## DOCUMENT 1 ## --- 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 ## DOCUMENT 2 ## --- 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 ## DOCUMENT 3 ## --- 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 ## DOCUMENT 4 ## --- 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 ## DOCUMENT 5 ## --- 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 ## DOCUMENT 6 ## --- 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 ## DOCUMENT 7 ## --- 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 ## DOCUMENT 8 ## --- 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: null - citation: Oellrich, Walls et al., 2015 doi: 10.1186/s13007-015-0053-y pmid: 25774204 ## DOCUMENT 9 ## --- 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 ## DOCUMENT 10 ## --- 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 ## DOCUMENT 11 ## --- 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 ## DOCUMENT 12 ## --- 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 ## DOCUMENT 13 ## --- 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 ## DOCUMENT 14 ## --- 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 ## DOCUMENT 15 ## --- 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 ## DOCUMENT 16 ## --- 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 ## DOCUMENT 17 ## --- 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 ## DOCUMENT 18 ## --- 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: null 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 ## DOCUMENT 19 ## --- 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 ## DOCUMENT 20 ## --- 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 ## DOCUMENT 21 ## --- 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 ## DOCUMENT 22 ## --- 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 ## DOCUMENT 23 ## --- 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 ## DOCUMENT 24 ## --- 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 ## DOCUMENT 25 ## --- 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 ## DOCUMENT 26 ## --- gene_symbols: - MtCre1 gene_symbol_long: Cytokinin Response1 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, Mt RR4, 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 ## DOCUMENT 27 ## --- 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 ## DOCUMENT 28 ## --- 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: null 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 ## DOCUMENT 29 ## --- 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 ## DOCUMENT 30 ## --- 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 ## DOCUMENT 31 ## --- 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: TO:0000748 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 ## DOCUMENT 32 ## --- 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 ## DOCUMENT 33 ## --- gene_symbols: - EIN2 - Skl1 gene_symbol_long: Ethylene Insensitive2 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: TO:0000757 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 ## DOCUMENT 34 ## --- 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 ## DOCUMENT 35 ## --- 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 ## DOCUMENT 36 ## --- gene_symbols: - ERN1 gene_symbol_long: Ethylene Response Factor Required for Nodulation1 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 ## DOCUMENT 37 ## --- gene_symbols: - ERN2 gene_symbol_long: Ethylene Response Factor Required for Nodulation2 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 ## DOCUMENT 38 ## --- 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 ## DOCUMENT 39 ## --- 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 ## DOCUMENT 40 ## --- 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 ## DOCUMENT 41 ## --- 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 ## DOCUMENT 42 ## --- 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