The jasmonate (JA)-dependent signalling gene network in Arabidopsis thaliana differentially regulates responses to biotic (e.g. pathogens, wounding) and abiotic (e.g. drought) stress. In this study, three transcriptional networks using gene expression data (a large data set of microarray experiments) have been constructed in order to model the interactions between individual genes. The modelling procedures make use of gene co-expression signatures measured by partial correlation. This study presents the novel idea of integrating these signatures by generating edges between two genes in the network on the basis of profiles of partial correlations to a curated set of genes known to be involved in the response. The networks assess the interactions between regulators in the JA pathway and their cross-talk with other hormone-dependent pathways. The results confirm previously known relationships between genes based on experimental evidence and highlight additional connections to test experimentally. This method gives new insights for the discovery of novel genes in the transcriptional coordination of the JA signalling pathway.

Bambara groundnut (Vigna subterranea (L.) Verdc.) is an important underutilised legume crop, grown mainly by female subsistence farmers in Africa under traditional low input agricultural systems. Bambara groundnut is known as being of high nutritional value, as an atmospheric nitrogen fixer and to possess high levels of drought, pest and disease tolerance. Bambara groundnut is a predominantly self-pollinated crop and is grown as locally adapted landraces. These are expected to exist as non-identical inbred lines and are generally low yielding. Strategies involving genetic analysis of this species could provide important data for breeding programmes that could enhance food security in Africa. A set of 124 SSR primers designed from different library sources were tested to screen a ‘narrow’ genetic cross (F3) and a ‘wide’ genetic cross (F2) . The former is a cross between domesticated landraces (DipC and Tiga necaru) while the latter is a cross between a domesticated landrace and a wild ancestor (DipC and VSSP11). Residual heterozygosity in the F3 ‘narrow’ cross was confirmed to be around 25% based on 33 polymorphic SSR primers, consistent with an F3 population. A ‘narrow’ cross linkage map was constructed for the first time in bambara groundnut using 269 polymorphic markers (236 DArT and 33 SSR). The map consisted of 238 markers in 21 linkage groups of two or more linked markers, totalling 608.1cM and covering a predicted 54% of the bambara groundnut genome, although the high marker-marker linkage (at 89%) suggests a more comprehensive coverage. QTL analysis was carried out for 73 bulked lines of an F3 population and plants were evaluated for traits in a controlled glasshouse suite and a field trial in Indonesia. Data from single plant analysis of the F2 generation of this cross grown in a controlled environment glasshouse was also used. Most of the QTLs detected were clustered on linkage groups 1, 4 and 12. Major QTLs for internode length and biomass dry weight were detected on LG4 and LG1, respectively, for the FutureCrop glasshouse and field datasets. The highest LOD score of 9.7 was detected for peduncle length and was located within the confidence interval for a QTL for internode length locus. Marker locus bgPabg-596774 was detected to be associated with QTL for six traits; node no./plant, pod no/plant, pod weight, seed no./plant, seed yield and biomass dry weight, on LG1 within one LOD score of confidential interval, potentially suggesting pleiotropic effects of a more limited number (or even one) gene(s). One hundred and fifty-nine additional markers (136 DArT and 23 SSR) were used to improve the existing partial ‘wide’ map (141 AFLP, 1 SSR) constructed in an F2 population of 98 plants. A total of 194 markers were assigned to 20 linkage groups spanning a total of 901 cM. The linkage map derived from the ‘wide’ cross (DipC x VSSP11) had an expected genome coverage of 79.6%. An attempt to combine both maps through 32 common markers allowed a common QTL for days to emergence to be detected in both populations in close association with the common DArT markers 601384 and 601748. The main segregating traits were found to be plant spread, internode length, growth habit, peduncle length, pod weight, seed yield and biomass dry weight. Detecting the same QTL positions for a number of traits, suggested that common underlying genes might be responsible. The QTL-DNA marker associations developed in this study could be used practically for MAS in a future breeding program of this crop.

