TABLE 3.
List of soybean genes edited for functional genetics study and trait improvement using genome editing technology.
| Trait | Gene/targeting location | GE platform | Delivery method | Edited events | Editing outcomes | References |
| Yield | ||||||
| Plant architecture | GmLHY1a (Glyma.16G017400), GmLHY1b (Glyma.07G048500), GmLHY2a (Glyma.19G260900), and GmLHY2b (Glyma.03G261800) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Cheng et al., 2019 |
| GmSPL9a (Glyma.02G177500), GmSPL9b (Glyma.09G113800), GmSPL9c (Glyma.03G143100), and GmSPL9d (Glyma.19G146000) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Bao et al., 2019 | |
| GmAP1a (Glyma.16G091300), GmAP1b (Glyma.08G269800), GmAP1c (Glyma.01G064200), and GmAP1d (Glyma.02G121600) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Chen et al., 2020d | |
| Seed weight and organ size | GmPPD1 (Glyma.10G244400) and GmPPD2 (Glyma.20G150000) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Kanazashi et al., 2018 |
| GmSWEET10a (Glyma.15G049200) and GmSWEET10b (Glyma.08G183500) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Wang et al., 2020c | |
| GmKIX8-1 (Glyma.17G112800) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Nguyen et al., 2021 | |
| Seed number | GmJAG1 (Glyma.20G25000) and GmJAG2 (Glyma.10G42020) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Cai et al., 2021 |
| Photoperiod | GmFT2a (Glyma.16G26660) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Cai et al., 2018 |
| GmE1 (Glyma.06G207800) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Han et al., 2019 | |
| GmFT2a (Glyma.16G26660) and GmFT5a (Glyma.16G04830) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Cai et al., 2020b | |
| GmFT2a (Glyma.16G150700) and GmFT4 (Glyma.08G363100) | BE base editor | A. tumefaciens | Whole plant | Base editing | Cai et al., 2020a | |
| GmFT2b (Glyma.16G26690) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Chen et al., 2020c | |
| GmAP1a (Glyma.16G091300), GmAP1b (Glyma.08G269800), GmAP1c (Glyma.01G064200), and GmAP1d (Glyma.02G121600) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Chen et al., 2020d | |
| GmPRR37 (Glyma.12G073900) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Wang et al., 2020b | |
| GmLUX1 (Glyma.12G060200) and GmLUX2 (Glyma.11G136600) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Bu et al., 2021 | |
| GmLNK2a (Glyma.04G141400), GmLNK2b (Glyma.11G154700), GmLNK2c (Glyma.13G199300), and GmLNK2d (Glyma.15G237600) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Li et al., 2021c | |
| Nutrition and quality | ||||||
| Storage protein | Glyma.20G148400, Glyma.20G146200, Glyma.10G246300, Glyma.20G148200, Glyma.10G037100, Glyma.03G163500, Glyma.19G164900, Glyma.13G123500, and Glyma.19G164800 | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Li et al., 2019 |
| Seed oil | GmFAD2-1A (Glyma.10G278000) and GmFAD2-1B (Glyma.20G111000) | TALENs | A. rhizogenes and disarmed A. rhizogenes | Hairy root and whole plant | Knockout (multiplex) | Haun et al., 2014 |
| GmFAD2-2 | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | al Amin et al., 2019 | |
| GmFAD2-1A (Glyma.10G278000) | ZFNs | Biolistic method | Whole plant | Knock in (NHEJ) | Bonawitz et al., 2019 | |
| GmFAD2-1A (Glyma.10G278000) and GmFAD2-1B (Glyma.20G111000) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Do et al., 2019 | |
| GmGOLS1A (Glyma.03G222000) and GmGOLS1B (Glyma.19G219100) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Le et al., 2020 | |
| GmFAD2–1A (Glyma.10G278000) and GmFAD2–2A (Glyma.19G147300) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Wu et al., 2020 | |
