ant1.2

ant1.4

ant1.56

Bonus ant1.1 (Bonus)

Bonus

ant1.1 (B

onus)0

5

10

15

20

25

auricle

awn

A535

/ fr

esh

wei

ght (

g)

* *: p < 0.05

0.5 cm

Supplementary Fig. S1

b c

d e

f

a

Bonus ant1.1

7DS-2CS 7DS

-47DS-1

7DS-5

7DS-3

7BS-1CS 7BS

-27BS-3

TaC1-B1a(LP10-RP8)

TaC1-D1a(LP7-RP11)

7BS-1, -2 (0.27)

7BS-3 (0.16)

7DS-2, -6 (0.73)

7DS-4 (0.61)

7DS-1 (0.37)7DS-5 (0.36)

7DS-3 (0.15)

a

b

Supplementary Fig. S2

TaC1-A1b (Hope) 1:TTGAGCTCGCAGATATAGCATCGATCGAGACTTAATGAAGTCTCTACTTAGCAAGACTGCTCCAATAATATAGCAATGGG 80TaC1-B1b (Hope) 1:---------------------------------------------CTTTAGCAAGACTGTTACAATAATATTGCAATGGA 35TaC1-D1b (NS67) 0:-------------------------------------------------------------------------------- 0 ............ . ......... .......

TaC1-A1b (Hope) 81:GGGAGTAACGTTTCAGCCACTTGGAGATAAAAGGCAGCTATGAACAAGCCTCTGTTATAGAAATATGACACCGAATTTGG 160TaC1-B1b (Hope) 36:GGGAGTAATGTTTCCGCCACTTGGAGATAAAAGGCAACTATGAATAAGCCTCTGTTATAGAAATATGACATCGAATTTGG 115TaC1-D1b (NS67) 0:-------------------------------------------------------------------------------- 0 ........ ..... ..................... ....... ......................... .........

TaC1-A1b (Hope) 161:ACGGATATCATCGCCCCTGCCAGCGATATATAACGGCGGCTG-------------------------------------- 202TaC1-B1b (Hope) 116:ACAGAAATCATCGCTGCTGCCAGCGATATATAACGGCTGATGAACGGCCGTCCTGGTTCACCCGCAAAAAAAAAAAAAAA 195TaC1-D1b (NS67) 0:-------------------------------------------------------------------------------- 0 .. .. ........ ..................... . ..

TaC1-A1b (Hope) 203:---AACGGCCGTTCTGGTTACGTCCCTGTTCATGCACACATGGAAGCCTTCCCGGCCTTCTGGTCCATCTAACACTTTGA 279TaC1-B1b (Hope) 196:AAAAACGGCCGTCCTGGTTACGTCCCTGTTCATGCACACATGGAAGCCCTCCCGGCCGTGTGGTCCATCTAACACTTTGA 275TaC1-D1b (NS67) 0:-------------------------------------------------------------------------------- 0 ......... ................................... ........ . ....................

TaC1-A1b (Hope) 280:GG------------CCG-TGGCCGTGGATTGCCTTAAAGGTGCTAAGCCGGCCACGTAGTCGCGCTGCGGCGCCGGTGTA 346TaC1-B1b (Hope) 276:GGAAAGTGCCGCTCCCGATGGCCGTGGATAGCCTTAAAGGTGCTAAGCCGGCCACGTAGTCGCGCTGCGGCGCCGGTGTA 355TaC1-D1b (NS67) 0:-------------------------------------------------------------------------------- 0 .. ... ........... ..................................................

TaC1-A1b (Hope) 347:TAAATACCCCAACCACCCCTGCTGCCCGCAGACCACTCCCCCTCTCTCTAACAAAGCACACACGGCGAGATAGAGAT--- 423TaC1-B1b (Hope) 356:TAAATACCCCAACCATCCCTTCTGCCCGCAGACCACTCCCC--CTCTCTAACAAAGCACACACGGCGAGATAGAGAT--- 430TaC1-D1b (NS67) 1:----------------------------------------------TCTAACAAAGCACACACGGCGAGATAGAGATAGG 34 ............... .... .................... ...*******************************

TaC1-A1b (Hope) 424:-----------AGAGGGAGAGAGAGGATGGGGAGGAGGGCGTGCTGTGCCAAGGAAGGGGTGAAGCGAGGGGCCTGGACG 492TaC1-B1b (Hope) 431:-----------AGAGGGAGAGAGAGGATGGGGAGGAGGGCGTGCTGTGCCAAGGAAGGGGTGAAGCGAGGGGCGTGGACG 499TaC1-D1b (NS67) 35:GAGAGGGGTTGAGAGAGGGAGAGGGGATGGGGAGGAGGGCGTGCTGTGCCAAGGAAGGGGTGAAGCGAGGGGCCTGGACG 114 ****.*.*****.*************************************************.******

