Genetic Relationships and Molecular Signatures of Divergence in Traditional Landraces and Morphotypes of Brassica oleracea

Brassica oleracea is a complex species incorporating a great variety of vegetable types, including cabbage, cauliflower, broccoli, kale, and others. Southern Italy, and especially the Puglia region, is rich in B. oleracea landraces. In this study, genotyping-by-sequencing (GBS) was applied to a germplasm panel of 82 samples, mostly landraces and some commercial varieties, belonging to various morphotypes of B. oleracea. Population structure (K = 2), principal component (PCA), and phylogenetic analyses resulted in a general subdivision of our samples into two large lineages: the types used for their leaves (LHL) and those consumed for their flower heads (AIL). Going deeper inside, the different morphotypes were mostly grouped into specific clusters, and a clear separation of particular landraces, such as the Mugnoli and Cima nera broccoli, was observed in the structure analysis (K = 7), as well as in the PCA and in the Neighbor-Joining tree. The calculation of the pairwise fixation index (FST, threshold > 0.50) between LHL and AIL types (based on population structure analysis at K = 2) provided 456 outlier single nucleotide polymorphisms (SNPs). Among the corresponding orthologs annotated in Arabidopsis, we identified several genes involved in flower/inflorescence development, cellular proliferation, etc. Overall, our investigation provides useful information on the knowledge of early domesticated landraces of B. oleracea and allows for the attribution of unknown material to the appropriate taxonomical ranking. The analysis of outlier SNPs has highlighted signatures of molecular divergence between LHL and AIL lineages.