| GmFATB1a (Glyma.05G012300) and GmFATB1b (Glyma.17G012400) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Ma J. et al., 2021 | |
| Glyma.15G117700 | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Qu et al., 2021 | |
| Bean flavor-free soybean | GmLox1 (Glyma.13G347600), GmLox2 (Glyma.13G347500), and GmLox3 (Glyma.15G026300) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Wang et al., 2020a |
| Disease resistance | ||||||
| Cyst nematode resistance | GmSyn12 (Glyma.12G194800), GmSyn13 (Glyma.13G307600), GmSyn16 (Glyma.16G154200), and GmSyn02 (Glyma.02G072900) | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Dong et al., 2020 |
| Rps1 families (Glyma.03G034400, Glyma.03G0034800, Glyma.03G039200, Glyma.03G039500, Glyma.03G037100, Glyma.03G037300, Glyma.03G037400, Glyma.03G037400, Glyma.03G037000, Glyma.03G034500, Glyma.03G039300, Glyma.03G045700, Glyma.03G043600, Glyma.03G045300, Glyma.03G043000, Glyma.03G043500, Glyma.03G044000, Glyma.03G043200, Glyma.03G045000, Glyma.03G046500, Glyma.03G047000, Glyma.03G043900) and Rpp1L families (Glyma.18G281700, Glyma.18G281600, Glyma.18G281500, and Glyma.18G280300) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Nagy et al., 2021 | |
| Rhg1-locus (Glyma.18G02270), DELLA18 (Glyma.18G040000), and DELLA11 (Glyma.11G216500) | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Dong and Hudson, 2022 | |
| Insect resistance | GmUGT (Glyma.07G110300) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout | Zhang et al., 2022b |
| Abiotic stress tolerance | ||||||
| Drought tolerance | GmLHY1a (Glyma.16G017400), GmLHY1b (Glyma.07G048500), GmLHY2a (Glyma.19G260900), and GmLHY2b (Glyma.03G261800) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Wang et al., 2021a |
| Salt tolerance | GmNAC06 (Glyma06G21020) | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout | Li et al., 2021b |
| Nitrogen fixation | ||||||
| GmNSP1a (Glyma.07G039400) and GmNSP1b (Glyma.16G008200) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | He et al., 2021 | |
| Herbicide resistance | GmALS1 (Glyma.04G37270.1), GmALS2 (Glyma.06G17790.1), GmALS3 (Glyma.13G31470.1), and GmALS4 (Glyma.15G07860.1) | CRISPR/Cas9 | Biolistic method | Whole plant | Knockin (HDR) | Li et al., 2015 |
| Root nodulation | GmRIC1 (Glyma.13G292300), GmRIC2 (Glyma.06G284100), GmRDN1-1 (Glyma.02G279600), GmRDN1-2 (Glyma.14G035100), and GmRDN1-3 (Glyma.20G040500) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Bai et al., 2020 |
| GmSPL9d (Glyma.19G146000) and GmmiR156 | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Yun et al., 2022 | |
| Allergy reduction | Gly m Bd 28K (Glyma.U020300) and Gly m Bd 30K (Glyma.08G116300) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Sugano et al., 2020 |
| GE platform adoption in soybean | GmDCL1a (Glyma.03G42290), GmDCL1b (Glyma.19G45060), GmDCL4a (Glyma.17G11240), GmDCL4b (Glyma.13G22450), GmRDR6a (Glyma.04G07150), GmRDR6b (Glyma.06G07250), and GmHEN1a (Glyma.08G08650) | ZFNs | A. rhizogenes | Hairy root | Knockout (multiplex) | Curtin et al., 2011 |
| GmDCL4a (Glyma.17G11240) and GmDCL4b (Glyma.13G22450) | ZFNs | A. rhizogenes | Hairy root | Knockout | Sander et al., 2011 | |
| Bar transgene, GmFEI1 (Glyma.01G35390), GmFEI2 (Glyma.09G34940), and GmSHR | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Cai et al., 2015 | |
| GmGS (Glyma.18G04660 and Glyma.18G041100) and GmCHI20 (Glyma.20G38560 and Glyma.20G241500) | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout | Michno et al., 2015 | |
