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RTO-1.0.obo
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RTO-1.0.obo
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format_version: 1.1
saved_by: xzyao
default_namespace: rice_trait_ontology
[Term]
id: RTO:0000001
name: Rice Trait
[Term]
id: TO:0000001
name: carbon sensitivity
def: "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]
synonym: "CBSN (related)" RELATED []
synonym: "carbon deficiency (related)" RELATED []
is_a: TO:0000252 ! non-mineral nutrient sensitivity
[Term]
id: TO:0000002
name: epigenetic trait
def: "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]
is_obsolete: true
[Term]
id: TO:0000003
name: alkali soil sensitivity
def: "Plant sensitivity to soils with alkali conditions (pH>7)." [IRRI:SES, TO:moorel]
comment: 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.
synonym: "AlkS (related)" RELATED []
synonym: "alkali sensitivity (related)" RELATED []
is_a: TO:0000481 ! alkali sensitivity
[Term]
id: TO:0000004
name: reversible male sterility
def: "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]
synonym: "RMS (related)" RELATED []
is_a: TO:0000111 ! genetically engineered male sterility
[Term]
id: TO:0000006
name: calcium sensitivity
def: "Sensitivity to the calcium content in the growth medium. Plays an important role in cell wall synthesis and enzyme activities." [Gramene:pankaj_jaiswal]
synonym: "calcium deficiency (related)" RELATED []
synonym: "CALSN (related)" RELATED []
is_a: TO:0000251 ! secondary macronutrient sensitivity
[Term]
id: TO:0000007
name: sulfur sensitivity
def: "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]
synonym: "sulfur deficiency (related)" RELATED []
synonym: "SFSN (related)" RELATED []
is_a: TO:0000251 ! secondary macronutrient sensitivity
[Term]
id: TO:0000008
name: potassium sensitivity
def: "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]
synonym: "potassium deficiency (related)" RELATED []
synonym: "KSN (related)" RELATED []
is_a: TO:0000248 ! primary macronutrient sensitivity
[Term]
id: TO:0000009
name: genic male sterility-photoperiod sensitive
def: "Male sterility affected by photoperiod." [Gramene:pankaj_jaiswal, IRRI:SES]
synonym: "PGMS (related)" RELATED []
synonym: "photoperiod sensitive genic male sterility (related)" RELATED []
synonym: "PPDSNGMS (related)" RELATED []
is_a: TO:0000199 ! genic male sterility
[Term]
id: TO:0000010
name: magnesium sensitivity
def: "Sensitivity to the magnesium content in the growth medium. It is important for chlorophyll biosynthesis and metal ion homeostasis." [Gramene:pankaj_jaiswal]
synonym: "magnesium deficiency (related)" RELATED []
synonym: "MGSN (related)" RELATED []
is_a: TO:0000251 ! secondary macronutrient sensitivity
[Term]
id: TO:0000011
name: nitrogen sensitivity
def: "Sensitivity to the nitrogen content in the growth medium. It is important for protein synthesis, chlorophyll etc." [Gramene:pankaj_jaiswal]
synonym: "NISN (related)" RELATED []
synonym: "nitrogen deficiency (related)" RELATED []
is_a: TO:0000248 ! primary macronutrient sensitivity
[Term]
id: TO:0000012
name: hydrogen sensitivity
def: "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]
synonym: "hydrogen ion sensitivity (related)" RELATED []
synonym: "molecular hydrogen sensitivity (related)" RELATED []
is_a: TO:0000252 ! non-mineral nutrient sensitivity
[Term]
id: TO:0000013
name: resistance to disease by mycoplasma-like organism
def: "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]
comment: 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.
synonym: "MLO (related)" RELATED []
synonym: "MLORS (related)" RELATED []
is_a: TO:0000112 ! disease resistance
is_a: TO:0000242 ! microbial damage resistance
[Term]
id: TO:0000014
name: panicle weight
def: "Average weight of the panicle from the plants or tillers in a given study." [Gramene:pankaj_jaiswal]
synonym: "PNWT (related)" RELATED []
is_a: TO:0000583 ! infructescence weight
is_a: TO:0000803 ! inflorescence weight
is_a: TO:0000847 ! panicle inflorescence morphology trait
[Term]
id: TO:0000015
name: oxygen sensitivity
def: "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]
synonym: "oxygen deficiency (related)" RELATED []
is_a: TO:0002657 ! oxidative stress
is_a: TO:0000252 ! non-mineral nutrient sensitivity
[Term]
id: TO:0000016
name: cobalt sensitivity
def: "Sensitivity to the cobalt content in the growth medium." [Gramene:pankaj_jaiswal]
xref: WTO:0000533
synonym: "COSN (related)" RELATED []
is_a: WTO:0000463 ! heavy metal toxicity
is_a: TO:0000247 ! other nutrient sensitivity
[Term]
id: TO:0000017
name: plant morphology trait
def: "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]
comment: 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).
