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. 2019 Apr 16;26(3):243–260. doi: 10.1093/dnares/dsz005

Table 3.

DNA polymorphisms in nine genes significantly associated with flowering time variation in the mini-core collection as revealed by the single linear regression analysis

Glyma ID Gene description Gene symbola Chromosome Position (bp) Reference sequence Alternative sequence SNP name P value of association tests
 Functional effect Amino acid change Functional class
2011 2012 2013
Glyma.06G207800 B3 domain- containing protein E1 Chr06 20207322 C G rs123612969 (e1-as) 0.0226 0.0153 0.0333 Missense_variant p.Thr75Arg/c.224C>G MISSENSE
Glyma.10G221500 GIGANTEA E2 Chr10 45310798 A T rs124971350 (e2) 2E-16 2E-16 2E-16 Stop-gained p.Lys527*/c.1582A>T HIGH
                           
Glyma.12G073900 Two-component response regulator-like - Chr12 5508242 T G rs125308101 0.00258 0.0082 0.0019 Upstream_gene_ variant    
      Chr12 5508672 CT C rs745192414 0.00155 0.00261 0.00503 Intron_variant c.-120 + 219delT  
      Chr12 5508702 T C rs743387935 0.0211 0.0228 0.0109 Intron_variant c.-119-198T>C  
      Chr12 5509310 G A rs388619068 0.0146 0.0119 0.00907 Missense_variant p.Asp98Asn/c.292G>A MISSENSE
      Chr12 5509317 C T rs125308103 0.00107 0.00148 0.00319 Missense_variant p.Ser100Leu/c.299C>T MISSENSE
      Chr12 5519728 A C rs125308115 0.00229 0.00749 0.00169 Missense_variant p.Lys378Gln/c.1132A>C MISSENSE
      Chr12 5520578 A G rs389122657 0.014 0.0112 0.00865 Synonymous_ variant p.Ala504Ala/c.1512A>G SILENT
      Chr12 5520945 T C rs125308117 8.96E-10 1.76E-08 7.74E-11 Stop_lost p.Ter627Glnext*?/c.1879T>C MISSENSE
HIGH      Chr12 5521029 G T rs743179814 0.0244 0.0203 0.0089 3_Prime_UTR_ variant c.*82G>T  
Glyma.15G140000 Phytochrome B - Chr15 11436193 G A rs388435741 5.17E-06 7.93E-06 8.47E-06 3_Prime_UTR_ variant c.*218C>T  
      Chr15 11441207 C T rs126279495 5.17E-06 7.93E-06 8.47E-06 Missense_variant p.Val394Ile/c.1180G>A MISSENSE
      Chr15 11442400 A C rs126279502 0.0753 0.0769 0.0431 5_Prime_UTR_ variant c.-14T>G  
Glyma.16G150700 FLOWERING LOCUS T GmFT2a/GmFTL3 Chr16 31110004 TATAAGAAAGC T rs392064733_1 0.0397 0.117 0.0266 5_Prime_UTR_ variant c.-50_-59delATAAGAAAGC  
      Chr16 31110004 TATAAGAAAGCA TA rs392064733_2 0.0397 0.117 0.0266 5_Prime_UTR_ variant c.-49_-58delTAAGAAAGCA  
      Chr16 31110991 A AATAT rs864598505_1 6.24E-05 0.000274 0.000111 Intron_variant c.202-56_202-55insATAT  
      Chr16 31111033 T A rs126829817 6.24E-05 0.000274 0.000111 Intron_variant c.202-15T>A  
      Chr16 31111042 T C rs126829818 0.0697 0.21 0.0419 Splice_region_ variant c.202T>C  
      Chr16 31111349 A G rs126829819 6.24E-05 0.000274 0.000111 Intron_variant c.304 + 72A>G  
      Chr16 31114633 G A Chr16_31114633 5.46E-06 4.14E-06 3.05E-07 Missense_ variant p.Gly169Asp/c.506G>A MISSENSE
      Chr16 31114658 AGA AA Chr16_31114658_2 0.0765 0.0538 0.043 3_Prime_UTR_ variant c.*1delG  
      Chr16 31114930 G T rs126829846 6.24E-05 0.000274 0.000111 3_Prime_UTR_ variant c.*272G>T  
Glyma.16G200700 MADS box protein - Chr16 36179909 T G rs126888526 1.13E-07 3.18E-06 3.35E-07 3_Prime_UTR_ variant c.*218A>C  
      Chr16 36180002 G A rs126888527 1.09E-07 1.63E-06 1.98E-07 3_Prime_UTR_ variant c.*125C>T  
      Chr16 36180087 T TGA Chr16_36180087 8.8E-08 2.16E-06 2.07E-07 3_Prime_UTR_ variant c.*39_*40insTC  
