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

Fusarium head blight (FHB) caused by Fusarium graminearum is a fungal disease of wheat that can result in severe yield losses and contaminate grain with deoxynivalenol (DON). Wheat cultivars with different levels of FHB resistance were combined with fungicides application to control FHB. Results showed that foliar fungicide Prosaro™ combined with moderately resistant cultivars greatly reduced the risk of FHB. Integrating fungicide application with moderately resistant cultivars can be an effective strategy in controlling FHB. Quantitative trait loci (QTL) for resistance to FHB related traits were analyzed using a double haploid population. Four QTL associated with FHB resistance was detected on chromosomes 2B, 2D, 4D and 7A. The QTL on chromosome 2B and 4D were found to reduce multiple FHB-related traits and were more frequently detected than QTL on chromosome 2D and 7A. QTL on chromosome 2B and 4D could be valuable for improving FHB resistance in wheat. / October 2015

Infectious disease is an important issue for animal breeders, farmers and governments. Solutions to control infectious disease are needed and research focused on the genetic loci determining variation in immune-related traits has the potential to deliver solutions. The primary aim of this thesis is to discover regions of the bovine genome which influence the immune response post immunisation. To accomplish this two types of immunising agents, a Foot-and-Mouth Disease Virus (FMDV) peptide (FMDV15) and a commercial vaccine for Bovine Respiratory Syncytial Virus (BRSV), were used to immunise the second generation (F2 and backcrosses) of the Roslin Bovine Genome (RoBoGen) herd, a Charolais Holstein cross population. The FMDV15 peptide consisted of two sections of the VP1 protein located on the FMDV capsid, together encompassing the major neutralising antibody sites that are known to be immunogenic. Protection against FMDV is generally believed to relate to the levels of neutralising antibody and has been correlated with IgG1 and IgG2 levels as well as interferon- . In addition it has been shown that T cell responses also play a role in protection against FMDV. Thus all of these were used as phenotypic measurements post immunisation to the FMDV15 peptide. The BRSV vaccine used was an attenuated live vaccine. Protective mechanisms against BRSV infection include IgA, IgG1, IgG2 and IgM BRSV-specific antibodies and antibody titres particularly those of the IgG isotypes are considered to be correlates of protection. Thus, IgG1 and IgG2 antibody levels were measured post vaccination with the BRSV vaccine. All phenotypes were measured across time, and allowed analysis of the primary and secondary adaptive immune responses. Both agents caused considerable variation in the phenotypes measured post immunisation, with significant responses detected two weeks post immunisation. REstricted Maximum Likelihood (REML) analysis attributed much of this variation to sire, highlighting the heritable component, and environmental effects. Significant positive correlations were detected across time within each trait for both the FMDV and BRSV responses. The FMDV and BRSV antibody levels also correlated with each other at later time points, suggesting that there may be animals which are genetically predisposed to be high or low responders in general. Initially a linkage mappingapproach was followed using 165 microsatellite markers, which detected 77 QTL in response to the FMDV peptide and 27 QTL in response to the BRSV vaccine. There were some overlapping QTL, for example QTL which spanned the Major Histocompatibility Complex. Further analysis was conducted by developing a Perl scripted program which genotyped the RoBoGen herd in two ways; 1) Single Nucleotide Polymorphism(s) (SNP) were genotyped within the confidence intervals of the previously discovered QTL and 2) SNP were genotyped via a candidate gene approach. Association study methodology, accounting for relationship stratification via principal components of the genetic relationship matrix, was used to detect significant SNP, in response to both the FMDV peptide and the BRSV vaccine. Twenty significant SNP associations were discovered across 19 traits, with some SNP located in genes with known biological relevance to an immune response, such as the Toll-Like Receptors (TLR), TLR4 and TLR8. This thesis has detected regions of the genome which are significantly associated with the immune responses elicited by two different agents, suggesting similar pathway(s)/gene(s) may be used in defence of multiple pathogens. Once regions of significance were detected, further analysis using SNP markers identified significant, non-synonymous SNP that were associated with the immunising agents. The novel markers discovered in this study may aid breeding for resistance to disease via marker assisted selection. In addition, they may also have highlighted new targets for vaccinologists to develop ‘next generation’ vaccines.

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

Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual the extreme progeny may be selected by multiple generations of asexual reproduction and selection. In this thesis I will analyse this method of measuring phenotype in asexual cross progeny. The aim is to examine the behaviour of marker allele frequency due to selection over many generations, and also to identify statistically significant changes in frequency in the selected population. I will show that stochasticity in marker frequency in the selected population arises due the finite initial population size. For Mendelian traits, the initial population size should be at least in the low to mid hundreds to avoid spurious changes in marker frequency in the selected population. For quantitative traits the length of time selection is applied for, as well as the initial population size, will affect the stochasticity in marker frequency. The longer selection is applied for, the more chance of spurious changes in marker frequency. Also for quantitative traits, I will show that the presence of epistasis can hinder changes in marker frequency at selected loci, and consequently make identification of selected loci more difficult. I also show that it is possible to detect epistasis from the marker frequency by identifying reversals in the direction of marker frequency change. Finally, I develop a maximum likelihood based statistical model that aims to identify significant changes in marker frequency in the selected population. I will show that the power of this statistical model is high for detecting large changes in marker frequency, but very low for detecting small changes in frequency.