xref: TO_GIT:54
synonym: "plant structure trait (related)" RELATED []
synonym: "plant architecture trait (related)" RELATED []
is_a: TO:0000387 ! plant trait
[Term]
id: TO:0000018
name: boron sensitivity
def: "Sensitivity to the boron content in the growth medium. It plays an important role in cell division." [Gramene:pankaj_jaiswal]
xref: WTO:0000453
synonym: "BOSN (related)" RELATED []
synonym: "boron deficiency (related)" RELATED []
is_a: WTO:0000331 ! metalloid toxicity
is_a: TO:0000080 ! micronutrient sensitivity
[Term]
id: TO:0000019
name: seedling height
def: "Average height measurements of 10 seedlings, in centimeters from the base of the shoot to the tip of the tallest leaf blade." [IRRI:SES]
synonym: "SH (related)" RELATED []
is_a: TO:0000207 ! plant height
[Term]
id: TO:0000020
name: black streak dwarf virus resistance
synonym: "BSDVRS (related)" RELATED []
is_a: TO:0000148 ! viral disease resistance
[Term]
id: TO:0000021
name: copper sensitivity
def: "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]
xref: WTO:0000534
synonym: "CUSN (related)" RELATED []
is_a: WTO:0000463 ! heavy metal toxicity
is_a: TO:0000080 ! micronutrient sensitivity
[Term]
id: TO:0000022
name: stink bug resistance
def: "Causal agent: Oebalus pugnax." [Gramene:pankaj_jaiswal]
synonym: "SBUGRS (related)" RELATED []
is_a: TO:0000261 ! insect damage resistance
[Term]
id: TO:0000023
name: fungal infection related grain discoloration
def: "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]
synonym: "grain discoloration (related)" RELATED []
synonym: "Gd (related)" RELATED []
is_a: TO:0000439 ! fungal disease resistance
[Term]
id: TO:0000024
name: ligule length
def: "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]
comment: Refer to length PATO:0000122: A 1-D extent quality which is equal to the distance between two points.
xref: PATO:0000122
synonym: "LIGLG (related)" RELATED []
synonym: "LgL (related)" RELATED []
is_a: TO:0000135 ! leaf length
is_a: TO:0002748 ! ligule morphology trait
[Term]
id: TO:0000025
name: molybdenum sensitivity
def: "Important for nitrate fixation." [Gramene:pankaj_jaiswal]
is_a: TO:0000080 ! micronutrient sensitivity
[Term]
id: TO:0000026
name: aborted tri-nucleate stage
def: "Abortion at tri-nucleate stage of microspore development." [Gramene:pankaj_jaiswal, IRRI:SES]
comment: An example is CMS-boro in rice.
synonym: "TNUABR (related)" RELATED []
is_a: TO:0000218 ! pollen abortion type
[Term]
id: TO:0000027
name: culm number
def: "Actual count of the total number of tillers after full heading, Specify if per plant, hill or area." [IRRI:SES]
synonym: "CmN (related)" RELATED []
is_a: TO:0000077 ! shoot system morphology trait
[Term]
id: TO:0000028
name: unfilled grain number
def: "Number of unfilled florets in a grass inflorescence." [Gramene:pankaj_jaiswal]
synonym: "unfilled florets per panicle (related)" RELATED []
synonym: "unfilled grain (related)" RELATED []
synonym: "UNFILGRNB (related)" RELATED []
is_a: TO:0002759 ! grain number
[Term]
id: TO:0000029
name: chlorine sensitivity
def: "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]
synonym: "CHLORSN (related)" RELATED []
is_a: TO:0000080 ! micronutrient sensitivity
[Term]
id: TO:0000030
name: sedge weed
def: "A common sedge weed Cyperus iria (rice flatsedge), Cyperus difformis (Small flower umbrella sedge), Rice field bulrush Scirpus mucronatus, River bulrush Scirpus fluviatilis. Grows as a weed in the rice field. Can be distinguished from grass plant by the leaf shape, venation, stem cross-section and plant shape leaf shape." [Gramene:pankaj_jaiswal, http//www.ipm.ucdavis.edu/PMG/r682700999.html, ISBN:9712200299]
is_a: TO:0000347 ! weed damage
[Term]
id: TO:0000031
name: silicon sensitivity
is_a: TO:0000247 ! other nutrient sensitivity
[Term]
id: TO:0000032
name: selenium sensitivity
is_a: TO:0000247 ! other nutrient sensitivity
[Term]
id: TO:0000033
name: iodine sensitivity
is_a: TO:0000247 ! other nutrient sensitivity
[Term]
id: TO:0000034
name: chromium sensitivity
def: "Sensitivity to the chromium content in the growth medium." [Gramene:pankaj_jaiswal]
xref: WTO:0000532
synonym: "CHRSN (related)" RELATED []
is_a: WTO:0000463 ! heavy metal toxicity
is_a: TO:0000247 ! other nutrient sensitivity
[Term]
id: TO:0000035
name: incompatibility trait
is_a: TO:0000392 ! sterility or fertility trait
is_a: TO:0000398 ! whole plant morphology trait
[Term]
id: TO:0000036
name: hybrid incompatibility
synonym: "HYBIC (related)" RELATED []
is_a: TO:0000035 ! incompatibility trait
[Term]
id: TO:0000037
name: male sterility extent
def: "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]
synonym: "degree of male sterility of male sterile lines (related)" RELATED []
synonym: "male sterility measure (related)" RELATED []
is_obsolete: true
[Term]
id: TO:0000038
name: fluorine sensitivity
is_a: TO:0000247 ! other nutrient sensitivity
[Term]
id: TO:0000039
name: yield component
def: "OBSOLETE. Defines the components that determine the over all yield from a plant" [Gramene:pankaj_jaiswal]
is_obsolete: true
[Term]
id: TO:0000040
name: panicle length
def: "A panicle morphology trait (TO:0000847) which is the measurement in centimeters from panicle base to tip." [IRRI:SES]
comment: Evaluated at growth stage:8 in rice.
