Doctor of Philosophy / Department of Statistics / Weixing Song / In this dissertation, we proposed a new robust estimation procedure for two multivariate mixture regression models and applied this novel method to functional mapping of dynamic traits. In the first part, a robust estimation procedure for the mixture of classical multivariate linear regression models is discussed by assuming that the error terms follow a multivariate Laplace distribution. An EM algorithm is developed based on the fact that the multivariate Laplace distribution is a scale mixture of the multivariate standard normal distribution. The performance of the proposed algorithm is thoroughly evaluated by some simulation and comparison studies. In the second part, the similar idea is extended to the mixture of linear mixed regression models by assuming that the random effect and the regression error jointly follow a multivariate Laplace distribution. Compared with the existing robust t procedure in the literature, simulation studies indicate that the finite sample performance of the proposed estimation procedure outperforms or is at least comparable to the robust t procedure. Comparing to t procedure, there is no need to determine the degrees of freedom, so the new robust estimation procedure is computationally more efficient than the robust t procedure. The ascent property for both EM algorithms are also proved. In the third part, the proposed robust method is applied to identify quantitative trait loci (QTL) underlying a functional mapping framework with dynamic traits of agricultural or biomedical interest. A robust multivariate Laplace mapping framework was proposed to replace the normality assumption. Simulation studies show the proposed method is comparable to the robust multivariate t-distribution developed in literature and outperforms the normal procedure. As an illustration, the proposed method is also applied to a real data set.

Submitted by MARCOS LEANDRO TEIXEIRA DE OLIVEIRA (marcosteixeira@ufv.br) on 2018-08-24T12:59:01Z No. of bitstreams: 1 texto completo.pdf: 3178737 bytes, checksum: 5041c62a2f0856a630f7f0f0865ee43b (MD5) / Made available in DSpace on 2018-08-24T12:59:01Z (GMT). No. of bitstreams: 1 texto completo.pdf: 3178737 bytes, checksum: 5041c62a2f0856a630f7f0f0865ee43b (MD5) Previous issue date: 2016-08-12 / Fundação de Amparo à Pesquisa do Estado de MInas Gerais / Para identificar regiões genômicas envolvidas na regulação de processos fisiológicos fundamentais, como fotossíntese, respiração e aqueles relacionados, uma população de ILs de Solanum pennellii em fundo genético de S. lycopersicum (M82) foi analisada. Foram estudados parâmetros fisiológicos, metabólicos e de crescimento, que vão desde troca gasosa (por exemplo, taxa de assimilação de CO 2 e condutância estomática), fluorescência da clorofila (por exemplo, taxa de transporte de elétrons e de extinção fotoquímica), bem como parâmetros de crescimento (por exemplo, taxa de crescimento relativo, matéria seca da raiz e parte aérea). Em paralelo, nós também analisamos, por meio de uma plataforma robotizada, os principais intermediários metabólicos (por exemplo, açúcares, amido, nitrato, aminoácidos e proteínas), e a atividade de nove enzimas representativas do metabolismo central do C e N. O objetivo do estudo foi: (1) combinar informações sobre as atividades enzimáticas e os níveis de metabólitos de caule, pecíolo e folha com a biomassa e rendimento de frutos; (2) através do estudo desses três órgãos interligados, examinar o quanto há de conectividade entre a atividade das enzimas e os níveis de metabólitos; (3) fornecer informações preditivas sobre as diferenças de particionamento do C e assimilação N inorgânico; (4) investigar a diversidade genética natural e identificar QTLs relacionados ao metabolimo central e a atividade enzimática no caule, pecíolo e folha. As análises dos dados permitiram a identificação de 67 QTL relacionados à parametros fisiológicos e metabólicos. Além disso, uma anotação abrangente e detalhada destas regiões permitiu apontar um total de 87 genes candidatos que possam controlar as características investigadas. Desses, 70 genes apresentou variantes alélicas relacionadas inserções de elementos transponíveis entre os dois genótipos parentais. As análises metabólicas e enzimática revelaram alta frequência de correlações positivas entre as enzymas, frequência moderada de correlações entre metabólitos relacionados, e baixa correlações entre a atividade das enzimas e os níveis de metabólitos. Tomados em conjunto, vapresentamos o maior estudo de parâmetros de fotossíntese e crescimento em plantas de tomate até à data. Os resultados permitiram a identificação de genes candidatos que podem estar envolvidos na regulação da fotossíntese, metabolismo primário e crescimento da planta, e fornece um recurso genético valioso para a compreensão dos mecanismos bioquímicos envolvidos na regulação do metabolismo primário em tomateiro. / To identify genomic regions involved in the regulation of fundamental physiological processes such as photosynthesis, respiration and underlying traits, a population of 71 Solanum pennellii introgression lines (ILs) in the genetic background of S. lycopersicum (M82) was analyzed. We determined IL phenotypes physiological, metabolic and growth related traits, ranging from gas- exchange parameters (e.g. CO 2 assimilation rates and stomatal conductance), chlorophyll fluorescence parameters (e.g. electron transport rate and photochemical quenching) as well as growth related traits (e.g. relative growth rate, shoot and root dry matter accumulation). In parallel, we also analyzed by robotized platform the major metabolic intermediates (e.g. sugars and starch), and the activities of nine representative enzymes from central C and N metabolism. We aimed: (1) combine information about enzyme activities and metabolite levels from stem, petiole and leaf with biomass and fruit yield; (2) by studying these three interconnected organs, examine how much connectivity exists between enzyme activities and metabolite levels; (3) provide predictive information about differences in C partitioning and inorganic N assimilation; (4) investigate the natural genetic diversity and identify QTL controlling variation of enzyme activities and metabolite levels in stem, petiole and leaf. Data analyses allowed identification of 67 physiological and metabolic QTL. Additionally, a comprehensive and detailed annotation of these regions allowed to point out a total of 87 candidate genes that might control the investigated traits. Out of those, 70 genes showed allelic variants related to differentially transposable element insertions pattern between both parental genotypes. Furthermore, the results revealed high frequency of positive correlations between enzyme activities, moderate frequency of correlations between related metabolites, and few correlations between enzyme activities and metabolite levels. Taken together, we present the largest study of photosynthetic and growth parameters in tomato plants to date. Our results allowed the identification of candidate genes that might be involved in the regulation of photosynthesis, primary metabolismo and plant growth, and provide an valuable genetic resource to understanding of the biochemical mechanisms involved in the regulation of primary metabolism in tomato plants.

