Es wurden mehrere Experimente durchgeführt, um - basierend auf 208 hochgradig homozygoten Inzuchtlinien - genetisch die Frosttoleranz von Ackerbohnen (Vicia faba L.) zu analysieren. Die Inzuchtlinien sind in drei Sätzen organisiert: Original-Satz (N=208, O-Satz), Winterbohnen-Satz (N=196, WB-Satz; eine Untermenge des O-Satzes), und Assoziations-Satz (N=186, A-Satz; eine Untermenge des WB-Satzes). Alle Experimente fanden statt: in der sog. Frost-Kammer (Pflanzenwuchskammer), im Gewächshaus, im Molekulargenetischen Laboratorium, oder im Zuchtgarten (Versuchsstation Reinshof der Georg-August-Universität Göttingen). Insgesamt wurden 65 morphologische Merkmale (Saison 2011/2012 und 2012/2013), physiologische Merkmale (Saison 2011/2012), und Feld-Merkmale (Saison 2012/2013) erfasst. Daraus werden 25 Merkmale für diese Studie hier verwendet. Mittels des A-Satzes und mit 156 polymorphen SNP-Markern wurde eine Assoziationsanalyse durchgeführt. Das Ziel dieser Untersuchung war, eine markergestützte Züchtung auf Frosttoleranz bei der Ackerbohne vorzubereiten, und also QTLs für Frosttoleranz für zukünftige Zuchtprogramme zu detektieren. Die Ergebnisse können wie folgt zusammengefasst werden. 1- Es wurde eine hohe genetische Variation zwischen allen Linien (Original-Satz) beobachtet, für alle acht morphologische Merkmale, die an Spross und Wurzel von Ackerbohnen-Jungpflanzen erfasst wurden. Die Pflanzen wurden über 10 Tage (5°C) gehärtet und dann während dreier Nächte einem Frost ausgesetzt (-16°C, -18°C, -19°C). Alle Merkmale zeigten eine hohe Wiederholbarkeit (h²), die Schätzwerte reichten von h2=59,45 für Wurzel-Frostempfindlichkeit bis zu h2=94,71 für den Blattturgor- und Blattfarbverlust. Darüber hinaus wurden hochsignifikante phänotypische und genotypische Korrelationen zwischen den morphologischen Merkmalen unter Froststress entdeckt. Die genotypischen Korrelationen zwischen den Merkmalen waren höher als die phänotypischen Korrelationen. Die höchste genetische (rg=-0,96) und phänotypische (rp= -0,83**) Korrelation wurde zwischen dem Wiederaufwuchs und der Wurzel-Frostempfindlichkeit gefunden. Zur Charakterisierung der Frosttoleranz von Ackerbohnen wurden drei Selektionsindices berechnet. Der wichtigste war der Frosttoleranz-Index, weil er zwei Schlüsselaspekte kombiniert: die Überlebensneigung und den Wiederaufwuchs. Diese hohe genetische Variation, phänotypische Korrelation, genotypische Korrelation, und hohe Wiederholbarkeit versprechen, dass ein Ausleseprozess zur erblichen Verbesserung der Frosttoleranz fruchtbar und effektiv wäre. 2- Als physiologische Parameter mit Beziehung zur Frosttoleranz der Ackerbohne wurde die Fettsäurezusammensetzung nach Härtung (5°C) und der relative Sproßwassergehalt (vor und nach Frost) studiert. Für diese physiologischen Parameter wurde der WB-Satz benutzt. Die genetische Variation in den aufgefundenen Fettsäure-Gehalten und im relativen Sproßwassergehalt wurde festgehalten. Alle physiologischen Kennwerte zeigten sehr hohe Wiederholbarkeitsschätzwerte (62,78 < h2 < 89,04). Wir erwartet war die Korrelation zwischen den ungesättigten Fettsäuren und den gesättigten Fettsäuren negativ (rp = -0,62, rg = -0,84**). Eine Erhöhung der ungesättigten Fettsäuren geht in Ackerbohnen bekanntermaßen mit einer Verringerung der gesättigten Fettsäuren einher. Eine ähnlich negative und signifikante Korrelationen (r = -0,20**) wurde zwischen dem Wassergehalt nach Frost und dem Wassergehalt vor Frost (nach Härtung) gefunden. Es ist gängiges Wissen, dass die Frosttoleranz von Pflanzen mit der Fähigkeit