Estrela' were the most susceptible parents, while 'IAC-4' was unstable. Jinks-Hayman's analysis reaffirmed the environment effect on the genetic control of the resistance to SDS foliar symptoms, which was quantitatively controlled. In the 2001 experiments there was observed only additive genic effects, but in one experiment recessive genes had controlled the resistance, while in the other, in major part, dominant genes had controlled the resistance to SDS. In the 2002 experiment it was showed mainly dominance effects and also some additive genic effects. In the last experiment, for the group of parents used, the genetic parameters indicated that: the average degree of dominance showed the presence of overdominance; there were more recessive than dominants genes in the group of the parents; at least three loci or genic blocks that exhibited dominance were responsible for the genetic control of the resistance to SDS; the heritability in the narrow-sense had middle values (0.33 to 0.62), and in the broad-sense had high values (0.90 to 0.96), reinforcing the presence of dominance effects; the resistance to SDS was controlled, mostly, by dominant genes; the decreasing order of dominance of the parents were: 'Conquista', 'Cristalina', 'Forrest', 'Estrela' and 'IAC-4'; and the exclusion of 'Cristalina' of the diallel for disease index by suspect of gene correlated distribution with 'Conquista' and 'Estrela' improved the fitting of the data to Jinks-Hayman's additive-dominant model. Five microsatellite markers (Satt163, Satt309, Satt354, Satt371 and Satt570), reported as linked to five SDS QRLs, were used and showed the possibility of occurrence of multiallelism in those loci, but this evidence did not invalidate the fitting of the data to Jinks-Hayman's model. The molecular analysis in 126 plants of 'Conquista' x 'Estrela' cross with the markers Satt163 and Satt354, in the first experiment of 2001, showed the tendency of weakly association (P<0,10), between those loci and the QRLs. This analysis showed also tendency that the recessive genes controlled the resistance to SDS in both loci, in according to the results obtained in the diallel analysis for this experiment.

Au cours de leur vie, les individus doivent constamment prendre des décisions qui peuvent fortement affecter leur valeur sélective. Pour optimiser leur prise de décisions, ces individus peuvent utiliser des informations soit issues de leurs propres interactions avec l’environnement (informations personnelles), soit issues de l’observation d’autres individus (informations sociales). La propension à utiliser des informations sociales et leur signification dépend certainement de paramètres individuels et environnementaux. Pour comprendre le potentiel évolutif de ce comportement à priori adaptatif, il est nécessaire de comprendre les causes de ces variations inter- et intra-individuelles. Le but de cette thèse était donc de déterminer les sources de variations individuelles dans l’utilisation d’information sociales hétérospécifiques pour le choix d’habitat de reproduction, chez le gobe-mouche à collier (Ficedula albicollis). A partir de données à long terme et d’expérimentations en nature dans la population de Gotland (Suède), j’ai montré que l’utilisation d’informations sociales n’est pas héritable dans cette population, mais dépend de l’âge et de l’agressivité des mâles, ainsi que de la taille de ponte des compétiteurs au moment où les gobe-mouches font leur choix. A partir d’une expérience de repasse, j’ai également montré que les femelles peuvent ajuster, en fonction de leur propre niveau d’agressivité, leur choix de site de nidification en fonction de caractéristiques de chants supposément liés à la qualité des mésanges charbonnières (Parus major). Cette thèse souligne l’importance de la personnalité dans l’utilisation d’informations sociales hétérospecifiques pour la sélection d’habitat de reproduction dans cette population, et montre que des caractéristiques fines de signaux à l’intention de congénères peuvent aussi être utilisées par d’autres espèces. Cela nous aide ainsi à mieux comprendre les mécanismes évolutifs de ce comportement / All their life, individuals have to make decisions that may strongly affect their fitness. To optimize their decisions, they can use personally acquired information but also information obtained from observing other individuals (“social information”). The propensity to gather and use social information and the information meaning might depend on both individual and environmental factors. Studying what drives within- and between-individual differences in social information use should help us understand the evolutionary potential of this supposedly adaptive behaviour. The aim of my PhD was to empirically investigate sources of variability in heterospecific social information use for breeding habitat selection. I worked on a natural population of collared flycatchers (Ficedula albicollis, Gotland Island, Sweden), a passerine species shown to cue on the presence, density, reproductive investment and nest site preference of dominant titmice for settlement decisions. Using both long term and experimental data, I showed that the use of heterospecific social information, measured as the probability to copy tit nest preference, is not heritable but depends on male age and aggressiveness and on tit apparent breeding investment at the time of flycatcher settlement. Using a playback experiment, I also showed that female flycatchers can fine-tune nest site choice according to (i) song features supposedly reflecting great tit (Parus major) quality and (ii) their own aggressiveness level. This thesis highlights the importance of personality in the use of heterospecific social information for breeding site selection in this population, and broadens the traditionally known sources of heterospecific information to fine song characteristics reflecting heterospecifics’ quality. To fully understand the evolutionary mechanisms and consequences of heterospecific social information use, genetically based plasticity and fitness consequences remains to be explored