Doctor of Philosophy / Department of Plant Pathology / Scot H. Hulbert / The rice cultivar Oryzica Llanos 5 (OL5) possesses a high level of resistance to the fungus Magnaporthe grisea. The number and chromosomal location of quantitative trait loci (QTL) conferring resistance against eight isolates of the blast fungus were tested in two different populations of recombinant inbred lines from the cross Fanny x OL5. Twenty one QTL were detected and associated with the resistance traits, disease leaf area and lesion type, on 9 rice chromosomes. Eight of these 21 resistance loci had significant resistance effects in both experiments, while the others had effects that were only statistically significant in one experiment. Most, but not all, of the QTL occurred in the same genomic regions as either genes with major race-specific effects or other resistance QTL that had been described in previous experiments. Most of the QTL appeared to be race-specific in their effects but it is possible some of the QTL with smaller effects were nonspecific. One of the blast isolates used was FL440, which causes limited disease on OL5 and was probably virulent on most or all of the major genes from OL5. Three QTL affected resistance to FL440 in both experiments, one of which mapped to a region on chromosome 9 where no blast resistance genes have yet been mapped. An advanced backcross strategy with marker-assisted selection for OL5 alleles in QTL regions was used to generate five BC2F3 populations carrying five different target regions associated with partial resistance to rice blast disease. Three of five of these populations were analyzed for segregation for resistance to the M. grisea isolate FL440. One QTL designated qrbr-11.3 near the bottom of rice chromosome 11 was found to be significantly associated with partial blast resistance in 120 lines of a BC2F3 population (P< 0.01). This QTL accounted for 12.4% and 8.0% of the phenotypic variation in diseased leaf area and lesion type observed under greenhouse inoculation. Examination of the genomic sequence at the qrbr-11.3 locus showed that twenty-nine candidate resistance genes are present at that locus (~1.8 Mb), twenty-seven of which are predicted NBS-LRR genes. Ultimately, the information from this study can be integrated into the development of improved lines with OL5-derived QTL for resistance.

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.

