Supporting information
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure).
SNP
0_15361_01-oldSnpPosition_64
0_4588_01-oldSnpPosition_172
0_11324_01-oldSnpPosition_170
CL180Contig1_03-oldSnpPosition_418
1_3086_01-oldSnpPosition_202
2_7532_01-oldSnpPosition_152
CL1521Contig1_01-oldSnpPosition_160
0_6116_01-oldSnpPosition_289
0_6116_01-oldSnpPosition_455
0_10054_01-oldSnpPosition_151
CL3421Contig1_03-oldSnpPosition_149
UMN_3847_01-newSnpIndex_235
0_2433_01-newSnpIndex_126
0_15329_01-oldSnpPosition_418
CL2332Contig1_01-newSnpIndex_186
CL463Contig2_02-oldSnpPosition_128
CL3495Contig1_03-oldSnpPosition_205
CL3062Contig1_03-oldSnpPosition_158
0_3372_02-oldSnpPosition_136
Pila_comp2709_c0_262
2_1818_01-oldSnpPosition_190
2_10502_03-oldSnpPosition_115
UMN_7021_02-newSnpIndex_182
UMN_4966_01-newSnpIndex_82
Pila_comp11517_c0_979
UMN_915_01-newSnpIndex_181
Pila_isogroup07763_471
0_17641_01-oldSnpPosition_138
CL572Contig1_02-oldSnpPosition_69
CL1720Contig1_06-oldSnpPosition_213
CL1692Contig1_05-oldSnpPosition_214
CL263Contig2_03-oldSnpPosition_85
0_13240_01-oldSnpPosition_192
CL3832Contig1_05-oldSnpPosition_133
CL1694Contig1_04-oldSnpPosition_240
2_4723_01-newSnpIndex_93
2_4723_01-newSnpIndex_349
Pila_isogroup07475_315
CL4478Contig1_03-oldSnpPosition_157
2_9280_01-newSnpIndex_308
0_17161_01-oldSnpPosition_366
2_9940_01-oldSnpPosition_235
E-value
1.2E-23
4.2E-15
5.6E-28
4E-117
2E-15
0.33
1.5E-127
4.9E-30
4.9E-30
2.2E-12
8.7E-11
0.000039
1.5E-21
0.037
2.9E-92
2.6E-67
8.4E-38
6.5E-66
1.6E-16
1.5E-28
2.3E-64
1.9E-94
4.3E-110
7.1E-17
3.7E-130
9.7E-29
4.3E-112
1.7E-37
9.8E-202
2.8E-169
2.8E-89
2.5E-94
8.9E-67
1.8E-65
2E-88
3.9E-51
3.9E-51
0.0000026
1.1E-95
0.0053
5.2E-26
3.8E-146
Annotation [Species]
PREDICTED: UPF0497 membrane protein 11 [Vitis vinifera]
PREDICTED: aldehyde dehydrogenase family 2 member B4, mitochondrial-like [Glycine max]
heat shock protein 70 (HSP70)-interacting protein, putative [Ricinus communis]
Quasimodo1-like protein [Selaginella moellendorffii]
PREDICTED: eukaryotic translation initiation factor 1A [Vitis vinifera]
60S ribosomal protein L34, putative [Ricinus communis]
PREDICTED: aquaporin PIP2-7 [Vitis vinifera]
Ankyrin repeat containing protein. (Os10t0178200-01) [Oryza sativa Japonica Group]
Ankyrin repeat containing protein. (Os10t0178200-01) [Oryza sativa Japonica Group]
NAC domain protein, IPR003441 [Populus trichocarpa]
TCP transcription factor 11 [Solanum lycopersicum]
EGF-type aspartate/asparagine hydroxylation site domain containing protein. (Os08t0501500-00) [Oryza sativa Japonica Group]
protein histidine triad nucleotide-binding 4 [Arabidopsis thaliana]
PREDICTED: metal tolerance protein A2-like [Vitis vinifera]
PREDICTED: calcium-dependent protein kinase 3-like isoform 1 [Glycine max]
PREDICTED: expansin-A8 [Glycine max]
PREDICTED: 5'-nucleotidase domain-containing protein DDB_G0275467 [Vitis vinifera]
WD40-like domain containing protein. (Os10t0498700-01) [Oryza sativa Japonica Group]
PREDICTED: TPR repeat-containing thioredoxin TTL1-like [Glycine max]
leucine-rich repeat-containing protein, putative [Ricinus communis]
PREDICTED: chalcone synthase-like [Glycine max]
PREDICTED: peptidyl-prolyl cis-trans isomerase B-like [Vitis vinifera]
PREDICTED: uncharacterized protein KIAA0090 homolog [Vitis vinifera]
Limkain-b1 [Medicago truncatula]
PREDICTED: F-box/LRR-repeat protein 2-like [Glycine max]
PREDICTED: U-box domain-containing protein 43-like [Brachypodium distachyon]
chitinase-like protein 1 [Arabidopsis thaliana]
PREDICTED: laforin-like [Glycine max]
alcohol dehydrogenase class III [Solanum lycopersicum]
PREDICTED: DEAD-box ATP-dependent RNA helicase 30-like [Vitis vinifera]
Ubiquitin-protein ligase bre-1, putative [Ricinus communis]
PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like isoform 2 [Vitis vinifera]
PREDICTED: L-aspartate oxidase 1-like [Vitis vinifera]
PREDICTED: xyloglucan galactosyltransferase KATAMARI1 [Vitis vinifera]
elongation factor 2 (EF-2, EF-TU) [Volvox carteri f. nagariensis]
PREDICTED: coatomer subunit gamma-2-like [Vitis vinifera]
PREDICTED: coatomer subunit gamma-2-like [Vitis vinifera]
Rhodanese-like domain containing protein. (Os01t0889800-01) [Oryza sativa Japonica Group]
PREDICTED: eukaryotic translation initiation factor 3 subunit D-like [Vitis vinifera]
PREDICTED: SWI/SNF complex subunit SWI3D-like [Glycine max]
bel1 homeotic protein, putative [Ricinus communis]
cholesterol transport protein [Populus trichocarpa]
Classification
Control
Non-neutral
Non-neutral
Control
Control
Control
Non-neutral
Non-neutral
Non-neutral
Control
Control
Control
Control
Control
Non-neutral
Control
Control
Control
Non-neutral
Control
Non-neutral
Non-neutral
Control
Control
Non-neutral
Non-neutral
Non-neutral
Control
Control
Non-neutral
Non-neutral
Control
Non-neutral
Control
Control
Control
Control
Control
Control
Control
Non-neutral
Control
Reference
Seki et al. (2002)
Sarkar et al. (2013)
Almeida-Rodriguez et al. (2007)
Seong et al. (2007)
Seong et al. (2007)
Hettenhausen et al. (2016)
Rosado et al . (2006)
Kawaguchi et al. (2004)
Sharma and Singh (2003)
Seki et al.(2002)
Yee and Goring (2009)
Kwon et al. (2007)
Macovei et al. (2012)
Seki et al.(2002)
Seki et al. (2002)
Yuan et al. (2012)
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
0_15361_01-oldSnpPosition_64
0_4588_01-oldSnpPosition_172
0_11324_01-oldSnpPosition_170
CL180Contig1_03-oldSnpPosition_418
1_3086_01-oldSnpPosition_202
2_7532_01-oldSnpPosition_152
CL1521Contig1_01-oldSnpPosition_160
0_6116_01-oldSnpPosition_289
0_6116_01-oldSnpPosition_455
0_10054_01-oldSnpPosition_151
CL3421Contig1_03-oldSnpPosition_149
UMN_3847_01-newSnpIndex_235
0_2433_01-newSnpIndex_126
0_15329_01-oldSnpPosition_418
CL2332Contig1_01-newSnpIndex_186
CL463Contig2_02-oldSnpPosition_128
CL3495Contig1_03-oldSnpPosition_205
CL3062Contig1_03-oldSnpPosition_158
0_3372_02-oldSnpPosition_136
Pila_comp2709_c0_262
2_1818_01-oldSnpPosition_190
2_10502_03-oldSnpPosition_115
UMN_7021_02-newSnpIndex_182
UMN_4966_01-newSnpIndex_82
Pila_comp11517_c0_979
UMN_915_01-newSnpIndex_181
Pila_isogroup07763_471
0_17641_01-oldSnpPosition_138
CL572Contig1_02-oldSnpPosition_69
CL1720Contig1_06-oldSnpPosition_213
CL1692Contig1_05-oldSnpPosition_214
CL263Contig2_03-oldSnpPosition_85
0_13240_01-oldSnpPosition_192
CL3832Contig1_05-oldSnpPosition_133
