This study comprised three major parts: a comparative physiological study of drought responses under controlled conditions; a genetic study to construct the skeleton map of a doubled haploid (DH) population; and a quantitative trait loci (QTL) analysis to identify QTLs associated with drought tolerance traits in the field. In the first part (Chapter 3), three cultivars of wheat (Triticum aestivum L.) adapted to South Australian conditions were tested for drought tolerance under cyclic drought in growth rooms and glasshouse. Extensive physiological traits, including stomatal conductance, chlorophyll content and fluorescence, ABA content, water status traits (e.g. osmotic adjustment, RWC and leaf water potential), water soluble carbohydrates (WSC) and carbon isotope discrimination (Δ¹ ³C) were measured during experiments. Through these experiments, the drought responses of the three cultivars were physiologically dissected and the likely processes contributing most to drought tolerance were identified. In the South Australian wheatbelt, cyclic drought is a frequent event, represented by intermittent periods of rainfall which can occur around anthesis and post-anthesis in wheat. Three South Australian bread wheat cultivars, Excalibur, Kukri and RAC875, were evaluated in two growth room experiments under cyclic water-limiting conditions. In the first experiment, where plants were subjected to severe water stress, RAC875 and Excalibur (drought tolerant) showed significantly (P < 0.05) higher grain yield under cyclic water availability compared to Kukri (drought susceptible), producing 44% and 18% more grain yield compared to Kukri, respectively. In the second growth room experiment, where plants were subjected to a milder drought stress, the differences between cultivars were less pronounced, with only RAC875 showing significantly higher grain yield under the cyclic water treatment. Grain number per spike and the percentage of aborted tillers were the major yield components that affected yield under cyclic water stress. Excalibur and RAC875 adopted different morpho-physiological traits and mechanisms to reduce water stress. Excalibur was most responsive to cyclic water availability and showed the highest level of osmotic adjustment (OA), highest stomatal conductance, lowest ABA content and most rapid recovery from stress under cyclic water stress. RAC875 was more ‘conservative’ in its responses, with moderate OA, high leaf waxiness, high chlorophyll content and slower recovery from stress. Within this germplasm, the capacity for osmotic adjustment was the main physiological attribute associated with tolerance under cyclic water stress, which enabled plants to recover from water deficit. In the second part (Chapter 4), the genetic linkage map of a DH population including 368 lines, which was developed from a cross between ‘RAC875’ and ‘Kukri’, was constructed. The genetic linkage map consisted of about 500 molecular markers including ~300 DArT (Diversity array technology) and ~200 SSR (Microsattelite markers). In the third part (Chapter 5), Quantitative Trait Loci (QTLs) linked to plant phenology and production traits under irrigated and drought stress conditions were mapped by means of a DH population. To phenotype the population, 368 DH lines were cultivated in two replicates in five environments (three sites across South Australian wheatbelt in collaboration with Australian Grain Technology (AGT) in 2006, and two trials in Mexico in collaboration with CYMMIT, 2007). Data of grain yield, yield components, maturity related traits and some morpho-physiological traits such as leaf chlorophyll content, leaf waxiness, plant height, peduncle length, flag leaf and spike length were measured. Raw data were then analysed for spatial variation for each single trial using the REML procedure in GenStat (version 6). The DH lines showed significant variation for plant phenology, grain yield and yield components under irrigated and drought stress conditions. QTL analyses were performed using QTLCartographer and QTLNetwork for each trait in each site. Two major QTL for maturity traits were identified on chromosomes 2BS and 2DS corresponding to Ppd-B1 and Ppd-D1, respectively. A region was identified on chromosome 7A that harbored major QTL for grain yield, number of grains per square meter, number of grain per spike and spike fertility under drought stress. For yield data in the irrigated trial, two major QTL were identified on chromosome 3B which were not detected in drought stress environments. By using different datasets in the QTL analysis (splitting the population into two subpopulation based