Genetic variation in the lettuce pangenome

Lettuce is an important and valuable leafy vegetable showing extensive morphological and genetic variation. To utilise this genetic variation without bias to any specific cultivar, a pangenomic approach is needed. A pangenome integrates genetic variation across cultivars or even species into a single representation to which novel genomic data can be compared.  In this thesis, we contributed to this holistic understanding of genetic variation in lettuce and its wild relatives by constructing new annotated genome assemblies for wild relatives of lettuce, developing novel methods for the construction and analysis of large plant pangenomes, and analysing a lettuce pangenome of cultivated and wild lettuce. We found variations in genes and gene organisation that are relevant for lettuce breeding. Moreover, we pioneered pangenomics methodology necessary to support genomics-based breeding in lettuce and other crops.