TaC1-A1b (Hope) 493:AGCAAGGAGGACGAGATCCTGGCTTCCTACGTCAAGGCCCATGGCGAGGGCAGGTGGAGGGAGCTCCCCCAGAGAGCTGG 572TaC1-B1b (Hope) 500:AGCAAGGAGGACGAAATCCTGGCTTCCTACGTCAAAGCCCATGGCGAAGGCAGGTGGAGGGAGCTCCCCCAGCGAGCTGG 579TaC1-D1b (NS67) 115:AGCAAGGAGGACGAGATCCTGGCTTCCTACGTCAAGGCCCATGGCGAAGGCAGGTGGAGGGAGCTCCCGCAGCGAGCTG- 193 **************.********************.***********.********************.***.******.

TaC1-A1b (Hope) 573:TACGTACTGATCCATCGTAAACGCAT-------------------------------TCTGGTTCTAT-CAATGGGGAGC 620TaC1-B1b (Hope) 580:TACGTACTAATCCATCGTAATGACGTAATCCCTAGCTAGCCATATACACAGGACCACTCTGATTCTAT-CAATGGCGAGC 658TaC1-D1b (NS67) 194:---GTACTACTC--GCGAGATGTTATCAT-GTTAGCTACCGATCCATCGTAAACCGTTCTGGTTCTATCCAATGGAGAGC 267 ...*****..**...**..*.. ..* .. ...... . .. . ... ****.****** ****** ****

TaC1-A1b (Hope) 621:TGGA-------ATGGAAGTGACGCATGCT---AACTGAATGAATCTGCATGCAGGTCTGCGGCGGTGCGGCAAGAGCTGC 690TaC1-B1b (Hope) 659:TGGACGGAGAGCGGGAGTTGACGCATG-TG--AACTGAATGAATCTGCATGCAGGTCTGCGGCGGTGCGGCAAGAGCTGC 735TaC1-D1b (NS67) 268:TGGA-------ATGGAAGTGACGCATGCTGCTAACTGAATGAATCTGCATGCAGGTCTGCGGCGGTGCGGCAAGAGCTGC 340 **** ..***..*********.*. ************************************************

TaC1-A1b (Hope) 691:CGGCTGCGGTGGCTGAACTACCTCCGGCCGAACATCAAGCGGGGCAACATCTCCGACGACGAGGAGGAGCTCATCGTCAG 770TaC1-B1b (Hope) 736:CGGCTGCGGTGGCTGAACTACCTCCGGCCGAACATCAAGCGGGGCAACATCTCCGACGACGAGGAGGAGCTCATCGTCAG 815TaC1-D1b (NS67) 341:CGGCTGCGGTGGCTGAACTACCTCCGGCCGAACATCAAGCGGGGCAACATCTCCGACGACGAGGAGGAGCTCATCGTCAG 420 ********************************************************************************

TaC1-A1b (Hope) 771:GCTCCACGGCCTGCTTGGCAATAGGTGGTCCATCATCGCCGGCAGGCTGCCCGGCCGAACAGATAACGAAATCAAGAACT 850TaC1-B1b (Hope) 816:GCTCCACGGCCTGCTCGGCAACAGGTGGTCCATCATCGCCGGCAGGCTGCCCGGCCGAACAGACAACGAAATCAAGAACT 895TaC1-D1b (NS67) 421:GCTCCACGGCCTGCTCGGCAACAGGTGGTCCATCATCGCCGGCAGGCTGCCCGGCCGAACAGACAACGAAATCAAGAACT 500 ***************.*****.*****************************************.****************

TaC1-A1b (Hope) 851:ACTGGAACAGCACGCTCGGCAGGAAGGCGCTCCCCGCCCGCCCCACCATTGCCGCGGCGAGGACCGTCGTCGCCACGCCC 930TaC1-B1b (Hope) 896:ACTGGAACAGCACGCTCGGCAGGAAGGCGCTCCCCGCCCGCCCCGCCATTGCCGCGGCGAGGAC---CATCGCCACGCCC 972TaC1-D1b (NS67) 501:ACTGGAACAGCACGCTCGGCAGGAAGGCGCTCCCCGCCCGCCCCGCCATTGCCGCGGCGAGGA---------------CC 565 ********************************************.******************. . .........**

