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.

Doctor of Philosophy / Department of Agronomy / Guihua Bai / Growing resistant cultivars is an economically effective method to control wheat disease Fusarium head blight (FHB) caused by Fusarium graminearum. Ninety-five wheat lines mainly from China and Japan were evaluated for resistance to initial infection (type I), spread of symptoms within a spike (type II), and deoxynivalenol (DON) accumulation in infected grains (type III). Most of lines were resistant or moderately resistant, 15 lines had DON content lower than 2 ppm and six lines showed a high level of resistance for all the three types. Deoxynivalenol content was significantly correlated with type II, but not type I resistance. Fifty-nine of the ninety-five lines were evaluated for genetic diversity on the basis of amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs). Genetic relationships among these lines were consistent with pedigrees and their geographic distribution. Chinese lines had broader genetic diversity than Japanese lines. Sumai 3 is a widely used Chinese variety for FHB-resistant breeding in the US and elsewhere. Haplotype patterns of the SSR markers linked to FHB resistance quantitative trait loci (QTL) on chromosomes 3BS, 5AS and 6BS of Sumai 3 indicated that only a few Sumai 3 derivatives carry all of these Sumai 3 QTL. SSR data also suggested that these QTL in Sumai 3 were derived from Chinese landrace Taiwan Xiaomai. Some highly resistant lines may carry novel QTL for FHB-resistance QTL, and need further investigation. A mapping population of 139 recombinant inbred lines derived from the cross of Wangshuibai (resistant Chinese landrace)/Wheaton (susceptible cultivar) was genotyped with more than 1300 SSR and AFLP markers. Five QTL for type I resistance were detected on chromosome arms 3BS, 4BS, 5DL, 3AS, and 5AS; seven QTL for type II resistance on 3BS, 1AL, 5AS, 5DL, 7AL, and 3DL; and seven QTL for type III resistance on 3BS, 5AS, 1AS, 5DL, 1BL, and 7AL. These QTL together explained 31.7%, 64%, and 52.8% of the phenotypic variation for FHB type I, II, and III resistance, respectively. QTL on 5AS, the distal end of 3BS, and 5DL contributed to all three types of resistance. FHB resistance QTL identified in Wangshuibai can be used in developing wheat cultivars with enhanced FHB resistance by pyramiding FHB resistance QTL from other sources.

Doctor of Philosophy / Department of Plant Pathology / James C. Nelson / The aim of quantitative trait locus (QTL) mapping is to identify association between DNA marker genotype and trait phenotype in experimental populations. Many QTL mapping methods have been developed to improve QTL detecting power and estimation of QTL location and effect. Recently, shrinkage Bayesian and penalized maximum-likelihood estimation approaches have been shown to give increased power and resolution for estimating QTL main or epistatic effect. Here I describe a new method, shrinkage interval mapping, that combines the advantages of these two methods while avoiding the computing load associated with them. Studies based on simulated and real data show that shrinkage interval mapping provides higher resolution for differentiating closely linked QTLs and higher power for identifying QTLs of small effect than conventional interval-mapping methods, with no greater computing time. A second new method developed in the course of this research toward increasing QTL mapping efficiency is the extension of multi-trait QTL mapping to accommodate incomplete phenotypic data. I describe an EM-based algorithm for exploiting all the phenotypic and genotypic information contained in the data. This method supports conventional hypothesis tests for QTL main effect, pleiotropy, and QTL-by-environment interaction. Simulations confirm improved QTL detection power and precision of QTL location and effect estimation in comparison with casewise deletion or imputation methods.

京都大学 / 0048 / 新制・論文博士 / 博士(農学) / 乙第13343号 / 論農博第2886号 / 新制||農||1079(附属図書館) / 学位論文||R2||N5250(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 奥本 裕, 教授 白岩 立彦, 教授 森 直樹 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

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

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21377号 / 農博第2301号 / 新制||農||1069(附属図書館) / 学位論文||H30||N5150(農学部図書室) / 京都大学大学院農学研究科農学専攻 / (主査)教授 奥本 裕, 教授 白岩 立彦, 教授 稲村 達也 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM