--- scientific_name: Medicago truncatula gene_symbols: - ENOD40 gene_symbol_long: Abnormal tissue development gene_model_pub_name: CAD48198.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Use of antisense constructs of Mtenod40 arrested callus growth of Medicago explants, while overexpressing Mtenod40 embryos developed into teratomas. Enod40 genes might have a role in plant development, acting as 'riboregulators'. traits: - entity_name: plant tissue development trait entity: TO:0006015 references: - citation: Campalans, Kondorosi et al., 2017 doi: 10.1105/tpc.019406 pmid: 15037734 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - cyp716A12 gene_symbol_long: cytochrome P450 monoxygenase gene_model_pub_name: Medtr3g021350 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g021350 confidence: 5 curators: - Steven Cannon phenotype_synopsis: A cytochrome P450 gene (CYP716A12) is involved in an early step in saponin biosynthesis and is found in most tissues. CYP716A12 loss-of-function mutants do not produce hemolytic saponins and only synthetize soyasaponins, and were thus named lacking hemolytic activity (lha). CYP716A12 catalyzes the oxidation of _-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of the triterpenic saponin biosynthetic pathway, which includes squalene cyclization, _-amyrin oxidation, and glycosylation. Growth of homozygous lha/lha plants was stunted. traits: - entity_name: plant structure growth and development trait entity: TO:0000928 - entity_name: whole plant entity: PO:0000003 references: - citation: Carelli, Biazzi et al., 2014 doi: 10.1111/nph.13162 pmid: 25406544 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - HAP2.1 gene_model_pub_name: Medtr1g056530 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g056530 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Small and nonfunctional nodules arrested in growth when both normally spliced and alternatively spliced variants repressed. When only the alternative spliced form repressed the nodules are small but still fix nitrogen successfully. traits: - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: root nodule entity: PO:0003023 references: - citation: Chen, Liu et al., 2015 doi: 10.3389/fpls.2015.00575 pmid: 26284091 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtFULc gene_symbol_long: FRUITFULL gene_model_pub_name: Medtr7g016630 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g016630 confidence: 5 curators: - Raegan Nelson comments: - MtFULc is required for the secondary inflorescence identity - MtFULc regulates secondary inflorescence meristem identity by repressing the expression of MtTFL1 and MtAP1 - MtFULc was highly expressed in secondary inflorescence meristems, but not detectable in primary inflorescence meristem or any other floral organs phenotype_synopsis: MtFULc regulates secondary inflorescence meristem identity traits: - entity_name: secondary branching of inflorescence entity: TO:0000142 - entity_name: inflorescence morphology trait entity: TO:0000373 references: - citation: Cheng, Li et al., 2018 doi: 10.1242/dev.158766 pmid: 29361570 --- scientific_name: Medicago truncatula gene_symbols: - MtTFL1 gene_symbol_long: TERMINAL FLOWER 1 gene_model_pub_name: Medtr7g104460 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g104460 confidence: 5 curators: - Raegan Nelson comments: - Mutated MtTFL1 changes the inflorescence branching pattern from monopodial to sympodial - MtTFL1 is epistatic to MtFULc in the regulation of inflorescence development - MtTFL1 is highly expressed in the central part of the primary inflorescence meristem, but was not detected in secondary inflorescence meristem and floral primordia - MtTFL1 was also expressed in the center of axillary meristems phenotype_synopsis: MtTFL1 regulates primary inflorescence development traits: - entity_name: primary branching of inflorescence entity: TO:0000052 - entity_name: shoot meristem development entity: TO:0002638 - entity_name: inflorescence morphology trait entity: TO:0000373 references: - citation: Cheng, Li et al., 2018 doi: 10.1242/dev.158766 pmid: 29361570 --- scientific_name: Medicago truncatula gene_symbols: - MtSGL1 gene_symbol_long: SINGLE LEAFLET 1 gene_model_pub_name: Medtr8g066260 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g066260 confidence: 5 curators: - Raegan Nelson comments: - MtSGL1 plays a synergistic role with MtAP1 in floral meristem identity - Mutated MtSGL1 exhibited simple leaves and cauliflower-like structures consisting of reiterated sepals and carpels - SGL1 expression was detected in the leaf primordia, floral meristems, and floral organ primordia phenotype_synopsis: MtSGL1 regulates floral meristem identity traits: - entity_name: compound leaf morphology trait entity: TO:0001121 - entity_name: floral meristem determinacy entity: GO:0010582 - entity_name: inflorescence morphology trait entity: TO:0000373 references: - citation: Cheng, Li et al., 2018 doi: 10.1242/dev.158766 pmid: 29361570 --- scientific_name: Medicago truncatula gene_symbols: - MtAP1 gene_symbol_long: APETALA 1 gene_model_pub_name: Medtr3g098560 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g098560 confidence: 5 curators: - Raegan Nelson comments: - The MtAP1 mutant developed proliferating mixtures of abnormal flowers, vegetative shoots or leaf-like structures at the end of pedicels instead of one or two flowers as seen on the WT - MtAP1 was detectable in sepals and petals, but not in stamen primordia and carpel primordia. In lates stage floral development MtAP1 is only found in the petals - MtAP1 represses MtTFL1 expression in floral meristems phenotype_synopsis: MtAP1 regulates floral meristem identity traits: - entity_name: floral organ identity entity: TO:0006019 - entity_name: floral meristem determinacy entity: GO:0010582 - entity_name: inflorescence morphology trait entity: TO:0000373 references: - citation: Cheng, Li et al., 2018 doi: 10.1242/dev.158766 pmid: 29361570 --- scientific_name: Medicago truncatula gene_symbols: - SGL1 gene_symbol_long: single leaflet1 gene_model_pub_name: Medtr3g098560 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g098560 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Mutant displays simple, unifoliate (not compound) leaves. Petiole length is decreased. Defective, fused flowers traits: - entity_name: petiole length entity: TO:0000766 - entity_name: flower morphology trait entity: TO:0000499 - entity_name: leaf shape entity: TO:0000492 - entity_name: petiole entity: PO:0020038 - entity_name: flower entity: PO:0009046 references: - citation: Cheng, Li et al., 2021 doi: 10.1093/plphys/kiaa005 pmid: 33631796 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - NAM - NAM-2 gene_symbol_long: No Apical Meristem (weak allele) gene_model_pub_name: AFI56799.