Understanding the genetic basis of complex traits

Recent advances in genetics and genomics have provided numerous opportunities to study the genetic basis of complex traits. Nevertheless, dissecting the genetic basis of complex traits is still challenged by the complex genetic architecture, in which many genes are involved, and many have small contributions to phenotypic variation, interactions with other genes or environmental factors. The aim of this thesis is to evaluate the genetic basis of the complex traits by exploring available genomic resources and analytical approaches. Four studies included in this thesis explore: the genetic basis of global transcriptome variation in natural population (Study I); the genetic basis of 8-week body weight in artificial selected chicken lines (Study II); the genetic basis of flowering time variation for Arabidopsis thaliana sampled from a wide range of ecological conditions (Study III and Study IV). Findings from this thesis show that the genetic architecture of complex traits involves many polymorphisms with variable effect sizes. Some of those polymorphisms are multi-allelic and have interactions with each other and environmental factors at the same time. The presence of many alleles with minor contributions to phenotypic variation in natural and artificially selected population demonstrates that response to natural and artificial selection has been achieved by polygenic adaptation. Furthermore, population-specific large-effect loci with long-range LD to QTL in functionally related pathways indicate that emergence and fixation of loci with large effects and co-evolution of loci in the related pathway is contributing to the local adaptation of Arabidopsis thaliana. Overall, this thesis shows the complexity of complex trait genetics and provides a few insights into study designs and analysis approaches for understanding the genetic basis of complex traits