      Chr16 36180122 A C rs126888528 4.19E-07 9.01E-06 1.03E-06 3_Prime_UTR_ variant c.*5T>G  
      Chr16 36180183 T A rs389022394 4.96E-07 1.03E-05 1.32E-06 Missense_variant p.Thr219Ser/c.655A>T MISSENSE
      Chr16 36182854 T TA Chr16_36182854 6.15E-06 4.11E-05 3.79E-06 Intron_variant c.511-49_511-50insT  
      Chr16 36182857 T A rs126888574 8.41E-07 7.3E-06 5.2E-07 Intron_variant c.511-52A>T  
      Chr16 36183423 T G rs126888580_2 6.9E-06 5.27E-06 2.61E-06 Intron_variant c.427-19A>C  
      Chr16 36183426 G C rs126888581_1 0.00286 0.00159 0.0018 Intron_variant c.427-22C>G  
      Chr16 36183435 G C rs126888582 6.8E-06 5.07E-06 2.66E-06 Intron_variant c.427-31C>G  
      Chr16 36183450 G A rs126888583 0.0104 0.00721 0.00804 Intron_variant c.427-46C>T  
      Chr16 36183510 C T rs126888584 0.000219 0.00275 0.000461 Intron_variant c.427-106G>A  
      Chr16 36183518 A G rs126888585 3.22E-10 9.24E-09 3.46E-10 Intron_variant c.427-114T>C  
      Chr16 36183541 C A rs126888586 2.98E-10 8.83E-09 3.27E-10 Intron_variant c.427-137G>T  
      Chr16 36183556 T C Chr16_36183556 0.0507 0.0363 0.048 Intron_variant c.427-152A>G  
      Chr16 36183568 T A rs126888588 0.00193 0.0172 0.00328 Intron_variant c.427-164A>T  
      Chr16 36183573 T A rs126888589 0.00193 0.0172 0.00328 Intron_variant c.427-169A>T  
      Chr16 36184165 T C rs126888605 4.71E-05 3.54E-05 0.000019 Intron_variant c.327-41A>G  
      Chr16 36184729 T C rs126888609 2.18E-09 2.34E-08 6.84E-10 Missense_variant p.Thr79Ala/c.235A>G MISSENSE
      Chr16 36184733 C T rs126888610 2.18E-09 2.34E-08 6.84E-10 Synonymous_ variant p.Ser77Ser/c.231G>A SILENT
      Chr16 36184819 A T rs126888611 0.0341 0.0817 0.0244 Intron_variant c.183-38T>A  
      Chr16 36187211 A C rs744233319 0.000287 0.000744 0.00118 Synonymous_ variant p.Ser36Ser/c.108T>G SILENT
      Chr16 36187552 T G rs126888636 0.0383 0.0315 0.0302 Upstream_gene_ variant    
      Chr16 36187600 A G rs126888637 0.0383 0.0315 0.0302 Upstream_gene_ variant    
Glyma.17G052100 WD repeat-containing protein 61 WDR61 Chr17 3955280 A AT rs126942305_1 0.00214 0.00191 0.00197 Downstream_gene_ variant    
      Chr17 3955411 A G rs126942313 2.56E-10 3.12E-10 1.07E-10 Downstream_gene_ variant    
      Chr17 3955475 TC AA rs126942314_1 0.00359 0.00645 0.00279 Downstream_gene_ variant    
      Chr17 3955476 C A rs126942315 0.00359 0.00645 0.00279 Downstream_gene_ variant    
      Chr17 3955546 T A rs126942316 0.00374 0.00157 0.00264 3_Prime_UTR_ variant c.*125A>T  
      Chr17 3955554 T C rs126942317 0.031 0.0299 0.0358 3_Prime_UTR_ variant c.*117A>G  
      Chr17 3955716 A G rs388258139 0.00418 0.00761 0.00338 Synonymous_ variant p.Ala307Ala/c.921T>C SILENT
      Chr17 3955763 C CG Chr17_3955763 0.00444 0.00194 0.00318 Frameshift_ variant p.Val291_Ala292fs/c.873_874insC HIGH
      Chr17 3955764 A G rs126942318 0.00374 0.00157 0.00264 Synonymous_ variant p.Val291Val/c.873T>C SILENT
      Chr17 3955884 G C rs126942319 0.00374 0.00157 0.00264 Synonymous_ variant p.Val251Val/c.753C>G SILENT
      Chr17 3956142 T C rs126942321 6.36E-08 3.72E-08 1.25E-08 Synonymous_ variant p.Ala165Ala/c.495A>G SILENT
      Chr17 3956163 T C rs126942322 0.00644 0.00295 0.00466 Synonymous_ variant p.Lys158Lys/c.474A>G SILENT
      Chr17 3958319 C G rs126942340 9.03E-10 4.86E-10 1.98E-10 Synonymous_ variant p.Ser16Ser/c.48G>C SILENT