CL1694Contig1_04-oldSnpPosition_240
2_4723_01-newSnpIndex_93
2_4723_01-newSnpIndex_349
Pila_isogroup07475_315
CL4478Contig1_03-oldSnpPosition_157
2_9280_01-newSnpIndex_308
0_17161_01-oldSnpPosition_366
2_9940_01-oldSnpPosition_235
Probe sequence
GTTTGTTTCATGGTACTGTCCCTGCTTTCTGCACACAAACTGTTCAGCAA[A/G]TACGAGRCTCCYATAGTAAATAAGGGCCCCCATACAGCCTTCTCACAC
GGGTCGAGGGTGTTTGTTCAAGAGGGCATCTATGATGAGTTTCTRAAGAA[A/G]GCGGTGGCAAGAGCCAAACAACAAGTGGTGGGAGACCCTTTTAAGCCTGG
AGTAGAAGACCCAAGCAAAGAACCTAATAAGCAGGTATCCTTGGAGGAAG[C/G]TTGTAAAGACAAAACTGGGGATGAGCTTGAAGGCAAAGAAGTTGAAATTG
AAATTAAAATGAATTATTGAGAAAGGATTGTATTTCTAATTGCTGGAATG[T/C]ATTTAGTTGCCCAGAGACAAATATATTCTTAAGGTGCTGCATTCCCTTGG
CATAACATTGACAGTGAAGACGAGAATAATTAGATTTTGTCAATGTCTTC[A/G]TCTTCAAACTCAATATAGTCATCGGCGCCGCCTTCCTCATCTTCATCGAG
AGGTTGGCGACTTTCATTATCAGGGRCATAACTTGATCTGATAGACAACT[A/G]TTTGACTAATTCAGTACCGTGCCATTCTTTCATGACAAGAATCAAAACCA
GAAGTTGCTGTGAAGATATCTGTGTCTGTTTGTAKAGATGGCAAAAGAAA[C/G]TGGAACTGATATAGAGCCTCCTGCCAAGGACTACCAAGACCCCCCACCAG
GCAGTCAAGGGTCACATCAACAACAAGCTGCTAAGGCTTGGAATGCTTGC[C/G]TCGGCATTAGGATCAATAATGGGATGCGTATTCTTGATGTTGTCTATGGT
AGCTTAGAGGACAGTGGCGCTTGTGATGCAGGTGAAGACATTG[T/C]TAAGAACCTTTTGATATTTGAGGTGACGTCATTCAGTGCATTTCTATTCT
AACTGTGATGTTGATCTCTGGAGCTTTGCAGGAAAATGAACAGCCCTCTC[T/C]CTCAAAAATTACATGAACAAATGGTAACTTTAACTGGCTTTTCATGTACA
ATAACTGCAATTCAAGCTTCTGCAACATAGGTTTCATTCAATCTGATGCA[T/G]GCAGGATTACTTATTAATTGTGGATCCCTTAYTCGGCTGGAGTTCTAACA
TTCAGAKATTATCAGRACAATGGGGGCTATGCTTGTAATAATATTAGTAG[C/G]ATCACAGATTCTGGACGCGGGAGCCGTAATGACAGGAGGCTGCAGGACGT
TTACATAACCCTTCTTATGATGCATAACCGTGCGTTAGTTTATATTTTCA[T/C]GTTATAAATTATGAGTAGACATGAAGCCATTTTTTGATCTCTATGAATGT
GCATTTGGAAGCTCGCCTTCTTCTGTTCGGTCATAGGAAGATTCTACAAG[A/T]TCCTGCTCTTGATCTCGACCAGCAGGATCMAGTGGATCAAAAGGCATTGA
GATCATCATACTTTTTCATTCTTGCTAATCAKTGTTGGTCCTGATGCTAG[A/G]CCATCCATGGGTGAGAGAAGATGGTGAGGCACCAGACAAACCACTTGACA
ATGTCACGCAACTGGGGACAGAATTGGCAAAGCAATTCATACTTGAATGG[C/G]CAGAGCCTGTCCTTCAAGGTCACCACCAGTGAYGGGCGGACAGTTKTTTC
GAAGGTAAATCACCTTGAAATTATTTTTTCACTTTCTGCTTACATCTTTT[T/C]AAAACACTGGGTATAGCAGTGTACGCCATCCTGCAGTATGAAGTTATACT
ACCCTGGGTTCATGTAGTCTAGTTACTAGTTTTGTACAAATCTCTCGGGA[T/C]TTCTGCAGCTCCTGTAAAATAGCTTCATTCCATTATACCC
TATAATTGCTCAAGTGCACCAAATGAACCCATAGCACCCACCAATTTGAT[A/C]ATGTTTTCAGTGAGAGAAGTCAAAACAGAATGAGAATGTATTTGCAAATT
ATTTCCAGCAAATCTTCGAGCAAGGAACTCAGGCAAAAGCTCTTAAGCCT[C/G]AAGCCTACCATTGATCAAATCTCTAAGATTTCTTCTGACGCAGACTCTTC
TGGGTSGTTCATCCCGGAGGACGYGCCATTCTGGACCAGGTGGAGGCCAG[A/G]GTCAACCTGGATCCTAAAAAACTGAGAGCCACTAGGCACATTCTGAGCGA
GCAGCGTACCCTGCTCCAGCTGCCTGCGGGCGCAGAGAGCTCGTAATCCT[T/C]ACAGCCCTCGCAGCGGCCCCTGCYAGAGCCGAGGAGGAGGAAGTTGAGGT
TTAGATGAGAGTCCAGCTGTTCTGATAATAGGAAAATGTGGTCTAGGACC[C/G]GATGATACAGGAATTCTTTCATTTGTAGATTCTCACAGTGGCAAAGAACT
GGGGTGAGCCRGCTCTTCAAAATTCTCTGCAGGACTCTGAACAAACAGAG[A/C]AAAAGGGTAATTCTAATGTTTCAAATGATGTTCCGAAAACAGATGTTCCA
TTCTAGTTGTAGAATTCTTAGGCTCGGACCACAAACAGAAGCAAGTGCTT[C/G]AATGGCTTCATCTGATACGAGTCTGCACCCTCCAATCATCAGAACCTCAA
GCAATATGTACTCTTGTCAGTGATTCGGTTGATGTGGAACGTGGGGTTAA[T/C]ATTTTGGATAAAGCGGATGCTATACAGCATATCCTAGATATTCTACAAGA
GTTGAAACAGGGTTAAGAGGAACTTGCTGGCCACAGTCAAGATTCTCACC[A/G]GCTTTTTCACGCCCAATGCCCATCAAATCGAGGAAATACAGGTAATGTGA
GCATATGATATGGTGACATCAAAAAGACCTTGTGGACCAAAGAGAGATGC[A/T]ATTAGAGGTGCCACGTATGATCTGGCAAAAAATGATCCGTGGAAGGCATC
CAGCTTGTTACAGGACGTGTGTGGAAGGGTACAGCTTTTGGTGGTTTCAA[A/G]AGCCGTTCTCAAGTGCCATGGCTTGTAGAGAAGTATATGAAAAAGGTTAG
AAGGGCACAGCATATTCATTCTTTACTGCTGCAAATGGAAGATTTGCAAG[A/G]GAGTTGGTTAGCATTCTTCAAGAAGCCGGGCAGCGTGTTAATCCTGAATT
AAGTAGGTACCATAGGATCTGTAAATCATTTGAAGTGTTTTAGCTCCAAT[A/G]CTATTGGTTACTTTTCTACTTTCAAAGTAAACTATCTGTGTTTTTTCCTT
TCTGGCATKRATTTTGCCAAATTTTGGCATCTGAGAATGTRTTMTATGTT[T/G]CCTTCTGAACCAGCAACCTCAGCCACAGGGGCAACAGCCTCAGTCTGATC
ACAAGGATGAAATTGCAAAAGATCATGTGGGACTATGTTGGAATTGTTCG[A/T]TCTATTGATTGTCTTAAAATAGCTGAGAAGTCTTTGGCAGATTTAGAACT
ATTTATGATCMTGTGGTAGACGTTGCGGCACTTACCCGATCTGAGAAACT[T/G]GAGATCGGGGAGGAGGGACTGCTGTCGGATTCTGCTGAATTCAGATTCAA
AACAAATTTTTCGATGATCCTATGTTACTTGAGATGGCAAGGCAAGATGC[A/C]GATTTTCAGCAGATCTTGTAGGTTGAACTATACACCTACTCTGCTGCTGA
AGGAATGATGAAAGATCCCTGCACCCTTAGCCATTAGCAACAATTTCATG[T/G]ATGGCRTCGCTTACAAATTGGTCTTCCGACCGCACTGCAAGCTTCATAGC
ATTAGCATTACAGAYTGCAAGATGCCAATATCTAGAAGATGGGCACTCAT[T/G]CCTGAATCTTACCTCACAAGCCTGCATTCCAAGAAGATTGATTACTGCCT
TTGAGATGCTAAATCAaTTCCATCTCCTCCActgAAAGATGAcAaGACTG[T/C]TGCAGATTTATTtGTTgcaGGaGAGGCATCAACCTTTtGATTAGAAaTAG
TGTCTAAAACTGAATGAAGGAAAATATGTCTTTGTTAAAGATCCTTCAAA[A/G]CCTCAGGTGAGAATATATGAGGTTCCTACTGATGCATTTGAGAACGATTA
CTTGGCAGAGGACCAGGAATGTTGGAACGAGCTGCTGCTAATATCTGTGC[A/G]CGTTCAAAATGTAATCTATGTCTGGCCCTTTCAATCTGCTCTCGTTCTTT
AGTTCAGTGATGAAAGGCAGAACACTGAAGATTACAGCTTTGTCCATAAT[A/G]CCATGGTTCATCCAGATAATAGTGGAAGTTTTGGGTCATATCAGATTGGA
ACCATGGTTTTTGACTGCATTGCCATCTGCAGATTGTTCAAAAGGGGGTT[A/T]TGGTGCTTACACCAATAGTGTTGATTTCAAAGGATATGAGAATGGAGTAA
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
2_1668_01-newSnpIndex_257
CL263Contig2_03-newSnpIndex_331
2_4183_01-newSnpIndex_83
CL1758Contig1_04-oldSnpPosition_200
0_10754_01-newSnpIndex_144
0_444_01-newSnpIndex_159
2_10059_02-newSnpIndex_66
0_7793_01-oldSnpPosition_175
CL1213Contig1_01-oldSnpPosition_110
0_3073_01-newSnpIndex_247
2_89_01-oldSnpPosition_177
0_2354_01-oldSnpPosition_58
2_3941_01-newSnpIndex_78
2_4029_01-oldSnpPosition_209
2_3941_01-oldSnpPosition_289
CL4470Contig1_01-newSnpIndex_367
CL4481Contig1_04-oldSnpPosition_229
2_3941_01-oldSnpPosition_588
0_6878_01-oldSnpPosition_278
CL1767Contig1_02-oldSnpPosition_100
CL1045Contig1_03-oldSnpPosition_113
0_9408_01-oldSnpPosition_361
2_6351_01-oldSnpPosition_366
2_5724_02-oldSnpPosition_74
2_9455_01-oldSnpPosition_89
0_4054_02-oldSnpPosition_225
0_13957_02-oldSnpPosition_291
UMN_6393_01-newSnpIndex_185
0_9513_01-oldSnpPosition_251
2_8852_01-oldSnpPosition_289
0_9568_01-newSnpIndex_373
Pila_isogroup08223_368
0_9577_01-oldSnpPosition_303
0_8683_01-oldSnpPosition_419
0_9749_01-oldSnpPosition_306
CL4354Contig1_01-oldSnpPosition_76
0_13240_01-oldSnpPosition_294
CL1367Contig1_03-newSnpIndex_84
0_846_01-oldSnpPosition_213
UMN_3055_01-oldSnpPosition_135
0_13240_01-oldSnpPosition_139
CL4138Contig1_01-oldSnpPosition_138
E-value
3.8E-24
2.5E-94
4.8E-65
2.7E-95
1.1E-63
0.000024
1.1E-47
4.1E-35
1.7E-71
1.7E-30
6.6E-40
3.8E-52
0.00003
1.9E-52
0.00003
4E-58
2.8E-50
0.00003
7.3E-74
2E-60
9E-49
1.7E-43
6.9E-52
0.0015
6.5E-59
0.00001
4.9E-47
7.8E-34
7E-22
9.7E-39
3.3E-44
6E-20
3.7E-34
1.3E-82
1.4E-24
4.8E-97
8.9E-67
6.1E-84
1.5E-18
4.6E-41
8.9E-67
9.9E-82
Annotation [Species]
