Many important traits in plants, animals and humans are quantitative, and most such traits are generally believed to be affected by multiple genetic loci. Standard computational tools for mapping of quantitative traits (i.e. for finding Quantitative Trait Loci, QTL, in the genome) use linear regression models for relating the observed phenotypes to the genetic composition of individuals in an experimental population. Using these tools to simultaneously search for multiple QTL is computationally demanding. The main reason for this is the complex optimization landscape for the multidimensional global optimization problems that must be solved. This thesis describes parallel algorithms, implementations and tools for simultaneous mapping of several QTL. These new computational tools enable genetic analysis exploiting new classes of multidimensional statistical models, potentially resulting in interesting results in genetics. We first describe how the standard, brute-force algorithm for global optimization in QTL analysis is parallelized and implemented on a grid system. Then, we also present a parallelized version of the more elaborate global optimization algorithm DIRECT and show how this can be efficiently deployed and used on grid systems and other loosely-coupled architectures. The parallel DIRECT scheme is further developed to exploit both coarse-grained parallelism in grid systems or clusters as well as fine-grained, tightly-coupled parallelism in multi-core nodes. The results show that excellent speedup and performance can be archived on grid systems and clusters, even when using a tightly-coupled algorithm such as DIRECT. Finally, we provide two distinctly different front-ends for our code. One is a grid portal providing a graphical front-end suitable for novice users and standard forms of QTL analysis. The other is a prototype of an R-based grid-enabled problem solving environment. Both of these front-ends can, after some further refinement, be utilized by geneticists for performing multidimensional genetic analysis of quantitative traits on a regular basis. / eSSENCE

Master of Science / Department of Statistics / Gary L. Gadbury / QTL (quantitative-trait locus) analysis aims to locate and estimate the effects of genes that are responsible for quantitative traits, such as grain protein content and yield, by means of statistical methods that evaluate the association of genetic variation with trait (phenotypic) variation. Quantitative traits are typically polygenic, i.e., controlled by multiple genes, with varying degrees of in uence on the phenotype. Several methods have been developed to increase the accuracy of QTL location and effect estimates. One of them, multiple interval mapping (MIM) (Kao et al. 1999), has been shown to be more accurate than conventional methods such as composite interval mapping (CIM) (Zeng 1994). Other QTL analysis methods have been developed to perform additional analyses that might be useful for breeders, such as of pleiotropy and QTL-by-environment (QxE) interaction. It has been shown (Jiang and Zeng 1995) that these analyses can be carried out with a multivariate extension of CIM (MT-CIM) that exploits the correlation structure in a set of traits. In doing so, this method also improves the accuracy of QTL location detection. This thesis describes the multivariate extension of MIM (MT-MIM) using ideas from MT-CIM. The development of additional multivariate tests, such as of pleiotropy and QxE interaction, and several methods pertinent to the development of MT-MIM are also described. A small simulation study shows that MT-MIM is more accurate than MT-CIM and univariate MIM. Results for real data show that MT-MIM is able to provide a more accurate and precise estimate of QTL location.

Maize (Zea mays L.) inbred lines for hybrid breeding are usually developed within distinct heterotic groups. Breeders impose strong selection and maintain relatively small population sizes that are adapted to local environments, where the aim is to identify the desired recombinant types in the progeny. However, linkages between loci that control a trait may not permit breeders to obtain the desirable genetic recombination in these populations. It is hypothesized that different favorable and unfavorable alleles accumulate within the lines from different heterotic groups. In addition, within each inbred line, favourable alleles are linked with unfavourable alleles. Two early-season maize inbreds, CG60 (Iodent) and CG102 (Stiff Stalk), were used to develop a selfed recombinant inbred line (SRIL) and an intermated recombinant inbred line (IRIL) populations. Furthermore, individuals from within these populations were testcrossed with an inbred tester from the Lancaster Sure Crop heterotic group, to give rise to selfed SRIL testcross (SRIL-TC) and IRIL testcross (IRIL-TC) populations. The inbred and inbred-testcross populations were evaluated for trait variation and QTL mapping. The genetic variance was high in inbred populations (SRIL and IRIL) with transgressive segregation for flowering time and agronomic traits. However, genetic variances and correlation coefficients did not significantly differ between the inbred populations. Results suggested that pleiotropic genes were prevalent for these traits. In addition, linkages between the loci that control these traits were not common within parental genomes. Genetic linkage maps developed from the IRIL population were larger than those of the SRIL population. In the inbred-testcross populations (SRIL-TC and IRIL-TC) high means and high levels of trait variation were observed for all traits. The genetic variances and correlation coefficients of hybrid traits did not significantly differ between the SRIL-TC and IRIL-TC populations. Twenty five significant small to moderate QTL were detected, but only one, for grain moisture, was shared between inbred-testcross populations. Overall, the two inbred parents from different heterotic groups have many distinct alleles that contribute to traits. The recombinant inbred line populations had high means and variances for grain yield and related traits, which opens the possibility of utilizing these lines for hybrid breeding.

