--- scientific_name: Glycine max gene_symbols: - GmPLDγ gene_symbol_long: Phospholipase D gamma gene_model_pub_name: Glyma.01G215100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G215100 confidence: 5 curators: - Greg Murrell - Scott Kalberer phenotype_synopsis: Overexpression of GmPLDγ introduced from soybean results in higher seed oil content and fatty-acid remodeling in Arabidopsis. traits: - entity_name: seed oil content entity: CO_336:0000048 - relation_name: positively regulates relation: RO:0002213 - entity_name: fat and essential oil composition related trait entity: TO:0000491 - entity_name: seed weight entity: TO:0000181 - relation_name: positively regulates relation: RO:0002213 - entity_name: triglyceride metabolic process entity: GO:0006641 - relation_name: positively regulates relation: RO:0002213 references: - citation: Bai, Jing et al., 2020 doi: 10.1016/j.plantsci.2019.110298 pmid: 31779909 --- scientific_name: Glycine max gene_symbols: - GmTIR1A gene_symbol_long: Transport Inhibitor Response 1A gene_model_pub_name: Glyma.02G152800 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G152800 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - TIR1A is strongly expressed in developing nodules, main and lateral roots, and especially in main root tips and lateral root primordia. - Expression in roots decreases as nodulation progresses. - TIR1A is upregulated by auxin. phenotype_synopsis: TIR1A is an auxin receptor which positively regulates root growth and nodulation. traits: - entity_name: auxin receptor activity entity: GO:0038198 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: root development entity: GO:0048364 - relation_name: positively regulates relation: RO:0002213 - entity_name: positive regulation of lateral root development entity: GO:1901333 references: - citation: Cai, Wang et al., 2017 doi: 10.1111/nph.14632 pmid: 28598036 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmTIR1B gene_symbol_long: Transport Inhibitor Response 1B gene_model_pub_name: Glyma.10G021500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G021500 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - TIR1B is most strongly expressed in developing nodules and main and lateral roots. - Expression in roots decreases as nodulation progresses. - RNAi knockdowns of TIR1B have reduced nodulation. phenotype_synopsis: TIR1B is an auxin receptor which positively regulates root growth and nodulation. traits: - entity_name: auxin receptor activity entity: GO:0038198 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: root development entity: GO:0048364 - relation_name: positively regulates relation: RO:0002213 - entity_name: positive regulation of lateral root development entity: GO:1901333 references: - citation: Cai, Wang et al., 2017 doi: 10.1111/nph.14632 pmid: 28598036 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmTIR1C gene_symbol_long: Transport Inhibitor Response 1C gene_model_pub_name: Glyma.19G206800 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G206800 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - TIR1C is most strongly expressed in developing nodules and root meristems. - Expression in roots is upregulated by Bradyrhizobium japonicum and auxin but downregulated by miR393d. phenotype_synopsis: TIR1C is an auxin receptor which positively regulates root growth and nodulation. traits: - entity_name: auxin receptor activity entity: GO:0038198 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: root development entity: GO:0048364 - relation_name: positively regulates relation: RO:0002213 - entity_name: regulation of root meristem growth entity: GO:0010082 - relation_name: positively regulates relation: RO:0002213 references: - citation: Cai, Wang et al., 2017 doi: 10.1111/nph.14632 pmid: 28598036 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmTIR1D gene_symbol_long: Transport Inhibitor Response 1D gene_model_pub_name: Glyma.03G209400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G209400 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - TIR1D is most strongly expressed in developing nodules, main and lateral root tips, and lateral root primordia. - RNAi knockdowns of TIR1D have reduced nodulation. phenotype_synopsis: TIR1D is an auxin receptor which positively regulates root growth and nodulation. traits: - entity_name: auxin receptor activity entity: GO:0038198 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: root development entity: GO:0048364 - relation_name: positively regulates relation: RO:0002213 - entity_name: positive regulation of lateral root development entity: GO:1901333 references: - citation: Cai, Wang et al., 2017 doi: 10.1111/nph.14632 pmid: 28598036 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmAFB3A gene_symbol_long: Auxin-Signaling F-Box 3A gene_model_pub_name: Glyma.19G100200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G100200 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - AFB3A is most strongly expressed in developing nodules, main and lateral roots, and especially in main root tips and lateral root primordia. - AFB3A is upregulated by the presence of auxin but downregulated by miR393d. - RNAi knockdowns of AFB3A have reduced nodulation. - Transgenic overexpression of AFB3A did not increase nodulation. phenotype_synopsis: AFB3A is an auxin receptor which has a minor role in the positive regulation of root growth and nodulation. traits: - entity_name: auxin receptor activity entity: GO:0038198 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: root development entity: GO:0048364 - relation_name: positively regulates relation: RO:0002213 - entity_name: positive regulation of lateral root development entity: GO:1901333 references: - citation: Cai, Wang et al., 2017 doi: 10.1111/nph.14632 pmid: 28598036 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmAFB3B gene_symbol_long: Auxin-Signaling F-Box 3B gene_model_pub_name: Glyma.16G050500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G050500 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Expression of AFB3B is barely detectable in roots and developing nodules. - It is likely involved in shoot development rather than in root growth and nodulation. - RNAi knockdowns of AFB3B have reduced nodulation. phenotype_synopsis: AFB3B is an auxin receptor. traits: - entity_name: auxin receptor activity entity: GO:0038198 - relation_name: positively regulates relation: RO:0002213 - entity_name: shoot system development entity: GO:0048367 references: - citation: Cai, Wang et al., 2017 doi: 10.1111/nph.14632 pmid: 28598036 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmChlI1a gene_symbol_long: Mg-Chelatase Subunit Chl1a gene_model_pub_name: Glyma.13G232500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G232500 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - The MinnGold and T219H phenotypes cosegregate with ChlI1a. Transformation of WT ChlI1a into mutant soy reinstated normal phenotype. phenotype_synopsis: Defective Mg-Chetelase is responsible for chlorophyll deficient MinnGold (y11-2) and T219H (y11) phenotypes. traits: - entity_name: magnesium chelatase activity entity: GO:0016851 - entity_name: leaf chlorophyll content entity: TO:0012002 references: - citation: Campbell, Mani et al., 2014 doi: 10.1534/g3.114.015255 pmid: 25452420 --- scientific_name: Glycine max gene_symbols: - GmChlI1b gene_symbol_long: Mg-Chelatase Subunit Chl1b gene_model_pub_name: Glyma.15G080200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G080200 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - The CD-5 phenotype cosegregates with ChlI1b. phenotype_synopsis: Defective Mg-chetelase is responsible for chlorophyll deficient CD-5 phenotype. traits: - entity_name: magnesium chelatase activity entity: GO:0016851 - entity_name: leaf chlorophyll content entity: TO:0012002 references: - citation: Campbell, Mani et al., 2014 doi: 10.1534/g3.114.015255 pmid: 25452420 --- scientific_name: Glycine max gene_symbols: - GmSACPD-C gene_symbol_long: Delta-9-Stearoyl-Acyl-Carrier Protein Desaturase C gene_model_pub_name: Glyma.14G121400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G121400 confidence: 4 curators: - Ella Townsend - Jacqueline Campbell - Scott Kalberer comments: - GmSACPD-C is one of three SACPD genes involved in delta-9-stearyol-acyl-carrier proteins. - Has homology with SACPD-A and SACPD-B which are also linked to roles in increased stearic acid. - SACPD-B and SACPD-C are both shown to increase stearic acid content in the seed when a deletion occurs in the genes. - SACPD-A has no evidence that mutations increased stearic acid seed content. phenotype_synopsis: GmSACPD-C encodes for the delta-9-stearoyl-acyl-carrier protein desaturase enzyme and is an important gene involved in the conversion of stearic acid into oleic acid. traits: - entity_name: oleic acid content entity: TO:0005002 - entity_name: stearic acid content entity: TO:0005003 - entity_name: acyl carrier activity entity: GO:0000036 - entity_name: unsaturated fatty acid biosynthesis process entity: GO:0006636 - entity_name: sterol desaturase activity entity: GO:0070704 - entity_name: seed entity: PO:0009010 references: - citation: Carrero-Colon, Abshire et al., 2014 doi: 10.1371/journal.pone.0097891 pmid: 24846334 --- scientific_name: Glycine max gene_symbols: - GmFT2b gene_symbol_long: Flowering Locus T-like Protein 2b gene_model_pub_name: Glyma.16G151000 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G151000 confidence: 4 curators: - Greg Murrell - Scott Kalberer comments: - Overexpression of GmFT2b upregulates expression of genes that are important in flowering time regulation. - The major FT2b haplotype Hap3 is associated with significantly earlier flowering at higher latitudes. phenotype_synopsis: GmFT2b promotes flowering under long-day conditions traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 - entity_name: positive regulation of long-day photoperiodism, flowering entity: GO:0048578 references: - citation: Chen, Cai et al., 2020 doi: 10.1111/pce.13695 pmid: 31981430 --- scientific_name: Glycine max gene_symbols: - GmSYP24 - GmLEA2-96 gene_symbol_long: Syntaxin-24 gene_model_pub_name: Glyma.19G198600 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G198600 confidence: 5 curators: - Greg Murrell - Scott Kalberer comments: - GmSYP24 was identified as a dehydration-responsive gene with the expressed protein located on the cell membrane. - Overexpression of SYP24 in soybean and heteroexpression in Arabidopsis produced insensitivity to osmotic/drought stress and high salinity levels. - SYP24-transgenic soybeans had greater water content and higher activities of peroxidase and superoxide dismutase compared with non-transgenic controls following exposure to abiotic stresses. - SYP24-transgenic soybeans showed altered expression of some aquaporins under osmotic/drought, salt, or ABA treatment. - Leaf stomatal density and opening were reduced in SYP24-transgenic Arabidopsis, and ABA-responsive genes were up-regulated. - Sensitivity to ABA was decreased during seed germination of both SYP24-transgenic soybean and Arabidopsis. phenotype_synopsis: GmSYP24 plays an important role to enhance drought response and salt tolerance as part of the ABA signaling pathway. traits: - entity_name: drought tolerance entity: TO:0000276 - relation_name: positively regulates relation: RO:0002213 - entity_name: salt tolerance entity: TO:0006001 - relation_name: positively regulates relation: RO:0002213 - entity_name: abscisic acid-activated signaling pathway entity: GO:0009738 - entity_name: seed germination entity: GO:0009845 references: - citation: Chen, Fang et al., 2019 doi: 10.1038/s41598-019-42332-5 pmid: 30979945 --- scientific_name: Glycine max gene_symbols: - GmDGAT1A gene_symbol_long: Diacylglycerol Acyltransferase 1A gene_model_pub_name: Glyma.13G106100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G106100 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of DGAT1A enhances triacylglycerol biosynthesis in seeds (and in other tissues to a lesser extent). - It is involved in stress response and downregulated by stressors like cold, insect bites, and jasmonate. - DGAT1A produces similar results when transformed into other species. phenotype_synopsis: DGAT1A controls synthesis of many triacylglycerols, using 18:3 acyl CoA as an acyl donor. Oil mostly accumulates in seeds. traits: - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: seed development entity: GO:0048316 references: - citation: Chen, Wang et al., 2016 doi: 10.1038/srep28541 pmid: 27345221 - citation: Li, Hatanaka et al., 2013 doi: 10.1007/s10142-012-0306-z pmid: 23322364 - citation: Zhau, Bi et al., 2019 doi: 10.1016/j.jplph.2019.153019 pmid: 31437808 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmDGAT2D gene_symbol_long: Diacylglycerol Acyltransferase 2D gene_model_pub_name: Glyma.01G156000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G156000 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of DGAT2D enhances triacylglycerol biosynthesis in flower tissues. - DGAT2D is upregulated by temperature stress but downregulated by insect bites and jasmonate. - DGAT2D produces similar results when transformed into other species. phenotype_synopsis: DGAT2D controls synthesis of many triacylglycerols, using 18:1 and 18:2 acyl CoA as acyl donors. Oil accumulates most in flowers. traits: - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: seed development entity: GO:0048316 references: - citation: Chen, Wang et al., 2016 doi: 10.1038/srep28541 pmid: 27345221 --- scientific_name: Glycine max gene_symbols: - GmLHY2a - GmLCL3 - GmMYB156 gene_symbol_long: Late Elongated Hypocotyl 2a gene_model_pub_name: Glyma.19G260900 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G260900 confidence: 5 curators: - Greg Murrell - Scott Kalberer phenotype_synopsis: GmLHY2a encodes a MYB transciption factor that affects plant height through mediating the gibberellin pathway in soybean. traits: - entity_name: plant height entity: TO:0000207 - relation_name: negatively regulates relation: RO:0002212 - entity_name: gibberellin metabolic process entity: GO:0009685 references: - citation: Cheng, Dong et al., 2019 doi: 10.1186/s12870-019-2145-8 pmid: 31852439 --- scientific_name: Glycine max gene_symbols: - GmIFS1 gene_symbol_long: Isoflavone Synthase 1 gene_model_pub_name: EU391460.1 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.07G202300 confidence: 4 curators: - Ella Townsend - Jacqueline Campbell - Scott Kalberer - Steven Cannon comments: - A cytochrome P450 superfamily protein phenotype_synopsis: Involved in producing soybean isoflavonoids, isoflavonoids involved in health benefits for soybean consumption, and more importantly, involved with soybean environmental stress response. traits: - entity_name: plant stress trait entity: TO:0000164 - entity_name: abiotic plant stress trait entity: TO:0000168 - entity_name: biotic plant stress trait entity: TO:0000179 - entity_name: isoflavonoid biosynthetic process entity: GO:0009717 - entity_name: secondary metabolite biosynthetic process entity: GO:0044550 - entity_name: oxidation-reduction process entity: GO:0055114 references: - citation: Cheng, Wang, et al., 2013 doi: 10.1371/journal.pone.0054154 pmid: 23342093 - citation: Jung, Yu, et al. 2013 doi: 10.1038/72671 pmid: 10657130 --- scientific_name: Glycine max gene_symbols: - GmIFS2 gene_symbol_long: Isoflavone Synthase 2 gene_model_pub_name: EU391493.1 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G173500 confidence: 4 curators: - Ella Townsend - Jacqueline Campbell - Scott Kalberer - Steven Cannon comments: - A cytochrome P450 superfamily protein - glyma.Wm82.gnm4.ann1.Glyma.13G173401 is a second equally good match to EU391493, close to the other GmIFS2 gene on chromosome 13 phenotype_synopsis: Involved in producing soybean isoflavonoids, isoflavonoids involved in health benefits for soybean consumption, and more importantly, involved with soybean environmental stress response. traits: - entity_name: plant stress trait entity: TO:0000164 - entity_name: abiotic plant stress trait entity: TO:0000168 - entity_name: biotic plant stress trait entity: TO:0000179 - entity_name: isoflavonoid biosynthetic process entity: GO:0009717 - entity_name: secondary metabolite biosynthetic process entity: GO:0044550 - entity_name: oxidation-reduction process entity: GO:0055114 references: - citation: Cheng, Wang, et al., 2013 doi: 10.1371/journal.pone.0054154 pmid: 23342093 - citation: Jung, Yu, et al. 2013 doi: 10.1038/72671 pmid: 10657130 --- scientific_name: Glycine max gene_symbols: - GmF3H2 gene_symbol_long: Flavanone 3-Hydroxylase 2 gene_model_pub_name: EU391427.1 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.02G048600 confidence: 4 curators: - Ella Townsend - Scott Kalberer - Jacqueline Campbell - Steven Cannon comments: - A cytochrome P450 superfamily protein - glyma.Wm82.gnm4.ann1.Glyma.02G048400 is also a very strong match to EU391427 - GmF3H2 is under more selective pressure than GmIFS1 & GmIFS2. phenotype_synopsis: Involved in flavone 3-hydroxylase synthase and involved in environmental stress responses. traits: - entity_name: plant stress trait entity: TO:0000164 - entity_name: abiotic plant stress trait entity: TO:0000168 - entity_name: biotic plant stress trait entity: TO:0000179 - entity_name: isoflavonoid biosynthetic process entity: GO:0009717 - entity_name: secondary metabolite biosynthetic process entity: GO:0044550 - entity_name: oxidation-reduction process entity: GO:0055114 references: - citation: Cheng, Wang, et al., 2013 doi: 10.1371/journal.pone.0054154 pmid: 23342093 - citation: Jung, Yu, et al. 2013 doi: 10.1038/72671 pmid: 10657130 --- scientific_name: Glycine max gene_symbols: - GmbHLHm1 - GmSAT1 gene_symbol_long: bHLH transcription factor gene_model_pub_name: Glyma08g06880 gene_model_full_id: glyma.gnm2.ann1.Glyma.07g184900 confidence: 5 curators: - Steven Cannon phenotype_synopsis: GmbHLHm1 is important to the soybean rhizobium symbiosis because loss of activity results in a reduction of nodule fitness and growth. Transcriptional changes in nodules highlight downstream signaling pathways involving circadian clock regulation, nutrient transport, hormone signaling, and cell wall modification. comments: - Established using mutation, expression, and related functional tests. - Originally named GmSAT1 (Symbiotic Ammonium Transporter 1) by Kaiser et al., 1998, but does not encode an NH4+ transporter. traits: - entity_name: plant organ growth and development trait entity: TO:0000927 - entity_name: root nodule entity: PO:0003023 references: - citation: Chiasson, Loughlin et al., 2014 doi: 10.1073/pnas.1312801111 pmid: 24707045 - citation: Kaiser, Finnegan et al., 1998 doi: 10.1126/science.281.5380.1202 pmid: 9712587 --- scientific_name: Glycine max gene_symbols: - GmPHYE1 gene_symbol_long: Phytochrome E1 gene_model_pub_name: Glyma.09G088500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.09G088500 confidence: 3 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmTOC1 gene_symbol_long: Timing of CAB Expression 1 gene_model_pub_name: Glyma.06G196200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G196200 confidence: 2 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmGA2OX5 gene_symbol_long: Gibberellin 2 Oxidase 5 gene_model_pub_name: Glyma.13G218200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G218200 confidence: 2 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmGA2OX6 gene_symbol_long: Gibberellin 2 Oxidase 6 gene_model_pub_name: Glyma.13G259400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G259400 confidence: 2 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmMSI1 gene_symbol_long: Multicopy Suppressor of IRA 1 gene_model_pub_name: Glyma.05G131200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G131200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Wu, Kang et al., 2019 doi: 10.3389/fpls.2019.01221 pmid: 31787988 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmKASI gene_symbol_long: Beta-Ketoacyl-Acyl Carrier Protein Synthase I gene_model_pub_name: Glyma.08G084300 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.08G084300 confidence: 4 curators: - Greg Murrell - Scott Kalberer comments: - GmKASI is a fatty acid synthesis enzyme involved in the conversion of sucrose into