POC Conf. Call 9-24-13

POC meeting, Skype Conference Call; Date: Tuesday Sept 24th, 2013 10:30am PST/1:30pm EST

In attendance:

Absent:

- please see the Items_for_future_meetings page, will be moved here before the meeting

leaf development stage (PO:0001050)

• Continued from POC_Conf._Call_9-10-13.
• See Google Doc for revisions in progress.

• leaf development stage (PO:0001050):

old def'n: A phyllome development stage (PO:0025579) that has as a primary participant a leaf (PO:0025034).

Revised def'n: A phyllome development stage (PO:0025579) in which the development of vascular leaves (PO:0009025) and non-vascular leaves (PO:0025075) occurs.

• No comment currently

multi-tissue plant structure development stage (PO:new PO:0025571)

• New upper level term: multi-tissue plant structure development stage (PO:0025571): A plant structure development stage (PO:0009012) that has as primary participant a multi-tissue plant structure (PO:0025496).

This is also be the parent for seed development and plant organ development, these definitions have been re-written.

non-vascular leaf development stage (new PO:0025573) and child terms:

* non-vascular leaf development stage (new PO:0025573): A leaf development stage (PO:0001050) that has as a primary participant a non-vascular leaf (PO:0025075). To be revised....

background references

• For further information on the development of the non-vascular leaf

see also: moss phyllides, moss info and Background_info_on_Physco_biology_and_culture.

vascular leaf development stage and child terms

Proposed new term and definition:

• vascular leaf development stage (new PO:0025570): A leaf development stage (PO:0001050) which begins with the onset of the vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
  • No comment currently

vascular leaf initiation stage (PO:0007040) and child terms:

• vascular leaf initiation stage (PO:0007040):

• Old def'n: The earliest histological evidence of leaf initiation, i.e, a change in the orientation of cell division both in the epidermis and in internal layers of the shoot meristem occurs at this stage (Poethig S, 1997, Plant Cell 9:1077-1087).

* Revised def'n: A vascular leaf development stage (PO:0025570) which begins with the onset of the vascular leaf anlagen formation stage (PO:0001003) and ends with the termination of the vascular leaf primordium polarity determination stage (PO:0001052).

• Revised Comment: Localized cell divisions in the peripheral zone (PO:0000225) transition from anticlinal to periclinal divisions.

vascular leaf anlagen formation stage (PO:0001003)

• Old name and definition: formation of the leaf founder cells stage (PO:0001003): The initial stage of leaf development when cells in the SAM are already determined to form a leaf primordium, but the primordium itself is not distinguishable morphologically.

• Revised name and definition: vascular leaf anlagen formation stage (PO:0001003): A vascular leaf initiation stage (PO:0007040) when the cells of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).

Revised comment: The vascular leaf primordium (PO:0000017) is not yet distinguishable.

Added Revised synonym (exact): vascular leaf founder cell formation stage

Question: Are the leaf founder cells the same as the leaf analgen? It would appear so.

• Definition from Nature Review: Tsiantis1 & Hay, 2003:

LEAF FOUNDER CELLS: A group of cells that encompasses several layers of the shoot apical meristem and from which a leaf primordium is derived. Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.

vascular leaf anlagen (PO:0025431): A phyllome anlagen (PO:0025430) that will give rise to a vascular leaf primordium (PO:0000017) and is part of a peripheral zone (PO:0000225) of a vegetative shoot apical meristem (PO:0008016). [source: PMID:14732442, POC:curators]

Comment: This is the region where you have the maximum concentration of auxin in the SAM (at least in a few species that have been studied).

See image: founder-cell population (FC) that will give rise to the next leaf primordium

vascular leaf primordium formation stage (PO:0001019)

-was formerly a child of leaf expansion, moved to leaf initiation stage

• Old name and def'n: formation of leaf primordium stage PO:0001019: Stage of leaf development when leaf primordium is formed as a small protrusion on the flank of SAM. [source: TAIR:Katica_Ilic]

• Revised name and def'n: vascular leaf primordium formation stage (PO:0001019): A vascular leaf initiation stage (PO:0001051) during which a vascular leaf primordium (PO:0000017) forms in the peripheral zone (PO:0000225) of the shoot apical meristem (PO:0020148). should this be "vegetative shoot apical meristem"?

Revised comment: The vascular leaf primordium (PO:0000017) develops from the vascular leaf anlagen (PO:002543).

vascular leaf primordium polarity determination stage (new PO:0025572)

* vascular leaf primordium polarity determination stage (PO:0025572): A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).

Comment: The vascular leaf primordium adaxial side (PO:0004726) is the closest side to the meristem. This stage leads to the development of a bifacial vascular leaf.

