Dissertations / Theses on the topic 'QTL analysi'

Brown rot (BR) disease, caused by Monilinia spp., causes significant pre-and post-harvest losses in stone fruit production, especially in humid and warm temperatures. In this thesis, we tried to tackle the subject with three complementary approaches. First, the recent progress in BR resistance in peach fruit was reviewed. Then we highlighted best practices in phenotyping BR susceptibility/resistance procedures in field and in vitro. We concluded that the main factors contributing to disease development are Monilinia inocula availability, environmental conditions, cultivars, fruit stage and management practices. Secondly, we investigated the anti-fungal effect of some phenolics such as chlorogenic and ferulic acids and triterpenoids such as oleanolic, betulinic, and ursolic acids. Furthermore, fruit surface compound (FSC) extracts of peach fruit at two developmental stages on Monilinia fructicola and M. laxa characteristics during in vitro growth were studied. A new procedure for assaying anti-fungal activity of triterpenoids, which are notoriously difficult to assess in vitro because of their hydrophobicity, has been developed. Also, a follow-up of this study revealed that certain phenolics and triterpenoids showed modest anti-fungal activity while dramatically modulating M. fructicola gene expression. MfRGAE1 gene was overexpressed by chlorogenic and ferulic acids and MfCUT1 by betulinic acid at 4- and 7-days post-inoculation. The third objective was to investigate the genetic background responsible for disease resistance in peach by detecting Quantitative Trait Loci (QTL) and attempts to identify molecular markers for assisted selection (MAS) in peach. For this, three F2 progenies, derived from three selfied F1 selections obtained from "Contender" (C, resistant) × "Elegant Lady" (El, susceptible), were investigated for two seasons (2019 and 2021). The whole progeny was genotyped by Single-Primer Enriched Technology (SPET) and a recently developed 18K SNP array. The genome-wide QTL analysis showed intriguing areas relevant to disease resistance, mainly the QTLs on chromosomes 2 and 4, which may be candidates for future MAS applications. Several new QTLs were detected for other fruit quality traits, including maturity date, soluble solid content and fruit weight.

Les buts de cette thèse étaient l'acquisition de connaissances sur l'architecture génétique de caractères complexes et l'étude de la variabilité des taux de recombinaison chez le porc. La première partie de cette thèse présente une analyse sur l'ensemble du génome des locus influençant des caractères quantitatifs (QTL) au sein de croisements F2 entre des verrats de race Duroc blanc et des truies Erhulian, protocole développé en Chine à l'université d'agriculture du Jiangxi (JXAU). La population étudiée dans le cadre de cette thèse regroupe de 750 à 1030 animaux F2 mesurés sur 80 caractères concernant la composition de la carcasse (17 caractères), la qualité de la viande (58 caractères) et les caractères morphologiques des oreilles (5 caractères). Au total nous avons identifié 253 QTL pour ces caractères, dont la moitié est significatif au niveau du génome entier. Les chromosomes rassemblant le plus de QTL pour ces caractères sont les chromosomes 4, 7, 8 & X. Les niveaux de signification les plus élevés sont observés pour un (ou des) QTL affectant la longueur de carcasse, le poids de la tête et le poids des oreilles situé au sein d'un intervalle de 3 cM situé sur le chromosome 7 (Sw1856-S0066) expliquant jusqu'à 50 % de la variance phénotypique. L'allèle Duroc blanc étant l'allèle favorable pour une majorité des QTL affectant la composition de la carcasse, tandis que les allèles favorables pour la qualité de la viande présentent des origines tantôt asiatique tantôt européenne. L'INRA avait réalisé il y a près de 20 ans un programme de détection de QTL entre animaux Large White & Meishan. La localisation parallèle sur le chromosome X de QTL influençant l'engraissement et la muscularité des animaux au sein des pédigrées français et chinois nous a amené a travaillé sur la cartographie fine de ce(s) QTL qui a été développée dans la deuxième partie de cette thèse réalisée en cotutelle. Dans un premier temps afin de préciser la position du QTL située sur le chromosome X, nous avons étudié les variations de taux de recombinaison entre différentes régions du chromosome ainsi que les variations inter individuelles. .
The aims of this thesis are to gain knowledge on genetic architecture of complex traits and on fine-scale structure of recombination rate variation in pigs. The first part of this thesis presents a genome-wide scan for quantitative trait loci (QTL) in a cross between White Duroc boars and Erhualian sows that was developed at Jiangxi Agricultural University (JXAU) in China. The mapping population comprised 750-1030 F2 individuals that were evaluated for a total of 80 traits related to carcass composition (17 traits), meat quality (58 traits) and ear traits (5 traits). In total, we identified 253 QTL for these traits, of which about half reached genome-wide significance level. Numerous QTL for these traits have been found on porcine chromosomes 4, 7, 8 and X. The greatest significance levels were found for a QTL affecting carcass length, head weight and ear weight on SSC7 in an interval of 3 cM (SW1856-S0666), which explained up to 50% of the phenotypic variance. White Duroc alleles at a majority of QTL detected were favorable for carcass composition, while favorable QTL alleles for meat quality originated from both White Duroc and Erhualian. INRA performed a genome scan to reveal QTL in a Large White × Meishan cross 8 years ago. Coincidently, both INRA and JXAU mapped strong QTL for fatness and muscling traits in a similar region of the porcine chromosome X (SSCX). Thus, both sides wished to collaborate to fine map the QTL. .

Ziel der vorliegenden Arbeit war die Identifizierung genetischer Faktoren, die das Plasmaproteom regulieren. Die Untersuchungen wurden im Modellsystem einer F2-Kreuzung zweier Inzucht-Mausstämme (FVB.LDLR-/-, C57BL/6.LDLR-/-) durchgeführt, die sich in ihrer Atheroskleroseausprägung unterscheiden. Von jedem der 453 Tiere der F2-Generation wurden Plasmaproteomprofile mittels Massenspektrometrie (MALDI-TOF) generiert. Diese Spektren wurden in zwei unabhängigen Datenanalysen ausgewertet und eine Kopplungsanalyse (QTL-Analyse, quantitative trait loci) der Phänotypen mit jeweils 192 genetischen Markern in jedem der F2-Tiere durchgeführt. So wurden die Datensätze von Proteom und Genom miteinander kombiniert, um Genorte, die mit unterschiedlich regulierten Proteinen in Verbindung stehen, zu identifizieren. Dieser Ansatz ist bisher in der Literatur nicht beschrieben worden. In der vorliegenden Arbeit wird sowohl die Methodik der statistischen Auswertung als auch die weitere Analyse der generierten Daten beschrieben. Es wurden zahlreiche hochsignifikante Kopplungssignale gefunden, von denen zwei durch die Identifizierung von Proteinen verifiziert werden konnten. Es handelt sich hierbei um das Apo-A2 des HDL auf Chromosom 1 und Hämoglobin subunit alpha auf Chromosom 11. Eine Kolokalisation der gefundenen Proteine mit Loci der Atherosklerosedisposition konnte nicht identifiziert werden. Dieser Ansatz zeigt erstmals, dass eine hypothesenfreie Verbindung proteomischer und genomischer Daten möglich ist und zur Identifizierung genetisch regulierter Plasmaproteine beitragen kann.

Cette thèse avait pour but de préciser les facteurs génétiques responsables des différences de cortisolémie entre les races de porc Meishan et Large White. Lors d'études précédentes d'analyse de liaisons génétiques sur le croisement F2 Meishan x Large White, un QTL influençant les taux de cortisol basal et induit par un stress a été cartographié sur le chromosome 7 porcin. Par l'analyse comparative des cartes humaine, murine et porcine nous avons révélé la présence d'un gène candidat positionnel codant pour la transcortine ou CBG (corticosteroid binding globulin). En premier lieu nous avons vérifié la localisation de ce gène chez le porc. Cela a été réalisé d'abord par cartographie sur des panels d'hybrides somatiques et irradiés à l'aide d'un fragment du gène Cbg. De plus ce fragment de Cbg porcin nous a servi pour isoler un clone BAC que nous avons utilisé pour cartographier ce gène par hybridation in situ sur un étalement de chromosomes porcins. L'ensemble de ces techniques nous a permis de localiser la CBG porcine en 7q26, entre les marqueurs flanquant le QTL de cortisolémie. L'évaluation de paramètres de liaison de la transcortine pour le cortisol (fait par la technique de radioliaison en utilisant la Concanavaline A-Sepharose) a montré que les porcs de race Meishan possédaient une capacité maximale de la CBG plasmatique pour le ligand 1. 6 fois supérieure à celle des porcs de race Large White. Les mêmes mesures biochimiques sur la population de porcs F2 ont abouti à l'établissement d'une liaison génétique forte entre les taux de la CBG et la même région du chromosome 7q24-q26 où le QTL de cortisolémie a été placé. Les études moléculaires ont montré l'absence de variation de l'expression des ARNm Cbg entre les deux races porcines. Nous avons déterminé la séquence de la partie codante et promotrice du gène Cbg porcin. Les premiers résultats d'analyse d'haplotype du gène Cbg (partie promotrice, codante et 3'UTR) chez les porcs F1 et leurs parents sont discutés
This thesis was directed to precise the genetic factors underlying the variations of cortisol levels vetween pig races Large White and Meishan. Previous studies had identified on chromosome 7 a QTL associated with the levels of cortisol, basal and after a novelty stress. Comparative mapping data between human, mouse and pig genomes has suggested that transcortine or CBG (corticosteroid binding globulin) incoding gene might be a causal gene for this QTL. Firstly, using a porcine Cbg gene fragment we have mapped the porcine Cbg gene on somatic cell hybrid and radiation hybrid panels. Thereafter isolation of a BAC Cbg clone using the same DNA probe has allowed us to localise the gene Cbg on pig metaphase chromosomes by FISH. These methods together has assigned the Cbg gene to band q26 of pig chromosome 7, between the markers flanking the QTL associated with cortisol levels. Estimation of transcortin binding parameters realised using cortisol binding capacity assay after absorption on solid phase (concanacalin A-Sepharose) revealed that Meishan pigs had a maximal CBG binding capacity 1. 6 times higher than Large White pigs. Using the same biochemical measures on the F2 pig population, we showed a strong genetic linkage between CBG binding capacity and the chromosomal region 7q24-7q26 where the QTL associated with cortisol levels was localised. Molecular expression studies indicated no differences in Cbg mRNA expression in the liver of the two parental breeds. The sequence of exons and promoter region of porcine Cbg gene has been determined. The preliminary results of haplotype analysis of Cbg gene (proximal promoter, coding sequence, 3'UTR) of F1 pigs and their parents are discussed

