Genetic Resources and Crop Evolution
TaqSH1-D, wheat ortholog of rice seed shattering gene qSH1, maps to the interval of a rachis fragility QTL on chromosome 3DL
Mazen Katkout1, Shun Sakuma1, Kanako Kawaura1, Yasunari Ogihara1,*
1 Kihara Institute for Biological Research and Department of Life and Environmental System Science, Graduate School of Nanobioscience, Yokohama City University, Maioka-cho 641-12, Totsuka-ku, Yokohama 244-0813, Japan
* Corresponding author. E-mail:
Table S1 Primers used for gene isolation and sequencing from both parental lines, Chinese Spring (CS) and the synthetic wheat line S-6214Primer name / 5′-Sequence-3′ / Amplicon size
For PCR
WBLH4-1/F / ACAGCAGCGGAGACAGAG / 2536 bp
TaqSH1-D-1669/R / ACGGCCGATCTTATTAGCTCC
WBLH4b/F / CAACACCAGCAAGATGCCG / 1924 bp
WBLH4b/R / CATTGGCTTCCAGAGCCG
Cg352b/F / TGGTGCTAGACTGATAAAAGC / 2176 bp in CS
Cg3615/R / TTTGGGGCACTGTGGCATTA / 1987 bp in S-6214
Cg3615/F / TCCTTGTTTATGCCCAAAAGTTT / 1148 bp
Cg2717/R / TATGGCCATGAATAAACAGC
For sequencing
WBLH4-317/F / GCTTCATAACCATGCACACCAC
WBLH4-310/R / GCATGGTTATGAAGCAGCATG
WBLH4-811/F / AGGAGATCTGCGACGTGG
WBLH4-811/R / CCACGTCGCAGATCTCCT
Cg6717/F / CATCCACATGAAATCCAAAGCTC
Cg6717/R / GAGCTTTGGATTTCATGTGGATG
Cscg1/R / AAGTGCTCGAAGAGCCAAGC
wblh4b-w/F / GGCCTGGACCTCTAGTTGTT
wblh4b-w/R / GGATGTAATAGGCAAAACAACCA
cg352b/R / AGGATACCTGCAAAGTTTCAA
Syncg1/F / GGCTCACCAGCACTCGTC
Syncg2/R / CGAACGAGCCCATCACGT
Cg2717/F / CGAGCCTGTCTGAGCTACC
1 ACAGCAGCGGAGACAGAGGGAGATACCACCAGCACCAGGCCAGCCAGCCAGGCCCGGCGC 60
61 TCGGAAAGTGCGGAGCCGTTTCCCCTCCACCTCCACTCTCTCCAGGGCCACCCACCCAGC 120
121 CCCAGCCCCAGCCCAGCCAGGTGCTCCTGCTCCTCCTGCTCTACCTCGCTGCCCGCCACC 180
181 CACCGCGTACGTACGTGCGGTGCGGGCGCTCGCCATGTCGTCTCCCGCCGGCGGGTACGG 240
1 M S S P A G G Y G 9
241 CGGCGCCGAGGCCCACCACCACCAGCAGCACCACGGCCACATGCTGCTTCATAACCATGC 300
10 G A E A H H H Q Q H H G H M L L H N H A 29
301 ACACCACATGGCGACCGCGGCCGCCGCGGCGTCGGGCGGGCAGCTCTACCACGTGCCGCA 360
30 H H M A T A A A A A S G G Q L Y H V P Q 49
361 GCACAGCCGGCGCGAGAAGCTCCGGTTCCCGCCGGACGCCGCCGCGGAGGACTCGCCACC 420
50 H S R R E K L R F P P D A A A E D S P P 69
421 GACCCCTCTCGCCCACCACCACCAGCAGCAGCACCAGCAGCACCAGGCCGGGGCGTGGCC 480
70 T P L A H H H Q Q Q H Q Q H Q A G A W P 89
481 GCCCCCGGCCTTCTACTCCTACGCGTCCTCCTCCTCCTCCTACTCGCCGCACAGCCCGAC 540
