Online Resource S3

Table S4 Assignment of 708 flax accessions into 20 BAPS clusters by passport data

A. By section and user type

Cluster 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Total breeding lines 3 3 5 6 11 46 8 0 21 8 4 5 3 0 9 24 5 0 12 5 178 landraces 5 2 5 33 12 2 7 3 6 39 2 8 4 0 6 0 3 1 0 5 143 cultivars 21 33 19 13 6 2 8 82 36 16 9 19 26 33 7 0 12 21 0 24 387 fibre use 14 18 11 27 21 24 16 37 18 40 11 21 16 16 13 13 11 3 4 17 351 combined use 1 0 7 9 6 6 3 5 10 7 1 1 4 5 4 6 2 1 3 5 86 oil use 14 20 11 16 2 17 4 43 37 16 3 10 13 13 5 5 8 18 5 12 272

Total 29 38 29 52 29 50 23 85 63 63 15 32 33 33 22 24 20 22 12 34 708

B. By. country of origin

Cluster 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Total CSK 4 5 3 8 11 38 8 1 19 6 5 5 2 0 8 20 7 0 12 7 169 NLD 3 4 4 2 3 0 3 6 6 1 1 3 4 6 3 0 2 1 0 4 56 USA 3 1 5 2 3 0 1 13 10 6 0 4 3 3 0 3 0 1 0 0 58 SUN 1 0 0 2 1 2 2 10 2 7 1 2 0 0 0 0 1 1 0 2 34 GER 4 4 0 10 0 0 0 1 0 2 0 0 0 0 1 0 0 3 0 3 28 ARG 2 8 2 5 0 0 0 9 10 2 1 3 5 1 0 0 0 11 0 4 63 BRA/URY 4 5 1 0 0 0 0 8 4 0 2 3 2 1 0 0 2 0 0 1 36 BGR 0 0 0 1 2 0 0 3 0 2 2 5 1 18 0 0 0 0 0 1 35 Other countries 7 12 9 22 9 10 9 33 12 37 3 7 16 4 10 1 8 5 0 12 227 Table S5 Analysis of molecular variance (AMOVA) of all flax genotypes used to partition the total genetic variation to among- and within-population components.

Source of variation Number Sum of squares Variance components % of variation

Total 708 3109.68 25.20 Among sections 3 478.56 6.68 23.45 Within populations 708 2156.43 16.52 76.55 Within cultivars 387 504.36 11.45 Within landraces 143 1142.20 20.33 Within breeding lines 178 509.87 12.56 Within fiber use 351 806.35 12.67 Within oil use 86 1023.46 21.30 Within combined use 271 1256.33 25.20 Table S6 Inter-population distance (phi-statistic=Φst) estimates among germplasm sections detected by AMOVA. The significance of each Φst value is based on a permutation test (n=1000). Comparison Inter-population distance Φst P value breeding lines vs. landraces 0.296 *** landraces vs. cultivars 0.254 ** breeding lines vs. cultivars 0.103 ** oil vs. fibre 0.116 ** oil vs. combined 0.058 fibre vs. combined 0.063

*** significant at P < 0.001 ** significant at P < 0.05 Fig S1 Neighbor joining tree of 20 BAPS clusters In group I, there are 88 breeding lines, 107 landraces, 176 cultivars of which 200 accessions are fibre type, 39 combined and 129 of oil type use. In group II, there are 266 breeding lines, 36 landraces, 211 cultivars of which 151 accessions are fibre type, 47 combined and 143 of oil type use.

Group I

Group II Fig S2 Multidimensional scaling (MDS) plot of the clusters based on average pair-wise Hamming distances between the accessions they contain.