oil during seed development via elongation of ACP-bound acyl species. phenotype_synopsis: Soybean seeds from a mutagenized plant exhibited doubled sucrose and halved oil content relative to wild type because of disruption to a Beta-Ketoacyl-Acyl Carrier Protein Synthase ortholog (GmKASI) by chromosomal translocation. traits: - entity_name: sucrose content entity: TO:0000328 - relation_name: negatively regulates relation: RO:0002212 - entity_name: fat & essential oil content entity: TO:0000604 - relation_name: positively regulates relation: RO:0002213 - entity_name: fatty acid biosynthetic process entity: GO:0006633 references: - citation: Dobbels, Michno et al., 2017 doi: 10.1534/g3.116.038596 pmid: 28235823 --- scientific_name: Glycine max gene_symbols: - GmMYB118 gene_model_pub_name: GLYMA_17G094400 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.17G094400 confidence: 4 curators: - William Hardison - Scott Kalberer comments: - The GmMYB118 protein is located in the nucleus and is highly responsive to drought, salt, and high temperature stresses as suggested by quantitative real-time PCR. - MYB118 increased tolerance to drought and salt stress and regulated stress-associated gene expression in transgenic Arabidopsis thaliana. MYB118-overexpressing soybeans generated by transformation of the hairy roots with Agrobacterium rhizogenes also showed improved drought and salt tolerance. - Clustered, regularly interspaced, short palindromic repeat (CRISPR)-transformed plants showed reduced drought and salt tolerance. - Proline and chlorophyll contents in MYB118-overexpressor plants were greater than control levels, and their contents in the controls were greater than levels in CRISPR plants under drought and salt stress. Reactive oxygen species and malondialdehyde contents were lower in overexpressor plants than in control plants, whose contents were in turn lower than levels in CRISPR plants under stress conditions. phenotype_synopsis: Improved tolerance to drought and salt stress by GmMYB118 may result from promoting stress-associated gene expression and maintaining cell homeostasis through regulation of osmotic and oxidizing substances. traits: - entity_name: drought tolerance entity: TO:0000276 - entity_name: salt tolerance entity: TO:0006001 - entity_name: plant stress trait entity: TO:0000164 references: - citation: Du, Zhao et al., 2018 doi: 10.1186/s12870-018-1551-7 pmid: 30509166 --- scientific_name: Glycine max gene_symbols: - GmFT2b gene_symbol_long: Flowering Time 2b gene_model_pub_name: Glyma.16G151000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G151000 confidence: 5 curators: - Steven Cannon - Greg Murrell phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Fan, Hu et al., 2014 doi: 10.1186/1471-2229-14-9 pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 - citation: Chen, Cai et al., 2020 doi: 10.1111/pce.13695 pmid: 31981430 --- scientific_name: Glycine max gene_symbols: - GmFT3a gene_symbol_long: Flowering Time 3a gene_model_pub_name: Glyma.16G044200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Fan, Hu et al., 2014 doi: 10.1186/1471-2229-14-9 pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmFT3b gene_symbol_long: Flowering Time 3b gene_model_pub_name: Glyma.19G108100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108100 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Fan, Hu et al., 2014 doi: 10.1186/1471-2229-14-9 pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmFT5b gene_symbol_long: Flowering Time 5b gene_model_pub_name: Glyma.19G108200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G108200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Fan, Hu et al., 2014 doi: 10.1186/1471-2229-14-9 pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max classical_locus: D1 gene_symbols: - GmD1 gene_model_pub_name: Glyma01g42390 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma01g42390 confidence: 5 curators: - William Hardison phenotype_synopsis: chlorophyll retention in mature tissues traits: - entity_name: negative regulation of chlorophyll catabolic process entity: GO:1903647 references: - citation: Fang, Li et al., 2014 doi: 10.1111/tpj.12419 pmid: 24372721 - citation: Schmutz et al., 2010 doi: 10.1038/nature08670 pmid: 20075913 - citation: Chao et al., 1995 doi: 10.1104/pp.107.1.253 pmid: 12228359 --- scientific_name: Glycine max classical_locus: D2 gene_symbols: - GmD2 gene_model_pub_name: Glyma11g02980 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g02980 confidence: 4 curators: - William Hardison phenotype_synopsis: chlorophyll retention in mature tissues traits: - entity_name: negative regulation of chlorophyll catabolic process entity: GO:1903647 references: - citation: Fang, Li et al., 2014 doi: 10.1111/tpj.12419 pmid: 24372721 - citation: Schmutz et al., 2010 doi: 10.1038/nature08670 pmid: 20075913 - citation: Chao et al., 1995 doi: 10.1104/pp.107.1.253 pmid: 12228359 --- scientific_name: Glycine max gene_symbols: - cqSP003 gene_symbol_long: cq SeedProtein-003 gene_model_pub_name: Glyma.20g085100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G085100 confidence: 4 curators: - Raegan Nelson comments: - silencing of the low protien version of Glyma.20g085100 increases seed protien concentration - controls seed protien phenotype - The allele in Williams 82 is 321 bases longer than the higher-protein version in PI 468916. - The low-protein allele in Williams 82 is likely due to a transposon insertion in the low-protein ancestral lineage. - fine mapping of the cqSeed protein-003 shows that it is found between BARCSOYSSR_20_0670 and BARCSOYSSR_20_0674 phenotype_synopsis: Glyma.20g085100 regulates seed protein content by being coincident with the causative polymorphism in cqSeed protein-003 traits: - entity_name: seed protien content entity: TO:0000490 references: - citation: Fliege, Ward et al.,2022 doi: 10.1111/tpj.15658 pmid: 34978122 --- scientific_name: Glycine max gene_symbols: - GmBS1 gene_symbol_long: Big Seeds 1 gene_model_pub_name: Glyma10G38970 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma10G38970 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Downregulation of BS1 increases seed size, weight, and amino acid content. phenotype_synopsis: BS1 negatively regulates the size of seeds, seed pods, and leaves. traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed size entity: TO:0000391 - relation_name: negatively regulates relation: RO:0002212 - entity_name: fat and essential oil content entity: TO:0000604 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Ge, Yu et al., 2016 doi: 10.1073/pnas.1611763113 pmid: 27791139 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max classical_locus: R gene_symbols: - GmR gene_symbol_long: Black or brown seed coat color gene_model_pub_name: Glyma09g36990 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.09G235100 confidence: 3 curators: - Ella Townsend - Jacqueline Campbell - Steven Cannon - Scott Kalberer comments: - The classical R locus is associated with brown coloration of seed coats and hilums. - A loss of function mutation altering the R2R3 MYB transcription factor gene GmR (Glyma09g36990) was proposed as a candidate for the brown hilum phenotype. Expression of this gene is specific to the seed coat. - Gene expression of the functional GmR gene candidate was correlated with expression of an UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT) gene. UF3GT is responsible for the final step in anthocyanin biosynthesis. Conversely, gene expression of this functionless allele of Glyma09g36990 was associated with a failure to upregulate the UF3GT gene. phenotype_synopsis: Gene expression of functional transcription factor GmR is associated with up-regulation of the UF3GT gene and consequent anthocyanin production. traits: - entity_name: Seed coat color entity: TO:0000190 - entity_name: Hilum color entity: TO:0000968 - entity_name: Transcription factor binding entity: GO:0008134 references: - citation: Gillman, Tetlow et al., 2011 doi: 10.1186/1471-2229-11-155 pmid: 22070454 - citation: Zabala, Vodkin, 2014 doi: 10.1371/journal.pone.0111959 pmid: 25369033 - citation: Palmer, Pfeiffer et al., 2004 doi: 10.2134\/agronmonogr16.3ed.c5 pmid: null --- scientific_name: Glycine max gene_symbols: - GmFT1a gene_symbol_long: Flowering Time 1a gene_model_pub_name: Glyma.18G298900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G298900 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Guo, Xu et al., 2015 doi: 10.1371/journal.pone.0136601 pmid: 26371882 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmFT1b gene_symbol_long: Flowering Time 1b gene_model_pub_name: Glyma.18G299000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G299000 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Guo, Xu et al., 2015 doi: 10.1371/journal.pone.0136601 pmid: 26371882 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmKASII-A gene_symbol_long: beta-ketoacyl-ACP synthase II gene_model_pub_name: Glyma17g05200 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g05200 confidence: 3 curators: - Wei Huang comments: - Mutations in the soybean 3-ketoacyl-ACP synthase gene are correlated with high levels of seed palmitic acid phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control traits: - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity entity: GO:0033817 references: - citation: Head, Katie, et al., 2012 doi: 10.1007\/s11032-012-9707-x pmid: null --- scientific_name: Glycine max gene_symbols: - GmKASII-B gene_symbol_long: plastid 3-keto-acyl-ACP synthase II-B gene_model_pub_name: Glyma13g17290 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g17290 confidence: 3 curators: - Wei Huang phenotype_synopsis: Palmitic acid levels were significantly higher in the mutants than in the Williams-82 wild type control traits: - entity_name: beta-ketoacyl-acyl-carrier-protein synthase II activity entity: GO:0033817 references: - citation: Head, Katie, et al., 2012 doi: 10.1007\/s11032-012-9707-x pmid: null --- scientific_name: Glycine max gene_symbols: - GmFAD3-2a - GmFAD3C gene_symbol_long: Omega-3 fatty acid desaturase 3 2a gene_model_pub_name: Glyma18g06950 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g06950 confidence: 5 curators: - Wei Huang comments: - There are four FAD3 homologs (Glyma02g39230, Glyma11g27190, Glyma14g37350 and Glyma18g06950) in the soybean genome with relatively little variation. - Combining three non-functional alleles (GmFAD3-1a, GmFAD3-1b, and GmFAD3-2a), soybean lines containing < 2% α-linolenic acid in their seeds were generated. phenotype_synopsis: GmFAD3-2a plays a critical role in the production of the seed oil α-linolenic acid, and mutations within GmFAD3-2a reduces α-linolenic acid content. traits: - entity_name: alpha-linolenic acid content entity: TO:0005005 - entity_name: omega-3 fatty acid content entity: TO:0005004 - entity_name: omega-3 fatty acid desaturase entity: GO:0042389 references: - citation: Hoshino, Watanabe et al., 2014 doi: 10.1270/jsbbs.64.371 pmid: 25914592 --- scientific_name: Glycine max gene_symbols: - GmFAD3-1a - GmFAD3B gene_symbol_long: Omega-3 fatty acid desaturase 3 1a gene_model_pub_name: Glyma02g39230 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma02g39230 confidence: 5 curators: - Wei Huang comments: - GmFAD3-1a (Glyma02g39230) is one of the FAD3 genes that, along with GmFAD3-1b and GmFAD3-2a, are expressed in soybean seeds and control ALA content in the seed oil. - Non-functional alleles for both GmFAD3-1a and another homolog, GmFAD3-1b (Glyma14g37350), as contributing factors to the overall reduction of α-linolenic acid levels. phenotype_synopsis: By combining non-functional alleles of GmFAD3-1a, GmFAD3-1b, and GmFAD3-2a, soybean lines with reduced ALA content (<2%) in their seeds were obtained. traits: - entity_name: alpha-linolenic acid content entity: TO:0005005 - entity_name: omega-3 fatty acid content entity: TO:0005004 - entity_name: omega-3 fatty acid desaturase entity: GO:0042389 references: - citation: Hoshino, Watanabe et al., 2014 doi: 10.1270/jsbbs.64.371 pmid: 25914592 - citation: Anai, Yamada et al., 2005 doi: 10.13039\/501100001700 pmid: null --- scientific_name: Glycine max gene_symbols: - GmFAD3-1b gene_symbol_long: Omega-3 fatty acid desaturase 3 1b gene_model_pub_name: Glyma14g37350 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma14g37350 confidence: 5 curators: - Wei Huang comments: - GmFAD3-1b (Glyma14g37350) is one of the homologs responsible for the synthesis of α-linolenic acid in soybeans, along with GmFAD3-1a and GmFAD3-2a. phenotype_synopsis: By combining non-functional alleles of GmFAD3-1a, GmFAD3-1b, and GmFAD3-2a, soybean lines with reduced ALA content (<2%) in their seeds were obtained. traits: - entity_name: alpha-linolenic acid content entity: TO:0005005 - entity_name: omega-3 fatty acid content entity: TO:0005004 - entity_name: omega-3 fatty acid desaturase entity: GO:0042389 references: - citation: Hoshino, Watanabe et al., 2014 doi: 10.1270/jsbbs.64.371 pmid: 25914592 - citation: Anai, Yamada et al., 2005 doi: 10.13039\/501100001700 pmid: null --- scientific_name: Glycine max classical_locus: D1 gene_symbols: - GmFLD gene_symbol_long: Flowering Locus D gene_model_pub_name: Glyma02g18610 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma02g18610 confidence: 4 curators: - William Hardison phenotype_synopsis: early flowering time traits: - entity_name: flowering time trait entity: TO:0002616 references: - citation: Hu, Jin et al., 2014 doi: 10.1186/s12870-014-0263-x pmid: 25287450 --- scientific_name: Glycine max gene_symbols: - GmNFR1α gene_symbol_long: Nod Factor Receptor 1α gene_model_pub_name: Glyma.02G270800 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G270800 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Mutants lacking NFR1α don't form nodules. - Transgenic overexpression increased the number of nodules per plant and allowed plants to form nodules in unfavorable conditions. phenotype_synopsis: NFR1α codes for a receptor kinase which positively regulates nodule number. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 references: - citation: Indrasumunar, Searle et al., 2011 doi: 10.1111/j.1365-313X.2010.04398.x pmid: 21175888 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmNFR1β gene_symbol_long: Nod Factor Receptor 1β gene_model_pub_name: Glyma.14G046200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G046200 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Mutants with functional NFR1β but nonfunctional NFR1α have very minimal nodulation. - Overexpression of NFR1β did not increase nodule number. - Expression of NFR1β is not sufficient to induce a healthy level of nodulation. phenotype_synopsis: NFR1β codes for a redundant receptor kinase with unstable mRNA transcripts. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Indrasumunar, Searle et al., 2011 doi: 10.1111/j.1365-313X.2010.04398.x pmid: 21175888 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmERD15B gene_symbol_long: Early Responsive to Dehydration 15B gene_model_pub_name: Glyma.11G149900 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.11G149900 confidence: 4 curators: - Greg Murrell - Steven Cannon - Scott Kalberer comments: - Protein–protein interaction network analysis showed that five out of the top 10 potential interacting proteins of GmERD15B were GmPAB proteins. Two of the GmPAB genes, GmPAB-14G and GmPAB-17G, have annotations related to salt stress responses. phenotype_synopsis: Gene overexpression in Glycine enhanced salt tolerance probably by increasing the expression levels of genes related to ABA-signalling, proline content, catalase peroxidase, dehydration response and cation transport. traits: - entity_name: salt tolerance entity: TO:0006001 - relation_name: positively regulates relation: RO:0002213 references: - citation: Jin, Sun et al., 2021 doi: 10.1111/pbi.13536 pmid: 33368860 --- scientific_name: Glycine max gene_symbols: - GmDMI1-3 gene_symbol_long: Doesn't Make Infections 1-3 gene_model_pub_name: Glyma.19G263500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G263500 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Transgenic overexpression of DMI1 reduces Heterodera glycines parasitism and increases nodulation. RNAi silencing of DMI1 increases suceptibility to H. glycines and reduces nodulation. phenotype_synopsis: DMI genes confer resistance to H. glycines nematodes and are necessary for establishing symbiosis. DMI1 encodes a channel protein that controls the signalling pathway leading to nodulation. traits: - entity_name: biological process involved in symbiotic interaction entity: GO:0044403 - entity_name: nodulation entity: GO:0009877 - entity_name: defense response to nematode entity: GO:0002215 references: - citation: Khatri, Pant et al., 2022 doi: 10.3389/fpls.2022.842597 pmid: 35599880 --- scientific_name: Glycine max gene_symbols: - GmDMI2-7 gene_symbol_long: Doesn't Make Infections 2-7 gene_model_pub_name: Glyma.11G246200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G246200 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Transgenic overexpression of DMI2 reduces Heterodera glycines parasitism and increases nodulation even without rhizobia. RNAi silencing of DMI2 increases suceptibility to H. glycines and reduces nodulation. phenotype_synopsis: DMI genes confer resistance to H. glycines nematodes and are necessary for establishing symbiosis. DMI2 encodes a kinase. traits: - entity_name: biological process involved in symbiotic interaction entity: GO:0044403 - entity_name: nodulation entity: GO:0009877 - entity_name: defense response to nematode entity: GO:0002215 - entity_name: protein kinase activity entity: GO:0004672 references: - citation: Khatri, Pant et al., 2022 doi: 10.3389/fpls.2022.842597 pmid: 35599880 --- scientific_name: Glycine max gene_symbols: - GmDMI3-2 gene_symbol_long: Doesn't Make Infections 3-2 gene_model_pub_name: Glyma.15G222300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.15G222300 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Transgenic overexpression of DMI3 reduces Heterodera glycines parasitism and increases nodulation even without rhizobia. RNAi silencing of DMI3 increases suceptibility to H. glycines and reduces nodulation. phenotype_synopsis: DMI genes confer resistance to H. glycines nematodes and are necessary for establishing symbiosis. DMI3 encodes a kinase. traits: - entity_name: biological process involved in symbiotic interaction entity: GO:0044403 - entity_name: nodulation entity: GO:0009877 - entity_name: defense response to nematode entity: GO:0002215 - entity_name: protein kinase activity entity: GO:0004672 references: - citation: Khatri, Pant et al., 2022 doi: 10.3389/fpls.2022.842597 pmid: 35599880 --- scientific_name: Glycine max classical_locus: E9 gene_symbols: - GmFT2a gene_symbol_long: Flowering Time 2a gene_model_pub_name: Glyma.16g150700 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G150700 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Kong, Liu et al., 2010 doi: 10.1104/pp.110.160796 pmid: 20864544 - citation: Kong, Nan et al., 2014 doi: 10.13039\/501100001809 pmid: null - citation: Takeshima, Hayashi et al., 2016 doi: 10.1093/jxb/erw283 pmid: 27422993 - citation: Zhao, Takeshima et al., 2016 doi: 10.1186/s12870-016-0704-9 pmid: 26786479 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmFT5a gene_symbol_long: Flowering Time 5a gene_model_pub_name: Glyma.16G044100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G044100 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Kong, Liu et al., 2010 doi: 10.1104/pp.110.160796 pmid: 20864544 - citation: Fan, Hu et al., 2014 doi: 10.1186/1471-2229-14-9 pmid: 24397545 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmVPS8a gene_symbol_long: Vacuolar Protein Sorting 8 gene_model_pub_name: Glyma.07g049700 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.07g049700 confidence: 5 curators: - Wei Huang comments: - GmVPS8a plays a conserved and essential role in controlling plant architecture. - This study revealed that GmVPS8a influences key pathways involved in auxin signaling, sugar transport, and lipid metabolism, which collectively modulate plant growth and development. phenotype_synopsis: Mutation of GmVPS8a leads to a compact plant architecture characterized by shorter plant