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 Construction of Identity in Edwidge Danticat's The Farming of Bones

The Farming of Bones deals with issues surrounding the dynamic connections between identity and boundary construction in post-colonial context. It will present an analysis of how the novelist problematizes and communicates her idea of social and national identity construction to her readers and how the readers can identify themselves with the struggles and challenges of the protagonist Amabelle who is trying to find her own identity. This essay will show how Danticat’s novel contributes to an understanding of national identity beyond borders and makes the reader take the role of an individual who constructs her identity by uncovering moments of raw humanness. Until now, no literary scholar has examined the protagonist’s therapeutic role in bridging this social and national gap. Instead critics have discussed other issues of the novel like crossing and re-crossing the border, love, dreams, etc. Although this scholarship has been very effective and rewarding, it lacks any focus on the complexity of the characters’ identity construction. Therefore, this paper will reconsider Danticat’s The Farming of Bones with a closer attention to the question of identity.