Genetics of Nodulation and Nitrogen fixation in Legumes

This table catalogs all plant genes currently known to be required for SNF in two model legume species, Medicago truncatula and Lotus japonicus, and two crop species, Glycine max (soybean) and Phaseolus vulgaris (common bean), based on genetic studies (RNAi, antisense-RNA, EMS, Tnt1, LORE1, FNB, CRISPR-Cas9).
  1. Each reference indicates the first study describing a mutant in which the gene was identified and the genes are annotated with the two letter code to the corresponding species, example MtVAPYRIN, LjEPR.
  2. Studies describing gene overexpression phenotypes or genes with expression data alone are not included.
  3. Phenotypes associated with lines where multiple genes have been knocked down or edited are entered only once, example MtVAMP721d/MtVAMP721e.
  4. Phenotypic descriptions included here are strictly based on published literature and do not include any interpretation of the data.
  5. Where ever possible, Gene IDs were taken from the original reference. Gene homology information was derived from searching genomes of the four legumes Medicago truncatula (Mt_reanno_pep); Lotus japonicus (Version 3.0); Glycine max (Wm82.a2.v1); Phaseolus vulgaris (Ver2.1) and publicly accessible phylogeny information, if available (Phytozome).
If you would like to help us keep this table up-to-date or have any suggestions/comments please contact the Functional Genomics Laboratory at the Noble Research Institute:

GeneSymbol Infection NoduleOrgaogenesis Fixation Reference Edit
GmACP n/a Nod+/- n/a Wang et al., 2014
PvAGO5, GmAGO5 Inf- Nod+/-, White++ n/a Reyero-Saavedra et al., 2017
LjAMSH Inf+/-, Inf* Nod+/- Fix* Malolepszy et al., 2015
LjAMT1.1 n/a Nod++ Fix+/- Rogato et al., 2008
PvANN1 Inf+/- Nod+/- Fix+/- Carrasco-castilla et al., 2018
LjAPN1 n/a Nod+, Nod* Fix- Yamaya-Ito et al., 2018
MtARF16a Inf+/- Nod+ n/a Breakspear et al., 2014
GmARF8a/GmARF8b n/a Nod++ n/a Wang et al., 2015
MtARP3 n/a n/a Fix* Gavrin et al., 2015
LjARPC1 Inf+/- Nod++, White++ n/a Hossain et al., 2012
PvBECLIN1 n/a Nod+/- n/a Estrada-Navarrete et al., 2016
GmBCH1/GmBCH2 n/a Nod* Fix+/- Kim et al., 2013
GmBEHL1 n/a Nod++ n/a Yan et al., 2018
MtBG2 Inf++ Nod++ n/a Gaudioso-Pedraza et al., 2018
MtBHLH1 n/a Nod+ Fix+ Laurence Godiard et al., 2011
MtBHLH476 Inf+ Nod+/- Fix+ Ariel et al.,2012
PvBPS1 Inf++ Nod+/- n/a Arthikala et al., 2018
MtBRI1 n/a Nod+/-, Nod* n/a Cheng et al., 2017