Soybeans (Glycine max L.) are an important crop globally for its food, feed, and oilpurposes. It is impacted by many diseases, including Cercospora sojina, the causal agent of Frogeye Leaf Spot (FLS). Chemical and cultural controls to this fungal pathogen are insufficient, so genetic resistance must be acquired for adequate control. To this end, two recombinant inbred populations were screened in a greenhouse setting for their relative resistance to FLS, and their genomes were analyzed for contributing quantitative trait loci (QTL). In the Essex ́ Forrest population, one QTL was discovered on chromosome 13, and in the Forrest ́ Williams 82 population, two QTL were identified on chromosomes 6 and 11, respectively. These populations were then also screened in a field setting for agronomic traits. These traits were analyzed to detect one superior line for both FLS resistance and advanced agronomic traits, F ́W 125. This line should be used in future breeding projects to increase FLS resistance and reduce linkage drag for other desired characteristics.

Bread wheat (Triticum aestivum L.) is an important cereal crop that provides over 20% of the global calorie intake. With the world population constantly growing, yield production must increase to meet food demands. Wheat plays a significant role on nutritional and food security especially in rural areas, however, bread wheat grains are known to be inherently deficient in micronutrients, particularly Fe and Zn, which makes them important biofortification targets. To date, South African wheat genotypes have not been explored for their nutritional micronutrient variation; hence there is a need to investigate the variation of nutritional quality and its association with yield components. Bread wheat cultivars, TugelaDN and Elands were used in this study based on their known high yield potential, resistance to insect pests and diseases as well as their good-to-excellent bread-making quality. The goal of this study was to use a doubled haploid (DH) mapping population, developed from a cross between cultivars Tugela-DN and Elands, to identify single nucleotide polymorphism (SNP) and genotyping-by-sequencing (GBS)-based markers linked to high nutritional quality and yield-related traits. This was achieved by (i) determining grain micronutrient (Fe and Zn) concentration variation in 139 lines of a DH mapping population; (ii) evaluating the mapping population for yield-related traits; (iii) determining the correlation between micronutrient and yield-related traits among the genotypes; (iv) identifying SNP GBS-based markers linked to the high minerals and yield-related traits. The analysis of variance (ANOVA) showed significant (P<0.001) differences between genotypes for all traits evaluated. A wide variation was observed for both GFeC and GZnC. The statistical analysis revealed significant variation for Zn concentration (P < 0.001) among genotypes and not significant Fe concentration. DArT-Seq was used to genotype Tugela-DN and Elands cultivars and 139 DH genotypes. Quantitative trait loci (QTL) were detected using SNP GBS-based markers on chromosome 2D, 5B, 5D, 6A, and 6B for GZnC, and on chromosome 2D, 5B, 5D and 7D for GFeC. Most QTLs identified for GFeC and GZnC shared the genomic interval and some of them also co-located with few yield-related traits. The results of this study will contribute to breeding programmes to improve nutritional quality of bread wheat and food security of the country. / Life and Consumer Sciences

One of the great aims of statistics, the science of collecting, analyzing, and interpreting data, is to protect against the probability of falsely rejecting an accepted claim, or hypothesis, given observed data stemming from some experiment. This is generally known as protecting against a Type I Error, or controlling the Type I Error rate. The extension of this protection against Type I Errors to the situation where thousands upon thousands of hypotheses are examined simultaneously is known as multiple hypothesis testing. This dissertation presents an improvement to an existing multiple hypothesis testing approach, the Focus Level method, specific to gene set testing (a branch of genomics) on Gene Ontology graphs. This improvement resolves a long standing computational difficulty of the Focus Level method, providing more than a 15.000-fold increase in computational efficiency. This dissertation also presents a solution to a multiple testing problem in genetics where a specific approach to mapping genes underlying quantitative traits of interest requires a multiplicity adjustment approach that both corrects for the number of tests while also ensuring logical consistency. The power advantage of the solution is demonstrated over the current standard approach to the problem. A side issue of this model framework led to the development of a new bivariate approach to quantitative trait marker detection, which is presented herein. The overall contribution of this dissertation to the statistics literature is that it provides novel solutions that meet real needs of practitioners in genetics and genomics with the aim of ensuring both that truth is discovered and that discoveries are actually true.