on heading time and also adjusting the phenotypic data for heading time to eliminate heading time effect), a QTL for grain yield was consistently detected on chromosome 7A in drought-affected environments. The coincidence of a drought response index QTL on this chromosome indicated that it might be a QTL for yield response under drought. This study demonstrated that the region on the long arm of chromosome 7A identified for grain yield and yield components is a drought response QTL which is closely linked to, but separate from, a heading time QTL. This QTL cluster on chromosome 7A could be used as a good target for positional cloning and gene isolation. However further work would be required to confirm and validate the identified QTLs in this preliminary QTL analysis. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1340056 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

This study comprised three major parts: a comparative physiological study of drought responses under controlled conditions; a genetic study to construct the skeleton map of a doubled haploid (DH) population; and a quantitative trait loci (QTL) analysis to identify QTLs associated with drought tolerance traits in the field. In the first part (Chapter 3), three cultivars of wheat (Triticum aestivum L.) adapted to South Australian conditions were tested for drought tolerance under cyclic drought in growth rooms and glasshouse. Extensive physiological traits, including stomatal conductance, chlorophyll content and fluorescence, ABA content, water status traits (e.g. osmotic adjustment, RWC and leaf water potential), water soluble carbohydrates (WSC) and carbon isotope discrimination (Δ¹ ³C) were measured during experiments. Through these experiments, the drought responses of the three cultivars were physiologically dissected and the likely processes contributing most to drought tolerance were identified. In the South Australian wheatbelt, cyclic drought is a frequent event, represented by intermittent periods of rainfall which can occur around anthesis and post-anthesis in wheat. Three South Australian bread wheat cultivars, Excalibur, Kukri and RAC875, were evaluated in two growth room experiments under cyclic water-limiting conditions. In the first experiment, where plants were subjected to severe water stress, RAC875 and Excalibur (drought tolerant) showed significantly (P < 0.05) higher grain yield under cyclic water availability compared to Kukri (drought susceptible), producing 44% and 18% more grain yield compared to Kukri, respectively. In the second growth room experiment, where plants were subjected to a milder drought stress, the differences between cultivars were less pronounced, with only RAC875 showing significantly higher grain yield under the cyclic water treatment. Grain number per spike and the percentage of aborted tillers were the major yield components that affected yield under cyclic water stress. Excalibur and RAC875 adopted different morpho-physiological traits and mechanisms to reduce water stress. Excalibur was most responsive to cyclic water availability and showed the highest level of osmotic adjustment (OA), highest stomatal conductance, lowest ABA content and most rapid recovery from stress under cyclic water stress. RAC875 was more ‘conservative’ in its responses, with moderate OA, high leaf waxiness, high chlorophyll content and slower recovery from stress. Within this germplasm, the capacity for osmotic adjustment was the main physiological attribute associated with tolerance under cyclic water stress, which enabled plants to recover from water deficit. In the second part (Chapter 4), the genetic linkage map of a DH population including 368 lines, which was developed from a cross between ‘RAC875’ and ‘Kukri’, was constructed. The genetic linkage map consisted of about 500 molecular markers including ~300 DArT (Diversity array technology) and ~200 SSR (Microsattelite markers). In the third part (Chapter 5), Quantitative Trait Loci (QTLs) linked to plant phenology and production traits under irrigated and drought stress conditions were mapped by means of a DH population. To phenotype the population, 368 DH lines were cultivated in two replicates in five environments (three sites across South Australian wheatbelt in collaboration with Australian Grain Technology (AGT) in 2006, and two trials in Mexico in collaboration with CYMMIT, 2007). Data of grain yield, yield components, maturity related traits and some morpho-physiological traits such as leaf chlorophyll content, leaf waxiness, plant height, peduncle length, flag leaf and spike length were measured. Raw data were then