30S ribosomal protein S31, mitochondrial precursor, putative [Ricinus communis]
PREDICTED: uncharacterized RNA-binding protein C23E6.01c-like isoform 2 [Vitis vinifera]
cation:cation antiporter, putative [Ricinus communis]
ATMLO14 [Arabidopsis lyrata subsp. lyrata]
Peptidase M24 family protein. (Os04t0321600-01) [Oryza sativa Japonica Group]
embryo sac development arrest 6 protein [Arabidopsis thaliana]
PREDICTED: cell division topological specificity factor homolog, chloroplastic-like [Vitis vinifera]
PREDICTED: ABC transporter B family member 19-like [Glycine max]
tolB-related protein [Arabidopsis thaliana]
mitochondrial import inner membrane translocase subunit Tim17 [Arabidopsis thaliana]
PREDICTED: RING-H2 finger protein ATL72 [Vitis vinifera]
armadillo/beta-catenin repeat family protein [Arabidopsis lyrata subsp. lyrata]
B3 domain-containing protein [Medicago truncatula]
Kinase-like protein [Medicago truncatula]
B3 domain-containing protein [Medicago truncatula]
Isoflavone reductase-like protein [Medicago truncatula]
OB-fold nucleic acid binding domain-containing protein [Arabidopsis thaliana]
B3 domain-containing protein [Medicago truncatula]
PREDICTED: F-box protein ORE9-like [Glycine max]
PREDICTED: mitochondrial nicotinamide adenine dinucleotide transporter 1-like [Vitis vinifera]
WD-repeat protein, putative [Ricinus communis]
PREDICTED: transcription factor MYC2-like [Vitis vinifera]
DnaJ homolog subfamily C member 2 [Arabidopsis thaliana]
Homeodomain-related containing protein. (Os07t0568200-01) [Oryza sativa Japonica Group]
PREDICTED: putative pentatricopeptide repeat-containing protein At3g23330-like [Brachypodium distachyon]
Protein of unknown function DUF789 family protein. (Os01t0138500-01) [Oryza sativa Japonica Group]
receptor-like protein kinase HSL1-like [Glycine max]
PREDICTED: probable receptor-like protein kinase At2g42960 [Vitis vinifera]
PREDICTED: activating signal cointegrator 1 complex subunit 2-like [Glycine max]
PREDICTED: galactokinase [Vitis vinifera]
mitochondrial import inner membrane translocase subunit TIM14 precursor [Zea mays]
Disease resistance gene [Medicago truncatula]
Toll interleukin receptor [Medicago truncatula]
wall-associated kinase, putative [Ricinus communis]
receptor protein kinase, putative [Ricinus communis]
PREDICTED: serine/threonine-protein phosphatase PP2A-3 catalytic subunit [Vitis vinifera]
PREDICTED: L-aspartate oxidase 1-like [Vitis vinifera]
PREDICTED: monocopper oxidase-like protein SKU5-like [Glycine max]
PREDICTED: transcription factor RF2b [Glycine max]
PREDICTED: proline-rich receptor-like protein kinase PERK8 [Vitis vinifera]
PREDICTED: L-aspartate oxidase 1-like [Vitis vinifera]
cinnamoyl-CoA reductase, putative [Ricinus communis]
Classification
Control
Control
Control
Control
Control
Control
Control
Non-neutral
Non-neutral
Non-neutral
Control
Control
Control
Control
Control
Non-neutral
Control
Control
Non-neutral
Control
Control
Non-neutral
Control
Control
Control
Control
Control
Control
Control
Control
Non-neutral
Control
Control
Control
Control
Non-neutral
Non-neutral
Control
Control
Non-neutral
Non-neutral
Non-neutral
Reference
Kuromori et al. (2011)
Shaar-Moshe et al. (2015)
Van Aken et al. (2009)
Salekdeh et al . (2002)
Seki et al.(2002)
Abe et al. (1997)
Van Aken et al. (2009)
País et al . (2009)
Seki et al. (2002)
Seki et al.(2002)
Seki et al. (2002)
Srivastava et al . (2015)
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
2_1668_01-newSnpIndex_257
CL263Contig2_03-newSnpIndex_331
2_4183_01-newSnpIndex_83
CL1758Contig1_04-oldSnpPosition_200
0_10754_01-newSnpIndex_144
0_444_01-newSnpIndex_159
2_10059_02-newSnpIndex_66
0_7793_01-oldSnpPosition_175
CL1213Contig1_01-oldSnpPosition_110
0_3073_01-newSnpIndex_247
2_89_01-oldSnpPosition_177
0_2354_01-oldSnpPosition_58
2_3941_01-newSnpIndex_78
2_4029_01-oldSnpPosition_209
2_3941_01-oldSnpPosition_289
CL4470Contig1_01-newSnpIndex_367
CL4481Contig1_04-oldSnpPosition_229
2_3941_01-oldSnpPosition_588
0_6878_01-oldSnpPosition_278
CL1767Contig1_02-oldSnpPosition_100
CL1045Contig1_03-oldSnpPosition_113
0_9408_01-oldSnpPosition_361
2_6351_01-oldSnpPosition_366
2_5724_02-oldSnpPosition_74
2_9455_01-oldSnpPosition_89
0_4054_02-oldSnpPosition_225
0_13957_02-oldSnpPosition_291
UMN_6393_01-newSnpIndex_185
0_9513_01-oldSnpPosition_251
2_8852_01-oldSnpPosition_289
0_9568_01-newSnpIndex_373
Pila_isogroup08223_368
0_9577_01-oldSnpPosition_303
0_8683_01-oldSnpPosition_419
0_9749_01-oldSnpPosition_306
CL4354Contig1_01-oldSnpPosition_76
0_13240_01-oldSnpPosition_294
CL1367Contig1_03-newSnpIndex_84
0_846_01-oldSnpPosition_213
UMN_3055_01-oldSnpPosition_135
0_13240_01-oldSnpPosition_139
CL4138Contig1_01-oldSnpPosition_138
Probe sequence
GACGAACCATGAAACTCCCGTTGTATGCGGCCGTGGAGACAAGAAGACGA[A/G]GAAGGGCAAACGCTTCAAGGGCTCCTATGGCAATTCCAGGCCCAAAAAAG
AACTATACGTCTTTCTTGGGGTCGAAGCCCTGCAAACAAGCAGGTAAAAT[T/G]TGTACAAGTACTTAAACAATTATGTGCTAAGTRTACATTCTTTTRCTTCT
GTTATGAGTGTGTGTTGGATTTCATTTATAGCTGGAGAGCTGTTGGGTTG[T/C]TTAGCGGCRCTTGGTGTCATATTAAAGTTGTCACCAGCTTTATTGGGTCT
AAATGCATTTACTGTGGCTTTTGTCAAGAAGCTTGTCCCGTTGATGCTAT[T/C]GTTGAAGGGCCTAATTTTGAATTCGCCACAGAAACACATGAAGTGAGTTT
TTTATTGAAGACGGTGGYTGGGAATTCTTAAATATGGAAGCTAGTGATTC[T/C]GATTCAGAGGGTTCAGAGGAATCTGATCAAGGATACGAACCCTCAGATGT
CATAAAATAGCACAACAGCCTATGGACAACGCATGTCAAATTTGAACTGA[A/G]ATGTTTCTGTAAATCATCCATTAGAATCCACTCCAATCCAATCTAATCCC
CAGGAGCATGTTGCAATACACAAACAGAGATTCTTACAGTGTATGTCTAG[T/G]TTCCTCCTCAATGCTTTCCAAAGTGAATTGCAGAAAAATGCRTATMGAAT
GATGCAGAATCAGAGATTATTGTTCAAGAAGCTTTGGAGAGRTTGATGTG[T/C]GGAAGAACAACAGTGGTAGTTGCTCATCGTTTGTCAACAATTCGAAATGT
GGTTTTCAGATCAGGTCGTTCTGGGCACAAGAATTTGTACATTATGGATG[T/C]AGAACAGGGCGAGGAGGGMGGAATCCGTGCCCTTACHGAAGGCCCCTGGA
ACGGCTGGCAGACCGGKGACCAATCAGATGAACCCAAATCAGCAGCAAGG[T/C]GGGTCAACAATGGGTGAATTCTCAAAGGATAGCACCTCAGGTATGTCATC
GGCCTCAACTCGGTGCTCAAATGCGTGCGTTGCTACAGCAGACGAATGKC[A/T]GGGGATCCATCCGATGGCGTGGTTATCAGGTTCGCGGACACTGGATTGAA
TTCGAGACGGCTTTTGGCCTCTGGAAGAAGGCTCTCCAAA[T/C]GGGGATTCTGAATGAGAGAAACCTGCTTAGATGCCCATTCCAGCGCTGAC
TTTGACTTGTGTTTCTCATTTTCGTCATTGACCTTACCTGACTTTTTCAA[A/C]GCACTTTTCCCATCCTTCGCTTCTGAAGACGTCTCCTTTTCATTCACTGT
GAGCAGTGGAAGCCTGCCAACACGGATKCCGAGGACTGCTACGGTATTGA[T/C]CTTGATGTGCCCCTCTCCCAGGCGCTCAAGCGATGGCAGGCCGTTGAAGG
GATTTGAGGCCTCATGTTCCTGCAACTCCCTGTCAGAATCATCTGCTTCA[T/C]TCTGTAATTCCTCTGGAGGATTATCCGCTTCGTTCTGTAAATTTTCAGTG
AAGCATGCAGTTACATTTCAGCGCATTCCTTTGCCACCCTAAAATCAAAT[T/C]AATTACAGTATAGTCTAGCACAGATGTACAACTGATTACCAGTATCCCAC
