Table S 1. SSR, RGA-STS and SNP markers developed from shotgun sequence assembly data of wheat cv. Chinese Spring, T. monococcum and
T. boeoticum
S.
No
Primer Sequence (5’----------------3’)
Marker/Contig IDa
Forward
Mapped as
Matrix for
resolution
Revers
SSR Markers
1
Ta7AL-2101772
AGGAATGGGATGTGATGAGG
CGTAGTGTAGGAAGTGAAGG
Codominant
PAGE_Licor
2
Ta7AL-4430604
CGCCTAATACACCATTTCAG
ACTAAGTTTGTACTGTGTCC
Dominant
PAGE_Licor
3
Ta7AL-4442119
CTAGTAATGGCGCATCAGTG
TTTAATCCGAGTTCGTATGC
Codominant
PAGE_Licor
4
Ta7AL-4534299
AGCAGTCAAGTATAATCAGCA
C
CTGTCTCAACTAATGGATTCTC
Codominant
PAGE_Licor
5
Ta7AL-4541312
GCCTGTCAAGTTCACATCAC
TTTGTCATGTCGCATAGCCA
Codominant
PAGE_Licor
6
Ta7AL-4554964-1b
ACAGTGAGGAGATCGACCC
Codominant
PAGE_Licor
7
Ta7AL-4554964-2
ACAGTGAGGAGATCGACCC
Codominant
PAGE_Licor
8
Ta7AL-4555302
GTATCTCACAGCACCATCAG
TACACATACGTAAACCAAGCC
Dominant
Agarose
TATGATTTACCATCCTTGACCG
AG
TATGATTTACCATCCTTGACCG
AG
RGA-STS Markers
9
Ta7AL-4367420-1
CATCTTACCACTCGGTCCAC
AATGAGCTGTCTTTGACTTGAG
Codominant
Agarose
10
Ta7AL-4367420-2
GTGTAGATATGGTGTAGAGAA
GAC
CAPS_HindIIIc
Agarose
11
Ta7AL-4426363
GAATCCTCCAAAGCCTCCAC
GTGAAACAATCCGAGGTAAAC
TG
GGCATATCTCATGTGAAGAAC
TG
CAPS_HphI
Agarose
12
Ta7AL-4437049
GGGACAAGATCGAAGAAGAC
CCAACTCCTTGTAGTAATGTG
CAPS_BsrG1
Agarose
13
Ta7AL-4442999
CACACTAGTTCATCATTGGCAG
CATGAAGCAGATTGTGGATGG
CAPS_XhoI
Agarose
14
Ta7AL-4444971
GACAGAGACAAGATTGTGTTT
GAG
AAGTGAAATAAAGAGCGGCGA
CAPS_BtgI
Agarose
1
Primer Sequence (5’----------------3’)
S.
No
Marker/Contig IDa
Mapped as
Matrix for
resolution
15
Ta7AL-4445409-1
CTTACGTTCTTGGTCCTCAC
AGCTGAGAAACTCAAATCTG
Co-dominant
PAGE_Licor
16
Ta7AL-4445409-2
TTGAGCCACATGATAAGAGAT
GTC
CCACACTAGATGCCGAACTG
CAPS_BtgI
Agarose
17
Ta7AL-4449952
ATATAGATCGAGACACATGGC
CAATGAGGTGGTCCATGC
Dominant
Agarose
18
Ta7AL-4459571
CGAGTCAGCCAACTAGATCAG
TGAGGACGTATAGATTCCGA
Dominant
Agarose
19
Ta7AL-4491418
GAAGACACAAAGTGTATCCA
CAPS_SphI
Agarose
20
Ta7AL-4503710
CATTACAGATTTGGACGGTTAA
GG
Dominant
Agarose
21
Ta7AL-4504413
CAGTCTTCTAAAGCCAACAC
CTTGCCAATTATATGCACCT
CAPS_EcoRI
Agarose
22
Ta7AL-4535243
AGTCCAGCAATTCAGAAGATC
C
TGAGCCTAGATAATCGAGCA
Dominant
Agarose
23
Ta7AL-4544237
CACTACAATGATGGTAAGCGA
GCAAGAAGAAACAAGGAGAG
CAPS_TaqI
Agarose
24
Ta7AL-4552644
CGTTCAACTCGGTACAATGG
CACTCCCAAAGAGCAAACAC
CAPS_XmaI
Agarose
25
Ta7AL-4553495
AATTCGTAACGGGCTTATTGTG
TGATGAGATTGCCAAGTGTCC
CAPS_NdeI
Agarose
26
Ta7AL-4555017
GGGTTCTACATATTGAATCTAC
GG
TACATCACATACCACTTCCT
CAPS_HaeIII
Agarose
27
Ta7AL-4556232
TTTCAAATAACGGCTTCTGG
GAGACGAGCAAATAGATATGG
Codominant
PAGE_Licor
28
Ta7AL-4557825
GATACCACGGAATCACACCA
GATACTGTTGACTTCCTGCCA
Codominant
PAGE_Licor
29
Ta7AL-4558388
CAGATTAAGATGAAGCCTGGT
GAGTGCTCAAACAAATCAAGA
C
Codominant
PAGE_Licor
ATTCTTCATTGTCTTCCCTG
CATTCCTACTTCCGTACCTG
HRMd
Bio-Rad CFX96
Forward
GAACAGAAACATGTAAGGACA
C
GGGAAGACTGGTATAGAGATG
AG
Revers
SNP Markers
30
Tm-147865483
2
S.
