POC Conf. Call 9-24-13

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

In attendance: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Pankaj Jaiswal (OSU), Barry Smith (OBO), Marie Alejandra Gandolfo (Cornell)

Absent: Brian Atkinson (OSU), Dennis W Stevenson (NYBG)

Strawberry Genomics Annotation Project

LC has been working with Omar Darwish on annotating the samples and stages for their project.

You can view the annotations here: Strawberry Annotations

They have a nice page where you can view the samples they used: see slide #2 Strawberry Genomics

Suggest we need to create a specific term for receptacle cortex and receptacle pith:

Proposed new terms:

receptacle cortex (new po:ID): A cortex which is part of the receptacle (PO:0009064).

We should get rid of mass nouns if possible and make the specific types of cortex all a child of cortex, rather than a child of portion of ground tissue. Some of the cortex terms are is_a portion of ground tissue and others are is a cortex. See examples below:

Existing terms:

• receptacle (PO:0009064): A cardinal organ part that is the region at the distal end of either a peduncle or a pedicel where the floral appendages (e.g.: sepals, petals, stamens and pistils) are attached.

• cortex (PO:0005708): A maximal portion of ground tissue (PO:0025059) between the vascular system (PO:0000034) and the epidermis (PO:0005679) in a plant.

• portion of ground tissue (PO:0025059): Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015).

This needs to be worked on since there are numerous children now of PoPT that are not ground tissue, suce as bark and seed coat.

MAG: ground tissue of plants is made up of: parenchyma cells, collenchyma cells and sclerenchyma cells.

See tracker: portion of ground tissue

• pedicel cortex (PO:0004722): A portion of ground tissue that is part of a cortex and part of a pedicel.

revised def'n: A cortex which is part of a pedicel.

- make pedicel cortex a child of cortex, rather than a child of PoGT

• pedicel (PO:0009052): An inflorescence branch (PO:0009081) that supports an individual flower in an inflorescence (PO:0009049).

• pith (PO:0006109): A maximal portion of parenchyma (PO:0005421) in the center of a shoot axis (PO:0025029) or root (PO:0009005).

• shoot axis pith : A portion of pith (PO:0006109) that is part of a shoot axis (PO:0025029).

revised: shoot axis pith: A pith (PO:0006109) which is part of a shoot axis (PO:0025029).

See continued discussion Items_for_future_meetings#Revisions_to_cortex_.28PO:0005708.29_and_other_portion_of_ground_tissue_.28PO:0025059.29_children

Question about using the plant embryo stages, as these refer to the developmental stages of the whole plant. rather than an individual embryo (sporophyte development stage (PO:0028002)). I related the samples to the 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

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.

-def'n accepted, OK

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 also: [http://www.public.iastate.edu/~bot.512/papers/Eshed.pdf Eshed et al,

NOTE: Based on the discussion, the founder cells are not the same as the anlagen so we will change the name of vascular leaf anlagen formation stage (PO:0001003) back to vascular leaf founder cells formation stage (PO:0001003) with a revised def’n: The initial stage of leaf development when cells in the shoot apical meristem (PO:0020148) are already determined to form a leaf primordium, but the primordium itself is not distinguishable morphologically. We also realize the def'n needs some work. It is still not clear how to distinguish the two though.

We also created a new term vascular leaf anlagen formation stage (PO:0025586): A vascular leaf initiation stage (PO:0007040) when the cells of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).

phyllome anlagen (PO:0025430): A portion of meristem (PO:0009013) tissue that is part of a part_of peripheral zone (PO:0000225) and will give rise to a phyllome primordium (PO:0025128).

comment: The phyllome anlagen is only detectable by gene expression, not morphology.

references for anlagen and founder cells

"The development of a leaf begins with a regional shift in the polarity and rate of cell division and expansion within a group of leaf founder cells on the flank of shoot apical meristem." Smith and Hake 1992

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

Goh et al, 2012 Development

PO-dev Feb.06

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 differentiation stage (new PO:0025574)

This term was proposed during last POC conference call to emphasize the importance of cell and tissue differentiation.

Proposed new term and def'n vascular leaf differentiation stage (new PO:0025574): A vascular leaf development stage (PO:0025570) that begins with the formation of cambial initial cells (PO:0000295) and epidermal initial cells (PO:0000349) and ends with the formation of the leaf epidermis (PO:0006016) and the leaf vascular system (PO:0000036).

Proposed comment: tba

* cambial initial cell (PO:0000295): An initial cell (PO:0004011) that is part of the vascular cambium (PO:0005598) or cork cambium (PO:0005599), and by periclinal divisions, produces cells to the outside or inside of the cambial axis.

• • phloem mother cell PO:0000400
  • fusiform initial cell PO:0000079
  • ray initial cell PO:0000082

* epidermal initial cell (PO:0000349): An initial cell (PO:0004011) that is part of an epidermis (PO:0005679) and gives rise to specialized cell types of the epidermis.

• • stomatal initial cell (PO:0000062)

Gonzalez et al 2012, Trends in Plant Science

vascular leaf expansion stage PO:0001052

old name and def'n: 2 leaf expansion stage (PO:0001052): Stage of leaf development which begins when cell differentiation and cell expansion occurs and finishes when the leaf reaches its full size.

Proposed revised name and def'n vascular leaf expansion stage (PO:0001052): A vascular leaf development stage (PO:0025570) during which vascular leaf size increases primarily through cell expansion.

Proposed comment: During this stage leaf shaping (GO:0010358) occurs which is defined as the developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

• Note: The majority of cell division occurs early in leaf development and cell expansion is the major agent of leaf expansion link or see above image.

From Esau 1965: It appears that leaf differentiation occurs during the intercallary growth of the leaf. The difference between palisade and spongy mesophyll/cells is a matter of individual growth or elongation.

vascular leaf post-expansion stage (PO:0001053):

old name and def'n: 3 leaf fully expanded stage (PO:0001053): Stage of leaf development when leaf is fully expanded.

Proposed new Name and def'n: vascular leaf post-expansion stage: A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and ends with the onset of the vascular leaf senescence stage (PO:0001054).

from 9-10-13: Perhaps change term to "vascular leaf mature stage", or maybe keep the "leaf fully expanded stage"???. Examples of leaves with indeterminate growth, ferns, viney leaves, some Mahogany plants, but they are the exceptions. Could add as a comment (get names from DWS).

vascular leaf senescence stage (PO:0001054)

• vascular leaf senescence stage (PO:0001054): A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.

Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf. Need to add the references to the GO terms.

Need to look at this more- abscission zone (PO:0000146) starts in the petioles (are part of the leaf), starts with cell senescence, should refer to 'point of attachment'. Don't need to specify where the abscission zone forms. Note all leaves abscise, end with death of the vascular leaf

Need to review leaf senescence- see plant cell resource

• 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
  • Gleissberg 2002
  • 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.

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