LjBRUSH Inf+/- Nod+/- (C) n/a Chiasson et al., 2018
LjBZF n/a Nod++ n/a Nishimura et al., 2002
MtCAS31 n/a Nod+, Pink +/- (C) Fix+/- (C) Li et al., 2018
MtCBS1 Inf++ Nod++ Fix+/- Sinharoy et al., 2016
LjCCD7 Inf+ Nod+/- n/a Liu et. al., 2013
MtCCS52a n/a Nod+/-, Nod* Fix* Vinardell et al., 2003
MtCDC16 n/a Nod++ Fix+ Kuppusamy et al.,2009
MtCDPK1 Inf* Nod+/- n/a Ivashuta et al.,2005
LjCHIT5 Inf+/- Nod+, Pink +/- Fix+/- Malolepszy et al., 2018
MtCHR n/a Nod+/- n/a Zhang et al., 2009
MtCHS n/a Nod+/- n/a Zhang et al., 2009
LjCIP73 Inf+/- Nod+/- n/a Kang et al., 2011
LjCKX3 Inf+/- Nod+/- n/a Reid et al., 2016
LjCLC1 n/a Nod+/- n/a Wang et al., 2015
LjCLE-RS1 n/a Nod++ n/a Nishida et al., 2018
LjCLE-RS2 n/a Nod++ n/a Nishida et al., 2018
LjCLV2 n/a Nod++ n/a Krusell et al., 2011
MtCNGC15a Inf+/- Nod+/- n/a Charpentier et al., 2016
MtCNGC15b Inf+/- Nod+/- n/a Charpentier et al., 2016
MtCNGC15c Inf+/- Nod+/- n/a Charpentier et al., 2016
MtCOPT1 n/a Nod+ n/a Senovilla et al., 2018
MtCP6 n/a Nod+/-, Nod* Fix++ Pierre et al., 2014
MtCPK3 n/a Nod++ n/a Gargantini et al., 2006
MtCRA2 n/a Nod+/- n/a Huault et al., 2014
MtCRE1 (L.O.F) Inf++ Nod+/- n/a Gonzalez-Rizzo et al., 2006
LjCRE1 (G.O.F) Inf+/- White++ (spontaneous) n/a Tirichine et al., 2007
MtCRN n/a Nod++ n/a Crook et al., 2016
LjCYCLOPS (MtIPD3) Inf- Nod* n/a Yano et al., 2008
MtIPD3L Inf- Nod- n/a Jin et al., 2018
MtCYP15a n/a Nod* Fix* Sheokand S., et al., 2005
MtDELLA1 Inf+/- Nod+/- n/a Fonouni-Farde et al., 2016; Jin et al., 2016
MtDELLA2 Inf+/- Nod+/- n/a Fonouni-Farde et al., 2016; Jin et al., 2016
MtDELLA3 Inf+/- Nod+/- n/a Fonouni-Farde et al., 2016; Jin et al., 2016
MtDME Inf+ Nod+, Nod*, White++ Fix+/- Carine Satgé et al., 2016
MtDMI1(LjPOLLUX) Inf- Nod- Fix- Ane et al., 2004
LjCASTOR Inf- Nod- n/a Imaizumi-Anraku et al., 2005
LjSYMRK Inf- Nod- Fix- Stracke et al., 2002
MtCCaMK (L.O.F) Inf- Nod- Fix- Levy et al., 2004; Mitra et al., 2004
LjCCaMK (G.O.F) Inf- White++ (spontaneous) n/a Tirichine et al., 2006
MtDGD1 n/a Nod+/- Fix+/- Si et al., 2019
MtDNF1 n/a Nod*, White++ Fix-, Fix* Wang et al., 2010; Van de Velde et al., 2010
MtDNF2 n/a Nod++, White++ Fix-, Fix* Bourcy et al., 2014
MtDNF4 n/a Nod*, White++ Fix* Kim et al., 2015
MtDNF7 n/a Nod*, White++ Fix-, Fix* Horvath et al, 2015
MtEFD Inf++ Nod++ n/a Vernie et al., 2008
MtSKL(LjEIN2a) Inf++ Nod++ n/a Penmetsa et al., 2008
LjEIN2b Inf++ Nod++ Fix-/- Reid et al., 2018
