Fig. 1

Geographic distribution, population structure, and genetic diversity of garlic accessions. a Geographic distribution of 230 garlic accessions, which are represented by dots on the world map. b Principal components (PC) analysis plots of the first three components of 230 accessions. c Phylogenetic tree and model-based clustering analysis of 230 accessions. The rooted tree constructed using neighbor-joining method. Model-based clustering analysis with different cluster numbers (k = 2–8). The y-axis quantifies cluster membership, and the x-axis lists the different accessions. The orders and positions of these accessions on the x-axis are consistent with those presented in the neighbor-joining tree. Three Allium ampeloprosum accessions were used as the outgroup species. d Nucleotide diversity (π) and population divergence (F_ST) across the four groups. The value in each circle represents an estimation of nucleotide diversity for each group, and values on each line indicate pairwise population divergence between groups. Value in black or red indicates that it was estimated using the SNPs from genotyping-by-sequencing and whole-genome resequencing. e Comparison of the trait value in the origin group (OG) and two cultivated groups of East Asia, CG1 and CG2 for four bulb traits. ns indicates no significant difference, and *, **, *** indicates the significance at the level of 0.05, 0.01, and 0.001, respectively