Vrn1_T4 (AS_ITA_21_HQ910536) genomic sequence vs. corresponding fragment from T. aestivum Vrn-A1:

F primer

Exon 3 Intron 3

Intron 3 Exon 4

Exon 4 Intron 4

- Majority

ACT GAXGGCGAAGGT T GAXACAAT ACAXAAAT GT CAAAAGT AAT T XGXAXXGXT T T T GXT T GXT T GCCAGT AT XXMajority

10 20 30 40 50 60 70

ACT GA- GGCGAAGGT T GAKACAAT ACAAAAAT GT CAAAAGT AAT T AGRAGKGRT T T T GAT T GGT T GCCAGT AT GA 74AS_ITA_21_HQ910536_genomicACT GAAGGCGAAGGT T GAGACAAT ACAGAAAT GT CAAAAGT AAT T T GT AACGAT T T T GGT T GAT T GCCAGT AT AT 75Taestivum_AY747601_genomic_frag

- Majority

T GT AT AXXXT XT XAAGAT AXAT GXGAXXGXXT T XXXACAT XCT GCAXCT GCXGGCAT CT XAT GGGAGAGGAT CT XMajority

80 90 100 110 120 130 140 150

T GT AT AT YYT WT T AAGAT AT AT GT GAT AGGCT T - - - ACAT T CT GCACCT GCRGGCAT CT GAT GGGAGAGGAT CT C 146AS_ITA_21_HQ910536_genomicT GT AT ACACT CT GAAGAT AAAT GGGACT GAAT T T CT ACAT CCT GCAT CT GCAGGCAT CT CAT GGGAGAGGAT CT T 150Taestivum_AY747601_genomic_frag

- Majority

GAAT CT T T GAAT CT XAAXGAGT T GCAGCAACT XGAGCAGCAGCT XGAAAGXT CACT XAAACAT AT CAGAT CCAGXMajority

160 170 180 190 200 210 220

GAAT CT T T GAAT CT T AAAGAGT T GCAGCAACT AGAGCAGCAGCT AGAAAGT T CACT AAAACAT AT CAGAT CCAGA 221AS_ITA_21_HQ910536_genomicGAAT CT T T GAAT CT CAAGGAGT T GCAGCAACT GGAGCAGCAGCT GGAAAGCT CACT GAAACAT AT CAGAT CCAGG 225Taestivum_AY747601_genomic_frag

- Majority

AAGGT AXXXAT XXXXAT GXXT T XAT XCXGXXGCAXAAT AT AT XAAAAXXXXXXXAACXXT T GCAGAXAAGXT CAGMajority

230 240 250 260 270 280 290 300

AAGGT AGAAAT - - - - AT GT GT T T AT GCT GT GGCAGAAT AT AT CAAAA- - - - - - - AACT AT T GCAGAAAAGCT CAG 285AS_ITA_21_HQ910536_genomicAAGGT ACT GAT T T AAAT GAT T T GAT ACAGCAGCACAAT AT AT AAAAAGAAGAAAAACACT T GCAGAGAAGT T CAG 300Taestivum_AY747601_genomic_frag

Supplement 4: alignments for putative Vrn1 clone used for RFLP mapping (November, 2011):

Intron 4 Exon 5

Exon 5 Intron 5

R primer

Intron 5 Exon 6

79% identity

- Majority

XAAAGT AXAT CT GAAXT CXGAT T CT AGACT GAGAT XT T XXAXAT XAT GT XT AT GCXT T T XXGT CAT AT GCT CT XXMajority

310 320 330 340 350 360 370

T AAAGT ACAT CT GAAT T CGGAT T CT AGACT GAGAT AT T T T ACAT T AT GT GT AT GCGT T T - - GT CAT AT GCT CT GT 358AS_ITA_21_HQ910536_genomicCAAAGT AT AT CT GAAAT CAGAT T CT AGACT GAGAT GT T CAAAAT - AT GT AT AT GCAT T T T AGT CAT AT GCT CT T C 374Taestivum_AY747601_genomic_frag

- Majority

XT AXT T XAAXAXXT GACXAAT XT XXXT XXXT XXXT GT AXXT GCAGAXCCAXCT T AT GCACGAAT CCAT T T CXGAGMajority

380 390 400 410 420 430 440 450

GT A- T T CAAGAGCT GACAAAT AT AACT - - - T CCCT GT AT GT GCAGAGCCAGCT T AT GCACGAAT CCAT T T CCGAG 429AS_ITA_21_HQ910536_genomicAT AGT T AAAAAAAT GACT AAT T T T T T T CAT T T T T T GT ACT T GCAGAACCAACT T AT GCACGAAT CCAT T T CT GAG 449Taestivum_AY747601_genomic_frag

- Majority

CT T CAXAAGAAGGT AAXXT GXCAACCT T GXCAT ACCT XAT T CXGXAT XXGAACT GGXXAXCT T GT XAT GAXXXCTMajority

460 470 480 490 500 510 520

CT T CAAAAGAAGGT AAAGT GGCAACCT T GGCAT ACCT GAT T CAGCAT CGGAACT GGCT ACCT T GT T AT GAT AT CT 504AS_ITA_21_HQ910536_genomicCT T CAGAAGAAGGT AAGCT GT CAACCT T G- CAT ACCT T AT T CGGT AT T CGAACT GGT CAACT T GT CAT GAAGCCT 523Taestivum_AY747601_genomic_frag