京都大学 / 0048 / 新制・論文博士 / 博士(工学) / 乙第13016号 / 論工博第4141号 / 新制||工||1650(附属図書館) / 32944 / (主査)教授 跡見 晴幸, 教授 森 泰生, 教授 梅田 眞郷 / 学位規則第4条第2項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM

Fusarium head blight (FHB) is one of the most destructive diseases of common wheat (Triticum eastivum L.) worldwide. Resistance to FHB is an ideal trait for which molecular marker assisted selection (MAS) would facilitate breeding and cultivar development efforts. Validation of quantitative trait loci (QTL) conferring FHB resistance is a prerequisite for MAS. This study was conducted to validate and evaluate the effect of two major QTL, previously reported on chromosomes 3BS and 5AS, on multiple FHB resistance components in two independent studies, one involving a mapping population derived from a cross between a known resistance source W14 and a susceptible soft red winter (SRW) wheat cultivar Pioneer2684, and the other involving seventy adapted SRW wheat lines. The first study confirmed that the 3BS and 5AS QTL were significantly associated with FHB resistance and further indicated that the 3BS QTL has a larger effect on three FHB resistance components (type II and III resistance and resistance to Fusarium Damaged kernels) evaluated in greenhouse experiments, while the 5AS QTL has a larger effect on type I resistance evaluated in a field experiment. Six simple sequence repeat (SSR) and two sequence targeted site (STS) markers associated with FHB resistance in the two QTL regions identified in the first experiment were then used to characterize FHB QTL marker haplotypes and their effect on FHB resistance in seventy wheat genotypes. Five main haplotype groups (1-5) were characterized among the elite lines on the basis of allelic differences of four marker loci linked to the 3BS QTL and two marker loci linked to the 5AS QTL. Haplotype group 5 was comprised of marker allele combinations of both 3BS and 5AS QTL and elite lines with this haplotype have improved type I and type II resistance compared to the other haplotypes. This again validated the presence of QTL on chromosomes 3BS and 5AS, and illustrated the utility of SSR and STS markers in the two QTL regions in selection of FHB resistance in elite backgrounds. Four favorable marker alleles including two (Xbarc133 and XSTS3B142) on 3BS and two (Xbarc117 and Xbarc056) on 5AS are recommended for MAS of the two QTL for improved FHB resistance in wheat. Wheat lines having favorable marker alleles identified in the current study will provide breeding programs with a source of unique and adapted FHB resistant parents and some of the lines also may have potential for release as cultivars. / Ph. D.

<p>&nbsp / </p> <p align="left">The domesticated apple (<i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">x </font><i><font face="TimesNewRomanPS-ItalicMT">domestica </font><font face="TimesNewRomanPSMT">Borkh.), belonging to the </font><i><font face="TimesNewRomanPS-ItalicMT">Malus </font><font face="TimesNewRomanPSMT">genus of the Rosaceae family, is one of the edible pomaceous fruits. Since it is one of the important commercial fruit crops worldwide, the quality of the fruit is crucial to breeders and farmers as it ultimately determines acceptance of a cultivar for consumption. Fruit quality is also a critical determinant factor that is used to estimate the potential of apples to have a long shelf life. The introduction of marker-assisted selection (MAS) has allowed hastening of traditional breeding and selection of high-quality apple cultivars. The availability of genetic linkage maps, constructed by positioning molecular markers throughout the apple genome, enables the detection and analysis of major genes and quantitative trait loci (QTLs) contributing to the quality traits of a given genotype.&nbsp / herefore, the primary aim of this study was to construct a genetic linkage map of the &lsquo / Golden Delicious&rsquo / x &lsquo / Dietrich&rsquo / population for the identification of QTLs associated with fruit quality traits and then to examine the apple fruit pulp proteome with a specific focus on fruit firmness. In this regard, genomic DNA was extracted from leaves of the &lsquo / Golden Delicious&rsquo / x Dietrich&rsquo / population and used in megaplex PCR reactions. The PCR products were analysed prior to scoring of alleles. Polymorphic markers were then used to construct genetic linkage maps. The genetic linkage maps constructed in this study comprise of 167 simple sequence repeats (SSR) markers, 33 of these were newly developed markers. The 17 linkage groups of apple were constructed and aligned to existing apple genetic maps. The maps span 1,437.8 cM and 1,491.5 cM for &lsquo / Golden Delicious&rsquo / and &lsquo / Dietrich&rsquo / , respectively.</font></i></i></i></p>