No
Primer Sequence (5’----------------3’)
Marker/Contig IDa
Mapped as
Forward
Revers
Matrix for
resolution
31
Tm-147956055
CGATGATATCCATCTTGGCAC
ATGACGATGATTTGTGGCCT
HRM
Bio-Rad CFX96
32
Tm-148019499
ATCACCATCAATTAGAAGCC
GAAGACATAATTAGCAGTGGG
HRM
Bio-Rad CFX96
33
Tm-148064849
TGTGCATCTCAAATGACCGT
HRM
Bio-Rad CFX96
34
Tm-148129757
GATTACGGAGCGAATGAAGG
CAAGAAGATGATGAGGTTGGT
GACAACTTGAAACAAGACTTC
C
HRM
Bio-Rad CFX96
35
Tm-148138043-1
CCTCTTACAAACACTCGGCA
GCTTCAGTATGTTGTTTGTTCG
HRM
Bio-Rad CFX96
36
Tm-148138043-2
GTACACATAGCCTGAGCAGAG
TATATTTGTGAACGGATGGAGT
GG
HRM
Bio-Rad CFX96
37
Tm-148139701
GTAACTTGCTTCTTGTCATGTC
AGTGTCCGAAATTCTTTGCC
HRM
Bio-Rad CFX96
38
Tm-148142453
AAACAAACAGGACTAATGCCC
TTCCTTTAGACTAAAGGTGGAG
HRM
Bio-Rad CFX96
39
Tm-148149679
ACCACCTTCACTGAATAGTC
TGAAGATAGTTCCTTCCACAG
HRM
Bio-Rad CFX96
AAACGAGTGGCTGAAATAATG
HRM
Bio-Rad CFX96
G
GCCTTCAAGAGGAAACATACC
41 Tm-148162417-1
ACGATGCTTGGTCATTGCT
HRM
Bio-Rad CFX96
A
GCTGCTTTCAACTTCATCAATC GCTCTAGTATCTTCTTCGATCT
42 Tm-148162417-2
HRM
Bio-Rad CFX96
TC
G
a
Ta7AL denotes the contig from shotgun sequence assembly data of Triticum aestivum chromosome 7AL and number represent the contig ID.
b
Markers designed from the same contig
c
Restriction enzyme used for generating the CAPS marker.