Master of Science
Department of Agronomy
Allan Fritz
Fusarium head blight (FHB) is one of the most devastative diseases in wheat. Growing resistant cultivars is one of the most effective strategies to minimize the disease damage. Huangcandou (HCD) is a Chinese wheat landrace showing a high level of resistance to FHB spread within a spike (type II). To identify quantitative traits loci (QTL) for resistance in HCD, a population of 190 recombinant inbred lines (RILs) were developed from a cross between HCD and Jagger, a susceptible hard winter wheat (HWW) released in Kansas. The population was evaluated for type II resistance at the greenhouses of Kansas State University. After initial marker screening, 261 polymorphic simple-sequence repeats (SSR) between parents were used for analysis of the RIL population. Among three QTL identified, two from HCD were mapped on the short arms of chromosomes 3B (3BS) and 3A (3AS). The QTL on the distal end of 3BS showed a major effect on type II resistance in all three experiments. This QTL coincides with a previously reported Fhb1, and explained 28.3% of phenotypic variation. The QTL on 3AS explained 9.7% of phenotypic variation for mean PSS over three experiments. The third QTL from chromosome 2D of Jagger explained 6.5% of phenotypic variation. Allelic substitution using the closest marker to each QTL revealed that substitution of Jagger alleles of two QTL on 3AS and 3BS with those from HCD significantly reduced the PSS. HCD containing both QTL on 3AS and 3BS with a large effect on type II resistance can be an alternative source of FHB resistance for improving FHB type II resistance in wheat. Besides, meta-analyses were used to estimate 95% confidence intervals (CIs) of 24 mapped QTL in five previously mapped populations derived from Chinese landraces: Wangshuibai (WSB), Haiyanzhong (HYZ), Huangfangzhu (HFZ), Baishanyuehuang (BSYH) and Huangcandou (HCD). Nineteen QTL for FHB type II resistance were projected to 10 QTL clusters. Five QTL on chromosomes 1A, 5A, 7A, and 3BS (2) were identified as confirmed QTL that have stable and consistent effects on FHB resistance and markers in these meta-QTL regions should be useful for marker-assisted breeding.

The purpose of this study was to design and test five SNP markers in an inbred chicken cross between Red Junglefowl and domestic White Leghorn of the 8th generation. The markers lie in a region affecting the tonic immobility behaviour which differs significantly between the two species. The markers could be identified by usage of PCR and pyrosequencing. The data obtained were further used in a small scale quantitative trait locus (QTL) analysis. QTL analysis is a statistical method to link phenotypic traits to genotypic data. Four out of five markers could be genotypes and thereby, made it possible to proceed with the QTL analysis. The results showed that there is no QTL associated with the markers identified. The two flanking markers were closest to a significant difference between genotypes and it is therefore a possibility that a QTL lies close further down or up the searched region. From the line map it is indicated that there is little recombination in the marker region.

Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach. This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL). Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 % and 23 % for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 % of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis. The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.
Pflanzen sind die Primärproduzenten von Biomasse und damit Grundlage allen Lebens. Sie werden nicht nur zur Gewinnung von Nahrungsmitteln, sondern zunehmend auch als Quelle erneuerbarer Energien kultiviert. Aufgrund der Begrenztheit der weltweit zu Verfügung stehenden Anbaufläche ist eine zielgerichtete Selektion und Verbesserung der verwendeten Sorten unabdingbar. Um solch eine kontinuierliche Verbesserung zu gewährleisten, ist ein grundlegendes Verständnis des biologischen Systems Pflanze nötig. Diese Arbeit hatte zum Ziel, den Primärmetabolismus der Modellpflanze A. thaliana mit Methoden der quantitativen Genetik zu untersuchen und in Beziehung zu Wachstum und Biomasse zu stellen. Insbesondere sollte Heterosis, die Abweichung von Hybriden in ihren Merkmalen vom Mittelwert der Eltern, auf Stoffwechselebene charakterisiert werden. Mit Hilfe der Gas Chromatographie/ Massen Spektrometrie (GC-MS) wurden über 2000 Proben von rekombinanten Inzucht Linien (RIL) und Introgressions Linien (IL) der Akzessionen Col 0 und C24 bezüglich des Vorkommens von 181 Metaboliten untersucht. Die beobachtete Varianz erlaubte die Bestimmung von 157 metabolischen QTL (mQTL), genetischen Regionen, die für die Metabolitkonzentrationen relevante Gene enthalten. Durch die Untersuchung von Testkreuzungen der RILs und ILs konnten weiterhin 385 heterotische metabolische QTL (hmQTL) identifiziert werden. Im Rahmen dieser Arbeit wurde eine robuste Methode zur Auswertung von GC-MS Analysen entwickelt. Es wurde eine hoch signifikante kanonische Korrelation (r=0.73) zwischen Biomasse und Metabolitprofilen gefunden. Die unterschiedlichen Ansätze zur QTL Analyse, RILs und ILs, wurden verglichen. Dabei konnte gezeigt werden, daß die Methoden komplementär sind, da mit RILs gefundene mQTL zu 56% und hmQTL zu 23% in ILs bestätigt wurden. Durch den Vergleich mit Datenbanken wurden für 67% der mQTL Kandidatengene identifiziert. Um diese zu überprüfen wurden acht dieser Gene resequenziert und insgesamt 23 Polymorphismen darin bestimmt. Die Heterosis in den Hybriden ist für die meisten Metabolite gering (<20%). Für hmQTL konnten weniger Kandidatengene als für mQTL bestimmt werden und sie zeigten eine geringere Übereinstimmung in den beiden Populationen. Dies deutet darauf hin, daß regulatorische Loci und epistatische Effekte einen wichtigen Beitrag zur Heterosis besteuern. Die gewonnenen Daten stellen eine reiche Quelle für die weitergehende Untersuchung und Annotation relevanter Gene dar und ebnen den Weg für ein besseres Verständnis des Systems Pflanze.

The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools. The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures. The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS).
eSSENCE

L'objectif de la thèse est la cartographie fine de QTL de fertilité femelle (FF) chez les races bovines Françaises : la Prim'Holstein (PH), la Normande (NO) et la Montbéliarde (MO). La première étape du projet consiste en une primo-localisation, sur un dispositif de 78 familles, de QTL de FF dans 12 régions génomiques. Six QTL de FF ont été détectés chez la PH et deux chez la NO. La deuxième étape consiste en une cartographie des QTL détectés sur les chromosomes BTA01, BTA02, BTA03 et BTA21 sur un échantillon de 41 familles des trois races. La localisation de ces QTL a été confirmée et précisée pour les QTL détectés sur les chromosomes BTA01 et BTA03. Le QTL sur le chromosome BTA03 a été finement cartographié en utilisant 437 SNP ce qui a permis de réduire son intervalle de localisation à quelques centimorgans et de sélectionner six gènes candidats. Les régions flanquant les exons de ces six gènes ont été séquencées sur quatre pools d'ADN d'individus de phénotypes extrêmes afin de trouver des polymorphismes intéressants dans les régions séquencées qui pourront ensuite être validés sur l'ensemble du dispositif. La mise à disposition récente d'une puce de 54000 SNP situés dans tout le génome bovin a changé la stratégie de cartographie de QTL de FF. Des gènes pouvant influencer la FF ont été sélectionnés et suggérés comme étant des gènes candidats positionnels et fonctionnels responsables de la dégradation de la FF chez les bovins laitiers.

La recherche du polymorphisme causal d’un QTL est une étape encore longue et difficile dans la plupart des espèces d’animaux domestiques. Dans ce cadre, ce travail porte sur l’intégration d’informations à haut débit sur l’expression des gènes dans un tissu. La démarche traditionnelle consiste à détecter des QTL sur ces données d’expression de gènes (détection de eQTL) en mettant en oeuvre, gène par gène, des méthodes de cartographie d’intervalle. Hors, il apparaît qu’il existe un biais sur la position estimée des QTL, biais aboutissant sur ces données de grande dimension à un nombre anormalement élevé de eQTL détectés sur les positions des marqueurs. La première partie de ce travail vise à caractériser ce biais afin de proposer des itinéraires pour mieux le maîtriser. Les paramètres affectant le biais sont étudiés, puis un algorithme pour améliorer l’estimation de la position du QTL est proposé. Dans une seconde partie, le test de la co localisation entre eQTL et QTL est abordé. L’objectif est de réduire la liste des eQTL déclarés « colocalisant » avec un QTL afin de permettre le passage à une étude individuelle de ces gènes. Dans ce contexte, les conditions favorables pour assurer l’efficacité des méthodes de régression existant dans la littérature sont recherchées. Des méthodes permettant de lever ces éventuelles conditions sont ensuite proposées. Enfin, en perspectives de ce travail, nous proposons des pistes de recherche pour l’utilisation des modèles d’équations structurelles (Structural Equation Modeling) pour finaliser la construction d’un réseau unissant QTL, eQTL et caractères
Identifying the causal polymorphism of a QTL remains a long and difficult step in most species of domestic animals. Under this framework, this work focuses on the integration of high throughput information on the expression of genes in a tissue. The traditional approach consists in detecting QTL on gene expression data (eQTL detection) by carrying out, gene by gene, the interval mapping methods. However, it appears that there is a bias on the estimated position of QTL. That leads, based on these high-dimensional data, to a high number of eQTL abnormally detected at the positions of the markers. The first part of this work is dedicated to the characterization of this bais in order to propose some ways to better control it. The parameters affecting the bias are discussed and an algorithm to improve the accuracy of the estimated position of the QTL is proposed. In the second part, the test of the co localization between eQTL and QTL is discussed. The aim is to reduce the list of eQTL declared "co localizing" with a QTL so that one could pass an individual study for these genes. In this framework, the conditions to guarantee the efficacy for the regression methods existing in the literature are sought. Then, some methods allowing to improve these conditions are proposed. Finally, perspectives of this work, we propose some tracks by the use of structural equation models to construct a network linking QTL, eQTL and traits

Durum (2n=4x=28; AABB) wheat is the grain of choice for the production of high-quality pasta products. Fusarium spp. are causal pathogens for Fusarium Head Blight (FHB). Limited host resistance to this disease exists among adapated durum cultivars. The use of Tunisian-derived durum lines for integration of FHB resistance in cultivars was evaluated. The genetic characterization of FHB resistance was evaluated, and markers assosciated with FHB resistance are presented in two populations. Two backcross inbred line (BIL) populations derived from cross between a resistant durum genotype `Tunisian 108' and susceptible durum wheat cultivars `Ben' and `Lebsock' were screened to identify QTL for FHB resistance. Analysis of variance showed significant effect of genotypes on FHB severity and incidence despite high level of interaction between environment and genotypes. A total of 329 and 331 DArT and microsatellite markers covered a distance of 1887.6 and 1748 cM in two populations respectively. Composite interval mapping using two linkage maps and the phenotypic data revealed 11 different FHB resistance QTL on seven different chromosomes (1A, 1B, 2B, 3B, 5A, 5B, and 7B) in Tunisian/Ben derived population and 15 different FHB resistant QTL on seven different chromosomes (1A, 1B, 3A, 3B, 4A, 5A, and 6B) in population derived from cross between Tunisian/Lebsock. At least two novel QTL were identified on chromosome 2B (Qfhb.ndsu-2B) 4A (Qfhs.ndsu-4A) in Tunisian/Ben//Ben and Tunisian/Lebsock//Lebsock population respectively. Location of the two FHB resistance QTL on chromosome 1B and two QTL on 5A were identical in both populations. Owing to cumulative effects of resistance QTL, high level of transgressive segregation was observed in both populations. Our finding revealed an alternative tetraploid FHB resistance source from Tunisian genomic background that can be utilized with associated markers for wheat geremplasm enhancement.

