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Table 3 Twelve new and sixteen known candidate genes around mQTLs clusters for metabolites and lipids in soybean

From: 4D genetic networks reveal the genetic basis of metabolites and seed oil-related traits in 398 soybean RILs

Candidate gene for metabolites and lipids Quantitative trait locus mapping Comparative genomics analysis
mQTL cluster Chr Markers associated Effect LOD score r2 (%) Metabolite class Metabolites and lipids Gene-name 1.1 Arabidopsis homologs KEGG pathway References
GmPHS Known mQTL-C6 8 Marker706158, Marker750703 − 0.97~ 0.52 3.14~3.63 2.48~8.16 Carbohydrates d-Glucose Glyma08g45210 AT3G46970 gmx00500 Satoh et al. [69]
GmFPBP New mQTL-C4 7 Marker399016, Marker384918 − 0.72~0.69 2.60~2.82 7.33~7.40 Mannose Glyma07g17180 AT3G54050 gmx00051 Strand et al. [109]
GmFBA Known mQTL-C11 13 Marker2849746, Marker2767659 0.45~ 0.76 2.56~2.74 3.06~3.14 Mannose, d-fructose 2,6-bisphosphate Glyma13g21540 AT2G36460 gmx00051 Carrera et al. [110]
GmZF351 Known mQTL-F17 6 Marker1996457, Marker2044143 0.27~ 0.35 2.59~3.25 3.47~4.34 Fatty acids FA(18:0), FA(20:0), FA(22:1) Glyma06g44440 AT1G03790   Li et al. [25]
GmPLDγ Known mQTL-G115 1 Marker1801142, Marker1822692 − 0.44~ 0.46 2.62~4.71 5.92~10.87 Glycerolipids DG(16:0/16:0), DG(20:0/18:2), DG(20:0/18:3), TG(18:1/18:2/18:3), DG(18:0/16:0), DG(18:0/18:0), DG(18:1/18:1) Glyma01g42420 AT2G42010 gmx04144 Bai et al. [16]
GmPLDε1 Known mQTL-G109 15 Marker29446, Marker5035 − 0.27~ 0.26 2.56~5.36 0.24~5.73 DG(16:0/16:0), DG(18:0/16:0), DG(18:0/18:0), DG(18:3/18:3) Glyma15g02710 AT1G55180 gmx04144 Yang et al. [59]
GmPECT1 Known mQTL-G21 18 Marker920733, Marker926627 − 0.45~ 0.41 2.72~4.45 5.97~11.39 DG(18:0/18:1), DG(16:0/18:1), DG(18:1/18:1), DG(18:0/18:0), DG(16:0/16:0) Glyma18g45210 AT2G38670 gmx00564 Mizoi et al. [111]
GmnsPLC New mQTL-G40 3 Marker2485779, Marker2406610 − 0.21~ 1.44 3.24~31.92 3.49~10.22 DGDG(16:0/18:2) Glyma03g22860 AT3G03520 gmx00564 Cai et al.[15]
GmDREBL New mQTL-G94 12 Marker2668097, Marker2705284 − 0.12~ 0.05 3.07~4.57 0.46~3.16 DG(20:1/18:2), TG(18:0/16:0/18:1), DG(18:3/18:3), LPC(16:0), LPC(18:0) Glyma12g11150 AT2G40340   Zhang et al. [24]
GmLPAAT4 Known mQTL-G9 17 Marker182106, Marker181452 − 0.23~ 0.22 2.51~5.41 0.10~11.01 TG(16:0/16:0/18:2), DG(18:2/18:2), TG(16:0/18:2/18:3), TG(16:0/16:0/18:1), TG(16:0/18:1/18:1), TG(18:3/18:2/18:2), TG(18:1/18:2/18:2), TG(18:0/16:0/18:1), TG(20:0/18:1/18:2), TG(16:0/16:0/18:3) Glyma17g36670 AT1G75020 gmx00561 Kim et al. [112]
GmDGAT1a Known mQTL-G100 13 Marker2790748, Marker2850221 − 0.39~ 0.32 2.83~5.40 0.02~10.08 TG(16:0/18:2/18:3), TG(20:1/18:3/18:3), TG(18:3/18:3/18:3), TG(20:2/18:2/18:2) Glyma13g16560 AT2G19450 gmx00561 Torabi et al. [10]
