Supplementary material
List of supplementary material
Supplementary Tables 1a to 6s: Polymorphic sites and haplotypes observed in each segment for genes Sh2, Bt2, SssI, Ae1, Wx and O2.
Supplementary Table 7: Correspondence between the names of the polymorphic sites used in this study and their physical position on the sorghum pseudomolecules v1.0.
Supplementary Figure 1: Positions of Sh2, Bt2, SssI, Ae1, Wx and O2 on a synthetic genetic map of sorghum.
Supplementary Figure 2: Position of the sequenced segments on Sh2, Bt2, SssI, Ae1, Wx and O2.
Supplementary Tables 1a to 6s: Polymorphic sites and haplotypes observed in each segment for genes Sh2, Bt2, SssI, Ae1, Wx and O2.
Polymorphic sites are labeled "s" followed by the site starting position in bp in the segment minus 1. Alleles at Indels are defined by reference to the longest insertion with an insertion of any length represented by allele 0, and the deletion by a number corresponding to the number of deleted bp. In comparison with de Alencar Figueiredo et al. (2008), rare SNPs are not represented. The most frequent allele at the SNP/deletion is in bold. SNP/deletion frequencies can be deduced from haplotype frequencies. nc stands for non coding, c for coding, s for synonymous and ns for non synonymous. Haplotypes in brackets in italics are haplotypes represented by less than five accessions that were not included in the association analyses.
Supplementary Table 1a: Sh2, segment A polymorphic sites and haplotypes (184 accessions; 693 bp; exon 1 to exon 2)
Sh2 A / E1s87
cns / I1
s253
nc / I1
s264
nc / I1
s281
nc / I1
s480
nc / I1
s525
nc / I1
s570
nc / I1
s636
nc / Freq.
A1 / G / 1 / A / C / T / C / T / T / 81.5
A2 / G / 0 / A / C / T / C / T / T / 9.3
A3 / A / 1 / G / T / C / T / G / G / 9.2
Supplementary Table 1b: Sh2, segment B polymorphic sites and haplotypes (169 accessions; 638 bp; intron 12 to 3’UTR)
Sh2 B / I12s88
nc / I12
s116
nc / I12
S125
nc / E13
s240
cs / I13
s294
nc / E14
s377
cs / I14
s423
nc / I14
s427
nc / I14
s440
nc / I14
s474
nc / 3'
s626
nc / Freq.
B1 / G / C / T / A / G / T / A / G / C / T / C / 84.6
B2 / G / C / T / G / G / T / A / G / C / T / C / 6.5
B3 / T / A / A / G / C / C / G / A / T / C / A / 8.9
Supplementary Table 1c: Sh2, gene haplotype from concatenated segments A and B (159 accessions; 1,331 bp)
Sh2 / Sh2 A / Sh2 B / Freq.H1 / A1 / B1 / 73.6
H2 / A2 / B1 / 9.4
H3 / A3 / B3 / 7.6
H4 / A1 / B2 / 6.9
[H5 / A3 / B1 / 2.5]
Supplementary Table 2a: Bt2, segment A polymorphic sites and haplotypes (177 accessions; 510 bp; exon 4 to exon 5)
s333
nc / I4
s530
nc / I4
s578
nc / I4
s627
nc / Freq.
A1 / 0 / T / G / 1 / 65.0
A2 / 0 / T / G / 0 / 3.4
A3 / 1 / T / G / 1 / 20.3
A4 / 0 / C / A / 1 / 9.6
[A5 / 1 / T / G / 0 / 1.1]
[A6 / 0 / C / A / 0 / 0.6]
Supplementary Table 2b: Bt2, segment B polymorphic sites and haplotypes (191 accessions; 496 bp; exon 9 to exon 10)
Bt2 B / I9s145
nc / I9
s178
nc / I9
s252
nc / Freq.