der Pflanzen assoziiert ist, die Eiskristallbildung während des Frosts im Spross- und Wurzelgewebe zu modulieren. Es wurden signifikante Korrelationen zwischen morphologischen und physiologischen Merkmalen gefunden. Der Gehalt an ungesättigten Fettsäuren war mit dem Frosttoleranz-Index positiv korreliert (r = 0,22**). Darüber hinaus war die Verringerung des Wassergehaltes durch Froststress hochsignifikant korreliert mit allen morphologischen Merkmalen. Solche Korrelationen bieten eine verbesserte Beschreibung des physiologischen Verhaltens, welches die Pflanzen dem Frost gegenüber zeigen. 3- Der WB-Satz wurde auch benutzt, um die genetische Variation der Winterhärte der Genotypen in einem einjährigen Feldversuch zu überprüfen. Eine hohe, signifikante Variation wurde für alle Feldmerkmale gefunden. Die Wiederholbarkeitsschätzwerte reichten von 61,98 für Kornertrag (g/2m2) bis zu 92,03 für Blühbeginn. Die Linien S_299 und S_271 kombinierten hohe Winter-Überlebensraten mit niedriger Frostanfälligkeit des Blattes und mit hohem Kornertrag unter Feldbedingungen. Dieselben Genotypen rangierten bei den Besten für Frosttoleranz in den Frostkammer-Experimenten. Interessanterweise zeigten mehrere Feldmerkmale signifikante Korrelationen mit Merkmale aus der Frostkammer. Die höchste Korrelation (r=0,39**) war die zwischen Wiederaufwuchs (Frostkammer) und Winter-Überlebensrate (Feld). 4- Um die Verbesserung der Frosttoleranz der Ackerbohne weiter nach vorne zu bringen, wurde ein Assoziationsanalyse-Ansatz mit dem A-Satz gefahren. Als Ergebnis liegen nun 70 mutmaßliche QLTs vor, die sieben morphologische Merkmale (Überlebensneigung, Blattturgor- und Blattfarbverlust, Frosttoleranz-Index, Wuchshöhe, Index1, Index2, und Sproß-Frischmasse nach Frost) und sechs physiologische Merkmale (Gehalt an gesättigten Fettsäuren, Gehalt an ungesättigten Fettsäuren, relativer Wassergehalt vor Frost, relativer Wassergehalt nach Frost, Verringerung des Wassergehaltes durch Froststress, und C16:0-Gehalt, also Palmitinsäuregehalt) betreffen. Das Gametenphasenungleichgewicht zwischen Marker-Loci zeigte ein sehr niedriges Niveau (r2=0,00075). Darüber hinaus zeigt die Hauptkoordinatenanalyse für genetische Distanzen zwischen den A-Satz-Linien keine offensichtliche Struktur in dieser Linienpopulation. Mehrere Marker zeigten eine signifikante Assoziation mit mehr als einem Merkmal, was ernstlich die Hoffnung erhöht, dass der markergestützte Ausleseansatz für die Verbesserung der Frosttoleranz bei der Ackerbohne genutzt werden kann.

Breast cancer is a heterogeneous, polygenic disease and is influenced by genetic, environmental and life-style factors. Many single nucleotide polymorphisms (SNPs) associated with breast cancer risk have been identified in genome-wide association studies (GWASs) by several research groups for different populations. However, the variants identified so far contribute to a small proportion of disease risk. The objectives of the work described in this thesis were (i) to seek relevance/replicability of reported risk alleles from SNP scans to our study population; and (ii) to perform an independent GWAS for identification of additional/novel polymorphisms in the Albertan population. We approached these two end points by using cases and controls recruited in Alberta (total sample size, n=3064) in a two-stage association study (discovery study followed by replication study). We reproduced 14 of the 28 variants reported by others and also identified seven novel variants associated with breast cancer risk in our study population.