La plupart des maladies humaines ont une étiologie complexe avec des facteurs génétiques et environnementaux qui interagissent. Utiliser des phénotypes corrélés peut augmenter la puissance de détection de locus de trait quantitatif. Ce travail propose d'évaluer différentes approches d'analyse bivariée pour des traits corrélés en utilisant l'information apportée par les marqueurs au niveau de la liaison et de l'association. Le gain relatif de ces approches est comparé aux analyses univariées. Ce travail a été appliqué à la variation de la densité osseuse à deux sites squelettiques dans une cohorte d'hommes sélectionnés pour des valeurs phénotypiques extrêmes. Nos résultats montrent l'intérêt d'utiliser des approches bivariées en particulier pour l'analyse d'association. Par ailleurs, dans le cadre du groupe de travail GAW16, nous avons comparé les performances relatives de trois méthodes d'association dans des données familiales.

Sucrose content is one of the important seed quality traits in soybean, especially for oriental soyfood production. However, little genetic information is available on this quantitative trait yet. A previous study was conducted on seed sucrose content of soybean using a population of F2-derived lines from an interspecific cross between an adapted high-sucrose (8.3%) G. max breeding line (V71-370) and a low sucrose (1.6%) G. soja plant introduction (PI407162). Nineteen marker loci, mapping to seven linkage groups (A1, A2, E, F, L1, I, and M), were significantly associated with seed sucrose content after screening 178 polymorphic genetic markers, including RFLPs, SSRs, RAPDs and morphological markers. The replicated field experiments were planted in 1993 and 1995. The objective of my study was to evaluate QTLs associated with seed sucrose content utilizing an additional 153 F2:3 families from the same cross. DNA samples from the additional families were analyzed with the nineteen genetic markers associated with sucrose in the previous study. Sucrose data were obtained from seeds harvested from a field experiment conducted in 1995. Single factor analysis of variance results for the sucrose data obtained from the 153 F2:3 families were compared to the 1995 data for the 144 F2:3 families of the previous study. Of the nineteen genetic markers significantly associated with seed sucrose content in the previous study, seven were also significantly associated in this study. These genetic markers include sgA458a on linkage group A2, NBS61 on linkage group E, sgB164, R-B4a and sgB162 on linkage group L1, and R-B4b and sgA144 on linkage group I. The percent phenotypic variation explained by significant individual markers varied from 2.9 to 6.8% in the 153 F2:3 families. This study shows that seed sucrose content, a quantitative trait, may be improved using the molecular marker technology. Further research is necessary in different genetic backgrounds of G. max in order to implement these markers in a breeding program for selection.
Master of Science

Breeding programmes that use elite sires with the best estimated breeding values for muscling traits have achieved significant improvement in lamb production in the UK. Further acceleration of the rate of genetic gain for the desirable production traits could be achieved using DNA marker-assisted selection (MAS) breeding strategies. The underlying causal genetic variants associated with improved muscling may be unknown and lying between a cluster of genes known as quantitative trait loci (QTL) or could be single nucleotide polymorphisms (SNP). LoinMAXTM, Texel muscling QTL (TM-QTL) and c.*1232G > A myostatin mutation were genetic variants that reported to be associated with improved muscling characteristics and hence subjected to further analysis in this project. It is essential before incorporating segregating genetic variants in any breeding scheme to comprehensively evaluate their effects on carcass traits. In-vivo scanning (ultrasound scanning (US) and computed tomography scanning (CT)), and carcass video image analyses (VIA) were used in the current studies. Objective VIAprediction weights of the carcass primal cuts could be the backbone of a value-based marketing system that is suggested to replace the current Meat and Livestock Commission (MLC) carcass grades for conformation scores (MLC-C) and fat class (MLC-F). The effect of a single copy of LoinMAXTM QTL (LM-QTL) compared to noncarriers was evaluated in UK crossbred lambs out of Scottish Mule ewes. M. longissimus lumborum (MLL) width, depth and area, as measured by CT scanning, were significantly greater in lambs heterozygous for LM-QTL compared to noncarriers. VIA detected a significant effect of the LM-QTL on the predicted weight of saleable meat yield in the loin primal cut (+2.2%; P < 0.05). The effects of the ovine c.*1232G > A myostatin mutation (MM), found on sheep chromosome 2, on carcass traits in heterozygous crossbred lambs sired by Texel and Poll Dorset rams were studied. Texel crossbred lambs carrying MM had increased loin depth and area. In both crossbred lambs, MM-carriers had significantly higher CT-estimated lean weight and proportion (2 to 4%) and muscle to bone ratios (by ~3%). Poll Dorset heterozygous crossbred animals had higher muscle to fat ratio (28%) and significantly lower fat-related measurements. The c.*1232G > A (MM) mutation as well as TM-QTL effects were evaluated in a different genetic background of Texel x Welsh Mountain crossbreed lambs. Carrying two copies of MM was associated with a significant positive effect on 8 week weight, a negative effect on ultrasound fat depth, a substantial decrease in MLC-fat score, positive impact on VIA-estimated weight of the hind leg, chump and loin primal cuts, as well as the muscularity of the hind leg and loin regions with greater loin muscle width, depth and area. Two copies of MM altered lambs‟ morphological traits with significantly wider carcasses across the shoulders, breast and hind legs and greater areas of the back view of the carcass when measured by VIA. TM-QTL significantly increased US-muscle depth and TM-QTL carriers had significantly greater loin muscle width and area measurements. Comparing TM-QTL genetic groups (homozygote allele carriers (TM/TM), heterozygote carriers of paternal and maternal origin of allele (TM/+ and +/TM, respectively) and homozygote non-carriers (+/+)) and TM-QTL mode of action were then studied. TM/TM carcasses were significantly heavier than non-carriers by 1.6 kg and scored higher conformation values when compared to heterozygote groups only. TM/+ lambs had significantly higher VIA-predicted weight and muscularity in the hind leg and loin, and higher loin dimensions relative to some other genotypic groups. The effect of TM-QTL on some carcass shape measurements was significant. TM-QTL mode of action results on the loin muscling traits supports the earlier reports of polar over dominance. In the light of growing calls to replace the current subjective carcass payment system with the objective VIA system that values the carcass according to the superiority of its cuts, I investigated the ability of US and CT measurements to predict the VIAestimated weights of the carcass primal cuts. Several prediction equations were examined but the best could be achieved when ultrasound measurement, CT linear measurements and live weight were fitted in the model. Since CT scanning information of elite sires is now being used for genetic selection for carcass merit, genetic parameters and genetic relationships between CT scanning measurements and post mortem traits (VIA and MLC-FC) were estimated. However, results were not sufficiently accurate to be of practical use due to lack of data.

Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.

Orientadores: Claudio Lopes de Souza Junior, Anete Pereira de Souza
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A maior parte dos caracteres de importância agronômica e econômica do milho estão sob o controle de diversos locos gênicos, denominados locos de caracteres quantitativos (QTL). A possibilidade do uso de marcadores moleculares e o aperfeiçoamento dos modelos estatístico-genéticos possibilitaram o mapeamento desses locos gênicos que afetam tais caracteres. Pouco enfoque no estudo de mapeamento de QTL foi dado em populações derivadas do germoplasma do milho tropical, o qual possui uma base genética ampla com maior diversidade do que o germoplasma temperado. Da mesma forma, pouco se conhece sobre as interações dos QTL nos diferentes ambientes (QTL X E). Duzentos e cinqüenta e seis progênies F2:3, derivadas do cruzamento de duas linhagens de milho tropical, foram avaliadas em cinco ambientes. O mapa genético foi desenvolvido com 139 marcadores microssatélites, utilizando o programa MAPMAKER/EXP versão 3.0b. As análises de mapeamento de QTL e a detecção da interação QTL X E foram realizadas utilizando o procedimento JZmapQTL do programa Windows QTL-Cartographer versão 2.5, que se baseia na análise de mapeamento em ambientes múltiplos (mCIM). A extensão total do mapa genético foi de 1.858,61 cM com intervalo médio entre marcadores de 13,47 cM. Dezesseis QTL foram mapeados para produção de grãos, oito para espiga por planta, seis para acamamento, seis para altura de planta, nove para altura de espiga e dois para número de folhas. Os efeitos genéticos dos QTL mapeados apresentaram variação em sinal e magnitude, demonstrando que cada QTL contribui de forma particular para a expressão dos caracteres. A maioria destes QTL apresentou ação gênica sobredominante, e muitos deles também apresentaram significante interação QTL X E. Esses resultados forneceram dados para uma melhor compreensão da arquitetura genética do genoma do milho tropical. Estas informações podem ser utilizadas em programas de seleção assistida dessa espécie, utilizando marcadores moleculares, gerando mais eficiência nos programas brasileiros de melhoramento
Abstract: Most of important agricultural and economical traits in maize are under the control of several gene loci, named quantitative trait loci (QTL). The possibility of using molecular markers and the statistic-genetic models made possible the mapping of these gene loci that affect such traits. Little focus has been given to QTL mapping study in populations derived from tropical maize germplasm, which has a broad genetic base with greater variability than temperate maize germplasm. Also, not much is known about the interaction of QTL in various environments (QTL X E). Two-hundred and fifty-six F2:3 progenies, derived from a crossing between two tropical maize inbred lines, were evaluated in five environments. The genetic map was developed with 139 microsatellite markers, using the software MAPMAKER/EXP version 3.0b. The analyses of QTL mapping and the detection of QTL X E interaction were performed using the Windows QTL-Cartographer version 2.5, JZmapQTL procedure, which is based on multiple-environment joint analysis (mCIM). The genetic map spanned 1,858.61 cM in length with an internal average of 13.47 cM between markers. Sixteen QTL were mapped for grain yield, eight for ears per plant, six for plant lodging, six for plant height, nine for ear height and two for number of leaves. The genetic effects of the mapped QTL presented varied signal and magnitude, displaying that each QTL contributes in a particular way for trait expression. Most of these QTL displayed gene action overdominance, many of them with significant QTL X E interaction detected. These results provide data for a better comprehension of genetic architecture on tropical maize genome. This information can be used in the marker-breeding selection of this species, leading more efficiency to Brazilian breeding programs
Doutorado
Genetica Vegetal e Melhoramento
Doutor em Genetica e Biologia Molecular