B1 / C / C / G / 75.9
B2 / C / T / A / 5.8
B3 / C / T / G / 2.6
B4 / T / C / G / 15.7
Supplementary Table 2c: Bt2, gene haplotypes from concatenated segments A and B (169 accessions; 1,006 bp)
Bt2 / Bt2 A / Bt2 B / Freq.H1 / A1 / B1 / 63.8
H2 / A3 / B4 / 13.8
H3 / A3 / B1 / 6.3
H4 / A4 / B2 / 5.7
H5 / A2 / B1 / 3.4
H6 / A4 / B3 / 3.0
[H7 / A1 / B4 / 1.1]
[H8 / A4 / B1 / 1.1]
[H9 / A5 / B1 / 0.6]
[H10 / A6 / B2 / 0.6]
[H11 / A7 / B4 / 0.6]
Supplementary Table 3a: SssI, segment A polymorphic sites and haplotypes (185 accessions; 861 bp; exon 5 to intron 9)
s57
nc / I7
s491
nc / I7
s509
nc / E8
s610
cs / I9
s859
nc / Freq.
A1 / T / T / T / G / C / 82.7
A2 / C / A / A / A / C / 12.4
A3 / C / A / A / A / G / 4.9
Supplementary Table 3b: SssI, segment B polymorphic sites and haplotypes (191 accessions; 664 bp; exon 15 to 3’UTR)
SssI B / 3'Us189
nc / 3'U
s193
nc / 3'U
s197
nc / 3'U
s624
nc / Freq.
nc
B1 / C / 3 / 2 / A / 84.3
B2 / T / 0 / 0 / G / 13.6
[B3 / T / 0 / 0 / A / 2.1]
Supplementary Table 3c: SssI, gene haplotypes from concatenated segments A and B (183 accessions; 1,525 bp)
SssI / SssI A / SssI B / Freq.H1 / A1 / B1 / 83.6
H2 / A2 / B2 / 9.3
H3 / A3 / B2 / 4.9
[H4 / A2 / B3 / 1.6]
[H5 / A2 / B1 / 0.6]
Supplementary Table 4a: Ae1, segment A polymorphic sites and haplotypes (185 accessions; 603 bp; exon 1 to exon3)
s19
cns / I1
s49
nc / I1
s109
nc / E2
s143
nc / E2
s167
cs / E2
s181
cs / E2
s189
cns / E2
s194
cns / E2
s197
cns
A1 / C / 0 / G / G / A / C / A / G / A
A2 / C / 0 / G / G / A / C / A / G / A
A3 / T / 2 / G / G / A / C / A / G / A
A4 / T / 2 / G / G / A / C / A / G / A
A5 / T / 0 / C / A / C / G / G / T / G
(continued)
Ae1 A / E2s241
cs / E2
s244
cs / E2
s246
cns / E2
s291
cns / I2
s343
nc / I2
s370
nc / I2
s393
nc / I2
s517
nc / Freq.
A1 / T / G / A / A / 1 / C / T / 7 / 32.4
A2 / C / A / G / A / 0 / A / C / 7 / 24.3
A3 / C / A / G / A / 0 / A / C / 7 / 23.2
A4 / C / A / G / A / 0 / A / C / 0 / 14.2
A5 / C / G / G / G / 0 / C / T / 7 / 5.9
Supplementary Table 4b: Ae1, segment B polymorphic sites and haplotypes (174 accessions; 774 bp; exon 20 to exon 22)
Ae1 B / I20s161
nc / I20
s187
nc / I20
s189
nc / I20
s202
nc / I20
s222
nc / I20
s224
nc / I20
s239
nc / I20
s244
nc / I20
s401
nc / I20
s471
nc / I21
s705
nc / Freq.