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g078700 confidence: 5 curators: - Steven Cannon phenotype_synopsis: The mtnam mutants display unique simplified floral organ phenotypes in addition to the common fused-cotyledon and leaflet phenotypes shared with other cuc/nam mutants. traits: - entity_name: shoot apical meristem development entity: TO:0006020 - entity_name: carpel morphology trait entity: TO:0006012 - entity_name: trichome morphology trait entity: TO:0000911 - entity_name: cotyledon morphology trait entity: TO:0000749 - entity_name: male sterility entity: TO:0000437 - entity_name: vascular leaf morphology trait entity: TO:0000419 - entity_name: female sterility entity: TO:0000358 - entity_name: stamen morphology trait entity: TO:0000215 - entity_name: embryo shape entity: TO:0000193 - entity_name: carpel trichome entity: PO:0025208 - entity_name: reproductive shoot system entity: PO:0025082 - entity_name: leaflet entity: PO:0020049 - entity_name: cotyledon entity: PO:0020030 - entity_name: plant ovule entity: PO:0020003 - entity_name: flower entity: PO:0009046 - entity_name: carpel entity: PO:0009030 - entity_name: stamen entity: PO:0009029 - entity_name: plant embryo entity: PO:0009009 - entity_name: fruit entity: PO:0009001 - entity_name: juvenile vascular leaf entity: PO:0006339 references: - citation: Cheng, Peng et al., 2012 doi: 10.1111/j.1469-8137.2012.04147.x pmid: 22530598 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtNOOT1 gene_symbol_long: NODULE ROOT 1 gene_model_pub_name: Medtr7g090020 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g090020 confidence: 5 curators: - Raegan Nelson comments: - MtNOOT1 is an ortholoug of A. thaliana BLADE-ON-PETIOLE genes - A homozygous noot genotype is linked with a petal abscission defect - Petiole and fruit abscission defects are associated with a different cellular organization at the site of organ detachment in MtNOOt1 mutants - NOOT and BLADE-ON-PETIOLE promoter activites overlap in A. thaliana which strongly suggests a conservation of the transcriptional regulation between these genes - MtNOOT1 is expressed in the transition zone and root vasculature - MtNOOT1 is required for the coordinated development of the primary root in medicago - MtNOOT1 mutants have thinner roots then compared to the WT - MtNOOT1 mutants have delayed root radical growth which correlates with the growth defects seen in its vasculature phenotype_synopsis: MtNOOT1 is necessary for fruit abscission and primary root development traits: - entity_name: root development trait entity: TO:0000656 - entity_name: fruit senescing quality trait entity: TO:0002729 - entity_name: fruit abscission entity: GO:0060867 - entity_name: floral organ abscission entity: GO:0010227 - entity_name: root radial pattern formation entity: GO:0090057 - entity_name: primary root development entity: GO:0080022 references: - citation: Couzigou, Magne et al., 2015 doi: 10.1111/nph.13634 pmid: 26390061 - citation: Shen, Kulikova et al., 2019 doi: 10.1186/s12870-019-2194-z pmid: 31856724 --- scientific_name: Medicago truncatula gene_symbols: - MtCLV2 gene_symbol_long: CLAVATA 2 gene_model_pub_name: Medtr7g079550 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g079550 confidence: 5 curators: - Raegan Nelson comments: - MtCLV2 is found in the ER and the plasma membrane - MtCLV2 can form homomers with MtCRN and SUNN - MtCLV2 is trancribed in both the roots and shoots of Medicago - Inactivation of the PsCLV2 (Pisum sativum) causes hypernodulation of the roots - PsCLV2 mutants had shorter internode length between flowering nodes compared to the WT phenotype_synopsis: MtCLV2 regulates root nodule number and internode length traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: shoot axis internode length entity: TO:0000145 references: - citation: Crook, Schnabel et al., 2016 doi: 10.1111/tpj.13234 pmid: 27296908 - citation: Krusell, Sato et al., 2010 doi: 10.1111/j.1365-313x.2010.04474.x pmid: 21276104 --- scientific_name: Medicago truncatula gene_symbols: - MtCRN gene_symbol_long: CORYNE gene_model_pub_name: Medtr7g020850 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g020850 confidence: 5 curators: - Raegan Nelson comments: - MtCRN mutants showed a three-fold increase in nodule number compared to wild type - MtCRN is found in the ER and the plasma membrane - MtCLV2 can form homomers with MtCRN and SUNN - MtCRN is trancribed in both the roots and shoots of Medicago - AtCRN (Arabidopsis thaliana) muntants increase the size of floral meristems and floral organ number compared to the WT - CRN function is not required for root meristem development, it is involved in transmitting CLE signals that inhibit its activity phenotype_synopsis: MtCRN regulates root nodule number, floral organ number and root meristem activity traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root meristem development entity: TO:0002692 - entity_name: floral organ number entity: TO:0006038 - entity_name: floral organ size entity: TO:0002600 references: - citation: Crook, Schnabel et al., 2016 doi: 10.1111/tpj.13234 pmid: 27296908 - citation: Muller, Bleckmann et al., 2008 doi: 10.1105/tpc.107.057547 pmid: 18381924 --- scientific_name: Medicago truncatula gene_symbols: - MtSUNN gene_symbol_long: SUPER NUMERIC NODULES gene_model_pub_name: AY769943 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr4g0035451 confidence: 5 curators: - Raegan Nelson comments: - MtSUNN is expressed in roots, flowers and shoots of medicago - SUNN is concentrated in parts of the plasma membrane that are specifically associated with the plasmodesmata - MtSUNN mutants display shortened roots and hypernodulation phenotype_synopsis: MtSUNN plays a role root nodule number and root length traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root length entity: TO:0000227 references: - citation: Crook, Schnabel et al., 2016 doi: 10.1111/tpj.13234 pmid: 27296908 - citation: Schnabel Journet et al., 2005 doi: 10.1007/s11103-005-8102-y pmid: 16240175 --- scientific_name: Medicago truncatula gene_symbols: - MtCCD1 gene_symbol_long: carotenoid cleavage dioxygenase 1 gene_model_pub_name: CAR57918.