## DOCUMENT 1 ## --- 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_summary: 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 ## DOCUMENT 2 ## --- 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 ## DOCUMENT 3 ## --- 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 ## DOCUMENT 4 ## --- 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 ## DOCUMENT 5 ## --- 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 ## DOCUMENT 6 ## --- 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 ## DOCUMENT 7 ## --- 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 ## DOCUMENT 8 ## --- 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 ## DOCUMENT 9 ## --- 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 ## DOCUMENT 10 ## --- 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 ## DOCUMENT 11 ## --- 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 ## DOCUMENT 12 ## --- 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 ## DOCUMENT 13 ## --- 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 ## DOCUMENT 14 ## --- 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 ## DOCUMENT 15 ## --- 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 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 ## DOCUMENT 16 ## --- 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 ## DOCUMENT 17 ## --- 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 ## DOCUMENT 18 ## --- 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 ## DOCUMENT 19 ## --- 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 ## DOCUMENT 20 ## --- 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 ## DOCUMENT 21 ## --- 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 ## DOCUMENT 22 ## --- scientific_name: Glycine max gene_symbols: - GmMYB118 gene_model_pub_name: GLYMA_17G094400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G094400 confidence: 4 curators: - William Hardison comments: - The accession number of the maker gene located in the nucleus is At2g30250 - also known as glyma.Wm82.gnm4.ann1.Glyma.17G094400.1 phenotype_synopsis: improved tolerance to drought and salt stress traits: - entity_name: drought tolerance entity: TO:0000276 - entity_name: stress trait entity: TO:0000164 references: - citation: Du, Zhao, et al., 2018 doi: 10.1186/s12870-018-1551-7 pmid: 30509166 ## DOCUMENT 23 ## --- 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 ## DOCUMENT 24 ## --- 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 ## DOCUMENT 25 ## --- 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 ## DOCUMENT 26 ## --- 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 ## DOCUMENT 27 ## --- scientific_name: Glycine max classical_locus: D1 gene_symbols: - GmD1 gene_model_pub_name: Glyma01g42390 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma11g02980 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 ## DOCUMENT 28 ## --- 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 ## DOCUMENT 29 ## --- 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 ## DOCUMENT 30 ## --- 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 ## DOCUMENT 31 ## --- 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 ## DOCUMENT 32 ## --- 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 ## DOCUMENT 33 ## --- 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 ## DOCUMENT 34 ## --- 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 ## DOCUMENT 35 ## --- 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 ## DOCUMENT 36 ## --- 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 ## DOCUMENT 37 ## --- 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_summary: 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 ## DOCUMENT 38 ## --- 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 ## DOCUMENT 39 ## --- 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 ## DOCUMENT 40 ## --- 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 ## DOCUMENT 41 ## --- 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: 10.2135/cropsci2014.03.0228 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 ## DOCUMENT 42 ## --- 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 ## DOCUMENT 43 ## --- 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 ## DOCUMENT 44 ## --- 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 ## DOCUMENT 45 ## --- 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 ## DOCUMENT 46 ## --- 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 ## DOCUMENT 47 ## --- 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 ## DOCUMENT 48 ## --- 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 ## DOCUMENT 49 ## --- 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: null pmid: null ## DOCUMENT 50 ## --- 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 ## DOCUMENT 51 ## --- 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 ## DOCUMENT 52 ## --- 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 ## DOCUMENT 53 ## --- 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 ## DOCUMENT 54 ## --- 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 ## DOCUMENT 55 ## --- 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 ## DOCUMENT 56 ## --- 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 ## DOCUMENT 57 ## --- 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 ## DOCUMENT 58 ## --- 