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Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
O mercado consumidor tem sido cada vez mais exigente quanto à qualidade da carne e, portanto, a pecuária precisa melhorar sua eficiência e fornecer produtos diferenciados, padronizados e com qualidade. Entre as características de qualidade de carne, a maciez é a que mais influencia na satisfação dos consumidores. Considerando a importância dada à maciez da carne, pesquisas têm sido desenvolvidas para melhor compreender os mecanismos relacionados à expressão fenotípica desta característica. Os estudos de genes candidatos têm possibilitado a identificação de polimorfismos que modificam as estruturas das proteínas ou ainda, que estejam em desequilíbrio de ligação com alterações funcionais no DNA. Com a automatização dos polimorfismos de nucleotídeo único (SNPs) muitas regiões ao longo do genoma foram identificadas como responsáveis pela variação fenotípica da maciez da carne. No entanto, os marcadores SNPs podem ter baixa capacidade de identificar locos que atuam nas características quantitativas (QTL) por serem, na grande maioria, bi-alélicos e, mesmo que aconteçam mutações, as mudanças nas frequências alélicas dos SNPs podem permanecer quase inalteradas. Por outro lado, com a utilização de haplótipos, mutações tendem a causar mudanças nas frequências dos haplótipos, aumentando as chances de identificação dos QTL. Sendo assim, este estudo teve como objetivos detectar QTL e mutações causais em genes candidatos e identificar QTL por meio de uma análise de associação genômica ampla, para a característica maciez da carne em bovinos da raça Nelore, utilizando haplótipos como unidades fundamentais dos testes de associação. Foram utilizadas informações fenotípicas, genotípicas e de pedigree de animais provenientes de fazendas que integram os programas de melhoramento genético DeltaGen e PAINT. Cinquenta e dois genes candidatos foram escolhidos para serem analisados utilizando haplótipos construídos com base no desequilíbrio de ligação, utilizando 1.616 animais. Do total de haplótipos, dois foram significativos, sendo que os éxons próximos e dentro destes foram sequenciados visando buscar a mutação causal. O sequenciamento foi realizado com 298 animais e os SNPs identificados foram imputados para os 1.318 animais remanescentes. Foram realizadas análises de associação utilizando haplótipos construídos com base na metodologia de janelas sobrepostas, sendo que seus efeitos foram estimados pelo método Genomic Best Linear Unbiased Predictor (GBLUP). Os valores genéticos dos animais foram estimados para cada haplótipo e SNP e, após, as variâncias genéticas aditivas foram calculadas. Utilizando haplótipos construídos com base em janelas sobrepostas, verificou-se que o aumento do número de SNPs no haplótipo permitiu capturar maior proporção da variância genética aditiva da característica maciez da carne. Seis possíveis QTL foram identificados explicando as maiores proporções de variância genética aditiva para maciez da carne, dos quais um está no gene CAPN1 e cinco no gene ASAP1. Não houve evidências de que a mutação causal para a maciez da carne tenha sido identificada nos dois genes. Uma análise de associação genômica ampla foi realizada utilizando haplótipos construídos com base na metodologia de janelas sobrepostas de tamanhos variados. Foram utilizados nesta análise 1.405 animais genotipados com o painel Illumina Bovine HD e 1.756 animais genotipados com painel de menor densidade (70 K Neogen) e, posteriormente, imputados para o painel HD, em um total de 3.161 animais analisados. Os efeitos dos haplótipos e SNPs foram estimados pelo método GBLUP e as variâncias genética aditivas de cada haplótipo e SNP foram calculadas. Os genes NOS1AP, SUCLG1, PHLDB2 e LOC107132946 foram associados com a característica maciez da carne em bovinos da raça Nelore, por meio de análises de associação genômica ampla utilizando SNPs individuais e haplótipos. A análise utilizando SNPs identificou QTL diferentes das análises com haplótipos e, em alguns casos, SNPs apresentaram variâncias genéticas aditivas maiores do que as apresentadas pelos haplótipos. A análise que utilizou haplótipos construídos com cinco SNPs identificou mais QTL do que as análises de haplótipos construídos com sete e nove SNPs. Sugere-se que análises utilizando haplótipos, baseados em janelas sobrepostas, sejam realizadas para complementar análises de SNPs individuais em estudos de associação genômica ampla.
The consumer market has been increasingly demanding about the meat quality and therefore livestock needs to improve its efficiency and provide differentiated products, standardized and with quality. Considering the importance given to the meat tenderness, research has been undertaken to better understand the mechanisms related to the phenotypic expression of this trait. The candidate gene studies have allowed the identification of polymorphisms that change the structures of the proteins or that are in linkage disequilibrium with functional alterations in the DNA. With the advent of single nucleotide polymorphisms (SNPs) throughout many regions of the genome have been identified as responsible for phenotypic variation in meat tenderness. However, SNPs markers may have low ability to identify mutations, because SNPs are commonly bi-allelic and even when mutations have occurred, allelic frequencies can remain unaltered. On the other hand, using haplotype, mutations tend to cause major changes in haplotype frequencies, increasing the chances of identification of QTL. Thus, this study aimed to detect QTL and causal mutations by the approach of candidate genes and identify possible QTL through a genome-wide association analysis, for the trait meat tenderness in Nelore cattle using haplotypes as fundamental units of association tests. Information of the phenotypic, genotypic and pedigree were used from farms that belong to the breeding programs DeltaGen and PAINT. Fifty-two candidate genes were chosen for analysis using haplotypes constructed based on linkage disequilibrium using 1,616 animals. Two haplotypes were significant, and the exons near and within these haplotypes were sequenced to search for the causal mutation. The sequencing was performed using 298 animals and the identified SNPs were imputed for 1,318 remaining animals. Association analysis using haplotypes constructed based on the method of overlapping sliding windows were carried out and the SNPs and haplotypes effects were estimated using Genomic Best Linear Unbiased Predictor (GBLUP) method. The breeding values were estimated for each haplotype and SNPs and the additive genetic variances were calculated. Using haplotypes constructed based on overlapping sliding windows, we found that increasing the number of SNPs in the haplotype allowed to capture a greater proportion of additive genetic variance of meat tenderness. Six putative QTL were identified with the greatest additive genetic variances for meat tenderness, which one was in CAPN1 gene and five in ASAP1 gene. There was no evidence that the causal mutation for meat tenderness trait has been identified in these genes. A genome-wide association analysis was performed using haplotypes constructed based on the methodology of overlapping sliding windows of varying sizes. In this analysis, 1,405 animals genotyped with the Illumina Bovine HD panel and 1,756 genotyped animals with lower density panel (Neogen 70 K) were used and then, the genotypes of the 1,756 were imputed to the HD panel, in a total of 3,161 animals analyzed. The haplotypes and SNPs effects were estimated by the method GBLUP and the additive genetic variances were calculated for each haplotype and SNP. The NOS1AP, SUCLG1, PHLDB2 and LOC107132946 genes were associated with the meat tenderness trait in Nelore cattle through genome-wide association analysis using individual SNPs and haplotypes. The analysis using SNPs identified different QTL of the haplotype analyzes, and in some cases, the SNPs showed additive genetic variance greater than those presented by the haplotypes. The analysis used haplotypes constructed with five SNPs identified more QTL than analysis of haplotypes constructed with seven and nine SNPs. Analyzes using haplotypes based on overlapping sliding windows, should be conducted as additional analyzes for individual SNPs in genome-wide association studies.
FAPESP: 2013/00035-9

Les strongles gastro-intestinaux, dont Haemonchus contortus constituent un problème majeur pour l'élevage des ovins allaitants. Ils entrainent des pertes de production et le recours aux anthelminthiques est remis en question par l'apparition de souches de vers résistantes. La sélection d'ovins plus résistants fait partie des stratégies complémentaires de lutte les plus sérieuses. Cependant sa mise en oeuvre requiert une meilleure compréhension des mécanismes sous-jacents. Cette thèse vise à identifier les régions du génome ovin impliquées dans la résistance aux strongles gastro-intestinaux. Une analyse statistique d'association entre des marqueurs génétiques et des mesures de résistance d'un troupeau d'ovins croisés Martinik Black-belly x Romane a mis en évidence un nombre limité de régions d'intérêt. Parmi celles-ci, un segment du chromosome 12 a été choisi pour effectuer des accouplements raisonnés et valider son rôle dans la résistance à H. contortus. L'effet de cette région a été validé chez les descendants issus d'accouplements assistés par marqueurs génétiques. Cette région semble limiter fertilité des vers femelles tout en contribuant à une réponse immunitaire plus forte. Le rôle d'une région du chromosome 21 dans la variation de concentration plasmatique en pepsinogène, un marqueur de lésions abomasales, a également été confirmé. Un gène candidat sous-jacent est en cours de séquençage et l'analyse des polymorphismes devrait contribuer à la validation de son rôle. Deux autres gènes très proches pourraient également être impliqués et mériteraient une considération future. Ces travaux illustrent à la fois la variation génétique disponible pour les caractères de résistance à H. contortus et la complexité des mécanismes mis en jeu. Des études complémentaires de séquençage et d'étude d'expression par séquençage devrait contribuer à une meilleure compréhension des fonctions des gènes impliqués et de leurs interactions
Gastro-intestinal nematodes, among which Haemonchus contortus are a major threat to the meat sheep industry. They are responsible for production losses and the apparition of worm populations resistant to drugs limits their use as worm control strategy. Breeding more resistant sheep is among the most practicable alternative strategy. However its implementation requires a deeper understanding of underlying mechanisms. This PhD aims at identifying regions of the ovine genome affecting resistance to gastro-intestinal nematodes. A statistical analysis of existing associations between genetic markers and resistance traits of a Martinik Black-belly x Romane cross-bred sheep flock unraveled a limited number of key players. Among these, a fragment of the chromosome 12 was chosen to perform marker-assisted matings and to validate its role in resistance to H. contortus. The effect of this region was validated in the progenies born from matings. It seems this chromosomic fragment limits female worms fertility and is associated to a stronger immune response. The putative role played by a fragment of the chromosome 21 in plasmatic pepsinogen concentration (a biomarker of abomasal lesions) was also confirmed in this work. A candidate gene underlying this region has been sequenced and the analysis of the detected polymorphisms should confirm its role. Further, two other genes in its vicinity could also play a role in this biological phenomenon and they should also deserve future considerations. This work illustrated both the existing genetic variation for resistance to H. contortus and the associated complexity of underlying mechanisms. Additional sequencing and gene expression sequencing studies should help understanding gene functions and interactions