Abstract With the phenomenal growth of electronic data and information, there are many demands for the development of efficient and effective systems (tools) to perform the issue of data mining tasks on multidimensional databases. Association rules describe associations between items in the same transactions (intra) or in different transactions (inter). Association mining attempts to find interesting or useful association rules in databases: this is the crucial issue for the application of data mining in the real world. Association mining can be used in many application areas, such as the discovery of associations between customers’ locations and shopping behaviours in market basket analysis. Association mining includes two phases. The first phase, called pattern mining, is the discovery of frequent patterns. The second phase, called rule generation, is the discovery of interesting and useful association rules in the discovered patterns. The first phase, however, often takes a long time to find all frequent patterns; these also include much noise. The second phase is also a time consuming activity that can generate many redundant rules. To improve the quality of association mining in databases, this thesis provides an alternative technique, granule-based association mining, for knowledge discovery in databases, where a granule refers to a predicate that describes common features of a group of transactions. The new technique first transfers transaction databases into basic decision tables, then uses multi-tier structures to integrate pattern mining and rule generation in one phase for both intra and inter transaction association rule mining. To evaluate the proposed new technique, this research defines the concept of meaningless rules by considering the co-relations between data-dimensions for intratransaction-association rule mining. It also uses precision to evaluate the effectiveness of intertransaction association rules. The experimental results show that the proposed technique is promising.

A soja está entre as principais culturas mundiais, uma vez que é uma excelente fonte de proteínas e óleo. Além disso, a espécie é aproveitada também pela indústria de biocombustíveis. Considerando a importância das novas mudanças climáticas no agronegócio; para a soja, esta situação é agravada em virtude das condições de temperatura e latitude recomendadas para a semeadura. Dessa forma, para aumentar a produtividade da cultura mesmo frente ao aquecimento global, fazse fundamental o desenvolvimento de cultivares com alta produtividade e tolerantes às altas temperaturas. Neste contexto, o objetivo geral deste trabalho foi selecionar genótipos de soja tolerantes ao calor. Uma população composta por 80 PI\'s de soja e 15 testemunhas foi avaliada sob condições de altas temperaturas, com experimentos instalados nas cidades de Teresina-PI, Piracicaba-SP e Jaboticabal- SP, no ano agrícola 2013/2014. Para a avaliação dos genótipos, foram realizadas análises univariadas e multivariadas. A seleção dos genótipos mais tolerantes a altas temperaturas foi realizada via análise de componentes principais. Nas análises de variâncias univariadas, todos os caracteres mostraram efeitos de tratamentos significativos pelo teste F. Pela análise de componentes principais no experimento conduzido em Teresina-PI, os caracteres que mais contribuíram para a variabilidade dos genótipos avaliados foram: data que metade da parcela atingiu o estádio R5, altura da planta na maturidade, período de granação e valor agronômico. Em Piracicaba-SP, os caracteres que mais contribuíram para a variabilidade foram o período de granação, massa de 100 sementes e o número de dias para a maturidade. Para a seleção dos genótipos mais tolerantes ao calor em Jaboticabal- SP, considerou-se principalmente a altura e a produtividade. Para a análise de mapeamento associativo, a fenotipagem foi realizada em Teresina-PI e avaliados quatro caracteres: altura da planta na maturidade, valor agronômico, massa de cem sementes e produtividade. A genotipagem foi realizada utilizando o chip da empresa Affymetrix. O desequilíbrio de ligação entre pares de marcadores foi calculado pelo coeficiente de determinação r2 e a análise de associação entre marcadores e o fenótipo de interesse foi realizada utilizando a abordagem de modelo linear generalizado. Foram identificadas 16 associações significativas. / Soybean (Glycine max) is one of most important crops in the world. This crop is an source of protein and oil. Beyond that, the species is also utilized for the biofuels industry. The recent climate changes are important on agribusiness, the ones on soybean crop are worse than on other crops because of the conditions of temperature and latitude recommended for planting. Thus, to increase the productivity of the crop even in face of global warming, it is essential that soybean breeding programs promote the development of cultivars highly productive and tolerant to high temperatures. In this context, the aim of this study was to select genotypes for heat tolerance. A population composed of 80 soybean PI\'s and 15 experimental checks was evaluated under high temperature conditions. The experiments were conducted in the cities of Teresina-PI, Piracicaba-SP and Jaboticabal-SP, in the 2013/2014 season. For the evaluation of the genotypes, univariate and multivariate analysis were performed, and the selection of the most genotypes for heat tolerance was performed by principal component analysis (PCA). In the univariate analyzes of variance, all characters showed significant effects of treatments by test F. In the PCA in the experiment conducted in Teresina-PI, the variables that most contributed to the variability of genotypes were: date in which half of the parcel reached R5 stage, height of the plant at maturity, grain filling period and agronomic value. In Piracicaba-SP PCA, the variables that most contributed to the variability were: grain filling period, 100-grain weight and the number of days to maturity. For the selection of the most heat-tolerant genotypes in Jaboticabal-SP, the height and the yield were the variables that most contributed to the variability. In the the association mapping analysis, the genotypes were evaluated under conditions of high temperatures in Teresina-PI and evaluated for four traits: height of the plant at maturity, agronomic value, 100 grain weight and yield. The genotyping was carried out using the Affymetrix chip. The linkage disequilibrium between pairs of markers was calculated by the determination coefficient r2 and the association analysis between markers and the phenotype of interest was performed using the generalized linear model approach. A total of 16 significant marker-trait associations were detected for the four traits.