analysed for spatial variation for each single trial using the REML procedure in GenStat (version 6). The DH lines showed significant variation for plant phenology, grain yield and yield components under irrigated and drought stress conditions. QTL analyses were performed using QTLCartographer and QTLNetwork for each trait in each site. Two major QTL for maturity traits were identified on chromosomes 2BS and 2DS corresponding to Ppd-B1 and Ppd-D1, respectively. A region was identified on chromosome 7A that harbored major QTL for grain yield, number of grains per square meter, number of grain per spike and spike fertility under drought stress. For yield data in the irrigated trial, two major QTL were identified on chromosome 3B which were not detected in drought stress environments. By using different datasets in the QTL analysis (splitting the population into two subpopulation based on heading time and also adjusting the phenotypic data for heading time to eliminate heading time effect), a QTL for grain yield was consistently detected on chromosome 7A in drought-affected environments. The coincidence of a drought response index QTL on this chromosome indicated that it might be a QTL for yield response under drought. This study demonstrated that the region on the long arm of chromosome 7A identified for grain yield and yield components is a drought response QTL which is closely linked to, but separate from, a heading time QTL. This QTL cluster on chromosome 7A could be used as a good target for positional cloning and gene isolation. However further work would be required to confirm and validate the identified QTLs in this preliminary QTL analysis. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1340056 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

This study comprised three major parts: a comparative physiological study of drought responses under controlled conditions; a genetic study to construct the skeleton map of a doubled haploid (DH) population; and a quantitative trait loci (QTL) analysis to identify QTLs associated with drought tolerance traits in the field. In the first part (Chapter 3), three cultivars of wheat (Triticum aestivum L.) adapted to South Australian conditions were tested for drought tolerance under cyclic drought in growth rooms and glasshouse. Extensive physiological traits, including stomatal conductance, chlorophyll content and fluorescence, ABA content, water status traits (e.g. osmotic adjustment, RWC and leaf water potential), water soluble carbohydrates (WSC) and carbon isotope discrimination (Δ¹ ³C) were measured during experiments. Through these experiments, the drought responses of the three cultivars were physiologically dissected and the likely processes contributing most to drought tolerance were identified. In the South Australian wheatbelt, cyclic drought is a frequent event, represented by intermittent periods of rainfall which can occur around anthesis and post-anthesis in wheat. Three South Australian bread wheat cultivars, Excalibur, Kukri and RAC875, were evaluated in two growth room experiments under cyclic water-limiting conditions. In the first experiment, where plants were subjected to severe water stress, RAC875 and Excalibur (drought tolerant) showed significantly (P < 0.05) higher grain yield under cyclic water availability compared to Kukri (drought susceptible), producing 44% and 18% more grain yield compared to Kukri, respectively. In the second growth room experiment, where plants were subjected to a milder drought stress, the differences between cultivars were less pronounced, with only RAC875 showing significantly higher grain yield under the cyclic water treatment. Grain number per spike and the percentage of aborted tillers were the major yield components that affected yield under cyclic water stress. Excalibur and RAC875 adopted different morpho-physiological traits and mechanisms to reduce water stress. Excalibur was most responsive to cyclic water availability and showed the highest level of osmotic adjustment (OA), highest stomatal conductance, lowest ABA content and most rapid recovery from stress under cyclic water stress. RAC875 was more ‘conservative’ in its responses, with moderate OA, high leaf waxiness, high chlorophyll content and slower recovery from stress. Within this germplasm, the capacity for osmotic adjustment was the main physiological attribute associated with tolerance under cyclic water stress, which enabled plants to recover from water deficit. In the second part (Chapter 4), the genetic linkage map of a DH population including 368 lines, which was developed from a cross between ‘RAC875’ and ‘Kukri’, was constructed. The genetic linkage map consisted of about 500 molecular markers including ~300 DArT (Diversity array technology) and ~200 SSR (Microsattelite markers). In the third part (Chapter 5), Quantitative Trait Loci (QTLs) linked to plant phenology and production traits under irrigated and drought stress conditions were mapped by means of a DH population. To phenotype the population, 368 DH lines were cultivated in two replicates in five environments (three sites across South Australian wheatbelt in collaboration with Australian Grain Technology (AGT) in 2006, and two trials in Mexico in collaboration with CYMMIT, 2007). Data of grain yield, yield components, maturity related traits and some morpho-physiological traits such as leaf chlorophyll content, leaf waxiness, plant height, peduncle length, flag leaf and spike length were measured. Raw data were then analysed for spatial variation for each single trial using the REML procedure in GenStat (version 6). The DH lines showed significant variation for plant phenology, grain yield and yield components under irrigated and drought stress conditions. QTL analyses were performed using QTLCartographer and QTLNetwork for each trait in each site. Two major QTL for maturity traits were identified on chromosomes 2BS and 2DS corresponding to Ppd-B1 and Ppd-D1, respectively. A region was identified on chromosome 7A that harbored major QTL for grain yield, number of grains per square meter, number of grain per spike and spike fertility under drought stress. For yield data in the irrigated trial, two major QTL were identified on chromosome 3B which were not detected in drought stress environments. By using different datasets in the QTL analysis (splitting the population into two subpopulation based on heading time and also adjusting the phenotypic data for heading time to eliminate heading time effect), a QTL for grain yield was consistently detected on chromosome 7A in drought-affected environments. The coincidence of a drought response index QTL on this chromosome indicated that it might be a QTL for yield response under drought. This study demonstrated that the region on the long arm of chromosome 7A identified for grain yield and yield components is a drought response QTL which is closely linked to, but separate from, a heading time QTL. This QTL cluster on chromosome 7A could be used as a good target for positional cloning and gene isolation. However further work would be required to confirm and validate the identified QTLs in this preliminary QTL analysis. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1340056 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Fusarium head blight (FHB) is a major challenge in global wheat production. In the United States, the disease is predominantly caused by the fungus Fusarium graminearum. Utilization of FHB-resistant wheat cultivars integrated with other measures such as fungicide application is the most effective approach for the management of this disease. This study aimed to 1) identify novel quantitative trait loci (QTL) for resistance to FHB in a Brazilian spring wheat cultivar ‘Surpresa’ through bi-parental mapping, 2) detect QTL for FHB resistance in a global panel of 233 spring wheat accessions by genome-wide association analysis (GWAS), and 3) localize genomic regions governing traits associated with virulence in Fusarium graminearum. Using phenotypic and genotypic data from 187 recombinant inbred lines derived from the cross between Surpresa and a susceptible spring wheat cultivar ‘Wheaton’, four QTL (Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, Qfhb.ndwp-3B, and Qfhb.ndwp-4D) were mapped on chromosomes 2A, 3B, and 4D of Surpresa, respectively. Qfhb.ndwp-2AS, Qfhb.ndwp-2AL, and Qfhb.ndwp-3B were found to be novel based on physical locations of the markers tightly linked to these QTL. Two significant marker-trait associations (Qfhb.ndwp-3A and Qfhb.ndwp-2BL) were detected by GWAS of 233 spring wheat accessions, which conferred type II and type III FHB resistance and mapped on chromosomes 3A and 2B, respectively. Both QTL were novel based on the physical locations of tightly linked markers. GWAS of virulence and fungicide sensitivity using 183 F. graminearum isolates collected from North Dakota identified two significant marker-trait associations in chromosomes 1 and 3 for virulence, and two for fungicide sensitivity. The genes associated with virulence that were detected in this study were not previously reported. Identification of these novel genes in metabolic pathways of F. graminearum could help to develop new strategies for the management FHB.

