La sélection génomique offre de nouvelles perspectives en amélioration des plantes pour la sélection de caractères complexes. Le travail proposé porte sur l’évaluation de son intérêt dans le cadre d’un programme de sélection réciproque pour la valeur d’hybrides entre deux groupes génétiques de maïs complémentaires. Il s’appuie sur un dispositif expérimental original constitué de 900 hybrides produits dans un plan factoriel entre deux dispositifs multiparentaux connectés. L’objectif de la sélection est d’améliorer le rendement ensilage des hybrides tout en améliorant leur digestibilité. Une réflexion sur les modèles permettant de prédire la valeur hybride sera conduite et testée sur les données expérimentales et par simulations. Ce travail, conduit en collaboration avec sept sociétés de sélection (au sein de PROMAÏS) devrait permettre d’améliorer les dispositifs de sélection classiques et de produire des hybrides d’intérêt agronomique. Il s’inscrit dans le cadre plus général de l’amélioration pour la valeur en croisement commune à de nombreuses espèces végétales allogames et à certaines espèces animales. / Genomic selection opens new prospects in plant breeding for the selection of complex traits. The proposed study aims to evaluate its efficiency in the context of a reciprocal selection schemes for the hybrid value between two complementary maize groups. The work will rely on an original experimental design including 900 hybrids produced from a factorial between two multiparental connected designs. The selection objective is to increase the hybrids silage yield as well as their digestibility. Several models for the hybrid value prediction will be proposed and tested on the experimental data and by simulations. This study, carried out in close connection with seven plant breeding companies (members of PROMAÏS) will contribute to the improvement of breeding designs and will produce new interesting hybrids. It falls within the general context of the selection for hybrid value which is common to numerous plant allogamous species and animal species.

Le maïs (Zea mays L.) est la plante la plus cultivée au monde. Pour valoriser le fort effet d’hétérosis pour les caractères liés à la biomasse, la diversité génétique du maïs est structurée en groupes hétérotiques et les variétés cultivées sont majoritairement des hybrides F1 entre lignées de groupes complémentaires. La valeur hybride se décompose comme la somme de l’Aptitude Générale à la Combinaison (AGC) de chacune des lignées parentales et de l’Aptitude Spécifique à la Combinaison (ASC) du couple. En Europe du Nord, le maïs est souvent utilisé en ensilage destiné à l'alimentation animale. L’objectif de sélection est d’améliorer la productivité et d'assurer une bonne digestibilité du maïs ensilage. Les objectifs de cette thèse étaient : (i) d’estimer l’importance de l’AGC et de l’ASC dans la variance génétique hybride pour les caractères de qualité de l’ensilage, (ii) d’identifier les locus (QTL) impliqués dans ces caractères et d’étudier leur colocalisation avec des QTL de productivité, (iii) d’évaluer l’intérêt de la sélection génomique pour la prédiction des performances hybrides et (iv) de comparer l’efficacité de deux dispositifs de calibration des prédictions basés sur un factoriel ou l’utilisation classique de testeurs du groupe complémentaire. Dans le cadre du projet SAM-MCR, 6 familles biparentales connectées ont été créés dans les groupes « corné » et « denté » à partir de 4 lignées fondatrices. Dans une première phase, 822 lignées cornées et 802 dentées ont été génotypées pour 20k SNP et croisées selon un factoriel incomplet pour produire 951 hybrides, phénotypés pour des caractères de qualité et de productivité (étudiés par H. Giraud pendant sa thèse). L’analyse des caractères de qualité a montré une prédominance de l’AGC par rapport à l’ASC ainsi qu’une corrélation négative entre les caractères de qualité et le rendement. De nombreux QTLs multi-alléliques ont été détectés, la plupart spécifiques d’un groupe et dont certains colocalisent avec des QTL de rendement. Par validation croisée, la qualité de prédictions basées sur les QTL détectés s’est avérée plus faible que celle obtenue par prédiction génomique. La prise en compte de l’ASC n‘a pas permis d’améliorer sensiblement la qualité de prédictions des modèles. Dans une seconde phase, 90 lignées ont été choisies par groupe : 30 sélectionnées sur la base de leurs prédictions génomiques pour la productivité et la valeur énergétique et 60 choisies aléatoirement parmi les 6 familles. Ces lignées ont été croisées selon un factoriel incomplet pour produire 360 nouveaux hybrides : 120 issus des lignées sélectionnées et 240 issus des lignées choisies au hasard. Les 90 lignées de chaque groupe ont aussi été croisées à deux lignées fondatrices du groupe complémentaire (testeurs). Les hybrides issus des lignées sélectionnées se sont avérés plus productifs mais de moins bonne qualité. Nous avons confirmé la bonne qualité des prédictions génomiques obtenus dans le factoriel initial sur les nouveaux hybrides évalués dans d’autres environnements et après sélection et observé une bonne corrélation entre les AGC estimées dans le factoriel et dans le dispositif testeurs. Des dispositifs factoriels et testeurs ont été simulés en faisant varier la part d’ASC, le nombre d’hybrides et la contribution de chaque lignée dans le jeu de calibration. A moyens expérimentaux égaux, le dispositif factoriel s’est avéré plus efficace en termes de capacité prédictive et de gain génétique cumulé que le dispositif testeur (jusqu’à +50%) pour un caractère présentant de l’ASC et équivalent pour un caractère purement additif. Les résultats de cette thèse ouvrent de nouvelles perspectives pour revisiter les schémas de sélection hybrides en remplaçant l’évaluation des lignées candidates, classiquement faite sur testeur, par l’évaluation directe d’hybrides issus d’un factoriel incomplet. La mise en œuvre de tels dispositifs nécessitera de réorganiser la logistique des programmes de sélection. / Maize (Zea mays L.) is the most cultivated crop in the world. To exploit the strong heterosis for traits related to biomass, the genetic diversity of maize is structured into heterotic groups and cultivated varieties are mainly F1 hybrids obtained by crossing lines from complementary groups. The hybrid value can be decomposed as the sum of the General Combining Ability (GCA) of each parental line and the Specific Combining Ability (ASC) of the cross. In northern Europe, maize is often used as silage for animal feed and the breeding objective is to improve productivity while ensuring a good energetic value and digestibility of the silage. The objectives of this thesis were: (i) to estimate the importance of GCA and SCA in hybrid genetic variance for silage quality traits, (ii) to identify loci (QTL) involved in these traits and to study their colocalization with QTL for productivity traits, (iii) to evaluate the interest of genomic selection for the prediction of hybrid performances and (iv) to compare the prediction accuracies of two calibration designs either based on a factorial or on the conventional use of testers from the complementary group. As part of the SAM-MCR project, 6 biparental connected families were created in the "flint" and "dent" groups from 4 founder lines. In a first phase, 822 flint and 802 dent lines were genotyped for 20k SNPs and crossed according to an incomplete factorial to produce 951 hybrids which were phenotyped for quality traits and for productivity traits (studied by H. Giraud during her phD). Quality trait analysis showed a predominance of GCA over SCA and a negative correlation between digestibility traits and silage yield. Several multi-allelic QTLs were detected, most of them being specific to one group. Several colocalizations were found with yield QTL. Using cross-validation, we observed that the predictive ability of models based on detected QTLs was lower than that obtained by genomic predictions. Considering the SCA did not improve model predictive abilities for most of the traits. In a second phase, 90 lines were chosen per group: 30 were selected based on their genomic predictions for productivity and the energetic value and 60 were randomly sampled from the 6 families. These lines were crossed according to an incomplete factorial to produce 360 new hybrids: 120 from selected lines and 240 from randomly chosen lines. The 90 lines of each group were also crossed to two lines of the complementary group (testers). Hybrids from the selected lines were more productive but had a lower silage quality. We confirmed the good accuracy of the genomic predictions obtained in the initial factorial on the new hybrids evaluated in other environments and after selection. We also observed good correlations between GCA estimated in the factorial and in the testcross design. Different factorial and testcross designs were simulated by varying the proportion of dominance/SCA, the number of hybrids and the contribution of each line to the calibration set. Considering the same number of hybrids in the calibration set, the factorial was more efficient in terms of predictive ability and cumulative genetic gain (up to + 50%) than the testcross design for traits showing SCA and was similar for purely additive traits. The results of this thesis open new perspectives to revisit hybrid breeding schemes by replacing the evaluation of candidate lines, classically made on testcross, by the direct evaluation of hybrids resulting from an incomplete factorial. The implementation of such designs will require reorganizing the logistics of selection programs.

