An ontology that describes phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant. Plant Trait Ontology plant_trait_ontology 1.2 cooperl definition term replaced by Terms_used_for_leek Terms_used_for_squash Terms_used_for_soybean Term_used_for_barley Terms_used_for_sugarcane Terms_used_for_the_Solanaceae Terms_used_for_wheat Terms_used_for_maize_or_corn subset_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym in_subset shorthand BFO:0000050 plant_trait_ontology part_of part_of part of BFO:0000051 plant_trait_ontology has_part has_part has part BFO:0000066 plant_trait_ontology occurs_in occurs_in occurs in RO:0000052 plant_trait_ontology inheres_in inheres_in inheres in plant_trait_ontology evaluation_location evaluation location plant_trait_ontology from_country from country plant_trait_ontology has_absolute_phenotype has absolute phenotype plant_trait_ontology has_dividend_entity has dividend entity plant_trait_ontology has_dividend_quality has dividend quality plant_trait_ontology has_divisor_entity has divisor entity plant_trait_ontology has_divisor_quality has divisor quality plant_trait_ontology has_phenotype_score has phenotype score plant_trait_ontology has_phenotype_variable has phenotype variable plant_trait_ontology has_ratio_quality has ratio quality plant_trait_ontology has_relative_phenotype has relative phenotype plant_trait_ontology relative_to relative to Sensitivity to the carbon content in the growth medium. It plays an important role in the synthesis of various inorganic and organic metabolites such as carbohydrates, lipids, amino acids and peptides and plays a role in various metabolic processes. plant_trait_ontology CBSN (related) carbon deficiency (related) TO:0000001 carbon sensitivity Sensitivity to the carbon content in the growth medium. It plays an important role in the synthesis of various inorganic and organic metabolites such as carbohydrates, lipids, amino acids and peptides and plays a role in various metabolic processes. Gramene:pankaj_jaiswal OBSOLETE. An epigenetic trait is a distinguishable feature or a characteristic or a quality of character or a phenotypic feature of a developing or developed individual but have arisen as a result of mechanisms regulating the expression of the genes rather than differences in the gene sequence. plant_trait_ontology TO:0000002 OBSOLETE epigenetic trait true OBSOLETE. An epigenetic trait is a distinguishable feature or a characteristic or a quality of character or a phenotypic feature of a developing or developed individual but have arisen as a result of mechanisms regulating the expression of the genes rather than differences in the gene sequence. Gramene:pankaj_jaiswal ISBN:0198506732 Plant sensitivity to soils with alkali conditions (pH>7). plant_trait_ontology AlkS (related) alkali sensitivity (related) TO:0000003 Observed by general growth conditions in relation to standard resistant and susceptible checks. Since some soil problems are very heterogeneous in the field, several replications may be needed to obtain precise reading. Leaf is counted as discolored or dead if more than half of its area is discolored or dead. alkali soil sensitivity Plant sensitivity to soils with alkali conditions (pH>7). IRRI:SES TO:moorel Trait of a plant in which the action of the cytotoxic gene used to introduce male sterility is suppressed by the application of a chemical to the plant. Reversion of the sterility allows the RMS parent to be self-fertilized, a step that overcomes the need to remove fertile sib plants prior to making the hybrid cross. plant_trait_ontology RMS (related) TO:0000004 reversible male sterility Trait of a plant in which the action of the cytotoxic gene used to introduce male sterility is suppressed by the application of a chemical to the plant. Reversion of the sterility allows the RMS parent to be self-fertilized, a step that overcomes the need to remove fertile sib plants prior to making the hybrid cross. PMID:10645437 true Sensitivity to the calcium content in the growth medium. Plays an important