Diverses lésions ostéochondrales peuvent affecter les articulations des jeunes chevaux et réduire leurs futures performances en course. L’objectif de cette thèse est d’identifier les régions du génome, appelées locus à caractère quantitatif (QTL), associées avec des caractères mesurant l’ostéochondrose (OC) enregistrés dans le programme GENEQUIN sur une population de Trotteurs Français. Le génotypage a été réalisé à l’aide de la puce SNP Illumina BeadChip EquineSNP50, qui est dense et permet d’exploiter le déséquilibre de liaison par des analyses d’association. Ces analyses sont sujettes à certains problèmes en présence d’une structure familiale des données. Dans la première partie de la thèse, une comparaison de la puissance et de la robustesse d’un choix restreint de méthodes d’analyses est effectuée. L’originalité de ce travail réside dans la dérivation algébrique des moments des distributions des statistiques de test comparées, donnant ainsi plus de généralité à nos résultats et permettant une meilleure compréhension des différences. Les résultats peuvent notamment servir à l’optimisation du dispositif expérimental. La deuxième partie est consacrée à la cartographie des régions QTL des caractères mesurant l’OC en différents sites articulaires dans une population de 583 Trotteurs Français. Cette étude a permis de mettre en évidence plusieurs régions QTL d’effets moyens et faibles à un niveau significatif mais pas hautement significatif. Nous montrons que l’OC est un caractère polygénique et qu’aucun QTL, ayant un effet à la fois sur l’OC du jarret et l’OC du boulet, n’est détectable dans ce protocole QTL, ce qui infirme l’hypothèse simple d’une cause génétique commune de la sensibilité à cette maladie sur les différents sites anatomiques. Suite à ces travaux, l’identification des gènes candidats et des mutations causales devrait clarifier la physiopathologie moléculaire de l’OC et ainsi permettre de développer des stratégies efficaces pour l’évaluation des risques. Pendant ce temps, les marqueurs peuvent être utilisés dans un contexte de sélection assistée par marqueurs afin d’améliorer la santé et le bien-être du cheval. / Osteochondral lesions are commonly observed in young horses and may be responsible for reduced performances in racing. The purpose of the PhD thesis was to identify genome regions, called quantitative trait loci (QTL), associated with various traits measuring osteochondrosis (OC) and recorded in the GENEQUIN program in a population of French Trotters horses. Genotyping was performed using the EquineSNP50 Illumina high density chip, which allows to exploit the linkage disequilibrium with genome-wide association studies. These analyses are subject to several problems in presence of family structure. We hence first proposed a comparison of power and robustness of a limited choice of models for this type of analysis. The originality of this work lies in the algebraic derivation of the distribution moments of the test statistics compared, making the outcome of this comparison more general and allowing a better understanding of differences. The results can be used to establish an experimental design. The second part was devoted to the QTL fine mapping of traits that measure OC in different joint sites. This study highlighted several significant QTL with low and medium effects but none of them were highly significant. We showed that OC is a polygenic trait and we were not able to identify QTL affecting both OC on the hock and the fetlock, rejecting the hypothesis of a single genetic determinism of susceptibility to this desease accross anatomical sites. Further studies will now focus on the identification of candidate genes and screening for mutation in an attempt to clarify the molecular physiopathology of OC and develop efficient strategies for risk assessment. Meanwhile, markers could be used in a marker-assisted selection context to improve horse health and welfare.

Made available in DSpace on 2015-03-26T13:42:02Z (GMT). No. of bitstreams: 1 texto completo.pdf: 365530 bytes, checksum: 14eb9333accf37cc0f88b5dbb33077f0 (MD5) Previous issue date: 2008-02-25 / Conselho Nacional de Desenvolvimento Científico e Tecnológico / Molecular markers can be used to identify chromosomal regions harboring quantitative trait locos (QTL) that control traits of economic importance in farm animals. To study these locos in the pig, a resource population has been generated from a cross between two Naturalized Brazilian Piau grand sires and eighteen Commercial grand dams (Landrace x Large White x Piétrain). A total of 614 F2 progeny from 50 matings of F1 parents were produced. Phenotypic data on performance, carcass, internal organs, viscera, carcass cuts and meat quality traits were collected on the F2 animals. Parentals, F1 e F2 animals were genotyped for 17 microsatellite markers covering the chromosomes 5, 7 e 8. The loci were considered appropriate for quantitative analysis, when it was analysed their values for observed heterogosity (Ho), expected heterozigosity (He) and polimorfic information content (PIC). In the chromosome 5, the average values of the Ho, He; and PIC found were 0,73; 0,66 and 0,61; in