Triticeae T-CAP traits

[planteome-user]

Hi Pankaj,

I've completed the spreadsheet for the 27 new Trait Ontology terms that the T-CAP participants would like to add to the ontology. Brian Steffenson, a pathologist at Univ. of Minnesota approved all of the pathology terms and Tom Blake, a malt barley breeder approved the remaining. For all, I got the sources from 2-3 places and paraphrased.

Thanks for all of your suggestions. I did eliminate the Winter Hardiness trait and used the Cold Tolerance trait as it suits our phenotype as well. I left a note about phenolics to you, i.e. these vary so staying generic is ok. I also used the Ontology term spike exsertion, as it existed in the Ontology, was distinct from panicle exsertion but had no definition. I provided one if you wish to use it.

Can you please let me know when these are added and I can update the databases supporting the T-CAP data to reflect the more granular TO terms.

Cheers, Victoria

Reported by: jaiswalp

Original Ticket: obo/plant-trait-ontology-to-requests/41

[planteome-user]

Traits from T-CAP

Original comment by: jaiswalp

[planteome-user]

Added the TO terms for following 27 barley/wheat/triticea traits)

From TO file: Revision 1191 Available at: http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators\_ontology/gramene/traits/trait.obo?view=log

[Term] id: TO:0020051 name: barley leaf scald disease resistance def: "Causal agent: Rhynchosporium secalis." [T-CAP:Victoria Corollo Blake] comment: Symptoms include, oval, water-soaked, blue-grey spots (1.0-1.5 cm long) developing into lesions with dry necrotic centers and dark brown margins. Lesions will coalesce under high infection levels and are not delimited by veins. synonym: "scald" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:12:24Z

[Term] id: TO:0020052 name: barley spot blotch disease resistance def: "Causal agent: Cochliobolus sativus (Bipolaris sorokiniana)." [T-CAP:Victoria Corollo Blake] comment: Symptoms include, uniform chocolate brown lesions that eventually merge forming irregular necrotic patches on leaves. Lesions may be surrounded by yellow zones of varying width. synonym: "spot blotch" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:19:00Z

[Term] id: TO:0020053 name: wheat spot blotch disease resistance def: "Causal agent: Cochliobolus sativus (Bipolaris sorokiniana)." [T-CAP:Victoria Corollo Blake] comment: Symptoms include, elongated to oval shaped dark brown lesions. Centers often lighten to dark brown or tan surrounded by an irregular dark brown ring. synonym: "Helminthosporium leaf blotch" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:21:53Z

[Term] id: TO:0020054 name: barley stripe rust disease resistance def: "Causal agent: Puccinia striiformis f. sp. hordei." [T-CAP:Victoria Corollo Blake] comment: Symptoms: chlorotic flecks at the infection site initially appear, followed by yellow uredinia (spore masses) in prominent stripes along the leaf veins. Black telia (overseasoning structures) readily develop from uredinia as infected plants mature. synonym: "BSR" EXACT [] synonym: "yellow rust" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:25:00Z

[Term] id: TO:0020055 name: wheat stripe rust disease resistance def: "Causal agent: Puccinia striiformis f. sp. tritici." [T-CAP:Victoria Corollo Blake] comment: Symptoms: pustules (spore masses) containing yellow to orange-yellow urediniospores form narrow stripes on leaves, leaf sheaths and glumes. synonym: "yellow rust" BROAD [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:27:45Z

[Term] id: TO:0020056 name: barley leaf rust disease resistance def: "Causal agent: Puccinia hordei." [T-CAP:Victoria Corollo Blake] comment: Symptoms: small round orange brown pustules producing a mass of orange-brown urediniospores on the upper leaf surfaces and leaf sheaths. synonym: "brown rust" BROAD [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:29:57Z

[Term] id: TO:0020057 name: wheat leaf rust disease resistance def: "Causal agent: Puccinia recondita f. sp. tritici." [T-CAP:Victoria Corollo Blake] comment: Symptoms: circular to slightly elliptical pustules containing masses of orange to orange-brown urediniospores on the leaf surfaces and leaf sheaths. synonym: "brown rust" BROAD [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:31:09Z

[Term] id: TO:0020058 name: barley common root rot resistance def: "Causal agents: Cochliobolus sativus (Bipolaris sorokiniana), Fusarium culmorum and Fusarium pseudograminearum." [T-CAP:Victoria Corollo Blake] comment: Symptoms: brown lesions on the roots, especially the subcrown internode. Under severe conditions, lesions can become nearly black with brown tissue extending into the crown and leaf sheaths. Stunted plants with reduced tillering and yield. Heads can be white with fewer kernels that are small and shriveled. synonym: "crown rot" BROAD [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:33:03Z