Sorghum downy mildew (SDM) of maize is caused by the oomycete Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw. The disease can cause devastating yield losses in maize (Zea mays L.). Quantitative trait loci (QTLs) mediating resistance to SDM were mapped using both restriction fragment length polymorphisms (RFLPs), and simple sequence repeats (SSRs) in 220 F2 individual maize progeny derived from a cross between two extremes; highly susceptible inbred parent SC-TEP5-19-1-3-1-4-1-1 (white) and highly resistant inbred P345C4S2B46-2-2-1-2-B-B-B (yellow). The phenotypic expression was assessed on F2:3 families in a wide range of environments under natural field infection and in a controlled greenhouse screening method. Heritability estimates of disease reaction ranged from 93.3% in Thailand sit 1 to 48% in Thailand sit 2. One hundred and thirty three polymorphic markers were assigned to the ten chromosomes of maize with LOD scores exceeding 4.9 covering about 1265 cM with an average interval length between markers of 9.5 cM. About 90% of the genome was located within a 10 cM distance to the nearest marker. Three putative QTLs were detected in association with resistance to SDM in different environments using composite interval mapping. Despite environmental and symptom differences, one QTL on chromosome 2 bin 9 had a major effect in all trials and explained up to 70% of the phenotypic variation in Thailand where the highest disease pressure was experienced. Two other QTLs on chromosome 3 bin 5 and chromosome 9 bin 2 had a minor effect, each explaining no more than 4% of the phenotypic variation. These results revealed one major gene and two minor genes that control sorghum downy mildew resistance. These markers should be very useful in breeding programs in facilitating the introgression of the resistance genes into commercial varieties. Marker-assisted selection for these loci should be useful in incorporating SDM resistance genes in maize across environments, even in the absence of the pathogen.

Sorghum (Sorghum bicolor [L.] Moench) is the world's fifth most economically important cereal crop, grown worldwide as a source of food for both humans and livestock. Sorghum is a C4 grass that is well adapted to hot and arid climes and is popular for cultivation on lands of marginal quality. Recent interest in development of biofuels from lignocellulosic biomass has drawn attention to sorghum, which can be cultivated in areas not suitable for more traditional crops, and is capable of generating plant biomass in excess of 40 tons per acre. While the quantity of biomass and low water consumption make sorghum a viable candidate for biofuels growth, the biomass composition is enriched in lignin, which is problematic for enzymatic and chemical conversion techniques. The genetic basis for stem composition was analyzed in sorghum populations using a combination of genetic, genomic, and bioinformatics techniques. Utilizing acetyl bromide extraction, the variation in stem lignin content was quantified across several sorghum cultivars, confirming that lignin content varied considerably among sorghum cultivars. Previous work identifying sorghum reduced-lignin lines has involved the monolignol biosynthetic pathway; all steps in the pathway were putatively identified in the sorghum genome using sequence analysis. A bioinformatics toolkit was constructed to allow for the development of genetic markers in sorghum populations, and a database and web portal were generated to allow users to access previously developed genetic markers. Recombinant inbred lines were analyzed for stem composition using near infrared reflectance spectroscopy (NIR) and genetic maps constructed using restriction site-linked polymorphisms, revealing 34 quantitative trail loci (QTL) for stem composition variation in a BTx642 x RTx7000 population, and six QTL for stem composition variation in an SC56 x RTx7000 population. Sequencing the genome of BTx642 and RTx7000 to a depth of ~11x using Illumina sequencing revealed approximately 1.4 million single nucleotide polymorphisms (SNPs) and 1 million SNPs, respectively. These polymorphisms can be used to identify putative amino acid changes in genes within these genotypes, and can also be used for fine mapping. Plotting the density of these SNPs revealed patterns of genetic inheritance from shared ancestral lines both between the newly sequenced genotypes and relative to the reference genotype BTx623.