90 P P A F Y S Y A S S S S S Y S P H S P T 109
541 GGTGCCGCAGGGCCAGCAGCTGGTGCTCAACGGGCTCACCGCCCAGCAGGTCACCGCGCA 600
110 V P Q G Q Q L V L N G L T A Q Q V T A Q 129
601 GCAGTTCCCGCAGATCCCCACGCAGAACTTCTCGCTCTCCCTCTCCTCCGCCTCGTCCAA 660
130 Q F P Q I P T Q N F S L S L S S A S S N 149
661 CCCCGCCACCACGCCCCCGGCGCCCAGGAAGCAGGAGCCAGGAGCCGCCGCGCCGGCCGC 720
150 P A T T P P A P R K Q E P G A A A P A A 169
721 GTGGCCGTACGGGCCCTTCACCGGCTACGCCACGGTGCTCGGGCGATCCAGGTTCCTCGG 780
170 W P Y G P F T G Y A T V L G R S R F L G 189
SKY domain
781 CCCGGCGCAGAAGCTGCTCGAGGAGATCTGCGACGTGGGGGGCGCGGCCGCGCACGCCGA 840
190 P A Q K L L E E I C D V G G A A A H A D 209
841 CACCAGCGTCCCGGACGAGGGCCCGCTCGACGCGGACGCCATGGACGGCGCCGACGACGC 900
210 T S V P D E G P L D A D A M D G A D D A 229
901 GGCCGGCCACGAGCTGGACACCTCCGGCCCCATGTCCGGCGCCGAGCAGCAGTGGAAGAA 960
230 A G H E L D T S G P M S G A E Q Q W K K 249
BEL domain
961 GACGAGGCTCATCTCCATGATGGAAGAGGTGAGCTAGCCACGACGCCGCTCGCTCCAAAT 1020
250 T R L I S M M E E V 259
1021 TTCCGACTTTTTCCGCCTCGTTCGCTTCGACGCCGCCACTGCAATTCTCCGGCTGGCTCC 1080
1081 TCGGCCGGGAGCGCGAAGAATCTTGCACATAGCGGTCACATCGCCAGCGACGCGGCCGTG 1140
1141 GCTTTGCCTGCTTTTATTCACTGTGCTTCCGCGGTTGCATGTGCTTTTGATTTGATGATC 1200
1201 ATTTCCATTGCTGCTGTTACATTTGCTCGGATTTTCCTTTTCTCCTTTCTCCACAGTGCC 1260
1261 GCACTGTTGGCGCCCAACAATTTGCTGCTCGCCTTTTTTTCTCATCAGAGGATCAAAGAT 1320
1321 TGGATGTTGATTAGTTTCACCGCACTAAGCACACCTTTTGCAAATATCATCTGCTACATG 1380
1381 AAACCACAACTGATTAGCAGCGTCCTCGAACGCTTTGGGAGGGTAGGTGATGCTGGAAAC 1440
1441 TAGTAGCAAAACTTTGGCCTGTCATGTCAAGAAAACCGTGTTGTTTCATCTCTCACATGG 1500
1501 TTAGGATAGGAGTACTTGACCCTCCCGCAGCGTCCTCTTCCAGCCTCTGGGGCAATACTG 1560
1561 TACATAACATGGGAGTCTACGTACGATGTAGAAAGCTTCCATTTATGGAGCTCTCAGTCT 1620
1621 GAGTCTCAGCCTCAGTAGGCGAAGTTGCTTGTCTGACTTCTTTATTAATGGCGTCTTACT 1680
1681 TCTATAGTTGGGAAGTAGGCTTTGCTTTGTTCATGTCACATCCACATGAAATCCAAAGCT 1740
1741 CCCAGCAAACAGCAAAGAAAATCTTTCCCATCTTCATGAGTAGTAGCTGCTTATCTCCTC 1800
1801 TAATCAAGTACCGTACTCACTTACCAATCCAGCTGCAATTAACCTCTCATCTCATTCTAC 1860
1861 TTCTAGGTGTGCAAGAGGTACCGGCAGTACTACCAGCAGGTCCAGGCCGTGATCGCGTCG 1920
260 C K R Y R Q Y Y Q Q V Q A V I A S 276
BEL domain
1921 TTCGAGAGCGTGGCTGGGTTCAGCAACGCCGCCCCGTTCACGGCGCTGGCGCTGAGGGTG 1980
277 F E S V A G F S N A A P F T A L A L R V 296