role in cell wall synthesis and enzyme activities. plant_trait_ontology CALSN (related) calcium deficiency (related) TO:0000006 calcium sensitivity Sensitivity to the calcium content in the growth medium. Plays an important role in cell wall synthesis and enzyme activities. Gramene:pankaj_jaiswal Response by the plant in terms of sensitivity to sulfur content in the growth medium. It is important for synthesis of some amino acid residues. plant_trait_ontology SFSN (related) sulfur deficiency (related) TO:0000007 sulfur sensitivity Response by the plant in terms of sensitivity to sulfur content in the growth medium. It is important for synthesis of some amino acid residues. Gramene:pankaj_jaiswal Sensitivity to the potassium ion content in the growth medium. It plays an important role in controlling water by osmosis and also in the metal ion homeostasis. plant_trait_ontology KSN (related) potassium deficiency (related) TO:0000008 potassium sensitivity Sensitivity to the potassium ion content in the growth medium. It plays an important role in controlling water by osmosis and also in the metal ion homeostasis. Gramene:pankaj_jaiswal Male sterility affected by photoperiod. plant_trait_ontology PGMS (related) PPDSNGMS (related) photoperiod sensitive genic male sterility (related) TO:0000009 genic male sterility-photoperiod sensitive Male sterility affected by photoperiod. Gramene:pankaj_jaiswal IRRI:SES Sensitivity to the magnesium content in the growth medium. It is important for chlorophyll biosynthesis and metal ion homeostasis. plant_trait_ontology MGSN (related) magnesium deficiency (related) TO:0000010 magnesium sensitivity Sensitivity to the magnesium content in the growth medium. It is important for chlorophyll biosynthesis and metal ion homeostasis. Gramene:pankaj_jaiswal Sensitivity to the nitrogen content in the growth medium. It is important for protein synthesis, chlorophyll etc. plant_trait_ontology NISN (related) nitrogen deficiency (related) TO:0000011 nitrogen sensitivity Sensitivity to the nitrogen content in the growth medium. It is important for protein synthesis, chlorophyll etc. Gramene:pankaj_jaiswal Sensitivity to the molecular hydrogen or hydrogen ion content in the growth medium. It plays an important role in the synthesis of various inorganic and organic metabolites such as carbohydrates, lipids, amino acids and peptides and plays a role in the energy metabolism, osmolarity, etc. plant_trait_ontology hydrogen ion sensitivity (related) molecular hydrogen sensitivity (related) TO:0000012 hydrogen sensitivity Sensitivity to the molecular hydrogen or hydrogen ion content in the growth medium. It plays an important role in the synthesis of various inorganic and organic metabolites such as carbohydrates, lipids, amino acids and peptides and plays a role in the energy metabolism, osmolarity, etc. Gramene:pankaj_jaiswal An assay to determine the resistance exhibited by a plant or a group of plants (population) in response to the disease caused by a mycoplasma-like pathogen infection as compared to the susceptible and/or the reference plants of the same species. plant_trait_ontology MLO (related) MLORS (related) TO:0000013 The factors needed for successful test are the presence of sources and vectors, inoculation at the susceptible growth stage of the test plants and favorable environmental conditions. resistance to disease by mycoplasma-like organism An assay to determine the resistance exhibited by a plant or a group of plants (population) in response to the disease caused by a mycoplasma-like pathogen infection as compared to the susceptible and/or the reference plants of the same species. Gramene:pankaj_jaiswal IRRI:SES Average weight of the panicle from the plants or tillers in a given study. plant_trait_ontology PNWT (related) TO:0000014 panicle weight Average weight of the panicle from the plants or tillers in a given study. Gramene:pankaj_jaiswal Sensitivity to the molecular oxygen or reactive oxygen ion content in the growth medium. It plays an important role in