synonym: "PNLG (related)" RELATED []
synonym: "PnL (related)" RELATED []
is_a: TO:0000271 ! inflorescence length
is_a: TO:0006032 ! panicle inflorescence size
[Term]
id: TO:0000041
name: brown rice length
def: "A grain length (TO:0000734) monitored after dehulling but before polishing. The grain should contain pericarp (PO:0009084)." [IRRI:SES, PO:0009084, TO:moorel]
comment: Refer to length (PATO:0000122): A 1-D extent quality which is equal to the distance between two points.
xref: PATO:0000122
synonym: "Len (related)" RELATED []
synonym: "BRWLG (related)" RELATED []
is_a: TO:0000734 ! grain length
[Term]
id: TO:0000042
name: f1-hybrid incompatibility
synonym: "F1HYBIC (related)" RELATED []
is_a: TO:0000036 ! hybrid incompatibility
[Term]
id: TO:0000043
name: root morphology trait
def: "A plant axis morphology trait (TO:0000738) which is a quality of a root (PO:0025025)." [Gramene:pankaj_jaiswal, PO:0025025, TO:cooperl]
xref: TO_GIT:58
is_a: TO:0000738 ! plant axis morphology trait
[Term]
id: TO:0000044
name: stigma exsertion
def: "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]
comment: 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.
synonym: "STIEX (related)" RELATED []
synonym: "stigma exsertion of male sterile lines (related)" RELATED []
is_a: TO:0006012 ! carpel morphology trait
[Term]
id: TO:0000045
name: udbatta disease resistance
def: "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]
synonym: "UDb (related)" RELATED []
is_a: TO:0000439 ! fungal disease resistance
[Term]
id: TO:0000046
name: f2-generation sterility
synonym: "F2GST (related)" RELATED []
is_a: TO:0000036 ! hybrid incompatibility
[Term]
id: TO:0000047
name: sporophytic incompatibility
is_a: TO:0000310 ! self-incompatibility
[Term]
id: TO:0000048
name: kernel smut disease resistance
def: "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]
synonym: "KSm (related)" RELATED []
synonym: "KSRS (related)" RELATED []
is_a: TO:0000439 ! fungal disease resistance
[Term]
id: TO:0000049
name: gametophytic incompatibility
synonym: "GPHIC (related)" RELATED []
is_a: TO:0000310 ! self-incompatibility
[Term]
id: TO:0000050
name: inflorescence branching
def: "An inflorescence morphology trait (TO:0000373) which is the extent of branching. (PO:0009049)." [Gramene:pankaj_jaiswal, PO:0009049, TO:moorel]
comment: Branching usually determines the shape and compactness of the inflorescence
xref: TO_GIT:96
synonym: "panicle branching (related)" RELATED []
is_a: TO:0000621 ! inflorescence development trait
is_a: TO:0000268 ! inflorescence shape
[Term]
id: TO:0000051
name: stem strength
def: "A stem morphology trait (TO:0000361) which is the strength of a stem (PO:0009047)." [Gramene:pankaj_jaiswal, IRRI:SES, PO:0009047, TO:moorel]
comment: Refer to strength (PATO:0001230): A quality inhering in a bearer by virtue of the bearer's power or force.
xref: PATO:0001230
synonym: "STEMSTR (related)" RELATED []
synonym: "Cs (related)" RELATED []
synonym: "CULMSTR (related)" RELATED []
synonym: "culm strength (related)" RELATED []
is_a: TO:0000361 ! stem morphology trait
[Term]
id: TO:0000052
name: primary branching of inflorescence
def: "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)." [Gramene:pankaj_jaiswal, PO:0009049, TO:moorel]
synonym: "primary branching of panicle (related)" RELATED []
synonym: "PBR (related)" RELATED []
is_a: TO:0000050 ! inflorescence branching
[Term]
id: TO:0000053
name: pollen sterility
def: "Observed under a microscope at magnification 10x10 after staining with 1% iodine potassium iodide (IKI) solution. Samples for pollen are collected from anthers and fixed in 70% alcohol. Two to three anthers are extracted from each floret and pollen grains are squeezed out into the IKI solution drop. At least three fields are used to count the sterile pollen grains; unstained withered, unstained spherical and partially stained round and fertile, from stained round pollen grains. Percentage sterility is calculated as = (unstained withered+unstained spherical+partially stained) x 100/total number of pollen grains in the field including the fertile." [Gramene:pankaj_jaiswal, IRRI:SES]
is_a: TO:0000437 ! male sterility
[Term]
id: TO:0000054
name: animal damage resistance
def: "Response by the plant in terms of resistivity or sensitivity to the animals infesting them." [Gramene:pankaj_jaiswal]
synonym: "pest resistance (related)" RELATED []
is_a: TO:0000236 ! crop damage resistance
[Term]
id: TO:0000055
name: leaf lamina pubescence
def: "A leaf lamina morphology trait (TO:0000829) which is the extent of pubescence (presence of hairs) on a leaf lamina (PO:0020039)." [IRRI:SES]
comment: Refer to pubescent hair (PATO:0001320): A pilosity quality of being covered with short hairs or soft down.
xref: PATO:0001320
synonym: "LFLPUBES (related)" RELATED []
synonym: "LBP (related)" RELATED []
synonym: "leaf blade pubescence (related)" RELATED []
synonym: "LFLHR (related)" RELATED []
is_a: TO:0000829 ! leaf lamina morphology trait
[Term]
id: TO:0000056
name: stem color
def: "A stem morphology trait (TO:0000361) which is the color of a stem (PO:0009047)." [Gramene:pankaj_jaiswal, PO:0009047, TO:moorel]
comment: Refer to color (PATO:0000014): A composite chromatic quality composed of hue, saturation and intensity parts.