Rust diseases caused by Puccinia spp. are specialised to different economically important crops such as wheat and barley and can cause significant crop failure when severe. For many decades, genetic resistance has proven effective in protecting crops against rust pathogens. However, the ability of rust pathogens to evolve rapidly can lead to the emergence of new virulent races that can overcome genetic resistance. Therefore, the identification of new durable sources of resistance is essential for crop production and food security. Barley is a diploid crop with a reference genome sequence that is a near non-host to some non-adapted rust pathogens. Thus, the barley-Puccinia pathosystem is amenable for studies of the genetic architecture of resistance to rust pathogens. This thesis aims to determine the genetic basis of specificity of resistance in different barley-Puccinia pathosystems and to identify valuable sources of resistance in barley that can be used for genetic improvement of cereal crops. Chapter one contains a detailed review of the literature, addressing aspects of biology of barley and rust pathogens as well as mechanisms of host and non-host resistance. Chapter two investigates the genetic architecture of non-host resistance in barley using diverse Puccinia isolates and identifies non-host resistance (NHR) QTL that are suitable for either map-based or rapid cloning approaches. Chapter three examines the isolate specificity and polygenic inheritance of resistance in barley to different P. striiformis isolates. Chapter four generates a high-density linkage map using DArT-Seq markers with the aim of mapping loci for seedling and adult plant resistance to adapted stripe, leaf and stem rust pathogens. Chapter five delivers an overall conclusion based on the findings of the thesis and includes future paths and perspectives.

Le tocophérol, le phytostérol, le pourcentage de protéines des graines, l'huile et les teneurs en acides gras ont été mesurés dans une population de lignées recombinantes (RILS) de tournesol, cultivées sous conditions de sécheresse, irrigation et semis tardif. Une analyse génétique de QTL a été réalisée à partir de ces mesures, en utilisant une carte génétique basée sur des marques SSR et avec des gènes candidats (1) impliqués dans la voie métabolique de tocophérol et phytostérol, (2) des gènes codant des antioxydants enzymatiques, (3) des gènes liés à la sécheresse et (4) des gènes homologues à SEC14 chez Arabidopsis. Trois gènes candidats importants (VTE4, VTE2 et HPPD), qui codent pour des enzymes impliquées dans la biosynthèse du tocophérol, ont été cartographiés sur les groupes de liaison LG8 et LG14. Quatre SNPs sont identifiés pour PAT2, le gène homologue chez Arabidopsis SEC14, entre les deux parents (PAC2 et RHA266) et un SNP, identifié par alignement de séquences est converti en marqueur CAPS pour permettre l'analyse génotypique des RIL. Les gènes homologues à SFH3, HPPD, CAT et CYP51G1 ont été cartographiés grâce à la mise au point de marqueurs dominants, tandis que des marqueurs co-dominants ont permis la cartographie des gènes homologues à SEC14-1, VTE4, DROU1, POD, SEC14-2 et AQUA. Les gènes POD, CAT et GST, codant pour des antioxydants enzymatiques, ont également été cartographiés sur les groupes de liaison 17, 8 et 1, respectivement. Le QTL majeur pour la teneur en tocophérol a été identifié sur le groupe de liaison 8, qui explique 59,5% de la variation phénotypique (6.TTC.8). Il colocalsie également avec le QTL identifié pour la teneur en phytostérol (7.TPC.8). Sous condition de semis tardif, un QTL spécifique de la teneur en acide palmitique a été identifié sur le groupe de liaison 6 (PAC-LS.6). Il est situé entre les marqueurs ORS1233 et SSL66_1. Les QTLs pour le pourcentage d'huile de graines et la teneur en acide stéarique colocalisent sur les groupes de liaison 10 (PSO-PI.10 et SAC-WI.10) et 15 (PSO-PI.15 et SAC-LS.15). Sept QTLs associés à teneur en acides palmitique, stéarique, oléique et linoléique sont identifiés sur le groupe de liaison 14. Ils sont liés à l’homologue du gène HPPD. Par ailleurs, les caractères agronomiques tels que les jours du semis à la floraison, la hauteur des plantes, le rendement et la morphologie foliaire ont été étudiés. Des analyses association génétique ont permis d’identifier des QTLs intérêts sur les groupes de liaison 2, 10 et 13 pour les caractères étudiés, d’autres QTLs identifies sur les groupes de liaison 9 et 12 mettent en avant l'importance de ces régions génomiques pour les caractères de morphologie foliaire. Nous avons finalement identifié des marqueurs AFLP et quelques gènes candidats liés aux caractères impliqués dans la qualité des graines sous conditions irriguée et stress hydrique chez une population de mutants (M8). Deux lignées mutantes, M8-826-2-1 et M8-39-2-1, produisent un niveau significativement élevé d'acide oléique peuvent être utilisées dans les programmes de sélection en raison de la haute stabilité à l'oxydation et des propriétés cardiovasculaire apportés par l’acide oléique qu’elles produisent. L'augmentation du niveau de tocophérol dans les lignées mutantes, M8-862-1N1 et M8-641-2-1, est justifiée par le polymorphisme observé pour le gène, MCT, impliqué dans la voie métabolique du tocophérol. Le marqueur le plus important pour le contenu en tocophérol total est E33M50_16 qui explique 33,9% de la variation phénotypique. Un des gènes candidats les plus importants concernant la biosynthèse des acides gras, FAD2 (FAD2-1), est lié à la teneur en acides oléique et linoléique. Il explique plus de 52% de la variation phénotypique
The genetic control of tocopherol, phytosterol, percentage of seed protein, oil and fatty acids content in a population of recombinant inbred lines (RILs) of sunflower under various conditions are studied through QTL analysis using genetic-linkage map based on SSR markers and introducing some important tocopherol and phytosterol pathway-related genes, enzymatic antioxidant-related genes, droughtresponsive family genes and Arabidopsis SEC14 homologue genes. Three important candidate genes (HPPD, VTE2 and VTE4), which encode enzymes involved in tocopherol biosynthesis, are mapped to linkage group 8(LG8) and LG14. One of the most important candidate genes coding for sterol methyltransferase II (SMT2) enzyme is anchored to LG17 by CAPS marker. Four SNPs are identified for PAT2, Arabidopsis Sec14 homologue gene, between two parents (PAC2 and RHA266). PAT2 is assigned to LG2 by CAPS marker. Squalene epoxidase (SQE1) is also assigned to LG15 by InDel marker. Through other candidate genes, POD, CAT and GST encoding enzymatic antioxidants are assigned to LG17, LG8 and LG1, respectively. The major QTL for total tocopherol content on linkage group 8 accounted for 59.5% of the phenotypic variation (6.TTC.8), which is overlapped with the QTL of total phytosterol content (7.TPC.8). Under late-sowing condition, a specific QTL of palmitic acid content on linkage group 6 (PAC-LS.6) is located between ORS1233 and SSL66_1 markers. Common chromosomic regions are observed for percentage of seed oil and stearic acid content on linkage group 10 (PSO-PI.10 and SACWI. 10) and 15 (PSO-PI.15 and SAC-LS.15). Overlapping occurs for QTLs of oleic and linoleic acids content on linkage groups 10, 11 and 16. Seven QTLs associated with palmitic, stearic, oleic and linoleic acids content are identified on linkage group 14. These common QTLs are linked to HPPD homologue, HuCL04260C001. QTLs controlling various traits such as days from sowing to flowering, plant height, yield and leaf-related traits are also identified under well-, partial-irrigated and late-sowing conditions in a population of recombinant inbred lines (RILs). The results do emphasis the importance of the role of linkage group 2, 10 and 13 for studied traits. Genomic regions on the linkage group 9 and 12 are important for QTLs of leaf-related traits in sunflower. We finally identified AFLP markers and some candidate genes linked to seed-quality traits under well-irrigated and water-stressed conditions in gammainduced mutants of sunflower. Two mutant lines, M8-826-2-1 and M8-39-2-1, with significant increased level of oleic acid can be used in breeding programs because of their high oxidative stability and hearthealthy properties. The significant increased level of tocopherol in mutant lines, M8-862-1N1 and M8- 641-2-1, is justified by observed polymorphism for tocopherol pathway-related gene; MCT. The most important marker for total tocopherol content is E33M50_16 which explains 33.9% of phenotypic variance. One of the most important candidate genes involving fatty acid biosynthesis, FAD2 (FAD2-1), is linked to oleic and linoleic acids content and explained more than 52% of phenotypic variance

Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be affected by multiple genetic loci. Standard computational tools for mapping of quantitative traits (i.e. for finding Quantitative Trait Loci, QTL, in the genome) use linear regression models for relating the observed phenotypes to the genetic composition of individuals in an experimental population. Using these tools to simultaneously search for multiple QTL is computationally demanding. The main reason for this is the complex optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms, implementations and tools for simultaneous mapping of several QTL. These new computational tools enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics. We first describe how the standard, brute-force algorithm for global optimization in QTL analysis is parallelized and implemented on a grid system. Then, we also present a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be efficiently deployed and used on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid systems or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithm such as DIRECT. Finally, we provide two distinctly different front-ends for our code. One is a grid portal providing a graphical front-end suitable for novice users and standard forms of QTL analysis. The other is a prototype of an R-based grid-enabled problem solving environment. Both of these front-ends can, after some further refinement, be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis.
eSSENCE