1981 ATGGCCAGGCACTTCAGGTGCATCAAGGGCATGATACTCAGCCAGCTGCGCAACACCAGC 2040
297 M A R H F R C I K G M I L S Q L R N T S 316
2041 AAGATGCCGGTCAAGGAAGGCATGAGCAAGGACATCACCATCTTCGGCCTCGGCGGCGGC 2100
317 K M P V K E G M S K D I T I F G L G G G 336
2101 GGCGGCGCCCCCGTCGGCGGCTTCCAGAGGGGTGGCAGCGTGAACGGCTTCGGCCAGCCG 2160
337 G G A P V G G F Q R G G S V N G F G Q P 356
2161 CACAACATCTGGCGCCCCCAGAGGGGCCTCCCCGAGCGCTCCGTCACGGTCCTCCGGGCT 2220
357 H N I W R P Q R G L P E R S V T V L R A 376
Homeodomain
2221 TGGCTCTTCGAGCACTTCCTGCACCCGTAAGTTGTTTTACTACCATCTGCTTATGGTAAT 2280
377 W L F E H F L H P Y 386
2281 TAGCATTAGCACTAGACGACGTACGTACTCTGCGCCTTTCCAAGATAATAATGTGTCTTT 2340
2341 GCGGTGCTACATCAACATGATTATGCTGGGCCTGGACCTCTAGTTGTTTTAGCTGATGGC 2400
2401 AAGCAATCCTCGGTGTCGAAATCATTAGGATGGCCAAGGCCAAGGCCAAGCATGAGTGAT 2460
2461 GGAGTGTCATGGCATGGCATGCCTTGCCTTGGCTTGGCTTCCAAATCATTCTATTGGAGC 2520
2521 TAATAAGATCGGCCGTCAGCTTTTTAAGACATTGTGTTTTTTGAGCTGTGCACATCATCA 2580
2581 ATTTGCTAACAGTCCGGGTCCTCCATTTTGCATCTTTCTTAGACATTTGCATGACTTTCT 2640
2641 AACTATCATCAGGTGAGCGGCTTTATGGATTTGGTTAGGGCGTCCAATTACTTGTATGTT 2700
2701 GCTTGTTTTGTTATACACTGATTGCGAAACAACTTGTGAGTGAGATTACTTCTAATCCAG 2760
2761 TTTTAGGGGGGCACCTACCTATAGGAAGATGAAACATCATCATTATTTTGGTTGTTTTGC 2820
2821 CTATTACATCCATCTTTTGTACTACTACAATCTGGTTTTTCCATGATGTATGACCTGGTG 2880
2881 GTTACATCAGGTTGATTGGTGCAATGTTAGCATATTCAGTTGTTGTTCATTATAACTTTA 2940
2941 TAATGCCAGATCTTTCCATTTCCAACTGGATTTAGTATTATAAATTGAGTAGTACCCTTT 3000
3001 CTTCATTATTGCTGTCAATATTTGAAGCCTCTAGAAAGAAAGGCTGATAATTGTCAATTC 3060
3061 ATGTCCTTTTGTGTGATCCCACACCAATCAGTGCTTAGATTTAACTTACTCTTCTTTACA 3120
3121 AAAAGGCCTACTTGGATGGCGCTAGAATGATAAGAAAAATTCTTTAAGATGAAACCTTTA 3180
3181 TTTTTGGTATGTCGATTGGAGTTATGAATGTTTAAGCTGAATAAAAAACCCATGACAGGC 3240
3241 ATCCTAGCACAAGAATTTTGTTTGATCCCCTGATCTAACACTACCTGGCTTGTTTTCCAG 3300
3301 GACCCCTTTTCTATTCACACTGGGCAATCAAATATAATTGTTCCTCACATCAATCAGTGC 3360
3361 TTAGATTTGAACATACTCTTAAAGGGGTGCATGGATGGTGCTAGACTGATAAAAGCCTGA 3420
3421 ATCAAATATAATTGTTCCTCACATCAATCAGTGCTTAGATTTGAACATACTCTTAAAGGG 3480
3481 GTGCATGGATGGTGCTAGACTGATAAAAGCAATTCTTGTGGATGCTGCCCGGACTTATGG 3540
3541 ATGTTAAGCCTGAATAAAGAAAGCCATGACAGGCACCGGCATCCCAATCTGGCTTGTTTT 3600
3601 GCACTCATTTTCTATTCACACTGGGCAATCTCGTATAATAGTTGCGTGCAGAACGTCTTT 3660