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g034835 confidence: 5 curators: - Steven Cannon phenotype_synopsis: RNA interference (RNAi) was used to repress a M. truncatula CCD1 gene in hairy roots colonized by the arbuscular mycorrhizal (AM) fungus Glomus intraradices. The normal AM-mediated accumulation of apocarotenoids (C13 cyclohexenone and C14 mycorradicin derivatives) was reduced in repressed plants; mycorradicin derivatives were reduced to 3% to 6% of the controls and the cyclohexenone derivatives were reduced to 30% to 47%. The RNAi roots turned a yellow-orange color because of C27 apocarotenoid accumulation (the probable substrate of the CCD1 enzyme). More degenerating arbuscules was observed in RNAi roots. traits: - entity_name: carotene content entity: TO:0000289 - entity_name: root entity: PO:0009005 references: - citation: Floss, Schliemann et al., 2008 doi: 10.1104/pp.108.125062 pmid: 18790999 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - CPK3 gene_symbol_long: calcium dependent protein kinase 3 gene_model_pub_name: ABE72958.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g051770 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Expression of MtCPK3 in Medicago truncatula is regulated during nodulation. RNAi silenced CPK3 in transformed roots but no major phenotype was detected. When infected with rhizobia the nodule number was twice as high as the controls. traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Gargantini, Gonzalez-Rizzo et al., 2006 doi: 10.1111/j.1365-313x.2006.02910.x pmid: 17132148 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - bHLH1 gene_symbol_long: basic helix loop helix 1 gene_model_pub_name: Medtr3g099620 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g099620 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Repressing MtbHLH1 (using Chimeric REpressor Silencing Technology) caused an assymetrical pattern of nodule vascular bundle development with variable angles of growth in inoculated roots. The growth and vigor of aerial parts of the plant was impaired; the nodules were still able to fix atmospheric Nitrogen but the aboveground tissues could not benefit for whatever reason. Nodules on repressed plants appeared later than in control plants and were smaller in size. traits: - entity_name: vascular bundle development trait entity: TO:0020109 - entity_name: plant organ growth and development trait entity: TO:0000927 - entity_name: shoot system entity: PO:0009006 - entity_name: vascular bundle entity: PO:0005020 - entity_name: root nodule entity: PO:0003023 references: - citation: Godiard, Lepage et al., 2011 doi: 10.1111/j.1469-8137.2011.03718.x pmid: 21679315 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - LYK3 gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 3 gene_model_pub_name: Medtr5g086130 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086130 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Doesn't make nodules; infection thread aborts traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Herrbach, Chirinos et al., 2017 doi: 10.1093/jxb/erw474 pmid: 28073951 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - LYK4 gene_symbol_long: LYSIN MOTIF RECEPTOR-LIKE KINASE 4 gene_model_pub_name: Medtr5g086120 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g086120 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Doesn't make nodules; infection thread aborts traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Herrbach, Chirinos et al., 2017 doi: 10.1093/jxb/erw474 pmid: 28073951 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtCRA2 gene_symbol_long: compact root architecture 2 gene_model_pub_name: MtrunA17_Chr3g0140861 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr3g0140861 confidence: 5 curators: - Raegan Nelson comments: - MtCRA2 negatively regulates lateral root development - MtCRA2 positively regulates symbiotic nodule development - The root-dependent regulation of the lateral root number is independent of the shoot-regulation of the nodule number - MtCRA2 encodes an LRR-RLK (Leucine-Rich Repeat–Receptor-Like Kinase) belonging to subfamily XI phenotype_synopsis: MtCRA2 negatively regulates lateral root development and positively regulates symbiotic nodule development traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root morphology trait entity: TO:0000043 - entity_name: negative regulation of lateral root development entity: GO:1901332 references: - citation: Huault, Laffont et al., 2014 doi: 10.1371/journal.pgen.1004891 pmid: 25521478 --- scientific_name: Medicago truncatula gene_symbols: - MtAOC gene_symbol_long: Allene-oxide cyclase gene_model_pub_name: CAI29046.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g417750 confidence: 5 curators: - Steven Cannon phenotype_synopsis: MtAOC (allene oxide cyclase) gene expression was partially suppressed in roots following transformation with cDNA in the antisense direction. These roots exhibited lower jasmonic acid levels and delayed colonization by Glomus intraradices. The number of arbuscles decreased and their development was delayed, yet their physical structure was unaltered. traits: - entity_name: root system entity: PO:0025025 - entity_name: root entity: PO:0009005 references: - citation: Isayenkov, Mrosk et al., 2005 doi: 10.1104/pp.105.069054 pmid: 16244141 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - CDPK1 gene_symbol_long: calcium-dependent protein kinase 1 gene_model_pub_name: Medtr5g022030 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g022030 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Reduced root hair and root cell lengths; diminution of rhizobial and mycorrhizal symbiotic colonization traits: - entity_name: root cortical cell length entity: TO:0020108 - entity_name: root hair length entity: TO:0002665 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 - entity_name: root hair cell entity: PO:0000256 references: - citation: Ivashuta, Liu et al., 2005 doi: 10.1105/tpc.105.035394 pmid: 16199614 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - PALM1 gene_symbol_long: PALMATE-LIKE PENTAFOLIATA1 gene_model_pub_name: Medtr5g014400 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g014400 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Forms dissected leaves with five leaflets clustered at the tip (palmate-like pentafoliate in contrast to the trifoliate WT leaves). The distal lateral leaflets developed in a manner morphologically/anatomically similar to terminal leaflets. The length of the petiole increased and that of the rachis decreased. traits: - entity_name: petiole length entity: TO:0000766 - entity_name: leaf morphology trait entity: TO:0000748 - entity_name: leaf entity: PO:0025034 - entity_name: leaf rachis entity: PO:0020055 - entity_name: petiole entity: PO:0020038 references: - citation: Jiao, Wang et al., 2020 doi: 10.1186/s12870-020-02619-6 pmid: 32867687 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - ANS gene_symbol_long: Anthocyanidin synthase gene_model_pub_name: Medtr5g011250 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g011250 confidence: 5 curators: - Steven Cannon phenotype_synopsis: MtANS (anthocyanidin