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 ## DOCUMENT 59 ## --- 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 ## DOCUMENT 60 ## --- 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 ## DOCUMENT 61 ## --- 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 ## DOCUMENT 62 ## --- 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 ## DOCUMENT 63 ## --- 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 ## DOCUMENT 64 ## --- 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 ## DOCUMENT 65 ## --- 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 ## DOCUMENT 66 ## --- 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 ## DOCUMENT 67 ## --- 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 ## DOCUMENT 68 ## --- 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: 10.1007/s11032-019-0972-9 pmid: null - citation: Zuo, Ikram et al., 2022 doi: 10.1016/j.csbj.2022.06.014 pmid: 35782726 ## DOCUMENT 69 ## --- 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: 10.1007/s11032-019-0972-9 pmid: null ## DOCUMENT 70 ## --- 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 ## DOCUMENT 71 ## --- 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 ## DOCUMENT 72 ## --- 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 ## DOCUMENT 73 ## --- 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 ## DOCUMENT 74 ## --- 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 ## DOCUMENT 75 ## --- 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 ## DOCUMENT 76 ## --- 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 ## DOCUMENT 77 ## --- 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: 10.1016/j.cj.2021.08.009 pmid: null ## DOCUMENT 78 ## --- 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: 10.1016/j.cj.2021.08.009 pmid: null ## DOCUMENT 79 ## --- 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 ## DOCUMENT 80 ## --- 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 ## DOCUMENT 81 ## --- scientific_name: Glycine max gene_symbols: - GmGA3ox_1a gene_symbol_long: ARRAY(0x832e73060) 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 ## DOCUMENT 82 ## --- 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 ## DOCUMENT 83 ## --- 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.gnm1.ann1.Glyma16g33780 confidence: 4 curators: - Greg Murrell phenotype_synopsis: Some alleles of Rj2 restrict nodulation to specific rhizobial strains. traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Sugawara, Umehara et al., 2019 doi: 10.1371/journal.pone.0222469 pmid: 31518373 ## DOCUMENT 84 ## --- scientific_name: Glycine max gene_symbols: - GmCIF1 gene_symbol_long: Cell Wall Invertase Inhibitor gene_model_pub_name: Glyma17G036300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G036300 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Ectopic expression and RNAi silencing show that CIF1 has a role in suppressing extracellular invertases. - Silencing of CIF1 increases seed weight as well as protein and starch content. - CIF1 is strongly expressed in flowers, mature leaves, and developing seeds. - CIF1 is activated by ABA signaling, draught, and senescence. phenotype_synopsis: CIF1 is an invertase inhibitor which represses CWI (cell wall invertase). traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed size entity: TO:0000391 - 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 ## DOCUMENT 85 ## --- scientific_name: Glycine max gene_symbols: - GmC/VIF2 gene_symbol_long: Cell Wall or Vacuolar Inhibitor of β-Fructosidase 2 gene_model_pub_name: Glyma17G036400 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.17G036400 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Ectopic expression and RNAi silencing show that C/VIF2 has a role in suppressing extracellular invertases. - Silencing of C/VIF2 increases seed weight as well as protein and starch content. - C/VIF2 is most strongly expressed in flowers, roots, and developing seeds. - C/VIF2 is activated by ABA signaling, draught, and senescence but suppressed by fungal infections. phenotype_synopsis: C/VIF2 is an invertase inhibitor which represses CWI (cell wall invertase). traits: - entity_name: regulation of seed growth entity: GO:0080113 - entity_name: seed development entity: GO:0048316 - entity_name: seed size entity: TO:0000391 - 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 ## DOCUMENT 86 ## --- 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 ## DOCUMENT 87 ## --- 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 ## DOCUMENT 88 ## --- 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 ## DOCUMENT 89 ## --- 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 ## DOCUMENT 90 ## --- 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 ## DOCUMENT 91 ## --- scientific_name: Glycine max gene_symbols: - GmSTF3 gene_symbol_long: Soybean TGACG-motif Binding Factor 3 gene_model_pub_name: Glyma.14G088300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G088300 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of STF3 increased nodulation, RNAi knockdown decreased nodulation. - STF3 is induced by the blue light activated transcription factor CRY1 and expressed mainly in leaves. - The protein product of STF3 migrates from shoots to roots. - After migration, it is phosphorylated by calcium/calmodulin dependent protein kinase (CCaMK), which