- Majority

XT AGCT T GT T T CAAGXT T T XT GXCAT XAT AXCAT GT AXGXAXGXAAXT XXT CXXXXXXXXXXXXACCT CAT T ACXMajority

530 540 550 560 570 580 590 600

GT AGCT T GT T T CAAGT T T T AT GGCAT CAT AGCAT GT ACGT AT GCAAGT ACT C- - - - - - - - - - - - ACCT CAT T ACC 567AS_ITA_21_HQ910536_genomic- T AGCT T GT T T CAAGAT T T GT GACAT T AT AACAT GT AT GCAAGT AACT GGT CT ACAT GCACGT AACCT CAT T ACA 597Taestivum_AY747601_genomic_frag

- Majority

T CGT T CT T GXT GCAGGAGAGGT CACT GCAGGAGGAGAAMajority

610 620 630

T CGT T CT T GGT GCAGGAGAGGT CACT GCAGGAGGAGAA 605AS_ITA_21_HQ910536_genomicT CGT T CT T GCT GCAGGAGAGGT CACT GCAGGAGGAGAA 635Taestivum_AY747601_genomic_frag

AS_ITA_21_HQ910536 spliced sequence* vs. A. strigosa Fruitful-like cDNA and spliced T. aestivum Vrn-A1 sequence:

* Two sequencing errors corrected to match oat Vrn1 consensus sequence

- Majority

ACT GAAGGCGAAGGT T GAGACAAT ACAAAAAT GT CAAAAGCAT CT GAT GGGAGAGGAT CT CGAAT CT T T GAAT CTMajority

10 20 30 40 50 60 70

ACT GAAGGCGAAGGT T GAGACAAT ACAAAAAT GT CAAAAGCAT CT GAT GGGAGAGGAT CT CGAAT CT T T GAAT CT 75AS_ITA_21_HQ910536_splicedACT GAAGGCGAAGGT T GAGACAAT ACAAAAAT GT CAAAAGCAT CT GAT GGGAGAGGAT CT CGAAT CT T T GAAT CT 75Astrigosa_DQ792964_cDNA_fragACT GAAGGCGAAGGT T GAGACAAT ACAGAAAT GT CAAAAGCAT CT CAT GGGAGAGGAT CT T GAAT CT T T GAAT CT 75Taestivum_AY747601__spliced_frag

- Majority

T AAAGAGT T GCAGCAACT AGAGCAGCAGCT AGAAAGT T CACT AAAACAT AT CAGAT CCAGAAAGAGCCAGCT T ATMajority

80 90 100 110 120 130 140 150

T AAAGAGT T GCAGCAACT AGAGCAGCAGCT AGAAAGT T CACT AAAACAT AT CAGAT CCAGAAAGAGCCAGCT T AT 150AS_ITA_21_HQ910536_splicedT AAAGAGT T GCAGCAACT AGAGCAGCAGCT AGAAAGT T CACT AAAACAT AT CAGAT CCAGAAAGAGCCAGCT T AT 150Astrigosa_DQ792964_cDNA_fragCAAGGAGT T GCAGCAACT GGAGCAGCAGCT GGAAAGCT CACT GAAACAT AT CAGAT CCAGGAAGAACCAACT T AT 150Taestivum_AY747601__spliced_frag

- Majority

GCACGAAT CCAT T T CCGAGCT T CAAAAGAAGGAGAGGT CACT GCAGGAGGAGAAMajority

160 170 180 190 200

GCACGAAT CCAT T T CCGAGCT T CAAAAGAAGGAGAGGT CACT GCAGGAGGAGAA 204AS_ITA_21_HQ910536_splicedGCAT GAAT CCAT T T CCGAGCT T CAAAAGAAGGAGAGGT CAT T GCT GGAGGAGAA 204Astrigosa_DQ792964_cDNA_fragGCACGAAT CCAT T T CT GAGCT T CAGAAGAAGGAGAGGT CACT GCAGGAGGAGAA 204Taestivum_AY747601__spliced_frag

Nucleotide Substitution per 100 residues0

4.1

24

Astrigosa_DQ792964_cDNA_fragAS_ITA_21_HQ910536_splicedTaestivum_AY747601__spliced_frag

AS_ITA_21_HQ910536 translated sequence vs. Z. mays TF15 protein sequence and translated A. strigosa Fruitful-like and T. aestivum Vrn-A1 sequences:

K-box motif

- Majority

L KAKVET I QKCQKHL MGEDL ESL NL KEL QQL EQQL ESSL KHI RSRKSQL MHESI SEL QKKERSL QEEMajority

10 20 30 40 50 60

L KAKVET I QKCQKHL MGEDL ESL NL KEL QQL EQQL ESSL KHI RSRKSQL MHESI SEL QKKERSL QEE 67AS_ITA_21_HQ910536_translatedL KAKVET I QKCQKHL MGEDL ESL NL KEL QQL EQQL ESSL KHI RSRKSQL MHESI SEL QKKERSL L EE 67Astrigosa_DQ792964_trans_fragL KAKVET I QKCQKHL MGEDL ESL NL KEL QQL EQQL ESSL KHI RSRKNQL MHESI SEL QKKERSL QEE 67Taestivum_AY747601_trans_fragL KAKI ET I QKCHKHL MGEDL ESL NPKEL QQL EQQL DSSL KHI RSRKSHL MAESI SEL QKKERSL QEE 67Zmays_ACG35179_pro_frag

Amino Acid Substitution per 100 residues0

5.7

24

Astrigosa_DQ792964_trans_fragTaestivum_AY747601_trans_fragAS_ITA_21_HQ910536_translatedZmays_ACG35179_pro_frag