1.7-kb insertion

2-kb insertion

AAC(N) -> GAC(D)

Supplementary Fig. S3

TaC1-A1b (Hope) 931:GTCGCCTCCGGCTCCTCCAGCTCCA---CGGGGAGCGCCGCGGCGCCGCTGTCCACCTCCGTCCCTGCCCTCCTCCACGC 1007TaC1-B1b (Hope) 973:GTCGCCTCCGGCTCCTCCAGCTCCACCGCAGGAAACGCAGCTGTGGCGCTGT---CCACCGTCCCTGCTGTCCTCCACGC 1049TaC1-D1b (NS67) 566:GTCGCCTCCGGCTCCTCCAGCTCCA---CGGGGAGCGCCGCGGCGGCGCTGTCTACCTCCGTCCCTGCCGTCCTCCATGG 642 ************************* *.**.*.***.**.*.*.******. .**.**********..*******.*.

TaC1-A1b (Hope) 1008:CGCGGCGCCTTCGTCGCTGGCCGCCGCGGTGTGGGCGCCCAAGCCCGTGAGGTGCACGGGCGGCCTCTTCTTCCGCCGGG 1087TaC1-B1b (Hope) 1050:TGCGGCGCCTTCGTCGCCGACCGCCGCGGTGTGGGCGCCCAAGCCCGTGAGGTGCACGGGCGGCCTCTTCTTCCGC---- 1125TaC1-D1b (NS67) 643:CGCGGCGCCTTCGTCGCCGGCCGGCGCGGTGTGGGCGCCCAAGCCCGTGAGGTGCACGGGCGGCCTCTTCTTCCGCAGGG 722 .****************.*.***.**************************************************** ...

TaC1-A1b (Hope) 1088:AGCAGGAGACGCCGCCGCCCGCGCCGGTCGTAGAGGAGACGCGGGCCGGGGGAG---AAGAGGGAGATGCCTGCAGCGGC 1164TaC1-B1b (Hope) 1126:--CGGGAGACGCCGCCGCCCGCGCCGGTCGTCGCGGAGACGCGGGCCGGGGGAG---AAGAGGGAGATGCCTGCAGCG-- 1198TaC1-D1b (NS67) 723:AGCAGGAGACGCCGCCGCCCGCGCCGGTCGTCGAGGAGACGCGGGCCGGAGGAGATCAAGAGGGAGACGCCTGCAGCG-- 800 ..*.***************************.*.***************.**** **********.**********

TaC1-A1b (Hope) 1165:AGCAGCAGCTCGGAGACGTCGTCGGCCGAGCCGTGCTCGTCGGGGTCGGGCGGGGGAGACTGGATGGACGACGTGAGAGC 1244TaC1-B1b (Hope) 1199:-GCAGCTGCTCGGAGACGTCGTCGGCCGAGCCGTGCTCGTCGGGGTCGGGCGGGGGAGACTGGATGGACGACGTGAGAGC 1277TaC1-D1b (NS67) 801:-GCAGCAGCTCGGAGACGTCGTCGGCCGAGCCGTGCTCGTCGGGGTCGGGCGGCGGAGACTGGATGGACGACGTGAGAGC 879 *****.**********************************************.**************************

TaC1-A1b (Hope) 1245:CCTGGCGTCATTCCTCGAGTCCGACGAGGAATGGCTCAAGTCCCTGCACATGGCCGGTTAA--AACCTCTCACACGTGAT 1322TaC1-B1b (Hope) 1278:CTTGGCCTCGTTCCTGGAGTCCGACGAGGAATGGCTCAAGTCCCTGCACATGGCCGGTTAATTAACCTCTCACACGTGAT 1358TaC1-D1b (NS67) 880:CCTGGCGTCGTTCCTGGAGTCCGACGAGGAATGGCTCAAGTCCCTGCACATGGCCGGTTAATTAACCTCTCACACGTGAT 959 *.****.**.*****.*********************************************..*****************

TaC1-A1b (Hope) 1323:CGA----------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1359:CGATCCAGTTCAGTCACATGTACGTGGGTGCGCCGCTGCACGTACGCTTTTAGAAAAGGAAACTGTATGTGTACTTGAAC 1438TaC1-D1b (NS67) 960:CGATCTGGTTCAGTCACATGTACGTGGGTGCGCCGCTGCACGTACGCTTTTCGAAAAGGAAACTGTATGTATGCTTGAGC 1039 ***.. ............................................ .................. . .....

