Table 3.

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

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]