[Term] id: TO:0020059 name: wheat common root rot resistance def: "Causal agents: Cochliobolus sativus (Bipolaris sorokiniana)." [T-CAP:Victoria Corollo Blake] comment: Symptoms: browning of the root, crown and basal culm tissues. Plants may lodge. White spikes can appear. is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:36:24Z

[Term] id: TO:0020060 name: barley powdery mildew disease resistance def: "Causal agent: Blumeria graminis f. sp. hordei." [T-CAP:Victoria Corollo Blake] comment: Symptoms: first visible signs are fuzzy white to pale grey tufts of mycelia and conidia on the upper surfaces of leaves and leaf sheaths (especially on lower leaves) and sometimes on the spikes. Older fungal tissue is yellowish grey and can be easily rubbed off. Plant tissue becomes chlorotic or necrotic. Spherical black cleistothecia may develop. is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:39:36Z

[Term] id: TO:0020061 name: wheat powdery mildew disease resistance def: "Causal agent: Blumeria graminis f. sp. tritici." [T-CAP:Victoria Corollo Blake] comment: Symptoms: first visible signs are fuzzy white to pale grey tufts of mycelia and conidia on the upper surfaces of leaves and leaf sheaths (especially on lower leaves) and sometimes on the spikes. Older fungal tissue is yellowish grey and can be easily rubbed off. Plant tissue becomes chlorotic or necrotic. Spherical black cleistothecia may develop. is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:39:36Z

[Term] id: TO:0020062 name: barley net form net blotch disease resistance def: "Causal agent: Pyrenophora teres f. teres." [T-CAP:Victoria Corollo Blake] comment: Symptoms: in adult plants, initial symptoms are small pinpoint to elliptical brown spots which expand to form narrow, tan to light brown lesions, often delimited by leaf veins. Within lesions, dark brown longitudinal and transverse striations appear forming a net-like pattern. In seedlings, greenish grey, water-soaked areas appear forming brown lesions with netted striations. synonym: "NFNB" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:39:36Z

[Term] id: TO:0020063 name: barley spot form net blotch disease resistance def: "Causal agent: Pyrenophora teres f. maculata." [T-CAP:Victoria Corollo Blake] comment: Symptoms: dark brown, circular to elliptical lesions surrounded by bands of chlorosis. synonym: "SFNB" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:39:36Z

[Term] id: TO:0020064 name: barley septoria disease resistance def: "Causal agent: Septoria passerinii and Stagonospora avenae f. sp. triticea (teleomorph: Phaeosphaeria avenaria f. sp. triticeae)." [T-CAP:Victoria Corollo Blake] comment: Symptoms: in seedlings, S. passerinii causes faint, yellowish areas that turn greenish gray then straw colored with time forming a distinct demarcation next to healthy green tissue. On adult plants S. passerinii infection produces long, rectangular lesions delimited by veins that first appear graying then turn tan or straw colored. S. avenae f. sp. triticea produces yellow brown lesions that traverse veins and are shield or lens shaped. synonym: "SSLB" EXACT [] is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:39:36Z

[Term] id: TO:0020065 name: wheat septoria leaf blotch disease resistance def: "Causal agent: Septoria tritici (Mycosphaerella graminicola), Septoria nodorum (Leptosphaeria nodorum), Septoria avenae f. sp. triticea (Leptosphaeria avenaria f. sp. triticea)." [T-CAP:Victoria Corollo Blake] comment: Symptoms: Initial infection sites tend to be irregular in shape, oval to elongated chlorotic spots or lesions. As these sites expand, the centers of the lesions become pale, straw colored, and slightly necrotic, often with numerous small black dots (pycnidia). The lesions of septoria tritici blotch tend to be linear and restricted laterally, while those of septoria nodorum blotch and septoria avenae blotch are more lens shaped. All above ground plant parts can be affected. is_a: TO:0000439 ! fungal disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:39:36Z

[Term] id: TO:0020066 name: barley leaf streak resistance def: "Causal agent: Xanthomonas translucens pv. translucens and pv. undulosa." [T-CAP:Victoria Corollo Blake] comment: Symptoms: small, light to pale green spots which later expand into linear streaks. Streaks can extend the entire length of the leaf, that will become translucent. Infected leaves will turn yellow then brown as it dies. is_a: TO:0000315 ! bacterial disease resistance created_by: jaiswalp creation_date: 2011-08-19T12:58:34Z