height, reduced leaf petiole length, and altered leaf shape. traits: - entity_name: plant height entity: TO:0000207 - entity_name: petiole length entity: TO:0000766 - entity_name: leaf width entity: TO:0000370 - entity_name: protein binding entity: GO:0005515 - entity_name: intracellular protein transport entity: GO:0006886 - entity_name: vesicle-mediated transport entity: GO:0016192 references: - citation: Kong, Xu et al., 2023 doi: 10.1016/j.plantsci.2023.111677 pmid: 36931563 --- scientific_name: Glycine max classical_locus: O gene_symbols: - GmANR1 gene_symbol_long: Anthocyanidin Reductase 1 gene_model_pub_name: Glyma08G06630 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.08G062000 confidence: 3 curators: - Ella Townsend - Scott Kalberer comments: - The seed-coat color phenotypes Brown (O) and red-brown (o) are controlled by the O locus in an irT (brown) genetic background (alternative to iRT black background). - GmANR1 (Glyma08G06630) is 70% identical to GmANR2 (Glyma08G06640). - ANR1 is highly and predominantly expressed in the seed coat. - Lines associated with red-brown seed coat color showed strong decreases in soluble proanthocyanidin (PA) levels and small increases in anthocyanins relative to brown-pigmented lines. - Spontaneous mutant and EMS-mutagenized lines with red-brown seed coats exhibited reduced ANR1 gene expression in the testa and lower ANR1 activity in vitro, respectively. - ANR1 mutations that either impair gene expression or enzyme activity may result in a red-brown seed coat phenotype and possibly redirect cyanidin substrate towards enhanced anthocyanin biosynthesis. phenotype_synopsis: GmANR1 (Glyma08G06630) produces brown seed coat color through the reduction of cyanidin (a reddish-purple anthocyanidin) to (-)-epicatechin, a monomer used to build flavonoid proanthocyanidins. traits: - entity_name: Seed coat color entity: TO:0000190 - entity_name: Flavonoid metabolic process entity: GO:0009812 - entity_name: Anthocyanidin reductase activity entity: GO:0033729 references: - citation: Kovinich, Saleem et al., 2012 doi: 10.1021/jf2033939 pmid: 22107112 - citation: Palmer, Pfeiffer et al., 2004 doi: 10.2134\/agronmonogr16.3ed.c5 pmid: null --- scientific_name: Glycine max gene_symbols: - GmANR2 gene_symbol_long: Anthocyanidin Reductase 2 gene_model_pub_name: Glyma08G06640 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.08G062100 confidence: 2 curators: - Ella Townsend - Scott Kalberer comments: - GmANR2 is not highly expressed within the seed coat. - ANR2 is expressed at low levels throughout all organs. phenotype_synopsis: An anthocyanidin reductase of undetermined significance that is found in many tissues. traits: - entity_name: Flavonoid metabolic process entity: GO:0009812 references: - citation: Kovinich, Saleem et al., 2012 doi: 10.1021/jf2033939 pmid: 22107112 --- scientific_name: Glycine max classical_locus: Gp11 gene_symbols: - GmPRR3A gene_symbol_long: Pseudo Response Regulator 3A gene_model_pub_name: Glyma11g15580 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g15580 confidence: 3 curators: - William Hardison comments: - Glyma11g15580 pseudo-response regulator 3 - Gp11 and Gp12 regulate the expression of GmFT2a and GmFT5a phenotype_synopsis: Shorter growth period traits: - entity_name: days to maturity entity: TO:0000469 references: - citation: Li, Liu et al., 2019 doi: 10.1093/pcp/pcy215 pmid: 30418611 --- scientific_name: Glycine max classical_locus: Gp12 gene_symbols: - GmPRR3B gene_symbol_long: Pseudo Response Regulator 3B gene_model_pub_name: Glyma12g07861 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12g07861 confidence: 3 curators: - William Hardison comments: - Gp11 and Gp12 regulate the expression of GmFT2a and GmFT5a - Glyma12g07861 pseudo-response regulator 7 phenotype_synopsis: Shorter growth period traits: - entity_name: days to maturity entity: TO:0000469 references: - citation: Li, Liu et al., 2019 doi: 10.1093/pcp/pcy215 pmid: 30418611 --- scientific_name: Glycine max gene_symbols: - GmRIN1 - GmSPA3a gene_symbol_long: reduced internode 1 gene_model_pub_name: Glyma.12G224600 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.12G224600 confidence: 5 curators: - Raegan Nelson comments: - A positive regulator of node number and internode length, which together determine soybean height - RIN1 is strongly expressed in the shoot axillary meristems, trifoliate leaves and the leaf primordia - High RIN1 expression in the shoot apical meristem at early phases of vegetative suggests the potential function in node number and size - RIN1 can interact directly with both STF1 and STF2 and promote degradation of STF1 and STF2 - Suppresses the expression of GA2ox7a and GA2ox7b, which negatively regulates the shoot apical meristem development - RIN1 improves soybean yield under high-density planting conditions compared to HN35 (Heinong 35) which is a popular cultivar known for its high yield - RIN1 functions might be upstream of STF1 and STF2 and partially depends on STF1 and STF2 phenotype_synopsis: RIN1 is a positive regulator of node number and internode length and a negative regulator of the shoot apical meristem traits: - entity_name: stem internode morphology trait entity: TO:0000756 - entity_name: yield trait entity: TO:0000371 - entity_name: Stem node number entity: TO:0000634 - entity_name: negative regulation of shoot apical meristem development entity: GO:1902184 references: - citation: Li, Sun et al., 2023 doi: 10.1038/s41467-023-42991-z pmid: 38040709 --- scientific_name: Glycine max gene_symbols: - GmSTF1 gene_symbol_long: TGACG-motif binding factor 1 gene_model_pub_name: Glyma.18G117100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.18G117100 confidence: 5 curators: - Raegan Nelson comments: - soybean homoloug of Arabidopsis ELONGATED HYPOCOTYL 5 (HY5) - Directly activates GA2ox expression, which promotes the elongation of soybean internodes - RIN1 can interact with STF1 and promote degregation - RIN1 functions might be upstream of STF1 and STF2 and partially depends on STF1 and STF2 phenotype_synopsis: STF1 controls internode elgonation by regulating transcription of GA2ox7 genes traits: - entity_name: stem internode morphology trait entity: TO:0000756 references: - citation: Li, Sun et al., 2023 doi: 10.1038/s41467-023-42991-z pmid: 38040709 --- scientific_name: Glycine max gene_symbols: - GmSTF2 gene_symbol_long: TGACG-motif binding factor 2 gene_model_pub_name: Glyma.08G302500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G302500 confidence: 5 curators: - Raegan Nelson comments: - soybean homoloug of Arabidopsis ELONGATED HYPOCOTYL 5 (HY5) - Directly activates GA2ox expression, which promotes the elongation of soybean internodes - RIN1 can interact with STF2 and promote degregation - RIN1 functions might be upstream of STF1 and STF2 and partially depends on STF1 and STF2 phenotype_synopsis: STF2 controls internode elgonation by regulating transcription of GA2ox7 genes traits: - entity_name: stem internode morphology trait entity: TO:0000756 - entity_name: positive regulation of shoot apical meristem development entity: GO:1902185 references: - citation: Li, Sun et al., 2023 doi: 10.1038/s41467-023-42991-z pmid: 38040709 --- scientific_name: Glycine max gene_symbols: - GmGA2ox7a gene_symbol_long: gibberellin 2 oxidase 7a gene_model_pub_name: Glyma.20G141200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G141200 confidence: 5 curators: - Raegan Nelson comments: - plays a role in the CRY1–STF–gibberellin module to regulate low-blue-light-mediated plant height in soybean - inhibits gibberellin catabolism in the shoot apical meristem - RIN1 represses GA2ox7a expression in shoot apical meristems, STF1 and STF2 promote GA2ox7a expression phenotype_synopsis: GA2ox7a supresses gibberellin catabolism, which promotes shoot apical meristem development traits: - entity_name: stem internode morphology trait entity: TO:0000756 - entity_name: positive regulation of shoot apical meristem development entity: GO:1902185 - entity_name: gibberellin catabolic process entity: GO:0045487 references: - citation: Li, Sun et al., 2023 doi: 10.1038/s41467-023-42991-z pmid: 38040709 --- scientific_name: Glycine max gene_symbols: - GmGA2ox7b gene_symbol_long: gibberellin 2 oxidase 7b gene_model_pub_name: Glyma.11G003200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G003200 confidence: 5 curators: - Raegan Nelson comments: - plays a role in the CRY1–STF–gibberellin module to regulate low-blue-light-mediated plant height in soybean - inhibits gibberellin catabolism in the shoot apical meristem - RIN1 represses GA2ox7b expression in shoot apical meristems, STF1 and STF2 promotes GA2ox7b expression phenotype_synopsis: GA2ox7b supresses gibberellin catabolism, which promotes shoot apical meristem development traits: - entity_name: stem internode morphology trait entity: TO:0000756 - entity_name: positive regulation of shoot apical meristem development entity: GO:1902185 - entity_name: gibberellin catabolic process entity: GO:0045487 references: - citation: Li, Sun et al., 2023 doi: 10.1038/s41467-023-42991-z pmid: 38040709 --- scientific_name: Glycine max classical_locus: null gene_symbols: - GmDT2 gene_symbol_long: Determinacy 2 gene_model_pub_name: SoyZH13_18G242900 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.18G273600 confidence: 5 curators: - Brandon Jordan phenotype_synopsis: In the presence of Dt1, Dt2 impacts determinacy, maturity, and branch number. comments: - knockout of SoyZH13_18g242900 produces plants with increased branch number and delayed flowering and maturity relative to wildtype. traits: - entity_name: shoot branching entity: TO:0002639 - relation_name: increased amount relation: PATO:0000470 references: - citation: Liang, Chen, et al., 2022 doi: 10.1038/s41467-022-34153-4 pmid: 36307423 - citation: Ping, Liu, et al., 2014 doi: 10.1105/tpc.114.126938 pmid: 25005919 --- scientific_name: Glycine max classical_locus: E4 gene_symbols: - GmphyA2 gene_symbol_long: Earliness 4 gene_model_pub_name: Glyma.20G090000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G090000 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Liu, Jiang et al., 2008 doi: 10.1111/nph.14884 pmid: 29120038 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmVTL1a gene_symbol_long: Vacuolar Iron Transporter Like 1A gene_model_pub_name: Glyma.05G121600 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05G121600 confidence: 3 curators: - William Hardison comments: - also known as glyma.Wm82.gnm2.ann1.Glyma.08G076300.1 - iron import into symbiosomes from infected cell cytosol phenotype_synopsis: Nitrogen fixation in the nodules traits: - entity_name: indeterminate root nodule nitrogen fixation zone entity: ENVO:01000171 references: - citation: Liu, Liao et al., 2020 doi: 10.1111/nph.16506 pmid: 32119117 --- scientific_name: Glycine max gene_symbols: - GmVTL1b gene_symbol_long: Vacuolar Iron Transporter Like 1B gene_model_pub_name: Glyma.08G076300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G076300 confidence: 3 curators: - William Hardison comments: - Failed to keep wildtype phenotype phenotype_synopsis: lack of iron homeostasis traits: - entity_name: indeterminate root nodule nitrogen fixation zone entity: ENVO:01000171 references: - citation: Liu, Liao et al., 2020 doi: 10.1111/nph.16506 pmid: 32119117 --- scientific_name: Glycine max gene_symbols: - GmDT1 gene_symbol_long: Determinacy 1 gene_model_pub_name: Glyma.19g194300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G194300 confidence: 5 curators: - Brandon Jordan phenotype_synopsis: determinate stem growth habit traits: - entity_name: meristem identity entity: TO:0006017 - relation_name: terminal relation: PATO:0002476 references: - citation: Liu, Watanabe et al., 2010 doi: 10.1104/pp.109.150607 pmid: 20219831 --- scientific_name: Glycine max gene_symbols: - GmPHR1 gene_symbol_long: Phosphate Starvation Response 1 gene_model_pub_name: Glyma.01G009600 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G009600 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmPHR1 is expressed throughout nodules and expression increases as nodules develop. - Transgenic overexpression increased nodule size and increased the concentration of N and P. - PHR1 and GmPHR4 promote each other's expression. - When phosphorus is abundant, overexpression of PHR1 represses GmPHT1-4. - PHR1 positively regulates GmPAP12 (see Wang, Yang et al., 2020). phenotype_synopsis: GmPHR1 is a constitutively expressed transcription factor which induces expression of GmPHT1s to promote phosphate uptake. Together, PHRs and PHT1s maintain inorganic phosphate (Pi) homeostasis in nodules. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Lu, Cheng et al., 2020 doi: 10.1104/pp.19.01209 pmid: 32680974 - citation: Isidra-Arellano, Pozas-Rodríguez et al., 2020 doi: 10.1111/tpj.14789 pmid: 32344464 - citation: Wang, Yang et al., 2020 doi: 10.3389/fpls.2020.00450 pmid: 32499790 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmPHR4 gene_symbol_long: Phosphate Starvation Response 4 gene_model_pub_name: Glyma.02G108500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G108500 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmPHR4 is expressed in noninfected nodule tissues. Transgenic overexpression increased nodule size but decreased nodule number. - PHR4 targets GmPHT1-1, GmPHT1-4, and GmPHT1-11. - PHR4 and GmPHR1 promote each other's expression. - When phosphorus is abundant, overexpression of PHR4 increases expression of PHT1-4. - Silencing of PHR4 had no effect on PHT1-4 expression. phenotype_synopsis: GmPHR4 is a constitutively expressed transcription factor which induces expression of GmPHT1s to promote phosphate uptake. Together, PHRs and PHT1s maintain inorganic phosphate (Pi) homeostasis in nodules. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Lu, Cheng et al., 2020 doi: 10.1104/pp.19.01209 pmid: 32680974 --- scientific_name: Glycine max gene_symbols: - GmPHT1-1 gene_symbol_long: Phosphate Transporter 1-1 gene_model_pub_name: Glyma10G33030 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma10G33030 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Expression is enhanced by GmPHR1 in N2-fixing regions. - Expression is enhanced in non N2-fixing regions by both PHR1 and GmPHR4. - Expression of GmPHT1-1 is positively correlated with nitrogen fixation. phenotype_synopsis: GmPHT1-1 is a target of GmPHR1 and GmPHR4. It encodes a plasma membrane phosphate transporter. traits: - entity_name: inorganic phosphate transmembrane transporter activity entity: GO:0005315 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Lu, Cheng et al., 2020 doi: 10.1104/pp.19.01209 pmid: 32680974 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmPHT1-4 gene_symbol_long: Phosphate Transporter 1-4 gene_model_pub_name: Glyma.10G036800 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G036800 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmPHR1 and GmPHR4 enhance expression of GmPHT1-4 in non N2-fixing regions. - When phosphorus concentration is low, PHR4 enhances PHT1-4 expression. - When phosphorus is readily available, overexpression of PHR1 represses PHT1-4. - Expression of GmPHT1-1 is positively correlated with nitrogen fixation. phenotype_synopsis: GmPHT1-4 is a target of GmPHR1 and GmPHR4. It encodes a plasma membrane phosphate transporter. traits: - entity_name: inorganic phosphate transmembrane transporter activity entity: GO:0005315 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Lu, Cheng et al., 2020 doi: 10.1104/pp.19.01209 pmid: 32680974 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmPHT1-11 gene_symbol_long: Phosphate Transporter 1-11 gene_model_pub_name: Glyma.14G188000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G188000 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmPHT1-11 is expressed in noninfected nodule tissues. - RNAi silencing of PHT1-11 increased nodule number but decreased nodule size and nitrogenase activity. - Transgenic overexpression of PHT1-11 enhanced nitrogenase activity. - Expression of PHT1-11 is enhanced by GmPHR1, except in N2-fixing regions, where PHR1 represses PHT1-11. - PHT1-11 is repressed by GmPHR4. - Overexpression of PHT1-11 represses GmPHT1-4. phenotype_synopsis: GmPHT1-11 is targeted by GmPHR1 and GmPHR4. It encodes a plasma membrane phosphate transporter. traits: - entity_name: inorganic phosphate transmembrane transporter activity entity: GO:0005315 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Lu, Cheng et al., 2020 doi: 10.1104/pp.19.01209 pmid: 32680974 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - Tof11 - PRR3a gene_symbol_long: Time of Flowering 11 gene_model_pub_name: SoyZH13_11G141200 gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_11G141200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Lu, Dong et al., 2020 doi: 10.1038/s41588-020-0604-7 pmid: 32231277 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - Tof12 - PRR3b gene_symbol_long: Time of Flowering 12 gene_model_pub_name: SoyZH13_12G067700 gene_model_full_id: glyma.Zh13.gnm1.ann1.SoyZH13_12G067700 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Lu, Dong et al., 2020 doi: 10.1038/s41588-020-0604-7 pmid: 32231277 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmNFYA gene_symbol_long: Nuclear Transcription Factor Y Subunit gene_model_pub_name: Glyma.02G303800 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G303800 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression enhances seed oil content and salt tolerance. phenotype_synopsis: NFYA is a transcription factor which is induced by salt stress and regulates seed oil metabolism by acting as a positive regulator of lipid biosynthesis. traits: - entity_name: salt tolerance entity: TO:0006001 - entity_name: fatty acid biosynthetic process entity: GO:0006633 - entity_name: regulation of metabolic process entity: GO:0019222 references: - citation: Lu, Wei et al., 2021 doi: 10.1111/pbi.13668 pmid: 34265872 - citation: Lu, Li et al., 2016 doi: 10.1111/tpj.13181 pmid: 27062090 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max classical_locus: J gene_symbols: - GmELF3 gene_symbol_long: Early Flowering 3 gene_model_pub_name: Glyma.04G050200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G050200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Lu, Zhao et al., 2017 doi: 10.1038/ng.3819 pmid: 28319089 - citation: Yue, Liu et al., 2017 doi: 10.1016/j.molp.2016.12.004 pmid: 27979775 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - LHY1a gene_symbol_long: Leafy 1a gene_model_pub_name: Glyma.16G017400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G017400 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Lu, Zhao et al., 2017 doi: 10.1038/ng.3819 pmid: 28319089 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - LHY1b gene_symbol_long: Leafy 1b gene_model_pub_name: Glyma.07G048500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.07G048500 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Lu, Zhao et al., 2017 doi: 10.1038/ng.3819 pmid: 28319089 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - LHY2a - GmLHY2a - LCL3 - MYB156 gene_symbol_long: Leafy 2a gene_model_pub_name: Glyma.19G260900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G260900 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation comments: - Encodes a MYB transciption factor that affects plant height through mediating the GA pathway in soybean traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Lu, Zhao et al., 2017 doi: 10.1038/ng.3819 pmid: 28319089 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 - citation: Chen, Cai et al., 2020 doi: 10.1111/pce.13695 pmid: 31981430 --- scientific_name: Glycine max gene_symbols: - LHY2b gene_symbol_long: Leafy 2b gene_model_pub_name: Glyma.03G261800 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G261800 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: positively regulates relation: RO:0002213 - entity_name: days to maturity entity: TO:0000469 - relation_name: positively regulates relation: RO:0002213 references: - citation: Lu, Zhao et al., 2017 doi: 10.1038/ng.3819 pmid: 28319089 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmLEC2a - GmLEC2 gene_symbol_long: Leafy Cotyledon 2 gene_model_pub_name: Glyma.20G035700 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G035700 