LjENOD40-1/ENOD40-2 Inf+ Nod+/- n/a Kumagai et al., 2006
GmENOD93 n/a Nod+/-, Nod* n/a Yan et al., 2015
LjEPR3 Inf+/-, Inf* Nod* n/a Kawaharada et al., 2015
LjERF1 n/a Nod+/- n/a Asamizu et al., 2008
MtERN1 Inf+/-, Inf* Nod-, Nod* n/a Middleton et al., 2007
MtERN2 Inf+, Inf* Nod+, Nod* Fix+, Fix* Cerri et al., 2016
MtEXO70H4 Inf+/-, Inf* Nod+ n/a Liu et al., 2019
GmEXPB2 n/a Nod+/-, Nod* Fix+/- Li et al., 2015
LjFEN1 Inf+ Nod* Fix- Hakoyama et al., 2009
MtFER2 n/a Nod+ Fix+/- Dhanushkodi et al., 2018
MtFER3 n/a Nod+ Fix+/- Dhanushkodi et al., 2018
MtFLOT2 Inf+/- Nod+/- Fix+/- Haney et al., 2010
MtFLOT4 Inf+/- Nod+/- Fix+/- Haney et al., 2010
MtFNSII n/a Nod+/- n/a Zhang et al., 2009
GmFWL1 n/a Nod+/- n/a Libault et al., 2010
MtGA2ox10 Inf+/- Nod+/-, Nod* n/a Kim et al., 2019
GmGa n/a Nod++ n/a Choudhury and Pandey, 2015
LjGLB1 Inf+/- Nod+/- Fix+/- Fukudome et al., 2016
GmGß1/GmGß2/GmGß3/GmGß4 n/a Nod+/-, Nod* Fix* Choudhury and Pandey, 2013
GmG?1/GmG?2/GmG?3/GmG?4/GmG?5/GmG?6/GmG?7/GmG?8/GmG?9,GmG?10 n/a Nod+/-, Nod* Fix* Choudhury and Pandey, 2013
LjHIP n/a Nod++ n/a Kang et al., 2015
MtHMGR1 Inf- Nod- n/a Kevei et al., 2007
GmIFS1/GmIFS2 n/a Nod+/- n/a Subramanian et al., 2006
LjGLE1 n/a Nod+/-, Nod* Fix+/-, Fix* Imai et al., 2019
LjIGN1 n/a Nod+, Nod* Fix-, Fix* Kumagai et al., 2007
GmINS1 n/a Nod+/- Fix+/- Li et al., 2018
LjIPT3 n/a Nod++ n/a Sasaki et al., 2014
LjKLV n/a Nod++, Nod* n/a Miyazawa et al., 2010
MtKNAT3/MtKNAT5/MtKNAT9/MtKNAT10 Inf+ Nod+, Nod* n/a Di Giacomo et al., 2017
LjLAN Inf- Nod+/- Fix+/- Suzaki et al., 2019
MtLAX2 n/a Nod+/- n/a Roy et al., 2017
LjLB1/LjLB2/LjLB3 Inf+ Nod+ Fix- Ott et al., 2005
MtLIN, LjLIN Inf+/-, Inf* Nod*, White++ n/a Yano et al., 2009; Kiss et al., 2009
LjLNP Inf- Nod- n/a Roberts et al., 2013
MtLOG1 n/a Nod+/- n/a Mortier et al., 2014
LjLSK1 n/a Nod++, Nod* n/a Garagounis et al., 2018
LjNFR1, MtLYK3 Inf- Nod- Fix- Radatoiu et al., 2003; Limpens et al., 2003
LjMATE1 n/a Nod* Fix+/-, Fix* Takanashi et al., 2013
GmmiR160 Inf++ Nod++ n/a Nizampatnam et al., 2015
GmmiR167 n/a Nod+/- n/a Wang et al., 2015
GmmiR172c n/a Nod+/- n/a Wang et al., 2014
MtMMPL Inf* Nod++ n/a Combier et al., 2007
MtMOT1.2 n/a Nod* Fix+/- Gil-Diez et al., 2018
MtMOT1.3 n/a Nod* Fix+/- Tejada-Jiménez et al., 2017
MtMTP2 n/a Nod* Fix+/- León-Mediavilla et al., 2018
LjMPK6 n/a Nod+/- n/a Yin et al., 2016
MtN5 Inf* Nod+/- n/a Pii et al., 2012
MtNAC969 n/a Nod+ Fix* De Zélicourt et al., 2012
