Table 2.
Summary of GWAS regions, genes of interest, and overlapping QTLs. Counts of candidate genes are given for regions defined by two methods: by flanking non-significant markers (column “Genes in region - A”) and within a window defined by the significant SNP(s) plus 100 kb before and after the significant SNP(s) (column “Genes in region - B”). Known QTLs are abbreviated IN: Node number; PH: Plant height; SY: seed yield; SW: seed weight. Also see a more detailed version of the table in Additional file 3 (including full *QTL names), and a list of all genes within GWAS regions in Additional file 4
| Start SNP | End SNP | Chrom | Gene count A | Gene count B | P-value | stable 3 locs | Genes of special interest | Annotation | Known QTLs* |
|---|---|---|---|---|---|---|---|---|---|
| Internode Number (IN) | |||||||||
| ss715578706 | ss715578717 | Gm01 | 8 | 24 | 7E-05 | Glyma.01 g022500 | AP2-like ethylene-responsive TF | NN | |
| ss715579430 | ss715579430 | Gm01 | 1 | 17 | |||||
| ss715578432 | ss715578590 | Gm01 | 3 | 3 | |||||
| ss715578480 | ss715578480 | Gm01 | 4 | 9 | |||||
| ss715578432 | ss715578590 | Gm01 | 4 | 3 | 0.0004 | Glyma.01 g074000 | ubiquitin protein ligase | NN, PH | |
| ss715589109 | ss715589108 | Gm04 | 0 | 25 | |||||
| ss715590708 | ss715590708 | Gm05 | 6 | 24 | |||||
| ss715598728 | ss715598728 | Gm07 | 3 | 21 | |||||
| ss715614000 | ss715614000 | Gm13 | 3 | 23 | 8E-05 | Glyma.13 g101400 | Putative lysophospholipase | NN, PH | |
| ss715625429 | ss715625429 | Gm16 | 0 | 21 | |||||
| ss715623458 | ss715623458 | Gm16 | 3 | 22 | 0.0005 | Glyma.16 g016400 | NAC domain containing protein 62 | NN, PH | |
| ss715631395 | ss715631424 | Gm18 | 14 | 24 | 8E-05 | X | Glyma.18 g203800 | Metallopeptidase protein | PH |
| ss715635223 | ss715635190 | Gm19 | 4 | 29 | 4E-05 | Glyma.19 g002900 | NAC domain-containing protein 8-like | PH | |
| ss715635454 | ss715635456 | Gm19 | 5 | 24 | 4E-05 | X | Glyma.19 g194300 | Phosphatidylethanolamine binding prot (Dt1) | PH |
| ss715635024 | ss715635024 | Gm19 | 1 | 22 | 0.0002 | Glyma.19 g146000 | squamosa promoter binding | PH | |
| same | same | Glyma.19 g145700 | pectinesterase | PH | |||||
| same | same | Glyma.19 g145400 | plant phosphoribosyltransferase protein | PH | |||||
| Plant Height (PH) | |||||||||
| ss715582992 | ss715582994 | Gm02 | 3 | 23 | 9E-05 | X | Glyma.02G245600 | Gibberellin-regulated family protein | PH |
| ss715585780 | ss715585783 | Gm03 | 10 | 25 | 4E-05 | ||||
| ss715585781 | ss715585784 | Gm03 | 9 | 24 | 0.0002 | ||||
| ss715585788 | ss715585790 | Gm03 | 8 | 23 | 0.0002 | ||||
| ss715588701 | ss715588703 | Gm04 | 3 | 25 | 0.0001 | ||||
| ss715592575 | ss715592573 | Gm05 | 1 | 20 | 0.0002 | ||||
| ss715602866 | ss715602868 | Gm08 | 6 | 36 | 9E-05 | ||||
| ss715635355 | ss715635357 | Gm19 | 3 | 26 | 0.0001 | X | Glyma.19G187800 | pectinesterase 11 | PH, SL |
| ss715635405 | ss715635407 | Gm19 | 3 | 17 | 7E-05 | X | Glyma.19G192400 | ethylene-responsive transcription factor 12 | PH, SL |
| same | same | X | Glyma.19G192700 | growth-regulating factor 4 | PH, SL | ||||
| ss715635424 | ss715635459 | Gm19 | 17 | 36 | 1E-06 | X | Glyma.19 g194300 | Phosphatidylethanolamine binding prot (Dt1) | PH, SL |
| Seed Weight (SW) | |||||||||
| ss715579653 | ss715579702 | Gm01 | 18 | 26 | |||||
| ss715583620 | ss715583627 | Gm02 | 5 | 35 | |||||
| ss715582341 | ss715582351 | Gm02 | 5 | 26 | 8E-06 | Glyma.02 g04660 | histidine kinase 1 | SW | |
| ss715584321 | ss715584321 | Gm02 | 1 | 16 | |||||
| ss715588755 | ss715588756 | Gm04 | 3 | 27 | 5E-05 | X | Glyma.04 g228200 | Late embryogenesis protein (LEA) | SW |
| ss715594571 | ss715594571 | Gm06 | 3 | 17 | |||||
| ss715608522 | ss715608522 | Gm10 | 2 | 16 | |||||
| ss715609333 | ss715609333 | Gm11 | 3 | 14 | |||||
| ss715613704 | ss715613704 | Gm12 | 8 | 17 | |||||
| ss715612715 | ss715612715 | Gm12 | 7 | 23 | |||||
| ss715614263 | ss715614263 | Gm13 | 3 | 19 | 2E-06 | X | Glyma.13 g149000 | Late embryogenesis abundant (LEA) | SW |
| ss715624623 | ss715624628 | Gm16 | 4 | 18 | |||||
| ss715635103 | ss715635103 | Gm19 | 1 | 24 | 9E-05 | Glyma.19 g151900 | Hpt domain | SW | |
| ss715635205 | ss715635205 | Gm19 | 6 | 20 | 0.0004 | X | Glyma.19 g163900 | AP2 domain protein | SW |
| Seed Yield per Plant (SYP) | |||||||||
| ss715586641 | ss715586641 | Gm03 | 7 | 30 | |||||
| ss715602684 | ss715602688 | Gm08 | 4 | 29 | |||||
| ss715603479 | ss715603479 | Gm09 | 0 | 8 | |||||
| ss715603626 | ss715603626 | Gm09 | 5 | 27 | 0.0004 | X | Glyma.09 g040000 | Response regulator receiver | SY, SW |
| ss715615670 | ss715615670 | Gm13 | 16 | 35 | |||||
| ss715618757 | ss715618757 | Gm14 | 1 | 22 | |||||
| ss715620375 | ss715620383 | Gm15 | 6 | 28 | 0.0003 | Glyma.15 g145200 | Response regulator | SY, SW | |
| ss715634241 | ss715634241 | Gm19 | 0 | 14 | |||||
| ss715637551 | ss715637574 | Gm20 | 13 | 37 | 0.0002 | Glyma.20 g112200 | Inner centromere protein | SY, SW | |