| GFP transgene, Glyma07g14530, 01gDDM1 (Glyma.11G38150), 11gDDM1 (Glyma.11G07220), Glyma04g36150, Glyma06g18790, miR1509, and miR1514 | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout | Jacobs et al., 2015 | |
| Glyma.06G14180, Glyma.08G02290, and Glyma.12G37050 | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Sun et al., 2015 | |
| GmPDS11 (Glyma.11G253000) and GmPDS18 (Glyma.18G003900) | TALENs | A. tumefaciens | Whole plant | Knockout | Du et al., 2016 | |
| FAD2-1A (Glyma.10G42470) and FAD2-1B (Glyma.20G24530) | CRISPR/AsCpf1 or LpCpf1 | Protoplast transfection | Protoplast | Knockout (RNP) | Kim et al., 2017 | |
| GmIPK1 (Glyma.14G072200) and GmIPK2 (Glyma.12G240900) (STU and TCTU system*) | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Carrijo et al., 2021 | |
| Glyma.15G249000 and Glyma.13G259100 | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Luo et al., 2021 | |
| GmPDS11g (Glyma.11g253000) and GmPDS18g (Glyma.18g003900) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Lu and Tian, 2022 | |
| Transgene-free edited events | Target sites DD38 and DD51 | CRISPR/Cas9 | O. haywardense H1-8 | Targeted insertion | Kumar et al., 2022 | |
| Gly m Bd 30K (Glyma.08G116300) | CRISPR/Cas9 | Biolistic method | Whole plant | Knockout | Adachi et al., 2021 | |
| Egg cell promoter driving Cas9 | GmAGO7a (Glyma.01G053100) and GmAGO7b (Glyma.02G111600) | CRISPR/Cas9 | A. rhizogenes andA. tumefaciens | Hairy root and whole plant | Knockout (multiplex) | Zheng et al., 2020 |
| Targeted deletions of DNA fragments | GmFT2a (Glyma.16G26660) and GmFT5a (Glyma.16G04830) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (4.5 kb in GmFT2a) | Cai et al., 2018 |
| Growth of soybean trichomes | GmCPR5 (Glyma.06G145800) | CRISPR/Cas9 | Biolistic method | Whole plant | Knockout | Campbell et al., 2019 |
| Fertility | GmMs1 (Glyma.13G114200) | CRISPR/Cas9 | Biolistic method | Whole plant | Knockout | Nadeem et al., 2021 |
| GmMs1 (Glyma.13G114200) | CRISPR/Cas9 | Biolistic method | Whole plant | Knockout | Jiang et al., 2021 | |
| miRNA pathway and small RNA processing | GmDCL1a (Glyma.03G42290), GmDCL1b (Glyma.19G45060), GmDCL4a (Glyma.17G11240), GmDCL4b (Glyma.13G22450), GmRDR6a (Glyma.04G07150), GmRDR6b (Glyma.06G07250), GmHEN1a (Glyma.08G08650), and GFP transgene | ZFNs | A. rhizogenes | Hairy root | Knockout | Curtin et al., 2011 |
| GmDRB2a (Glyma.12G075700), GmDRB2b (Glyma.11G145900), GmDCL3a (Glyma.04G057400), GmHEN1a (Glyma.08G081600), and GmHEN1b (Glyma.05G126600) | CRISPR/Cas9 | A. rhizogenes | Hairy root | Knockout (multiplex) | Curtin et al., 2018 | |
| GmDCL2a (Glyma.09G025400), GmDCL2b (Glyma.09G025300), and GmDCL3a (Glyma.04G057400) | TALENs | Disarmed A. rhizogenes | Whole plant | Knockout (multiplex) | Curtin et al., 2018 | |
| Sucrose export related embryo development | GmSWEET15a (Glyma.05G126600) and GmSWEET15b (Glyma.05G1266000) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Wang et al., 2019b |
| Circadian rhythmicity | GmLCLa1 (Glyma.16G01980), GmLCLa2 (Glyma.07G05410), GmLCLb1 (Glyma.03G42260), and GmLCLb2 (Glyma.19G45030) | CRISPR/Cas9 | A. tumefaciens | Whole plant | Knockout (multiplex) | Wang et al., 2020e |
| Soybean knockout library | 70 sgRNAs to target 102 genes | CRISPR/Cas9 | A. tumefaciens (pooled) | Whole plant | Knockout (multiplex) | Bai et al., 2020 |
*STU, single transcriptional unit; SpCas9 and sgRNA are driven by only one promoter; and the two-component transcriptional unit (TCTU) in the conventional system, and SpCas9 and sgRNA are under the control of different promoters.