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Table 4 Thirty-eight genetic sub-networks that were partly validated by previous molecular biology studies

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

Subnetworks constructed in this study Evidences from previous studies Subnetworks constructed in this study Evidences from previous studies
No.a Class Knownb Sub-network No.a Class Knownb Sub-network
3 3D-I New Oil content (T)-GmDHLAT-DG(18:0/18:0) GPDH-oil content [9] 60 4D-II New DG(18:0/16:0) -GmPLDγ-GmARF16-miR160b-linolenic acid (T) GmPLDγ-oil content [16]
4 3D-I New Oil content (T)-GmDHLAT-DG(16:0/16:0) GPDH-oil content [9] 61 4D-II New DG(16:0/16:0) -GmPLDγ-GmARF16-miR160b-linolenic acid (T) GmPLDγ-oil content [16]
7 3D-I Known Linolenic acid (T)-GmCK-PC(16:0/18:3) CK-PC [72] 62 4D-II New DG(18:0/18:0) -GmPLDγ-GmARF16-miR160b-linolenic acid (T) GmPLDγ-oil content [16]
11 3D-I New Oleic acid (T)-GmPHS-d-glucose GmPHS-d-glucose [69] 64 4D-II Known Oleic acid (T) -GmPLDα1-GmARF8a-miR167d-PI(16:0/18:2) GmPLDα1-oleic acid [13]
19 3D-II New Stearic acid (T)-GmMDH1-succinic acid-GmDGAT1a ChMDH2-oil content [19], GmDGAT1-oil content [10] 65 4D-II Known FA(18:0)-GmABI4-GmARF8a-miR167b-oil content (T) ABI3-oil content [56], miR167-ARF8a [45]
20 3D-II New Stearic acid (T)-GmMDH1-citric acid-GmDGAT1a ChMDH2-oil content [19], GmDGAT1-oil content [10] 78 4D-II New Palmitic acid (T)-GmPLDα1-GmGAMYB1-miR159a-pyruvate GmPLDα1-oleic acid [13]
22 3D-II New Palmitic acids (T)-GmSPT-oleic acid-GmHAD AtHAD-fatty acids [121] 84 4D-II Known TG(16:0/18:1/18:2)-GmbZIP123-GmHD-ZIPIII-10-miR166s-oil content (T) GmbZIP123-lipid content [22], miR166-HD-ZIPIII10 [67]
24 3D-II Known Linolenic acid (T)-GmKASI-TG(18:1/18:2/18:3)-GmKAR AtKAS-fatty acids [121] 86 4D-II Known TG(18:1/18:1/18:3)-GmTAGL-GmHD-ZIPIII-10-miR166s-oil content (T) miR166-HD-ZIPIII10 [67]
35 3D-III Known Oil content (T)-GmDHLAT-GmFUM-Pyruvate GPDH-palmitic acid [9] 90 4D-II Known TG(18:3/18:2/18:2)-GmFatB1-GmHD-ZIPIII-10-miR166f-oleic acid (T) GmFatB-fatty acid [57], miR166-HD-ZIPIII10 [67]
37 3D-III Known Oleic acid (T)-GmSEI-GmDGAT1a-TG(16:0/18:2/18:3) GmDGAT1-linolenic acid [9] 100 4D-II Known Linolenic acid (T)-GmPI4Kβ-GmHD-ZIPIII-10-miR166g-PI(16:0/18:2) miR166-HD-ZIPIII10 [67]
38 3D-III Known Linoleic acid (T)-GmPDAT1-GmDGAT1a-TG(16:0/18:2/18:3) GmDGAT1-linolenic acid [9], GmPDAT-stearic acid [12] 102 4D-II Known Oil content (T)-GmPLDζ2-GmHD-ZIPIII-10-miR166j-CerG1(d18:2/22:1) GmPLDζ2-oil content [59],
miR166-HD-ZIPIII10 [67]
39 3D-III Known Oil content (T)-GmPLDζ2-GmDAGK-TG(18:0/16:0/18:1) GmPLDζ2-oil content [59] 105 4D-II Known Stearic acid (T)-GmLEC1-b-GmHD-ZIPIII-10-miR166j-FA(18:0) AtLEC1-stearic acid [58], miR166-HD-ZIPIII10 [67]
40 3D-III Known Stearic acid (T)-GmLEC1-b-GmDGAT1a-TG(18:3/18:3/18:3) AtLEC1-stearic acid [56], GmDGAT1-linolenic acid [9] 114 4D-II Known FA(22:1)-GmZF351-GmHD-ZIPIII-10-miR166k-linoleic acid (T) GmZF351-oil content [25], miR166-HD-ZIPIII10 [67]
44 3D-III New Palmitic acid (T)-GmBCCP1-GmFUS3-ethanolamine AtFUS3-palmitic acid [21] 118 4D-II New Stearic acid (T)-GmABI3b-GmNLP6-miR1516b-palmitic acid ABI3-oil content [56]
45 3D-III Known Linolenic acid (T)-GmKAR-GmPK-leucine AtPK-linoleic acid [6] 119 4D-II New Stearic acid (T)-GmLEC1-b-GmNLP6-miR1516b-palmitic acid AtLEC1-stearic acid [56]
49 4D-I New Linoleic acid (T)-GmABI4-miR530d-TG(18:1/18:1/18:1) ABI3-oil content [56] 121 4D-II New PE(16:0/18:1)-GmDof11-GmNLP6-miR1516b-palmitic acid (T) GmDof11-lipid content [26]
53 4D-I New Linolenic acid (T)-GmOBO-miR5036-TG(16:0/16:0/18:1) OBO-miR5036 [66] 125 4D-II New LPC(16:0)-GmDREBL-GmTCP-miR319h-linolenic acid (T) GmDREBL-lipid content [24]
55 4D-II New Oleic acid (T)-GmPLDα1-GmARF16-miR160d-TG(18:0/16:0/18:1) GmPLDα1-oleic acid [13] 127 4D-II New Linolenic acid (T)-GmbZIP123-GmTCP-miR319h-TG(16:0/18:1/18:2) GmbZIP123-lipid content [22]
59 4D-II New Stearic acid (T)-GmLEC1-b-GmARF16-miR160d-TG(18:0/18:1/18:1) AtLEC1-stearic acid [56] 128 4D-II New Oil content (T)-GmDHLAT-GmTCP2-miR319f-TG(18:1/18:1/18:3) GPDH-oil content [9]
  1. aThe number of sub-networks in Additional file 1: Table S21
  2. b‘Known’ subnetworks could be found at the KEGG PATHWAY website (https://www.kegg.jp/kegg/pathway.html) and ‘new’ subnetworks were constructed in this study