confidence: 4 curators: - Greg Murrell phenotype_synopsis: Regulation of genes involved in biosynthesis and catabolism of seed storage and development. traits: - entity_name: seed growth and development trait entity: TO:0000653 - entity_name: triglyceride catabolic process entity: GO:0019433 - relation_name: negatively regulates relation: RO:0002212 - entity_name: carbohydrate biosynthetic process entity: GO:0016051 - relation_name: negatively regulates relation: RO:0002212 - entity_name: regulation of gene expression entity: GO:0010468 references: - citation: Manan, Ahmad et al., 2017 doi: 10.3389/fpls.2017.01604 pmid: 28979275 --- scientific_name: Glycine max gene_symbols: - GmZTL3 gene_symbol_long: Zeitlupe 3 gene_model_pub_name: glyma.15G174800 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15G174800 confidence: 2 curators: - Raegan Nelson comments: - GmZTL3 expression remains constant regardless of short or long day conditions - GmZTL3 is detectable in many different organs includeing roots, stem and pod wall - Constitutive expression of GmZTL3 delayed flower time and produced more leaves in Arabidopsis phenotype_synopsis: GmZTL3 functions as a photoreceptor and plays a role in flowering time and leaf development traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: leaf yeild trait entity: TO:0000870 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Xue, Zhang et al., 2012 doi: 10.1007/s11033-011-0875-2 pmid: 21617948 --- scientific_name: Glycine max gene_symbols: - GmSOC1 gene_symbol_long: Supressor of overexpression of constans 1 gene_model_pub_name: NM_001249448 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.18G224500 confidence: 3 curators: - Raegan Nelson comments: - High expression of GmSOC1 was found in the shoot apex during the transition from vegetative growth to flowering - GmFT2a may regulate the expression of GmSOC1 during flowering - Expression of GmSOC1 in the shoot apex follows a circadian rhythm during SD conditions increaseing at night phenotype_synopsis: GmSOC1-like is a floral inducer traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: positive regulation of short-day photoperiodism, flowering entity: GO:0048576 - entity_name: positive regulation of long-day photoperiodism, flowering entity: GO:0048578 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Na, Jian et al., 2013 doi: 10.1007/s00299-013-1419-0 pmid: 23636663 --- scientific_name: Glycine max gene_symbols: - GmSOC1-like gene_symbol_long: Supressor of overexpression of constans like gene_model_pub_name: XM_003534550 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.09G266200 confidence: 3 curators: - Raegan Nelson comments: - High expression of GmSOC1-like was found in the shoot apex during the transition from vegetative growth to flowering - Regulatory function of GmSOC1-like may be diversified in various plant organs, but its main function might be the same as GmSOC1 - The up-regulation of GmFT5a is earlier than that of GmSOC1-like suggesting that it is apart of promotion of GmSOC1-like - Expression of GmSOC1-like in the shoot apex follows a circadian rhythm during SD conditions increaseing at night phenotype_synopsis: GmSOC1-like is a floral inducer traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: positive regulation of short-day photoperiodism, flowering entity: GO:0048576 - entity_name: positive regulation of long-day photoperiodism, flowering entity: GO:0048578 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Na, Jian et al., 2013 doi: 10.1007/s00299-013-1419-0 pmid: 23636663 --- scientific_name: Glycine max classical_locus: qFT12-2 gene_symbols: - GmPRR37 gene_symbol_long: Pseudo response regulator 37 gene_model_pub_name: Glyma.12G073900 gene_model_full_id: glyma.Wm82.gnm6.ann1.Glyma.12G073900 confidence: 5 curators: - Raegan Nelson comments: - GmPRR37 is primarily expressed in unifoliate and trifoliolate leaves - GmPRR37 showed diurnal expression that peaked in the afternoon ~8 h after the lights were turned on under both LD and SD conditions - GmPRR37 promotes Ft1a and supressed Ft2a and FT5a expression under only LD conditions phenotype_synopsis: GmPRR37 delays flowering time traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: negative regulation of long-day photoperiodism, flowering entity: GO:0048579 - entity_name: positive regulation of long-day photoperiodism, flowering entity: GO:004857 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Wang, Sun et al., 2020 doi: 10.1111/pbi.13346 pmid: 31981443 --- scientific_name: Glycine max gene_symbols: - GmSVP1 gene_symbol_long: Short vegetative stage 1 gene_model_pub_name: Glyma01g02880 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.01G023500 confidence: 5 curators: - Raegan Nelson comments: - GmSVP1 is found in all floral organs - GmSVP1 induces flowering - GmSVP1 shows high expression in reaction to low temperature, wounding and salt treatments but low expression when reacting to heat stress phenotype_synopsis: GmSVP1 acts as a regulator for flowering traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: floral organ development entity: GO:0048437 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Zhang, Yan et al., 2016 doi: 10.13039\/501100012166 pmid: null --- scientific_name: Glycine max gene_symbols: - GmSVP2 gene_symbol_long: Short vegetative stage 2 gene_model_pub_name: Glyma02g04710 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.02G041500 confidence: 5 curators: - Raegan Nelson comments: - GmSVP2 is found in all floral organs - GmSVP2 induces flowering - GmSVP2 maintained relatively low expression levels to no change in expression when put under the four stressors phenotype_synopsis: GmSVP2 acts as a regulator for flowering traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: floral organ development entity: GO:0048437 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Zhang, Yan et al., 2016 doi: 10.13039\/501100012166 pmid: null --- scientific_name: Glycine max classical_locus: D gene_symbols: - GmFDL19 gene_symbol_long: Flower Locus D-like 19 gene_model_pub_name: Glyma19g30230 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G122800 confidence: 5 curators: - Raegan Nelson comments: - Overexpression of GmFDL19 causes early flowering - GmFDL19 is required for GmFT2a- and GmFT5a-regulated flowering system - GmFT2a promotes early flowering through both transcriptional upregulation of and physical interaction with GmFDL19 while GmFT5a only promotes flowering through physical interaction with the protien phenotype_synopsis: GmFDL19 promotes flowering in soybeans traits: - entity_name: Flowering time trait entity: TO:0002616 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Nan, Cao et al., 2014 doi: 10.1371/journal.pone.0097669 pmid: 24845624 --- scientific_name: Glycine max gene_symbols: - GmCRY1a gene_symbol_long: Cryptochrome 1a gene_model_pub_name: DQ401046 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.04G101500 confidence: 5 curators: - Raegan Nelson comments: - GmCRY1a is found in the nuclei of soybean leaf tissues and expressed throughout soybean development - GmCRY1a promotes flowering by stimulating mRNA expression of the flowering time locus - GmCRY1a has a circadian rhythm in long day and short day conditions - GmCRY1a is associated with the latitudinal cline in photoperiodic flowering of soybean phenotype_synopsis: GmCRY1a is a positive regulator of floral initiation in soybean traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: positive regulation of long-day photoperiodism, flowering entity: GO:004857 - entity_name: positive regulation of short-day photoperiodism, flowering entity: GO:0048576 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Shang, Li et al., 2008 doi: 10.1073/pnas.0810585105 pmid: 19106300 --- scientific_name: Glycine max gene_symbols: - GmCRY2a gene_symbol_long: Cryptochrome 2a gene_model_pub_name: DQ401047 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G180600 confidence: 5 curators: - Raegan Nelson comments: - GmCRY2a is found in the nuclei of soybean leaf tissues and expressed throughout soybean development - GmCRY2a is follows a circadian rhythm in LD conditions, but is not in SD conditions - GmCRY2a is degraded in response to blue light phenotype_synopsis: GmCRY2a a role in blue light inhibition of cell elongation traits: - entity_name: cell elongation trait entity: TO:0002687 - entity_name: cellular response to blue light entity: GO:0071483 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Shang, Li et al., 2008 doi: 10.1073/pnas.0810585105 pmid: 19106300 --- scientific_name: Glycine max gene_symbols: - GmVRN1-like gene_symbol_long: Vernalization 1-like gene_model_pub_name: Glyma11g13220 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.11G124200 confidence: 5 curators: - Raegan Nelson comments: - GmVRN1-like is involved in the late flowering phenotype in soybeans - GmVRN1-like may play a role in low temperature induced flowering in soybean - GmVRN1-like is photoperiod responsive in soybean - Ectopic expression of GmVRN1-like causes early flowering in Arabidopsis phenotype_synopsis: GmVRN1 is involved in flowering regulation in soybeans traits: - entity_name: Flowering time trait entity: TO:0002616 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Li, Suo et al., 2015 doi: 10.1186/s12870-015-0602-6 pmid: 26420429 - citation: Suo, Lu et al., 2016 doi: 10.1007\/s11738-016-2136-4 pmid: null --- scientific_name: Glycine max gene_symbols: - GmAP1 gene_symbol_long: APETALA1 gene_model_pub_name: Glyma16g13070 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G091300 confidence: 5 curators: - Raegan Nelson comments: - GmAP1 transcription was detected in both the apical inflorescence meristem and lateral floral meristems - GmAP1 is a nuclear-localized transcription activator - Overexpression of GmAP1 in tobacco leads to early flowering phenotype and some flower morphology changes in the stamen - GmAP1 is a MADS-box transcription factor phenotype_synopsis: GmAP1 is involved in flowering time and morphology in soybeans traits: - entity_name: Flowering time trait entity: TO:0002616 - entity_name: Flowering morphology trait entity: TO:0000499 references: - citation: Molinari, Fuganti-Pagliarini et al., 2021 doi: 10.1590/1678-4685-GMB-2021-0016 pmid: 34919115 - citation: Chi, Huang et al., 2011 doi: 10.1016/j.jplph.2011.08.007 pmid: 21963279 --- scientific_name: Glycine max gene_symbols: - GmELF5 gene_symbol_long: Early Flowering 5 gene_model_pub_name: Glyma.05G031100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G031100 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Noh, Bizzell et al., 2004 doi: 10.1111/j.1365-313X.2004.02072.x pmid: 15125772 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmTEM1a gene_symbol_long: Tempranillo 1a gene_model_pub_name: Glyma.20G186200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.20G186200 confidence: 3 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Noh, Bizzell et al., 2004 doi: 10.1111/j.1365-313X.2004.02072.x pmid: 15125772 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmCAMTA12 gene_symbol_long: Calmodulin Binding Transcription Activator 12 gene_model_pub_name: Glyma.17G031900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G031900 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of GmCAMTA12 increases drought tolerance in Glycine max and Arabidopsis thaliana. phenotype_synopsis: GmCAMTA12 affects the expression of many genes involved in stress tolerance. traits: - entity_name: abiotic plant stress trait entity: TO:0000168 - entity_name: drought tolerance entity: TO:0000276 - entity_name: calmodulin binding entity: GO:0005516 references: - citation: Noman, Jameel et al., 2019 doi: 10.3390/ijms20194849 pmid: 31569565 - citation: Wang, Zeng et al., 2015 doi: 10.1007\/s11104-014-2267-6 pmid: null --- scientific_name: Glycine max gene_symbols: - GmABCC8 gene_symbol_long: ATP-Binding Cassette Transporter 8 gene_model_pub_name: Glyma.07G011600 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.07G011600 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of GmABCC8 in transgenic plants created glyphosate resistance. ABCC8 knockout plants had decreased resistance to glyphosate. phenotype_synopsis: GmABCC8 codes for an efflux pump that extrudes the herbicide glyphosate out of a cell's cytoplasm, making the plant glyphosate resistant. traits: - entity_name: glyphosate sensitivity entity: TO:0005006 - entity_name: herbicide resistance entity: OMIT:0025284 - entity_name: ABC-type transporter activity entity: GO:0140359 references: - citation: Pan, Yu et al., 2021 doi: 10.1073/pnas.2100136118 pmid: 33846264 --- scientific_name: Glycine max gene_symbols: - ASPGB1a gene_symbol_long: asparaginase 1a gene_model_pub_name: Glyma14g09510 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma14g09510 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat of developing seeds - Lower transcription levels in the cotyledon compared to the seed coat - very low levels of transcription of ASGB1 in embryo of developing seeds - ASPGB1a is primarily expressed in seed coat compared to other paralougs of ASPGB1 - Transcription levels are more highly expressed in the high protien developing seed (AC Proteus) phenotype_synopsis: ASPGB1a codes for asparaginase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: Hydrolase Activity entity: GO:0016787 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - ASPGB1b gene_symbol_long: asparaginase 1b gene_model_pub_name: Glyma17g35650 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g35650 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat of developing seeds - Lower transcription levels in the cotyledon compared to the seed coat - very low levels of transcription of ASGB1 in embryo of developing seeds - Transcription levels are more highly expressed in the high protien developing seed (AC Proteus) phenotype_synopsis: ASPGB1 codes for asparaginase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: Hydrolase Activity entity: GO:0016787 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - ASPGB2a gene_symbol_long: asparaginase 2a gene_model_pub_name: Glyma04g04470 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma04g04470 confidence: 2 curators: - Raegan Nelson comments: - predominantly expressed in the cotyledon compared to other ASPG genes - Transcription levels are more highly expressed in the cotyledon of low protien seed (Maple Arrow) - low trancription of ASPGB2 paralougs may explain the higher free asparagine levels in the embryo of developing seeds phenotype_synopsis: ASPGB2a codes for asparagine traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: Hydrolase Activity entity: GO:0016787 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - ASPGB2b gene_symbol_long: asparaginase 2b gene_model_pub_name: Glyma06g04590 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g04590 confidence: 2 curators: - Raegan Nelson comments: - predominantly expressed in the cotyledon - Transcription levels are more highly expressed in the cotyledon of low protien seed (Maple Arrow) - low trancription of ASPGB2 paralougs may explain the higher free asparagine levels in the embryo of developing seeds phenotype_synopsis: ASPGB2b codes for asparagine traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: Hydrolase Activity entity: GO:0016787 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - AS1a gene_symbol_long: asparaginase synthetase 1a gene_model_pub_name: Glyma11g27480 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g27480 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat during early seed development and decline steadily as seed weight increases - AS genes are likely responsible for the high levels of free asparagine found in the embryo - relatively stable expression in embyro - more predomiently expressed in high protien seed (AC Proteus) phenotype_synopsis: AS1a codes for asparaginase synthetase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: metabolic process entity: GO:0008152 - entity_name: asparagine biosynthetic process entity: GO:0006529 - entity_name: asparagine synthase (glutamine-hydrolyzing) activity entity: GO:0004066 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - AS1b gene_symbol_long: asparaginase synthetase 1b gene_model_pub_name: Glyma11g27720 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g27720 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat during early seed development and decline steadily as seed weight increases - AS genes are likely responsible for the high levels of free asparagine found in the embryo - relatively stable expression in embyro - more predomiently expressed in high protien seed (AC Proteus) phenotype_synopsis: AS1b codes for asparaginase synthetase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: metabolic process entity: GO:0008152 - entity_name: asparagine biosynthetic process entity: GO:0006529 - entity_name: asparagine synthase (glutamine-hydrolyzing) activity entity: GO:0004066 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - AS1c gene_symbol_long: asparaginase synthetase 1c gene_model_pub_name: Glyma18g06840 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g06840 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat during early seed development and decline steadily as seed weight increases - AS genes are likely responsible for the high levels of free asparagine found in the embryo - relatively stable expression in embyro - more predomiently expressed in high protien seed (AC Proteus) - predomiently expressed in seed coat compared to other AS genes phenotype_synopsis: AS1c codes for asparaginase synthetase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: metabolic process entity: GO:0008152 - entity_name: asparagine biosynthetic process entity: GO:0006529 - entity_name: asparagine synthase (glutamine-hydrolyzing) activity entity: GO:0004066 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - AS2b gene_symbol_long: asparaginase synthetase 2b gene_model_pub_name: Glyma14g37440 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma14g37440 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat during early seed development and decline steadily as seed weight increases - AS genes are likely responsible for the high levels of free asparagine found in the embryo - relatively stable expression in embyro phenotype_synopsis: AS2b codes for asparaginase synthetase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: asparagine synthase (glutamine-hydrolyzing) activity entity: GO:0004066 - entity_name: asparagine biosynthetic process entity: GO:0006529 - entity_name: metabolic process entity: GO:0008152 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - AS3a gene_symbol_long: asparaginase synthetase 3a gene_model_pub_name: Glyma11g38130 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g38130 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat during early seed development (50mg) and decline steadily as seed weight increases (150mg) - AS genes are likely responsible for the high levels of free asparagine found in the embryo - relatively stable expression in embyro - predomiently expressed in cotyledon compared to other AS genes phenotype_synopsis: AS3a codes for asparaginase synthetase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: metabolic process entity: GO:0008152 - entity_name: asparagine biosynthetic process entity: GO:0006529 - entity_name: asparagine synthase (glutamine-hydrolyzing) activity entity: GO:0004066 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - AS3b gene_symbol_long: asparaginase synthetase 3b gene_model_pub_name: Glyma18g02060 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g02060 confidence: 2 curators: - Raegan Nelson comments: - strongly expressed in the seed coat during early seed development (50mg) and decline steadily as seed weight increases (150mg) - AS genes are likely responsible for the high levels of free asparagine found in the embryo - relatively stable expression in embyro - predomiently expressed in cotyledon compared to other AS genes phenotype_synopsis: AS3b codes for asparaginase synthetase traits: - entity_name: Seed protien content entity: TO:0000490 - entity_name: metabolic process entity: GO:0008152 - entity_name: asparagine biosynthetic process entity: GO:0006529 - entity_name: asparagine synthase (glutamine-hydrolyzing) activity entity: GO:0004066 references: - citation: Pandurangan_Pajak_2012 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - GmFAD2-1A gene_symbol_long: Fatty Acid Desaturase 2-1A gene_model_pub_name: Glyma.10G278000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G278000 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - If GmFAD2-1A and GmFAD2-1B are both downregulated or have loss-of-function mutations, seeds will have high oleic acid content. - Knockout studies confirm that functional FAD2-1A decreases accumulation of oleic acid in seeds. phenotype_synopsis: GmFAD2-1A converts the precursors of oleic acid into linoleic acid. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 references: - citation: Pham, Lee et al., 2010 doi: 10.1186/1471-2229-10-195 pmid: 20828382 - citation: Combs, Bilyeu, 2019 doi: 10.13039\/100012009 pmid: null - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmFAD2-1B gene_symbol_long: Fatty Acid Desaturase 2-1B gene_model_pub_name: Glyma.20G111000 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G111000 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - If GmFAD2-1A and GmFAD2-1B are both downregulated or have loss-of-function mutations, seeds will have high oleic acid content. - FAD2-1B is more active at low temperatures. - Knockout studies confirm that functional FAD2-1B decreases accumulation of oleic acid in seeds. phenotype_synopsis: Normal GmFAD2-1B converts the precursors of oleic acid into linoleic acid. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 references: - citation: Pham, Lee et al., 2010 doi: 10.1186/1471-2229-10-195 pmid: 20828382 - citation: Combs, Bilyeu, 2019 doi: 10.13039\/100012009 pmid: null --- scientific_name: Glycine max gene_symbols: - GmCHX1 gene_symbol_long: cation/H(+) antiporter 1 gene_model_pub_name: Glyma.03G171600 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.03G171600 confidence: 4 curators: - Greg Murrell phenotype_synopsis: Impacts salt tolerance traits: - entity_name: salt tolerance entity: TO:0006001 - relation_name: positively regulates relation: RO:0002213 references: - citation: Qi, Li et al., 2014 doi: 10.1038/ncomms5340 pmid: 25004933 --- scientific_name: Glycine max gene_symbols: - GmBADH2 gene_symbol_long: betaine aldehyde dehydrogenase 2 gene_model_pub_name: Glyma05g01770 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma05g01770 confidence: 5 curators: - Wei Huang comments: - Mutated GmBADH2 may be responsible for the aroma of three aromatic soybean cultivars. - A perfect association between the marker genotypes and aroma phenotypes implied that GmBADH2 is a major aroma-conferring gene phenotype_synopsis: A Sequence Variation in GmBADH2 Enhances Soybean Aroma. traits: - entity_name: 3-chloroallyl aldehyde dehydrogenase activity entity: GO:0016491 - relation_name: positively regulates relation: RO:0002213 references: - citation: Qian, Jin et. al., 2022 doi: 10.3390/ijms23084116 pmid: 35456933 - citation: Juwattanasomran, Somta, et. al, 2011 doi: 10.1007/s00122-010-1467-6 pmid: 21046066 --- scientific_name: Glycine max gene_symbols: - GmBADH1 gene_symbol_long: betaine aldehyde dehydrogenase 1 gene_model_pub_name: Glyma06g19820 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g19820 confidence: 5 curators: - Wei Huang comments: - GmBADH1 gene may mainly regulate the salt tolerance of seedling stage - GmBADH2 expression level in the R6 stage seeds was significantly lower in the aromatic soybean varieties (QX1 and XD) than in the non-aromatic soybean variety (DBH), whereas there were no significant differences in the GmBADH1 expression levels - Knockout of the soybean (Glycine max) betaine aldehyde dehydrogenase genes GmBADH1 and GmBADH2 using CRISPR/Cas12i3 enhances the aroma of soybeans phenotype_synopsis: regulate the salt tolerance of seedling stage traits: - entity_name: 3-chloroallyl aldehyde dehydrogenase activity entity: GO:0004028 - entity_name: oxidoreductase activity entity: GO:0016491 references: - citation: Qian, Jin et. al., 2022 doi: 10.3390/ijms23084116 pmid: 35456933 - citation: Shi, Yang et. al., 2008 doi: 10.1007\/s11032-008-9165-7 pmid: null - citation: Xie, Song et. al., 2024 doi: 10.1111/jipb.13631 pmid: 38390811 --- scientific_name: Glycine max gene_symbols: - GmMIPS gene_symbol_long: Myo-Inositol-Phosphate Synthase gene_model_pub_name: Glyma.11G238800 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G238800 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Silencing of GmMIPS in transgenic lines (with RNAi and antisense) reduces accumulation of phytic acid in seeds. phenotype_synopsis: GmMIPS codes for the rate-limiting enzyme in phytic acid biosynthesis. Supression of MIPS reduces the phytic acid concentration in seeds which improves their nutritional value, but also reduces their germination rate. traits: - entity_name: biosynthetic process entity: GO:0009058 references: - citation: Redekar, Glover et al., 2020 doi: 10.1371/journal.pone.0235120 pmid: 32584851 - citation: Kumar, Kumar et al., 2019 doi: 10.1038/s41598-019-44255-7 pmid: 31123331 - citation: Yu, Jin et al., 2019 doi: 10.1186/s12870-019-2201-4 pmid: 31856712 - citation: Nunes, Vianna et al., 2006 doi: 10.1007/s00425-005-0201-0 pmid: 16395584 - citation: Hegeman, Good et al., 2001 doi: 10.1104/pp.125.4.1941 pmid: 11299373 --- scientific_name: Glycine max gene_symbols: - GmRIC1 gene_symbol_long: Rhizobia-Induced CLE 1 gene_model_pub_name: Glyma13G36830 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.13G292300 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - RT-qPCR studies conducted on tissue injected with Bradyrhizobium nodulation factor showed that GmRIC1 is upregulated hours after injection. - Introduction of plasmids carrying an extra dose of RIC1 inhibited nodulation. phenotype_synopsis: GmRIC1 reduces nodulation in Lotus japonicus and Medicago truncatula. It is induced by Bradyrhizobium nodulation factor. traits: - entity_name: plant organ growth and development trait entity: TO:0000927 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: root nodule entity: PO:0003023 references: - citation: Reid, Ferguson et al., 2011 doi: 10.1094/MPMI-09-10-0207 pmid: 21198362 --- scientific_name: Glycine max gene_symbols: - GmRIC2 gene_symbol_long: Rhizobia-Induced CLE 2 gene_model_pub_name: Glyma06G43680 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G284100 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - RT-qPCR studies conducted on tissue injected with Bradyrhizobium nodulation factor showed that GmRIC2 is upregulated a few days after injection. - Introduction of plasmids carrying an extra dose of RIC2 inhibited nodulation. phenotype_synopsis: GmRIC2 reduces nodulation in Lotus japonicus and Medicago truncatula. It is induced by Bradyrhizobium nodulation factor. traits: - entity_name: plant organ growth and development trait entity: TO:0000927 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: root nodule entity: PO:0003023 references: - citation: Reid, Ferguson et al., 2011 doi: 10.1094/MPMI-09-10-0207 pmid: 21198362 --- scientific_name: Glycine max gene_symbols: - GmNIC1 gene_symbol_long: Nitrate-Induced CLE 1 gene_model_pub_name: Glyma12G33660 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12G33660 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - RT-qPCR conducted on root tissue exposed to varying concentrations of nitrate showed that GmNIC1 expression is induced when roots are exposed to nitrate. - Introduction of plasmids carrying an extra dose of NIC1 inhibited nodulation. phenotype_synopsis: GmNIC1 reduces nodulation in Lotus japonicus and Medicago truncatula. It is induced by nitrate but inhibited by Bradyrhizobium nodulation factor. traits: - entity_name: plant organ growth and development trait entity: TO:0000927 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: root nodule entity: PO:0003023 references: - citation: Reid, Ferguson et al., 2011 doi: 10.1094/MPMI-09-10-0207 pmid: 21198362 --- scientific_name: Glycine max gene_symbols: - GmFg2 - GmF3G6R-b - GmF3G6_Rt-b gene_symbol_long: flavonol glycoside 2 mRNA for flavonol 3-O-glucoside (1->6) rhamnosyltransferase gene_model_pub_name: Glyma.10G194000 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G194000 confidence: 4 curators: - Greg Murrell phenotype_synopsis: Encodes a flavonol 3-O-glucoside (1 -> 6) rhamnosyltransferase. traits: - entity_name: glycoside biosynthetic process entity: GO:0016138 references: - citation: RojasRodas, Rodriguez et al., 2013 doi: 10.1007/s11103-013-0133-1 pmid: 24072327 --- scientific_name: Glycine max gene_symbols: - Gm-JAG1 gene_symbol_long: JAGGEED 1 gene_model_pub_name: Glyma20g25000 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.20G116200 confidence: 5 curators: - Wei Huang comments: - Gm-JAG1 is a transcription factor in soybean that controls the size of flowers, number of seeds, and shape of leaves. - Gm-JAG1 (Glyma20g25000), a gene controlling Ln gene. - The leaflets of the Gm-jag1 mutants were longer and narrower than those of the wild-type plants. - Soybean Ln gene pleiotropically controls leaflet shape and NSP. phenotype_synopsis: Gm-JAG1 is a transcription factor in soybean that controls the size of flowers, number of seeds, and shape of leaves. traits: - entity_name: C2H2 and C2HC zinc fingers superfamily protein entity: GO:0046872 - entity_name: multicellular organism development entity: GO:0007275 - entity_name: positively regulates entity: GO:0000496 references: - citation: Sayama, Tanabata et. al., 2017 doi: 10.1270/jsbbs.16201 pmid: 29085246 --- scientific_name: Glycine max gene_symbols: - GmNARK gene_symbol_long: Nodule Autoregulation Receptor Kinase gene_model_pub_name: Glyma.12G040000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.12G040000 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - All these studies identified the implicated gene by comparing mutant strains to each other and to wild type. - GmNARK is a negative regulator of miR172c, which affects the activity of nodulation gene GmNNC1 (see Wang, Wang et al., 2014). - NARK is expressed in roots, leaves, and shoots. - If the kinase domain of NARK is nonfunctional, most plants produce huge numbers of extra nodules, extra lateral roots, and more symbiotic interactions. - If NARK is less severely compromised, fewer extra nodules form. phenotype_synopsis: GmNARK exerts long-distance control on nodule proliferation by activating nodulation-suppressing genes. traits: - entity_name: kinase activity entity: GO:0016301 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - entity_name: root development entity: GO:0048364 references: - citation: Searle, Men et al., 2003 doi: 10.1126/science.1077937 pmid: 12411574 - citation: Kim, Van et al., 2005 doi: 10.1007/s00122-004-1887-2 pmid: 15731930 - citation: Meixner, Vegvari et al., 2007 doi: 10.1111\/j.1399-3054.2007.00903.x pmid: null - citation: Wang, Wang et al., 2014 doi: 10.1105/tpc.114.131607 pmid: 25549672 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmDRR1 gene_symbol_long: Disease Resistance Responsive 1 gene_model_pub_name: Glyma.11G150400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G150400 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - The importance of GmDRR1 in nodule formation was established through its overexpression in soybean, which increased the number of nodules relative to the wild-type. RNA interference had no effect on nodule number. - DRR1 is homologous with other dirigent proteins such as GmDRR2 and GmDRR3. - DRR1 promotes the synthesis of (+)-pinoresinol which is needed to increase lignin biosynthesis. Higher levels of lignin content and secondary cell wall deposition function as a physical barrier and inhibit the ability of Phytophthora sojae to infect soybeans. - The GmNAC1 transcription factor may bind to the DRR1 promoter to upregulate DRR1 expression and enhance Phytophthora sojae resistance. phenotype_synopsis: GmDRR1 was induced in soybean roots by the presence of rhizobia and helped establish a symbiotic relationship that resulted in development of root nodules and nitrogen fixation. Additionally, DRR1 expression increased the resistance of soybean to Phytophthora sojae. traits: - entity_name: nodulation entity: GO:0009877 - entity_name: biological process involved in symbiotic interaction entity: GO:0044403 - entity_name: microbial disease response entity: TO:0000112 - entity_name: nitrogen fixation entity: GO:0009399 references: - citation: Shi, Zhang et al., 2020 doi: 10.1094/MPMI-01-20-0017-R pmid: 32186464 - citation: Yu, Zou et al., 2021 doi: 10.13039\/100012548 pmid: null --- scientific_name: Glycine max gene_symbols: - GmDRR2 gene_symbol_long: Disease Resistance Responsive 2 gene_model_pub_name: Glyma.11G150300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.11G150300 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmDRR1 and GmDRR2 are homologous dirigent proteins. The function of DRR1 may depend on dimer formation with DRR2. phenotype_synopsis: GmDRR2 promoted a symbiotic relationship with rhizobia that resulted in development of root nodules and nitrogen fixation in soybeans. traits: - entity_name: nodulation entity: GO:0009877 - entity_name: biological process involved in symbiotic interaction entity: GO:0044403 - entity_name: microbial disease response entity: TO:0000112 - entity_name: nitrogen fixation entity: GO:0009399 references: - citation: Shi, Zhang et al., 2020 doi: 10.1094/MPMI-01-20-0017-R pmid: 32186464 - citation: Yu, Zou et al., 2021 doi: 10.13039\/100012548 pmid: null --- scientific_name: Glycine max gene_symbols: - GmbZIP123 gene_symbol_long: Basic Leucine Zipper 123 gene_model_pub_name: Glyma06G01240 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06G01240 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - The effect of GmbZIP123 was studied in transgenic Arabidopsis thaliana rather than in Glycine max. - Overexpression of bZIP123 increased lipid content in seeds of transgenic Arabidopsis. - The transcription factor bZIP123 bound to the promoters and upregulated Arabidopis genes for two sucrose transporters (SUC1 and SUC5) and three cell-wall invertases (cwINV1, cwINV3, and cwINV6). - Cell-wall invertase activity and sugar translocation were consequently boosted in Arabidopsis siliques. The result was greater levels of the sugars glucose, fructose, and sucrose within seeds. phenotype_synopsis: GmbZIP123 is a transcription factor which promotes expression of sucrose transporter and cell-wall invertase genes. Regulation of lipid accumulation in soybean seeds may be mediated by controlling transport of sugar into seeds from photoautotrophic tissues. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: seed development entity: GO:0048316 references: - citation: Song, Li et al., 2013 doi: 10.1093/jxb/ert238 pmid: 23963672 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmGA20ox_a gene_symbol_long: Gibberellic Acid 20-Oxidase a gene_model_pub_name: Glyma.04G244200 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.04G244200 confidence: 3 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmGA20ox_a is induced by inoculation with compatible rhizobia (e.g., Bradyrhizobium japonicum) in soybean root cortical cells during nodule primordia establishment. Mutant rhizobia (nodC-) that lack a chitin synthase gene, and thus cannot produce the Nod factor, don't induce nodulation and concomitant GA20ox_a gene expression. - GA20ox_a is expressed at the beginning of nodule development, with levels peaking at 12 hours after inoculation and then decreasing substantially by 48 hours post-inoculation. - GA20ox_a gene expression was substantially higher in newly-developing nodules than in other plant structures and is probably nodulation-specific. phenotype_synopsis: GmGA20ox_a is a gibberellic acid biosynthesis gene that increases levels of gibberellin during early nodulation. traits: - entity_name: gibberellin biosynthetic process entity: GO:0009686 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Song, Montes-Luz et al., 2022 doi: 10.3389/fpls.2022.820348 pmid: 35498680 - citation: Hayashi, Gresshoff et al., 2014 doi: 10.1111/jipb.12201 pmid: 24673766 - citation: Hayashi, Reid et al., 2012 doi: 10.1111/j.1467-7652.2012.00729.x pmid: 22863334 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmGA3ox_1a gene_symbol_long: Gibberellic Acid 3-Oxidase 1a gene_model_pub_name: Glyma.15G012100 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15G012100 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmGA3ox_1a is induced by inoculation with compatible rhizobia (e.g., Bradyrhizobium japonicum) in soybean root cortical cells during nodule primordia establishment. - GA3ox_1a is expressed at the beginning of nodule development, with levels peaking at 12 hours after inoculation and then decreasing substantially by 48 hours post-inoculation. - GA3ox_1a expression is not exclusive to nodule development, appearing in multiple tissues, and likely serves general roles. - Nodulation was reduced by RNAi silencing of GA3ox_1a in transgenic soybean hairy roots. phenotype_synopsis: GmGA3ox_1a is a gibberellic acid biosynthesis gene that increases levels of gibberellin during early nodulation. traits: - entity_name: gibberellin biosynthetic process entity: GO:0009686 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Song, Montes-Luz et al., 2022 doi: 10.3389/fpls.2022.820348 pmid: 35498680 - citation: Hayashi, Gresshoff et al., 2014 doi: 10.1111/jipb.12201 pmid: 24673766 - citation: Hayashi, Reid et al., 2012 doi: 10.1111/j.1467-7652.2012.00729.x pmid: 22863334 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmGA20ox_b gene_symbol_long: Gibberellic Acid 20-Oxidase b gene_model_pub_name: Glyma.06G119100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G119100 confidence: 2 curators: - Scott Kalberer comments: - GmGA20ox_b is induced by inoculation with compatible rhizobia (e.g., Bradyrhizobium japonicum) in soybean root cortical cells during nodule primordia establishment. phenotype_synopsis: GmGA20ox_b is a gibberellic acid biosynthesis gene that increases levels of gibberellin during early nodulation. traits: - entity_name: gibberellin biosynthetic process entity: GO:0009686 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 references: - citation: Song, Montes-Luz et al., 2022 doi: 10.3389/fpls.2022.820348 pmid: 35498680 --- scientific_name: Glycine max gene_symbols: - GmFT3b gene_symbol_long: Flowering Locus Time 3b gene_model_pub_name: Glyma19G28390 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G108100 confidence: 3 curators: - Ella Townsend - Scott Kalberer comments: - GmFT3b expression was induced by photoperiod and circadian rhythm and was more responsive to long-day (LD) conditions, but there were no significant differences in flowering time between the wild-type, the GmFT3b overexpressors, and the ft3b knockouts under natural long-day, short-day, or LD conditions. - GmFT3b acts redundantly in flowering time regulation and may be compensated by other FT homologs in soybean. phenotype_synopsis: A flowering time locus, orthologous to Arabidopsis FLOWERING LOCUS T (FT), but apparently redundant with other FT loci in soybean. traits: - entity_name: flowering time trait entity: TO:0002616 - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 - entity_name: photoperiodism, flowering entity: GO:0048573 references: - citation: Su, Chen et al., 2022 doi: 10.3390/ijms23052497 pmid: 35269637 --- scientific_name: Glycine max gene_symbols: - GmRj2 gene_symbol_long: Restriction of Nodulation 2 gene_model_pub_name: Glyma16G33780 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G212300 confidence: 5 curators: - Greg Murrell - Ella Townsend comments: - Cultivated soybean carrying the Rj2 allele restricts nodulation with specific Bradyrhizobium strains via host immunity, mediated by rhizobial type III secretory protein NopP and the host resistance protein Rj2. - The Rj2 gene appears to have been maintained during the process of soybean domestication to adapt to high rhizobial diversity. phenotype_synopsis: The Rj2 protein mediates nodulation compatibility with rhizobial strains. traits: - entity_name: root nodule entity: PO:0003023 - entity_name: nodulation entity: GO:0009877 - entity_name: root hair entity: GO:0035618 