GmbZIP123 Known mQTL-G51 6 Marker1991901, Marker1969292 − 0.33~ 0.22 2.62~4.27 1.46~8.53 TG(18:1/18:1/18:2), TG(20:1/18:1/18:2), TG(16:0/18:1/18:2), SQDG(16:0/18:2) Glyma06g01240 AT4G34590   Song et al. [22]
GmSWEET10a Known mQTL-G112 15 Marker107799, Marker23766 − 0.19~ 0.39 2.81~17.32 0.10~6.87 DG(16:0/18:1), DG(16:0/18:2), DG(18:1/18:2), DG(20:1/18:2), TG(18:1/18:2/18:3) Glyma15g05470 AT5G13170 gmx00500 Wang et al. [5]
GmCK Known mQTL-G33 20 Marker1374027, Marker1406581 − 2.96~ 1.16 2.58~7.15 1.44~7.58 Glycerophospholipids PC(16:0/18:3), PE(16:0/18:3), PE(18:3/18:2), PE(18:3/18:3), PE(20:0/18:3) Glyma20g31030 AT1G74320 gmx00564 Lin et al. [113]
GmDof11 Known mQTL-GP54 13 Marker2818991, Marker2827481 − 1.08~1.02 2.53~3.34 0.22~10.26 PE(16:0/18:1), PE(16:0/18:2), PE(16:0/18:3), PE(18:3/18:2) Glyma13g40420 AT5G60200   Wang et al. [26]
GmFBA New mQTL-O25 14 Marker1738741, Marker1763128 − 0.43~0.45 2.82~4.05 2.70~3.80 Organic acid d-Glyceric acid Glyma14g36850 AT2G36460 gmx01230 Carrera et al. [110]
GmMDH1 Known mQTL-O19 13 Marker2842700, Marker2759137 − 0.90~0.94 2.57~3.68 4.93~9.05 Isocitric acid, oxalic acid, succinic acid, citric acid Glyma13g16440 AT1G04410 gmx00020 Kong et al. [19]
GmGLYK New mQTL-O26 15 Marker114116, Marker114116 0.36 3.17 1.35 l-Malic acid Glyma15g01540 AT1G80380 gmx00260 Usuda and Edwards [114]
GmHXK New mQTL-O30 17 Marker169306, Marker169306 1.34 2.58 6.82 Oxalacetic acid Glyma17g37720 AT1G47840 gmx00500 Troncoso-Ponce et al. [115]
GmAAPT New mQTL-O2 2 Marker1193792, Marker1193792 − 0.91~ − 0.70 4.32~6.56 4.85~7.30 Pyruvate Glyma02g14211 AT1G13560 gmx00564 Bai et al. [16]
GmFUM Known mQTL-O14 9 Marker429142, Marker482975 − 0.54~ − 0.37 2.88~3.94 1.74~3.17 Pyruvate Glyma10g02040 AT2G47510 gmx00020 Behal and Oliver [116]
GmGAD New mQTL-O5 5 Marker2187077, Marker2178818 − 0.62~ 0.54 2.58~5.18 2.49~4.45 Succinic acid Glyma05g26660 AT2G02010 gmx00250 Matsuyama et al. [117]
GmALDH2 New mQTL-P8 6 Marker1993733, Marker2000797 − 0.55~ − 0.32 2.87~4.51 3.06~5.77 Amino acid beta-Alanine Glyma06g12010 AT1G44170 gmx00410 Shin et al. [118]
GmSD Known mQTL-P21 15 Marker12570, Marker12570 − 0.77~0.68 2.87~4.55 2.24~4.15 Ethanolamine Glyma15g05630 AT1G43710 gmx00340 Yunus et al. [119]
GmFUS3 New mQTL-P22 16 Marker2528893, Marker2589580 − 0.77~ − 0.50 3.97~4.10 1.94~8.71 Ethanolamine, isoleucine Glyma16g05480 AT3G26790   Zhang et al. [24]
GmPK New mQTL-P26 20 Marker1324457, Marker1324457 − 0.40~ − 0.39 3.14~3.14 1.21~1.29 Leucine Glyma20g02980 AT5G56350 gmx00620 Andre et al. [6]
GmGCL New mQTL-P1 1 Marker1898999, Marker1898999 − 0.74~ 0.70 4.05~6.02 2.62~4.38 Serine Glyma01g42900 AT4G23100 gmx00270 Franklin et al. [120]
GmSTYK Known mQTL-P3 2 Marker1188545, Marker1243816 − 1.15~− 0.70 2.67~2.81 3.08~9.01 Threonine Glyma02g43650 AT4G08850   Ramachandiran et al. [76]