B1 / A / T / T / C / G / 1 / C / 14 / 3 / T / T / 24.7
B2 / T / T / T / C / G / 1 / C / 14 / 3 / T / G / 24.7
B3 / T / T / T / C / G / 1 / C / 14 / 3 / T / T / 20.7
B4 / T / C / A / T / A / 2 / T / 0 / 0 / C / T / 22.4
B5 / T / C / A / T / A / 2 / T / 0 / 1 / T / G / 7.5
Supplementary Table 4c: Ae1, gene haplotypes from concatenated segments A and B (165 accessions; 1,377 bp)
Ae1 / Ae1 A / Ae1 B / Freq.H1 / A3 / B1 / 23.6
H2 / A1 / B4 / 23.0
H3 / A2 / B2 / 16.4
H4 / A4 / B3 / 14.5
H5 / A1 / B2 / 7.9
H6 / A5 / B5 / 5.5
H7 / A2 / B3 / 4.9
[H8 / A2 / B1 / 1.2]
[H9 / A3 / B3 / 1.2]
[H10 / A1 / B3 / 0.6]
[H11 / A1 / B5 / 0.6]
]H12 / A4 / B2 / 0.6]
Supplementary Table 5a: Wx, segment A polymorphic sites and haplotypes (165 accessions; 696 bp; exon 3 to intron 6)
s278
nc / I4
s293
nc / I4
s339
nc / E5
s437
cs / I5
s459
nc / I5
s461
nc / I5
s470
nc / I5
s492
nc / I5
s493
nc / I5
s508
nc / I5
s549
nc / I5
s568
nc / I5
s572
nc / I6
s674
nc / Freq.
A1 / T / 0 / T / A / A / C / G / T / C / 0 / T / 0 / T / A / 64.2
A2 / C / 2 / G / G / T / A / A / A / A / 8 / G / 2 / C / A / 29.7
A3 / C / 2 / G / G / T / A / A / A / A / 8 / G / 2 / C / G / 6.1
Supplementary Table 5b: Wx, segment B polymorphic sites and haplotypes (191 accessions; 393 bp; exon 7 to exon 9)
Wx B / I7s110
nc / E8
s187
cs / E8
s191
cs / I8
s263
nc / I8
s267
nc / I8
s318
nc / Freq.
B1 / C / A / T / G / T / G / 55.0
B2 / G / G / C / A / A / C / 31.9
B3 / G / G / C / A / A / G / 13.1
Supplementary Table 5c: Wx, segment C polymorphic sites and haplotypes (187 accessions; 561 bp; exon 11 to exon 14)
Wx C / I11s25
nc / Freq.
C1 / 15 / 65.2
C2 / 5 / 27.3
C3 / 10 / 7.5
Supplementary Table 5d: Wx, segment D polymorphic sites and haplotypes (189 accessions; 632 bp; exon 14 to 3' UTR)
Wx D / 3's121
nc / 3'
s399
nc / 3'
s445
nc / 3'
s471nc / 3'
s535
nc / 3'
s539
nc / 3'
s562
nc / Freq.
