Heat stress adversely affects wheat production in many regions of the world and is particularly detrimental during reproductive development. The objective of this study was to identify quantitative trait loci (QTL) associated with improved heat tolerance in hexaploid bread wheat (Triticum aestivum). To accomplish this objective, an analysis of both the phenotypic and genetic responses of two recombinant inbred line (RIL) populations was conducted. RIL populations Halberd x Cutter and Halberd x Karl 92 (H/K) both derive heat tolerance from Halberd and segregate in their response to heat stress. A heat susceptibility index (HSI) was calculated from the reduction of three yield components; kernel number, kernel weight, and single kernel weight, following a three-day 38 degrees C heat stress treatment during early grain-filling. The HSI, as well as temperature depression of the main spike and flag leaf were used as measurements of heat tolerance. Genetic linkage maps were constructed for both populations and were used in combination with phenotypic data and statistical software to detect QTL for heat tolerance. In a comparison across the two across populations, seven common QTL regions were identified for HSI, located on chromosomes 1B, 3B, 4A, 5A, 5B, and 6D. Subsequent analysis of temperature depression in the H/K population identified seven QTL that co-localized for both cooler organ temperature and improved HSI. Four of the beneficial alleles at these loci were contributed Halberd. The genetic effect of combining QTL, including QHkw.tam-1B, QHkwm.tam-5A.1, and QHskm.tam-6D showed the potential benefit of selection for multiple heat tolerant alleles simultaneously. Analysis of the H/K population in the field under abiotic stress detected QTL on chromosome 3B and 5A, which were in agreement with results from the greenhouse study. The locus QYld.tam-3B was pleiotropic for both temperature depression and HSI in both experiments and was associated with higher biomass and yield under field conditions. The results presented here represent a comprehensive analysis of both the phenotypic response of wheat to high temperature stress and the genetic loci associated with improved heat tolerance and will be valuable for future understanding and improvement of heat stress tolerance in wheat.

In the interest of understanding the genetic basis of adaption to environment, we developed F2 lines from an F1 interspecific cross between the rare serpentine endemic, Caulanthus amplexicaulis var. barbarae and the non-serpentine Caulanthus amplexicaulis var. amplexicaulis. Using genomic DNA from Caulanthus amplexicaulis var. barbarae, we developed a suite of microsatellite markers. In addition, we developed gene specific markers for genes known in Arabidopsis to be ecologically important. Our suite of markers was used to genotype 186 F2 plants, the basis for our F2 linkage map. In order to further resolve evolutionary relationships among related taxa, we constructed a molecular phylogeny for 52 taxa within the related genera Caulanthus, Guillenia, Sibaropsis, Streptanthella, and Streptanthus, using the sequences from the ribosomal ITS region and two chloroplast regions. To create a useful system to enable comparative genomics within the related taxa of the ecologically and morphologically diverse Streptanthoid Complex, we demonstrated that our molecular tools are portable across a large group of ecologically significant taxa. To use the significant genomic resources available in Arabidopsis, we constructed a collinear comparative map of Caulanthus and the model plant Arabidopsis thaliana based on ancestral linkage blocks with the Brassicaceae family. This comparative map acted as a guide for candidate gene selection in the mapping of sepal color. We identified a region of MYB transcription factors in an orthologous region of Arabidopsis. Sequence data from Caulanthus amplexicaulis var. barbarae and Caulanthus amplexicaulis var. amplexicaulis in this MYB region showed significant sequence divergence between the two taxa. To determine the genetic basis for the tolerance of high concentrations of magnesium in Caulanthus amplexicaulis var. barbarae, we phenotyped multiple individuals from 88 F2:3 families under two nutrient treatments, differing in the ratio of calcium to magnesium. Through QTL analysis, using our F2 linkage map as a framework for the analysis, we identified one major effect QTL on Caulanthus Linkage Group 8 and another QTL on Caulanthus Linkage Group 3. We identified candidate genes for the QTLs using our collinear comparative map to Arabidopsis.