xref: PATO:0000014
is_a: TO:0000361 ! stem morphology trait
[Term]
id: TO:0000057
name: grain moisture
is_a: TO:0000162 ! grain quality trait
[Term]
id: TO:0000058
name: herbicide sensitivity
def: "A chemical stress sensitivity (TO:0000482) which is the tolerance exhibited by a plant towards the applied herbicide." [Gramene:pankaj_jaiswal, TO:moorel]
comment: It is expected that the herbicide application must not affect the agronomic yield, if any.
xref: PECO:0007183
xref: WTO:0000342
synonym: "weedicide tolerance (related)" RELATED []
synonym: "herbicide tolerance (related)" RELATED []
is_a: TO:0002649 ! pesticide sensitivity
is_a: WTO:0000254 ! resistance to chemicals
[Term]
id: TO:0000059
name: node color
def: "Color of the stem node." [Gramene:pankaj_jaiswal]
synonym: "NDCL (related)" RELATED []
is_a: TO:1000003 ! shoot axis node color
[Term]
id: TO:0000060
name: aborted uni-nucleate stage
def: "Abortion at uni-nucleate stage of microspore development." [Gramene:pankaj_jaiswal, IRRI:SES]
comment: An example is CMS-WA in rice.
synonym: "UNUABR (related)" RELATED []
is_a: TO:0000218 ! pollen abortion type
[Term]
id: TO:0000061
name: node shattering
synonym: "brittle node (related)" RELATED []
is_a: TO:0000051 ! stem strength
is_a: TO:0000754 ! cardinal organ part morphology trait
[Term]
id: TO:0000062
name: phenol reaction
is_a: TO:0000489 ! carbohydrate composition related trait
[Term]
id: TO:0000063
name: mimic response
synonym: "disease mimic response (related)" RELATED []
synonym: "MIRP (related)" RELATED []
synonym: "lesion mimic (related)" RELATED []
is_a: TO:0000236 ! crop damage resistance
[Term]
id: TO:0000064
name: plant embryo morphology trait
def: "A whole plant morphology trait (TO:0000398) which is a quality of a plant embryo (PO:0009009)." [PO:0009009, TO:moorel]
xref: TO_GIT:140
is_a: TO:0000398 ! whole plant morphology trait
[Term]
id: TO:0000065
name: root color
def: "A root morphology trait (TO:0000043) which is the color of a root (PO:0009005)." [Gramene:pankaj_jaiswal]
synonym: "RTCL (related)" RELATED []
is_a: TO:0000043 ! root morphology trait
[Term]
id: TO:0000066
name: spot disease
def: "OBSOLETE." []
is_obsolete: true
[Term]
id: TO:0000067
name: genic male sterility-thermo sensitive
def: "Temperature sensitive male sterility, affected by environment." [Gramene:pankaj_jaiswal, IRRI:SES]
synonym: "TGMS (related)" RELATED []
synonym: "thermo sensitive genic male sterility (related)" RELATED []
is_a: TO:0000199 ! genic male sterility
[Term]
id: TO:0000068
name: lodging incidence
def: "Measure of percentage of plants that lodged." [IRRI:SES]
synonym: "Lg (related)" RELATED []
synonym: "LOI (related)" RELATED []
is_a: TO:0000250 ! plant vigor trait
[Term]
id: TO:0000069
name: variegated leaf
synonym: "leaf stripes (related)" RELATED []
synonym: "albino leaf striping (related)" RELATED []
is_a: TO:0000326 ! leaf color
is_a: TO:0000541 ! leaf position
[Term]
id: TO:0000070
name: variegated leaf necrosis
def: "Variegated leaf necrosis or scorching observed in response to stresses like drought, insecticides and cold temperature as evidenced by chlorotic and/or necrotic tissue." [Gramene:pankaj_jaiswal]
comment: In maize this trait is observed for chlorotic tissue between veins or older leaves, causing holes and torn appearance.
synonym: "VLFNEC (related)" RELATED []
synonym: "ragged leaf (related)" RELATED []
is_a: TO:0000069 ! variegated leaf
is_a: TO:0000652 ! leaf necrosis
[Term]
id: TO:0000071
name: anthocyanin content
def: "The anthocyanin content in a plant or plant part." [ISBN:198506732]
comment: Anthocyanin is the red to purple pigments composed of soluble glycosides of anthocyanidins, present in leaves and floral tissue. Usually the pigment is produced under stress conditions. Amounts of anthocyanin produced depend on stored sugar and sunlight. The more stored sugar in the leaf and brighter the autumn days, the more intense red. Anthocyanin production also increases as phosphates move out of the leaves; the lack of phosphates in young leaves can also lead to the production of anthocyanin.
synonym: "ANTHCN (related)" RELATED []
is_a: TO:0000494 ! pigment content trait
is_a: TO:0000290 ! flavonoid content
is_a: TO:0006008 ! carbohydrate derivative content
[Term]
id: TO:0000072
name: awn length
def: "An awn morphology trait (TO:0002718) which is the length of awn (PO:0025349)." [IRRI:SES, PO:0025349, TO:moorel]
comment: Refer to length PATO:0000122: A 1-D extent quality which is equal to the distance between two points.