the synthesis of various inorganic and organic metabolites such as carbohydrates, lipids, aminoacids and peptides and plays a role in the energy metabolism. plant_trait_ontology oxygen deficiency (related) TO:0000015 oxygen sensitivity Sensitivity to the molecular oxygen or reactive oxygen ion content in the growth medium. It plays an important role in the synthesis of various inorganic and organic metabolites such as carbohydrates, lipids, aminoacids and peptides and plays a role in the energy metabolism. Gramene:pankaj_jaiswal Sensitivity to the cobalt content in the growth medium. plant_trait_ontology COSN (related) TO:0000016 cobalt sensitivity Sensitivity to the cobalt content in the growth medium. Gramene:pankaj_jaiswal A plant trait (TO:0000387) which is a morphological quality of a plant anatomical entity (PO:0025131) or a constituent cellular component (GO:0005575) contained therein. https://github.com/Planteome/plant-trait-ontology/issues/54 TO_GIT:54 plant_trait_ontology plant architecture trait (related) plant structure trait (related) TO:0000017 Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161). plant morphology trait A plant trait (TO:0000387) which is a morphological quality of a plant anatomical entity (PO:0025131) or a constituent cellular component (GO:0005575) contained therein. GO:0005575 Gramene:pankaj_jaiswal PO:0025131 TO:cooperl Sensitivity to the boron content in the growth medium. It plays an important role in cell division. plant_trait_ontology BOSN (related) boron deficiency (related) TO:0000018 boron sensitivity Sensitivity to the boron content in the growth medium. It plays an important role in cell division. Gramene:pankaj_jaiswal Average height measurements of 10 seedlings, in centimeters from the base of the shoot to the tip of the tallest leaf blade. plant_trait_ontology SH (related) TO:0000019 seedling height Average height measurements of 10 seedlings, in centimeters from the base of the shoot to the tip of the tallest leaf blade. IRRI:SES plant_trait_ontology BSDVRS (related) TO:0000020 black streak dwarf virus resistance Sensitivity to the copper ion content in the growth medium. Plays a role as cofactor in synthesis of some enzymes important in photosynthesis. plant_trait_ontology CUSN (related) TO:0000021 copper sensitivity Sensitivity to the copper ion content in the growth medium. Plays a role as cofactor in synthesis of some enzymes important in photosynthesis. Gramene:pankaj_jaiswal Causal agent: Oebalus pugnax. plant_trait_ontology SBUGRS (related) TO:0000022 stink bug resistance Causal agent: Oebalus pugnax. Gramene:pankaj_jaiswal Causal agent: species of Sarocladium, Bipolaris, Alternaria, Gerlachia, Fusarium, Phoma, Curvularia, Trichoconiella and Psaudomonas etc. Symptoms: darkening of glumes of spikelets, brown color to black including rotten glumes caused by one or more pathogens. Intensity ranges from sporadic discoloration to discoloration of the whole glume. Severity of grain discoloration can be estimated by counting of grains with more than 25% of glume surface affected. plant_trait_ontology Gd (related) grain discoloration (related) TO:0000023 fungal infection related grain discoloration Causal agent: species of Sarocladium, Bipolaris, Alternaria, Gerlachia, Fusarium, Phoma, Curvularia, Trichoconiella and Psaudomonas etc. Symptoms: darkening of glumes of spikelets, brown color to black including rotten glumes caused by one or more pathogens. Intensity ranges from sporadic discoloration to discoloration of the whole glume. Severity of grain discoloration can be estimated by counting of grains with more than 25% of glume surface affected. Gramene:pankaj_jaiswal IRRI:SES A ligule morphology trait (TO:0002748) which is a length of a ligule measured in millimeters from the base of the leaf collar to the tip of the ligule (PO:0020105). PATO:0000122 plant_trait_ontology LIGLG (related) LgL (related) TO:0000024 Refer to length PATO:0000122: A 1-D extent quality which is equal to the distance between two points. ligule length A ligule