TaC1-A1b (Hope) 1325:-------------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1439:AGTGTGTATACGTACAAATGCACTTACGCCCGGGCTTATGTGACGGTACGTGGGTGGCTAGCTCCCGTACGTTACGACTG 1518TaC1-D1b (NS67) 1040:AGTGTGCATACGTACAAACGTACTTACGCCCGCGCGTATGTGGCGGTACGTGGCTGGCTAGCTCCCGTACGTTACGACTG 1119 ...... ........... . ........... .. ...... .......... ..........................

TaC1-A1b (Hope) 1325:-------------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1519:TACTGAGTTGTTCATATGTAAAC-------------------------------GTGGTTTTGAGAAAAATACGTAAGCT 1567TaC1-D1b (NS67) 1120:TACTGAGTTTTTTATTTATAAACTACGACTGTACTGAGTTGTTCATATGTAAACGTGGTTTTGAG-AAAATACGTAAGCT 1198 ......... .. .. . ..... ........... ..............

TaC1-A1b (Hope) 1325:-------------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1568:AGCGTCGCTCCTCGCATGTGCACGACAGCGCAACAGAAAAAGTCATGTGATGGATGGACGTCGGCGTCGGTGGAGACGTA 1647TaC1-D1b (NS67) 1199:AGCGTCGCTCCTGGCATGTGCACGACAGCGCAACAGAAAAAGTCATGTGATGGATGGGCATCGGCGTCGGCGGAG-CGTA 1277 ............ ............................................ . .......... .... ....

TaC1-A1b (Hope) 1325:-------------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1648:CTTTGCAGTAAACGACATACGCTAGTAAGATTTCCTCACTGTACTTGCTGCTTTCCGCGAGGTATCGTTTTCTGCAGCCA 1727TaC1-D1b (NS67) 1278:CTTTGCAGTAAACGACATACGCTAGTGAGATTTCCTCACTGTACTTGCTGCTTTCCGCGAGGTATCGTTTTCTGCAGCCA 1357 .......................... .....................................................

TaC1-A1b (Hope) 1325:-------------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1728:CGGGCCACCGATCATAGTTGTTAGAAAGCTAGGGCTCGTGCAAGCATCTCAACCGTGCAAGAAGATGAATCGTGCATTCG 1807TaC1-D1b (NS67) 1358:CGGGCCACTGATCATAGTTGTTAGAAAGCTAGGGCTCGTGCAAGCATCTCAACCGTGGAAGAAGATGAA--------TCG 1429 ........ ................................................ ........... ...

TaC1-A1b (Hope) 1325:-------------------------------------------------------------------------- 1325TaC1-B1b (Hope) 1808:TGCTCCCCCTCTATTAGGCCTTGTTTGGTTACACCACTTCTCAAGGGATAGAAGAGGATCGGAGAGGATTTAAA 1881TaC1-D1b (NS67) 1430:TGCTCCCCCTCTA----GCCTTGTTTGGTTACATCCCTTCTCAAGGGATAGAAGAGGATTGGAGAGGATCTCA- 1498 ............. ................ . ....................... ......... . .

1-bp deletion

PmlI ClaI

Supplementary Fig. S3 continued

LP10-RP8

LP11-RP8

CS Hope8019R1 NS67 Douson

1 M808 Cornell Ardito AUS1408

OW104

Rc-B1 a a b a a a a a a a

LP7-RP11

LP3-RP11

CS Hope8019R1 NS67 Douson

1 M808 Cornell Ardito AUS1408

OW104

Rc-D1 a a a b b b b b b b

CS Hope8019R1 NS67 Douson1

- + - + - + - + - + (ApaI)

Rc-A1 a ab b a

M808 Cornell Ardito AUS1408 OW104

- + - + - + - + - + (ApaI)

a a a a aRc-A1

a

b

Supplementary Fig. S4

c

d

LP15-RP4

LP15-RP4

Hope8019R1 NS67 Douson1

- + - + - + - +

b b a aRc-A1

(EcoRV)

LP6-RP15

GATATC:EcoRV

AtATCTCCGACGACGAGGAGGA-5’TaC1-A1(Hope) AACATCAAGCGGGGCAACATCTCCGACGACGAGGAGGATaC1-A1(NS67) AACATCAAGCGGGGCGACATCTCCGACGACGAGGAGGA

RP15

e

Supplementary Table S1 Barley and wheat lines for this study 　 　 　　 Line name 　 　 　 　 　Barley Sheath color Mutagen note

Bonus purple the original cultivar of ant1 mutantsant1.1 white alpha-raysant1.2 white neutronsant1.4 purple neutronsant1.56 purple iso-propyl methanesulfonateBetzes purple Donor of wheat-barley addition lines