the chromosome 7, the values found were 0,81, 071 and 0,67 and in the chromosome 8 had the average values for Ho, He and PIC of 0,65; 0,65 and 0,61 respectively. After the genotype scoring, it was constructed the linkage map for these markers in the population. Association analyses were performed using interval mapping by regression for QTL detection. Seventeen QTL were mapped for carcass and cuts carcass traits on the three chromosomes, while just one QTL for feed intake were found for performance trait in the eight chromosome. One QTL for Total (bone-in) loin weight (Kg) and for bacon depth were mapped and not yet described in the literature on the seven chromosome. The generated information of significant QTL will be useful for future studies dealing fine mapping with and identification of genes that could provide a better understanding of physiology and production traits of pigs. / Marcadores moleculares podem ser usados para identificar regiões cromossômicas que contêm locos de características quantitativas (QTL) que controlam fenótipos de importância econômica em animais de produção. Para estudá-los em suínos, foi gerada uma população de um cruzamento entre dois varrões da raça naturalizada Piau e dezoito fêmeas da linha comercial (Landrace x Large White x Pietrain). Uma progênie de 614 animais na F2 foi produzida de 50 acasalamentos da F1. Os dados fenotípicos de desempenho, carcaça, órgãos internos, vísceras, corte de carcaça e qualidade de carne foram coletados nos animais F2. Os animais parentais, F1 e F2 foram genotipados para 17 marcadores tipo microssatélites cobrindo os cromossomos 5, 7 e 8. Os locos foram considerados adequados para estudos de características quantitativas, quando foram analisados os valores de heterozigosidade observada (Ho), heterozigosidade esperada (He) e conteúdo de informação polimórfica (PIC). No cromossomo 5, os valores das médias de Ho, He e PIC encontrados foram 0,73; 0,66 e 0,61; no cromossomo 7, os valores encontrados foram 0,81, 071 e 0,67 e no cromossomo 8 os valores foram 0,65; 0,65 e 0,61. Com o resultado da genotipagem foi construído o mapa de ligação específico dos marcadores para a população desenvolvida. As análises de associação foram feitas utilizando mapeamento por intervalo por regressão para detecção de QTL. Foram detectados 17 QTL para características de carcaça e corte de carcaça nos três cromossomos, enquanto para característica de desempenho apenas um QTL para conversão alimentar foi encontrado no cromossomo oito. Não foram encontrados nas literaturas consultadas QTL para Peso de Carré e Espessura de Bacon no cromossomo sete. As informações dos QTL significativos encontrados servem para estudos futuros como o mapeamento fino e identificação de genes que ajudam no melhor entendimento da fisiologia e características de produção de suínos.

<p>The focus of this thesis is on numerical algorithms for efficient solution of QTL analysis problem in genetics.</p><p>Firstly, we consider QTL mapping problems where a standard least-squares model is used for computing the model fit. We develop optimization methods for the local problems in a hybrid global-local optimization scheme for determining the optimal set of QTL locations. Here, the local problems have constant bound constraints and may be non-convex and/or flat in one or more directions. We propose an enhanced quasi-Newton method and also implement several schemes for constrained optimization. The algorithms are adopted to the QTL optimization problems. We show that it is possible to use the new schemes to solve problems with up to 6 QTLs efficiently and accurately, and that the work is reduced with up to two orders magnitude compared to using only global optimization.</p><p>Secondly, we study numerical methods for QTL mapping where variance component estimation and a REML model is used. This results in a non-linear optimization problem for computing the model fit in each set of QTL locations. Here, we compare different optimization schemes and adopt them for the specifics of the problem. The results show that our version of the active set method is efficient and robust, which is not the case for methods used earlier. We also study the matrix operations performed inside the optimization loop, and develop more efficient algorithms for the REML computations. We develop a scheme for reducing the number of objective function evaluations, and we accelerate the computations of the derivatives of the log-likelihood by introducing an efficient scheme for computing the inverse of the variance-covariance matrix and other components of the derivatives of the log-likelihood.</p>

