Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

The program and treatment effect of summer jobs on girls’ post-schooling incomes

Public programs (of disputed effect) offering summer jobs or work while in high school to smooth the transition from school to work is commonplace. In this paper, 1447 girls in their first grade of high school between 1997-2003 and randomly allotted summer jobs via a program in Falun (Sweden) are followed 5-12 years after graduation. The program led to a substantially larger accumulation of income while in high school. The causal effect of the high school income on post-schooling incomes was substantial and statistically significant. The implied elasticity of 0.4 is however potentially inflated dueto heterogeneous effects.

Degree projects improving co-operation between the teacher education program and schools : - Swedish experiences

In 1977, when teacher education inSwedenwas incorporated into the university system, the main reason was to transform it into an academic tradition. Now, nearly 30 years later, there is still tension between the academic and the vocational tradition; they show up as different and separated elements in a program that is meant to prepare students for a career as a teacher and for a possible future career as a researcher in this field. This tension gives rise to a risk of allowing parallel “tracks” to develop and of isolating the degree thesis work from other courses. On the teacher-training program in which we are involved, close co-operation with partner-schools, where the practical part of the program takes place, has been established. Here, the students´ degree theses are an important factor in making this co-operation work on a concrete level. Accordingly, the purpose of the degree thesis is both to reflect problems in schools and contribute to better teaching in the individual school, but also to offer relevant educational subject matter to the students, which may be adapted as an element in the university’s research environments. From these points of view, the degree thesis is an important part of teacher education and rather more than just a single course. The degree thesis should be an element that gives the students an opportunity to show that they have reached central goals in the teacher education program. It should also be an integral part in the development of critical and scholarly thinking, deepening pedagogical and didactic knowledge and giving the students an opportunity to apply research methods. We will here use two minor case studies: one that compares teacher education programs in five Swedish universities and one minor study at one of those universities, in order to elaborate on the questions: - What purpose has a degree thesis and what role does it play in teacher education? - What criteria are relevant to assessing a degree thesis and what qualities do the degree theses have? - Is it possible to assess a degree thesis fairly and what happens to students who do not pass? - How could the degree thesis be used to improve the contact between the teacher education program and its partner schools in order to contribute to the development of the individual school?