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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]