Domestication history and genetic changes for the newly evolved flower color in the ornamental plant <i>Lobularia maritima</i> (Brassicaceae)

<i>Lobularia maritima</i> (sweet alyssum) is a popular ornamental plant that displays a range of flower colors, particularly white and purple. However, the genetic underpinning and evolutionary history of flower colors have remained unknown. To address this, we performed a <i>de novo</i> assembly of a chromosome-level genome for this species and conducted comparative population genomic analyses of both domestic and wild representatives. These analyses revealed distinct genetic clusters corresponding to wild and domestic groups, with further subdivisions based on geographic and phenotypic differences. Importantly, all cultivars originated from a single domestication event within the Tunisia group. One wild group did not contribute genetically to the current cultivars. The new mutations in key gene of the anthocyanin biosynthetic pathway, <i>PAP1</i>, that arose following domestication led to the origin of purple flower coloration in the cultivars. Moreover, the contrasting <i>PAP1</i> haplotypes in white and purple varieties lead to differential expression of <i>CHS</i> and <i>DFR</i>, which in turn contributes to the observed flower color differences. These findings provide key insights into the domestication history and genetic regulation of flower color in <i>L. maritima</i>, laying the groundwork for future genetic breeding efforts focused on this plant, especially introducing genetic sources from other wild groups.