Carbohydrate content sucrose, raffinose, and stachyose are one of the important seed quality traits in soybean. However, little is known about the genetics of these quantitative traits. Recombinant inbred lines (RIL) were developed from the interspecific hybridization between a Glycine max breeding line (V71-370) and a Glycine soja plant introduction (PI407162). The 308 RILs, each parent, and one cultivar were arranged in a randomized complete block design with two replications and planted at two locations in Virginia. The main objective of the first part of this research was to devise a quick, economical, and reliable HPLC methodology to determine the amount of sucrose, raffinose, and stachyose in soybean seeds. Concentration of sucrose, raffinose and stachyose are quantitative traits, which are hard to manipulate genetically due to the influence of genotype, environment, and genotype by environment interactions on seed chemical composition. The objectives of the second study were to evaluate agronomic and quality traits over locations and to study correlations among traits. The agronomic traits analyzed in this study included; maturity, plant canopy height, canopy spread, leaflet length, leaflet width, yield, and seed size. Seed quality traits studied were sucrose, raffinose, and stachyose content. Although some correlation coefficients were statistically significant at P<0.001, many were not large enough to be of practical value. A positive correlation was observed between all three sugars. Significant variation was observed among RILs and locations for all traits studied. Genotype by environment interaction was significant for all of the agronomic traits, but was not significant for seed sucrose, stachyose, or raffinose. Maturity, seed size, and sucrose content were highly heritable traits, whereas plant height, canopy spread, yield, leaf length, leaf width, stachyose content, and raffinose content had relatively low broad-sense heritabilities. The RIL population was used to investigate the genetic basis for these agronomic and seed quality traits. Seven out of twenty soybean molecular linkage groups (MLG), A1, A2, E, F, G, I, and M, were selected on the basis of previous research and mapped in this population with restriction fragment length polymorphism (RFLP) and simple sequence repeat (SSR) markers. Five QTL for seed sucrose content, one QTL each for raffinose and stachyose, and one for each agronomic trait except yield and leaflet width, and two QTL each for yield and leaflet width were detected using the Blacksburg data. Four QTL for seed sucrose content, one QTL for raffinose, two QTL for stachyose, one QTL each for plot width and yield and two QTL for leaflet width were detected using the Warsaw data. Several QTL affecting different agronomic traits shared common genomic regions suggesting pleiotropy at some loci. The majority of the seed quality QTL was stable at both locations. Agronomic traits were more environmentally sensitive and no QTL were common to both locations. Epistasis analysis showed interactions between QTL that detected new genomic regions associated with raffinose content. These results suggest that these potential QTL are definitely on the genomic regions of interest and would be more powerful in marker-assisted selection when we find closer markers to each QTL.
Ph. D.

Polyploidization widely occurs in the evolutionary history of eukaryotes, especially for flowering plants. Exploring the evolutionary and agricultural important role by polyploidy is mystery and challenging job. In the first chapter of this thesis, I developed a quantitative genetics model based on orthogonal contrast scales, which would provide theoretical basis for any further bi-allelic QTL analysis in autotetraploid species. In the next chapter, I developed an interval mapping method for QTL mapping in outbred population for autotetraploid, considering both bivalent and quadrivalent pairing during meiosis. Extensive simulation work has been implemented to demonstrate the reliability of this method. This work would provide practical tools for breeding the world’s third most important crop, the cultivated potato. To give some insight into the evolutionary important role played by polyploidization, I developed a statistical method for inferring crossover interference based on three-locus analysis in autotetraploids in the third chapter and a method to predict genome-wide crossover rate for autotetraploid yeast in the final chapter.

Document incorrectly classified as a thesis on title page (decision to classify as a dissertation from NDSU Graduate School)
White mold caused by Sclerotinia sclerotiorumi s one of the most devastating diseases infecting field pea (Pisum sativum L.) which causes severe yield loss worldwide. Population 17 (Lifter/ PI240515), and Population 19 (PI169603/ Medora) were developed by single seed descent and screened by greenhouse evaluation and detached stem assay to identify potential sources of white mold resistance. Twenty-two partial resistant inbred lines were identified with short internode which met at least two resistance criteria based on lesion expansion inhibition (LEI) and nodal transmission inhibition (NTI). To find SNPs (single nucleotide polymorphism) responsible for white mold resistance, Populations 17 and 19 were genotyped using GBS (genotyping by sequencing) methodology and analyzed with the GBS-SNP-CROP pipeline. Linkage maps were constructed for each population and a composite map based on shared SNPs between the two populations was also generated. Nineteen QTL were identified as contributing to resistance to white mold. Seventeen were associated with LEI and two were associated with NTI. The QTL responsible for lesion expansion on LG VII were duplicated in the short internode subset of both populations. Partially resistant inbred lines and QTL responsible for white mold resistance identified in this study can be useful as resources for resistance to S. sclerotiorum in further experiments aimed at developing resistant cultivars.
National Sclerotinia Initiative in USDA ARS

Upland cotton (Gossypium hirsutum) is cultivated in many contrasting production environments and is often subjected to a combination of abiotic stresses such as high temperature (heat) and water deficit (drought) stress. In the present dissertation, two recombinant inbred line populations were constructed from heat-tolerant and -susceptible parental lines and evaluated in multiple environments under the presence of two treatments, well-watered (heat stress) and water-limited in the presence of high temperature (combination of heat and drought stresses). We assessed two agronomic traits, seed cotton yield and lint yield, as well as six fiber traits, lint percent, micronaire, length, strength, uniformity, and elongation. Fiber traits had moderate to very high broad-sense heritabilities, while heritabilities of agronomic traits were lower for both populations in each irrigation regime. Correlations between traits were not effected by the irrigation regimes. A stability analysis across the range of environments tested demonstrated that high seed cotton yield performance and greater stability may play a role in tolerance to the combination of heat and drought stresses. Additionally, we constructed linkage maps for both recombinant inbred line populations and mapped QTL controlling variation all eight traits. A total of 138 QTL were identified across populations for the eight traits. Climate change in the form of rising temperatures and reduced water availability will increase the occurrence of the combination of heat and drought stresses in a farmer's field. Thus, current cotton breeding programs will need to focus on the development of cotton varieties tolerant to heat, drought, and the combination of the two.

La maduixa representa el cultiu de baies més consumit a tot el món, amb una producció de 9,2 milions de tones l’any 2017. Els programes de millora tradicionalment s’han centrat en els trets agronòmics, però la qualitat dels fruits s’ha convertit recentment en un objectiu principal. El sabor és el principal factor responsable de la qualitat de la maduixa, sent atractiu per el consumidor. La maduixa diploide (Fragaria vesca) es un model per a el maduixot, gràcies al cicle de vida perenne, genoma reduït, curt període generacional, sistema de transformació genètica senzill i eficient, i als abundants recursos genètics. L’objectiu principal d’aquest treball ha estat estudiar la base genètica del sabor en la maduixa diploide mitjançant una col·lecció de línies isogéniques (NIL) desenvolupada per un encreuament entre un pare recurrent F. vesca i el progenitor donant F. bucharica. En primer lloc, hem millorat la col·lecció NIL desenvolupada anteriorment amb deu noves línies, cobrint en total el 94,8% del parental donant. És una eina genètica altament rellevant per mapar diversos trets de maduixa diploides. Per localitzar els loci dels caràcters quantitatius (QTL)de sabor es van analitzar el pH, l’àcid cítric i ºBrix. Es va mapar un QTL estable associat a l’augment del pH, dos QTL majors per la reducció del pH, dos QTL majors per la disminució dels nivells de l’àcid cítric i un QTL per l’augment dels ºBrix. Per localitzarQTL majors per a compostos volàtils al LG5, hem estudiat en profunditat els compostos aromàtics a les línies del LG5. Es van identificar disset compostos volàtils clau i es van assignar cinc QTL. Els QTL de metil 2-aminobenzoat i mirtenil acetat es van localitzar a LG5:20-35cM,el QTL per disminuir el contingut de metil butanoat a LG5:11-20cM i dos QTL per a compostos volàtils verds (CVV) (Z)-3-hexenil acetat i (E)-2-hexenil acetat a LG5:50-76cM. Onze gens van ser seleccionats percandidats a controlar l’acumulació de compostos volàtils.Es va analitzar el nivell de transcripció F. vesca i les NILs. Finalment, es van verificar tres gens en LG5:0-35cM i tres gens en LG5:50-76cM per presentar diferències significatives en l’expressió entre el pare recurrent i les NILs amb al·lels de F. bucharica en LG5. El gen FvH4_5g29270 que codifica una isomerasa 3Z-2E-enal es va seleccionar com a gen candidat per a CVV en LG5:50-76cM. Per verificar la funció del gen FvH4_5g29270, es va construir el vector de sobreexpressió gènica i es va expressar de forma transitòria en F. vesca i en dos NILs amb l’al·lel F. bucharica de FvH4_5g29270 mitjançant transfecció mediada per agrobacterium. Els resultats de contingut de CVVno van ser els esperats, principalment a causa de la baixa eficiència de la transformació. Un altre caràcter de qualitat important es l’aparença del fruit. Es va analitzar el color de la maduixa amb vuit paràmetres de color per a tres collites en la col·lecció. El color taronja es va observar en algunes NILs i es va mapar en LG5:35-39cM. Es van analitzar divuit gens candidats en aquesta regió per obtenir el nivell d’expressió de la transcripció en fruites madures. El gen FvH4_5g14770 que codifica per una proteïna d’unió al complex de clorofil·la A-B dependent de la llum es va seleccionar com a gen candidat, ja que mostrava un nivell de transcripció significativament superior en fruites de color taronja que en fruites vermelles,iaquest canvi pot estar relacionat amb el procés de reducció del contingut de clorofil·la. Tots aquests resultats van proporcionar una base fonamental per a la millora de l’aroma i el color de la maduixa.
La fresa representa el cultivo de bayas más consumido en todo el mundo, con una producción de 9,2 millones de toneladas en el año 2017. Los programas de mejora se han centrado en caracteres agronómicos, siendo la calidad del fruto un objetivo principal en los últimos años. El sabor es el factor responsable de la calidad en la fresa, actuando directamente sobre el consumidor. La fresa diploide (Fragaria vesca) es modelo para elfresón, debido a su ciclo de vida perenne, pequeño genoma, corto periodo generacional, un sistema de transformación genética simple y eficiente y abundantes recursos genéticos. El objetivo principal de este trabajo es estudiar la base genética del sabor del fruto en la fresa diploide utilizando una colección de líneas isogénicas (NIL) desarrollada por un cruce entre unparental recurrente F. vesca y un parental donante F. bucharica. En primer lugar, incrementamos la colección NIL desarrollada previamente con 10 nuevas líneas, con una cobertura del 94.8% del genoma del parental donante. Para posicionarlos loci de los caracteres cuantitativos (QTL),se analizaron pH, ácido cítrico y ºBrix enfresas maduras. Se mapeó un QTL estable asociado alincrementodel pH, dos QTL asociados con su disminución, dos QTL asociados con la reducción en ácido cítrico y un QTL relacionado con incremento deºBrix. Debido a la localización en LG5 de QTL asociados a compuestos volátiles, estudiamos su acumulaciónen todas las líneas del LG5. Se identificaron diecisiete compuestos volátiles clave y se maparon cinco QTL. Los QTL asociados al metil2-aminobenzoato y mirtenil acetato se localizan en LG5:20-35cM. El QTL asociado a la disminución de metil butanoato se localizó en LG5:11-20cM. Dos QTL ligados a la variación decompuestos volátiles verdes (CVV) (Z)-3-hexenil acetato y (E)-2-hexenil acetato están en LG5:50-76cM. Los genes candidatos que controlan la acumulación de compuestos volátiles aromáticos en LG5fueron once yse analizósu transcripción en frutas completamente maduras de F. vesca y de las líneas NIL de la región LG5.Se identificaron tres genes en LG5:0-35cM y tres genes en LG5:50-76cM que presentan diferencias significativas en la expresión entre el padre F. vesca y las NIL que albergan alelos de F. bucharica. El gen FvH4_5g29270 que codifica una 3Z-2E-enal isomerasa se seleccionó como gen candidato para CVV en LG5:50-76cM. Para verificar la función del gen FvH4_5g29270, se construyó el vector de sobreexpresión génica y se expresó de forma transitoria en F. vesca y en las NILs que contienen el alelo de FvH4_5g29270 en F. bucharica mediante transfección mediada por agrobacterium. Sin embargo, los resultados del contenido de CVVno fueron los esperados, principalmente debido a la baja eficiencia de transformación. La importancia de apariencia externa enfresa es el color,y se analizó aplicando ocho parámetros de color en tres cosechas distintas en la colección. Se observó el color del fruto anaranjado en algunas NILs y se mapeó en LG5:35-39cM. Se analizaron dieciocho genes candidatos en esta región para determinar el nivel de expresión de la transcripción en frutos maduros en plantas de F. vesca y en las NILs que albergan la introgresión LG5:35-39. El gen FvH4_5g14770 que codifica para una proteína de unión al complejo clorofila A-B dependiente de luz se seleccionó como un buen gen candidato ya que mostró un nivel de transcripción significativamente mayor en las fresas de color anaranjado que en las fresas rojas, y dicho cambio puede estar relacionado con la reducción del contenido de clorofila. Todos estos resultados proporcionaron una base fundamental para la mejora del aroma y la variación del color de la fresa.
Strawberry, belonging to Fragaria genus, Rosaceae family, is the most commonly consumed berry fruit crop worldwide, with a production of around 9.2 million tons during 2017. Although traditionally breeding programs have been focused on improving agronomic traits, fruit quality has become a main goal recently. Fruit flavor is the main factor responsible for the fruit quality that is a direct factor attracting customers. The diploid strawberry (Fragaria vesca) serves as an important model plant for cultivated strawberry and Rosaceae family, due to its perennial life cycle, small genome, short generation time, a simple and efficient genetic transformation system and abundant genetic resources. The main goal of this work was to study the genetic basis of fruit flavor in diploid strawberry using a isogenic lines collection (NIL) developed by a cross between the recurrent parent F. vesca and the donor parent F. bucharica. Firstly, we improved the previously developed NIL collection with 10 new lines added. Finally, this population consists of 49 lines with overlapping introgressions covering 94.8% of background of donor parental line. It is a highly relevant genetic tool for mapping a variety of traits for diploid strawberry. Fruit flavor traits, including pH, citric acid and oBrix of ripe fruits of the collection were statistically analyzed for mapping as quantitative traits loci (QTL). One stable QTL was mapped for increasing pH and two major QTL for decreasing pH. Two major QTL were mapped for decreasing citric acid and one QTL for increasing oBrix. Due to locating many major QTL for aroma volatile compounds in LG5, we deeply studied the aroma compounds in the new lines harboring introgressions in LG5. Seventeen key volatile compounds were identified and five QTL were mapped. The QTL for methyl 2-aminobenzoate and myrtenyl acetate were located in the same region LG5:20-35cM.The QTL for decreasing methyl butanoate content was located in LG5:11-20cM. Two QTL for green volatile compounds (Z)-3-hexenyl acetate and (E)-2-hexenyl acetate were located in LG5:50-76cM. In order to investigate the major genes controlling aroma volatile compounds accumulation, eleven genes were selected as important candidate genes to analyze the transcription level in fully ripe strawberry fruits of F. vesca and NILs harboring F. bucharica alleles. Finally, three genes in LG5:0-35cM and three genes in LG5:50-76cM were verified to present significant differences in expression between the recurrent parent F. vesca and the NILs harboring F. bucharica alleles in these LG5 regions. The gene FvH4_5g29270 encoding a 3Z-2E-enal isomerase was selected as candidate gene for green leaf volatile compounds in LG5:50-76cM. For verifying the function of gene FvH4_5g29270, the gene overexpression vector was constructed and transiently expressed in F. vesca and two NILs with the F. bucharica allele of FvH4_5g29270 via agrobacterium mediated transfection. However, the green volatile compounds content results were unexpected, mainly due to the low transformation efficiency. Attending to the important fruit appearance traits, the fruit color was analyzed with eight color parameters for three harvests. Orange fruit color was observed in some NILs and was mapped in LG5:35-39cM. Eighteen candidate genes in this region were analyzed for transcript expression level in fully ripen fruits from the recurrent parent F. vesca and NILs harboring the introgression containing LG5:35-39. The gene FvH4_5g14770 encoding light-harvesting complex chlorophyll A-B binding protein was selected as a good candidate gene since it showed significantly higher transcript level in orange colored fruits than in red fruits that can be related to chlorophyll content reduction. All these results provided fundamental basis for strawberry aroma and color breeding.

