POC Conf. Call 7-23-13

POC meeting, Webex Conference Call; Date: Tuesday July 23rd, 2013 10am PDT/1pm EDT

In attendance: Laurel Cooper (OSU), Justin Elser (OSU), Marie Alejandra Gandolfo (Cornell), Brian Atkinson (OSU), Barry Smith

Absent: Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU)

Streaming recording link: https://ontology.webex.com/ontology/ldr.php?AT=pb&SP=MC&rID=76811407&rKey=a0f26ae9a7ffde2f

Download recording link: https://ontology.webex.com/ontology/lsr.php?AT=dw&SP=MC&rID=76811407&rKey=f5d7af1633d4e208

Release #20

• Goals and Timeline for Release:
• Goal is end of July 2013; edits will be completed by the end of this week
• PO-Beta is loaded with new OBO file and new annotations sets

• Roughly 50 new terms and about 30 renamed terms
• See: Details_of_Changes_to_Release_20

Note: MAG is out for all of August, DWS is going to Colombia for August 5-14 and BA is out from the Aug 5th-21st.

New Annotation Files: Rice and Cotton

• Rice mutant phenotype set from the Plant Phenotype Pilot project- Lol and Laura. Example: leaf sheath

• still need a GR id for DSG1 [1] Should we just take it out?

• Cotton ESTs from a suppression subtractive hybridization study looking at cell wall biosynthesis in cotton suspension culture, derived from embryogenic callus tissue.

• Currently annotated to seed trichomes (PO:0004511) and seed trichome secondary wall biosynthesis stage (PO:0025372), but should be plant protoplasts (PO:0000006) and the associated plant-type cell wall biogenesis (GO:0009832) process term from GO.

• Reference: Expression profile analysis of genes involved in cell wall regeneration during protoplast culture in cotton by suppression subtractive hybridization and macroarray.

LC will contact Agbase curators about fixing the annotations

Translations

- Made a Google doc translations

- Spanish ones are almost complete- Thanks Ale!

- Sending to Yukiko today

Poster for BSA

Comments?

Items for discussion:

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

Flower development stage (PO:0021004) and subclasses

Continued from the POC Conf call 6-25-13 and 7-2-13

Link to spreadsheet: gdoc

• Added new relationship; preceded_by to show the order of the development stages:

Note: Should add as comment to all flower development terms that they should not be used in reference to whole plant development.

Revised definitions for flower development stages:

• Flower development stage (PO:0021004): A reproductive shoot system development stage (PO:0025530) which begins with the onset of the floral organ meristem development stage (PO:0007601) and ends after the post anthesis stage (PO:0007617).

Accepted, pending revisions to the post anthesis stage (PO:0007617)- if we get rid of it, then we should just refer to the flowering stage (was anthesis)

New and revised child terms:

flower meristem transition stage (new PO:0025588)

• flower meristem transition stage (new PO:0025588): A flower development stage (PO:0007615) which begins with the transition of a portion of meristem tissue (PO:0009013) to a flower meristem (PO:0000229) and ends with the onset of the floral organ formation stage (PO:0025585).

Accepted

floral organ formation stage (new PO:0025585)

• floral organ formation stage (new PO:0025585): A flower development stage (PO:0007615) which begins with the floral organ meristem development stage (PO:0007601) and ends with the onset of the flowering stage (PO:0025586).

Accepted

Children of floral organ formation stage (new PO:0025585):

• • floral organ meristem development stage (PO:0007601): A floral organ formation stage (PO:0025585) which begins with the development of the floral organ meristem (PO:0000229) from a portion of meristem tissue (PO:0009013) and ends with the beginning of the floral organ primordium development stage (PO:0007602).

• • floral organ primordium development stage (PO:0007602): A floral organ formation stage (PO:0025585) which begins with the appearance of the floral organ primordium (PO:0025477) and ends with the beginning of the floral organ differentiation stage (PO:0007600).

• • floral organ differentiation stage (PO:0007600): A floral organ formation stage (PO:0025585) which begins with the differentiation of floral organs (PO:0025395) from the floral organ primordium (PO:0025477) and ends with the onset of the anthesis stage (PO:0007616).

Accepted, pending changes to the anthesis stage (PO:0007616)

flowering stage (new PO:0025586)

• flowering stage (PO:0025586): A flower development stage (PO:0007615) during which a single flower (PO:0009046) participates in the process of flowering (GO:0010228). This needs to be revised...