references: - citation: Sugawara, Umehara et al., 2019 doi: 10.1371/journal.pone.0222469 pmid: 31518373 --- scientific_name: Glycine max gene_symbols: - GmCIF1 gene_symbol_long: Cell Wall Inhibitor of β-Fructosidase 1 gene_model_pub_name: Glyma.17G036300 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.17G036300 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Invertase enzymes may also be named β-fructosidase, β-fructofuranosidase, saccharase, glucosucrase, invertin, fructosylinvertase, alkaline invertase, and acid invertase. The Cell Wall Invertase (GmCWI) and Vacuolar Invertase (GmVI) are regulated in a post-translational manner by small inhibitory proteins. - Ectopic expression with fusions of fluorescent proteins and silencing through RNA interference (RNAi) show that the Cell Wall Inhibitor of β-Fructosidase 1 (GmCIF1) has a role in suppressing extracellular invertases. - The maximum inhibitory effects of recombinant CIF1 were a depression of 95% in CWI activity and 70% in VI activity. Both recombinant GmCIF1 and Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 (GmC/VIF2) exhibited higher inhibitory affinities to CWI than VI in vitro. - RNAi silencing of CIF1 expression increases seed weight as well as protein, starch, and hexose content in mature seeds. A marked elevation of CWI activity in maturing and germinating seeds was another impact of CIF1 suppression. On the other hand, VI activities were not significantly effected by RNAi of CIF1 except during early seed maturity. - CIF1 is most strongly expressed in flowers, mature leaves, and developing seeds. Transcript accumulation of CIF1 was more abundant than C/VIF2 expression. There was subcellular localization to the apoplast of tobacco leaf epidermis. - CIF1 transcription is activated by ABA treatment, ABA-triggered leaf senescence, and water-deficits. - Co-expression of CIF1 with putative CWI genes provided evidence that the CIF1 modulation of CWI impacting seed weight depends largely on post-translational mechanisms. phenotype_synopsis: Cell Wall Inhibitor of β-Fructosidase 1 (GmCIF1) is a protein that represses Cell Wall Invertase (GmCWI) and Vacuolar Invertase (GmVI) and thus promotes seed development through post-translational modulation. traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed weight entity: TO:0000181 - entity_name: protein content entity: TO:0000598 - entity_name: starch content entity: TO:0000696 references: - citation: Tang, Su et al., 2017 doi: 10.1093/jxb/erw425 pmid: 28204559 - citation: Su, Han et al., 2018 doi: 10.3390/ijms19082395 pmid: 30110937 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmC/VIF2 gene_symbol_long: Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 gene_model_pub_name: Glyma.17G036400 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.17G036400 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Invertase enzymes may also be named β-fructosidase, β-fructofuranosidase, saccharase, glucosucrase, invertin, fructosylinvertase, alkaline invertase, and acid invertase. The Cell Wall Invertase (GmCWI) and Vacuolar Invertase (GmVI) are regulated in a post-translational manner by small inhibitory proteins. - Ectopic expression with fusions of fluorescent proteins shows that the Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 (GmC/VIF2) has a role in suppressing extracellular invertases. - The maximum inhibitory effects of recombinant C/VIF2 were a depression of 80% in CWI activity and 75% in VI activity. Both recombinant Cell Wall Inhibitor of β-Fructosidase 1 (GmCIF1) and GmC/VIF2 exhibited higher inhibitory affinities to CWI than VI in vitro. - C/VIF2 is most strongly expressed in flowers, roots, and developing seeds. Transcript accumulation of CIF1 was more abundant than C/VIF2 expression. There was subcellular localization to the apoplast of tobacco leaf epidermis. - C/VIF2 transcription is activated by ABA treatment, ABA-triggered leaf senescence, and water-deficits. Fusarium solani infection caused a constant suppression of C/VIF2 transcription, whereas CIF1 expression was little affected, suggesting that C/VIF2 is a fungal pathogen-responsive gene (Su, Han et al., 2018). phenotype_synopsis: Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 (GmC/VIF2) is a protein that represses Cell Wall Invertase (GmCWI) and Vacuolar Invertase (GmVI) and thus promotes seed development through post-translational modulation. traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed weight entity: TO:0000181 - entity_name: protein content entity: TO:0000598 - entity_name: starch content entity: TO:0000696 references: - citation: Tang, Su et al., 2017 doi: 10.1093/jxb/erw425 pmid: 28204559 - citation: Su, Han et al., 2018 doi: 10.3390/ijms19082395 pmid: 30110937 --- scientific_name: Glycine max gene_symbols: - GmFLS2a gene_symbol_long: flagellin sensing 2 gene_model_pub_name: glyma.08g083300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G083300 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - GmFLS2a and GmFLS2b are likely redundant. They are not distinguishable by the VIGS knockout approach. When both of these genes are silenced, soy plants became much more suceptible to bacterial pathogens (Pseudomonas syringae pv. glycinea), but resistance to viral pathogens (Soybean mosaic virus) is not affected. phenotype_synopsis: GmFLS2a and GmFLS2b kinases start a phosphorylation cascade that activates GmMPK3 and GmMPK6, which are involved in the plant's response to bacterial infection. traits: - entity_name: bacterial disease resistance entity: TO:0000315 - entity_name: kinase activity entity: GO:0016301 references: - citation: Tian, Liu et al., 2019 doi: 10.1016/j.plantsci.2019.110386 pmid: 32005391 --- scientific_name: Glycine max gene_symbols: - GmFLS2b gene_symbol_long: flagellin sensing 2 gene_model_pub_name: glyma.05g128200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G128200 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - GmFLS2a and GmFLS2b are likely redundant. They are not distinguishable by the VIGS knockout approach. When both are silenced, soy plants became much more suceptible to bacterial pathogens (Pseudomonas syringae pv. glycinea), but resistance to viral pathogens (Soybean mosaic virus) is not affected. phenotype_synopsis: GmFLS2a and GmFLS2b kinases start a phosphorylation cascade that activates GmMPK3 and GmMPK6, which are involved in the plant's response to bacterial infection. traits: - entity_name: bacterial disease resistance entity: TO:0000315 - entity_name: kinase activity entity: GO:0016301 references: - citation: Tian, Liu et al., 2019 doi: 10.1016/j.plantsci.2019.110386 pmid: 32005391 --- scientific_name: Glycine max classical_locus: E2 gene_symbols: - GmGI gene_symbol_long: Earliness 2 gene_model_pub_name: Glyma.10G221500 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.10G221500 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Tsubokura, Watanabe et al., 2013 doi: 10.1093/aob/mct269 pmid: 24284817 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 - citation: Watanabe, Xia et al., 2011 doi: 10.1534/genetics.110.125062 pmid: 21406680 - citation: Xu, Yamagishi et al., 2015 doi: 10.1104/pp.15.00763 pmid: 26134161 --- scientific_name: Glycine max gene_symbols: - GmMYB176 gene_symbol_long: GmMYB176 gene_model_pub_name: Glyma.05g032200 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.05g032200 confidence: 4 curators: - Wei Huang comments: - A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max) phenotype_synopsis: GmMYB176 regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. traits: - entity_name: isoflavonoid biosynthetic process entity: GO:0009717 - entity_name: isoflavonoid phytoalexin metabolic process entity: GO:0046289 references: - citation: Vadivel, Anguraj AK, et al., 2021 doi: 10.1038/s42003-021-01889-6 pmid: 33742087 - citation: Yi, Jinxin et al., 2010 doi: 10.1111/j.1365-313X.2010.04214.x pmid: 20345602 --- scientific_name: Glycine max gene_symbols: - Gmbzip5 gene_symbol_long: GmbZIP5 gene_model_pub_name: Glyma.15g014800 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15g014800 confidence: 4 curators: - Wei Huang phenotype_synopsis: RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. traits: - entity_name: isoflavonoid biosynthetic process entity: GO:0009717 - entity_name: isoflavonoid phytoalexin metabolic process entity: GO:0046289 references: - citation: Vadivel, Anguraj AK, et al., 2021 doi: 10.1038/s42003-021-01889-6 pmid: 33742087 --- scientific_name: Glycine max gene_symbols: - GmSTF3 gene_symbol_long: Soybean TGACG-motif Binding Factor 3 gene_model_pub_name: Glyma.16G092700 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G092700 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of GmSTF3 in transgenic soybeans increased nodulation, whereas RNAi knockdown decreased nodulation. - STF3 is induced by the blue light activated transcription factor GmCRY1 and expressed mainly in leaves. - The protein product of STF3 migrates from shoots to the roots and signals nodule formation. - After migration, STF3 is phosphorylated by calcium/calmodulin-dependent protein kinase (GmCCaMK), which is activated by rhizobial infection of the roots. - Phosphorylation causes GmSTF3 and GmFT2a to form a complex that subsequently activates gene expression of nodulation signaling pathway 1 (GmNSP1), nodule inception (GmNIN), and nuclear factor Y (GmNF-YA1 and GmNF-YB1). phenotype_synopsis: Soybean TGACG-motif Binding Factor 3 (GmSTF3) promotes nodulation in conjunction with Flowering Locus T2a (GmFT2a) by inducing expression of nodule signalling pathway 1 (NSP1), nodule inception (NIN), and nuclear factor Y (NFY) genes. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: blue light signaling pathway entity: GO:0009785 references: - citation: Wang, Guo et al., 2021 doi: 10.1126/science.abh2890 pmid: 34591638 - citation: Hasan, Corpas et al., 2022 doi: 10.1016/j.tplants.2022.07.002 pmid: 35840482 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 - citation: Kong, Liu et al., 2010 doi: 10.1104/pp.110.160796 pmid: 20864544 - citation: Kong, Nan et al., 2014 doi: 10.13039\/501100001809 pmid: null - citation: Takeshima, Hayashi et al., 2016 doi: 10.1093/jxb/erw283 pmid: 27422993 - citation: Zhao, Takeshima et al., 2016 doi: 10.1186/s12870-016-0704-9 pmid: 26786479 - citation: Dietz, Chan et al., 2022 doi: 10.3389/fpls.2022.889066 pmid: 35574141 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max classical_locus: E9 gene_symbols: - GmFT2a gene_symbol_long: Flowering Locus T2a gene_model_pub_name: Glyma.16G150700 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G150700 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of GmFT2a in transgenic soybeans increased nodulation, whereas RNAi knockdown decreased nodulation. - FT2a is induced by the blue light activated transcription factor GmCRY1, as well as the transcription factor CONSTANS when acting as a florigen in response to long-day photoperiods. - FT2a is mainly expressed in leaves, and the translated product migrates from shoots to the roots in order to signal nodule formation. - At the roots, the FT2a protein forms a complex with the phosphorylated product of GmSTF3, which subsequently activates gene expression of nodulation signaling pathway 1 (GmNSP1), nodule inception (GmNIN), and nuclear factor Y (GmNF-YA1 and GmNF-YB1). phenotype_synopsis: Flowering Locus T2a (GmFT2a) is known for stimulating flowering, but it also positively regulates nodule organogenesis. Together with Soybean TGACG-motif Binding Factor 3 (GmSTF3) and calcium/calmodulin-dependent protein kinase (GmCCaMK), GmFT2a signals the root system that adequate photosynthate is available to power the rhizobial symbiosis and nitrogen fixation. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 - entity_name: blue light signaling pathway entity: GO:0009785 - entity_name: long-day photoperiodism, flowering entity: GO:0048574 references: - citation: Wang, Guo et al., 2021 doi: 10.1126/science.abh2890 pmid: 34591638 - citation: Hasan, Corpas et al., 2022 doi: 10.1016/j.tplants.2022.07.002 pmid: 35840482 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 - citation: Kong, Liu et al., 2010 doi: 10.1104/pp.110.160796 pmid: 20864544 - citation: Kong, Nan et al., 2014 doi: 10.13039\/501100001809 pmid: null - citation: Takeshima, Hayashi et al., 2016 doi: 10.1093/jxb/erw283 pmid: 27422993 - citation: Zhao, Takeshima et al., 2016 doi: 10.1186/s12870-016-0704-9 pmid: 26786479 - citation: Dietz, Chan et al., 2022 doi: 10.3389/fpls.2022.889066 pmid: 35574141 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmGA2ox8A gene_symbol_long: Gibberellin 2-Oxidase 8A gene_model_pub_name: Glyma.13G287600 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G287600 confidence: 3 curators: - William Hardison comments: - ncbi says the locus for gibberellin 2-beta-dioxygenase 8 [Glycine max] -> "LOCUS NP_001242439" - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height - glyma.Wm82.gnm2.ann1.Glyma.13G287600.1 also works phenotype_synopsis: Negatively correlated with shoot length and trailing growth traits: - entity_name: plant height entity: TO:0000207 references: - citation: Wang, Li et al., 2021 doi: 10.1111/tpj.15414 pmid: 34245624 --- scientific_name: Glycine max gene_symbols: - GmGA2ox8B gene_symbol_long: Gibberellin 2-Oxidase 8B gene_model_pub_name: Glyma.13G288000 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G288000 confidence: 5 curators: - William Hardison comments: - Cannot find plant trait ontology for trailing growth and shoot length -> "shoot height (related)" is for plant height - glyma.Wm82.gnm2.ann1.Glyma.13G288000.1 also works phenotype_synopsis: Negatively correlated with shoot length and trailing growth traits: - entity_name: plant height entity: TO:0000207 references: - citation: Wang, Li et al., 2021 doi: 10.1111/tpj.15414 pmid: 34245624 --- scientific_name: Glycine max gene_symbols: - GmEDS1a gene_symbol_long: enhanced disease susceptibility 1a gene_model_pub_name: Glyma04g34800 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma04g34800 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. traits: - entity_name: defense response to bacterium entity: GO:0042742 - enitity_name: defense response to virus entity: GO:0051607 references: - citation: Wang, Shine et al., 2014 doi: 10.1104/pp.114.242495 pmid: 24872380 - citation: Weirmer, Feys et al., 2005 doi: 10.1016/j.pbi.2005.05.010 pmid: 15939664 --- scientific_name: Glycine max gene_symbols: - GmEDS1b gene_symbol_long: enhanced disease suceptibility 1b gene_model_pub_name: Glyma06g19920 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g19920 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. traits: - entity_name: defense response to bacterium entity: GO:0042742 - enitity_name: defense response to virus entity: GO:0051607 references: - citation: Wang, Shine et al., 2014 doi: 10.1104/pp.114.242495 pmid: 24872380 - citation: Weirmer, Feys et al., 2005 doi: 10.1016/j.pbi.2005.05.010 pmid: 15939664 --- scientific_name: Glycine max gene_symbols: - GmPAD4 gene_symbol_long: phytoalexin deficient 4 gene_model_pub_name: Glyma08g00420 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g00420 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Silencing of GmEDS1a/b and GmPAD4 stopped accumulation of salicylic acid and increased the plant's suceptibility to Pseudomonas syringae pv glycinea and soybean mosaic virus infection. The phenotype is only altered if all three genes are silenced. phenotype_synopsis: responsible for basal and pathogen-inducible accumulation of salicylic acid, which helps the plant resist bacterial, oomycete, and viral infection. Gene activity is induced by infection. traits: - entity_name: defense response to bacterium entity: GO:0042742 - enitity_name: defense response to virus entity: GO:0051607 references: - citation: Wang, Shine et al., 2014 doi: 10.1104/pp.114.242495 pmid: 24872380 - citation: Weirmer, Feys et al., 2005 doi: 10.1016/j.pbi.2005.05.010 pmid: 15939664 --- scientific_name: Glycine max gene_symbols: - GmNNC1 gene_symbol_long: Nodule Number Control 1 gene_model_pub_name: Glyma12G07800 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.12G073300 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Nodule Number Control 1 (GmNNC1) activity is modulated by a noncoding microRNA named miR172c that fine-tunes nodulation and the rhizobium-legume symbiosis. - Expression patterns of NNC1 were studied with GAL4/UAS, GUS, and GFP reporter systems. NNC1 function was confirmed with RNAi knockdown and transgenic overexpression studies. - In the absence of rhizobia, NNC1 binds to the promoter of Early Nodulin 40 (GmENOD40) and represses gene transcription. ENOD40 is normally expressed in pericycle cells of root vascular bundles, dividing cortical cells, nodule primordia, and developing nodules. When rhizobia are present, Nod Factor Receptors (NFRs) in soybean roots recognize Nod Factors (NFs) produced by rhizobia and induce signaling that upregulates miR172c. - The miR172c targets and cleaves the mRNA of NNC1 resulting in a decrease in NNC1 gene expression. Consequently, the inhibition of ENOD40 transcription is curtailed, leading to elevated nodule numbers and nodule organogenesis. The mechanism may involve increasing the carbon sink strength of the dividing cells. - Negative feedback to prevent excessive nodulation is provided by Rhizobia-induced CLAVATA3/Embryo Surrounding Region-related peptides (GmRIC1 and GmRIC2) produced within roots during formation of nodule primordia. These short CLE-peptides activate a leucine-rich repeat receptor called Nodule Autoregulation Receptor Kinase (GmNARK). NARK, localized to the plasma membrane of leaf phloem parenchyma cells, induces shoot-derived cytokinins that travel to the roots to inhibit the transcriptional activity of miR172c (also see Searle, Men et al., 2003). phenotype_synopsis: GmNNC1 is a transcription factor that negatively regulates nodule number by repressing GmENOD40 and is itself controlled by the negative feedback of miR172c microRNA. traits: - entity_name: DNA-binding transcription factor activity entity: GO:0003700 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: negatively regulates relation: RO:0002212 - entity_name: miRNA-mediated post-transcriptional gene silencing entity: GO:0035195 references: - citation: Wang, Wang et al., 2014 doi: 10.1105/tpc.114.131607 pmid: 25549672 - citation: Searle, Men et al., 2003 doi: 10.1126/science.1077937 pmid: 12411574 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmVSPβ gene_model_pub_name: Glyma08g21410 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g21410 confidence: 3 curators: - William Hardison comments: - increased resistance to CCW (Common cutworm) phenotype_synopsis: increased resistance to insect infestations traits: - entity_name: insect damage resistance entity: TO:0000261 references: - citation: Wang, Wang et al., 2015 doi: null pmid: null --- scientific_name: Glycine max gene_symbols: - GmN:IFR gene_model_pub_name: Glyma01g37810 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma01g37810 confidence: 3 curators: - William Hardison comments: - increased resistance to CCW (Common cutworm) phenotype_synopsis: increased resistance to insect infestations traits: - entity_name: insect damage resistance entity: TO:0000261 references: - citation: Wang, Wang et al., 2015 doi: 10.13039\/501100001809 pmid: null --- scientific_name: Glycine max gene_symbols: - GmPAP12 gene_symbol_long: Purple Acid Phosphatase 12 gene_model_pub_name: Glyma.06G028200 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G028200 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Biological nitrogen (N) fixation within legume nodules necessitates large quantities of phosphorus (P) to meet energy and carbon demands. - Five Purple Acid Phosphatase (GmPAP) genes showed up-regulated expression under P-deficient as compared to P-sufficient conditions. P-starvation contributed to increasing acid phosphatase (APase) and phytase activities in soybean mature nodules. Purple Acid Phosphatase 12 (GmPAP12) had the highest level of expression amongst the five PAPs, its transcription gradually increased during nodule development, and the PAP12 promoter was activated by low-P stress. - Overexpression of PAP12 in transgenic hairy root nodules under