MtNAD1 n/a Nod*, Nod+/- Fix-, Fix* Wang et al., 2016
LjNAP1 Inf+/- Nod+/-, White++ Fix- Yokota et al., 2010
LjNDX1/LjNDX2 n/a Nod++, Nod* Fix* Grønlund et al., 2003
LjNENA Inf- Nod+/- n/a Groth et al., 2010
LjNFH1 Inf+/- Nod+/-, Nod* Fix++ Cai et al., 2018
LjNFR5 Inf- Nod- n/a Madsen et al., 2003
LjNFRe Inf+ Nod+/- n/a Murakami et al., 2018
MtNFS1 n/a n/a Fix++ (C) Yang et al., 2017
MtNFS2 n/a n/a Fix++ (C) Wang et al., 2017
MtNF-YA1 Inf* Nod+/-, Nod* Fix+/- Combier et al., 2006
PvNF-YC1 Inf+/- Nod+/-, Nod* n/a Zanetti et al., 2010
LjNiCK4 inf+ Nod+/- n/a Wong et al., 2019
LjNIN Inf++ Nod* Fix- Schauser et al., 1999
MtNIP/MtLATD/MtNPF1.7 Inf++, Inf* Nod+/-, Nod* Fix* Bagchi et al., 2012
MtNLP1 Inf++ (C) Nod++ (C) Fix++ (C) Lin et al., 2018
GmNMNa n/a Nod+/- Fix* Libault et al., 2011
GmNNC1 n/a Nod++, Nod* n/a Wang et al., 2014
pvNod22 Inf+/-, Inf* Nod++, Nod* Fix+/- Rodriguez-Lopez et al., 2019
MtNOOT Inf+ Nod+/-, Nod* Fix+ Couzigou et al., 2012
MtNPD1/MtNPD2/MtNPD3/MtNPD4/MtNPD5 n/a Nod*(C), White++ Fix* Trujillo et al., 2019
LjNPF8.6 Nod+ Fix+/- n/a Valkov et al., 2017
LjNPL Inf+/-, Inf* Nod+/-, Nod*, White++ n/a Xie et al., 2012
MtNRAMP n/a Nod+/- Fix+/- Tejada-Jiménez et al., 2015
LjNRSYM1 Inf++, (C) Nod++, (C) Fix++, (C) Nishida et al., 2018
MtNSP1 Inf- Nod- n/a Smit et al., 2005
MtNSP2 Inf- Nod- n/a Kaló et al., 2005;
LjnsRING Inf+/- Nod- n/a Shimomura et al., 2006
LjNUP133 Inf* Nod-, Nod*, (C) n/a Kanamori et al., 2006
LjNUP85 Inf+/- Nod- n/a Saito et al., 2007
MtPEN3-like n/a Nod+/- n/a Curtin et al., 2017
MtPHO2-like n/a Nod+/- n/a Curtin et al., 2017
MtPNO1-like n/a Nod+/- n/a Curtin et al., 2017
LjPHYB n/a Nod+/- n/a Suzuki et al., 2011
PvPI3K Inf++, Inf* Nod+/-, Nod* Fix+/-, Fix* Estrada-Navarrete et al., 2016
MtPIN2/MtPIN3/MtPIN4 n/a Nod+/- n/a Huo et al., 2006
LjPIR Inf+/- Nod+/-, White++ Fix- Yokota et al., 2009
MtPLT1/MtPLT2/MtPLT3/MtPLT4 n/a Nod+, Nod* n/a Franssen et al., 2015
PvPRAT3 n/a n/a Fix+/- Coleto et al., 2016
GmPT5 n/a Nod+/- (C), Nod* n/a Qin et al., 2012
GmPT7 n/a Nod* Fix+/- Chen et al., 2019
MtPUB1 Inf++ Nod++ n/a Mbengue et al, 2010
MtRab7a1/MtRab7a2 n/a Nod* Fix* Limpens et al.,2009
PvRabA2 Inf- Nod- n/a Blanco et al., 2009
PvRACK1 n/a Nod+/-, Nod* n/a Islas-flores et al., 2011
MtRbohA n/a n/a Fix+/- Marino et al., 2010
PvRbohA Inf+/- Nod+/- Fix+/- Arthikala et al, 2017
MtRDN1 n/a Nod+/-, Nod* n/a Schnabel et al., 2011