AATTGGTCAATATTGTGGAATGATATTTTAGCTGAAGAAATATGCAGTGA[A/G]GAGGCCTGTGATGCCGAGCTGGAGTTGATTGGATTTGAATATAGTCAATT
AATAACTAGTGTTGMAATTTTGGGCATTCGCAAAAACTTGGCGAACGGCT[A/G]GCATAAAGCTTAAACCTCAAAAAGCTCGAAAATACAGAACCTTGAATCTC
TACTGGCCTCCACAGGATAAAGACATGAATCGGAGAGGCCTTTCACTTCC[T/C]GCTGCAGGTCTTCTTTCAGAGTGTGCAACTCTTCGGAAACTCTTTGTTCA
GGTTATTACAGCAGCTGGTGTAGTCCTCATCAGGTTTGTCGCACATCCCC[T/G]ATAAAATCCATTAATCCCCTCCCTACGGAATACCTTTTTAACACAATCAA
AATGTCATAGATGAGGGACCCACATTAAAATATGTGATCACCACGTAAGA[A/G]ATAGGAGTTGGTTCAGAGCAAATATGCAAATATTCAATAGAAACAAATCA
ACTTCAAAGTAGAGTTCAAGAGATTGAAGCTGAGAAAAAGGAGCTTCAAG[C/G]CCAAATAGAAGCTACCAAGAAGGAATCCTCGTCTTCTCACTCTGCTTTCT
ACTGTTCTTTTGCAGAAGCCTGATACTGCAAATTCATTTGATTCTTTCCT[T/C]GAAAGAAGGAAGGCTGCGAATCCAATTGCGTCACCTTTGACAACTAGAGA
GCAATTCTAGATGTTTTATCTCACTTTGAACTTTGAAGAAACCRACTTAG[A/C]AAAGAGAAACAGGAATTCCCCAGGCAAAATATCCTCTTAGCAGTTTCTAC
GCGGTGATTGCCATRGGGCCACCAAGTTTATCTCTAAGGTTGTGGGGCGA[A/G]AAATCATAATGAGGGATGCTAACCGCTTCCATCACTTTAAGGATGGCYTT
TATTGTTCAATGCAATCAGTAACCTCTAGATGAATGTTCATTATCTACCG[C/G]TAACTAATTAAAACAAGAACTTCCTTACAGGTACCCAATATACAGGATAC
GAACAAGAGCTAAGCAAGCGCAGAAGCTACAAAGTAGCAGTAAATACAGA[A/C]GCCGAAGAAGAAAAGTCCAGGCCAAATGCAATTACCATCATGCCTATACA
CCCAAAAGTTTCAAAGGAAATAAAAGAAGTAAAGGTTGATAGGAAAGGGA[A/C]TAACAATCCTCCCCAAGGAGATGAAATTCGCCTCATTAATCAGGGCAATT
TTCACAAAACTGGTAACAGTGCTTACGGTAGAGGAAAACGGAAGGAAGAG[A/C]AGAAACCACAATTCTATCTCAAAGATGGAAAAAATTATAGCTACAAASTG
GGGTGGTTGTGCAGTTGCTTTAGTGAAAGATAATATAGTCCCTTCTTTCA[T/G]CTTAAATTTAAAGGTGACTGCTGCTGCTAAATTTTTGAGAATGTTTTAGC
TTAAAATGCCATTTTCTCTTGTATTCTCAACTTTATGGTAAATTATATGC[A/G]TGCAGGGAACGAGTTGCTATGGAAAAGATTAAGGAGGCACACAGAAGAGT
TGCATCTCATGATGGAAAGAGGAAAAGTCTATGGAAGAAGCTTGAGGAAT[T/C]TAGTGTTCCATCATTCCAGAGGCAACAACCATGGTGGGTTTGGGCTTCAA
GAGGTGAGACGCCAGCCTAAGCCCGGTTGTCTCTCCACAATAGAGAGTAT[T/C]GTTTATGCATTGAAAATGCTTGAACCCGGAACCGAARGGTTGGATTCTCT
GAAAAGAATGATGAGGTGAAGGCCATGGTAAGTGCTGTTGCAGAATTGAT[T/C]TTCCGATGCCTGGCGTCAGAAGGGGATGACAGACCACACA
GGGCTAGTTAGCGAATTAGTGGACCCCCTGCTACTTGGTTCAGATTCACA[T/C]GGTATTCTTCTTCCAGGCCTTGAAACCTTTGTGAACCTCGCGTTGAAGTG
TCCATTGACACATTAGATAACATAAGGAATTTTGACCGTRTTCAAGAAGT[A/G]CCTCATGAAGGACCCATGTGTGACCTTTTGTGGTCTGATCCAGATGATAG
TCAAATATTGACTTTGATGAGTCAGTTAAATGGCCTTTCCCTGTTGTACC[T/C]ACTGTGCTTGGGGTTTCACAACTCAATGAAGTAAAGCACATTACAGCATT
CAGGTATATTCACAAACTTAACAATGTTCCCTTTTTCTGCTGTACAAGTC[A/G]AGGGTTTAGATGAAATACACTCATGCTGATTTATTTTAATCGGGGTAACA
TTTGATGAAGAATCAGAAACATGATCAGGCTTTTGTTCCATCATCTGTGG[C/G]GATGAATTGTGCTCAAGCTTGCCAAACTGCTGCTGTTGCAAGTCATATGA
TTGAATACCATCTGCATGGTAGGAAACAATTCTTGGAAATCTAGTTAGAG[T/C]TTCTGAATGCTGATTTTTTTGCACCACTACTTCTTGAGCACACTTCCTTA
TATTGATTGTCTTAAAATAGCTGAGAAGTCTTTGGCAGATTTAGAACTTG[A/T]GTGGGAAGACCATCTATTTCGATTTCGGTGGAGGCCATACATGGTAAATC
TCTKTAGTTCTCCCTAGAAATGAATTTGATTGGACTATTTTGGTAATGGT[A/G]CCAAATGGTTGATAAGCACATGACTTGATTTGTGTAGATTTGGTATCCTG
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
2_4976_01-newSnpIndex_280
CL1848Contig1_01-oldSnpPosition_236
CL2172Contig1_09-oldSnpPosition_193
2_6355_02-oldSnpPosition_185
CL1879Contig1_02-oldSnpPosition_160
2_6491_01-oldSnpPosition_387
2_8443_01-oldSnpPosition_79
0_12588_01-newSnpIndex_328
CL1148Contig1_07-newSnpIndex_141
0_3128_02-oldSnpPosition_152
CL376Contig1_05-newSnpIndex_211
2_5724_02-oldSnpPosition_276
UMN_2174_01-oldSnpPosition_201
0_9389_01-newSnpIndex_228
2_9480_01-oldSnpPosition_77
CL1148Contig1_08-oldSnpPosition_232
UMN_689_01-oldSnpPosition_185
0_11270_01-oldSnpPosition_385
CL4138Contig1_01-oldSnpPosition_185
2_1160_01-newSnpIndex_233
0_3073_01-newSnpIndex_341
0_8111_01-oldSnpPosition_73
2_4892_01-oldSnpPosition_166
UMN_4748_01-newSnpIndex_160
0_13237_01-oldSnpPosition_84
2_8253_01-oldSnpPosition_141
Pila_isogroup00414_2430
CL1758Contig1_04-oldSnpPosition_118
2_7182_01-newSnpIndex_102
UMN_915_01-oldSnpPosition_115
CL730Contig1_04-newSnpIndex_51
2_10059_02-newSnpIndex_108
2_8443_01-oldSnpPosition_393
0_13237_01-oldSnpPosition_205
CL3097Contig1_01-newSnpIndex_192
CL1455Contig1_06-newSnpIndex_192
0_11772_01-newSnpIndex_230
CL4470Contig1_01-newSnpIndex_112
0_6683_01-oldSnpPosition_141
2_6906_01-oldSnpPosition_319
Pila_isogroup17105_203
CL1888Contig1_03-oldSnpPosition_137
E-value
2E-77
5.1E-48
8.4E-214
6.3E-31
2.3E-19
1.2E-12
2.9E-97
8.8E-11
3.3E-159
2.3E-18
3.8E-74
0.0015
4.7E-19
2.5E-24
8.9E-56
3.3E-159
3.1E-33
5.3E-29
9.9E-82
2.9E-88
1.7E-30
2.2E-34
5.7E-81
3.1E-87
3.5E-110
4.6E-27
2.9E-93
2.7E-95
1.7E-33
9.7E-29
7.4E-109
1.1E-47
2.9E-97
3.5E-110
0.12
3.8E-107
1.4E-107
4E-58
1.5E-17
5E-10
3.5E-31
1.4E-82
Annotation [Species]
PREDICTED: 26S proteasome non-ATPase regulatory subunit 11 isoform 1 [Vitis vinifera]
PREDICTED: DNA repair helicase XPB1-like [Vitis vinifera]
actin 7 [Populus trichocarpa]
PREDICTED: protein-tyrosine phosphatase mitochondrial 1-like protein-like [Glycine max]
PREDICTED: WPP domain-interacting protein 2-like [Vitis vinifera]
Coiled-coil domain-containing protein, putative [Ricinus communis]
EXTL2, alpha-1,4-N-acetylhexosaminyltransferase domain containing protein. (Os05t0540000-01) [Oryza sativa Japonica Group]
Similar to Disease resistance protein ADR1 (Activated disease resistance protein 1). (Os12t0586000-01) [Oryza sativa Japonica Group]
PREDICTED: malate dehydrogenase, glyoxysomal [Vitis vinifera]
f-box family protein [Populus trichocarpa]
Protein of unknown function DUF640 domain containing protein. (Os10t0478000-01) [Oryza sativa Japonica Group]
Homeodomain-related containing protein. (Os07t0568200-01) [Oryza sativa Japonica Group]
Protein of unknown function DUF604 family protein. (Os04t0578800-01) [Oryza sativa Japonica Group]
Alba, DNA/RNA-binding protein family protein. (Os06t0602600-01) [Oryza sativa Japonica Group]
PREDICTED: malate dehydrogenase, chloroplastic-like [Vitis vinifera]
PREDICTED: malate dehydrogenase, glyoxysomal [Vitis vinifera]
Similar to SUB1; calcium ion binding. (Os07t0633600-01) [Oryza sativa Japonica Group]
PREDICTED: probably inactive leucine-rich repeat receptor-like protein kinase At3g28040-like [Vitis vinifera]
cinnamoyl-CoA reductase, putative [Ricinus communis]
PREDICTED: 6-phosphogluconate dehydrogenase, decarboxylating-like [Glycine max]
mitochondrial import inner membrane translocase subunit Tim17 [Arabidopsis thaliana]
3-hydroxyisobutyrate dehydrogenase, putative [Ricinus communis]
ccaat-binding transcription factor, putative [Ricinus communis]
peptide transporter, putative [Ricinus communis]