synthase) gene expression was down-regulated in M. truncatula genotype R108 using an antisense construct. Anthocyanin levels were strongly reduced in leaf tissues of antisense lines. The presence of a red anthocyanin-rich circle at the base of the axial side of the leaflet and small red dots on the adaxial side results from anthocyanin deposition. Six independent transgenic antisense MtANS lines lacked the red circle and spots and another 10 such lines had reduced levels of pigmentation. There was a strong reduction in the levels of both soluble and insoluble PAs (Oligomeric proanthocyanidins) in seeds, consistent with involvement of ANS in PA biosynthesis. traits: - entity_name: anthocyanin content entity: TO:0000071 - entity_name: leaf entity: PO:0025034 - entity_name: seed entity: PO:0009010 references: - citation: Jun, Liu et al., 2015 doi: 10.1105/tpc.15.00476 pmid: 26410301 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - nork gene_symbol_long: nodulation receptor kinase gene_model_pub_name: Medtr5g030920 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g030920 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Lacks symbiotic root responses in the presence of compatible Sinorhizobium meliloti or Nod factor, and resists mycorrhizal colonization traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Kevei, Lougnon et al., 2007 doi: 10.1105/tpc.107.053975 pmid: 18156218 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - CDC16 gene_symbol_long: cell division cycle 16 gene_model_pub_name: Medtr8g058380 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g058380 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Partial suppression of the CDC16 gene homolog in Medicago truncatula leads to a decreased number of lateral roots, an increased number of nodules, and reduced auxin sensitivity. traits: - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: auxin sensitivity entity: TO:0000163 - entity_name: root system entity: PO:0025025 - entity_name: lateral root entity: PO:0020121 - entity_name: root entity: PO:0009005 - entity_name: root nodule entity: PO:0003023 references: - citation: Kuppusamy, Ivashuta et al., 2009 doi: 10.1104/pp.109.143024 pmid: 19789288 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - LIN gene_symbol_long: Lumpy infections gene_model_pub_name: Medtr1g090320 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g090320 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Rhizobial infection was reduced in quantity and infections were not persistent, i.e. infection threads were arrested after very limited progression within root hair cells. Nodule differentiation was arrested at an early primordial stage as an indirect result of the aborted infection. traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Lace, Su et al., 2023 doi: 10.7554/elife.80741 pmid: 36856086 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - SUNN gene_symbol_long: super numeric nodules gene_model_pub_name: Medtr4g070970 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g070970 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Shortened roots even in the absence of rhizobia. A dramatic increase in the number of root nodules. Nodulation occurred even under a high nitrogen regime. Unlike wild type, both infection by rhizobia and nodulation occur randomly throughout the circumference of the developing root. Nodulation is normally sensitive to ethylene, similar to wild type. traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root length entity: TO:0000227 - entity_name: root system entity: PO:0025025 - entity_name: root entity: PO:0009005 - entity_name: root nodule entity: PO:0003023 references: - citation: Laffont, Huault et al., 2019 doi: 10.1104/pp.18.01588 pmid: 30782966 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - FTa1 gene_symbol_long: Delayed flowering gene_model_pub_name: Medtr7g084970 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g084970 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Delayed flowering traits: - entity_name: flowering time trait entity: TO:0002616 references: - citation: Laurie, Diwadkar et al., 2011 doi: 10.1104/pp.111.180182 pmid: 21685176 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - FTc gene_symbol_long: Flower development normal under long days gene_model_pub_name: Medtr7g085040 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085040 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Normal flower development traits: - entity_name: flower development trait entity: TO:0000622 references: - citation: Laurie, Diwadkar et al., 2011 doi: 10.1104/pp.111.180182 pmid: 21685176 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - CYCLOPS gene_model_pub_name: Medtr5g026850 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g026850 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Symbiotic infection of roots by rhizobia bacteria and arbuscular mycorrhiza fungi was inhibited or blocked, i.e. infection threads were not observed despite colonization of root hairs by rhizobia and AM fungal hyphae formed abnormal hyphal swellings with no arbuscles observed. Nodule organogenesis was initiated but arrested prematurely at the level of primordia as an indirect consequence of the aborted infection. traits: - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: root system entity: PO:0025025 references: - citation: Liu, Breakspear et al., 2019 doi: 10.1104/pp.18.01572 pmid: 30710053 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - DMI1 gene_symbol_long: doesn't make infections 1 gene_model_pub_name: Medtr2g005870 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g005870 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Doesn't make nodules; infection thread aborts traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Liu, Lin et al., 2022 doi: 10.1073/pnas.2205920119 pmid: 35972963 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtKIX8 gene_symbol_long: KINASE-INDUCIBLE DOMAIN INTERACTING 8 gene_model_pub_name: Medtr4g114900 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g114900 confidence: 5 curators: - Raegan Nelson - Jacqueline Campbell comments: - MtKIX8 is a homolog of Arabidopsis KIX8 - MIO1(mini organ 1) can form a protein complex with MtKIX8 - MtKIX8 is a negative regulator of leaf and seed size - MtKIX8 is expressed throughout early floral primorida, and highly expressed during anthers development - MtKIX8 acts as a molecular adaptor to interact with BS1 phenotype_synopsis: MtKIX8 negatively regulates plant organ size traits: - entity_name: Seed size entity: TO:0000391 - entity_name: Leaf size entity: TO:0002637 - entity_name: anther development entity: GO:0048653 references: - citation: Mao, Zhou et