京都大学 / 新制・論文博士 / 博士(農学) / 乙第13519号 / 論農博第2907号 / 新制||農||1096(附属図書館) / 学位論文||R4||N5419(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 中﨑 鉄也, 教授 那須田 周平, 教授 吉田 健太郎 / 学位規則第4条第2項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

It is well documented that both quantitative and qualitative changes in the murine hematopoietic stem cell (HSC) population occur with age. In mice, the effect of aging on stem cells is highly strain-specific, thus suggesting genetic regulation plays a role in HSC aging. In C57BL/6 (B6) mice, the HSC population steadily increases with age, whereas in DBA/2 (D2) mice, this population declines. Our lab has previously mapped a quantitative trait locus (QTL) to murine chromosome 2 that is associated with the variation in frequency of HSCs between aged B6 and D2 mice. In these dissertation studies, I first aim to characterize the congenic mouse model which was generated by introgressing D2 alleles in the QTL onto a B6 background. Using a surrogate assay to mimic aging, I analyzed the cell cycle, apoptotic and self-renewal capabilities of congenic and B6 HSCs and show that D2 alleles in the QTL affect the apoptotic and selfrenewal capabilities of HSCs. In the second aim of these studies, I used oligonucleotide arrays to compare the differential expression of B6 and congenic cells using a population enriched for primitive stem and progenitor cells. Extensive analysis of the expression arrays pointed to two strong candidates, the genes encoding Retinoblastoma like protein 1 (p107) and Sorting nexin 5 (Snx5). B6 alleles were associated with increased p107 and Snx5 expression in old HSCs therefore both genes were hypothesized to be positive regulators of stem cell number in aged mice. Finally, in the third aim of these studies, I show that the individual overexpression of p107 and Snx5 in congeic HSCs increases day35 cobblestone area forming cell (CAFC) numbers, therefore confirming their roles as positive regulators of HSC number in vitro. These studies uncover novel roles for p107 and Snx5 in the regulation of HSC numbers and provide additional clues in the complex regulation of HSC aging.

The virulence of Plasmodium falciparum is largely attributed to the ability of asexual blood-stage parasites to cytoadhere to the microvascular endothelium of the human host. This pathogenic behavior is mediated by the primary parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1), an understanding of which is crucial to develop interventions to ameliorate the morbidity and mortality of P. falciparum malaria. The work presented in this thesis describes the application of a phenotype-to-genotype experimental approach to identify novel parasite proteins involved in the trafficking and display of PfEMP1. Guided by the overall hypothesis that the in vitro culture-adapted parasite line 3D7 harbors 1 or more genetic determinants of impaired PfEMP1 trafficking, surface PfEMP1 levels were first measured in 3D7, the presumably trafficking-competent parasite line HB3, and 16 unique progeny from an HB3 x 3D7 genetic cross (chapter 2). These phenotypes were then combined with genome-wide SNP data in QTL analysis to identify genetic polymorphisms potentially responsible for the impaired trafficking in 3D7 (chapter 3). A near-significant QTL containing a single protein-coding gene, the putative kinesin Pf3D7_1245600, was identified, characterized, and investigated in CRISPR-Cas9-driven allele-exchange parasite transfection experiments to establish a causal link between the gene and PfEMP1 trafficking (chapter 4). The parasite transfections were unsuccessful, but the potential role of Pf3D7_1245600 in PfEMP1 trafficking was indirectly assessed through the disruption of microtubules with colchicine (chapter 4), which significantly impacted the surface PfEMP1 levels of HB3 but not 3D7. The findings of this thesis suggest that kinesins and microtubules may play previously unconsidered roles in the regulation, production, or trafficking of PfEMP1.