Rice is one of the most important cereal crops for the world population. Flowering time and seed development of rice are directly related to plant regional and ecological adaptions, and productive yield. In this dissertation, to gain knowledge of seed development in rice, the status of post-translational modifications (PTMs) in developing rice seeds was investigated. Numerous modified lysine sites in developing rice seeds were identified utilizing antibody-based affinity enrichment approaches and nano-HPLC/MS/MS analyses of acetylated, succinylated, crotonylated and 2-hydroxyisobutyrylated peptides. Functional annotation analyses indicated that a wide variety of vital biological processes were targeted by lysine PTMs. A number of modified histone and non-histone proteins were found to harbor multiple PTMs, and our findings showed that many modified histone sites were conserved across plant, human, and animal systems. Comprehensive analyses of lysine modification sites illustrated that the sites were highly sequence-specific for distinct motifs. Overall, this study provides a systematic analysis of lysine PTM proteome in plants, which will serve as the basis for future investigations of the regulatory mechanisms and functions of lysine PTMs. The mechanisms of flowering time variances in response to different photoperiods were further studied in the rice mutant, HSS. QTL-seq analysis identified a major effect on chromosome 6 responsible for the phenotypic divergence between Nipponbare (wild-type) and HSS rice. Sequence and mRNA expression analyses confirmed that allelic variants of Hd1 make HSS plants less sensitive to photoperiod by altering expression level of Hd3a. Diurnal expression pattern analyses revealed that DTH8 transcripts were largely affected by Hd1 expression level in both LD and SD. This result suggested that Hd1 may able to regulate DTH8 and DTH8-Hd1 complex abundance in response to day length in rice flowering time regulation. In addition, we discussed the functions of PTMs in flowering time regulation in rice.

Caracteres quantitativos possuem herança complexa, que envolvem efeitos epistáticos, pleiotrópicos e interação com ambientes. Em razão da importância desses caracteres para o melhoramento genético, diversos estudos sobre sua natureza genética e herança têm sido conduzidos. Nesse contexto, o mapeamento de QTL é uma ferramenta útil, que permite mapear e estimar os efeitos dos locos que controlam os caracteres quantitativos além de obter outras importantes informações, como a ocorrência de QTL pleiotrópicos e interações QTL x ambientes. Os objetivos do presente trabalho foram mapear QTL e obter informações sobre a interação QTL x ambientes, QTL pleiotrópicos e herança de diversos caracteres de importância agronômica em uma população de milho tropical. Foram utilizadas 250 progênies F2:3 retrocruzadas para ambos os genitores conforme proposto no delineamento III, totalizando 500 progênies, as quais foram avaliadas em até seis ambientes. Para o mapeamento de QTL foi empregado o mapeamento por intervalo composto expandido para múltiplos ambientes ou caracteres (mCIM), considerando um mapa genético com 177 marcadores microssatélite. Os caracteres analisados foram produção de grãos (PG), prolificidade (PROL), peso de 500 grãos (P500), número de fileiras da espiga (NF) e de grãos por fileira (NGF), altura de planta (AP) e espiga (AE), dias para o florescimento feminino (FF) e masculino (FM), número de ramificações do pendão (RP) e stay green (SG). Os resultados das análises do delineamento III indicaram sobredominância para o caráter PG, dominância completa para NGF e dominância parcial para os demais caracteres. Estimativas elevadas de correlações genéticas foram obtidas entre os caracteres PG, PROL, NGF, FF, FM, AP e AE, sugerindo ocorrência de pleiotropia entre tais caracteres. No mapeamento considerando múltiplos ambientes foram mapeados 260 QTL para os onze caracteres analisados, distribuídos por todos os cromossomos do milho. O grau médio de dominância dos QTL foi de sobredominância para PG e AP, e dominância completa ou parcial para os demais caracteres. Devido ao desequilíbrio de ligação nesta população e ao modelo de mapeamento empregado, as estimativas que indicaram sobredominância foram, provavelmente, superestimadas. Para os caracteres PG, NF, NGF, P500, AE e SG, a maioria dos QTL mapeados interagiu significativamente com ambientes, indicando que experimentos conduzidos em vários locais e anos são necessários para identificar genótipos e QTL estáveis. Esses resultados sugerem que devido à elevada interação QTL x ambientes dos caracteres avaliados, os programas de melhoramento e a utilização de seleção assistida por marcadores (SAM) devem ser direcionados para ambientes específicos. No mapeamento de múltiplos caracteres foram identificados 43 QTL com efeitos significativos para dois ou mais caracteres analisados, distribuídos em todos os cromossomos do milho. A quantidade de QTL pleiotrópicos para combinações entre pares de caracteres não foi consistente com as magnitudes das correlações