PREDICTED: cyclic nucleotide-gated ion channel 4-like [Glycine max]
PREDICTED: protease Do-like 7-like [Vitis vinifera]
PREDICTED: probable disease resistance protein At4g33300-like [Vitis vinifera]
ATMLO14 [Arabidopsis lyrata subsp. lyrata]
PREDICTED: U-box domain-containing protein 4 [Vitis vinifera]
PREDICTED: U-box domain-containing protein 43-like [Brachypodium distachyon]
PREDICTED: peptide transporter PTR3-A-like [Glycine max]
PREDICTED: cell division topological specificity factor homolog, chloroplastic-like [Vitis vinifera]
EXTL2, alpha-1,4-N-acetylhexosaminyltransferase domain containing protein. (Os05t0540000-01) [Oryza sativa Japonica Group]
PREDICTED: cyclic nucleotide-gated ion channel 4-like [Glycine max]
PREDICTED: glucosidase 2 subunit beta-like [Vitis vinifera]
protein binding protein, putative [Ricinus communis]
PREDICTED: probable tRNA threonylcarbamoyladenosine biosynthesis protein osgep-like [Glycine max]
Isoflavone reductase-like protein [Medicago truncatula]
Zinc finger CCCH domain-containing protein [Medicago truncatula]
PREDICTED: probable protein phosphatase 2C 25-like [Glycine max]
chitinase, putative [Ricinus communis]
PREDICTED: ATP-dependent Clp protease proteolytic subunit 4, chloroplastic-like [Glycine max]
Classification
Control
Control
Control
Control
Control
Control
Control
Control
Non-neutral
Non-neutral
Control
Control
Control
Control
Non-neutral
Non-neutral
Non-neutral
Control
Non-neutral
Non-neutral
Non-neutral
Control
Control
Control
Non-neutral
Control
Control
Control
Non-neutral
Non-neutral
Control
Control
Control
Non-neutral
Non-neutral
Control
Control
Non-neutral
Non-neutral
Control
Non-neutral
Control
Reference
Seki et al.(2002)
Seki et al.(2002)
Seki et al.(2002)
Seki et al.(2002)
Syed et al. (2015)
Srivastava et al . (2015)
Hou et al. (2007)
Van Aken et al. (2009)
Mach (2012)
Yee and Goring (2009)
Yee and Goring (2009)
Mach (2012)
Xu et al. (2012)
Salekdeh et al . (2002)
Peng et al . (2012)
Lee et al. (2008)
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
2_4976_01-newSnpIndex_280
CL1848Contig1_01-oldSnpPosition_236
CL2172Contig1_09-oldSnpPosition_193
2_6355_02-oldSnpPosition_185
CL1879Contig1_02-oldSnpPosition_160
2_6491_01-oldSnpPosition_387
2_8443_01-oldSnpPosition_79
0_12588_01-newSnpIndex_328
CL1148Contig1_07-newSnpIndex_141
0_3128_02-oldSnpPosition_152
CL376Contig1_05-newSnpIndex_211
2_5724_02-oldSnpPosition_276
UMN_2174_01-oldSnpPosition_201
0_9389_01-newSnpIndex_228
2_9480_01-oldSnpPosition_77
CL1148Contig1_08-oldSnpPosition_232
UMN_689_01-oldSnpPosition_185
0_11270_01-oldSnpPosition_385
CL4138Contig1_01-oldSnpPosition_185
2_1160_01-newSnpIndex_233
0_3073_01-newSnpIndex_341
0_8111_01-oldSnpPosition_73
2_4892_01-oldSnpPosition_166
UMN_4748_01-newSnpIndex_160
0_13237_01-oldSnpPosition_84
2_8253_01-oldSnpPosition_141
Pila_isogroup00414_2430
CL1758Contig1_04-oldSnpPosition_118
2_7182_01-newSnpIndex_102
UMN_915_01-oldSnpPosition_115
CL730Contig1_04-newSnpIndex_51
2_10059_02-newSnpIndex_108
2_8443_01-oldSnpPosition_393
0_13237_01-oldSnpPosition_205
CL3097Contig1_01-newSnpIndex_192
CL1455Contig1_06-newSnpIndex_192
0_11772_01-newSnpIndex_230
CL4470Contig1_01-newSnpIndex_112
0_6683_01-oldSnpPosition_141
2_6906_01-oldSnpPosition_319
Pila_isogroup17105_203
CL1888Contig1_03-oldSnpPosition_137
Probe sequence
GARCCTTTTTCAAGGGTTGAAATATTGCATATAGCAGAGTTGATTGGATT[A/G]CCCGTGGATACTGTGGAAAATAAGCTGTCTCAGATGATTTTGGAGCGAAA
ACACCCTGGAGGATCAATTGGCACTTCTCACCAAGGTAACTATTTAGTTG[A/C]AAATTAGTTCTATGACAGAAAATTGGAACATCATCACTAGATCTAATATG
AGAGGTATTCTTACTTTGAAGTATCCTATTGAGCACGGAATTGTTACCAA[T/C]TGGGATGATATGGAAAAGATTTGGCATCATACCTTTTACAATGAGCTACG
ATTTGCACTACTTCTGTTTCTGCTTGGAAGCTTATTCTGAATACCAGATG[A/G]CATTGGGTGTATAGCAATGGAGTTCATCACTACACRACACATCTTGCAAC
TTGTACTAAATGGTCCTTTAACGAAAGAGCATGGCATTCAGTTTCTTTTA[T/G]CTTTAAAGCAGTTTGCAGTTGTCCAACGACTAGCCTTTTTTGTTCCTGAA
GCCTTTCTTTCTGATTCAACATGCTGCGAAGAAGGCGTAACTGTAACTTC[T/C]GTTTTATCAGAATTTGCCCCAAATGCAACATTCTTTTTGAGAAGGTTACG
CAGGGGCTGCATTCATGGATAGCCAGTCAGCATTTCAGAAGTACTTTAGC[A/G]ATGAAGCAAAAGAGGGGAGAGATATTGTTGACAAGTACTTCAACTGTGAA
TGATTGAACTTGGTTTTCCAAGCTTTGGAATAAGTTCATCATGCTCTTCT[A/G]AAACTACACTGATCATGTATTTAAGGGTAAGACCCTTCATAACCTCACCA
GGKATGACTAGGGACGATTTGTTCAATATAAATGCGGGAATCGTCCGCAC[A/C]CTGTGCGAAGGGGTAGCCAAGTGCTGTCCCAACGCAATTGTGAATATTAT
GGTCAGGGTGTATCTATCTACACATCCAGACCTATTTCAACTGAGTCAGC[A/G]CCACAATGGGATTTCCTGACTAGGGTAGGAGGATCCTTCGTCTTTAATTG
TACGAGGAGCACGGTGGGAAGCCGGAATCGAACCCTTTCGGTGCCCGGGC[T/G]GTTCGGCTCTATCTCAGGGAAGTTAGGGATCTCCAGTCCAAGGCCCGGGG
TCTTTAACAGGAYCCGTAGGAAGAGCATCTATGCTGAAGGGATGCAATGG[A/G]TATGACACTCAAATATGCTCGAAATCYCCAAATTGAYGTCAAGTSGCTGA
GCAGTTCTGGTATCAGGGGACAACGTTTTGCGAAAGCTTCATTCAGTGGA[A/C]ACCAGTGAGACGAGCTTGGAGCATATTGTTTTCGGRATTGCAGCTTCGGC
ACATATTTTTTAGACATGGTTATGTTGATGTAAATTCTATTAGTTTATGG[A/T]CTTGTTTCATAAATTTATCGTTTTGAGCAAAATTTTATGATTCTTTCAGA
AAGGCAAGCATTGAAAAGGGCATTGCTTTTGCAAACAAGTAAGCACCAGT[T/G]GGTAGTGCCGTTTGAAGGCATTCCATTTAACTTGAATTTTAGGACAAATA
TTCTAGGTGCGTGGATTTGTGGGCAAAGAGCAGCTGGAAGCAGCGTTGGT[A/G]GGAATGGATCTCGTGATCATCCCTGCCGGAATTCCACGGAAACCCGGKAT
TCTGTGGAGTTTTCTGTGTGCATTGGGTGAGGCTCGGTACTTGAATAGGA[T/C]TTTTGTAATGGAATTGGATGTTTGTTTGTCTGGGTCTAATAATCCGGGAC
TGGAGGATGATGTTGTGATCCTATGTGACAATGTGCGGTC[A/G]TTACTAGATGAAGGAAAGGCACTGACTTGTGTGGATTCGAGTTTATCTGA
GTTGGACTGATCTTGATTACTGCAAAGAAAATGGGGTGATAATTTGTTCT[T/G]TAGTTCTCCCTAGAAATGAATTTGATTGGACTATTTTGGTAATGGTRCCA
ATTATCAGGGCAGTTTTCTTGAATCGGATCAAGAGGGCCTATGAGCGAAA[T/C]CCGCAGCTTCCGAGTCTCTTGGTCGATCCGGAGTTTGCGAGAGAGATGGT
TGTCATCTGAGYTTGTTGGGCATGAAGAAAGAGGTGATCATAATGGGGCT[A/T]TTTTCTCTGGGTGGTTTGGGAAGAAGAAAACACAGGAACCCAAGARCGAG
TTGTCATGCCTTAATCACTGCCATCGAGAGGCTTAGTAACCATTCTTTGC[T/C]GTCACAACCGCCCTCAATCTGACATTGTAACWATAAATCCCTGCACTGCA
AAGAATGACATTGCAGCTGCCATAACTAGAACAGATATCTTTGATTTCCT[T/C]GTGGATATTGTACCAAGAGATGAGTTGAAGGAGGAGGGTCTCGGCATTCC
TACCCATGAGTATTTTTTGGCAAGTTCCCCAGTATTTCTTAGTAGGTGCT[T/G]CTGAAATTTTCACCTTCATAGGGCAACTAGAGTTCTTTTATGATCAAGCA
GCTGGGTCCGGGGAATTTCTGTGGGGATGAATTGCTGTCATGGTGTGTTC[C/G]GAGGCCATTTGTAGAGCGGCTGCCCACTTCGTCTTCGACATTCGTGAGCA
TAGTGATTTAAGGTGCTGAGAGTTTGTGTAGTGCTTTGGTGGTGTCTATA[A/C]CATGCCTACACTCWTGTCAGGCAATTAACCATGTAATATAAGAGTGAATC
CAAATGTCCAGTAATGCATCTGCCGAGGTTTTTTGATCCTCTGGAAATGA[T/C]CCCAAGTCTAAGAAGCATTCTCGTGCCTCCTCATCCAGGACATCAATACT
AAACACATGAAGTGAGTTTCTGAAATAGTTCTTTCCCAACGACCTGTTTT[T/G]CTCTTTTTCGTTTATTGTTTGGGGTATACGCAATGATGGTTTTTTTTCAA
GCCCAGAAAGAAGCCGTCTGCGAGCTCCGGCTGCTGGCCAAATGGGGCGA[T/C]GAGCACCGCATTTCGATAGCTCAAGCGGGCGCAGTGCCCTATCTTCTTGA