En l'estudi de l'ansietat, models animals com ara les soques de rates Roman High i Low-Avoidance (RHA-I i RLA-I respectivament), seleccionades per llur alta o baixa adquisició de l'evitació activa en dos sentits, han demostrat tenir una gran validesa. A la primera part d'aquest treball es presenta l'avaluació d'aquestes soques a la prova de resposta de sobresalt potenciada per por i a la de condicionament de por clàssic. Tal com seria predictible, en base a la seva conducta en altres proves d'ansietat, les rates RLA-I van mostrar més potenciació per por de la resposta de sobresalt i més condicionament de por, mesurat com a resposta de petrificació. En la segona part es presenta, per primera vegada, l'avaluació conductual d'una gran mostra de rates genèticament heterogènies N/Nih-HS en una bateria de sis proves d'ansietat incondicionada i condicionada. Les soques genèticament heterogènies són una eina molt valuosa pels estudis de mapeig genètic d'alta resolució de "QTLs" (Quantitative Trait Loci), que poden permetre la identificació de gens. L'anàlisi factorial de les dades mostra una estructura multidimensional de les conductes relacionades amb la por i l'ansietat. En tots dos sexes, s'obté ha un primer factor anomenat de "Timidesa" que agrupa totes les variables relacionades amb la por de les proves incondicionades, i un segon factor en el que pesen les mesures de resposta de sobresalt ("Fugida defensiva"). Així, el present treball proporciona evidència de que existeixen relacions entre conductes d'ansietat incondicionades i d'altres condicionades. Els diferents tipus d'anàlisis estadístiques mostren resultats coherents, proporcionant per tant un cert índex de consistència interna. Els resultats d'aquest treball representen un bon punt de partida per al posterior estudi de marcadors genètics ("QTLs") de la conducta ansiosa en rates. De fet, es presenten dades preliminars que indiquen l'existència d'un QTL per a la conducta ansiosa, obtingut amb mètodes d'alta resolució, a la posició 100 Mb del cromosoma 5 de les rates N/Nih-HS. En la regió cromosòmica definida per aquest QTL es troben menys d'una desena de gens coneguts. Actualment, s'estan portant a terme estudis per avaluar la possible expressió diferencial d'aquests gens en àrees cerebrals vinculades a l'ansietat i la por en les rates RHA-I (poc ansioses) i RLA-I (molt ansioses).

Beta-carotene presence or absence in muskmelon is controlled by two genes, green flesh gf and white flesh wf. In its dominant form the wf gene is responsible for orange flesh color; however, the epistatic interactions of gf and wf can create three flesh colors: orange, white and green. Two F2 populations, consisting of 77 greenhouse grown and 117 field grown plants, from the cross of ‘Sunrise’ (white fleshed) by ‘TAM Uvalde’ (orange fleshed), were used to examine the relationships of beta-carotene content, flesh color, and flesh color intensity. Bulk segregent analysis was used with RAPD markers to identify molecular markers associated with high beta-carotene content. Flesh color and flesh color intensity both had significant relationships with beta-carotene content. A significant correlation between total soluble solids and beta-carotene content was also found. Molecular markers were identified in both F2 populations and all significant, associated markers from ‘TAM Uvalde’ were linked with WF. A single QTL was also found to be linked with the WF locus. The identified QTL can be used to screen potential breeding lines for high beta-carotene. It was also confirmed that the visual ratings of flesh color intensity can be reliably used to select high beta-carotene content melons.

In wheat, cooler canopies have been associated with yield under high temperature stress. The objectives of this study were, i) to understand the role of leaf cuticular waxes as physiological adaptive mechanisms during reproductive stage high temperature stress ii) define quantitative trait loci (QTL) regulating leaf cuticular waxes and determine its link with the QTL for reproductive stage heat tolerance iii) define stable QTL associated with leaf cuticular waxes and yield stability across environments. For the first objective, thirteen wheat cultivars were subjected to a 2-day heat treatment at 38 degrees C at 10 days after pollination (DAP). Leaf cuticular waxes, canopy temperature depression and stomatal conductance were estimated during high temperature stress. At maturity the percent reduction in yield components in each cultivar was calculated. The wheat cultivars 'Kauz' and 'Halberd' had significantly high leaf cuticular wax content of 2.91mg/dm^-2 and 2.36mg/dm^-2 respectively and cooler canopies. Leaf cuticular waxes were significantly correlated with leaf temperature depression and reduction in yield components. A set of 121 recombinant inbred lines (RIL) population derived from the cross of heat tolerant wheat cultivar 'Halberd' and heat susceptible wheat cultivar 'Karl 92' was utilized for QTL mapping. The RIL population received a 2-day short-term high temperature stress at 38°C at 10DAP in 2008 and a long-term high temperature stress at 38 degrees C from 10DAP until maturity in 2009 in the greenhouse. The RIL population was also planted in College Station, Texas in 2009 and 2010 and in Uvalde, Texas in 2010. Leaf cuticular wax was estimated at 10DAP and leaf/spike temperatures were recorded during grain filling. Yield components were estimated after harvest. Heat susceptibility indexes for main spike yield components were estimated in the greenhouse. Overall ten significant QTL were identified for leaf cuticular waxes each explaining 8-19 percent of the variation respectively. Stable QTL for leaf cuticular waxes were located on chromosome 5A and 1B and co-localized with QTL for leaf/spike temperature depression and HSI for kernel weight and single kernel weight of main spike. Another QTL on chromosome 1B contributed by Karl92 was found in the greenhouse and field environments and co-localized with a previously identified QTL on 1B for spike non-glaucousness. The results suggest that leaf cuticular waxes may reduce leaf temperatures and improve adaptation during high temperature stress.