SAM restructuring suggestion

[Pankaj Jaiswal]

Please take a look at the following text. I proposed the re-organization 
based on the requirements for gene expression (rice and Arabidopsis). I 
need these terms for phenotype annotations as well. How we annotate the 
flowering time phenotypes is a different question and will be dealt in 
separate mails.

Thanks
Pankaj


FROM THE ARTICLE 
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=9482818&query_hl=38
):
Before transition to reproductive growth, RFL RNA was detected in 
epidermal cells at the marginal region in young leaves but not in the 
vegetative shoot apical meristem or stem tissue (Fig. 2B). .......The 
RFL RNA expression was observed in the vegetative apical meristem at a 
very early stage of panicle development (Fig. 2 B and C), then it 
started to diminish in the corpus of the panicle axis at the middle 
stage of primary branch differentiation (Fig. 2D). After all the 
primordia of primary branches had initiated, RFL RNA disappeared 
entirely from the main axis of the panicle (Fig. 2 E and F)
 
Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1979-82.
Down-regulation of RFL, the FLO/LFY homolog of rice, accompanied with 
panicle branch initiation.
Kyozuka J, Konishi S, Nemoto K, Izawa T, Shimamoto K.
   
FROM THE ARTICLE 
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=11440721&query_hl=40
): 
To investigate possible feedback regulation of WUS by AG, we examined 
WUS expression in ag mutants. In wild-type, WUS is expressed initially 
in floral meristems in a pattern similar to that of shoot meristems, but 
it is not maintained past stage 6, when the floral meristem is consumed 
in the formation of the central gynoecium (Figure 7A)

Cell. 2001 Jun 15;105(6):793-803.    
A molecular link between stem cell regulation and floral patterning in 
Arabidopsis.
Lohmann JU, Hong RL, Hobe M, Busch MA, Parcy F, Simon R, Weigel D.


There are lots of instances where a gene is expressed in SAM(vegetative) 
and may or may not in the reproductive (inflorescence/flower) meristems. 
Thus requiring us to make a specific annotation to the two types of 
meristem.  In the existing tree, The annotation for the same gene if 
expressed in both the vegetative and inflorescence meristems can be 
annotated to child term:inflorescence meristem and its parent term:SAM. 
But there is no way we can distinguish that the parent term is only 
representing vegetative SAM only. By virtue of representing children 
terms the current term is also saying the it is also a reproductive SAM 
as well, because by accumulating the annotations from the children 
terms, the generic term will show up the genes expressed in flower / 
inflorescence apical meristems.

Therefore to make a clear distinction, I suggest re-organizing the SAM 
section and introduce the concept of
vegetative and reproductive SAMs. Thus allowing the curators and users 
to particularly chose these terms for use and NOT use the current SAM 
term which is a generic term.

This will particularly help in the annotation of various MADs box genes 
and the transcription factors or other genes that are responsible 
especially in making a transition from vegetative to reproductive 
(vegetative-SAM to inflorescence-apical meristem and 
inflorescence-apical meristem to floral-apical meristem).

Both the above citations are such examples.




Pankaj Jaiswal wrote:

>
> <http://www.plantontology.org/amigo/go.cgi?action=plus_node&depth=1&search_constraint=terms&query=PO:00201482> 
>
>
>
> Refer to:
> http://www.plantontology.org/amigo/go.cgi?view=details&show_associations=terms&search_constraint=terms&depth=0&query=PO:0020148 
>
>
> Looks like we need a specific instance of SAM, ie. "vegetative shoot 
> apical meristem". The current term is too generic for curating 
> vegetative SAM.
>
> The reason being, I am curating a lot of flowering time genes and many 
> are involved in regulating the transition of vegetative SAM to 
> reproductive SAM. This event is critical in  short-day or long-day 
> light response resulting in early/delayed flowering.
>
> Current structure is like follows:
>
>
> #  PO:0020148 : shoot apical meristem   ( 32 )
>
>     * PO:0000224 : central zone
>     * PO:0006362 : embryonic shoot apical meristem
>     * PO:0000229 : floral meristem
>     * PO:0000230 : inflorescence meristem
>     * PO:0009020 : meristem L1
>     * PO:0009021 : meristem L2
>     * PO:0009022 : meristem L3
>     * PO:0000225 : peripheral zone
>     * PO:0005039 : primary thickening meristem
>     * PO:0000226 : rib zone
>     * PO:0006306 : shoot procambium
> --------------------------------------------------
>
> Proposed
>
> #  PO:0020148 : shoot apical meristem   ( 32 )
>   i PO:new : vegetative shoot apical meristem
>     p PO:0000224 : central zone
>     i PO:0006362 : embryonic shoot apical meristem
>     p PO:0009020 : meristem L1
>     p PO:0009021 : meristem L2
>     p PO:0009022 : meristem L3
>     p PO:0000225 : peripheral zone
>     p PO:0005039 : primary thickening meristem
>     p PO:0000226 : rib zone
>     p PO:0006306 : shoot procambium
>   i PO:new : reproductive shoot apical meristem
>     i PO:0000229 : floral meristem
>     i PO:0000230 : inflorescence meristem
>
>
> PO:0020148 : shoot apical meristem
> Def: current
>     Meristem formed in the apex of the shoot, including meristems 
> originating as axillary shoot meristems.
> Def: proposed
>     Meristem formed in the apex of the shoot or those originating as 
> axillary and reproductive meristems.
>
> PO:new : vegetative shoot apical meristem
> Def: proposed
>     Copy the original SAM definition.
>
> PO:new : reproductive shoot apical meristem
> Def: proposed
>     Meristem formed in the apex of the shoot originating as 
> inflorescence and or flower meristems.
>
> -Pankaj
>
>