A soja é uma das culturas mais importantes do mundo, além de ser a principal comodity brasileira. Entretanto apesar dos ganhos crescentes de produtividade a base genética da cultura no país é estreita. Sendo assim, é importante a identificação e caracterização de fontes de variabilidade para os programas de melhoramento de soja. Dado o exposto, os objetivos deste estudo foram i) avaliação da produtividade de grãos e caracteres agronômicos correlacionados; ii) caracterização da diversidade fenotípica; iii) caracterização da diversidade genética e estrutura de populações; e iv) mapeamento associativo para produtividade de grãos. Os acessos foram fenotipados nos anos agrícolas de 2012/2013 e 2013/2014, em cinco ambientes. As características avaliadas foram: altura da planta na maturidade, período de granação, valor agronômico, acamamento, massa de cem sementes, número de dias para a maturidade, inserção da primeira vagem, altura da planta no florescimento, teor de óleo e produtividade de grãos. A análise dos dados fenotípicos foi feita pelo software SELEGEN utilizando modelos mistos, e a árvore de regressão para identificação dos caracteres correlacionados foi feita pelo software JMP SAS. A diversidade fenotípica foi feita a partir de todas as características avaliadas anteriormente utilizando três tipos de análises: os métodos de agrupamento de Ward e Average Linkage no software Power Marker, e pela análise de componentes principais no software JMP SAS. A genotipagem dos acessos foi realizada pelo Axiom&reg; Soybean Genotyping Array contendo 10017 SNPs polimórficos para os acessos genotipados. A partir dos dados de marcadores foi feita a caracterização da diversidade genética pelo software Power Marker. Além disso, foram realizadas análises de estrutura de população pelo software STRUCTURE e pelo pacote do R, adegenet. A análise de associação foi efetuada pelo software TASSEL, utilizando o modelo misto MLM (Q+K). Duas abordagens foram utilizadas na análise de associação, a primeira utilizando as médias fenotípicas ajustadas para BLUP dos cinco ambientes e a segunda utilizando apenas as médias de cada local individualmente. Na análise fenotípica os acessos Dowling, PI 417563, PI200526, PI 377573 e PI 159922, apresentaram boa produtividade de grãos nos cincos ambientes avaliados. A caracterização molecular e fenotípica da diversidade indicou a presença de variabilidade genética no painel de acessos avaliados. Além disso, foi possível a identificação de dois grupos (k=2) em ambas as análises de estrutura da população utilizadas. No mapeamento associativo, foram detectadas sete associações marcador-característica com p<0,001 e com correção para múltiplos testes q<0,1. Dentre estas, quatro foram significativas no modelo de análise conjunta dos cinco ambientes e para o ambiente dois. As demais associações foram significativas somente para este último local. / Soybean is one of the most important crops in the world, and is Brazil\'s main commodity. However despite growing yield gains the genetic basis of culture in the country is narrow. Therefore, the identification and characterization of sources of variability for soybean breeding programs is important. On this basis, the objectives of this study were i) assessment of grain yield and agronomic traits correlated; ii) characterization of the phenotypic diversity; iii) characterization of genetic diversity and population structure; and iv) associative mapping for grain yield. The inbred lines were phenotyped in the agricultural years of 2012/2013 and 2013/2014, in five environments. The traits evaluated were: plant height at maturity, fruit filling period, agronomic value, lodging, mass of hundred seeds, number of days to maturity, first pod, plant height at flowering, oil content and grain yield. The analysis of phenotypic data was made by SELEGEN software using mixed models, and regression tree for identification of correlated traits was made by JMP SAS software. The phenotypic diversity was made from all the features previously evaluated using three types of analysis: the Ward clustering methods and Average Linkage from the Power Marker software, and the principal component analysis in SAS JMP software. Genotyping was performed by Axiom&reg; Soybean Genotyping Array containing 10017 polymorphic SNPs genotyped for the soybean lines. From the markers data was taken the genetic diversity analysis by Power Marker software. In addition, population structure analysis was performed by Structure software and the R package, adegenet. The association analysis was performed by TASSEL software using the mixed model MLM (Q + K). Two approaches were used in the association analysis, the first using the phenotypic average adjusted to BLUP values for the five enviroments and the second one using only the means of each site individually. In the phenotypic analysis the lines: Dowling, PI 417563, PI200526, PI 377573 and PI 159922 showed good grain yield in the five evaluated environments. The molecular and phenotypic characterization of diversity indicated the presence of geneticvariability in the inbreed lines. Moreover, it was possible to identify two groups (k = 2) in both population structure analysis used. In the associative mapping, were detected seven markertrait associations with p <0.001 and with correction for multiple tests q <0.1. Among these, four were significant in the pooled analysis model with five environments and at the individually environment two. The other variables were significant only for the latter location.