      Chr17 3958374 T G rs126942341 2.32E-10 9.96E-11 5.12E-11 5_Prime_UTR_ variant c.-8A>C  
Glyma.19G194300 TERMINAL FLOWER 1 Dt1/GmTFL1 Chr19 45183701 T A rs127928573 (dt1) 0.00122 0.00587 0.000401 Missense_variant p.Arg166Trp/c.496A>T MISSENSE
      Chr19 45183808 C T rs745009806 0.0319 0.0184 0.0153 Missense_variant p.Arg130Lys/c.389G>A MISSENSE
      Chr19 45183859 G A rs127928574 4.29E-11 3.71E-11 6.02E-10 Missense_variant p.Pro113Leu/c.338C>T MISSENSE
      Chr19 45184581 G T Chr19_45184581 0.014 0.153 0.0428 Splice_region_ variant c.202C>A  
      Chr19 45185131 C T Chr19_45185131 0.00805 0.00351 0.00764 5_Prime_UTR_ variant c.-142G>A  
Glyma.19G224200 Phytochrome A E3 Chr19 47633086 T TA Chr19_47633086 0.000763 0.000353 0.00085 5_Prime_UTR_ variant c.-693_-694insA  
      Chr19 47634596 A G rs127944661 0.0052 0.00108 0.00429 Synonymous_ variant p.Ser43Ser/c.129A>G SILENT
      Chr19 47635025 C T rs388644281 3.18E-05 3.43E-05 3.69E-05 Synonymous_ variant p.Ile186Ile/c.558C>T SILENT
      Chr19 47635737 C A rs389001110 0.0534 0.052 0.048 Missense_variant p.Leu424Ile/c.1270C>A MISSENSE
      Chr19 47636564 G A rs127944664 0.0098 0.00232 0.00888 Intron_variant c.2074 + 23G>A  
      Chr19 47636607 G T rs127944665 0.0127 0.0031 0.0113 Intron_variant c.2074 + 66G>T  
      Chr19 47637258 A G rs393405985_1 0.044 0.0447 0.0427 Missense_variant p.Thr832Ala/c.2494A>G MISSENSE
      Chr19 47638302 G A Chr19_47638302 (e3-Mo) 0.0433 0.0306 0.0485 Missense_variant p.Gly1050Arg/c.3148G>A MISSENSE
      Chr19 47638344 A T rs389636522 0.00508 0.00113 0.00433 Splice_region_ variant c.3183A>T  
      Chr19 47641562   15 kb deletion e3-tr 1.9E-13 1.61E-13 5.15E-14 Loss of exon 4   HIGH
Glyma.U034500 Two-component response regulator-like - Scaffold_32 197169 C T Scaffold_32_197169 0.000318 0.000771 0.000612 3_Prime_UTR_ variant c.*958G>A  
      Scaffold_32 197421 T C Scaffold_32_197421 0.000034 0.00007 8.54E-05 3_Prime_UTR_ variant c.*706A>G  
      Scaffold_32 197459 A T Scaffold_32_197459 1.23E-09 1.94E-08 2.71E-09 3_Prime_UTR_ variant c.*668T>A  
      Scaffold_32 198053 T A Scaffold_32_198053 2.16E-05 4.99E-05 0.000048 Intron_variant c.*133 + 29A>T  
      Scaffold_32 198773 A AT Scaffold_32_198773 1.85E-06 3.75E-06 2.85E-06 Frameshift_variant p.Met737_Ala738fs/c.2209_2210insA HIGH
      Scaffold_32 199551 A C Scaffold_32_199551 4.88E-09 6.54E-08 1.23E-08 Synonymous_ variant p.Ala529Ala/c.1587T>G SILENT
      Scaffold_32 199605 T G Scaffold_32_199605 2.16E-05 4.99E-05 0.000048 Intron_variant c.1575-42A>C  
      Scaffold_32 199656 TA T Scaffold_32_199656 0.0096 0.0104 0.011 Intron_variant c.1574 + 2delT  
      Scaffold_32 199722 C G Scaffold_32_199722 0.000318 0.000771 0.000612 Missense_variant p.Gly504Ala/c.1511G>C MISSENSE
      Scaffold_32 202754 G A Scaffold_32_202754 0.0142 0.01 0.0105 Stop_gained p.Arg308*/c.922C>T
HIGH      Scaffold_32 206717 A G Scaffold_32_206717 1.23E-09 1.94E-08 2.71E-09 Intron_variant c.792 + 27T>C  
      Scaffold_32 216494 C T Scaffold_32_216494 4.88E-09 6.54E-08 1.23E-08 Synonymous_ variant p.Val168Val/c.504G>A SILENT
      Scaffold_32 218380 A T Scaffold_32_218380 3.29E-09 4.29E-08 8.4E-09 Synonymous_ variant p.Pro73Pro/c.219T>A SILENT
a

Gene names refer to those in Kong et al.,8 Fan et al.,52 and Cao et al.53