xref: WTO:0000126
xref: PATO:0000122
synonym: "AWNLG (related)" RELATED []
synonym: "awning (related)" RELATED []
synonym: "An (related)" RELATED []
is_a: WTO:0000066 ! awn
is_a: TO:0002718 ! awn morphology trait
[Term]
id: TO:0000073
name: manganese sensitivity
def: "Sensitivity to the manganese content in the growth medium. It is important for activation of some enzymes and role in metal ion homeostasis." [Gramene:pankaj_jaiswal]
xref: WTO:0000537
synonym: "MNSN (related)" RELATED []
is_a: WTO:0000463 ! heavy metal toxicity
is_a: TO:0000080 ! micronutrient sensitivity
[Term]
id: TO:0000074
name: blast disease resistance
def: "Causal agent: Magnaporthe grisea." [Gramene:pankaj_jaiswal]
xref: TO_GIT:69
synonym: "blast disease resistance trait (exact)" EXACT []
synonym: "blast disease susceptibility (narrow)" NARROW []
is_a: TO:0000439 ! fungal disease resistance
[Term]
id: TO:0000075
name: light sensitivity
def: "Response shown by the plant in terms of sensitivity to light stress (quality and quantity of light)." [Gramene:pankaj_jaiswal]
is_a: TO:0000161 ! radiation response trait
[Term]
id: TO:0000076
name: inflorescence feature
def: "OBSOLETE. The instances define various distinguishing trait features associated with inflorescence and its instances." [Gramene:pankaj_jaiswal]
is_obsolete: true
[Term]
id: TO:0000077
name: shoot system morphology trait
def: "A collective plant organ structure morphology trait (TO:0000842) which is a quality of a shoot system (PO:0009006)." [Gramene:pankaj_jaiswal, PO:0009006, TO:cooperl]
comment: Does not include traits of fruit, parts of fruit and adventitious roots which are borne on the shoot.
xref: TO_GIT:57
is_a: TO:0000842 ! collective plant organ structure morphology trait
[Term]
id: TO:0000078
name: root dry weight
def: "The average dry weight of the root determined in a study." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "rdw/t (related)" RELATED []
synonym: "total root dry weight (related)" RELATED []
synonym: "RTDWT (related)" RELATED []
synonym: "rdw (related)" RELATED []
synonym: "root dry weight per tiller (related)" RELATED []
is_a: TO:0000279 ! root weight
[Term]
id: TO:0000079
name: flower bract morphology trait
def: "A bract morphology trait (TO:0000815) which is a quality of a flower bract (PO:0009034)." [Gramene:pankaj_jaiswal, PO:0009034, TO:cooperl]
xref: TO_GIT:390
is_a: TO:0000862 ! floral organ morphology trait
is_a: TO:0000815 ! bract morphology trait
[Term]
id: TO:0000080
name: micronutrient sensitivity
def: "Sensitivity response shown by the plant grown in either the excess or deficient amount of the micronutrient in the growth medium (soil)." [Gramene:pankaj_jaiswal]
xref: WTO:0000271
synonym: "micronutrient deficiency (related)" RELATED []
is_a: TO:0000480 ! nutrient sensitivity
[Term]
id: TO:0000081
name: deep root dry weight
def: "The average dry weight of the root, (for the root part 30cm below the soil surface) determined per tiller in a green house study." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "deep root weight (exact)" EXACT []
synonym: "deep root dry weight per tiller (exact)" EXACT []
synonym: "drw/t (exact)" EXACT []
synonym: "drw (exact)" EXACT []
synonym: "DRTDWT (exact)" EXACT []
is_a: TO:0000078 ! root dry weight
[Term]
id: TO:0000082
name: zigzag leafhopper resistance
def: "Causal agent: Recilia dorsalis (Motschulsky)." [Gramene:pankaj_jaiswal]
synonym: "ZLFHRS (related)" RELATED []
is_a: TO:0000261 ! insect damage resistance
[Term]
id: TO:0000083
name: penetrated root number
def: "Its the total number of roots penetrating the hard pans of the soil or the number of roots penetrated through the wax-petrolatum layer measured at 50 days after sowing (DAS)." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "PENRTNB (related)" RELATED []
synonym: "number of penetrating roots (related)" RELATED []
synonym: "npr (related)" RELATED []
is_a: TO:0000084 ! root number
[Term]
id: TO:0000084
name: root number
def: "A root system morphology trait (TO:0000985) which is the number of roots (PO:0009005) in a root system (PO:0025025)." [Gramene:jcl, Gramene:pankaj_jaiswal, PATO:0001555, TO:cooperl, TO_GIT:357]
synonym: "tnr (related)" RELATED []
synonym: "RTNB (related)" RELATED []
is_a: TO:0000043 ! root morphology trait
is_a: TO:0000985 ! root system morphology trait
[Term]
id: TO:0000085
name: leaf rolling
def: "A leaf morphology trait (TO:0000748) which is the rolling of a leaf preceding the leaf drying stage." [Gramene:jcl, Gramene:pankaj_jaiswal, TO:moorel]
comment: Leaf rolling is a feature observed in response to stresses like drought, water and temperature. If you are annotating to this term, please add an additional annotation to vascular leaf morphology (TO:0000419) or non-vascular leaf morphology trait (TO:0000925), depending on the species.