al., 2023 doi: 10.1111/ppl.14046 pmid: 37882293 - citation: Zhou, Yang et al., 2023 doi: 10.1093/jxb/erab033 pmid: 33506247 --- scientific_name: Medicago truncatula gene_symbols: - DMI3 gene_symbol_long: doesn't make infections 3 gene_model_pub_name: Medtr8g043970 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g043970 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Doesn't make nodules or mycorrhizae traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Mitra, Gleason et al., 2004 doi: 10.1073/pnas.0400595101 pmid: 15070781 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtNAP1 gene_symbol_long: Nick-associated protein 1 gene_model_pub_name: Medtr4g084140 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g084140 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Reduced levels of nodulation, reduced acetylene reduction, and limited nodule development. Aborted and deformed infection threads restricted to epidermal root hair cells. The few nodules that did form had very low rhizobial colonization and nitrogenase activity. traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: enzyme activity trait entity: TO:0000599 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 - entity_name: root hair cell entity: PO:0000256 references: - citation: Miyahara, Richens et al., 2010 doi: 10.1094/mpmi-06-10-0144 pmid: 20731530 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtLOG1 gene_symbol_long: LONELY GUY 1 gene_model_pub_name: Medtr7g101290 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g101290 confidence: 5 curators: - Raegan Nelson comments: - MtLOG1 expression depends on MtCRE1 (a gene that is essential for nodule organ formation) - MtLOG1 expression does not require MtCRE1 in the lateral root primordia - Overexpression of MtLOG1 leads to larger lateral root density and expansion of vascular tissue - Overexpression of MtLOG1 leads to a reduced number of nodules - MtLOG1 could be involved in MtCLE13 expression during nodulation - MtLOG1 is involved in cytokinin production - MtLOG1 and MtLOG2 share 87.8% similarity phenotype_synopsis: MtLOG1 negatively regulates lateral root formation and nodule formation and produces cytokinins traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: negative regulation of lateral root development entity: GO:1901332 - entity_name: nodulation entity: GO:0009877 - entity_name: cytokinin biosynthetic process entity: GO:0009691 references: - citation: Mortier, Wasson et al., 2014 doi: 10.1111/nph.12681 pmid: 24443934 --- scientific_name: Medicago truncatula gene_symbols: - MtLOG2 gene_symbol_long: LONELY GUY 2 gene_model_pub_name: Medtr1g064260 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g064260 confidence: 5 curators: - Raegan Nelson comments: - MtLOG2 expression depends on MtCRE1 (a gene that is essential for nodule organ formation) - MtLOG2 is involved in cytokinin production - MtLOG1 and MtLOG2 share 87.8% similarity phenotype_synopsis: MtLOG2 negatively regulates nodulation and produces cytokinins traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root nodule morphology trait entity: TO:0000898 - entity_name: nodulation entity: GO:0009877 - entity_name: cytokinin biosynthetic process entity: GO:0009691 references: - citation: Mortier, Wasson et al., 2014 doi: 10.1111/nph.12681 pmid: 24443934 --- scientific_name: Medicago truncatula gene_symbols: - CBF4 gene_symbol_long: C-repeat binding factor 4 gene_model_pub_name: Medtr1g101600 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g101600 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Expression of MtCBF4 (transcription factor) in M. truncatula was induced by most of the abiotic stresses, including salt, drought, cold, and abscisic acid, suggesting crosstalk between these abiotic stresses. Upon exposure to a salt medium the primary root growth in the MtCBF4-overexpressing lines was greater than that of the control plants. MtCAS31 belongs to the CBF regulon and is associated with salt tolerance; under salt treatment, expression of MtCAS31 increased more in d35S:MtCBF4 transgenic plants than in controls. To summarize, over-expression of MtCBF4 enhanced tolerance to salt stress. traits: - entity_name: salt tolerance entity: TO:0006001 - entity_name: root length entity: TO:0000227 - entity_name: primary root entity: PO:0020127 - entity_name: whole plant entity: PO:0000003 references: - citation: Pecrix, Staton et al., 2018 doi: 10.1038/s41477-018-0286-7 pmid: 30397259 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - FCL1 gene_symbol_long: fused compound leaf 1 gene_model_pub_name: Medtr6g071190 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g071190 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Leaflets fused or partially fused, rachis between leaflets is absent, petiole is foreshortened. traits: - entity_name: petiole length entity: TO:0000766 - entity_name: vascular leaf morphology trait entity: TO:0000419 - entity_name: leaf rachis entity: PO:0020055 - entity_name: leaflet entity: PO:0020049 - entity_name: petiole entity: PO:0020038 references: - citation: Peng, Yu et al., 2011 doi: 10.1105/tpc.111.089128 pmid: 22080596 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - VPY gene_symbol_long: Vapyrin gene_model_pub_name: ADC33495.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g027840 confidence: 5 curators: - Steven Cannon phenotype_synopsis: In Medicago truncatula, the Vapyrin (VPY) gene is essential for the establishment of the arbuscular mycorrhizal symbiosis. Analyses of mutants shows that the same VPYgene is also required for rhizobial colonization and nodulation. Plants mutated in this gene have abnormal rhizobial infection threads and fewer nodules, and in the case of interactions with AM fungi, epidermal penetration defects and aborted arbuscule formation. traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Pumplin, Mondo et al., 2009 doi: 10.1111/j.1365-313x.2009.04072.x pmid: 19912567 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - FLOT2 gene_symbol_long: Flotillin-like protein 2 gene_model_pub_name: Medtr3g106420 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106420 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Fewer nodules per plant, an increase in no-nodule plants, and a decrease in plants that form pink nodules. A decrease in primary root length and long primary lateral roots, reduced reduction of acetylene, and reduced number of infection events. traits: - entity_name: lateral root length entity: TO:0001012 - entity_name: root nodule number entity: TO:0000900 - entity_name: seminal root length entity: TO:0000586 - entity_name: root system entity: PO:0025025 - entity_name: primary root entity: PO:0020127 - entity_name: lateral root entity: PO:0020121 - entity_name: root nodule entity: PO:0003023 references: - citation: Qiao, Pingault et al., 2016 doi: 10.3389/fpls.2016.00034 pmid: 26858743 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - FLOT3 gene_symbol_long: Flotillin-like protein 3 gene_model_pub_name: Medtr3g106480 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106480 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Shorter roots and reduced root weight. traits: - entity_name: root weight entity: TO:0000279 - entity_name: root length entity: TO:0000227 - entity_name: root entity: PO:0009005 references: - citation: Qiao, Pingault et al., 2016 doi: 10.3389/fpls.2016.00034 pmid: 26858743 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - FLOT4 gene_symbol_long: Flotillin-like protein 4 gene_model_pub_name: Medtr3g106430 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g106430 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Decrease in plants that form pink nodules and an increase in numbers of secondary lateral roots, reduced reduction of acetylene. Weak association with reduction in nodule numbers. Both decreased number of infection events and defective infection thread elongation. traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: root number entity: TO:0000084 - entity_name: root system entity: PO:0025025 - entity_name: root nodule entity: PO:0003023 references: - citation: Qiao, Pingault et al., 2016 doi: 10.3389/fpls.2016.00034 pmid: 26858743 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - NFP gene_symbol_long: Nod Factor Perception gene_model_pub_name: Medtr5g019040 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g019040 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Root nodules did not form and infection threads aborted during development. traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Rey, Nars et al., 2013 doi: 10.1111/nph.12198 pmid: 23432463 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - GT3 - UGT73F3 gene_symbol_long: Glycosyltransferase 3 gene_model_pub_name: Medtr2g035020 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g035020 confidence: 5 curators: - Steven Cannon phenotype_synopsis: The uridine diphosphate glycosyltransferase (GT3, UGT73F3) showed specificity for multiple sapogenins and functions in saponin biosynthesis. Homozygous plants were retarded in growth relative to normal plants, whereas heterozygous plants did not show dwarfism. Homozygous plants could flower and produce a few pods. The seeds did not show visible morphological changes but took an unusually long time to germinate (at least 3 weeks). Roots in homozygous lines were very short and less branched compared with the wild type. Leaf saponin levels did not differ between controls and mutants. Levels of 5 different saponins were lower in mutant lines (approx. 3-fold) compared with controls, while only one saponin was higher in the mutants. The large (10-fold) increase of 3-Glc-28-Ara-Rha-Xyl-medicagenic acid in UGT73F3 knockout lines suggests that the UDP-glucose pool is being diverted toward increased formation of non-C-28-glucosylated sapogenins. Levels of the isoflavone formononetin and its conjugates were also increased in UGT73F3 knockouts. traits: - entity_name: plant structure growth and development trait entity: TO:0000928 - entity_name: germination rate entity: TO:0000430 - entity_name: root branching entity: TO:0000257 - entity_name: root length entity: TO:0000227 - entity_name: root entity: PO:0009005 - entity_name: whole plant entity: PO:0000003 references: - citation: Ribeiro, Lacchini et al., 2020 doi: 10.1105/tpc.19.00609 pmid: 32303662 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - chitIII-3 gene_symbol_long: class III chitinase gene_model_pub_name: Medtr8g055940 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g055940 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Mtchit 3-3 expression (class III chitinase gene) is specifically induced by arbuscular mycorrhizal (AM) fungi in roots of the model legume Medicago truncatula. Mtchit 3-3 expression was artificially induced with a CaMV 35S promoter in root cells; this stimulated spore germination of Glomus intraradices and Glomus constrictum, and in the case of G. intraradices resulted in a higher probability of root colonization and spore formation. There was no measurable effect on the abundance of arbuscules within colonized roots. traits: - entity_name: root system entity: PO:0025025 references: - citation: Salzer, Bonanomi et al., 2000 doi: 10.1094/mpmi.2000.13.7.763 pmid: 10875337 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtGS2b gene_symbol_long: PLASTID GLUTAMINE SYNTHETASE 2 b gene_model_pub_name: Medtr2g026360.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g021242 confidence: 4 curators: - Raegan Nelson comments: - MtGS2b transcripts were detected exculsivly in developing seeds and seed pods - MtGS2a has a high degree of homology with MtGS2b - MtGS2b plays a role in seed metabloism - The stronger and specific expression of MtGS2b during seed filling suggests that the enzyme plays a role in seed specific role related to reserve accumulation phenotype_synopsis: MtGS2b plays a role in seed metabloism and seed storage traits: - entity_name: seed maturation entity: TO:0002661 - entity_name: glutamine catabolic process entity: GO:0006543 references: - citation: Seabra, Vieria et al., 2010 doi: 10.1186/1471-2229-10-183 pmid: 20723225 --- scientific_name: Medicago truncatula gene_symbols: - MtGS2a gene_symbol_long: PLASTID GLUTAMINE SYNTHETASE 2 a gene_model_pub_name: Medtr2g026390.1 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr2g021255 confidence: 5 curators: - Raegan Nelson comments: - MtGS2a transcripts were detected in almost all organs of the plant, being generally more highly expressed in leaves, stems and cotyledon - MtGS2a transcripts remain constant from 3-14 DAP but are absent at 20 DAP - MtGS2a has a high degree of homology with MtGS2b - MtGSba plays a role in seed metabloism phenotype_synopsis: MtGSa plays a role in seed metabloism traits: - entity_name: seed maturation entity: TO:0002661 - entity_name: glutamine catabolic process entity: GO:0006543 references: - citation: Seabra, Vieria et al., 2010 doi: 10.1186/1471-2229-10-183 pmid: 20723225 --- scientific_name: Medicago Truncatula gene_symbols: - MtAGa gene_symbol_long: AGAMOUS a gene_model_pub_name: KF159804 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr2g0284911 confidence: 5 curators: - Raegan Nelson comments: - MtAGa transcripts were detected throughout the floral meristem including the petal and sepal primordia - MtAGa and MtAGb are largely restricted to devloping the male and female floral