D1 / C / 1 / G / 0 / G / T / G / 76.7
D2 / C / 1 / G / 0 / A / G / G / 5.3
D3 / C / 0 / G / 0 / G / T / G / 7.9
D4 / A / 1 / T / 34 / G / T / A / 10.1
Supplementary Table 5e: Wx, gene haplotypes from concatenated segments A, B, C, and D (152 accessions; 2,282 bp)
H1 / A3 / B1 / C1 / D4 / 25.0
H2 / A1 / B2 / C2 / D4 / 15.1
H3 / A3 / B3 / C1 / D1 / 9.2
H4 / A3 / B2 / C2 / D4 / 7.9
H5 / A1 / B1 / C1 / D4 / 5.9
H6 / A3 / B1 / C1 / D2 / 5.9
H7 / A1 / B2 / C1 / D4 / 4.6
H8 / A3 / B1 / C2 / D4 / 3.9
H9 / A3 / B2 / C1 / D4 / 3.3
[H10 / A2 / B1 / C1 / D3 / 2.6]
[H11 / A3 / B1 / C3 / D4 / 2.6]
[H12 / A1 / B1 / C3 / D4 / 1.3]
[H13 / A1 / B2 / C3 / D4 / 1.3]
[H14 / A2 / B3 / C1 / D4 / 1.3]
[H15 / A3 / B1 / C1 / D3 / 1.3]
[H16 / A3 / B1 / C3 / D2 / 1.3]
[H17 / A3 / B3 / C1 / D4 / 1.3]
[H18 / A3 / B3 / C2 / D1 / 1.3]
[H19 / A1 / B1 / C1 / D2 / 0.7]
[H20 / A1 / B3 / C1 / D4 / 0.7]
[H21 / A2 / B1 / C1 / D2 / 0.7]
[H22 / A2 / B1 / C1 / D4 / 0.7]
[H23 / A2 / B1 / C2 / D3 / 0.7]
[H24 / A2 / B2 / C2 / D4 / 0.7]
[H25 / A3 / B2 / C3 / D4 / 0.7]
Supplementary Table 6a: O2, segment A polymorphic sites and haplotypes (186 accessions; 755 bp; promoter)
s22
nc / P
s85
nc / P
s209
nc / P
s240nc / P
s242
nc / P
s258
nc / P
s276
nc / P
s409
nc / P
s419
nc / P
s482
nc / P
s634
nc / P
s735
nc / Freq.
A1 / T / 0 / T / G / 3 / C / G / G / T / T / G / 1 / 79.6
A2 / T / 0 / T / C / 3 / C / G / G / T / T / C / 1 / 7.0
A3 / T / 22 / T / G / 3 / T / G / G / T / T / G / 1 / 7.0
A4 / G / 0 / C / G / 0 / C / A / C / A / G / G / 0 / 6.4
Supplementary Table 6b: O2, segment B polymorphic sites and haplotypes (193 accessions; 495 bp; promoter)
O2 B / Ps37
nc / P
s94
nc / P
s136
nc / P
s141
nc / P
s360
nc / Freq.
B1 / G / A / A / C / C / 91.6
B2 / A / G / C / T / G / 8.4
Supplementary Table S6c: O2, segment C polymorphic sites and haplotypes (190 accessions; 607 bp; promoter to intron 1)
O2 C / E1s33
nc / E1
s127
nc / E1
s304
cns / E1
s316
cns / E1
s440
cns / E1
s481
cns / Freq.
C1 / C / 0 / A / A / C / G / 78.4
C2 / C / 0 / A / A / T / G / 6.8
C3 / C / 4 / A / A / C / G / 6.3
C4 / T / 0 / G / G / C / A / 8.5
Supplementary Table S6d: O2, segment D polymorphic sites and haplotypes (189 accessions; 497 bp; intron1)
O2 D / I1s39
nc / I1
s96
nc / I1
s328
nc / I1
s394
nc / I1
s489
nc / Freq.
D1 / A / G / G / A / 2 / 45.5
D2 / A / G / C / A / 2 / 40.2
D3 / C / G / G / A / 2 / 5.8
D4 / A / A / G / C / 0 / 8.5
Supplementary Table S6e: O2, segment E polymorphic sites and haplotypes (186 accessions; 631 bp; intron 1 to exon 3)
O2 E / I1s66
nc / I1
s94
nc / I1
s159
nc / I1
s181
nc / I1
s187
nc / I1
s195
nc / I1
s329
nc / I1
s439
nc / Freq.
E1 / G / 0 / A / A / A / G / T / 0 / 74.7
E2 / G / 0 / A / A / T / G / T / 0 / 16.7
E3 / A / 1 / C / T / A / C / A / 1 / 8.6
Supplementary Table S6f: O2, segment F polymorphic sites and haplotypes (183 accessions; 420 bp; exon 4 to exon 6)
s80
nc / E5
s215
cs / I5
s325
nc / Freq.