Visual quality is one of the major factors that determine the market value of field pea (Pisum sativum L.). Breeding for improved visual quality of pea seeds is currently a challenging task, because of the complexity and lack of sound genetic knowledge of the traits. The objectives of this research were to characterize the genetic basis and identify the genomic regions associated with four key visual quality traits (cotyledon bleaching in green pea, greenness in yellow pea, and seed shape and seed dimpling in both green and yellow types) in field pea. Biochemical and gene expression profiling to understand the molecular basis of post-harvest cotyledon bleaching in green pea was also addressed. Two F5:6 recombinant inbred line (RIL) populations (90 lines from Orb X CDC Striker cross, and 120 lines from Alfetta X CDC Bronco cross) were developed and evaluated for visual quality traits in two locations in Saskatchewan, Canada in 2006 and 2007. The four quality traits evaluated all displayed a continuous range of expression with moderate to high heritability. Two genetic linkage maps utilizing 224 markers (29 simple sequence repeat (SSR) (from Agrogene) and 195 amplified fragment length polymorphism (AFLP)) and 223 markers (27 SSR and 196 AFLP ) were constructed for the Orb X CDC Striker population and the Alfetta X CDC Bronco population, respectively. Multiple quantitative traits (QTL) mapping detected major QTLs on linkage group (LG) IV and LG V, as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance. Nine QTLs controlling yellow seed lightness, three for yellow seed greenness, 15 for seed shape and nine for seed dimpling were detected. Among them, 5 QTLs located on LG II, LG IV and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits. The bleaching resistant cultivar CDC Striker had a slower rate of chlorophyll degradation in cotyledons and a higher carotenoid to chlorophyll ratio in seed coats than the bleaching susceptible cultivar Orb when seed samples were exposed to high intensity light. An oligo-nucleotide microarray (Ps6kOLI1) was utilized to investigate the gene expression profiles of CDC Striker and Orb seed coats at different developmental stages. It clearly indicated that the expression of genes involved in the production and accumulation of secondary metabolites was significantly different between these cultivars. The results of both biochemical and gene expression studies suggested the bleaching resistance in CDC Striker was not due to the accumulation of chlorophyll pigments in the cotyledons, but rather due to the ability of seed coats to protect them from photooxidation. Accumulation of specific carotenoids which could bind with the reaction center protein complex more effectively and accumulation of phenolic secondary metabolites which could enhance the antioxidant properties and structural integrity of the seed coats may lead to the bleaching resistant phenotype. Therefore, breeding green pea cultivars with higher seed coat antioxidant properties would improve both visual and nutritional quality. This research has provided several insights into molecular approaches to improve field pea visual quality for food markets.

The growth and development of two sorghum drought tolerant genotypes BTx642 (post-flowering drought tolerant, “stay green”) and RTx7000 (pre-flowering drought tolerant) were characterized and compared. Differences in phenology and the growth and development of leaves and stalks were identified that could contribute to variation in shoot biomass, grain yield and response to water deficit. An F12 recombinant inbred line (RIL) population derived from the two parents was genotyped using the Illumina Genome Analyzer II platform and the information used to generate a genetic map useful for analysis of quantitative trait loci (QTL). Seventy-two different traits were measured in the RIL population at anthesis and at grain maturity. Plants were grown in well-watered environments in greenhouse conditions and in field conditions near College Station, TX in 2008-2010. QTL mapping was used to analyze the genetic basis of trait variation in the population and to detect associations between traits. A total of 477 QTL were identified that in combination modulate leaf size (length, width, and area), shoot biomass accumulation (shoot, stalk, stem, leaf, and leaf sheath), panicle weight, root size and architecture (length, surface area, and volume, number of tips, forks and nodal roots, and root biomass), stalk and stem length, and flowering time. Six flowering time QTL were identified and variation in time to anthesis affected the expression of several other traits including leaf size and biomass accumulation. However, QTL infrequently had an impact on traits associated with different organs. The specificity observed is consistent with independent genetic control of traits associated with leaves, stems and roots. Nine QTL that modulated shoot biomass accumulation were detected that were not affected by flowering time. Of these, four shoot biomass QTL co-localized with leaf size traits. Eight QTL for panicle biomass were detected with two coincident with QTL for upper leaf size. A QTL for leaf width at anthesis was found to co-localize with a stay green locus.