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

Le semis précoce du tournesol, d’un à deux mois par rapport à la période habituelle (Avril dans le sud ouest de la France), a été envisagé pour esquiver les périodes de sécheresses estivales. Cette stratégie conduit à un abaissement des températures de l’ordre de 5 à 10°C durant les premières phases de développement de la culture. L’objectif de ce travail est donc d’identifier des génotypes de tournesol adaptés à des conditions de basses températures en début de cycle, et de fournir des outils pour la sélection de ces nouveaux idéotypes. Dans un premier temps le modèle de culture SUNFLO, développé pour l’analyse des interactions génotype x environnement chez le tournesol, a été utilisé pour identifier par simulation un idéotype pour le semis précoce. Cette étude a révélé que le type variétal valorisant le mieux de semis précoce présente une levée précoce et un cycle tardif. Dans un deuxième temps, la variabilité génétique d’une population de lignées recombinantes de tournesol a été une analysée pour des traits agro-morphologiques et physiologiques caractérisant le développement (vitesse de germination, phénologie) et la croissance à basse température (élongation de l’hypocotyle, production de biomasse, et traits physiologiques impliqués dans la tolérance au froid). L’analyse génétique de ces caractères a permis d’identifier les régions chromosomiques impliquées dans la variation de ces caractères (QTLs) ainsi que les marqueurs moléculaires associés à ces QTLs qui représentent des marqueurs d’intérêts pour la sélection. L’analyse des processus impliqués dans la levée (germination et élongation de l’hypocotyle) montre que la température de base pour l’élongation de l’hypocotyle présente un gain génétique significatif à basse température. Ce trait est sous le contrôle génétique de deux QTLs majeurs dont l’un, qui explique 40% de la variabilité phénotypique observée, est lié au marqueur SSR ORS1128. Le temps thermique du semis à la floraison est un caractère contrôlé par des QTLs spécifiques en conditions de semis précoces, parmi lesquels deux sont colocalisés avec des QTLs identifiés pour des traits relatifs à la levée. L’étude des traits physiologiques impliqués dans la réponse aux basses températures a révélé que le tournesol a un potentiel de sélection pour la tolérance au froid, notamment pour le potentiel osmotique. Le maintien des membranes plasmiques stables à basses températures est également un trait jouant un rôle important dans la tolérance au froid. Un QTL à effet majeur lié au marqueur SSR ORS331_2 a été identifié pour ce trait et pourrait être utilisé pour aider à la sélection de génotypes de tournesol adaptés au froid
Early sowing to escape the drought during summer was studied in sunflower. Sowing one or two months earlier leads to reduce about 5 to 10°C during first stages of development compared with traditional sowing (April in south parts of France) in this species. The aim of this study is to identify sunflower genotypes adapted for low temperature and to identify tools for selecting them. Firstly the crop model SUNFLO, Which is developed to analyze “genotype x environment” interactions in sunflower, was used to identify by simulation favorable ideotypes for early sowing. Results show that they have to present early emergence and a late development cycle. Then, several experiments were undertaken to study genetic variability for agro-morphologic and physiologic traits under early sowing in sunflower. A population of 95 recombinant inbred lines and their two parents were used at low temperature in all experiments. Germination rate, hypocotyl elongation, biomass production and some physiological traits for cold tolerance were studied. Genetic analyses were performed and genomic regions (QTLs) involved in the variation of these traits as well as SSR markers associated with them were identified. Analysis of physiological processes related to emergence (germination and hypocotyl elongation) show that the base temperature of hypocotyl elongation presents a significant genetic gain at low temperature. This trait is controlled by two major QTLs and one of them explains 40% of the phenotypic variance and contains the SSR marker ORS1128. The thermal time from sowing to flowering is controlled by specific QTLs in early sowing and two of them are collocated with QTLs detected for emergence related-traits. The study of physiological traits implied with response to low temperature showed that sunflower present a high potential for cold tolerance variability, especially for the osmotic potential. The cell membrane stability at low temperature is also an important trait for cold tolerance. A major QTL associated with the SSR marker ORS331_2 was identified for this trait and should be used to select sunflower cold tolerant genotypes

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

Doctor of Philosophy
Department of Agronomy
Guihua Bai
Guorong Zhang
Fusarium head blight (FHB) is a devastating fungal disease in wheat, reducing not only grain yield but also quality. The pathogen produces the mycotoxin deoxynivalenol (DON) that induces severe toxicological problems in human and animals. Using host resistance has been the most efficient way to control the disease. To identify quantitative trait loci (QTLs) for FHB resistance in Chinese landrace Haiyanzhong (HYZ), a recombinant inbred lines (RILs) population derived from a cross between HYZ and Wheaton was developed. The RILs were evaluated for percentage of symptomatic spikelets (PSS) in three greenhouse experiments, and genotyped using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNPs) developed from genotyping-by-sequencing (GBS). Eight QTLs were identified for type II (PSS) resistance on chromosomes 5A, 6B, 7D, 2B (2), 3B, 4B, and 4D, with 5A as the major QTL. Ten SNPs closely linked to 5A, 6B, and 2B QTLs were successfully converted to Kompetitave allelic specific PCR (KASP) assays. To identify common QTLs across different populations, we constructed high-density GBS-SNP maps in an additional four RIL populations derived from the Chinese landraces, Wangshuibai (WSB), Baishanyuehuang (BSYH), Huangfangzhu (HFZ), and Huangchandou (HCD) and conducted meta-analysis of the QTLs for FHB resistance using a consensus map developed from the five populations. We identified six MQTLs on chromosomes 3BS (2), 3A, 3D, 2D, and 4D and 23 tightly linked GBS-SNPs to the MQTLs. These GBS-SNPs were successfully converted to KASPs. The KASPs linked to MQTLs can be used for pyramiding these QTL in breeding programs. To quickly reduce FHB damage in U.S. hard winter wheat (HWW), we transferred Fhb1, a major QTL with stable effects on FHB resistance, from Ning7840 into three adapted HWW cultivars Overland, Jagger, and Overley, by marker-assisted backcross (MAB), and assessed the effect of Fhb1 on FHB resistance in these different backgrounds. The results showed that Fhb1 can significantly lower FHB severity, Fusarium-damaged kernel (FDK), and DON accumulation in the all the three HWW backgrounds. Some of the selected lines showed high levels of FHB resistance, but agronomically similar traits as recurrent parents, can be used as resistant parents to improve HWW FHB resistance.

