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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

From: Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean

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