observadas. Em geral, para cada caráter, os QTL pleiotrópicos apresentaram magnitudes e graus de dominância distintos. Portanto, embora diversos QTL pleiotrópicos tenham sido mapeados, suas magnitudes e efeitos distintos para cada caráter indicaram grande complexidade da natureza genética das correlações, constituindo-se em um desafio para uso das informações desses QTL na SAM visando o melhoramento de múltiplos caracteres. / Quantitative traits have complex inheritance, including effects of epistasis, pleiotropy and interaction with environments. Due to the importance of these traits for plant breeding, many studies on their inheritance have been conducted. In this context, QTL mapping is a useful tool that allows mapping and estimating the effects of loci that control the quantitative traits besides obtaining other important information, such as the occurrence of pleiotropic QTL and QTL x environments interactions. The aims of the present study were to map QTL, obtain information about the QTL x environments interaction and the pleiotropic QTL of several relevant traits in a tropical maize population, using the design III. Two hundred and fifty F2:3 progenies backcrossed to both parents were used as proposed in the design III, totaling 500 progenies, which were evaluated in up to six environments. The components of the genetic variances and average degree of dominance were estimated using the design III. The QTL mapping was performed considering a genetic map with 177 microsatellite markers and the multi-trait composite interval mapping (mCIM). The evaluated traits were: grain yield (GY), prolificacy (PROL), 500 kernel weight (W500), kernel row number (KRN), number of kernel per row (NK), plant height (PH), ear height (EH), days to silk emergence (DS), days to anthesis (DA), number of tassel branches (NTB) and stay green (SG). The results from design III indicated occurrence of overdominance for GY, complete dominance for NK and dominance for the others traits. Higher genetic correlations were observed among GY, PROL, NK, DS, DA, PH and EH, suggesting occurrence of pleiotropy. The QTL mapping for multiple environments mapped 260 QTL for the eleven analyzed traits, distributed in all chromosomes. The average degree of QTL dominance was overdominance for GY and PH, and complete or partial dominance for the other traits. Estimates that indicated overdominance are probably biased due to the linkage disequilibrium in this population and the mapping model employed. For GY, KRN, NK, W500, EH and SG, most mapped QTL interacted significantly with environments, indicating that it is necessary to conduct experiments at many locations and years to identify stable QTL. These results suggests that, due to high number of QTL that showed significant interaction with the environment, assisted marker selection (MAS) must be targeted to specific geographic regions. The QTL mapping for multiple traits identified 43 pleiotropic QTL for two or more analyzed traits, distributed in all chromosomes of maize. The amount of pleiotropic QTL for combinations of pairs of traits was not consistent with the magnitudes of the observed correlations. In general, for each trait, the pleiotropic QTL exhibited different magnitude and estimate of the degree of dominance. Although several pleiotropic QTL have been mapped, their distinct magnitudes and effects on each trait indicated the great complexity of the genetic nature of the correlations, constituting a challenge to use QTL information in the MAS for simultaneous improvement of multiple traits.

Caracteres quantitativos possuem herança complexa, que envolvem efeitos epistáticos, pleiotrópicos e interação com ambientes. Em razão da importância desses caracteres para o melhoramento genético, diversos estudos sobre sua natureza genética e herança têm sido conduzidos. Nesse contexto, o mapeamento de QTL é uma ferramenta útil, que permite mapear e estimar os efeitos dos locos que controlam os caracteres quantitativos além de obter outras importantes informações, como a ocorrência de QTL pleiotrópicos e interações QTL x ambientes. Os objetivos do presente trabalho foram mapear QTL e obter informações sobre a interação QTL x ambientes, QTL pleiotrópicos e herança de diversos caracteres de importância agronômica em uma população de milho tropical. Foram utilizadas 250 progênies F2:3 retrocruzadas para ambos os genitores conforme proposto no delineamento III, totalizando 500 progênies, as quais foram avaliadas em até seis ambientes. Para o mapeamento de QTL foi empregado o mapeamento por intervalo composto expandido para múltiplos ambientes ou caracteres (mCIM), considerando um mapa genético com 177 marcadores microssatélite. Os caracteres analisados foram produção de grãos (PG), prolificidade (PROL), peso de 500 grãos (P500), número de fileiras da espiga (NF) e de grãos por fileira (NGF), altura de planta (AP) e espiga (AE), dias para o florescimento feminino (FF) e masculino (FM), número de ramificações do pendão (RP) e stay green (SG). Os resultados das análises do delineamento III indicaram