F1 / C / G / 0 / 92.3
F2 / T / C / 1 / 7.7
Supplementary Table S6g: O2, segment G (194 accessions; 429 bp; exon 6)
O2 G / E6s147
cns / Freq.
G1 / G / 91.8
G2 / A / 8.2
Supplementary Table S6h: O2, gene haplotypes from concatenated segments A, B, C, D, E, F, and G (183 sequences; 3,771 bp)
O2 / O2 A / O2 B / O2 C / O2 D / O2 E / O2 F / O2 G / Freq.H1 / A1 / B1 / C1 / D1 / E1 / F1 / G1 / 29.6
H2 / A1 / B1 / C1 / D2 / E1 / F1 / G1 / 23.7
H3 / A1 / B1 / C1 / D2 / E2 / F1 / G1 / 17.2
H4 / A1 / B1 / C3 / D1 / E1 / F1 / G1 / 6.5
H5 / A2 / B1 / C2 / D1 / E1 / F1 / G1 / 7.0
H6 / A3 / B2 / C4 / D4 / E3 / F2 / G2 / 8.0
H7 / A4 / B1 / C1 / D3 / E1 / F1 / G1 / 7.0
[H8 / A3 / B2 / C4 / D4 / E3 / F1 / G2 / 0.5]
[H9 / A1 / B1 / C2 / D1 / E1 / F1 / G1 / 0.5]
Supplementary Table 7: Correspondence between the names of the polymorphic sites used in this study and their physical position on the sorghum pseudomolecules v 1.0
Gene / Segment / Name in this study / Polymorphism type / Position on Sbi1 pseudomolecule / SNP flanking sequence (35 bp left) / SNP flanking sequence (35 bp right)Ae1 / A / 19 / SNP / chromosome_4:50601379 / GGATCATACGAGTTAAGAAGGGGCCGGTGCGCCGGA / AAGACCAGACTCCCCTCCTCGCCGCCGGTGAGTCGG
A / 49 / Indel (2) / chromosome_4:50601350 / GGAGGGGGAGGAGGAGGAAGTTGCGGCCGGGATCAT / TACGAGTTAAGAAGGGGCCGGTGCGCCGGAAGACCA
A / 109 / SNP / chromosome_4:50601291 / ACCACCAGTTCACCGCCACATCACTCACATACAGAC / CCCGAGGCAGGCCCACGCTTGATCGGAGGGGGAGGA
A / 143 / SNP / chromosome_4:50601257 / ACCTCCAACTCTAGCACCCCCTGCACCTGCACGCAC / CCACCAGTTCACCGCCACATCACTCACATACAGACC
A / 167 / SNP / chromosome_4:50601233 / GCGCATGGCCCCGTGCGTCCCGGAACCTCCAACTCT / TAGCACCCCCTGCACCTGCACGCACCACCAGTTCAC
A / 181 / SNP / chromosome_4:50601219 / GACGCGGCCGCCGCGCGCATGGCCCCGTGCGTCCCG / GGAACCTCCAACTCTAGCACCCCCTGCACCTGCACG
A / 189 / SNP / chromosome_4:50601211 / TCCTGGACGACGCGGCCGCCGCGCGCATGGCCCCGT / TGCGTCCCGGAACCTCCAACTCTAGCACCCCCTGCA
A / 194 / SNP / chromosome_4:50601206 / CGCCTTCCTGGACGACGCGGCCGCCGCGCGCATGGC / CCCCGTGCGTCCCGGAACCTCCAACTCTAGCACCCC
A / 197 / SNP / chromosome_4:50601203 / GACCGCCTTCCTGGACGACGCGGCCGCCGCGCGCAT / TGGCCCCGTGCGTCCCGGAACCTCCAACTCTAGCAC
A / 241 / SNP / chromosome_4:50601159 / TCAGCCTTCGATGCGAGGCCGTCGTTCTCGCCTTCG / GGCAACCACGACCGCCTTCCTGGACGACGCGGCCGC