Uncovering adaptation with a new <i>Arabidopsis thaliana</i> multiparent intercross population

Understanding the molecular basis of adaptation and the genetic architecture of complex traits are longstanding goals in biology. One problem impeding this understanding is the complexity of continental populations, with their complicated demographic histories, gene flow and secondary contact. In contrast, island populations represent simpler systems where uncovering the genetic basis of complex traits and tracing how traits built up is much more tractable. In Arabidopsis thaliana, the Cape Verde Islands populations represent a case of long-range colonization and adaptation to a divergent selective regime. Here, we describe the development and testing of a new multiparent intercross doubled haploid population of A. thaliana from the Cape Verde Islands. This population balances the representation of natural diversity and overcomes the shortcomings of existing resources, such as biparental recombinant inbred lines and genome-wide association populations. Specifically, it captures variation that segregates within the archipelago but is fixed on individual islands. We mapped the genetic basis of flowering time, rosette size, and photosystem II efficiency (ΦPSII) in this inter-island intercross population, representing traits that we hypothesized may be evolving under strong selection during the colonization of the archipelago. We identified functional loci underlying these traits, including FRI K232X and FLC R3X for flowering time, and IRT1 G130X for ΦPSII and rosette size. Our multiparent intercross population complements existing mapping resources and provides a robust framework for investigating the genetic basis of complex traits in A. thaliana. This work emphasizes the value of island systems and complementary approaches for advancing our understanding of genetic adaptation.