synonym: "wilting (related)" RELATED []
synonym: "LFRL (related)" RELATED []
is_a: TO:0000748 ! leaf morphology trait
[Term]
id: TO:0000086
name: sheath rot disease resistance
def: "Causal agent: Sarocladium oryzae. Symptoms: oblong or irregular brown to grey lesions on the leaf sheath near panicle; sometimes coalescing to prevent emergence of panicle." [Gramene:pankaj_jaiswal, IRRI:SES]
synonym: "SHROTRS (related)" RELATED []
synonym: "ShR (related)" RELATED []
is_a: TO:0000439 ! fungal disease resistance
[Term]
id: TO:0000087
name: grain aroma trait
def: "The aroma of the cooked/uncooked grains." [Gramene:pankaj_jaiswal, IRRI:SES]
comment: It is often associated with the accumulation of the aromatic compound 2-acetyl-1-pyrroline.
synonym: "Sct (related)" RELATED []
synonym: "odour (related)" RELATED []
synonym: "AROMA (related)" RELATED []
synonym: "scent (exact)" EXACT []
is_a: TO:0000162 ! grain quality trait
[Term]
id: TO:0000088
name: rice yellow mottle virus resistance
def: "Causal agent: rice yellow mottle virus (RYMV). Symptoms: stunting, reduced tillering, mottling and yellowish streaking of the leaves, delayed flowering or incomplete emergence of the panicle; in extreme cases, death of plants." [Gramene:pankaj_jaiswal, IRRI:SES]
synonym: "RYMV (related)" RELATED []
synonym: "RYMVRS (related)" RELATED []
is_a: TO:0000148 ! viral disease resistance
[Term]
id: TO:0000089
name: panicle inflorescence type
def: "A panicle inflorescence morphology trait (TO:0000847) which is the mode of branching, angle of primary branches, and spikelet density of a panicle inflorescence (PO:0030123)." [IRRI:SES, TO:moorel]
synonym: "PNTYPE (related)" RELATED []
synonym: "panicle attitude of branches (related)" RELATED []
synonym: "PnT (related)" RELATED []
is_a: TO:0000847 ! panicle inflorescence morphology trait
[Term]
id: TO:0000090
name: penetrated root thickness
def: "At 50 days after sowing (DAS), the thickness of roots penetrated through the wax-petrolatum layer is measured. Penetrated root thickness is measured on penetrated roots immediately below the wax layer." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "prt (related)" RELATED []
synonym: "PENRTTH (related)" RELATED []
is_a: TO:0000306 ! root thickness
[Term]
id: TO:0000091
name: leafhopper
def: "OBSOLETE." []
is_obsolete: true
[Term]
id: TO:0000092
name: deep root to shoot ratio
def: "The ratio of deep root length (for the roots found 30cm below the soil surface) and the shoot length determined in a study." [Gramene:pankaj_jaiswal]
synonym: "deep root/shoot ratio (related)" RELATED []
synonym: "deep root ratio (related)" RELATED []
synonym: "dr/s (related)" RELATED []
synonym: "DRTSHRO (related)" RELATED []
synonym: "deep root length to shoot length ratio (related)" RELATED []
is_a: TO:0000278 ! root to shoot ratio
[Term]
id: TO:0000093
name: root pulling force
synonym: "rpf (related)" RELATED []
synonym: "RTPF (related)" RELATED []
is_a: TO:0000043 ! root morphology trait
[Term]
id: TO:0000094
name: basal root thickness
def: "The thickness of the root present 2cm below the soil surface." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "brt (related)" RELATED []
synonym: "BARTTH (related)" RELATED []
is_a: TO:0000306 ! root thickness
[Term]
id: TO:0000095
name: osmotic response sensitivity
def: "Sensitivity to the osmoticum in the growth medium." [Gramene:pankaj_jaiswal]
synonym: "oa (related)" RELATED []
synonym: "OSRPSN (related)" RELATED []
is_a: TO:0000237 ! water stress trait
[Term]
id: TO:0000096
name: ratooning ability
def: "Regeneration of the main stem and tillers after harvesting in a grass plant." [Gramene:jn, Gramene:pankaj_jaiswal]
synonym: "RAAB (related)" RELATED []
is_a: TO:0000654 ! shoot system growth and development trait
is_a: TO:0000250 ! plant vigor trait
[Term]
id: TO:0000097
name: amylopectin content
def: "Amount of amylopectin present in the plant or plant part." [ISBN:198506732]
comment: It is a polysaccharide present in starch. Amylopectin is a polymer of alpha(1,4)-linked glucose units, as is amylose (see amylose). Unlike amylose, amylopectin contains branches of 2430 glucose units connected to the main chain by an alpha(1,6) linkage.
synonym: "AMYPCTCN (related)" RELATED []
is_a: TO:0006007 ! polysaccharide content
is_a: TO:0006008 ! carbohydrate derivative content
[Term]
id: TO:0000098
name: glutinous endosperm
def: "An endosperm morphology trait (TO:0000575) which is an opaque and hard endosperm (PO:0009089) with low or no amylose content (TO:0000196)." [Gramene:pankaj_jaiswal, PO:0009089, TO:moorel]
comment: If the endosperm has high amount of amylose it is called as non-glutinous endosperm. This is also an endosperm quality trait (TO:0000587).
xref: TO_GIT:133
synonym: "opaque endosperm (related)" RELATED []
synonym: "waxy endosperm (related)" RELATED []
is_a: TO:0000587 ! endosperm quality
is_a: TO:0000575 ! endosperm morphology trait
[Term]
id: TO:0000099
name: sugary endosperm
def: "An endosperm morphology trait (TO:0000575) which is a wrinkled and glassy endosperm (PO:0009089) when dry." [Gramene:pankaj_jaiswal, PO:0009089, TO:moorel]
comment: This is also an endosperm quality trait (TO:0000587).
