Fig. 7

Genomic diversity of the cultivated tomato collection. a STRUCTURE analysis of 244 S. lycopersicum genotypes with 37,317 SNP markers in the case of five clusters (K). The vertical coordinates of each subpopulation indicate the membership coefficient for each individual; each vertical bar represents one genotype. The coloured blocks correspond to the different clusters. b Maximum likelihood phylogenetic tree (unrooted). The initial tree for the heuristic search was obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Tamura-Nei model, and then selecting the topology with superior log likelihood value. The tree with the highest log likelihood (− 1,427,221.59) is shown. Internal colours correspond to clusters K1 to K5 (see panel a). c PCoA visualization of the genetic relationships between members of the association panel. Coloured symbols in the phylogenetic tree and the PCoA represent accessions from different cultivar group indicated in the legend