d
HRM (high resolution melting) curve analysis
40
Tm-148159657
CAACTGAATGCTCTTGTCTC
3
Table S2. Comparative genomics of Chinese Spring RGAs mapped on T. monococcum chromosome 7AL with Brachypodium and Oryza genes
Marker ID
Brachypodium
Gene ID
Ta7AL-4534299_ssr
Bradi1g30260
Ta7AL-4541312_ssr
Bradi1g29658
Ta7AL-4554964_ssr
Bradi1g31837
Ta7AL-4555302_ssr
Bradi1g33640
Ta7AL-4367420_rga
Bradi4g09957
Ta7AL-4426363_rga
Bradi4g04657
Ta7AL-4437049_rga
Bradi1g00237
Ta7AL-4442999_rga
Bradi2g59310
Ta7AL-4444971_rga
Bradi4g23880
Ta7AL-4445409_rga
Bradi2g52840
Ta7AL-4449952_rga
Bradi1g29370
Ta7AL-4459571_rga
Bradi3g00757
Ta7AL-4491418_rga
Bradi1g00237
Ta7AL-4503710_rga
Bradi1g01550
Ta7AL-4504413_rga
Bradi4g44217
Ta7AL-4535243_rga
Bradi4g09577
Ta7AL-4544237_rga
Bradi3g60337
Brachypodium Gene annotation
Oryza gene ID
Oryza Gene Annotation
LOC_Os06g43120
zinc finger C-x8-C-x5-C-x3-H type
family protein, expressed
LOC_Os02g16270
xa1, putative, expressed
Homeodomain-like superfamily protein
LOC_Os06g45410
MYB family transcription factor,
putative, expressed
S-locus lectin protein kinase family protein
LOC_Os04g34290
protein kinase, putative, expressed
LOC_Os06g16790
go35 NBS-LRR, putative, expressed
Zinc finger C-x8-C-x5-C-x3-H type family
protein
LRR and NB-ARC domains-containing
disease resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
LRR and NB-ARC domains-containing
disease resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
LOC_Os12g37740
LOC_Os05g16200
LOC_Os01g70080
resistance protein LR10, putative,
expressed
blight resistance protein T118, putative,
expressed
NB-ARC domain containing protein,
expressed
LOC_Os08g14850
resistance protein, putative, expressed
LOC_Os05g41290
disease resistance RPP13-like protein 1,
putative, expressed
LOC_Os08g14850
resistance protein, putative, expressed
LOC_Os08g10440
LOC_Os05g16200
LOC_Os08g14850
LOC_Os11g37870
LOC_Os02g19890
LOC_Os02g16270
NBS-LRR disease resistance protein,
putative, expressed
blight resistance protein T118, putative,
expressed
resistance protein, putative, expressed
stripe rust resistance protein Yr10,
putative, expressed
stripe rust resistance protein Yr10,
putative, expressed
xa1, putative, expressed
4
Marker ID
Brachypodium
Gene ID
Ta7AL-4552644_rga
Bradi4g16492
Ta7AL-4553495_rga
Bradi1g29427
Ta7AL-4555017_rga
Bradi1g00237
Ta7AL-4556232_rga
Bradi2g39537
Ta7AL-4557825_rga
Bradi3g61040
Ta7AL-4558388_rga
Bradi1g00237
Tm_147865483_snp
Bradi1g29370
Tm_147956055_snp
Bradi4g16492
Tm_148129757_snp
Bradi3g00757
Tm_148138043_snp-1
Bradi4g10037
Tm_148138043-snp-2
Bradi4g10037
Tm_148139701_snp
Bradi4g04657
Tm_148142453_snp
Bradi2g59310
Tm_148149679-snp
Bradi2g09434
Tm_148159657_snp
Bradi4g05870
Tm_148162417_snp-1
Bradi1g00237
Tm_148162417_snp-2
Bradi1g00237
Brachypodium Gene annotation
Disease resistance protein (CC-NBS-LRR
class) family
Disease resistance protein (CC-NBS-LRR
class) family
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
LRR and NB-ARC domains-containing
disease resistance protein
NB-ARC domain-containing disease
resistance protein
LRR and NB-ARC domains-containing
disease resistance protein
Disease resistance protein (CC-NBS-LRR
class) family
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
LRR and NB-ARC domains-containing
disease resistance protein
NB-ARC domain-containing disease
resistance protein
NB-ARC domain-containing disease
resistance protein
Oryza gene ID
LOC_Os11g34920
LOC_Os11g41540
LOC_Os05g16200
LOC_Os11g14380
Oryza Gene Annotation
stripe rust resistance protein Yr10,
putative, expressed
disease resistance RPP8-like protein 3,
putative, expressed
blight resistance protein T118, putative,
expressed
resistance protein LR10, putative,
expressed
LOC_Os11g44580
go35 NBS-LRR, putative, expressed
LOC_Os05g16200
blight resistance protein T118, putative,
expressed
LOC_Os08g14850
resistance protein, putative, expressed
LOC_Os11g34920
LOC_Os08g10440
LOC_Os11g44960
LOC_Os11g44960
LOC_Os12g37740
LOC_Os01g70080
LOC_Os10g22484
LOC_Os10g04120
LOC_Os05g16200
LOC_Os05g16200
stripe rust resistance protein Yr10,
putative, expressed
NBS-LRR disease resistance protein,
putative, expressed
NBS-LRR disease resistance protein,
putative, expressed
NBS-LRR disease resistance protein,
putative, expressed
resistance protein LR10, putative,
expressed
NB-ARC domain containing protein,
expressed
RGH2B, putative, expressed
powdery mildew resistance protein
PM3b, putative, expressed
blight resistance protein T118, putative,
expressed
blight resistance protein T118, putative,
expressed
5