xref: TO_GIT:133
synonym: "sugary kernel (related)" RELATED []
is_a: TO:0000587 ! endosperm quality
is_a: TO:0000575 ! endosperm morphology trait
[Term]
id: TO:0000100
name: shrunken endosperm
def: "An endosperm morphology trait (TO:0000575) which is a shrunken and opaque endosperm (PO:0009089)." [Gramene:pankaj_jaiswal, PO:0009089, TO:moorel]
comment: This is also an endosperm quality trait (TO:0000587). Refers to shrunken PATO:0000585 A decreased size quality inhering in a bearer by virtue of the bearer's exhibiting reduced size of a cell or constituent group of cells (for example, organ).
xref: PATO:0000585
xref: TO_GIT:133
synonym: "transluscent kernel (related)" RELATED []
synonym: "collapsed kernel (related)" RELATED []
is_a: TO:0000587 ! endosperm quality
is_a: TO:0000575 ! endosperm morphology trait
[Term]
id: TO:0000101
name: broad-leaved weed
def: "A common sedge weed Monochoria vaginalis (monochoria), California arrowhead Sagittaria montevidensis, Gregg arrowhead Sagittaria longiloba, Ducksalad Heteranthera limosa, Echinodorus berteroi and E. cordifolius (Burhead), Ammannia spp (Redstems), Bacopa spp. (Water hyssops), Alisma plantago-aquatica (Common water plantain). Grows as a weed in the rice field. Can be distinguished from rice plant by the leaf shape, venation, stem cross-section and plant shape leaf shape." [Gramene:pankaj_jaiswal, http://www.ipm.ucdavis.edu/PMG/r682700999.html, ISBN:9712200299]
is_a: TO:0000347 ! weed damage
[Term]
id: TO:0000102
name: phosphorus sensitivity
def: "Sensitivity to the phosphorus content in the growth medium. It is important in various biochemical pathways and storage of energy." [IRRI:SES]
synonym: "PHOSN (related)" RELATED []
synonym: "PDef (related)" RELATED []
synonym: "phosphorus deficiency (related)" RELATED []
is_a: TO:0000248 ! primary macronutrient sensitivity
[Term]
id: TO:0000103
name: deepwater stress
def: "The sensitivity response shown by the plant growing in a stagnant water for a long period of time (not unlike deepwater presence during flash flooding of the fields)." [Gramene:pankaj_jaiswal]
synonym: "DWSTR (related)" RELATED []
synonym: "deep water stress (related)" RELATED []
is_a: TO:0000237 ! water stress trait
[Term]
id: TO:0000104
name: floury endosperm
def: "An endosperm morphology trait (TO:0000575) which is an opaque and soft endosperm (PO:0009089)." [Gramene:pankaj_jaiswal, PO:0009089, TO:moorel]
comment: This is also an endosperm quality trait (TO:0000587).
xref: TO_GIT:133
is_a: TO:0000587 ! endosperm quality
is_a: TO:0000575 ! endosperm morphology trait
[Term]
id: TO:0000105
name: dull endosperm
def: "An endosperm morphology trait (TO:0000575) which is a glassy and tarnished endosperm (PO:0009089) with low amylose content (TO:0000196)." [Gramene:pankaj_jaiswal, PO:0009089, TO:moorel]
comment: This is also an endosperm quality trait (TO:0000587).
xref: TO_GIT:133
synonym: "glassy endosperm (related)" RELATED []
is_a: TO:0000587 ! endosperm quality
is_a: TO:0000575 ! endosperm morphology trait
[Term]
id: TO:0000106
name: male sterility type
def: "Represents the different types of male sterility found in plants." [Gramene:pankaj_jaiswal]
synonym: "MS (related)" RELATED []
is_a: TO:0000437 ! male sterility
[Term]
id: TO:0000107
name: endosperm storage protein-1 content
def: "Assay for the amount of 13kDa seed storage protein present in the endosperm." [Gramene:pankaj_jaiswal]
is_a: TO:0002653 ! endosperm storage protein content
[Term]
id: TO:0000108
name: leaf shattering
def: "A leaf growth and development trait (TO:0000655) which is the extent of leaf shattering based on the development of a leaf abscission zone (PO:0006501)." [Gramene:pankaj_jaiswal, PO:0006501, TO:cooperl]
comment: The leaf shattering trait is the occurence of the biological process of leaf abscission (GO:0060866): the controlled shedding of a leaf.
xref: GO:0060866
synonym: "leaf abscission (related)" RELATED [GO:0060866, SOY:0001342]
synonym: "LFSH (related)" RELATED []
is_a: TO:0000655 ! leaf growth and development trait
is_a: TO:0000419 ! vascular leaf morphology trait
[Term]
id: TO:0000109
name: endosperm storage protein-2 content
def: "Assay for amount of 57kDa seed storage protein present in the endosperm." [Gramene:pankaj_jaiswal]
is_a: TO:0002653 ! endosperm storage protein content
[Term]
id: TO:0000110
name: wild abortive CMS
def: "Abortion of microspore development at uni-nucleate stage." [Gramene:pankaj_jaiswal, IRRI:SES]
synonym: "CMS-WA (related)" RELATED []
synonym: "WACMS (related)" RELATED []
is_a: TO:0000060 ! aborted uni-nucleate stage
is_a: TO:0000232 ! rice cytoplasmic male sterility
[Term]
id: TO:0000111
name: genetically engineered male sterility
def: "The sterility induced by transgenes expressing cytotoxic component." [Gramene:pankaj_jaiswal, IRRI:SES]
is_a: TO:0000106 ! male sterility type
[Term]
id: TO:0000112
name: disease resistance
def: "An assay to determine the resistance exhibited by a plant or a group of plants (population) in response to the disease caused by a pathogen infection as compared to the susceptible and/or the reference plants of the same species." [Gramene:pankaj_jaiswal]
comment: It represents the damage done by the diease and/or the pathogen to the plant. The damage is a direct measure of resistance to the particular pathogen variety causing the disease.
