In this project we aim to conduct genomic analyses to better understand the genomic architecture of adaptive variation and the genomic impact of plant mating system shifts from outcrossing to self-fertilization. We aim to do so by studying the evolution of a classic supergene that governs a multi-trait balanced polymorphism called distyly, which constitutes an iconic example of convergent floral evolution. While distyly has attracted the attention of many generations of biologists, including Darwin himself, its molecular basis has remained unclear. Thanks to funding from the ERC and VR, we have identified and characterized the evolution of the genomic region, a so-called supergene, that governs distyly in wild flaxseed species (Linum spp.). To facilitate studies of supergene and mating system evolution in the classic Linum system, we have generated 10 high-quality genome assemblies to provide a genomic framework. The high-quality genome assemblies produced during this project paves the way for studies of the molecular basis of adaptive floral differences first identified by Darwin. The results from this project are important for an improved understanding of the processes that govern supergene evolution and the origins of coadapted gene complexes. More recently, we have also received funding from Formas to identify genetic variants that confer drought tolerance in crop wild relatives and that can be used for breeding climate resilient crops. To achieve this, we will undertake landscape genomic analyses and genome-wide association analyses in crop wild relatives. Taken together, the project will be both of broad and general importance for understanding the genetic basis of complex adaptive polymorphisms as well as of direct applied utility for breeding more climate resilient crops.