P-deficient conditions increased total nodule number, shoot weight, nodule nitrogenase activity, nodule APase activity, N content, and P content relative to controls. - When PAP12 was silenced by RNAi in transgenic hairy root nodules there was a reduction in total nodule number, shoot weight, nodule nitrogenase activity, nodule APase activity, N content, and P content under P-deficient conditions relative to controls. - PAP12 expression is induced by the transcription factor Phosphate Starvation Response Regulator 1 (GmPHR1), a member of the MYB transcription factor family. P1BS cis-elements were found in the PAP12 promoter, and yeast one-hybrid experiments showed that PHR1 bound to P1BS in the PAP12 promoter. PHR1 overexpression and suppression in nodules resulted in highly increased and decreased expression of PAP12, respectively. Therefore, PAP12 is probably regulated by PHR1 in soybean nodules. phenotype_synopsis: GmPAP12 promotes P uptake, efficient P usage, and maintains P homeostasis in nodules under low-P conditions. The enzyme thus contributes to nodulation, nitrogen fixation, and symbiosis with rhizobia. traits: - entity_name: nodulation entity: GO:0009877 - entity_name: nitrogen fixation entity: GO:0009399 - entity_name: phosphate ion homeostasis entity: GO:0055062 - entity_name: relative phosphorus uptake entity: TO:0000648 - entity_name: relative phosphorus utilization efficiency entity: TO:0000627 references: - citation: Wang, Yang et al., 2020 doi: 10.3389/fpls.2020.00450 pmid: 32499790 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 - citation: Lu, Cheng et al., 2020 doi: 10.1104/pp.19.01209 pmid: 32680974 --- scientific_name: Glycine max gene_symbols: - GmLCLb2 gene_symbol_long: LHY/CCA1-like b2 gene_model_pub_name: Glyma19g45030 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma19g45030 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Transgenic expression of LCLb2 shows that the gene maintains rhythmicity, is expressed most strongly at dawn, and is influenced by light/dark and temperature cycles. - The circadian cycle speeds up when the transgenic plant is exposed to higher intensity red or blue light. - Knockout of transcription factors LCLa1, LCLa2, LCLb1, and LCLb2 produces short circadian rhythms and delayed flowering time. - GmLCL genes share homology with AtCCA1, AtLHY, and VrCCA1L26 genes (see Liu_Zhang_2022.yml) phenotype_synopsis: Positive regulation of circadian clock. traits: - entity_name: transcription factor binding entity: GO:0008134 - entity_name: positive regulation of circadian rhythm entity: GO:0042753 references: - citation: Wang, Yuan, et. al., 2019 doi: 10.1111/pce.13678 pmid: 31724182 --- scientific_name: Glycine max gene_symbols: - GmFT6 gene_symbol_long: Flowering Time 6 gene_model_pub_name: Glyma.08G363200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Wang, Zhou et al., 2015 doi: 10.1105/tpc.114.135103 pmid: 25663621 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max classical_locus: E3 gene_symbols: - GmphyA3 gene_symbol_long: Earliness 3 gene_model_pub_name: Glyma.19G224200 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.19G224200 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Watanabe, Hideshima et al., 2009 doi: 10.1534/genetics.108.098772 pmid: 19474204 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - E1Lb gene_symbol_long: E1-like-b gene_model_pub_name: Glyma.04G143300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G143300 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Watanabe, Xia et al., 2011 doi: 10.1534/genetics.110.125062 pmid: 21406680 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmSWN gene_symbol_long: Swinger gene_model_pub_name: Glyma.03G224300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.03G224300 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - entity_name: days to maturity entity: TO:0000469 references: - citation: Wu, Kang et al., 2019 doi: 10.3389/fpls.2019.01221 pmid: 31787988 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 --- scientific_name: Glycine max gene_symbols: - GmCOL1a gene_symbol_long: CONSTANS-Like 1a gene_model_pub_name: Glyma08G28370 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.08G255200 confidence: 5 curators: - William Hardison - Scott Kalberer comments: - Phylogenetic analysis of full-length amino acid sequences classified CONSTANS homologs (GmCOLs) into three clades conserved among Angiosperms. - Clade I contained two soybean homeologous pairs (GmCOL1a, GmCOL1b and GmCOL2a, GmCOL2b) that clustered together with the flowering inducers Arabidopsis CONSTANS (CO) and rice HEADING DATE 1 (Hd1) based on sequence similiarity. - Transcript abundance of COL1a and COL1b exhibited a strong diurnal rhythm under flowering-inductive short days. Their mRNA levels reached a peak at dawn and coincided with the rise of GmFT5a expression. In contrast, the mRNA abundance of COL2a and COL2b was extremely low. - Transgenic experiments showed that COL1a, COL1b, COL2a and COL2b fully complemented the late flowering effect of the Arabidopsis co-1 mutant. - The gene_model_pub_name was found in Awal Khan, Zhang et al., 2022 and Supporting Table S1 of Wu, Price et al., 2014. phenotype_synopsis: GmCOL1a and GmCOL1b are potential inducers of short-day photoperiodic flowering in soybean. A rapid regulatory divergence between GmCOL1a/GmCOL1b and GmCOL2a/GmCOL2b was also suggested. traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 - entity_name: short-day photoperiodism entity: GO:0048572 references: - citation: Wu, Price et al., 2014 doi: 10.1371/journal.pone.0085754 pmid: 24465684 - citation: Awal Khan, Zhang et al., 2022 doi: 10.3389/fpls.2022.817544 pmid: 35371153 --- scientific_name: Glycine max gene_symbols: - GmCOL1b gene_symbol_long: CONSTANS-Like 1b gene_model_pub_name: Glyma18G51320 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.18G278100 confidence: 3 curators: - William Hardison - Scott Kalberer comments: - Phylogenetic analysis of full-length amino acid sequences classified CONSTANS homologs (GmCOLs) into three clades conserved among Angiosperms. - Clade I contained two soybean homeologous pairs (GmCOL1a, GmCOL1b and GmCOL2a, GmCOL2b) that clustered together with the flowering inducers Arabidopsis CONSTANS (CO) and rice HEADING DATE 1 (Hd1) based on sequence similiarity. - Transcript abundance of COL1a and COL1b exhibited a strong diurnal rhythm under flowering-inductive short days. Their mRNA levels reached a peak at dawn and coincided with the rise of GmFT5a expression. In contrast, the mRNA abundance of COL2a and COL2b was extremely low. - Transgenic experiments showed that COL1a, COL1b, COL2a and COL2b fully complemented the late flowering effect of the Arabidopsis co-1 mutant. - The gene_model_pub_name was found in Awal Khan, Zhang et al., 2022 and Supporting Table S1 of Wu, Price et al., 2014. phenotype_synopsis: GmCOL1a and GmCOL1b are potential inducers of short-day photoperiodic flowering in soybean. A rapid regulatory divergence between GmCOL1a/GmCOL1b and GmCOL2a/GmCOL2b was also suggested. traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 - entity_name: short-day photoperiodism entity: GO:0048572 references: - citation: Wu, Price et al., 2014 doi: 10.1371/journal.pone.0085754 pmid: 24465684 - citation: Awal Khan, Zhang et al., 2022 doi: 10.3389/fpls.2022.817544 pmid: 35371153 --- scientific_name: Glycine max classical_locus: E1 gene_symbols: - GmE1 gene_symbol_long: Flower Repressor 1 gene_model_pub_name: Glyma06g23040 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G207800 confidence: 5 curators: - Steven Cannon comments: - E1 transcripts negativly regulates the expression of GmFT2a and GmFT5a - High levels of expression in cotyledons, fully expanded leaves and mature leaves - E1 expression shows a bimodel pattern under long day conditions (16h light, 8h dark), transcription slows in the dark, reaching its minimmum at dawn - high level of E1 expression requires long-day conditions and functional photoreceptor genes (E3 and E4) - E1 inhibits GmFT2a/GmFT5a expression during long day conditions - Supression of E1 leads to early flowering phenotype_synopsis: E1 transcripts negativly regulates the expression of GmFT2a and GmFT5a to control flowering time traits: - entity_name: Flowering Time trait entity: TO:0002616 references: - citation: Xia, Watanabe et al., 2012 doi: 10.1073/pnas.1117982109 pmid: 22619331 --- scientific_name: Glycine max classical_locus: E1 gene_symbols: - E1 gene_symbol_long: Earliness 1 gene_model_pub_name: Glyma.06G207800 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G207800 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Xia, Zhai et al., 2012 doi: 10.3389/fpls.2021.632754 pmid: 33995435 - citation: Watanabe, Xia et al., 2011 doi: 10.1534/genetics.110.125062 pmid: 21406680 - citation: Dietz, Chan et al., 2023 doi: 10.3389/fpls.2022.889066 pmid: 35574141 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - E1La gene_symbol_long: E1-like-a gene_model_pub_name: Glyma.04G156400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.04G156400 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Xu, Yamagishi et al., 2015 doi: 10.1104/pp.15.00763 pmid: 26134161 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max gene_symbols: - GmBEHL1 - GmBES1-5 gene_symbol_long: BES1/BZR1 Homolog-Like protein 1 gene_model_pub_name: Glyma01G178000 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G178000 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - Overexpression of BEHL1 decreases nodulation, RNAi knockdown of BEHL1 increases nodulation. - BEHL1 interacts with the nodulation factor (NF) pathway as well as the brassinosteroid signalling (BR) pathway. - The product of BEHL1 binds to BR-responsive Responsive Elements (BRRE) and the gene GmBIN2 to regulate BR signalling. phenotype_synopsis: BEHL1 is a corepressor. It works with NNC1 (see Wang, Wang et. al., 2014) as a negative regulator of nodulation. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Yan, Wang et. al., 2018 doi: 10.1038/s41598-018-25910-x pmid: 29769571 - citation: Li, Guo et. al., 2019 doi: 10.1016/j.heliyon.2019.e01868 pmid: 31206092 - citation: Wang, Wang et. al., 2014 doi: 10.1105/tpc.114.131607 pmid: 25549672 - citation: Yang, Lan et. al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmIDD gene_symbol_long: Indeterminate Domain Transcription Factor gene_model_pub_name: Glyma.14G095900 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.14G095900 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmIDD, a zinc finger transcription factor, was induced by short days in soybean leaves and subject to circadian clock regulation. - Overexpression of IDD in transgenic wild-type Arabidopsis resulted in earlier flowering relative to control plants. Late-flowering idd mutants were rescued by overexpression of IDD and normal flowering times were restored. - Gene binding sites for the IDD-encoded transcription factor were identified by chromatin immunoprecipitation sequencing assays with IDD-overexpressing Arabidopsis. IDD reduced gene expression of the flower repressor transcription factor, AGAMOUS-like 18 (AGL18) through binding to the TTTTGGTCC motif of its promoter. - Arabidopis IDD overexpression increased the transcription of flowering time-related genes FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), LEAFY (LFY), and APETALA1 (AP1). phenotype_synopsis: GmIDD is induced by short days and promotes flowering in soybean and transgenic Arabidopsis. traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 - entity_name: flowering time trait entity: TO:0002616 - entity_name: short day length exposure entity: PECO:0007200 references: - citation: Yang, Zhang et al., 2021 doi: 10.3389/fpls.2021.629069 pmid: 33841461 --- scientific_name: Glycine max gene_symbols: - GmSFT gene_symbol_long: Seed-Flooding Tolerance gene_model_pub_name: Glyma.13g248000 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G248000 confidence: 3 curators: - William Hardison comments: - Genome-Wide Association Study (GWAS) - also known as glyma.Wm82.gnm2.ann1.Glyma.13G248000.1 - condifence is 4 because further functional validation is required to determine its [Glyma.13g248000] roles in seed-flooding tolerance of soybean - GmSFT(Glyma.13g248000) was considered to be the most likely candidate gene regulating seed-flooding tolerance in soybean phenotype_synopsis: Ability to grow in seed flooding conditions traits: - entity_name: flooding related trait entity: TO:0000114 references: - citation: Yu, Chang et al., 2019 doi: 10.3390/genes10120957 pmid: 31766569 --- scientific_name: Glycine max gene_symbols: - GmMIPS1 gene_symbol_long: d-myo-inositol 3-phosphate synthase gene 1 gene_model_pub_name: DQ323904 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.11G238800.1 confidence: 5 curators: - Raegan Nelson comments: - Gm-lpa-TW-1 lpa (low phytic acid) mutation resulted from a 2 bp deletion in MIPS1 - Gm-lpa-TW-1 had a significant increase in inorganic phosphorus levels and a decrease in organic phosphorus levels compared to the WT - Gm-lpa-TW-1 can negatively affect seed emergence when seeds are produced in unfavorable enviorments (spring season) phenotype_synopsis: involved in the early stages of phytic acid synthesis traits: - entity_name: myo-inositol hexakisphosphate metabolic process entity: GO:0033517 - entity_name: phosphorus content entity: TO:0001024 - entity_name: seed germination stage entity: PO:0007057 references: - citation: Yuan, Zhao et al., 2007 doi: 10.1007/s00122-007-0621-2 pmid: 17701395 - citation: DeMers, Raboy et al., 2021 doi: 10.3389/fpls.2021.708286 pmid: 34531883 --- scientific_name: Glycine max gene_symbols: - GmIPK1 gene_symbol_long: inositol 1,3,4,5,6 pentakisphosphate 2-kinase 1 gene_model_pub_name: Glyma14g07880 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma14g07880 confidence: 5 curators: - Raegan Nelson comments: - Gm-lpa-ZC-2 has a G to A point mutation on the 5th exon of IPK1 - the lpa mutation in Gm-lpa-ZC-2 does not affect seed emergence rate or seed yield - Gm-lpa-ZC-2 had a increase in inorganic phosphorus levels and a decrease in organic phosphorus levels compared to the WT - The point mutation affected the pre-mRNA splicing and resulted in the exclusion of the fifth exon of IPK1. This disrupted the kinase and led to low phytic acid levels in Gm-lpa-ZC-2 phenotype_synopsis: Involved in the conversion of InP5 into phytic acid traits: - entity_name: inositol-1,3,4,5,6-pentakisphosphate 2-kinase activity entity: GO:0035299 - entity_name: phosphorus content entity: TO:0001024 references: - citation: Yuan, Zhao et al., 2007 doi: 10.1007/s00122-007-0621-2 pmid: 17701395 - citation: Yuan, Zhu et al., 2012 doi: 10.1007/s00122-012-1922-7 pmid: 22733447 --- scientific_name: Glycine max gene_symbols: - GmFT5a - GmFTL4 gene_symbol_long: Flowering Locus T gene_model_pub_name: Glyma.16G044100 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.16G044100 confidence: 5 curators: - Greg Murrell phenotype_synopsis: Control of flowering time and shoot determinacy traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 - entity_name: plant height entity: TO:0000207 - entity_name: transcription factor AP-1 complex entity: GO:0035976 - relation_name: positively regulates relation: RO:0002213 references: - citation: Yue, Li et al., 2021 doi: 10.1111/jipb.13070 pmid: 33458938 - citation: Takeshima, Hayashi, et al., 2016 doi: 10.1093/jxb/erw283 pmid: 27422993 - citation: Cai, Wang, et al., 2020 doi: 10.1111/pbi.13199 pmid: 31240772 - citation: Takeshima, Nan, et al., 2019 doi: 10.1093/jxb/erz199 pmid: 31035293 - citation: Nan, Cao, et al., 2014 doi: 10.1371/journal.pone.0097669 pmid: 24845624 - citation: Jiang, Zhang, et al., 2019 doi: 10.1186/s12864-019-5577-5 pmid: 30894121 - citation: Liu, Jiang, et al., 2018 doi: 10.1111/nph.14884 pmid: 29120038 - citation: Cao, Takeshima, et al., 2017 doi: 10.1093/jxb/erw394 pmid: 28338712 - citation: Kong, Liu, et al., 2010 doi: 10.1104/pp.110.160796 pmid: 20864544 --- scientific_name: Glycine max gene_symbols: - GmDT1 - GmTFL - GmTFL1b - GmTFL1.1 - GmTFL1b gene_symbol_long: Terminal Flower 1-Like gene_model_pub_name: Glyma.19G194300 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.19G194300 confidence: 5 curators: - Greg Murrell comments: - photoperiodic flowering time phenotype_synopsis: Modification of flowering time and determinacy traits: - entity_name: soybean flowering time trait entity: CO_336:0000000 - entity_name: soybean plant height trait entity: CO_336:0000027 references: - citation: Yue, Li et al., 2021 doi: 10.1111/jipb.13070 pmid: 33458938 - citation: Tian, Wang, et al., 2010 doi: 10.1073/pnas.1000088107 pmid: 20421496 - citation: Liu, Watanabe, et al., 2010 doi: 10.1104/pp.109.150607 pmid: 20219831 - citation: Langewisch, Zhang, 2014 doi: 10.1371/journal.pone.0094150 pmid: 24727730 --- scientific_name: Glycine max classical_locus: R gene_symbols: - GmR gene_symbol_long: Black or brown seed coat color gene_model_pub_name: Glyma09g36983 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma09g36983 confidence: 5 curators: - Raegan Nelson comments: - Three different alleles RM55-r^m (variegated black-brown seed coat), RM30-R* (black seed coat), and RM38-r (brown seed coat) - 13 kb CACTA transposable element (TgmR*) insertion found in intron 2 in RM55-r^m and RM30-R* - “C”-nt deletion in Exon2 found in RM38-r - TgmR* insertion slightly represses expression of Glyma09g36983 - r allele of brown seed coats is expresssed at a higher level then the R* allele - R* allele Glyma09g36983 gene enhances expression/accumulation of ANS transcripts - TgmR* is stabilized by an increase of methylation in the R* line compared to the r allele line - TgmR* confirms the proposed existence of two subfamilies of CACTA transposons in soybean - ANS genes are highly expressed during early seed development stages - UGT78K1 gene may not be expressed in the seed coat but rather in the cotyledons phenotype_synopsis: Glyma09g36983 is associated with red-brown seed coat color, through modification of expression of genes in the ANS pathway traits: - entity_name: Seed coat color entity: TO:0000190 - entity_name: Regulation of anthocyanin metabolic process entity: GO:0031537 references: - citation: Zabala, Vodkin., 2014 doi: 10.1371/journal.pone.0111959 pmid: 25369033 - citation: Yang Y, Zhao T et al., 2023 doi: 10.3389/fpls.2023.1190503 pmid: 37384360 - citation: Song J, Liu Z et al., 2016 doi: 10.1371/journal.pone.0159064 pmid: 27404272 - citation: Palmer RG, Pfeiffer TW et al., 2004 doi: 10.2134\/agronmonogr16.3ed.c5 pmid: null --- scientific_name: Glycine max classical_locus: E10 gene_symbols: - GmFT4 gene_symbol_long: Earliness 10 gene_model_pub_name: Glyma.08G363100 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.08G363100 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Photoperiodic flowering time regulation traits: - entity_name: flowering time entity: TO:0002616 - relation_name: negatively regulates relation: RO:0002212 - entity_name: days to maturity entity: TO:0000469 - relation_name: negatively regulates relation: RO:0002212 references: - citation: Zhai, Lu et al., 2014 doi: 10.1371/journal.pone.0089030 pmid: 24586488 - citation: Samanfar, Molnar et al., 2017 doi: 10.1007/s00122-016-2819-7 pmid: 27832313 - citation: Lin, Liu et al., 2021 doi: 10.1111/jipb.13021 pmid: 33090664 --- scientific_name: Glycine max classical_locus: ARRAY(0x12dce9b68) gene_symbols: - SACPD-C gene_symbol_long: delta-9-Stearoyl-Acyl Carrier Protein Desaturase-C gene_model_pub_name: Glyma14g27990 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma14g27990 confidence: 3 curators: - Marlene Dorneich-Hayes comments: - Mutants with defective SACPD-C produce seeds with high stearic acid content. - Plants with defective or silent SACPD-C produce seeds high in stearic acid. - SACPD-C also has pleiotropic effects on nodule structure. phenotype_synopsis: SACPD-C codes for a seed-specific enzyme that converts stearic acid into oleic acid. traits: - entity_name: seed development entity: GO:0048316 - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 references: - citation: Zhang, Burton et. al., 2008 doi: 10.13039\/100012009 pmid: null - citation: Gillman, Stacey et. al., 2014 doi: 10.1186/1471-2229-14-143 pmid: 24886084 - citation: Carrero-Colon, Abshire