sobredominância para o caráter PG, dominância completa para NGF e dominância parcial para os demais caracteres. Estimativas elevadas de correlações genéticas foram obtidas entre os caracteres PG, PROL, NGF, FF, FM, AP e AE, sugerindo ocorrência de pleiotropia entre tais caracteres. No mapeamento considerando múltiplos ambientes foram mapeados 260 QTL para os onze caracteres analisados, distribuídos por todos os cromossomos do milho. O grau médio de dominância dos QTL foi de sobredominância para PG e AP, e dominância completa ou parcial para os demais caracteres. Devido ao desequilíbrio de ligação nesta população e ao modelo de mapeamento empregado, as estimativas que indicaram sobredominância foram, provavelmente, superestimadas. Para os caracteres PG, NF, NGF, P500, AE e SG, a maioria dos QTL mapeados interagiu significativamente com ambientes, indicando que experimentos conduzidos em vários locais e anos são necessários para identificar genótipos e QTL estáveis. Esses resultados sugerem que devido à elevada interação QTL x ambientes dos caracteres avaliados, os programas de melhoramento e a utilização de seleção assistida por marcadores (SAM) devem ser direcionados para ambientes específicos. No mapeamento de múltiplos caracteres foram identificados 43 QTL com efeitos significativos para dois ou mais caracteres analisados, distribuídos em todos os cromossomos do milho. A quantidade de QTL pleiotrópicos para combinações entre pares de caracteres não foi consistente com as magnitudes das correlações observadas. Em geral, para cada caráter, os QTL pleiotrópicos apresentaram magnitudes e graus de dominância distintos. Portanto, embora diversos QTL pleiotrópicos tenham sido mapeados, suas magnitudes e efeitos distintos para cada caráter indicaram grande complexidade da natureza genética das correlações, constituindo-se em um desafio para uso das informações desses QTL na SAM visando o melhoramento de múltiplos caracteres. / Quantitative traits have complex inheritance, including effects of epistasis, pleiotropy and interaction with environments. Due to the importance of these traits for plant breeding, many studies on their inheritance have been conducted. In this context, QTL mapping is a useful tool that allows mapping and estimating the effects of loci that control the quantitative traits besides obtaining other important information, such as the occurrence of pleiotropic QTL and QTL x environments interactions. The aims of the present study were to map QTL, obtain information about the QTL x environments interaction and the pleiotropic QTL of several relevant traits in a tropical maize population, using the design III. Two hundred and fifty F2:3 progenies backcrossed to both parents were used as proposed in the design III, totaling 500 progenies, which were evaluated in up to six environments. The components of the genetic variances and average degree of dominance were estimated using the design III. The QTL mapping was performed considering a genetic map with 177 microsatellite markers and the multi-trait composite interval mapping (mCIM). The evaluated traits were: grain yield (GY), prolificacy (PROL), 500 kernel weight (W500), kernel row number (KRN), number of kernel per row (NK), plant height (PH), ear height (EH), days to silk emergence (DS), days to anthesis (DA), number of tassel branches (NTB) and stay green (SG). The results from design III indicated occurrence of overdominance for GY, complete dominance for NK and dominance for the others traits. Higher genetic correlations were observed among GY, PROL, NK, DS, DA, PH and EH, suggesting occurrence of pleiotropy. The QTL mapping for multiple environments mapped 260 QTL for the eleven analyzed traits, distributed in all chromosomes. The average degree of QTL dominance was overdominance for GY and PH, and complete or partial dominance for the other traits. Estimates that indicated overdominance are probably biased due to the linkage disequilibrium in this population and the mapping model employed. For GY, KRN, NK, W500, EH and SG, most mapped QTL interacted significantly with environments, indicating that it is necessary to conduct experiments at many locations and years to identify stable QTL. These results suggests that, due to high number of QTL that showed significant interaction with the environment, assisted marker selection (MAS) must be targeted to specific geographic regions. The QTL mapping for multiple traits identified 43 pleiotropic QTL for two or more analyzed traits, distributed in all chromosomes of maize. The amount of pleiotropic QTL for combinations of pairs of traits was not consistent with the magnitudes of the observed correlations. In general, for each trait, the pleiotropic QTL exhibited different magnitude and estimate of the degree of dominance. Although several pleiotropic QTL have been mapped, their distinct magnitudes and effects on each trait indicated the great complexity of the genetic nature of the correlations, constituting a challenge to use QTL information in the MAS for simultaneous improvement of multiple traits.