TGCCTTTTGGAAGCAAAAGCAGTAACTAAGTTGGTCGCATGCCTAGATCA[T/C]GAAAATGTACTGGTGGTTGAATCATCTCTTGCAGCAATATGTACTCTTGT
CTATCAATGCTAATAACAACGGTGGTCTATGACCGAATATTAGTCCCCAT[A/C]TTCCGAAGATTCACAGGAAATCCCAARGGCATAACATCTCTGCARAGAAT
ATGTCTAGKTTCCTCCTCAATGCTTTCCAAAGTGAATTGCAGAAAAATGC[A/G]TATMGAATCTTAGAGATTACAGATTACTATTGAAAAGCATCACAACCTGC
TGTTATTTGGAATAAGGGCCAGCCTCCAAACCCCAATGACTTTGATTCAA[C/G]TGTACCAGTCCGTATAAGAGTTGAAAAGAAAAATTCTTTAAACAACCGTT
GCTCTGGAGGCGCAGGAGCTGAAGTACGTGACGCAGCACTTCCGGTACAC[A/G]TTTCTGAGCGAGAAGCTGAAGGGAACAGCGAGGTATTACTCTCCCGGGTG
ACTGCAATAATYGATGCAAGAACAATGATAGAAATCTCACCTGGAGAGTA[T/C]TAGGGCCCTTTTCTCTGCCTCTATTAATGACTTAGCTTTGGACAAGSATT
CAGTGCGTATTGCCTCAGGATCYCTGCCAAAAAGTCTTCATGTATTGGAT[T/C]TATCTAGAAACAAAATTACTGCGATTGAAGGGCTTAGGGAACTATGTCGG
TCTGCGGTGGTCGTCAGGATGCTTTCCCARCTCTGGAAGAAGCCCATCGT[C/G]GGAGTCAATCACTGCGTCGCCCATATWGAGATGGGCAGGRTCGTCACTGC
GGTGAGGCGAGTAATAGAGGCAGCCAATATTCCATACACTTACATCTCAG[T/C]GAACTGCTTTGCTAGAATCTTTTTAGGTGGACTTGGACAGTTTGGCCAAG
CACCAAGACAGGCGAAGTTACAGTTCACGGGACTTGGGTGCCCATTTACT[A/G]CCTRCTAGTTCAGACTGGGGCTCGCCAACTGGTAAATTGGACTGGGGAGT
GAGAGGCAGTCTAATTTGAAACCAGTAGGAGCTGGCCCTATAGATGCTTG[T/C]AAAAAGCTTGTAGAGCTTGCTGTAACCAGAAAATCTCAAGATGATGTCAG
GAGAACTCTGGCATATATGCCCAATTCCCCTTCCACTCCACACCCAAAGA[T/G]AAGACTtGATACCAGCAGAATATCAATTtCCAGAGAGAAGTTGAAGCTGA
ATTATGTATCATAAGAGCAATGTGACCAGAATAATATCTGAGAGAACAGG[A/G]CGTACAACTGAGCAGGTTGACAAAGATATGGACAGGGATCGCTACATGTC
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
2_2937_01-oldSnpPosition_185
CL4432Contig1_04-oldSnpPosition_297
0_11772_01-oldSnpPosition_112
CL1400Contig1_02-newSnpIndex_152
0_13552_02-oldSnpPosition_86
UMN_2001_01-newSnpIndex_329
UMN_1089_02-oldSnpPosition_209
0_11649_03-newSnpIndex_193
0_13929_02-oldSnpPosition_132
CL544Contig1_03-oldSnpPosition_99
CL1767Contig1_02-oldSnpPosition_256
2_8443_01-oldSnpPosition_272
0_4054_02-oldSnpPosition_65
UMN_2001_01-newSnpIndex_244
2_4723_01-newSnpIndex_313
0_4543_02-oldSnpPosition_254
0_12156_02-oldSnpPosition_294
2_9466_01-oldSnpPosition_333
0_4105_01-oldSnpPosition_187
CL91Contig1_01-oldSnpPosition_174
0_3073_01-oldSnpPosition_141
UMN_2001_01-newSnpIndex_432
2_1850_01-newSnpIndex_78
2_6596_01-newSnpIndex_128
0_4032_02-oldSnpPosition_325
CL635Contig1_01-newSnpIndex_70
CL2332Contig1_01-newSnpIndex_108
0_18470_01-oldSnpPosition_370
2_6731_01-oldSnpPosition_98
0_6683_01-oldSnpPosition_137
CL3116Contig1_03-oldSnpPosition_83
CL1061Contig1_03-oldSnpPosition_193
0_2433_01-oldSnpPosition_78
CL4023Contig1_01-oldSnpPosition_153
Pila_comp1359_c0_3133
0_9577_01-oldSnpPosition_266
2_9466_01-oldSnpPosition_234
UMN_2174_01-oldSnpPosition_63
0_17247_02-oldSnpPosition_91
CL1966Contig1_05-oldSnpPosition_178
CL1524Contig1_03-oldSnpPosition_207
0_10267_01-oldSnpPosition_345
E-value
3.6E-22
2.8E-96
1.4E-107
5.2E-51
2.4E-26
3.8E-103
0.000000002
2.8E-127
6.2E-43
2.8E-121
2E-60
2.9E-97
0.00001
3.8E-103
3.9E-51
1.1E-67
2.2E-78
5E-24
1.7E-15
3.1E-61
1.7E-30
3.8E-103
1E-26
7.7E-38
1.4E-71
2.1E-19
2.9E-92
0.00005
2.8E-22
1.5E-17
2E-102
8.1E-38
1.5E-21
2.3E-86
9.2E-188
3.7E-34
5E-24
4.7E-19
3.8E-56
1.8E-85
5.4E-113
6.8E-73
Annotation [Species]
PREDICTED: ADP, ATP carrier protein 1, chloroplastic-like [Brachypodium distachyon]
PREDICTED: serine/threonine-protein kinase AFC1 [Vitis vinifera]
PREDICTED: probable tRNA threonylcarbamoyladenosine biosynthesis protein osgep-like [Glycine max]
30S ribosomal protein S5, putative [Ricinus communis]
electron transporter, putative [Ricinus communis]
Pre-mRNA-processing-splicing factor [Medicago truncatula]
PREDICTED: abhydrolase domain-containing protein FAM108C1-like [Glycine max]
tubulin, beta chain [Populus trichocarpa]
PREDICTED: protein BASIC PENTACYSTEINE6 [Vitis vinifera]
PREDICTED: caffeoyl-CoA O-methyltransferase [Vitis vinifera]
PREDICTED: mitochondrial nicotinamide adenine dinucleotide transporter 1-like [Vitis vinifera]
EXTL2, alpha-1,4-N-acetylhexosaminyltransferase domain containing protein. (Os05t0540000-01) [Oryza sativa Japonica Group]
Protein of unknown function DUF789 family protein. (Os01t0138500-01) [Oryza sativa Japonica Group]
Pre-mRNA-processing-splicing factor [Medicago truncatula]
PREDICTED: coatomer subunit gamma-2-like [Vitis vinifera]
PREDICTED: probable cyclic nucleotide-gated ion channel 17-like [Vitis vinifera]
PREDICTED: ADP-ribosylation factor GTPase-activating protein AGD3-like [Glycine max]
peptidase M50-like protein [Arabidopsis thaliana]
PREDICTED: MORN repeat-containing protein 1-like [Vitis vinifera]
PREDICTED: GDP-mannose 3,5-epimerase 1 [Vitis vinifera]
mitochondrial import inner membrane translocase subunit Tim17 [Arabidopsis thaliana]
Pre-mRNA-processing-splicing factor [Medicago truncatula]
PREDICTED: G-type lectin S-receptor-like serine/threonine-protein kinase At2g19130-like [Glycine max]
Erythronate-4-phosphate dehydrogenase-like protein [Arabidopsis thaliana]
ubiquitin-protein ligase, PUB17 [Selaginella moellendorffii]
Spastin [Medicago truncatula]
PREDICTED: calcium-dependent protein kinase 3-like isoform 1 [Glycine max]
Protein of unknown function [Oryza sativa Japonica Group]
PREDICTED: F-box protein GID2-like [Vitis vinifera]
Zinc finger CCCH domain-containing protein [Medicago truncatula]
GTP-binding nuclear protein Ran-A1 [Medicago truncatula]
glutathione-s-transferase theta, gst, putative [Ricinus communis]
protein histidine triad nucleotide-binding 4 [Arabidopsis thaliana]
PREDICTED: tryptophan synthase beta chain 2, chloroplastic [Vitis vinifera]
PREDICTED: probable LRR receptor-like serine/threonine-protein kinase At5g45840-like [Vitis vinifera]
Toll interleukin receptor [Medicago truncatula]
peptidase M50-like protein [Arabidopsis thaliana]
Protein of unknown function DUF604 family protein. (Os04t0578800-01) [Oryza sativa Japonica Group]
PREDICTED: CLIP-associating protein-like [Vitis vinifera]
PREDICTED: nascent polypeptide-associated complex subunit alpha-like [Vitis vinifera]
PREDICTED: histidinol dehydrogenase, chloroplastic-like [Vitis vinifera]
R2R3-MYB transcription factor [Medicago truncatula]
Classification
Control
Control
Control
Control
Control
Control
Control
Control
Control
Non-neutral
Control
Control
Control
Control
Control
Non-neutral
Control
Control
Control
Non-neutral
Non-neutral
Control
Non-neutral
Control
Non-neutral
Control
Non-neutral
Control
Non-neutral
Non-neutral
Non-neutral
Non-neutral