D'importants progrès ont été réalisés dans les domaines du génotypage et du séquençage, ce qui permet de mieux comprendre la relation génotype/phénotype. Il est possible d'analyser l'architecture génétique des caractères (génétique d'association, GA), ou de prédire la valeur génétique des candidats à la sélection (sélection génomique, SG). L'objectif de cette thèse était de développer des outils pour mener ces stratégies de manière optimale. Nous avons d'abord dérivé analytiquement la puissance du modèle mixte de GA, et montré que la puissance était plus faible pour les marqueurs présentant une faible diversité, une forte différentiation entre sous groupes et une forte corrélation avec les marqueurs utilisés pour estimer l'apparentement (K). Nous avons donc considéré deux estimateurs alternatifs de K. Des simulations ont montré qu'ils sont aussi efficaces que la méthode classique pour contrôler les faux positifs et augmentent la puissance. Ces résultats ont été confirmés sur les panels corné et denté du programme Cornfed, avec une augmentation de 40% du nombre de SNP détectés. Ces panels, génotypés avec une puce 50k SNP et phénotypés pour leur précocité et leur biomasse ont permis de décrire la diversité de ces groupes et de détecter des QTL. En SG, des études ont montré l'importance de la composition du jeu de calibration sur la fiabilité des prédictions. Nous avons proposé un algorithme d'échantillonnage dérivé de la théorie du G-BLUP permettant de maximiser la fiabilité des prédictions. Par rapport à un échantillon aléatoire, il permettrait de diminuer de moitié l'effort de phénotypage pour atteindre une même fiabilité de prédiction sur les panels Cornfed. / Major progresses have been achieved in genotyping technologies, which makes it easier to decipher the relationship between genotype and phenotype. This contributed to the understanding of the genetic architecture of traits (Genome Wide Association Studies, GWAS), and to better predictions of genetic value to improve breeding efficiency (Genomic Selection, GS). The objective of this thesis was to define efficient ways of leading these approaches. We first derived analytically the power from classical GWAS mixed model and showed that it was lower for markers with a small minimum allele frequency, a strong differentiation among population subgroups and that are strongly correlated with markers used for estimating the kinship matrix K. We considered therefore two alternative estimators of K. Simulations showed that these were as efficient as classical estimators to control false positive and provided more power. We confirmed these results on true datasets collected on two maize panels, and could increase by up to 40% the number of detected associations. These panels, genotyped with a 50k SNP-array and phenotyped for flowering and biomass traits, were used to characterize the diversity of Dent and Flint groups and detect QTLs. In GS, studies highlighted the importance of relationship between the calibration set (CS) and the predicted set on the accuracy of predictions. Considering low present genotyping cost, we proposed a sampling algorithm of the CS based on the G-BLUP model, which resulted in higher accuracies than other sampling strategies for all the traits considered. It could reach the same accuracy than a randomly sampled CS with half of the phenotyping effort.

Sunflower (Helianthus annuus) consists of high levels of polyunsaturated fatty acids, making its oil susceptible to oxidation. Tocopherols can retard or prevented oxidation. The aim of this study is to determine the phenotypic tocopherol (vitamin E) composition and genetic diversity of the biosynthetic pathway genes. Seeds were characterized for fatty acid and tocopherol content. A positive correlation was found between oleic acid, γ (r =0.17) and δ (r =0.23) tocopherol but none between linoleic acid and all four tocopherol derivatives. Vitamin E gene homologues were identified and a concomitant pathway constructed, with genes of interest sequenced to determine their genetic variation. A sunflower gene database was developed for these genes and used to obtain 489 SNPs and 145 indels from the accessions evaluated. Only 139 of these SNPs were located in the exon regions of the gene candidates. These exon-based SNPs may influence tocopherol flow through possible enzyme structural modifications / School of Agriculture and Life Sciences / M. Sc. (Life Sciences)