Doctor of Philosophy / Genetics Interdepartmental Program / Allan K. Fritz / Wheat diseases cause significant economic losses every year. To ensure global food security, newly released cultivars must possess increased levels of broadly-effective resistance against wheat pathogens, acceptable end-use quality, and high yield potential. Genetic host resistance stands out from other management strategies as the most viable option for controlling diseases. New genotyping platforms allow whole genome marker discovery at a relatively low cost, favoring the identification of novel loci underlying traits of interest. The work presented here describes genomic approaches for mapping and predicting the resistance to Fusarium head blight (FHB) and wheat rusts. The first study used biparental mapping to identify quantitative trait loci (QTL) associated with Fusarium head blight (FHB) resistance. A doubled haploid population (DH) was originated from a cross of Everest and WB-Cedar, which are widely grown wheat cultivars in Kansas with moderately resistant and moderately susceptible reactions to FHB, respectively. We confirmed that neither of the parents carry known large-effect QTLs, suggesting that FHB resistance is native. Eight small-effect QTLs were identified as associated with multiple mechanisms of FHB resistance. All QTLs had additive effects, providing significant improvements in levels of resistance when they were found in combinations within DH lines. In the second study, a genome-wide association mapping (GWAS) and genomic selection (GS) models were applied for FHB resistance in a panel of 962 elite lines from the K-State Wheat Breeding Program. Significant single nucleotide polymorphisms (SNPs) associated with the percentage of symptomatic spikelets were identified but not reproducible across breeding panels tested in each year. Accuracy of predictions ranged from 0.25 to 0.51 depending on GS model, indicating that it can be a useful tool to increase levels of FHB resistance. GWAS and GS approaches were also applied to a historical dataset to identify loci underlying resistance to leaf and stem rust at seedling stage in a panel of elite winter wheat lines. Infection types of multiple races of wheat rusts from the last sixteen years of the Southern Regional Performance Nursery (SRPN) were used in this study. A total of 533 elite lines originating from several breeding programs were tested in the SRPN during this period of time. GWAS identified significant SNP-trait associations for wheat rusts, confirming the effectiveness of already known genes and revealing potentially novel loci associated with resistance.

Master of Science / Department of Statistics / Shie-Shien Yang / In fitting linear models, R[superscript]2 statistic has been wildly used as one of the measures to assess the goodness-of-fit and prediction power of the model. Unlike fixed linear models, at this time there is no single universally accepted measure for assessing goodness-of-fit and prediction power of a linear mixed model. In this report, we reviewed seven different approaches proposed to define a measure analogous to the usual R[superscript]2 statistic for assessing mixed models. One of seven statistics,Rc, has both conditional and marginal versions. Association mapping is an efficient way to link the genotype data with the phenotype diversity. When applying the R[superscript]2 statistic to the association mapping application, it can determine how well genetic polymorphisms, which are the explanatory variables in the mixed models, explain the phenotypic variation, which is the dependent variation. A linear mixed model method recently has been developed to control the spurious associations due to population structure and relative kinship among individuals of an association mapping. We assess seven definitions of R[superscript]2 statistic for the linear mixed model using data from two empirical association mapping samples: a sample with 277 diverse maize inbred lines and a global sample of 95 Arabidopsis thaliana accessions using the new method. R[superscript]2[subscript]LR statistic derived from the log-likelihood principle follows all the criterions of R[superscript]2 statistic and can be used to understand the overlap between population structure and relative kinship in controlling for sample relatedness. From our results,R[superscript]2[subscript]LR statistic is an appropriate R[superscript]2 statistic for comparing models with different fixed and random variables. Therefore, we recommend using RLR statistic for linear mixed models in association mapping.