is activated by rhizobial infection. - Phosphorylation causes STF3 and FT2a to form a complex. phenotype_synopsis: STF3 promotes nodulation 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: positive regulation of lateral root development entity: GO:1901333 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: 10.2135/cropsci2014.03.0228 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 ## DOCUMENT 92 ## --- 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.gnm2.ann1.Glyma.16G150700 confidence: 5 curators: - Marlene Dorneich-Hayes - Scott Kalberer comments: - Overexpression of FT2a increased nodulation while RNAi knockdown decreased nodulation. - FT2a is induced by the transcription factors GmCRY1 and CONSTANS. - It is mainly expressed in leaves and migrates from shoots to roots. - In the shoots, the product of FT2a forms a complex with the phosphorylated product of STF3. phenotype_synopsis: FT2a is known for stimulating flowering but it also positivley regulates nodulation. 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: positive regulation of lateral root development entity: GO:1901333 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: 10.2135/cropsci2014.03.0228 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 ## DOCUMENT 93 ## --- 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 ## DOCUMENT 94 ## --- 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 ## DOCUMENT 95 ## --- 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 ## DOCUMENT 96 ## --- 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 ## DOCUMENT 97 ## --- 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 ## DOCUMENT 98 ## --- 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.gnm2.ann1.Glyma.12G078000 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - Expression patterns of NNC1 were studied with GAL4/UAS, GUS, and GFP reporter systems. - Its function was confirmed with RNAi knockdown and transgenic overexpression studies. - The activity of NNC1 is modulated by miR172c to fine-tune nodulation and symbiosis. - miR172c cleaves the protein product of NNC1, allowing ENOD40 to be transcribed. - miR172c is, in turn, negatively regulated by NARK (see Searle, Men et. al., 2003). phenotype_synopsis: NNC1 is a transcription factor that negatively regulates nodule number by repressing GmENOD40. 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 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 ## DOCUMENT 99 ## --- 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 ## DOCUMENT 100 ## --- 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: 10.1007/s11240-015-0837-9 pmid: null ## DOCUMENT 101 ## --- scientific_name: Glycine max gene_symbols: - GmPAP12 gene_symbol_long: Purple Acid Phosphatase 12 gene_model_pub_name: Glyma06G170300 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.06G170300 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - When phosphate (P) is abuntant, overexpression of PAP12 increases nodule number, nitrogenase and phytase activity, and alkaline phosphatase (APase) activity. - When PAP12 is silenced, nodule number and APase activity are reduced. - PAP12 is induced by low-P conditions. - PAP12 is induced by transcription factor PHR1 (see Lu, Cheng et. al., 2020). phenotype_synopsis: ARRAY(0x833060eb8) traits: - entity_name: nodulation entity: GO:0009877 - entity_name: nitrogen fixation entity: GO:0009399 - entity_name: phosphate ion homeostasis entity: GO:0055062 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 ## DOCUMENT 102 ## --- 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 ## DOCUMENT 103 ## --- 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 ## DOCUMENT 104 ## --- 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 ## DOCUMENT 105 ## --- 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 ## DOCUMENT 106 ## --- 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 ## DOCUMENT 107 ## --- scientific_name: Glycine max gene_symbols: - GmCOL1a gene_symbol_long: CONSTANS-Like 1a gene_model_pub_name: Glyma08g28370 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma08g28370 confidence: 5 curators: - William Hardison comments: - Phylogenetic analysis of full-length amino acid sequences -> "Clade I, GmCOL1a, GmCOL1b, GmCOL2a and GmCOL2b clustered together with Arabidopsis CO and rice CO (Hd1), well-characterized flowering inducers" - gene_model_pub_name found in Awal Khan, Mohammad, et al., 2022 -> https://doi.org/10.3389/fpls.2022.817544 phenotype_synopsis: late long day flowering and early short day flowering traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 references: - citation: Wu, Price et al., 2014 doi: 10.1371/journal.pone.0085754 pmid: 24465684 - citation: Awal Khan, Mohammad, et al., 2022 doi: 10.3389/fpls.2022.817544 pmid: 35371153 ## DOCUMENT 108 ## --- scientific_name: Glycine max gene_symbols: - GmCOL1b gene_symbol_long: CONSTANS-Like 1b gene_model_pub_name: Glyma18g51320 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma18g51320 confidence: 3 curators: - William Hardison comments: - gene_model_pub_name found in Awal Khan, Mohammad, et al., 2022 -> https://doi.org/10.3389/fpls.2022.817544 phenotype_synopsis: late long day flowering and early short day flowering traits: - entity_name: photoperiod-sensitive flowering time trait entity: TO:0000934 references: - citation: Wu, Price et al., 2014 doi: 10.1371/journal.pone.0085754 pmid: 24465684 - citation: Awal Khan, Mohammad, et al., 2022 doi: 10.3389/fpls.2022.817544 pmid: 35371153 ## DOCUMENT 109 ## --- 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 ## DOCUMENT 110 ## --- 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 ## DOCUMENT 111 ## --- 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 ## DOCUMENT 112 ## --- scientific_name: Glycine max gene_symbols: - GmIDD gene_symbol_long: soybean indeterminate domain transcription factor gene_model_pub_name: Glyma.14G095900 gene_model_full_id: glyma.Wm82.gnm2.ann1.Glyma.14G095900 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - Comparisons between plants exposed to different day lengths indicated that GmIDD was induced by short days. Overexpression of GmIDD induces early flowering in WT Arabidopsis plants and restores normal flowering time to late-flowering Arabidopsis mutants. Genes acted on by the GmIDD-endcoded transcription factor identified by ChIP-Seq. phenotype_synopsis: GmIDD is induced by short days and promotes flowering in soy, maize, rice, and Arabidopsis. traits: - entity_name: photoperiod sensitive flowering time entity: TO:0000934 - entity_name: flowering time 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 ## DOCUMENT 113 ## --- 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 ## DOCUMENT 114 ## --- 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 ## DOCUMENT 115 ## --- 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 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 ## DOCUMENT 116 ## --- 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 ## DOCUMENT 117 ## --- scientific_name: Glycine max classical_locus: ARRAY(0x833126378) 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: null 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 ## DOCUMENT 118 ## --- 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 ## DOCUMENT 119 ## --- 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.gnm2.ann1.Glyma.15G049200 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Expression positively correlates to seed oil content and negatively correlates to seed protein content. phenotype_synopsis: SWEET39 codes for a sucrose efflux transporter in the plasma membrane which produces a pleiotropic affect 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 ## DOCUMENT 120 ## --- 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 ## DOCUMENT 121 ## --- scientific_name: Glycine max gene_symbols: - GmB1 gene_symbol_long: Bloom 1 gene_model_pub_name: Glyma13g31540 gene_model_full_id: glyma.Wm82.gnm1.ann1.Glyma13g31540 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - Expression of B1 in transgenic plants negatively correlates with the accumuation of oil and positively correlates with the amount of bloom. - Overexpression of B1 reduced fatty acid content in seed pods and increased bloom on the seed coat. phenotype_synopsis: ARRAY(0x8331f3318) 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., 2017 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 ## DOCUMENT 122 ## --- 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 ## DOCUMENT 123 ## --- 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 ## DOCUMENT 124 ## --- 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 ## DOCUMENT 125 ## --- 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 ## DOCUMENT 126 ## --- 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 ## DOCUMENT 127 ## --- 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: null pmid: null ## DOCUMENT 128 ## --- 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 ## DOCUMENT 129 ## --- 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 ## DOCUMENT 130 ## --- 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 ## DOCUMENT 131 ## --- 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 ## DOCUMENT 132 ## --- 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 ## DOCUMENT 133 ## --- 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 ## DOCUMENT 134 ## --- 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.gnm1.ann1.Glyma10g40820 confidence: 5 curators: - Marlene Dorneich-Hayes comments: - SPX5 is most strongly expressed in nodules. - Phosphate deficiency promotes expression of SPX5 in nodules but decreases SPX5 expression in roots. Nitrogen deficiency decreased SPX5 expression in roots. - SPX5 is upregulated by arbuscular mycorrhizal fungal infection in phosphate-deficient conditions. - SPX5 promotes binding of NF-YC4 to the promoter of ASL6, increasing expression of ASL6 during nodule development. phenotype_synopsis: SPX5 upregulates ASL genes to positively regulate nodule number. Unlike other SPX genes, SPX5 does not affect expression of PHR 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 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 ## DOCUMENT 135 ## --- 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.gnm1.ann1.Glyma06g17780 confidence: 4 curators: - Marlene Dorneich-Hayes comments: - NF-YC4 positively regulates nodule number and nitrogenase activity. - SPX5 promotes binding of NF-YC4 to the promoter of ASL6, increasing expression of ASL6 during nodule development. phenotype_synopsis: NF-YC4 is a transcription factor which upregulates ASL 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