3661 ATGATCTTTAAATCTTTATACGCATCTCCCTTTTGAACGTGTTGCAATCAAGAGTACTGC 3720
3721 TGCATTCGTCTGATATTCGGGTTGAAACTTTGCAGGTATCCTACCGATGGCGACAAGCAA 3780
387 P T D G D K Q 393
Homeodomain
3781 ATGCTGGCCAAGCAGACTGGCCTAACAAGGAATCAGGTGAACAGCAAAGCTGGTCGCTGT 3840
394 M L A K Q T G L T R N 404
3841 TACCACTAGCATGTCATTTTGTTTGTGGAGCTTGGTTGACGTGTTGGGTTAATAATGGCG 3900
3901 GTGCAGGTGTCGAACTGGTTCATCAACGCGAGGGTGCGGCTCTGGAAGCCAATGGTGGAG 3960
405 Q V S N W F I N A R V R L W K P M V E 423
Homeodomain
3961 GAGATCCACAACCTGGAGATGAGGCAGGTCCACAAGCACTCGCCGCACGACAAGGGCCAG 4020
424 E I H N L E M R Q V H K H S P H D K G Q 443
4021 CAGAACGGCGTCCACGGCCAGGCTCACCAACACTCGTCGCAGCAGCAGCAGCAGCAGCGC 4080
444 Q N G V H G Q A H Q H S S Q Q Q Q Q Q R 463
4081 AGCGGCAAGCGCTCCGAGCCCTGCGACTCGCACCCCGGCCAGAGCAGCGGCGTCACCAGG 4140
464 S G K R S E P C D S H P G Q S S G V T R 483
4141 AACCACCACCACCACAACGCCGCCGCCGCCGCCTCCTCCCACGGTGGTGGCTTCCCGGAC 4200
484 N H H H H N A A A A A S S H G G G F P D 503
4201 GACCTCTCCCAGATGTCCCACTCCATGCAGCAGGGCCAGGTGACCTTCGCCGGGTACGGC 4260
504 D L S Q M S H S M Q Q G Q V T F A G Y G 523
4261 GCGCTGCCCTCCCAGCAGCAGCACGGCAGCATGGCGTCGCCGCAGCACCACCACCACCAT 4320
524 A L P S Q Q Q H G S M A S P Q H H H H H 543
4321 CACGTCGGCGTCGGCGTCGGCGGGGCGGTGAATGCTGGCGGCGGTGGCGGCGTGTCGCTC 4380
544 H V G V G V G G A V N A G G G G G V S L 563
4381 ACCCTCGGCCTCCACCAGAACAACAGGGTCTGCTTCGGGGAGCCGCTGCCGGCCAACCTG 4440
564 T L G L H Q N N R V C F G E P L P A N L 583
4441 GCGCACCGGTTCGGGCTGGAGGACGTCGTCAGCGACCCCTACGTGATGGGCTCGTTCGGC 4500
584 A H R F G L E D V V S D P Y V M G S F G 603
4501 GGCCAGGACCGGCACTTCGCCAAGGAGATCGGCGGCCACCTCCTCCATGATTTCGTCGGG 4560
604 G Q D R H F A K E I G G H L L H D F V G 623
4561 TGATCGACGCCGCCGGTGCTCAGCTCGCTCCCCGCTGATGCACATTGTTGTAATGTACGC 4620
*
4621 ACGCTACGCACTGCTAGTATGCTAGGATGGTATATAGTAAGTCAATCATCACAATCACTT 4680
4681 GGCGGCTTGGCTCGATGATCGGTCGACATGAACACGGTCGATTCCTTTGGAGGGCGGATG 4740
4741 AAACATTGACATGCCCTCTCTCCCATGTACTAGATCCAAAATTCAAACAGCTGTCCAACA 4800
4801 TTGCTCTCAAACACCTTGTGGGCTACACAGAGCTTGAAGAGCAATGCTAGACGTACGGGC 4860
4861 GTTGTACGGGGGATTTACAGGCTCGTTGACTGTGATTGGTTGGAATATGATTAAGGGGGA 4920
4921 CGGCCCCACCCTGAAAATCAGGGGGGAAGCAATTAGATTAGGCCACGGTGTCATCCTGTA 4980
4981 AAACTTTGTACGATCATCCTGTACGTGTAGTATTATTGGAGCTTGAAAATACCTTCTTCC 5040