Control
Control
Control
Control
Control
Control
Control
Control
Control
Non-neutral
Reference
Giordano et al. (2016)
Mach (2012)
Ma et al. (2014)
Van Aken et al. (2009)
Sun et al. (2013)
Seki et al.(2002)
Hettenhausen et al. (2016)
Seki et al.(2002)
Peng et al. (2012)
Yang et al. (2014)
Rezaei et al. (2013)
Abe et al. (1997)
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
2_2937_01-oldSnpPosition_185
CL4432Contig1_04-oldSnpPosition_297
0_11772_01-oldSnpPosition_112
CL1400Contig1_02-newSnpIndex_152
0_13552_02-oldSnpPosition_86
UMN_2001_01-newSnpIndex_329
UMN_1089_02-oldSnpPosition_209
0_11649_03-newSnpIndex_193
0_13929_02-oldSnpPosition_132
CL544Contig1_03-oldSnpPosition_99
CL1767Contig1_02-oldSnpPosition_256
2_8443_01-oldSnpPosition_272
0_4054_02-oldSnpPosition_65
UMN_2001_01-newSnpIndex_244
2_4723_01-newSnpIndex_313
0_4543_02-oldSnpPosition_254
0_12156_02-oldSnpPosition_294
2_9466_01-oldSnpPosition_333
0_4105_01-oldSnpPosition_187
CL91Contig1_01-oldSnpPosition_174
0_3073_01-oldSnpPosition_141
UMN_2001_01-newSnpIndex_432
2_1850_01-newSnpIndex_78
2_6596_01-newSnpIndex_128
0_4032_02-oldSnpPosition_325
CL635Contig1_01-newSnpIndex_70
CL2332Contig1_01-newSnpIndex_108
0_18470_01-oldSnpPosition_370
2_6731_01-oldSnpPosition_98
0_6683_01-oldSnpPosition_137
CL3116Contig1_03-oldSnpPosition_83
CL1061Contig1_03-oldSnpPosition_193
0_2433_01-oldSnpPosition_78
CL4023Contig1_01-oldSnpPosition_153
Pila_comp1359_c0_3133
0_9577_01-oldSnpPosition_266
2_9466_01-oldSnpPosition_234
UMN_2174_01-oldSnpPosition_63
0_17247_02-oldSnpPosition_91
CL1966Contig1_05-oldSnpPosition_178
CL1524Contig1_03-oldSnpPosition_207
0_10267_01-oldSnpPosition_345
Probe sequence
ATGATAAGGGATTCATAGAAGGTAAGTATGAACCCTTTGTGGAGGATAGT[A/G]CCCCTTCAATTGACGAACAGCAGCAGCAACAACAGCAGGGGGAGGAGGTT
AGTTACCCCGACTACGGGTAGGGTTATTGTTTGTTTCTTTTAATGTTGTG[T/C]GATGCTCTTCTTAGGTAAGCATTGTATATGCATGTGAGCTAATTATTCWG
ATWGAGATGGGCAGGRTCGTCACTGCAGCCCATGACCCAGTCGTTTTGTA[T/C]GTTAGCGGAGGGAACACGCAGGTGATAGCTTAYAGTGAAGGGAGGTACAG
GCTAGGGCAGTTATTGATGCTGTTTTGCAAATGAGGCAGTTCCGTGAAGT[T/C]GCAGCGTACCGTGGTATCCCAATGGAGGAGCTATGGAAATGAGAGRAGAT
TGCGATGGTTGCGGTGACGTGAGGTTCATTCCTTGCCAAAACTGCGATGG[T/C]AGCCGCAAGATTTTTACAGAAGAGGAAGGTCAGGGCCTTTTCATCAGGTG
GGAAAGCGTGCTTAATGGTAAGGAATTTCGTTAAATACTTATTTTCCTTG[T/C]CATGGTTTATCAGGACTTAACATGCCATGCTCGAATCTTGGAGAATAATA
GTACAGATCACTTTGAGAAAGCAAGGGCTAGCATTGATCGTGGGGAAAGG[A/C]CATGACAAGCTGGGACTGGGAGAGCCATGAATATAGTCATACTTAAATTT
TTGGAGAGGATAAATGTGTACTACAATGAGGCCAGCTGTGGAAGATTTGT[T/C]CCCCGGGCAGTGCTCATGGATCTCGAACCCGGAACCATGGACAGTGTGAG
TTTTTACATCACTCTCCAGGAATTAGCACATACATGTGTTGAATAGCTAC[A/G]CGATCTGTATAGTACTTTCCTCTACTGGATTCTAATGTACCGATTGGTGC
CCTGRTGGATTGGAATTAATTGKGGRTTAATGTTTGGGATGACAGATTCT[A/G]GCCATGGACATCAACAGAGAGAACTATGATATCGGACTGCCCATTATTAA
CGAGCGCACAACCTGTTAAAAATTACGGTCCCCATAAATAACAGGTCTTT[A/C]TCCACAACAATCTTAAAAGTGCAGAGTATAAAGAGTTATACACTAGATAG
AAGACAAGAGCCGTACTTGAATTGGATGATGATATAATGATGACATGCAA[T/C]GATGTTGAAAGAGGGTTCAAAGCATGGCGTGAACATCCTGACAGACTTGT
TGCCAAGGACTTTCCACAGCTGAAAACCTTAAGAAGCATTGATCTGTTG[A/C]CAACAAGTTGGCTATCGGTTGCATGGTATGCCATCAATTATACTTGTGCA
CCCAACGAGCTTCCTCAATTATCACCTCAGGTTTGTTGTTTGATGTTTAA[T/C]TATTAGGGTAAAATARGAATGCCTTAATAGCTAAGGAAAGCGTGCTTAAT
CCTGTCAACAATCAAAAAATGCATCAAATACCAACCATTAGCATTACAGA[T/C]TGCAAGATGCCAATATCTAGAAGATGGGCACTCATKCCTGAATCTTACCT
GCAAATCAGTTCAGGCGTTTGCACAGCAAGAAGCTTCAACATACATTTCG[A/T]TTCTATTCTCACCAATGGAGGACATGGTCAGCCTGTTTTATACAAGCAGC
GTTCGACAACCCAATGCCCATTTATTAGTTTATGACCTCATTTCCAATGG[C/G]AGCCTTGCAGACGCTCTGAAGAAAATCAAGGATAACCAGCTGCAGCTGAG
GTTGAACAGGGCATTATGTCTTCTGGTATTGCATTGGTTTTTTTCCTTGG[C/G]ATTTTCCTGATTGTTCGTGATACTCTGAATCTTGATTTTGTTCAAGAAAT
GAAAACTGGTTTTACCCTATCTTATGAAAATGCCTGTAATAAGCAGACAT[A/C]TTTTCTTGTTTATGGGGAAGTATGCTGCATCAAAGTTAACAACCTGAACT
TACGTGGTCGGAATTCTGATAATGCATTGATCAAGGAAAAGCTAGGATGG[T/G]CACCGACCATGAAGCTGAAGGTAAGGTTCCATACCTTCTTCAGGAGTKAT
CAACAATGGGTGAATTCTCAAAGGATAGCACCTCAGGTATGTCATCTGAG[T/C]TTGTTGGGCATGAAGAAAGAGGTGATCATAATGGGGCTWTTTTCTCTGGG
CAGTGGGATGGAGAGAAGTGTATCATTCTTACATGCAGTTTCACTCCCGG[T/C]TCCTGCTCCTTAACTGCATATAAGCTTACTCCAACAGGTTATGAATGGGG
GGGCGAAGAAACATGGACGGGGACGAGGAATCCAGCGAGATGTTCTTTCC[A/C]GCATGGGCTGCAACTCAGATAAGCAGCGGAAACGCCATGGAGGTTCTTGA
ACCACCATAGGACCGTGGGTGTCGCGCTGGAGATTAATGGAGCCAGGATC[T/C]CGCCAGCGGAATCAGTGTCCCTGACCCTACGCAGGGACAGGGTCGACAAG
CCAGTCATTGTTTCTACCGGGCAAACATATGATCTATCATCCATTACCAG[A/G]TGGTTTGATGAGGGACACTCGACTTGTCCGAAGAATGGGCAGAAGCTTTT
AACTGAAAAAATCTATGTAAGTAGGCAGCTTATTTTCAAATTGAAGAATG[T/C]TGGAGCAGGAAAAGAGTGGCCAGCTAACCTCTGAGATACCAAGACCCTTA
CATATTATAAAGGACTGTTGTTAGATGCTAAAGAGCCCAAATTTGGTGGA[A/G]AATGGGTTTATATTTGATTTCTAATGGGATCATCATACTTTTTCATTCTT
AAGAGCTCGAGTTCGAAGAGGACGACGAAGAGGAGCTGCTCTGTAAGAAG[A/G]CCTTATCATGGCCTCTGCGACTGTGTGCAGATGGAGAAGACCACTGTAAC
TCTGCTACCCCTCTGAAAGCTTCCAAACATCCGATATTTGAAAATCCCAA[T/C]CCTAGCTTATCCAATTAGATGGACTCCAAATCAACCCCATCATACATATT
AAGACAGGCGAAGTTACAGTTCACGGGACTTGGGTGCCCATTTACTRCCT[A/G]CTAGTTCAGACTGGGGCTCGCCAACTGGTAAATTGGACTGGGGAGTTCAG
TCACCCTGCAGTGATCCTAATCTTCACTTTGTGGCCTCCCCTGCATTGAA[A/G]CCCCCAGAAGTTGATATTGATTTCTCACAGCAACAACACATTGAGGAAGA
TGGATGGAGGTGGAAAGCCAGACGTATAATCCTCCCAGTTCCA[T/C]TCTGGTATTTCAACTGGCATTCGCTCCGTTGTGGGGCATTCCTCAGAACC
GTTTCTGGCAGATGGAAAAAAATCAAATATTTGTCCTTCGGGCCACTTGG[T/C]GGCTTTATAGAGGCAGATGATCTATTGAAGAAAATTAAGCCCATTGACAA
AGYGCTGGGTAATATTCATGCAGAGATAAGACATCAATTCTATTGTGAAA[T/C]GCATTGGTGTAGCTTGATTCCATGACAGTTTTGTCTATGCTCTTTCTTTA
AGAGATATTACTTCAGAATTCAGAGTGGCTCTATCAATATCACCAGAGGC[T/C]GCATATCCAAAATTATCACCGTTATGGTGGGCAGAACTTGAAATCCTCTC
CAATAGAGAGTATYGTTTATGCATTGAAAATGCTTGAACCCGGAACCGAA[A/G]GGTTGGATTCTCTTCTGCAAGTTTTTGATTCCATGGTTGGAGACCAGAGG
ATGCTGTGATGAATTTGTGCTTGAAAGGCACAGATTGGAACATGGGGATA[T/G]CGTCTTCTGCTCACCAACGTGACAGGTCCATTCAAATATATGAGCGACGT
TGGTGAAAATGTCGGGGAGATTTGCTGGAAGGCTCTGAAAGGAGG[A/G]GGCGGATTTATTCTCTGCTGTTGGCTTTTCTATGTTTCTTTTCTCGTTCT
GTTCAAGAACCAATGCAATTTAGCAGCCATGTTGCTGGCCAGACAAATTC[A/G]GAAGAACCACCAAAGCACGTCTACCAAAATGAATCTTCTTTAAATCTTGA
GATCATTATCTCAATGCTTTTTGTTCTGTTACGTATAAATTCCATATTCT[T/G]ACCTGTAATTTGTGATCAGCAGAGCAAGGTGGTGATGCAAATGGAAAGTC
AAAATGCAGGTAATATGTYTSTATTTTAGTGTCCACATGAACAACATTGA[A/G]ATTATGAGTCTCTGATATTCAGAATTCTATGCATTTCTGGCATTCTTTAT
GTTGAAGACAACACTTTGATTGCCAGCGATTCCCAAGCAATGTTGCACAA[T/C]GGATTTATGAATTCCAACAGTACAACTACTACTACTACTGCTACTTCTAC
Table S1. Probe sequence, E-value and concomitant annotation of all 186 SNPs based on a BLAST analysis. SNPs were classified as
either control or putative non-neutral SNPs (see text for details on selection procedure) (continued).
