ddRAD-seq data reveals the significant population structure and potential causes of population divergence in Bougainvillea

Bougainvillea, an increasingly popular ornamental plant known for its vibrant colours and extended flowering period. Due to the complexities of classification systems and the serious phenomenon of homonym in Bougainvillea, this study utilized simplified genome sequencing technology (ddRAD) to explore the genetic background of 84 Bougainvillea varieties.756,078 SNPs were utilized to analyse the genetic diversity, genetic structure, and genetic relationships among these cultivars. The results indicated that all samples were categorized into six subpopulations (B1, B2, B3, B4, B5, B6), with low genetic diversity observed in all subpopulations except B5. Notably, there was significant gene flow and infiltration among different subpopulations, and most varieties exhibited no apparent kinship to one another. Additionally, selective sweep analysis identified 38 commonly selected sites across the six Bougainvillea subpopulations. These sites are primarily enriched in biosynthesis pathways related to sesquiterpenoids and triterpenoids, as well as glycerophospholipid metabolism, which may be associated with the directional artificial domestication of Bougainvillea and its susceptibility to bud mutation. This study not only uncovered the complex genetic background of Bougainvillea but also emphasized the considerable genetic differentiation within the subpopulations, thereby providing a foundation for future association studies and targeted breeding efforts.