response to wounding --jasmonic acid

[gocentral]

It's not clear to me that response to jasmonic acid should be a child of response to wounding. I think jasmonic acid can elicit other responses such as male fertility in plants. There might be a true-path violation here.

An example of a review for jasmonate pathway:

http://www.sciencemag.org/cgi/content/full/296/5573/16 49

Reported by: syrhee

Original Ticket: "geneontology/ontology-requests/3397":https://sourceforge.net/p/geneontology/ontology-requests/3397

[gocentral]

Logged In: YES user_id=436423

I agree ... which parents should we keep? At a glance, it seems we'd want to keep 'response to chemical stimulus' (42221). We could create child terms to go under the other parents, e.g.

response to jasmonic acid stimulus GO:0009753 [i] response to endogenous jasmonic acid stimulus GO:new1 --[i] jasmonic acid and ethylene-dependent systemic resistance, response to jasmonic acid stimulus GO:new3 [i] response to exogenous jasmonic acid stimulus GO:new2 GO:new3 would go under jasmonic acid and ethylene-dependent systemic resistance; that's the path that leads back to response to wounding.

would that work? m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=629839

It sounds OK to me, but I don't know if we need to have the 'endogenous' and 'exogenous' terms. It'd be good to get feedback from other curators, particularly Dong-hui.

Original comment by: syrhee

[gocentral]

Logged In: YES user_id=1561996

Although best known for its role in plant defense, jasmonic acid (JA) also performs critical roles in reproduction and development.

Male fertility in Arabidopsis: an essential role of jasmonate in reproduction was uncovered when Arabidopsis plants unable to perceive JA were found to be male-sterile (Feys et al. 1994). Here, jasmonate is vital for stamen and pollen maturation (Sanders et al. 2000).

Female fertility in tomato: in tomato, female fertility, rather than male fertility, requires jasmonic acid (Li et al. 2001).

Other developmental processes: developmental roles for the JA pathway are not restricted to sexual organs. Trichome production is to some extent dependant on JA signalling (Li et al., 2003). Tendril coiling (mechanotransduction) in the climbing plant Bryonia dioica may also be under the control of the jasmonate pathway (Weiler et al. 1993). Other roles in development may be uncovered as genetic screens for pathway mutants in Arabidopsis and other plants progress.

Currently there are three parent terms for this term:

[jasmonic acid and ethylene-dependent systemic resistance, GO:0009861]

[response to chemical stimulus, GO:0042221]

[response to endogenous stimulus, GO:0009719]

GO:0009861 is the path that leads back to [response to wounding GO:0009611]

A specific example: in a recent study published in The Plant Journal (June 2006, vol 46:984) the authors identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. These genes, mediating jasmonate response during stamen development, will be annotated to the GO term [response to jasmonic acid stimulus] [GO:0009753] among others. However, these genes may not be involved in [response to wounding] [GO:0009611].

In light of the above information, I agree that the paths that involve the GO term [response to jasmonic acid stimulus] [GO:0009753] need to be restructured.

My recommendation: remove the parent term [jasmonic acid and ethylene-dependent systemic resistance, GO:0009861], keep the other two: GO:0042221 and GO:0009719. I will look into Midori's suggestions in detail, but now my suggestion is that we do not create the new 'endogenous' and 'exogenous' terms, in part because these words are confusing: the normal function of these genes (as reported in the Plant J paper) is to respond to 'endogenous' JA in stamen development anyway.

I will also examine the term 0009861 [jasmonic acid and ethylene-dependent systemic resistance] and its parent terms in detail later.

Donghui Li

Original comment by: donghui

[gocentral]

Logged In: YES user_id=436423

OK, for now I've removed the relationship between GO:0009753 and GO: 0009861, and I've also added a new term as is_a GO:0009753 and part_of GO:0009861:

response to jasmonic acid stimulus during jasmonic acid and ethylene- dependent systemic resistance GO:0032260

Let me know whether you want anything else done for this item.

m

Original comment by: mah11

[gocentral]

Logged In: YES user_id=436423 Originator: NO

closing, since there have been no more comments reopen if anything else needs doing.

m

Original comment by: mah11

[gocentral]

• milestone: --> TAIR
• assigned_to: nobody --> gomidori
• status: open --> closed-fixed

Original comment by: mah11