5041 AAACGGCTTTATGGTCTCCTGCCATTTGTCCTAGTAGAGCTTTTGGATTATCCTTTGGTA 5100
5101 ATTAATGAAATGCACGCATGTGTTCCCACATGGCCAAGGAAAAGTTACCTCTTGTTTATG 5160
5161 CCCAAACGTAAATACCGTGCTGCAGCTCCTTGTTTATGCCCAAAAGTTTTACTACCATTA 5220
5221 CTGTGCCGCAGCTGAAGCTTTCAACCGGTCTCTGTAGAATATGACCATCTTCCGACCTGT 5280
5281 TATGTTAGCCTTTCGATGATATGATATGAACGAAACCTGCTGTATTAGTTAGTCTTTTGA 5340
5341 TGTGCGGTTATATTAATAGTACTAATCACGCCGTCGTTTCCGTTATCCCCTGTATACATC 5400
5401 GATGGGGGTAGCCTCCTAAAGTCTGGACAGCCCATGATTTGGACGCCTGTTGACCTCTAA 5460
5461 TTGGCCCCGTCACGCTAACAAATTATCTATCATCGGGGCTAGCAGCGGTAGATTCGGCCT 5520
5521 ACCCTTTCGATCACGGATCCACGCACTAAACTAATGCCACAGTGCCCCAAATGGCATGGC 5580
5581 ATGGCCATGATGATGGATCCTGGCTGCGCTGTCAGTGTCGTGCTGTGTAGAAGTATTATA 5640
5641 TTATCACTAGTAGGAGTATTATATTAAGCCCATGCATGGTAGAGCATGGTAATAGTACCT 5700
5701 GCCGCTGCATGGTTAACCGTGCTGTTCCTGTCCGGTTTCGCAGCGGTAGTATCGGATCTG 5760
5761 TATATATGTGTCTGGCGCGATGATTCTATAGGTGCGCTGTGTGTGTTGGCTGGTGATTGG 5820
5821 TGATGGGCAGCAGCAGCGTATCGGCCGTGGGTGGGGGTGGCGCCATGCACGTTGTTTTTC 5880
5881 CCGGGAGGGAATCCGCGCGCGCTGTAACTAGGGGGCTAGGGAGTACTTTGGCCTGCAGAG 5940
5941 ACTGCAGTGACTACAGCTCACGTTTTTAAAAGCGTCACTGTTTGCCTCCTCTCTTAGGCG 6000
6001 TGTCAGCTGCTACTGGTGGTGGATGGGGAGCGTAATTGTTCTTTCAATGTGTTGTTGTTG 6060
6061 GTCATGCAATGACCACTGTTACTACACATGGGTGATGGGCCGAGCCTGTCTGAGCTACCA 6120
6121 TAACTCGAAAGATCAGTTAAAAACATAATATCTCACATGGAATCAGAACCATGCAAGTGA 6180
6181 TATAGTACTCCTCTTGTTTACTTATATGTCCTGGCTGCATGGACTCTGGACATCACATCA 6240
6241 GCTAAGCTTGCCATCTCAGCGTAGAGAAAGCCAAGTTTGCTATTGGATGGCCTGTTAATT 6300
6301 TTGTGTGTTGTACTGCTGTTTATTCATGGCCATA 6334
Fig. S1 The structure of TaqSH1-D in Chinese Spring. The translated bases are 215–991, 1870–2249, 3759–3813, and 3904–4560 bp and the deduced polypeptide consists of 623 residues. Untranslated region sequences are double-underlined, and intron sequences are underlined. The stop codon is indicated by an asterisk. A 189-bp insertion in Chinese Spring compared to synthetic wheat S-6214 is indicated by gray shading. The adenine underlined in bold in exon 4 (at bp 4050) is a synonymous SNP in the parental lines (guanine in S-6214). The adenine underlined in bold at bp 5955 is thymine in S-6214. The three conserved protein domains (SKY, BEL, and homeodomain) are indicated by amino acids typed in bold