• • anthesis stage (PO:0007616): A flower development stage (PO:0007615) that begins when pollen (PO:0025281) is presented and/or the stigma (PO:0009073) is receptive and ends with pollination (GO:0009856). This needs to be revised...;

what is "pollen is presented"? pollen is released by anther dehiscecence

Refer to: anther dehiscence (GO:0009901): The dehiscence of an anther to release the pollen grains contained within it.

Proposed revised def'n: A flowering stage (PO:ID) that begins with anther dehiscence (GO:0009901) and/or the stigma (PO:0009073) is receptive and ends with pollination (GO:0009856).

just call it flowering??

• • post anthesis stage (PO:0007617): A flower development stage (PO:0007615) that occurs after the anthesis stage (PO:0007616) and lasts until flower morphogenesis is complete (GO:0048439). This needs to be revised...

Proposed getting rid of this stage as it is vaguely defined. There are a few annotations on it, but they can be re-assigned to more specific stages.

References for Anthesis:

• From PJ: section 1.10.3: "It definitely ends with pollination or anther dehiscence; fertilization can occur post anthesis".
• from DWS: "Anther dehiscence is the most common definition for the end."

This article clearly states that ad occurs either before or during the opening of lemma and palea. This is also true of other self-pollinated plants such as barley.

• barley dev

• In wheat

• Zadoks scale

• Anthesis in rice

• more rice stages

• Barley flowering

• Maize growth stages
  • Maize Flowering and fertilization and Maize growth stages with image

Refs for flower development:

• Simulation of Organ Patterning on the Floral Meristem Using a Polar Auxin Transport Model PLOSOne, 2012
• Pharbitis nil1 from MAG
• flower development in grasses; Review
• Grass Meristems I: Shoot Apical Meristem Maintenance, Axillary Meristem Determinacy and the Floral Transition; review
• RETARDED PALEA1 Controls Palea Development and Floral Zygomorphy in Rice
• LEAFY blossoms
• Genetics and Evolution of Inflorescence and Flower Development in Grasses
• Flower development in rice
• Link to BBCH scale

GO flower development terms and definitions:

flower development (GO:0009908): The process whose specific outcome is the progression of the flower over time, from its formation to the mature structure. The flower is the reproductive structure in a plant, and its development begins with the transition of the vegetative or inflorescence meristem into a floral meristem.

anther dehiscence (GO:0009901): The dehiscence of an anther to release the pollen grains contained within it.

Part_of Children:

floral meristem growth (GO:0010451): The increase in size or mass of a floral meristem, a population of undifferentiated cells in a plant that gives rise to a flower.

floral meristem determinacy (GO:0010582): The process in which a floral meristem becomes determinate (i.e. ceases to produce lateral organs and may or may not terminally differentiate).

floral organ development (GO:0048437): The process whose specific outcome is the progression of the floral organ over time, from its formation to the mature structure.

floral whorl development (GO:0048438): The process whose specific outcome is the progression of a floral whorl over time, from its formation to the mature structure. A floral whorl is a circular arrangement of parts of a flower arising from a stem of a plant.

flower morphogenesis (GO:0048439): The process in which the anatomical structures of the flower are generated and organized.

nectary development (GO:0010254): The process whose specific outcome is the progression of the floral nectaries over time, from its formation to the mature structure.

perianth development (GO:0090428): The process whose specific outcome is the progression of the perianth over time, from its formation to the mature structure. The perianth is a collective phyllome structure composed of two or more petals, sepals, or tepals.

specification of floral organ number (GO:0048833): Any process that modulates the number of floral organs formed in a floral whorl.

Is_a Children:

regulation of flower development (GO:0009909): Any process that modulates the frequency, rate or extent of flower development.

negative regulation of flower development (GO:0009910): Any process that stops, prevents, or reduces the frequency, rate or extent of flower development.

positive regulation of flower development (GO:0009911): Any process that activates or increases the frequency, rate or extent of flower development.

Upcoming meetings and Presentations 2013:

Botanical Society Meeting July 27-31st New Orleans

BSA 2013

- MAG will present the work she has been doing with the images and slides CUPAC- The Cornell University Plant Anatomy Collection: a web-based tool for the Plant Sciences teachers and researchers

- BA will present a talk on his work: New evidence for the radiation of basal Cupressaceae

- BA will also present a poster on the PO: Plant Ontology, a controlled and structured plant vocabulary for all botanical disciplines.