　 OUI026 purple 　 　 　 Mapping parentWheat-barley chromosome addition lines 　 　 　 　

1HS2H3H4H5H6H

　 7H 　 　 　 　 　7HS7HL

Deduced Rc genotype *1Wheat 　 Coleoptile color Rc-A1 Rc-B1 Rc-D1 References

Chinese Spring (CS) colorless a a aNovosibirskaya67 (NS67) red a a b Khlestkina et al, 2009Mironovskaya808 (M808) red a a b Khlestkina et al., 2002Hope red b b a Gale and Flavell, 19718019R1 red b a a

This study

Douson1 red a a bCornell595-W red a a bArdito red a a bAUS1408 red a a b

　 OW104 red a a bCS nulli-tetrasomic lines 　 　 　 　 　

N7AT7BN7AT7DN7BT7AN7BT7DN7DT7A

　 N7DT7B 　 　 　 　 　CS partial deletion line of the short arms of homoeologous group 7　 　 Fraction length 　 　 　 　

7AS-1 0.897AS-2 0.737AS-3 0.297AS-4 0.267AS-5 0.597AS-6 0.217AS-8 0.457AS-9 0.897AS-10 0.457AS-11 0.667AS-12 0.837AS-13 0.327BS-1 0.277BS-2 0.277BS-3 0.167DS-1 0.377DS-2 0.737DS-3 0.157DS-4 0.61

　 7DS-5 0.36 　 　 　 　*1 a: dysfunctional allele, b: normal allele.

Supplementary Table S2 Primers for this study 　Primer name Sequence (5' - 3') ReferenceGBMS0003F ATCCTATGGAAAACGGGGAG

Li et al. (2003)

GBMS0003R CCTGACATCGTTCATTGCTGGBMS0088F TTATTTCAGTGGAAGTCGGTTGGBMS0088R GCGTGCTTCCATACACACCGBMS0111F TTCATACCGCACATACAGAAGGGBMS0111R AATCTTGATGATGCGACGCGBMS0141F ACGACAACATTTTGTTGCCAGBMS0141R TGTGAATTTCTTGGACTTGGGGBMS0164F TTTCTCCCCCCACACATGGBMS0164R CTTGGACAGTTGGCGGTCGBMS0120F Dr.M.Roeder (personal communication)GBMS0120R Dr.M.Roeder (personal communication)HvC1-LP1 ACAGACCACTCCCCCTCTCT

AK359777

HvC1-RP1 AGCGTGCTGTTCCAGTAGTTCHvC1-LP2 CCGAACAGACAACGAAATCAHvC1-RP2 GAACGACGCCACCTTATCATHvC1-LP3 GACGTTGGTTTTGAGGGAAAHvC1-RP3 GGTTGTCGTGGCGAAACTAT7HS_48315-LP1 CAATATAGGCCCCAAGCAAA

morex_contig_483157HS_48315-RP1 TCGATGCCACTCACTAGACG7HS_137164-LP1 ACGCATTGTTTCATTGTTGC

morex_contig_1371647HS_137164-RP1 ACGGAATATGGTGAGCCAGT7HS_137164-LP2 GGCACACATGATCCATTCAG7HS_137164-RP2 TTTCTGTGTCTGCCCCTGAT7HS_1562627-LP1 TTCAAGTCCCCTTTCCACTG

morex_contig_1562627HS_1562627-RP1 GGCTTCGGTAGAAGTTGCTGTaC1-RP2 GAGCGTGCTGTTCCAGTAGTTTaC1-LP3 TCCCCCTCTCTAACAAAGCATaC1-LP4 ACTGGATGGACGACGTGAGTaC1-RP4 TCGATCACGTGTGAGAGGTTTaC1-LP5 GACGAGGAATGGCTCAAGTCTaC1-RP5 TTGACGTAGGAAGCCAGGATTaC1-LP6 ATCCTGGCTTCCTACGTCAATaC1-LP7 GGGCGTTGGTCACTAGAAAGTaC1-RP8 ATGCCCATCCATCACATGACTaC1-LP10 GCAAACCGGGTGTTGTTTATTaC1-LP11 TGAGCTCGCAGATATAGCATCTaC1-RP11 TGGCAGGGATTGAGATCCTTaC1-RP13 GAGCGCCTCGGATTTATTCTTaC1-LP15 ACTGGATGGACGACGTGAGGGTaC1-RP15 CGATGAGCTCCTCCTCGTCGTCGGAGATAT