synonym: "disease susceptibility (narrow)" NARROW []
synonym: "disease tolerance (exact)" EXACT []
synonym: "disease resistance trait (exact)" EXACT []
synonym: "disease control (exact)" EXACT []
is_a: TO:0000236 ! crop damage resistance
[Term]
id: TO:0000113
name: giant embryo
def: "An embryo shape trait (TO:0000193) that is a large sized plant embryo (PO:0009009)." [Gramene:pankaj_jaiswal, PO:0009009, TO:moorel]
is_a: TO:1000012 ! whole plant size
is_a: TO:0000193 ! embryo shape
[Term]
id: TO:0000114
name: flooding related trait
xref: WTO:0000221
is_a: TO:0000237 ! water stress trait
[Term]
id: TO:0000115
name: root mass density
def: "Determined as the dry mass of roots per unit soil volume at a given soil section." [Gramene:pankaj_jaiswal]
synonym: "rmd (related)" RELATED []
synonym: "RTMD (related)" RELATED []
is_a: TO:0000043 ! root morphology trait
[Term]
id: TO:0000116
name: root mass density 0-15
def: "Root mass density 0-15 cm was calculated as the dry mass of roots per unit soil volume at 0-15 cm soil section." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "rmd 0-15 (related)" RELATED []
is_a: TO:0000115 ! root mass density
[Term]
id: TO:0000117
name: rat damage resistance
def: "Since there is no genetic resistance to rats, the damage can be quantified as it does not represent resistance." [Gramene:pankaj_jaiswal, IRRI:SES]
synonym: "RD (related)" RELATED []
is_a: TO:0000054 ! animal damage resistance
[Term]
id: TO:0000118
name: root mass density 15-30
def: "Root mass density 15-30 cm was calculated as the dry mass of roots per unit soil volume at 15-30 cm soil section." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "rmd 15-30 (related)" RELATED []
is_a: TO:0000115 ! root mass density
[Term]
id: TO:0000119
name: root mass density 30-45
def: "Root mass density 30-45 cm was calculated as the dry mass of roots per unit soil volume at 30-45 cm soil section." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "rmd 30-45 (related)" RELATED []
is_a: TO:0000115 ! root mass density
[Term]
id: TO:0000120
name: percent root mass density
def: "Calculated as percent of root mass density over the total root mass density. Both parameters scored at the same depth." [Gramene:pankaj_jaiswal]
synonym: "prmd (related)" RELATED []
synonym: "PCENTRTMD (related)" RELATED []
is_a: TO:0000115 ! root mass density
[Term]
id: TO:0000121
name: ufra damage
def: "Causal agent: the stem nematode Dictylenchus angustus. Symptoms: leaf mottling or chlorotic discoloration in a splash pattern at base of young leaves in stem elongation or mid-tillering stage; brown stains may develop on leaves and sheaths which later intensify to a dark brown color. A characteristic distortion consisting of twisting and withering of young leaves. A distortion of panicle which either remains enclosed with in a swollen sheath, partially emerge but are twisted and with unfilled grains or emerge completely but with unfilled grains and resembling a whitehead." [Gramene:pankaj_jaiswal, IRRI:SES]
comment: Evaluated at growth stage:6-7 in rice.
synonym: "U (related)" RELATED []
is_a: TO:0000384 ! nematode damage resistance
[Term]
id: TO:0000122
name: percent root mass density 0-15
def: "Calculated as percent of root mass density in this section over the total root mass density. Both scored at the 0-15cm depth." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "prmd 0-15 (related)" RELATED []
is_a: TO:0000116 ! root mass density 0-15
is_a: TO:0000120 ! percent root mass density
[Term]
id: TO:0000123
name: percent root mass density 15-30
def: "Calculated as percent of root mass density in this section over the total root mass density. Both scored at the 15-30cm depth." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "prmd 15-30 (related)" RELATED []
is_a: TO:0000118 ! root mass density 15-30
is_a: TO:0000120 ! percent root mass density
[Term]
id: TO:0000124
name: flag leaf angle
def: "A flag leaf morphology trait (TO:0000832) which is an angle of the flag leaf (PO:0020103) measured near the collar, as the angle of attachment between the flag leaf blade and the main inflorescence axis in grass plants." [IRRI:SES, PO:0020103, TO:cooperl, TO:moorel]
synonym: "FLFAG (related)" RELATED []
is_a: TO:0000832 ! flag leaf morphology trait
is_a: TO:0000206 ! leaf angle
[Term]
id: TO:0000125
name: percent root mass density 30-45
def: "Calculated as percent of root mass density in this section over the total root mass density. Both scored at the 30-45cm depth." [Gramene:jcl, Gramene:pankaj_jaiswal]
synonym: "prmd 30-45 (related)" RELATED []
is_a: TO:0000119 ! root mass density 30-45