Master of Science / Department of Statistics / Gary L. Gadbury / QTL (quantitative-trait locus) analysis aims to locate and estimate the effects of genes that are responsible for quantitative traits, such as grain protein content and yield, by means of statistical methods that evaluate the association of genetic variation with trait (phenotypic) variation. Quantitative traits are typically polygenic, i.e., controlled by multiple genes, with varying degrees of in uence on the phenotype. Several methods have been developed to increase the accuracy of QTL location and effect estimates. One of them, multiple interval mapping (MIM) (Kao et al. 1999), has been shown to be more accurate than conventional methods such as composite interval mapping (CIM) (Zeng 1994). Other QTL analysis methods have been developed to perform additional analyses that might be useful for breeders, such as of pleiotropy and QTL-by-environment (QxE) interaction. It has been shown (Jiang and Zeng 1995) that these analyses can be carried out with a multivariate extension of CIM (MT-CIM) that exploits the correlation structure in a set of traits. In doing so, this method also improves the accuracy of QTL location detection. This thesis describes the multivariate extension of MIM (MT-MIM) using ideas from MT-CIM. The development of additional multivariate tests, such as of pleiotropy and QxE interaction, and several methods pertinent to the development of MT-MIM are also described. A small simulation study shows that MT-MIM is more accurate than MT-CIM and univariate MIM. Results for real data show that MT-MIM is able to provide a more accurate and precise estimate of QTL location.

BACKGROUND: Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. RESULTS: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F₂:₃ progenies and identified one major QTL and three minor QTLs. CONCLUSION: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

The goal of this thesis is to explore, improve and implement some advanced modern computational methods in statistics, focusing on applications in genetics. The thesis has three major directions. First, we study likelihoods for genetics analysis of experimental populations. Here, the maximum likelihood can be viewed as a computational global optimization problem. We introduce a faster optimization algorithm called PruneDIRECT, and explain how it can be parallelized for permutation testing using the Map-Reduce framework. We have implemented PruneDIRECT as an open source R package, and also Software as a Service for cloud infrastructures (QTLaaS). The second part of the thesis focusses on using sparse matrix methods for solving linear mixed models with large correlation matrices. For populations with known pedigrees, we show that the inverse of covariance matrix is sparse. We describe how to use this sparsity to develop a new method to maximize the likelihood and calculate the variance components. In the final part of the thesis we study computational challenges of psychiatric genetics, using only pedigree information. The aim is to investigate existence of maternal effects in obsessive compulsive behavior. We add the maternal effects to the linear mixed model, used in the second part of this thesis, and we describe the computational challenges of working with binary traits. / eSSENCE

Many phenotypes are controlled by factors which include the genes, the environment, interactions between genes and interaction between the genotypes and the environment. Great strides have been made to understand how these various factors affect traits of agricultural, medical and environmental importance. The chicken is regarded as a model organism whose study would not only assist efforts towards increased agricultural productivity but also provide insight into the genetic determination of traits with potential application in understanding human health and disease. Detection of genomic regions or loci responsible for controlling quantitative traits (QTL) in poultry has focussed mainly on growth and production traits with limited information on reproductive traits. Most of the reported results have used additive-dominance models which are easy to implement because they ignore epistatic gene action despite indications that it may be important for traits with low heritability and high heterosis. The thesis presents results on the detection of loci and genetic mechanisms involved in sexual maturity traits through modelling both additive-dominance gene actions and epistasis. The study was conducted on an F2 broiler x White Leghorn layer cross for QTL detection for age, weight, abdominal fat, ovary weight, oviduct weight, comb weight, number of ovarian yellow follicles, a score for the persistence of the right oviduct and bone density. In addition, body weight QTL at 3, 6, 12, 24, 48 and 72 weeks of age, QTL for growth rate between the successive ages and QTL for the parameters of the growth curve were also detected. Most of the QTL for traits at sexual maturity acted additively. A few of the QTL explained a modest proportion of the phenotypic variation with most of the QTL explaining a small component of the cumulative proportion of the variation explained by the QTL. Body weight QTL were critical in determining the attainment of puberty. The broiler allele had positive effects on weight at first egg and negative effects on age at first egg. Most QTL affecting weight at first egg overlapped with QTL for age at first egg and for early growth rate (6-9 weeks) suggesting that growth rate QTL are intimately related to the onset of puberty. Specific QTL for early and adult growth were detected but most QTL had varying influence on growth throughout life. Chromosome 4 harboured most of QTL for the assessed traits which explained the highest proportion of the phenotypic variation in the traits confirming its critical role in influencing traits of economic importance. There was no evidence for epistasis for almost all the studied traits. Evidence for role of epistasis was significant for ovary weight and suggestive for both growth rate and abdominal fat.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.