morphology trait (TO:0002748) which is a length of a ligule measured in millimeters from the base of the leaf collar to the tip of the ligule (PO:0020105). IRRI:SES PO:0020105 TO:cooperl Important for nitrate fixation. plant_trait_ontology TO:0000025 molybdenum sensitivity Important for nitrate fixation. Gramene:pankaj_jaiswal Abortion at tri-nucleate stage of microspore development. plant_trait_ontology TNUABR (related) TO:0000026 An example is CMS-boro in rice. aborted tri-nucleate stage Abortion at tri-nucleate stage of microspore development. Gramene:pankaj_jaiswal IRRI:SES Actual count of the total number of tillers after full heading, Specify if per plant, hill or area. plant_trait_ontology CmN (related) TO:0000027 culm number Actual count of the total number of tillers after full heading, Specify if per plant, hill or area. IRRI:SES Number of unfilled florets in a grass inflorescence. plant_trait_ontology UNFILGRNB (related) unfilled florets per panicle (related) unfilled grain (related) TO:0000028 unfilled grain number Number of unfilled florets in a grass inflorescence. Gramene:pankaj_jaiswal Sensitivity to the chlorine content in the growth medium. Chloride helps regulate the correct pH (acid/alkaline) balance. This is a major electrolyte in the living cell besides sodium and potassium. It is available to the cell mainly in the form of NaCl and KCl salts. plant_trait_ontology CHLORSN (related) TO:0000029 chlorine sensitivity Sensitivity to the chlorine content in the growth medium. Chloride helps regulate the correct pH (acid/alkaline) balance. This is a major electrolyte in the living cell besides sodium and potassium. It is available to the cell mainly in the form of NaCl and KCl salts. Gramene:pankaj_jaiswal A weed damage response (TO:0000347) trait which is the response of a plant to weed competition from sedge weeds. plant_trait_ontology TO:0000030 Sedges are perennial plants which resemble grasses, and commonly grow in shallow water or moist soils, such as rice production fields. Sedges may be distinguished from grasses by their stem cross-section (solid, triangular) and leaf shape (long, thin-textured, narrow and flat). Common sedge weeds in rice fields include Smallflower Umbrella Sedge (Cyperus difformis), Ricefield Bulrush (Scirpus mucronatus), and River Bulrush (Scirpus fluviatilis). sedge weed response A weed damage response (TO:0000347) trait which is the response of a plant to weed competition from sedge weeds. Gramene:pankaj_jaiswal ISBN:9712200299 TO:cooperl http://ipm.ucanr.edu/PMG/WEEDS/sedge_gallery.html plant_trait_ontology TO:0000031 silicon sensitivity plant_trait_ontology TO:0000032 selenium sensitivity plant_trait_ontology TO:0000033 iodine sensitivity Sensitivity to the chromium content in the growth medium. plant_trait_ontology CHRSN (related) TO:0000034 chromium sensitivity Sensitivity to the chromium content in the growth medium. Gramene:pankaj_jaiswal plant_trait_ontology TO:0000035 incompatibility trait plant_trait_ontology HYBIC (related) TO:0000036 hybrid incompatibility OBSOLETE. Determines the extent of male sterility of a male sterile line. Can be determined by either pollen sterility or spikelet fertility plant_trait_ontology degree of male sterility of male sterile lines (related) male sterility measure (related) TO:0000037 OBSOLETE male sterility extent true OBSOLETE. Determines the extent of male sterility of a male sterile line. Can be determined by either pollen sterility or spikelet fertility Gramene:pankaj_jaiswal IRRI:SES plant_trait_ontology TO:0000038 fluorine sensitivity OBSOLETE. Defines the components that determine the over all yield from a plant plant_trait_ontology TO:0000039 OBSOLETE yield component true OBSOLETE. Defines the components that determine the over all yield from a plant Gramene:pankaj_jaiswal A panicle morphology trait (TO:0000847) which is the measurement in centimeters from panicle base to tip. plant_trait_ontology PNLG (related) PnL (related) TO:0000040 Evaluated at growth stage:8 in rice. panicle length A