et. al., 2014 doi: 10.1371/journal.pone.0097891 pmid: 24846334 - citation: Zuo, Ikram et. al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmBTB/POZ gene_symbol_long: Broad Complex Tramtrack Bric-a-brac Pox Virus and Zinc finger gene_model_pub_name: XP_006578952 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.04G244900 confidence: 4 curators: - Marlene Dorneich-Hayes - Steven Cannon comments: - Overexpression of GmBTB/POZ increases resistance to Phytophthora sojae in GmLHP1 overexpressing plants. phenotype_synopsis: the product of GmBTB/POZ positively regulates the plant's response to Phytophthora sojae infection by marking the product of GmLHP1 for degradation, thus activating the transcription factor GmWRKY40. traits: - entity_name: defence response to fungus entity: GO:0050832 references: - citation: Zhang, Cheng et al., 2021 doi: 10.1038/s42003-021-01907-7 pmid: 33742112 - citation: Zhang, Gao et al., 2018 doi: 10.1111/mpp.12741 pmid: 30113770 --- scientific_name: Glycine max gene_symbols: - GmSWEET39 gene_symbol_long: Sugars Will Eventually be Exported Transporter 39 gene_model_pub_name: Glyma.15G049200 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.15G049200 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmSWEET39 is strongly expressed in soybean seed-coat parenchyma and integuments. This gene encodes a plasma membrane-localized sucrose efflux transporter. - Expression of SWEET39 positively correlates to seed oil content. There is a negative correlation between seed protein and seed oil content. - A two-nucleotide CC deletion resulted in a truncated C-terminus of SWEET39. This allele (CC-) was strongly associated with high seed oil and low seed protein. - SWEET39 may regulate oil and protein accumulation by affecting levels of sugar delivery from maternal seed coat to the filial embryo. - A CC deletion (CC-) haplotype H1 has been selected during domestication so as to produce high seed oil content alongside low protein; H1 is prominent worldwide and became fixed in North American cultivars. The protein-favored (CC+) haplotype H3 also underwent selection to enhance seed protein content alongside reduced oil amounts. There were more dramatic differences in both oil and protein content between CC- and CC+ accessions for cultivars than for landraces. phenotype_synopsis: GmSWEET39 codes for a sucrose efflux transporter in the plasma membrane that produces a pleiotropic effect on seed protein and oil content. traits: - entity_name: protein content entity: TO:0000598 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: efflux transmembrane transporter activity entity: GO:0015562 references: - citation: Zhang, Goettel et al., 2020 doi: 10.1371/journal.pgen.1009114 pmid: 33175845 - citation: Miao, Yang et al., 2020 doi: 10.1111/nph.16250 pmid: 31596499 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmTMT2a gene_symbol_long: glyma.Wm82.gnm1.ann1.Glyma12g01690 gene_model_pub_name: Glyma12g01690 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma12g01690 confidence: 5 curators: - Greg Murrell phenotype_synopsis: Catalyzes the conversion of γ-tocopherol to α-tocopherol. traits: - entity_name: vitamin E biosynthetic process entity: GO:0010189 - relation_name: positively regulates relation: RO:0002213 references: - citation: Zhang, Luo et al., 2013 doi: 10.1007/s11248-013-9713-8 pmid: 23645501 - citation: Fang, Feng, et al., 2017 doi: 10.1016/j.yrtph.2017.01.004 pmid: 28132846 - citation: Zhang, Luo, et al., 2020 doi: 10.1007/s11248-019-00180-z pmid: 31673914 --- scientific_name: Glycine max gene_symbols: - GmB1 gene_symbol_long: Bloom 1 gene_model_pub_name: Glyma.13G241700 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.13G241700 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Seed coat bloom proteins are synthesized within the pod endocarp and adhere to the surface of the seed coat. During Glycine max domestication, selection for the recessive mutant allele bloom 1 (Gmb1) gave rise to both the shiny no-bloom coat phenotype and elevated seed oil content. - A point mutation from C to T in the coding sequence of the dominant allele Bloom 1 (GmB1) causes an amino acid change from cysteine to arginine resulting in a loss of helix protein structure. - Gene expression levels of B1 were higher than b1 in transgenic Williams82, which suggests the C to T polymorphism impacts transcription. - Gene expression levels of the allele B1 in developing pods, pod endocarp, seeds, and seed coats were positively correlated with the amount of bloom deposition. The C to T polymorphism was associated with different seed coat bloom phenotypes among Glycine soja and G. max accessions. - High B1-allele expression in transgenic soybean plants was associated with reduced seed oil accumulation relative to b1 controls. Genome-wide SNP data from G. max accessions revealed a seed oil QTL associated with bloom in the 410 kb selective sweep region, suggesting the B1 locus may have pleiotropic effects on oil content. - The transcription factors GmWRI1a, GmLEC1a, GmLEC1b and GmABI3b upregulate fatty acid biosynthesis in soybean seeds. Overexpression of B1 was associated with reductions in gene expression for all four transcription factors in developing pods and pod endocarp, but didn't impact transcription or fatty acid biosynthesis in developing seed coat and seeds. phenotype_synopsis: Bloom 1 (GmB1) encodes a transmembrane transporter-like protein that not only controls seed coat bloom but also exerts pleiotropic effects on seed oil content following up-regulated oil biosynthesis in pods. traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: seed coat luster entity: TO:0000888 references: - citation: Zhang, Sun et al., 2018 doi: 10.1038/s41477-017-0084-7 pmid: 29292374 - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmNNL1 gene_symbol_long: Nodule Number Locus 1 gene_model_pub_name: Glyma.02G076900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.02G076900 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - NNL1 encodes an R protein that interacts with nodulation outer protein P (NopP) of Bradyrhizobium japonicum to prevent symbiosis. - Different NNL1 alleles provide immunity to different B. japonicum symbionts. - GmSINE1 may be inserted into NNL1, producing an inactive truncated protein. Infection proceeds normally when NNL1 is nonfunctional. - NNL1 is induced by innoculation with B. japonicum and expressed in root hairs. phenotype_synopsis: NNL1 gives soy plants immunity to root hair infection by B. japonicum, which inhibits nodulation and reduces nitrogen fixation. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: negatively regulates entity: RO:0002212 references: - citation: Zhang, Wang et. al, 2021 doi: 10.1038/s41477-020-00832-7 pmid: 33452487 - citation: Yang, Lan et. al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmRj2 gene_symbol_long: Resistance j2 gene_model_pub_name: Glyma16g33780 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G33780 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - Rj2 interacts with rhizobial NopP to determine compatibility of infecting rhizobia. - Different Rj2 alleles provide immunity to different Bradyrhizobium symbionts. - When invading NopP is incompatible with host Rj2, Rj2 activates defence gene PR-2 to prevent infection. - Regardless of rhizobial compatibility, Rj2 induces ENOD40. - Rj2 is expressed in nodules, root hairs, root tips, and shoot meristems. phenotype_synopsis: Rj2 is a resistance gene involved in sensing compatibility between soy and Bradyrhizobium symbionts. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: negatively regulates entity: RO:0002212 references: - citation: Zhang, Wang et. al, 2021 doi: 10.1038/s41477-020-00832-7 pmid: 33452487 - citation: Sugawara, Takahashi et. al., 2018 doi: 10.1038/s41467-018-05663-x pmid: 30087346 - citation: Sugawara, Umehara et al., 2019 doi: 10.1371/journal.pone.0222469 pmid: 31518373 - citation: Yang, Lan et. al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmDGAT1A gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1A gene_model_pub_name: Glyma13g16560 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g16560 confidence: 3 curators: - William Hardison comments: - soybean genome contains more DGAT genes -> duplicaiton events phenotype_synopsis: increased fat content, reduced protein content, and increased response to temperature stress traits: - entity_name: fat and essential oil content entity: TO:0000604 references: - citation: Zhao, Bi et al., 2019 doi: 10.1016/j.jplph.2019.153019 pmid: 31437808 --- scientific_name: Glycine max gene_symbols: - GmDGAT1B gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1B gene_model_pub_name: Glyma17g06120 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma17g06120 confidence: 3 curators: - William Hardison comments: - soybean genome contains more DGAT genes -> duplicaiton events phenotype_synopsis: increased fat content and reduced protein content traits: - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: temperature response trait entity: TO:0000432 references: - citation: Zhao, Bi et al., 2019 doi: 10.1016/j.jplph.2019.153019 pmid: 31437808 --- scientific_name: Glycine max gene_symbols: - GmDGAT1C gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 1C gene_model_pub_name: Glyma09g07520 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma09g07520 confidence: 2 curators: - William Hardison comments: - transcriptional analysis -> similarity to GmDGAT1A and GmDGAT1B, no knockdowns or other experiments phenotype_synopsis: increased fat content and reduced protein content traits: - entity_name: fat and essential oil content entity: TO:0000604 references: - citation: Zhao, Bi et al., 2019 doi: 10.1016/j.jplph.2019.153019 pmid: 31437808 --- scientific_name: Glycine max gene_symbols: - GmDGAT2D gene_symbol_long: Acyl-CoA:Diacylglycerol Acyltransferase 2D gene_model_pub_name: Glyma01g36010 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma01g36010 confidence: 3 curators: - William Hardison comments: - The gene model full id I pieced together from Information I found so it is probably wrong. (Williams 82, Glycine_Max_v4.0) - soybean genome contains more DGAT genes -> duplicaiton events phenotype_synopsis: increased response to temperature stress traits: - entity_name: temperature response trait entity: TO:0000432 references: - citation: Zhao, Bi et al., 2019 doi: 10.1016/j.jplph.2019.153019 pmid: 31437808 - citation: Zhao, Jiangzhe, et al. 2019 doi: 10.1016/j.jplph.2019.153019 pmid: 31437808 --- scientific_name: Glycine max gene_symbols: - GmGBP1 gene_symbol_long: GAMYB Binding Protein 1 gene_model_pub_name: DQ112540 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.01G008600 confidence: 4 curators: - William Hardison - Steven Cannon comments: - Could not determine the gene_model_pub_name from the paper. - Zhang, Zhao et al., 2013 [doi 10.1186/1471-2229-13-21] identifies GmGBP1 as GenBank DQ112540. - Zhao, Wang et al., 2013 [10.1007/s11103-013-0062-z] identifies GmGBP1 as Glyma16g08450. - Sequence analysis indicates this is a SNW/SKIP transcription factor, equivalent to glyma.Wm82.gnm2.ann1.Glyma.01G008600 phenotype_synopsis: increased flowering on short days traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0002616 - entity_name: days to maturity entity: TO:0000933 references: - citation: Zhao, Li et al., 2018 doi: 10.1111/tpj.14025 pmid: 30004144 - citation: Zhao, Wang et al., 2013 doi: 10.1007/s11103-013-0062-z pmid: 23636865 - citation: Zhang, Zhao et al., 2013 doi: 10.1186/1471-2229-13-21 pmid: 23388059 --- scientific_name: Glycine max classical_locus: E9 gene_symbols: - GmFT2a gene_symbol_long: Flowering time 2a gene_model_pub_name: Glyma.16g150700 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.16G150700 confidence: 5 curators: - Raegan Nelson comments: - FT2a recessive allele has a Ty1/copia–like retrotransposon (SORE-1) inserted in the first intron - SORE-1 only reduces FT2a by allele-specific transcriptional repression when highly methylated - E2 inhibits FT2a expression possibly through a pathway different from the E1–PHYA pathway - FT2a recessive allele ia a leaky allele and is still regulated by other genes involved in photoperiod response phenotype_synopsis: FT2a plays a role in flowering time, as the recessive homozygous allele is associated with late flowering time traits: - entity_name: Flowering Time trait entity: TO:0002616 - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 references: - citation: Zhao, Takeshima et al., 2016 doi: 10.1186/s12870-016-0704-9 pmid: 26786479 --- scientific_name: Glycine max gene_symbols: - GmAKT2 gene_symbol_long: soybean potassium transporter gene 2 gene_model_pub_name: Glyma08g20030 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g20030 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - Overexpression of GmAKT2 in transgenic SMV-susceptible soy plants increases resistance to SMV relative to WT phenotype_synopsis: GmAKT2 increases a soy plant's resistance to SMV by affecting distribution of potassium ions in the leaves. traits: - entity_name: soybean mosaic virus entity: NCBITaxon:12222 - entity_name: viral disease resistance entity: TO:0000148 - entity_name: mineral and ion transportation entity: TO:0020096 - entity_name: postassium ion concentration entity: TO:0000513 references: - citation: Zhou, He et al., 2014 doi: 10.1186/1471-2229-14-154 pmid: 24893844 --- scientific_name: Glycine max gene_symbols: - GmFATA1a gene_symbol_long: Fatty Acid Thioesterase A1a gene_model_pub_name: Glyma18g36130 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g36130 confidence: 3 curators: - Marlene Dorneich-Hayes comments: - Researchers studied the phenotypes of loss-of-function mutants and compared them to WT plants. - GmFATA1a loss-of-function mutatants accumulate high concentrations of oleic acid in their seeds. phenotype_synopsis: GmFATA1a is an acyl-acyl carrier protein thioesterase that hydrolizes 18:1 acyl-acyl carrier proteins. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: seed development entity: GO:0048316 references: - citation: Zhou, Lakhssassi et. al., 2021 doi: 10.1007/s00122-021-03917-9 pmid: 34319424 - citation: Zuo, Ikram et. al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max classical_locus: fap3 gene_symbols: - GmFATB1a gene_symbol_long: Fatty Acid Thioesterase B1a gene_model_pub_name: Glyma05G012300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.05G012300 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - CRISPR-Cas9 knockout study on genes identified in other species. - FATB1a knockouts have low palmitic and stearic acid but high oleic and linoleic acid. - FATB1a It is most strongly expressed in seeds and leaves. phenotype_synopsis: FATB1a codes for an enzyme that hydrolizes saturated acyl-ACPs. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: seed development entity: GO:0048316 references: - citation: Zhou, Lakhssassi et. al., 2021 doi: 10.1007/s00122-021-03917-9 pmid: 34319424 - citation: Ma, Sun et. al., 2021 doi: 10.3390/ijms22083877 pmid: 33918544 --- scientific_name: Glycine max gene_symbols: - GmFATB1b gene_symbol_long: Fatty Acid Thioesterase B1b gene_model_pub_name: Glyma.17G120400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G120400 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - CRISPR-Cas9 knockout study on genes identified in other species. - FATB1b knockouts have low palmitic and stearic acid but high oleic and linoleic acid. - FATB1b is most strongly expressed in seeds and leaves. phenotype_synopsis: FATB1b codes for an enzyme that hydrolizes saturated acyl-ACPs. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: seed development entity: GO:0048316 references: - citation: Zhou, Lakhssassi et. al., 2021 doi: 10.1007/s00122-021-03917-9 pmid: 34319424 - citation: Ma, Sun et. al., 2021 doi: 10.3390/ijms22083877 pmid: 33918544 - citation: Zuo, Ikram et. al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmFATB2b gene_symbol_long: Fatty Acid Thioesterase B2b gene_model_pub_name: Glyma06g23560 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma06g23560 confidence: 3 curators: - Marlene Dorneich-Hayes comments: - Researchers studied the phenotypes of loss-of-function mutants and compared them to WT plants. - FATB2b knockouts have low palmitic acid but high oleic acid. - FATB2b is most strongly expressed in flowers. phenotype_synopsis: FATB2b codes for an enzyme that hydrolizes saturated acyl-ACPs. traits: - entity_name: lipid metabolic process entity: GO:0006629 - entity_name: regulation of triglyceride biosynthetic process entity: GO:0010866 - entity_name: fat and essential oil content entity: TO:0000604 - entity_name: seed development entity: GO:0048316 references: - citation: Zhou, Lakhssassi et. al., 2021 doi: 10.1007/s00122-021-03917-9 pmid: 34319424 - citation: Zuo, Ikram et. al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 --- scientific_name: Glycine max gene_symbols: - GmSPX5 gene_symbol_long: SYG1/Pho81/Xpr1 5 gene_model_pub_name: Glyma10G40820 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.10G261900 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - GmSPX5 was most strongly expressed in soybean root nodules. Overexpression of SPX5 enhanced nodule development particularly under phosphate-sufficient conditions, whereas SPX5 suppression didn't cause any phenotypic differences. - Phosphorus concentration was unaffected in leaves, roots, and nodules of both SPX5 overexpression and suppression lines; nor was phosphate transporter gene expression altered in SPX5-overexpressing nodules. These facts contraindicate a role in phosphorus homeostasis as seen for homologous SPX proteins. - Phosphorus starvation typically inhibits nodulation in legumes. Yao, Tian et al. (2014) found that phosphorus deficiency promoted expression of SPX5 in roots and reduced expression in flowers and seeds. Conversely, SPX5 expression in roots was very low when phosphorus availability was high. Nitrogen and potassium deficiencies resulted in decreased and increased SPX5 expression in roots, respectively. - SPX5 expression was upregulated by arbuscular mycorrhizal fungal infection in phosphorus-deficient conditions (Yao, Tian et al., 2014). - SPX5 interacts with the transcription regulator Nuclear Factor Y Subunit C4 (GmNF-YC4) and promotes its binding to the promoter of Asparagine Synthetase-like Gene 6 (GmASL6), thus increasing expression of ASL6 during nodule development. However, nodule overexpression of SPX5 did not impact asparagine accumulation. phenotype_synopsis: GmSPX5 functions alongside GmNF-YC4 to upregulate GmASL6, positively regulate nodule number, and adapt to phosphorus deficiencies. SPX5 doesn't interact with or modulate expression of phosphate starvation response (PHR) genes involved in phosphorus homeostasis. traits: - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 references: - citation: Zhuang, Xue et al., 2021 doi: 10.1111/tpj.15520 pmid: 34587329 - citation: Yao, Tian et al., 2014 doi: 10.1093/aob/mcu147 pmid: 25074550 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095 --- scientific_name: Glycine max gene_symbols: - GmNF-YC4 gene_symbol_long: Nuclear Factor Y Subunit C4 gene_model_pub_name: Glyma06G17780 gene_model_full_id: glyma.Wm82.gnm4.ann1.Glyma.06G169600 confidence: 4 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Nuclear Factor Y Subunit C4 (GmNF-YC4) positively regulates nodule number and nitrogenase activity. - Overexpression of either GmSPX5 or NF-YC4 leads to upregulation of Asparagine Synthetase-like Genes ASL2,3,4,5,and 6. - SPX5 promotes binding of NF-YC4 to the promoter of GmASL6, increasing expression of ASL6 during nodule development and functionality of the asparagine synthesis pathway. phenotype_synopsis: GmNF-YC4 is a transcription factor which upregulates GmASL genes to positively regulate nodule number. traits: - entity_name: DNA-binding transcription factor activity entity: GO:0003700 - entity_name: regulation of biological process involved in symbiotic interaction entity: GO:0043903 - entity_name: nodulation entity: GO:0009877 - relation_name: positively regulates relation: RO:0002213 references: - citation: Zhuang, Xue et al., 2021 doi: 10.1111/tpj.15520 pmid: 34587329 - citation: Yang, Lan et al., 2022 doi: 10.1111/jipb.13207 pmid: 34962095