The focus of this thesis is on numerical algorithms for efficient solution of QTL analysis problem in genetics. Firstly, we consider QTL mapping problems where a standard least-squares model is used for computing the model fit. We develop optimization methods for the local problems in a hybrid global-local optimization scheme for determining the optimal set of QTL locations. Here, the local problems have constant bound constraints and may be non-convex and/or flat in one or more directions. We propose an enhanced quasi-Newton method and also implement several schemes for constrained optimization. The algorithms are adopted to the QTL optimization problems. We show that it is possible to use the new schemes to solve problems with up to 6 QTLs efficiently and accurately, and that the work is reduced with up to two orders magnitude compared to using only global optimization. Secondly, we study numerical methods for QTL mapping where variance component estimation and a REML model is used. This results in a non-linear optimization problem for computing the model fit in each set of QTL locations. Here, we compare different optimization schemes and adopt them for the specifics of the problem. The results show that our version of the active set method is efficient and robust, which is not the case for methods used earlier. We also study the matrix operations performed inside the optimization loop, and develop more efficient algorithms for the REML computations. We develop a scheme for reducing the number of objective function evaluations, and we accelerate the computations of the derivatives of the log-likelihood by introducing an efficient scheme for computing the inverse of the variance-covariance matrix and other components of the derivatives of the log-likelihood.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

Diplodia ear rot caused by the fungus Stenocarpella maydis (Berkeley) and Stenocarpella macrospora (Earle) have become one of the most important limiting factors for the production of Corn (Zea mays L.) in Brazil. The fungus can attack the stalks, leaves and the grain causing significant reductions on yield and the overall quality of the grain, since it can produce micotoxinas that are dangerous to livestock. Resistance to ear rot by Stenocarpella sp in corn is quantitative and highly influenced by the environment and even that artificial inoculation techniques are available to screen for the disease the overall cost is very expensive. The objective of this study was the identification of quantitative trait loci (QTL s) associated with ear rot resistance by Stenocarpella sp in one breeding population composed of 141 doublehaploid progenies resulted from the cross among the resistant inbred MONDR1 and the susceptible inbred MONDS1 in testcrosses with the susceptible tester MONDS5. Testcrosses were evaluated at harvest time after artificial inoculation for ear rot at three different locations in the central region of Brazil during the 2005/06 summer season. Thru Composite interval mapping (CIM), a total of three QTL s (LOD>2.5) for ear rot resistance were identified at chromosomes 2, 3 and 5, all together accounting for up 26% of total phenotypic variation for this character. The identification of two QTL s for ear rot resistance coming from the susceptible parent MONDS1 appear to indicate the presence of the phenomena of transgressive segregation. Additionally we were able to identify six double-haploid progenies with high level of resistance to ear rot by Stenocarpella (MDH15, MDH443, MDH95, MDH2, MDH120 e MDH81), being those recommended for their incorporation into the breeding program as new breeding sources for the Central Brazil regions. / Grãos ardidos causados pelos fungos Stenocarpella maydis (Berkeley) e Stenocarpella macrospora (Earle) tem se constituído num dos maiores fatores limitantes para a produção de milho (Zea mays L.) no Brasil. Estes fungos podem causar infecções no colmo, folhas e grãos, podendo ocasionar reduções significativas na produtividade e na qualidade do grão, pela produção de micotoxinas daninhas para aves e bovinos. A resistência para podridão de grão por Stenocarpella sp apresenta herança quantitativa e pode ser altamente influenciada pelo meio ambiente, e embora existam técnicas de inoculação que facilitam a discriminação de materiais suscetíveis, isto requer de grande quantidade de recursos. O objetivo do presente trabalho foi à identificação de locos de caracteres quantitativos (QTL) associados à resistência para podridão de grãos ( grãos ardidos ) ocasionados por Stenocarpella sp numa população de 141 progênies duplo-haplóides derivadas do cruzamento entre a linhagem resistente MONDR1 e a linhagem susceptível MONDS1 em testcross com o testador susceptível MONDS5. A porcentagem de espigas infectadas por Stenocarpella sp foi registrada para cada uma das testcrosses apos da inoculação artificial em três localidades na região Central de Brasil durante a Safra agrícola 2005/06. Mediante a análise de mapeamento por intervalo composto foram identificados três QTL s com LOD>2.5 para resistência à grãos ardidos nos cromossomos 2, 3 e 5, sendo estes em conjunto, responsáveis por ate 26% de variação fenotípica para este caráter. A identificação de dois QTL s para resistência a grãos ardidos por Stenocarpella sp com origem no progenitor susceptível parece indicar a presença do fenômeno de segregação transgressiva. Adicionalmente foram identificadas seis progênies duplohaplóides com alto nível de resistência a grãos ardidos (MDH15, MDH443, MDH95, MDH2, MDH120 e MDH81), sendo estas recomendadas para sua incorporação no programa de melhoramento para a região central do Brasil. / Mestre em Genética e Bioquímica