The yellowness of flour colour ranges is an important quality trait in wheat for end-use products and is determined by the accumulation of carotenoids in the endosperm. The aims of this study were to develop EST-based molecular markers for genes encoding enzymes of the carotenoid biosynthetic pathway leading to xanthophyll accumulation and identify quantitative trait loci for flour colour (b*) and xanthophyll content in Western Australian adapted germplasm. A novel bioinformatic strategy was developed to identify rice genes encoding key enzymes of the carotenoid biosynthetic pathway and to predict wheat orthologues on the short arm of chromosome 3 or long arm of chromosome 7. The bioinformatic strategy involved the identification of rice carotenoid genes on BAC/PAC contigs aligned to wheat mapped ESTs. Rice genes predicted to have wheat orthologues were selected based on ESTs mapping to regions on wheat homoeologous chromosomes 3 and 7 known to be involved in flour colour. The rice genes predicted to have wheat orthologues were Geranylgeranyltransferase I ƒÒ¡Vsubunit (GGT-Ibeta) and Rab geranylgeranyltransferase component A (RGGT-A) on the short arm of chromosome 3, Lycopene ƒÒ¡Vcylcase (LBC) on the long arm of chromosome 3 and Lycopene £`¡Vcylcase (LEC) on the long arm of chromosome 7. The prediction of these wheat orthologues provided the basis for development of EST-based molecular markers for detecting variation in xanthophyll content. Wheat ESTs with unknown chromosomal locations and having the highest similarity to GGT-Ibeta, RGGT-A and LBC were selected for the development of molecular markers. No EST homologues were identified for LEC and therefore this gene was not further considered. Orthology was confirmed by sequencing and deletion lines were used to confirm chromosomal locations. Two partial orthologues of GGT-Ibeta were identified on the short arms of chromosomes 3B and 3D. A partial orthologue of RGGT-A was mapped to the proximal regions of the short and long arms of chromosome 3B. At least two or more orthologues of LBC were identified from nullisomic-tetrasomic lines. An EST-based molecular marker for GGT-Ibeta was found to be involved in minor variation of xanthophyll content in a Westonia*2/Janz doubled haploid population. QTL analysis from three doubled haploid populations indicated variation in WA-adapted germplasm may be due to different alleles controlling flour colour. QTLs for b* and xanthophyll content were found to coincide on the short arms of chromosomes 3A, 4D, and 7B and the long arm of chromosomes 7A and 7B in WA-adapted germplasm. Homoeologous expression of regions controlling variation in b* and xanthophyll content on the long arm of chromosomes 7A and 7B suggests the shut-down of genes in the same region on chromosome 7D. The main outcome of this study is flour colour and identification of gene orthologues in wheat controlling variation in xanthophyll content is complex most likely because of the interaction of the carotenoid biosynthetic pathway with other pathways.

Second generation biofuels are seen as a sustainable solution to the problem of dwindling fossil fuels stocks. However, the process of converting lignocellulosic biomass to sugars for fermentation is expensive due the recalcitrance of these materials to enzymatic digestion. The identification of quantitative trait loci (QTL) in the model grass species Brachypodium distachyon was undertaken in order to improve our understanding of genes that affect straw digestibility. Initially, the study focused on the analysis of natural accessions to determine if there was variation, in terms of digestibility and cell wall composition, within the species and to identify lines suitable for producing recombinant inbred lines (RILs). This information was successfully used to initiate the production of a RIL population that can be used in future research. I made use of a pre-existing RIL population produced previously from a bi-parental cross between Bd21 and Bd3.1 to study pathogen resistance. This RIL population was screened for straw digestibility using a semi-automated robotic platform. This data together with the genotype data was used to identify QTL linked to digestibility. A single QTL was detected on chromosome 5 together with a further QTL on chromosome 3 that acted in epistasis. A candidate gene for each of the QTLs was identified by reviewing those located within the QTL regions. The chromosome 5 candidate gene encodes a glycosyl hydrolase family 43 family protein likely involved in xylan biosynthesis and the chromosome 3 candidate gene is a cellulose synthase-like subfamily A protein that has a possible glucomannan 4-beta-mannosyltransferase function. Functionality was analysed by studying the cell wall composition of selected RILs and corresponding Arabidopsis thaliana T-DNA lines to determine any differences in the secondary cell wall structure. The results indicated that the differences in digestibility are associated with subtle differences in cell wall composition.

The yellowness of flour colour ranges is an important quality trait in wheat for end-use products and is determined by the accumulation of carotenoids in the endosperm. The aims of this study were to develop EST-based molecular markers for genes encoding enzymes of the carotenoid biosynthetic pathway leading to xanthophyll accumulation and identify quantitative trait loci for flour colour (b*) and xanthophyll content in Western Australian adapted germplasm. A novel bioinformatic strategy was developed to identify rice genes encoding key enzymes of the carotenoid biosynthetic pathway and to predict wheat orthologues on the short arm of chromosome 3 or long arm of chromosome 7. The bioinformatic strategy involved the identification of rice carotenoid genes on BAC/PAC contigs aligned to wheat mapped ESTs. Rice genes predicted to have wheat orthologues were selected based on ESTs mapping to regions on wheat homoeologous chromosomes 3 and 7 known to be involved in flour colour. The rice genes predicted to have wheat orthologues were Geranylgeranyltransferase I beta-subunit (GGT-Ibeta) and Rab geranylgeranyltransferase component A (RGGT-A) on the short arm of chromosome 3, Lycopene beta-cylcase (LBC) on the long arm of chromosome 3 and Lycopene epsilon-cylcase (LEC) on the long arm of chromosome 7. The prediction of these wheat orthologues provided the basis for development of EST-based molecular markers for detecting variation in xanthophyll content. Wheat ESTs with unknown chromosomal locations and having the highest similarity to GGT-Ibeta, RGGT-A and LBC were selected for the development of molecular markers. No EST homologues were identified for LEC and therefore this gene was not further considered. Orthology was confirmed by sequencing and deletion lines were used to confirm chromosomal locations. Two partial orthologues of GGT-Ibeta were identified on the short arms of chromosomes 3B and 3D. A partial orthologue of RGGT-A was mapped to the proximal regions of the short and long arms of chromosome 3B. At least two or more orthologues of LBC were identified from nullisomic-tetrasomic lines. An EST-based molecular marker for GGT-Ibeta was found to be involved in minor variation of xanthophyll content in a Westonia*2/Janz doubled haploid population. QTL analysis from three doubled haploid populations indicated variation in WA-adapted germplasm may be due to different alleles controlling flour colour. QTLs for b* and xanthophyll content were found to coincide on the short arms of chromosomes 3A, 4D, and 7B and the long arm of chromosomes 7A and 7B in WA-adapted germplasm. Homoeologous expression of regions controlling variation in b* and xanthophyll content on the long arm of chromosomes 7A and 7B suggests the shut-down of genes in the same region on chromosome 7D. The main outcome of this study is flour colour and identification of gene orthologues in wheat controlling variation in xanthophyll content is complex most likely because of the interaction of the carotenoid biosynthetic pathway with other pathways.

The yellowness of flour colour ranges is an important quality trait in wheat for end-use products and is determined by the accumulation of carotenoids in the endosperm. The aims of this study were to develop EST-based molecular markers for genes encoding enzymes of the carotenoid biosynthetic pathway leading to xanthophyll accumulation and identify quantitative trait loci for flour colour (b*) and xanthophyll content in Western Australian adapted germplasm. A novel bioinformatic strategy was developed to identify rice genes encoding key enzymes of the carotenoid biosynthetic pathway and to predict wheat orthologues on the short arm of chromosome 3 or long arm of chromosome 7. The bioinformatic strategy involved the identification of rice carotenoid genes on BAC/PAC contigs aligned to wheat mapped ESTs. Rice genes predicted to have wheat orthologues were selected based on ESTs mapping to regions on wheat homoeologous chromosomes 3 and 7 known to be involved in flour colour. The rice genes predicted to have wheat orthologues were Geranylgeranyltransferase I beta-subunit (GGT-Ibeta) and Rab geranylgeranyltransferase component A (RGGT-A) on the short arm of chromosome 3, Lycopene beta-cylcase (LBC) on the long arm of chromosome 3 and Lycopene epsilon-cylcase (LEC) on the long arm of chromosome 7. The prediction of these wheat orthologues provided the basis for development of EST-based molecular markers for detecting variation in xanthophyll content. Wheat ESTs with unknown chromosomal locations and having the highest similarity to GGT-Ibeta, RGGT-A and LBC were selected for the development of molecular markers. No EST homologues were identified for LEC and therefore this gene was not further considered. Orthology was confirmed by sequencing and deletion lines were used to confirm chromosomal locations. Two partial orthologues of GGT-Ibeta were identified on the short arms of chromosomes 3B and 3D. A partial orthologue of RGGT-A was mapped to the proximal regions of the short and long arms of chromosome 3B. At least two or more orthologues of LBC were identified from nullisomic-tetrasomic lines. An EST-based molecular marker for GGT-Ibeta was found to be involved in minor variation of xanthophyll content in a Westonia*2/Janz doubled haploid population. QTL analysis from three doubled haploid populations indicated variation in WA-adapted germplasm may be due to different alleles controlling flour colour. QTLs for b* and xanthophyll content were found to coincide on the short arms of chromosomes 3A, 4D, and 7B and the long arm of chromosomes 7A and 7B in WA-adapted germplasm. Homoeologous expression of regions controlling variation in b* and xanthophyll content on the long arm of chromosomes 7A and 7B suggests the shut-down of genes in the same region on chromosome 7D. The main outcome of this study is flour colour and identification of gene orthologues in wheat controlling variation in xanthophyll content is complex most likely because of the interaction of the carotenoid biosynthetic pathway with other pathways.