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.

Phenotypic and genotypic characterization of hulled and hulless winter barley (Hordeum vulgare L.) is necessary for improvement using traditional and molecular breeding techniques.  Identification of genomic regions conferring resistance to Fusarium head blight (caused by Fusarium graminearum), leaf rust (caused by Puccinia hordei G. Otth), powdery mildew [caused by Blumeria graminis (DC.) E.O. Speer f. sp. hordei Em. Marchal], net blotch (caused by Pyrenophora teres) and spot blotch [caused by Cochliobolus sativus (Ito & Kuribayashi) Drechsler ex Dastur] will greatly aid in breeding for improved resistance.  Determining factors that contribute to yield differences between hulled and hulless genotypes, and identification of markers associated with yield and yield related traits will greatly aid in improvement of hulled and hulless genotypes.  The hulled cultivar Nomini, hulless cultivar Eve, and hulless line VA06H-48 were consistently resistant to Fusarium head blight (FHB) and had low deoxynivalenol (DON) accumulation.  Screening with molecular markers on chromosomes 2H and 6H for FHB and DON identified quantitative trait loci (QTL) which may confer resistance in Virginia Tech germplasm.  Evaluation of hulled and hulless full-sibs from four populations indicated  that  grain volume weight and protein concentration were significantly (P d 0.05) higher for hulless genotypes, while seedling emergence and grain ash concentration were significantly (P d 0.05) higher for hulled genotypes.  In linear regression analysis, none of the assessed traits explained yield variation in all populations and environments.  Identification of hulless genotypes having yield potentials similar to those of their hulled sibs should be possible after adjusting for hull weight.  A genome wide association study was used to identify chromosome regions governing traits of importance in six-rowed winter barley germplasm and to identify single nucleotide polymorphisms (SNPs) markers for use in a marker-assisted breeding program. Significant SNPs associated with previously described QTL or genes were identified for heading date, test weight, yield, grain protein, polyphenol oxidase activity, and resistance to leaf rust, powdery mildew, net blotch, and spot blotch.  Novel QTL also were identified for agronomic, quality, and disease resistance traits.  These SNP-trait associations provide the opportunity to directly select for QTL contributing to multiple traits in breeding programs. / Ph. D.

Doctor of Philosophy / Department of Agronomy / Tesfaye Tesso / Fusarium stalk rot and charcoal rot caused by Fusarium thapsinum and Macrophomina phaseolina respectively are devastating global diseases in sorghum that lead to severe quality and yield loss each year. In this study, three sets of interrelated experiments were conducted that will potentially lead to the development of resistance based control option to these diseases. The first experiment was aimed at identifying sources of resistance to infection by M. phaseolina and F. thapsinum in a diverse panel of 300 sorghum genotypes. The genotypes were evaluated in three environments following artificial inoculation. Out of a total of 300 genotypes evaluated, 95 genotypes were found to have resistance to M. phaseolina and 77 to F. thapsinum of which 53 genotypes were resistant to both pathogens. In the second experiment, a set of 79,132 single nucleotide polymorphisms (SNPs) markers were used in an association study to identify genomic regions underlying stalk rot resistance using a multi-locus mixed model association mapping approach. We identified 14 loci associated with stalk rot and a set of candidate genes that appear to be involved in connected functions controlling plant defense response to stalk rot resistance. The associated SNPs accounted for 19-30% of phenotypic variation observed within and across environments. An analysis of associated allele frequencies within the major sorghum subpopulations revealed enrichment for resistant alleles in the durra and caudatum subpopulations compared with other subpopulations. The findings suggest a complicated molecular mechanism of resistance to stalk rots. The objective of the third experiment was to determine the functional relationship between stay-green trait, leaf dhurrin and soluble sugar levels and resistance to stalk rot diseases. Fourteen genotypic groups derived from a Tx642 × Tx7000 RIL population carrying combinations of stay-green quantitative trait loci were evaluated under three environments in four replications. The stg QTL had variable effects on stalk rot disease. Genotypes carrying stg1, stg3, stg1,3 and stg1,2,3,4 expressed good levels of resistance to M. phaseolina but the combination of stg1 and stg3 was required to express the same level of resistance to F. thapsinum. Other stg QTL blocks such as stg2 and stg4 did not have any impact on stalk rot resistance caused by both pathogens. There were no significant correlations between leaf dhurrin, soluble sugar concentration, and resistance to any of the pathogens.