Visual quality is one of the major factors that determine the market value of field pea (Pisum sativum L.). Breeding for improved visual quality of pea seeds is currently a challenging task, because of the complexity and lack of sound genetic knowledge of the traits. The objectives of this research were to characterize the genetic basis and identify the genomic regions associated with four key visual quality traits (cotyledon bleaching in green pea, greenness in yellow pea, and seed shape and seed dimpling in both green and yellow types) in field pea. Biochemical and gene expression profiling to understand the molecular basis of post-harvest cotyledon bleaching in green pea was also addressed. Two F5:6 recombinant inbred line (RIL) populations (90 lines from Orb X CDC Striker cross, and 120 lines from Alfetta X CDC Bronco cross) were developed and evaluated for visual quality traits in two locations in Saskatchewan, Canada in 2006 and 2007. The four quality traits evaluated all displayed a continuous range of expression with moderate to high heritability. Two genetic linkage maps utilizing 224 markers (29 simple sequence repeat (SSR) (from Agrogene) and 195 amplified fragment length polymorphism (AFLP)) and 223 markers (27 SSR and 196 AFLP ) were constructed for the Orb X CDC Striker population and the Alfetta X CDC Bronco population, respectively. Multiple quantitative traits (QTL) mapping detected major QTLs on linkage group (LG) IV and LG V, as well as location- and year-specific QTLs on LG II and LG III associated with green cotyledon bleaching resistance. Nine QTLs controlling yellow seed lightness, three for yellow seed greenness, 15 for seed shape and nine for seed dimpling were detected. Among them, 5 QTLs located on LG II, LG IV and LG VII were consistent in at least two environments. The QTLs and their associated markers will be useful tools to assist pea breeding programs attempting to pyramid positive alleles for the traits. The bleaching resistant cultivar CDC Striker had a slower rate of chlorophyll degradation in cotyledons and a higher carotenoid to chlorophyll ratio in seed coats than the bleaching susceptible cultivar Orb when seed samples were exposed to high intensity light. An oligo-nucleotide microarray (Ps6kOLI1) was utilized to investigate the gene expression profiles of CDC Striker and Orb seed coats at different developmental stages. It clearly indicated that the expression of genes involved in the production and accumulation of secondary metabolites was significantly different between these cultivars. The results of both biochemical and gene expression studies suggested the bleaching resistance in CDC Striker was not due to the accumulation of chlorophyll pigments in the cotyledons, but rather due to the ability of seed coats to protect them from photooxidation. Accumulation of specific carotenoids which could bind with the reaction center protein complex more effectively and accumulation of phenolic secondary metabolites which could enhance the antioxidant properties and structural integrity of the seed coats may lead to the bleaching resistant phenotype. Therefore, breeding green pea cultivars with higher seed coat antioxidant properties would improve both visual and nutritional quality. This research has provided several insights into molecular approaches to improve field pea visual quality for food markets.

Domestication is the process by which animals become adapted to the environment provided by humans. The process of domestication has let to a number of correlated behavioural, morphological and physiological changes among many domesticated animal species. An example is the changes of plumage colour in the chicken. Plumage colour is one of the most readily observable traits that make distinction between breeds as well as between strains within a breed. Understanding the genetic architecture of pigmentation traits or indeed any trait is always a great challenge in evolutionary biology. The main aim of this study was to map quantitative trait loci (QTLs) affecting the red and metallic green coloration in the chicken plumage. In this study, a total of 572 F8 intercross chickens between Red Junglefowl and White Leghorn were used. Phenotypic measurements were done using a combination of digital photography and photography manipulating software. Moreover, all birds were genotyped with 657 molecular markers, covering 30 autosomes. The total map distance covered was 11228 cM and the average interval distance was 17 cM. In this analysis, a total of six QTLs (4 for red and 2 for metallic green colour) were detected on four different chromosomes: 2, 3 11 and 14. For red colour, the most significant QTL was detected on chromosome 2 at 165 cM. An additional QTL was also detected on the same chromosome at 540 cM. Two more QTLs were detected on chromosomes 11 and 14 at 24 and 203 cM respectively. Additionally, two epistatic pairs of QTLs were also detected. The identified four QTLs together can explain approximately 36% of the phenotypic variance in this trait. In addition, for metallic green colour, one significant and one suggestive QTLs were detected on chromosomes 2 and 3 at 399 and 247 cM respectively. Moreover, significant epistatic interactions between these two QTLs were detected. Furthermore, these two QTLs together can explain approximately 24% of the phenotypic variance in this trait. These findings suggest that the expression of pigmentation in the chicken plumage is highly influenced by both the epistatic actions and pleiotropic effects of different QTLs located on different chromosomes.