Cucurbit yellow stunting disorder virus (CYSDV) is a relatively new virus affecting cantaloupe production in South Texas and worldwide. No resistant commercial cultivars are available. A cross of ‘Dulce’ (susceptible) x ‘TGR1551’ (resistant) was made and populations were developed for screening. Although no complete resistance was recovered, ‘TGR1551’ showed some tolerance and may be useful in breeding efforts. Sugar components such as sucrose, fructose, glucose, and total soluble solids are major factors in determining mature melon fruit sweetness, and Vitamin C is important for human health. A F2 population was developed from the melon cross ‘Dulce’ (high values) x ‘TGR1551’ (low values) and bulked segregant analysis was used to detect random amplified polymorphic DNA (RAPD) markers associated with quantitative trait loci (QTL) for each trait. Out of 500 primers, fifteen RAPD markers were found to be significantly associated with fruit quality QTL. These markers could be useful in a marker assisted selection program to transfer these genes into a low quality cultivar or breeding line to enhance fruit quality. Gummy stem blight (Didymella brioniae) affects melon production in South Texas as well as other melon production areas in the U.S. A cross between ‘TMS’ (susceptible) and PI 140471 (resistant) was made and a F2 population was screened with a strain of the disease from South Texas. F2 plants exhibited symptoms ranging from resistant to susceptible. PI 140471 may be useful in developing commercial varieties of melon resistant to the disease in Texas. Monosporascus root rot and vine decline (Monosporascus cannonballus) affects melon production in South Texas as well as other melon production areas in the US. A cross was made between ‘TGR1551’ (moderately resistant) and ‘Deltex’ (resistant) to develop a F2 population. Both parents and the F2 were planted in infested soil. Once symptoms appeared, plant roots were removed from the soil and rated. ‘TGR1551’ showed greater resistance than ‘Deltex’ and should be utilized in breeding to develop improved resistant cultivars.

The Lake Malawi cichlid fishes are a pre-eminent example of adaptive evolutionary radiation. The diversity of species (nearly 1000 extant) is mirrored by an array of variation in dozens of phenotypes (e.g. trophic morphology, tooth shape, color patterns, behavior, development). The unique characteristics of this system have produced unparalleled diversity with very little genetic differentiation between species. This dissertation is composed of four studies addressing different aspects of the variation in the LM cichlids and the mechanisms generating and maintaining this level of diversity at multiple biological levels. Community-level diversity is investigated using null model analysis of species co-occurrence data. We detect signals of non-random community assembly at only the broadest and finest spatial scales. Based on the unique ecological and evolutionary characteristics of this assemblage we suggest that different mechanisms are responsible for these patterns. A core‟ group of species is posited to act as a foundation on which these diverse communities are created as a result of fine-scale species interactions. We identify both positive and negative depth-based correlations between species and suggest these interactions play an important role in species diversity in these fish. The Lake Malawi cichlids exhibit an array of trophic morphologies which may play a role in the fine-scale species interactions described in chapter one. In the second chapter we build a genetic model to predict the evolution of jaw morphology and a complex functional jaw trait. We use a complex biomechanical system, the 4-bar jaw linkage, to simulate trait evolution during interspecific hybridizations. We find rampant transgression (trait values beyond parental distributions) in jaw function in a large proportion of potential crosses. This result is characterized by a lack of novel morphological components but rather is the result of recombinations of existing component traits thus producing functional novelty. In the third chapter we create a laboratory cross of one of the parental combinations suggested from the genetic model. The results of this study serve as a proof of principle to the simulations as we observe a large proportion of transgressive 4-bar function in the F2. As predicted this diversity is produced in the absence of transgressive morphology. We contrast these results between this complex system and data generated from several simple jaw lever traits and report differences in the patterns. Using quantitative trait locus (QTL) mapping approaches we examine the genetic basis for complex and simple jaw traits and discuss correlative patterns within and between systems. Finally we examine the genetic architecture of sex-determination and color morphs in this hybrid cross. We find both ZW and XY sex systems segregating as well as linkage to sex-specific color patterns. Several loci and epistatic interactions are associated with sex-determination and color morphs in this cross. The orange-blotch (OB) color is found associated with ZW as predicted from previous work but a previously undescribed (in these species) male nuptial color (blue) is found associated with both ZW and XY genetic systems as well as other loci segregating for sex-determination. These results are discussed in the context of models of sex chromosome evolution as a result of sexual conflict and the potential importance of sexual selection in the diversification of Lake Malawi cichlids. Overall we observe various mechanisms generating and maintaining diversity at different levels of biological organization. We use community co-occurrence analyses, genetic simulation, and QTL analysis of an F2 hybrid population to examine these mechanisms in this rapidly radiating assemblage. These results bolster our understanding of the origins of diversity and the interplay between variation and aspects of evolution in all biological systems.

Common bacterial blight CBB, caused by Xanthomonas axonopodis pv. phaseoli, is an important disease of common bean (Phaseolus vulgaris L.). Genetic resistance is the most economically-efficient, environmentally-friendly, and socially-acceptable approach to control plant diseases including CBB. To examine the main and interaction effects of the previously-identified CBB-resistance quantitative trait loci (QTL), a resistant inter-cross population of OAC Rex and HR45 was evaluated under artificial inoculation. While the QTL on chromosome B6 of HR45 accounted for 37 to 46 % of phenotypic variation in the field, the QTL on chromosome B4 of OAC Rex was only significant in more sensitive assays using image analysis under controlled condition using a select number of lines, accounting for 15% of the variation. Broad sense heritability estimates of CBB resistance and the QTL associated with BC420 were high for severity and the area under disease progress curve, promoting the continued use of this marker in selecting CBB resistant genotypes, which in combination with SU91 marker on B8 seem to provide high levels of resistance.

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal

Fusarium Head Blight (FHB) is a destructive disease caused by Fusarium graminearum that affects wheat (Triticum aestivum L.) worldwide. Breeding for resistance to FHB is arguably the best way to combat this disease. However, FHB resistance is highly complex and phenotypic screening is difficult. Molecular markers are a promising tool but breeding programs face the challenge of allocating resources in such a way that the optimum balance between phenotypic and genotypic selection is reached. An F2:3 population derived from a resistant x susceptible cross was subjected to phenotypic and genotypic selection. For phenotyping, a novel air separation method was used to measure percentage of damaged kernels (FDK). Heritability estimates were remarkably high, which was attributed to the type of cross and the quality of phenotyping. Genotypic selection was done by selecting resistance alleles at quantitative trait loci (QTL) on the 3BS (Fhb1) and the 2DL chromosomes. Fhb1 conferred a moderate but stable FHB resistance while the 2DL QTL conferred a surprisingly high level of resistance but with significant interaction with the environment. Phenotypic selection conferred higher or lower genetic gains than genotypic selection, depending on the selection intensity. Based on these results, different selection strategies are discussed.

Brassica carinata is being actively pursued as a new industrial oil crop platform for the Canadian Prairies. A genetic assessment of B. carinata was performed to elucidate its evolutionary origins and create a genetic map to assist in locating genes and traits of interest that would help in marker-assisted breeding. First, genetic analysis using simple sequence repeat (SSR) markers, previously tested on B. juncea and B. napus, was performed, to examine the genetic diversity of 37 B. carinata lines. SSR analysis revealed world accessions were more diverse than lines conditioned to grow in the prairies. Diversity analysis revealed that the parental lines of a double haploid (DH) population, 179 and 345, obtained from the John Innes Centre (JIC), were among the more genetically diverse lines, supporting the use of this population for linkage mapping. Genetic markers created from 3’ targeted SNP discovery between 179 and 345, were tested on the DH population resulting in the generation of a B. carinata genetic linkage map essentially with no prior sequence data knowledge. This genetic map contained 341 SNP and 86 SSR loci identifying eight linkage groups belonging to the B genome, nine belonging to the C genome and two unidentified groups spanning 2041 cM. Comparative mapping of polymorphic markers identified in the amphidiploid B. carinata indicated the orientation of B and C genomes coincide with that of other Brassica species, and the two genomes have remained essentially unaltered, with no major chromosomal rearrangements since the formation of B. carinata. A lesser number of polymorphic markers were detected in the C genome, which suggested the B genome is more genetically diverse in B. carinata. Limited field trials of the 179 x 345 DH population were performed during the 2011 and 2012 growing seasons. Preliminary quantitative trait loci (QTLs) for agronomic traits including flowering time (FT), plant height (PH), and seed quality were identified.

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.

No description available.