SNP
CL1524Contig1_03-newSnpIndex_226
CL2637Contig1_04-oldSnpPosition_78
UMN_CL309Contig1_03-oldSnpPosition_145
CL2332Contig1_01-oldSnpPosition_97
2_684_01-oldSnpPosition_91
2_4594_01-oldSnpPosition_310
0_6259_01-newSnpIndex_167
2_5724_02-newSnpIndex_199
0_9568_01-newSnpIndex_245
UMN_5833_01-oldSnpPosition_264
1_1609_01-oldSnpPosition_303
2_8627_01-oldSnpPosition_421
2_8627_01-oldSnpPosition_174
Pila_comp383_c0_210
2_10059_02-oldSnpPosition_329
CL1915Contig1_03-oldSnpPosition_258
0_8111_01-oldSnpPosition_153
0_16068_01-oldSnpPosition_121
E-value
5.4E-113
5.9E-154
8.8E-23
2.9E-92
2.5E-42
6.2E-29
4.2E-26
0.0015
3.3E-44
3.5E-139
6.4E-21
1.8E-40
1.8E-40
4.3E-112
1.1E-47
9.3E-69
2.2E-34
1.2E-21
SNP
CL1524Contig1_03-newSnpIndex_226
CL2637Contig1_04-oldSnpPosition_78
UMN_CL309Contig1_03-oldSnpPosition_145
CL2332Contig1_01-oldSnpPosition_97
2_684_01-oldSnpPosition_91
2_4594_01-oldSnpPosition_310
0_6259_01-newSnpIndex_167
2_5724_02-newSnpIndex_199
0_9568_01-newSnpIndex_245
UMN_5833_01-oldSnpPosition_264
1_1609_01-oldSnpPosition_303
2_8627_01-oldSnpPosition_421
2_8627_01-oldSnpPosition_174
Pila_comp383_c0_210
2_10059_02-oldSnpPosition_329
CL1915Contig1_03-oldSnpPosition_258
0_8111_01-oldSnpPosition_153
0_16068_01-oldSnpPosition_121
Annotation [Species]
PREDICTED: histidinol dehydrogenase, chloroplastic-like [Vitis vinifera]
catalytic, putative [Ricinus communis]
PREDICTED: DUF246 domain-containing protein At1g04910-like [Vitis vinifera]
PREDICTED: calcium-dependent protein kinase 3-like isoform 1 [Glycine max]
extra sporogenous cells [Arabidopsis lyrata subsp. lyrata]
nuclear protein zap, putative [Ricinus communis]
Methyltransferase type 12 domain containing protein. (Os07t0667400-01) [Oryza sativa Japonica Group]
Homeodomain-related containing protein. (Os07t0568200-01) [Oryza sativa Japonica Group]
mitochondrial import inner membrane translocase subunit TIM14 precursor [Zea mays]
PREDICTED: probable methyltransferase PMT9-like [Vitis vinifera]
Similar to cDNA clone:002-182-C01, full insert sequence. (Os05t0574700-01) [Oryza sativa Japonica Group]
carbon-sulfur lyase, partial [Arabidopsis lyrata subsp. lyrata]
carbon-sulfur lyase, partial [Arabidopsis lyrata subsp. lyrata]
chitinase-like protein 1 [Arabidopsis thaliana]
PREDICTED: cell division topological specificity factor homolog, chloroplastic-like [Vitis vinifera]
PREDICTED: ATP synthase subunit d, mitochondrial [Vitis vinifera]
3-hydroxyisobutyrate dehydrogenase, putative [Ricinus communis]
Similar to Sterol glucosyltransferase-like protein (Fragment). (Os02t0210800-01), partial [Oryza sativa Japonica Group]
Classification
Control
Control
Control
Non-neutral
Control
Control
Control
Control
Non-neutral
Control
Control
Control
Control
Non-neutral
Control
Control
Control
Control
Probe sequence
AAGATGCAGATCAGTGGGTGGATTATATTGAAAATGCAGGTAATATGTYT[C/G]TATTTTAGTGTCCACATGAACAACATTGARATTATGAGTCTCTGATATTC
AAAGTGTTCATTTATGAGTTGCCCAGTAAATACAACAGGAAGATTTTGGC[T/G]AAAGATCCCAGATGCCTTACCCATATGTTTGCCACTGAGATCTTTATGAA
CAACAAAACAAAATTCTGCTGCTATGTTGTCAGATTCTGTATCACGTTAC[A/G]TTATTGACAAAAATCACTTAGCCTATTCATGCTTATGTTAGATTTCTGTG
AAAGTTGCTCTGAAGGTATGTTCCTATAATATCTAATGAGACAAACTTGC[A/G]TACCTTTTGTGCAGTCTAAAATTCTTTATCTYAATTCAGGTGATTGCTGA
RYGCTGATTYMAARTGGCCGGGGCGCTGAGGCTATTGATCCACTTYTGCT[T/C]GTTGAGCTTGGCGAAGGAAGCAGTCAATCATCAACACTAACATTTCCATC
TTTTCAATAGGTTGTGTTCCTCAGAGTAAGCGTGCTCTCATTATTGGACC[T/C]GGTGCTGGTTACAATGAGGTACAAGGATAGTTTTCTTGTGATGCCCCAAG
AACACCAGAATAAACTCAAGGGAAATTCTGATGCTGACAAAAGTGCATCA[A/C]CGCAGCCTTATTAGGCATGTTCTAGAGAACCCATCTTCATACATAAGTGC
GCAGCATCAGTATCCAGTAAATTTAAGGAAGGCATAACTTAACTTCCAGG[A/T]AAGTCTTTTCTTTTCTACTTCTTTAACAGGAYCCGTAGGAAGAGCATCTA
AATTTGTAAAGAAGCTGTACAAGGCAATTTAAGAAGCATCACAGGGGAGT[T/C]TGTGAGTTGTGACTATTACGTAGATTATATTTTCCATGTATGCATTGTTG
ATTGATTGGCTTCAGAGGGATGGCATATTGCTGCTAGAGTTGGACAGGTT[A/G]CTGAAGCCAGGGGGCTATTTTGCCTACTCTTCACCTGAAGCATATATGAA
GTTAACTTGTGGCTGCACTGTGRAAAATTTCTTATTTCATTAAGCAGAAC[T/C]GCTTCAAGCAAAGGGTTTGGATGAGAGGATCGCGCCCGGAAGAGGAAGAA
TACAGGTGCTGCTTTCACTAGACGTTGTAAAGCTTGCTAGCATATT[T/C]ACAGCTAGTAGGAATTTGTTGAGTTGACCCTCAGTTCCTGGTAATGGACG
CAGTTGCAAGAAGAATCTAAAGAGTGGCTAACAACCTACACTTTCGGAAC[T/C]CATACCGCAAAACATATATTCTGCAAGATCTGTGGCATAACTTCATACTA
TCACATTACCTGTATTTCCTCGATTTGATGGGCATTGGGCGTGAAAAAGC[T/C]GGTGAGAATCTTGACTGTGGCCAGCAAGTTCCTCTTAACCCTGTTTCAAC
TCCAATTTGATATCAAAYGCACTCACTTGCCCACTGACATCCTTGTACTC[T/C]AAATTCCTTAAATCTCCAAAGCCCCCACTGTACTCCTGATACTCTGGCTT
GAAGGTCAGCATTATCAGCTGTAATCTTATTGAAATTGAATTTTTAGACT[T/C]GTGGTACAAGGCTAGTTTAAATTCCTAGTTTTACTTTTATATTATTTGGT
ATGGGGRTTTCTCTGCCCGGGACCGCACTGCATCACCAGCTTTATCTGTC[T/C]ATGAAGGCCAATGGAGATGGGCTTCTTGGTTGTCATGCCTTAATCACTGC
CCACCTTTAGATGCTGCCATAAAATMTTTTKCTGGAGAATTTTTGGGTGC[T/C]GACAAACTTCATGATGCATCTGCCAATTACTGTGAAAGCAATACTGACCC
Reference
Hettenhausen et al. (2016)
Van Aken et al. (2009)
Kwon et al. (2007)
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Fig. S1. Correlations between original seasonal environmental variables and four retained
principal components. Variables are grouped by color (red: seasonal maximum temperature
(°C), white: seasonal minimum temperature (°C), blue: precipitation (mm), green: Hargreaves
reference evaporation, grey: Hargreaves climatic moisture deficit, orange: aridity index).
Seasons are abbreviated as follows: ‘wt’=winter, ‘sp’=sprin, ‘sm’=summer, ’at’=autumn.
Fig. S2. Correlation matrix of latitude, longitude, elevation and four most important PC’s.
Graphs below the diagonal depict a bivariate scatterplot. Blue and red pie charts refer to
respectively a positive and negative correlation. Magnitude of the correlation is represented by
the size and darkness of the filled portion of the pie (left panel). Table showing the Spearman
rank correlations (below the diagonal) and associated p-value (above the diagonal) between
latitude, longitude, elevation and four most important PC’s (right panel).
Fig. S3. Graphical display of levels of admixture provided by Bayesian clustering analyses
(STRUCTURE), optimal cluster sizes was determined at K=4. Similar color scheme of outer
band and dots on map is used as in Figure 1 to delineate the sample origin.
Fig. S4. Trace plots of each element of the variance-covariance matrix for 3 chains (red, black,
blue), only the lower portion of the symmetric matrix is shown. Dimensions of matrix equals the
number of populations (n=13). Horizontal axis denotes the iteration number, the vertical axis the
covariance of allele frequencies between populations. In the middle upper part of the graph the
first cell of matrix is enlarged. Right panel shows the distribution of Gewekes’ Z-statistic of each
cell of the matrix for the first (a), second (b) and third (c) chain.