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flowering photoperiod sensitivity #265

Open planteome-user opened 10 years ago

planteome-user commented 10 years ago

Request new terms for flowering response to photoperiod. This is to describe traits in a recent GWAS and QTL paper on maize, Hung et al 2012 , PMID 22711828. Request terms for male and female flowering, as child terms under another new term "flowering photoperiod sensitivity". They would fall under this part of the ontology: TO:0000229 : photoperiod sensitivity

Definitions would be something like this: "flowering photoperiod sensitivity" A difference in flowering dates when plants are grown under either long or short day environments.

"male flower photoperiod sensitivity" A difference in anthesis dates when plants are grown under either long or short day environments. COMMENT: In maize, long days are over 14 h, and short days under 12. Thermal time, expressed in growing degree days or GDD, is the recommended unit of measure.

"female flower photoperiod sensivitiy" A difference in dates for visible pistil formation, when plants are grown under either long or short day environments. SYNONYM silking, in maize. COMMENT: In maize, long days are over 14 h, and short days under 12. Thermal time, expressed in growing degree days or GDD, is the recommended unit of measure.

Reported by: mlschaeffer

Original Ticket: obo/plant-trait-ontology-to-requests/265

planteome-user commented 10 years ago

There may be several options on how we name the terms

1 days to flowering: photoperiod sensitive 2 response to photoperiod: days to flowering 3 photoperiod sensitive days to flowering

Didn't get a chance to look at the paper but I presume 'sensitivity' is the outcome (phenotype) of the response trait (#2), though I agree in other terms it can be scored by changes in the number if days or early/late flowering.

My suggestions are genetic ones, and they can be adjusted for male/female flowers

Pankaj

Original comment by: jaiswalp

planteome-user commented 10 years ago

After reviewing the literature, I think it would be better to describe this trait as:

A photoperiod response trait and make it a child of the flowering time trait (TO:0002616). This also matches the trait listed on MaizeGDB (http://www.maizegdb.org/cgi-bin/displaytraitrecord.cgi?id=64797)

Proposed new term: photoperiod response trait (new; TO:0000934): A flowering time trait (TO:0002616) which is associated with the difference between the time to flowering stage (PO:0007616) in long photoperiod and short photoperiod environments.

We can make the existing photoperiod sensitivity (TO:0000229) part_of the photoperiod response trait (new; TO:0000934).

Original comment by: cooperl09

planteome-user commented 10 years ago

It might be a child term of multiple parents, eg "flowering time" as Laurel proposes, and also "photoperiodism". Looking at the Gene Ontology, there are various terms for biological processes relating to photoperiod. One is "GO:0048573 photoperiodism, flowering", where synonyms include response to photoperiod, flowering, aka response to day length, flowering; aka response to night length flowering; etc. Perhaps we might parallel the GO here? In the GO, the term jsut mentioned,which is most similar to the TO term under discussion, "is_a photoperiodism (GO:0009648)" "Sensitivity to photoperiod might best be used as a synonym. While working on this part of TO, we might add terms for positive and negative regulation of both long and short day photoperiodism, flowering - per GO tree, but for traits.

Original comment by: mlschaeffer

planteome-user commented 10 years ago

Sure Here is a screen shot from OE I have worked quite a bit in the last few days on this part of the G+D traits branch. I think it is better but still needs a lot of attention. Still need to revise the children of flowering time trait, and add links to the other ontologies. I added the new term 'plant phenological trait' to group all the timing-related traits (tracker #266). The whole abiotic stress trait branch needs work.

On 5/7/14 2:43 AM, Pankaj Jaiswal wrote:
can you show me the ontology structure with is_a and part_of. I am unable to follow it from definition.

Original comment by: cooperl09

planteome-user commented 10 years ago

Renamed: photoperiod response trait (TO:0000934) to photoperiod-sensitive flowering time trait (TO:0000934) added synonym: flowering time response to photoperiod trait

Revised Def'n: A flowering time trait (TO:0002616) which is assayed as the difference between the time to flowering stage (PO:0007616) in long photoperiod (EO:0007199) and short photoperiod (EO:0007200) environments.

Removed the part_of relation between photoperiod sensitivity (TO:0000229) and photoperiod-sensitive flowering time trait (TO:0000934). Made photoperiod-sensitive flowering time trait (TO:0000934) a child of photoperiod sensitivity (TO:0000229).

Renamed photoperiod sensitivity (TO:0000229) --> photoperiod sensitivity trait.

Original comment by: cooperl09

planteome-user commented 10 years ago

This works for me. A related problem is the current "ancestor" term, light sensitivity (TO:0000075). I suggest using a broader term. The current tree suggests the extent of radiation triggers the response, rather than a cycle, or a certain threshold dark period, per much of the literature about flowering. It is also not a "stress trait", from the inferred tree, looking at the term neighborhood. It is more of an environmental response trait, without the judgemental term "stress". If stress were dropped from abiotic it would fit there.

Original comment by: mlschaeffer