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Trait variation within species is shaped by the genotype and the environment an individual is exposed to. Genomic information is inherited from the parents and forms the basis of the phenotype of an organism. The genetic variation between parents becomes differently distributed between their offspring, leading to trait variation in the offspring. Each trait can be affected by many genes, therefore the genetic architecture can be complex. In complex traits, multiple loci contribute to the ultimate trait value. However, complex traits are shaped not only by genetic variation but also by the environment and the interaction between genotype and environment. The interplay between genetic and environmental variation can affect the fitness of an organism. Chapter 2 discusses how genotype and environment have shaped the phenotype of the nematode Caenorhabditis elegans, the model species used in this thesis, resulting in a laboratory adapted domesticized strain known as Bristol N2. Bristol N2 has been cultivated in the laboratory for over a decade, leading to the fixation of novel mutations in several genes that strongly affect its phenotype. Genotypic variation arisen by novel mutations in the genes npr-1, glb-5, and nath-10 was fixed in N2 due to the laboratory environment. The allelic variation in npr-1 affects the behaviour of this animal in an environment dependent manner, showcasing the interplay between genotype and environment. However, the altered behaviour warrants caution for interpretation of results obtained in the N2 strain. The genotypic effects on trait variation can be large, and one of the more powerful population designs to study these effects are introgression lines. In chapter 3 the construction of a genome-wide introgression line (IL) panel between the N2 and the CB4856 strain is described. This panel contains loci of N2 introgressed in a homogeneous CB4856 background. It is demonstrated that together with CB4856-in-N2 ILs this new genome-wide introgres