460bp/Morex(24)

460bp/Strider(1)

520bp/OWB-D(1)

630bp/Baronesse(4)100

Insensitive/Baronesse(16)

Insensitive/OWB-D(1)

Insensitive/Morex(9)

Recessive/Strider(18)

Dominant/BCD12(10)

Dominant/Morex(60)

Dominant/OWB-R(2)

Dominant/OWB-D(10)

Recessive/Haruna Nijo(2)

64

66

66

Recessive/Hoody(3)

Recessive/Strider(3)

Dominant/Morex(37)

Recessive/OWB-D(6)

Recessive/OWB-R(4)

Recessive/Dicktoo(1)

Recessive/Kompolti korai(48)

100

100

100

Insensitive/Morex(15)

Insensitive/Baronesse(8)

Sensitive/Steptoe(1)

Sensitive/Arapiles(1)

Sensitive/Dicktoo(2)

Sensitive/Strider(3)

99

46

53

C) VRN-H3, 5670 bp, 102 accessions

B) HvSNF2 (VRN-H2 locus), 632 bp, 30 selected accessions

A) VRN-H1, 668 bp, 102 accessions

F) PPD-H1, 1355 bp, 30 selected accessions

D) VRS1, 1192 bp, 102 accessions

HvCBF3-Morex(12)

HvCBF3-Strider(2)

HvCBF3-Baronesse(4)

HvCBF3-88Ab536(3)

HvCBF3-Scarlett(9)

52

41

HvCBF6-Baronesse(4)

HvCBF6-OWB-D(1)

HvCBF6-88Ab536(1)

HvCBF6-Strider(3)

HvCBF6-Morex(12)

HvCBF6-Scarlett(9)

99

3532

HvCBF9-Morex(12)

HvCBF9-Scarlett(9)

HvCBF9-Baronesse(4)

HvCBF9-Strider(3)

HvCBF9-Kompolti korai(1)

HvCBF9-OWB-D(1)

34

27

vrs1.a1/Morex(9)

vrs1.a1/Kompolti korai(7)

vrs1.a2/Strider(3)

Vrs1.b2/OWB-D(14)

vrs1.a4/Belford(4)

Vrs1.b3/Harrington(41)

vrs1.a3/Dicktoo(24)90

67

45

65

E) PPD-H2, 1467 bp, 26 selected accessions

G) HvCBF3 (FR-H2 locus), 874bp, 30 selected accessions

H) HvCBF6 (FR-H2 locus), 913bp, 30 selected accessions

I) HvCBF9 (FR-H2 locus), 988bp, 30 selected accessions

Figure S1. Neighbor-Joining phylogenetic cluster analyses of 12 re-sequenced genes of the barley CAP Core set. Confidence values on the branches are based on 1000 bootstraps. Sequence length and number of lines used are indicated in the heading of each cluster. Number of genotypes per haplotype is indicated in brackets. Haplotypes are named after a representative cultivar