GmRj2/GmRFG1 Inf- Nod+/-, Nod* n/a Yang et al., 2010
GmRGS1 n/a Nod+/-, Nod* n/a Choudhury and Pandey, 2015
GmRGS2 n/a Nod+/-, Nod* n/a Choudhury and Pandey, 2015
LjRINRK1 Inf-, Inf* Nod+, Nod* Fix- Li et al., 2019
GmRj4 n/a Nod+/- (C), Nod* n/a Tang et al., 2016
LjROP6 Inf+/- Nod+/- n/a Ke et al., 2012
MtRPG Inf+, Inf* Nod+/-, Nod+ n/a Arrighi et al., 2008
MtRR5MtRR9/MtRR11 n/a Nod+/- n/a Op Den Camp et al., 2011
MtRSD Inf+ Nod+, Nod*, White++ Fix-, Fix* Sinharoy et al., 2013
GmSACPD-C n/a Nod+, Nod* Fix+ Gillman et al., 2014
GmbHLHm1 n/a Nod+/-, Nod* n/a Chiasson et al., 2014
LjSCARN Inf+/- Nod+/-, White++ Fix- Qiu et al., 2015
LjSEN1 n/a Nod++, White++ Fix- Hakoyama et al., 2011
MtSER6 n/a n/a Fix+/- Dhanoushkodi et al., 2018
GmSGF14c/GmSGF14l n/a Nod+/-, Nod*, White++ Fix* Radwan et al., 2012
MtSGR n/a Nod++ Fix+ Zhou et al., 2011
LjSIE3 Inf+/- Nod+/- Fix+ Yuan et al., 2012
PvSIN1 Inf+/- Nod+/-, Nod* Fix+ Battaglia et al., 2014
LjSIP1 Inf+ Nod+/- n/a Wang et. at., 2013
LjSIP2 Inf+/- Nod+/- n/a Chen et al., 2012
MtSNARP2 Inf+ Nod+, White++ Fix+/-, Fix* Laporte et al., 2010
MtSPK1 Inf+ Nod+/- n/a Andrio et al., 2013
LjSST1 n/a Nod++, White++,Nod* Fix- Krusell l., 2005
MtSUCS1 n/a Nod+/- Fix+/- Baier et al., 2007
LjSUNER1 Inf* Nod+/-, Nod* Fix+ Yoon et al., 2014
LjSUS1/LjSUS3 n/a n/a Fix+/- Horst et al., 2007
LjHAR1 n/a Nod++ Fix+ Krusell et al., 2002
MtSymCRK n/a Nod+, White++ Fix-, Fix* Berrabah et al., 2014
MtSymREM1 Inf++, Inf* Nod+/-, Nod* Fix-, Fix* Lefebvre et al., 2010
MtSYP132 n/a Nod+, Nod* Fix-, Fix* Ivanov et al., 2012
LjSYP71 n/a Nod+ Fix-, Fix* Hakoyama et al., 2012
MtSYT1/MtSYT2; MtSYT2/MtSYT3 n/a Nod+ Fix-, Fix* Gavrin et al., 2017
LjTCO Inf+/- Nod+/-, Nod* Fix-, Fix* Suzaki et at., 2013
MtTIP1g n/a Nod+ Fix-, Fix* Gavrin et al., 2014
LjTML (MtTML1) Inf++ Nod++ Fix+ Takahara et al., 2013
MtTML2 n/a Nod++ n/a Gautrat et al., 2019
PvTOR Inf+/-, Inf* Nod+/-, Nod* Fix- Nanjareddy et al., 2016
GmUPS1 n/a Nod+, Nod* Fix+/- Collier and Tegeder, 2012
MtVAMP721d/MtVAMP721e n/a, Inf* Nod+/-, Nod* Fix-, Fix* Ivanov et al., 2012
MtVPE n/a Nod* Fix++ Pierre et al., 2014
MtVPY Inf* Nod+/-, Nod* Fix- Murray et al., 2011
MtZIP6 n/a Nod+/-, White++ Fix+/- Abreu et al., 2018
MtZPT2 n/a Nod* Fix- Frugier et al., 2000
MtZR1 n/a Nod* Fix+/- Hopkins et al., 2013
Mt?ECS n/a Nod+ Fix+/- El Msehli et al., 2011
Gs52 n/a Nod+/-, Nod* Fix* Govindarajulu M, 2009
MsNADH-GOGAT n/a Nod++, Nod* Fix+/- Cordoba et al., 2003