panicle morphology trait (TO:0000847) which is the measurement in centimeters from panicle base to tip. IRRI:SES A grain length (TO:0000734) monitored after dehulling but before polishing. The grain should contain pericarp (PO:0009084). PATO:0000122 plant_trait_ontology BRWLG (related) Len (related) TO:0000041 Refer to length (PATO:0000122): A 1-D extent quality which is equal to the distance between two points. brown rice length A grain length (TO:0000734) monitored after dehulling but before polishing. The grain should contain pericarp (PO:0009084). IRRI:SES PO:0009084 TO:moorel plant_trait_ontology F1HYBIC (related) TO:0000042 f1-hybrid incompatibility A plant axis morphology trait (TO:0000738) which is a quality of a root (PO:0025025). TO_GIT:58 plant_trait_ontology TO:0000043 root morphology trait A plant axis morphology trait (TO:0000738) which is a quality of a root (PO:0025025). Gramene:pankaj_jaiswal PO:0025025 TO:cooperl Trait is monitored by counting number of flowers or florets that have completed anthesis on a given day and showing exserted stigma. Trait expressed as percent stigma exsertion. plant_trait_ontology STIEX (related) stigma exsertion of male sterile lines (related) TO:0000044 Scale, (%), Stigma exsertion; 1- Above 70, Well exserted; 3- 41-70, Moderately well exserted; 5- 21-40, Just exserted; 7- 11-20, Partly exserted; 9- 0-10, Enclosed. Evaluated at growth stage:6 and 7 in rice. stigma exsertion Trait is monitored by counting number of flowers or florets that have completed anthesis on a given day and showing exserted stigma. Trait expressed as percent stigma exsertion. Gramene:pankaj_jaiswal IRRI:SES Causal agent: Balanasia oryzae-sativae (Ephelis oryzae). Symptoms: a white mycelial mat ties the panicle branches together so that they emerge as single, small, cylindrical rods. plant_trait_ontology UDb (related) TO:0000045 udbatta disease resistance Causal agent: Balanasia oryzae-sativae (Ephelis oryzae). Symptoms: a white mycelial mat ties the panicle branches together so that they emerge as single, small, cylindrical rods. Gramene:pankaj_jaiswal IRRI:SES plant_trait_ontology F2GST (related) TO:0000046 f2-generation sterility plant_trait_ontology TO:0000047 sporophytic incompatibility Causal agent: Tilletia barclayana. Symptoms: infected grains show minute black pustules or streaks bursting through the glumes. In severe infection, the rupturing glumes produce short beak-like or spur-like outgrowths. plant_trait_ontology KSRS (related) KSm (related) TO:0000048 kernel smut disease resistance Causal agent: Tilletia barclayana. Symptoms: infected grains show minute black pustules or streaks bursting through the glumes. In severe infection, the rupturing glumes produce short beak-like or spur-like outgrowths. Gramene:pankaj_jaiswal plant_trait_ontology GPHIC (related) TO:0000049 gametophytic incompatibility An inflorescence morphology trait (TO:0000373) which is the extent of branching. (PO:0009049). TO:0000263 TO_GIT:96 plant_trait_ontology panicle branching (related) TO:0000050 Branching usually determines the shape and compactness of the inflorescence inflorescence branching An inflorescence morphology trait (TO:0000373) which is the extent of branching. (PO:0009049). Gramene:pankaj_jaiswal PO:0009049 TO:moorel A stem morphology trait (TO:0000361) which is the strength of a stem (PO:0009047). PATO:0001230 plant_trait_ontology CULMSTR (related) Cs (related) STEMSTR (related) culm strength (related) TO:0000051 Refer to strength (PATO:0001230): A quality inhering in a bearer by virtue of the bearer's power or force. stem strength A stem morphology trait (TO:0000361) which is the strength of a stem (PO:0009047). Gramene:pankaj_jaiswal IRRI:SES PO:0009047 TO:moorel An inflorescence morphology trait (TO:0000373) which is the extent of primary branching that usually sets the tone for shape and compactness of the inflorescence (PO:0009049) (rice panicle). plant_trait_ontology PBR (related) primary branching of panicle (related) TO:0000052 primary branching of inflorescence