Fig. 2

Population structure and LD decay in lotus. a The neighbor-joining tree of the 69 lotus accessions with bootstrap =1000 and the bootstrap values less than 100 were labelled. The accessions shown in red are wild sacred lotus, while yellow indicates American lotus, and purple, blue, and green represent flower lotus, rhizome lotus and seed lotus, respectively. b Principal component analysis (PCA) of the 69 lotus accessions. Two accessions of American lotus were from locations far from the sacred lotus accessions. The PCA of 67 accessions (Nelumbo nucifera) is shown on the left bottom side. c Population structure (k = 2–7) of the 69 lotus accessions determined by FRAPPE. Each accession is represented by a vertical bar, and the length of each colored segment in each vertical bar represents the proportion contributed by ancestral populations. d Differences in linkage disequilibrium (LD) between the wild and cultivated lotus groups. LD decay determined via squared correlations of allele frequencies (r2) against the distance between polymorphic sites in cultivated and wild lotus