[Term] id: TO:0020067 name: barley yellow dwarf virus disease resistance def: "Causal agent: The Barley Yellow Dwarf Viruses, Luteovirus (Group IV (+)ssRNA)." [T-CAP:Victoria Corollo Blake] comment: Symptoms: uneven blotches of bright yellow discoloration on the tips and margins of older leaves, eventually progressing down toward the base, covering the entire leaf within a few weeks. Reduced internode elongation causes stunting with severe infection possibly. synonym: "BYDV" EXACT [] is_a: TO:0000148 ! viral disease resistance created_by: jaiswalp creation_date: 2011-08-19T01:00:45Z

[Term] id: TO:0020068 name: beta-glucan content def: "Amount of beta-glucan present in the plant, plant part or product (ex. malt). beta-Glucans are polysaccharides of D-glucose linked by beta-glycosidic bonds that vary by molecular mass, solubility, viscosity and 3D configuration." [T-CAP:Victoria Corollo Blake] is_a: TO:0000291 ! carbohydrate content created_by: jaiswalp creation_date: 2011-08-19T01:03:01Z

[Term] id: TO:0020069 name: spike exsertion def: "A triticea trait measured in distance from the base of the spike to the flag leaf auricle." [T-CAP:Victoria Corollo Blake] is_a: TO:0001002 ! inflorescence exsertion created_by: jaiswalp creation_date: 2011-08-19T01:07:39Z

[Term] id: TO:0020070 name: beta-glucanase activity def: "Activity of beta-glucanase ((1-3 and/or 1-4)-beta-D-glucan, 4-glucanohydrolase), (E.C:3.2.1.73) in the hydrolysis of beta-glucans." [T-CAP:Victoria Corollo Blake] is_a: TO:0000599 ! enzyme activity trait created_by: jaiswalp creation_date: 2011-08-19T01:10:26Z

[Term] id: TO:0020071 name: beta-glucanase thermostability def: "The ability of beta-glucanase [(1-3,1-4)-beta-D-glucan, 4-glucanohydrolase], (E.C:3.2.1.73) to remain active under mashing (boiling grain in water) conditions during beer making." [T-CAP:Victoria Corollo Blake] is_a: TO:0000597 ! quality trait is_a: TO:0000599 ! enzyme activity trait is_a: TO:0020070 ! beta-glucanase activity created_by: jaiswalp creation_date: 2011-08-19T01:18:25Z

[Term] id: TO:0020072 name: residual beta-glucanase activity def: "Activity of beta-glucanase [(1-3,1-4)-beta-D-glucan, 4-glucanohydrolase], (E.C:3.2.1.73) in the barley wort (the boiled grain and water) during the beer making process." [T-CAP:Victoria Corollo Blake] synonym: "residual beta-glucanase" BROAD [] is_a: TO:0000597 ! quality trait is_a: TO:0000599 ! enzyme activity trait is_a: TO:0020070 ! beta-glucanase activity created_by: jaiswalp creation_date: 2011-08-19T01:20:23Z

[Term] id: TO:0020073 name: barley wort protein concentration def: "Concentration of protein in the wort after boiling the grain with water (mashing) in the beer making process." [T-CAP:Victoria Corollo Blake] synonym: "wort protein" BROAD [] is_a: TO:0000597 ! quality trait is_a: TO:0000598 ! protein content created_by: jaiswalp creation_date: 2011-08-19T01:24:05Z

[Term] id: TO:0020074 name: barley wort color def: "Color of the solution derived from boiling barley grain with water during the beer making process." [T-CAP:Victoria Corollo Blake] is_a: TO:0000597 ! quality trait created_by: jaiswalp creation_date: 2011-08-19T01:27:42Z

[Term] id: TO:0020075 name: barley malt protein def: "Percent protein in the malt prior to mashing (boiling the grain with water to produce a wort) in the beer making process." [T-CAP:Victoria Corollo Blake] is_a: TO:0000597 ! quality trait created_by: jaiswalp creation_date: 2011-08-19T01:29:00Z

[Term] id: TO:0020076 name: phenolic compound content def: "Amount of phenolics present in the plant, plant part or product ." [T-CAP:Victoria Corollo Blake] comment: In barley its evaluated in ex malt. is_a: TO:0000281 ! metabolite content related trait created_by: jaiswalp creation_date: 2011-08-19T01:29:58Z

[Term] id: TO:0020077 name: head drop def: "A triticea trait evaluated for fertile spikes dropped before harvest." [T-CAP:Victoria Corollo Blake] is_a: TO:0000373 ! inflorescence anatomy and morphology trait created_by: jaiswalp creation_date: 2011-08-19T01:33:35Z

Original comment by: jaiswalp