organs in the early stages of flower development - MtAGa overexpression causes the conversion of sepals and petals into carpels and stamens - The transcription factor LFY activates MtAGa phenotype_synopsis: MtAGa controls stamen and carpel development traits: - entity_name: floral organ identity entity: TO:0006019 - entity_name: stamen development entity: GO:0048443 - entity_name: carpel development entity: GO:0048440 references: - citation: Serwatowska, Roque et al., 2014 doi: 10.1371/journal.pone.0103770 pmid: 25105497 --- scientific_name: Medicago Truncatula gene_symbols: - MtAGb gene_symbol_long: AGAMOUS b gene_model_pub_name: KF159805 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr8g0380021 confidence: 5 curators: - Raegan Nelson comments: - MtAGb transcripts accumulate in the centre of the floral primordia before migrating to the common primordia which will give rise to the stamens and the central part of the floral apex where the carpel is developing - MtAGa and MtAGb are largely restricted to devloping the male and female floral organs in the early stages of flower development - MtAGb overexpression causes the conversion of sepals and petals into carpels and stamens - MTAGb is more efficent at at inducing reproductive organ fate when overexpressed compared to MTAGa - The transcription factor LFY activates MtAGb phenotype_synopsis: MtAGb controls stamen and carpel development traits: - entity_name: floral organ identity entity: TO:0006019 - entity_name: stamen development entity: GO:0048443 - entity_name: carpel development entity: GO:0048440 references: - citation: Serwatowska, Roque et al., 2014 doi: 10.1371/journal.pone.0103770 pmid: 25105497 --- scientific_name: Medicago truncatula gene_symbols: - MtTCP18 gene_symbol_long: TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR gene_model_pub_name: Medtr4g111935 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g111935 confidence: 5 curators: - Raegan Nelson comments: - The expression pattern of MtTCP18 suggests that it may play a role in axillary bud development - MtTCP18 is highly expressed in pods and axillary buds - MtTCP18 encodes a nuclear protein functioning as transcriptional activator - MtTCP18 likely supresses Auxin-related gene expression - MtTcP18 is highly conserved with Arabidopsis gene BRC1 (BRANCHED1) phenotype_synopsis: MtTCP18 regulates plant height, branch number and axillary bud synthesis traits: - entity_name: Plant Height entity: TO:0000207 - entity_name: Axillary bud morphology trait entity: TO:0000790 - entity_name: Primary Branch number entity: TO:0000547 references: - citation: Su, Zheng etal., 2024 doi: 10.3390/plants13071012 pmid: 38611541 --- scientific_name: Medicago truncatula gene_symbols: - MtCre1 gene_symbol_long: Cytokinin Response 1 gene_model_pub_name: Medtr8g106150 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g106150 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Roots growth was not inhibited by exogenous cytokinin application. Expression of the primary cytokinin response gene, MtRR4, was not induced by cytokinins. Plants had an increased number of lateral roots (higher lateral root density) and a strong reduction in numbers of root nodules. The development of infection threads was inhibited and early nodule primordia development was also impaired. Expression of early nodulation genes was reduced in plants in which expression of MtCre1 was interfered with by RNAi. traits: - entity_name: root nodule number entity: TO:0000900 - entity_name: cytokinin sensitivity entity: TO:0000167 - entity_name: root number entity: TO:0000084 - entity_name: root system entity: PO:0025025 - entity_name: lateral root entity: PO:0020121 - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - ERN1 gene_symbol_long: Ethylene Response Factor Required for Nodulation 1 gene_model_pub_name: EU038802 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr7g085810 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - ERN2 gene_symbol_long: Ethylene Response Factor Required for Nodulation 2 gene_model_pub_name: EU038803 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr6g029180 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - EXPA gene_symbol_long: EXPANSIN A7 gene_model_pub_name: DQ899790 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g102450 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - NIN gene_symbol_long: Nodule Inception gene_model_pub_name: Medtr5g099060 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g099060 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - NRT1.3 gene_symbol_long: Nitrate Transporter 1.3 gene_model_pub_name: GU966590 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g085850 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - NSP1 gene_symbol_long: Nodulation signaling pathway 1 gene_model_pub_name: AJ972478 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr8g020840 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - RR4 gene_symbol_long: Response Regulator 4 gene_model_pub_name: Medtr5g036480 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g036480 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Control of symbiotic nitrogen fixation traits: - entity_name: root nodule entity: PO:0003023 references: - citation: Vernie, Kim et al., 2015 doi: 10.1105/tpc.15.00461 pmid: 26672071 --- scientific_name: Medicago truncatula gene_symbols: - MtRH1 gene_symbol_long: RED HEART 1 gene_model_pub_name: XP_013442258 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0229101 confidence: 5 curators: - Raegan Nelson comments: - Upregulation of MtRH1 leads to enhanced leaf marking - MtRH1 activates anthocyanin biosynthetic genes - MtRH1 expression is primarily confinded to the red markings on the leaves - MtRH1 expression is mediated by binding to specific promoter regions and competes with MtRH2 - MtRH2 and MtRH1 are paralogs phenotype_synopsis: MtRH1 is a positive regulator of anthocyanin biosynthesis traits: - entity_name: anthocyanin content entity: TO:0000071 - entity_name: positive regulation of anthocyanin biosynthetic process entity: GO:0031542 references: - citation: Wang, Li et al., 2020 doi: 10.1111/nph.17097 pmid: 33222243 --- scientific_name: Medicago truncatula gene_symbols: - MtRH2 gene_symbol_long: RED HEART 2 gene_model_pub_name: XP_013442390 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0229131 confidence: 5 curators: - Raegan Nelson comments: - MtRH2 negativly regulates leaf markings - MtRH2 does not activate anthocyanin biosynthetic genes - MtRH2 and MtRH1 are paralogs - MtRH2 negatively regulates leaf anthocyanin markings by competing with RH1 in the MBW regulatory complex phenotype_synopsis: MtRH2 negatively regulates MtRH1 traits: - entity_name: anthocyanin content entity: TO:0000071 - entity_name: negative regulation of anthocyanin biosynthetic process entity: GO:0031541 references: - citation: Wang, Li et al., 2020 doi: 10.1111/nph.17097 pmid: 33222243 --- scientific_name: Medicago truncatula gene_symbols: - MtGSTF7 gene_symbol_long: Glutathione S-transferase family protein gene_model_pub_name: Medtr3g064700 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr3g064700 confidence: 5 curators: - Wei Huang phenotype_synopsis: MtGSTF7, a homolog of AtTT19, is essential for anthocyanin accumulation but not required for PA accumulation in Medicago truncatula. MtGSTF7 was induced by the anthocyanin regulator LEGUME ANTHOCYANIN PRODUCTION 1 (LAP1), and its tissue expression pattern correlated with anthocyanin deposition in M. truncatula. traits: - entity_name: anthocyanin accumulation entity: NCIT:C16641 references: - citation: Wang, Lu et al., 2022 doi: 10.1093/jxb/erac112 pmid: 35294003 - citation: Hasan, Singh et al. 2021 doi: 10.1371/journal.pone.0247170 pmid: 33606812 --- scientific_name: Medicago truncatula gene_symbols: - EIN2 - Skl1 gene_symbol_long: Ethylene Insensitive 2 gene_model_pub_name: Medtr7g101410 gene_model_full_id: medtr.A17.gnm5.ann1_6.MtrunA17Chr7g0264231 confidence: 5 curators: - Steven Cannon phenotype_synopsis: Absence of discrete nodules, increased persistant rhizobila infection, radial swelling of primary infection zone, larger cotyledons, reduced apical hook angle, reduced develoment of ectopic root hairs, no loss of geotropism,and a lack of inhibition of both hypocotyl and root growth. Reduced inhibition of root growth in response to application of exogenous cytokinin benzyl adenine. Increased primary mycorrhizal infections by Glomus versiforme and Glomus intraradices. Increased susceptability to damage caused by infection with R. solani necrotrophic fungus and P. medicaginis necrotrophic oomycete as well as larger numbers of P. medicaginis reproductive structures. Reduced biphasic ethylene production after inoculation with P. medicaginis, reduced gene expression for one isoform of ACC oxidase transcripts, and reduced responsiveness of ethylene levels to exogenous ACC (all indicators of impaired autocatalytic ethylene production). traits: - entity_name: gravity response trait entity: TO:0002693 - entity_name: root hair length entity: TO:0002665 - entity_name: root nodule number entity: TO:0000900 - entity_name: hypocotyl morphology trait entity: TO:0000757 - entity_name: seedling cotyledon size entity: TO:0000752 - entity_name: root development trait entity: TO:0000656 - entity_name: root system entity: PO:0025025 - entity_name: hypocotyl entity: PO:0020100 - entity_name: cotyledon entity: PO:0020030 - entity_name: root entity: PO:0009005 - entity_name: non-hair root epidermal cell entity: PO:0000263 - entity_name: apical hook entity: PO:0000012 references: - citation: Weller, Foo et al., 2015 doi: 10.1104/pp.15.00164 pmid: 25792252 - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 --- scientific_name: Medicago truncatula gene_symbols: - MtbZIP60 gene_symbol_long: basic leucine zipper 60 gene_model_pub_name: Medtr4g070860 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr4g070860 confidence: 5 curators: - Raegan Nelson comments: - MtbZIP60 expression level increases significantly as leaf ages - MtbZIP60 exhibits relatively high-level expression in leafs and moderate-level expression in roots and stems - MtbZIP60 inhibits leaf senescence through its interaction with MtWRKY40 phenotype_synopsis: MtbZIP60 acts as a negative regulator of leaf senescence traits: - entity_name: Leaf senescence duration entity: TO:0012012 - entity_name: negative regulation of leaf senescence entity: GO:1900056 references: - citation: Xing, Weng etal., 2024 doi: 10.3390/ijms251910410 pmid: 39408738 --- scientific_name: Medicago truncatula gene_symbols: - MtAGLF gene_symbol_long: AGAMOUS-LIKE FLOWER gene_model_pub_name: Medtr0007s0220 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr0007s0220 confidence: 5 curators: - Raegan Nelson comments: - MtAGLF possesses a MYB-like DNA-binding domain which suggests transcriptional regulator in flower development - MtAGLF is probably involved in the regulation of the class C gene - Loss-of-function of MtAGLF leads to the dysregulation of ABC genes - The knockout of MtAGLF leads to ectopic expression of MtAP1 and MtPI across the FM and to reduced MtAGa and MTAGb expression in the center phenotype_synopsis: MtAGLF regulates MtAGs which determine floral organ identity traits: - entity_name: floral organ identity entity: TO:0006019 - entity_name: floral organ development entity: GO:0048437 references: - citation: Zhao, Liu et al., 2019 doi: 10.1073/pnas.1820468116 pmid: 30782811 - citation: Serwatowska, Roque et al., 2014 doi: 10.1371/journal.pone.0103770 pmid: 25105497 --- scientific_name: Medicago truncatula gene_symbols: - MtMIO1 gene_symbol_long: Mini Organ 1 gene_model_pub_name: Medtr5g097060 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr5g097060 confidence: 5 curators: - Raegan Nelson comments: - MIO1 encodes an F-box protein SMALL LEAF AND BUSHY1(SLB1) which was identified as a key regulator of organ size - MIO1 is highly expressed in leaves, floral organs, and immature seeds - MIO1 plays a crucial role during lateral organ morphogenesis - MIO1 positively regulates organ size mainly by promoting the process of primary cell proliferation during plant development - MIO1 is also necessary for robust pulvinus development and leaf movement - MIO1/SLB1 could form part of SKP1/Cullin/F-box (SCF) E3 ubiquitin ligase complex to target MtBS1 phenotype_synopsis: MIO1 plays a role in plant organ size regulation and leaf movement traits: - entity_name: Pulvinus size entity: TO:0001075 - entity_name: Floral organ size entity: TO:0002600 - entity_name: Leaf size entity: TO:0002637 references: - citation: Zhou, Yang et al,. 2021 doi: 10.1093/jxb/erab033 pmid: 33506247 --- scientific_name: Medicago truncatula gene_symbols: - MtBS1 gene_symbol_long: Big seed 1 gene_model_pub_name: Medtr1g102900 gene_model_full_id: medtr.A17_HM341.gnm4.ann2.Medtr1g102900 confidence: 5 curators: - Raegan Nelson comments: - The stability of BS1 protein is negatively regulated by MIO1 - Loss of function BS1 caused enlarged lateral plant organs - BS1 is a negative regulator of meristemoid proliferation and primary cell division - BS1 is a ortholog of PPD (pea pod) phenotype_synopsis: MtBS1 is a repressor of primary cell cell division traits: - entity_name: Floral organ size entity: TO:0002600 - entity_name: Leaf size entity: TO:0002637 references: - citation: Zhou, Yang et al,. 2021 doi: 10.1093/jxb/erab033 pmid: 33506247