This term refers to the following two terms (children of phyllome primordium (PO:0025128); both have also been revised:

• Old name and def'n: adaxial side of leaf primordium (PO:0004726): "A portion of phyllome primordium tissue that is the adaxial/inner side of the leaf primordium develops into the adaxial/upper leaf blade.

• New name and def'n: vascular leaf primordium adaxial side (PO:0004726): "A portion of vascular leaf primordium (PO:0000017) that faces the shoot apical meristem (PO:0020148) and develops into the adaxial (upper) side of the leaf lamina (PO:0020039).

• Old name and def'n: abaxial side of leaf primordium (PO:0004725): A portion of phyllome primordium tissue that is the abaxial/outer side of a leaf primordium and develops into the abaxial/lower leaf blade.

• New name and def'n: vascular leaf primordium abaxial side (PO:0004725): A portion of vascular leaf primordium (PO:0000017) that faces away from the shoot apical meristem (PO:0020148) and develops into the abaxial (lower) side of the leaf lamina (PO:0020039).

Comments: The vascular leaves (PO:0009025) of some plants may not have an obvious adaxial or abaxial side such as the leaves of many xerophytic (arid-adapted) species. The adaxial and abaxial side may appear considerably more rounded and this could be due to early activity of the vascular leaf adaxial meristem (PO:0025401) and/or leaf abaxial meristem (PO:0025401).

vascular leaf expansion stage PO:0001052

• Links to Relevant References- vascular leaf development
  • Genetic Control of Leaf Development- Plant Cell teaching tools
  • Uchida et al (2010) Coordination of leaf development via regulation of KNOX1 genes. Journal of Plant Research 123: 7–14
  • Comparative plant development: the time of the leaf? Tsiantis & Hay, 2003 Nature Reviews Genetics
  • Li, Brutnell et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42: 1060–1067
  • Leaf adaxial–abaxial polarity specification and lamina outgrowth: evolution and development, Plant and Cell Physiology, 2012
  • FERNS: The evolution, morphology, and development of fern leaves, Vasco et al 2013
  • Independent recruitment of a conserved developmental mechanism during leaf evolution
  • Gonzalez et al, Trends in Plant Science 2012

Development of parts of the leaf

Need to consider if the following stage terms are appropriate under vascular leaf expansion stage (PO:0001052) due to the fact that these terms are for the development of specific parts of some plants.

• formation of vascular leaflet primordia stage (PO:0004500): A vascular leaf expansion stage (PO:0001052) at which a leaflet primordium (PO:0025481) is initiated on the leaf rachis (PO:0020055) of a compound leaf (PO:0020043).
• formation of ligule primordium stage (PO:0001021): A vascular leaf expansion stage (PO:0001052) when conical P3 leaf completely encloses SAM, and the ligule (PO:0020105) primordium is visible.
• hood-shaped primordium stage (PO:0001020): A vascular leaf expansion stage (PO:0001052) when a hood-shaped primordium is formed, partially enclosing P1 and SAM, as in Poaceae.
• rapid elongation of leaf sheath stage (PO:0001024): A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf sheath (PO:0020104) occurs.

Strwaberry Genomics Annotation Project

Yes, I have been working with Omar Darwish on annotating the samples and stages for their project. You can view the annotations here:https://docs.google.com/spreadsheet/ccc?key=0Ar1O1Y7eIKhsdHhObVd5UUZGT1BaalRKQ1FyMWx0dFE&usp=sharing

They have a nice page where you can view the samples they used: http://bioinformatics.towson.edu/strawberry/newpage/Tissue_Description.aspx see slide #2

I was planning for us to discuss this at tomorrow's meeting- I suggest we need to create a specific term for receptacle cortex and receptacle pith.

I also have a question about using the plant embryo stages, as these refer to the developemental stages of the whole plant. rather than an individual embryo ( sporophyte development stage (PO:0028002)). I related the samples tot he stages of development of the individual fruits- the achenes.

Pakanj asked about using the BBCH- here is a link to it: http://en.wikipedia.org/wiki/BBCH-scale_%28strawberry%29. It is more whole plant focused and call the whole strawberry a fruit.

OBO Foundry Review of Plant Ontology

Content of the review has been moved to a gdoc

Upcoming meetings and Presentations 2013-2014:

• The Plant Genomics Congress USA, St Louis, September 23rd & 24th, 2013

No one from PO is planning to attend

• PAG 2014 January 11-15, 2014 - San Diego, CA, USA

• • PJ has been contacted by PAG organizers; Suggest slightly new focus "Plant Ontologies and Systems Biology"
  • Ideas for speakers- someone from GO and others?>>

• • Registration is now open: PAG 2014. Early reg'n till Nov. 1st