POC Conf. Call 10-9-12

POC meeting, Webex Conference Call; Date: Tuesday Oct 9th, 2012 10am PDT/1pm EDT

In attendance:

POC members:

Absent:

Collaborators: none

Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_10-2-12?

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Change to gametophyte development stage

This change is urgent, because we need to address this in the manuscript in prep.

gametophyte development stage (PO:0028003) is currently defined as "A whole plant development stage that has as primary participant a whole plant during the interval between meiosis or apospory and its death or fertilization."

I think the last part about fertilization is misleading, because it suggests that the gametophyte stage could end in any plant with fertilization. Many gametophytic plants continue to live (and nourish the sporophyte) long after fertilization. In seed plants, the gametophyte does not exactly die after fertilization, but is transformed. I suggest we add something to the comment to help explain this, but keep the definition simpler.

New proposed definition: A whole plant development stage (PO:0007033) that has as primary participant a whole plant (PO:0000003) during the interval between meiosis or apospory and its death.

New addition to comment (rest stays the same): In seed plants, the gametophyte may be transformed by fertilization but not strictly die, such as when pollen (PO:0025281) germinates or when a plant embryo (PO:0009009) begins to develop within an embryo sac (PO:0025074) of an angiosperms.

Fruit development stages for whole plants

whole plant fruit development stage (PO:0025500)

New term

proposed defintion: A sporophyte reproductive stage that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

Comment: Includes whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010). An iteroparous plant will have a single whole plant fruit development stage during its life of whole plant (PO:0025337), while a semelparous plant may have multiple whole plant fruit development stages during its life, each of which will be part of the same instance of a sporophyte reproductive stage.

whole plant fruit formation stage (PO:0007042)

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) that has no other fruits as part enters a fruit initiation stage (PO:0025503) and ends with the onset of a whole plant fruit ripening stage (PO:0007010).

Comment: This term is to be used for a stage of development of a whole plant (PO:0000003). For the stages of development of an individual fruit, see fruit development stage (PO:0001002). An iteroparous plant will only have one fruit formation stage in its life, while a semelparous plant may have multiple whole plant fruit development stages during its life. In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the fruit ripening stage of whole plant (PO:0007042) has begun. Although the use of synonyms like 07-milk stage in rice properly refer to the development of an individual fruits, they are used as here to extrapolate to a whole plant.

Is it better to use whole plant fruit formation stage has_part fruit formation stage (new term, see below) or fruit formation stage part_of whole plant fruit formation stage?? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.

whole plant fruit ripening stage (PO:0007010)

under construction

New proposed def.: A whole plant fruit development stage (PO:0025500) that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with the earliest of either (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening, whichever comes first.

comment: This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing ripening (which is a type of senescence) during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An annual species generally will have only one fruit ripening stage in its life, followed by a sporophyte senescent stage (PO:0007017), as in case (1). A perennial species may have one fruit ripening stage for each growing season, followed by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species, the plant may remain in the sporophyte reproductive stage (PO:0007130) after all fruit has ripened, without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit development stage (PO:id) has ended. Although the use of stages like dough or particular ripening stages (see synonyms) properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.

Is it better to add whole plant fruit ripening stage has_part fruit ripening stage or fruit ripening stage has_part whole plant fruit ripening stage? Haven't added either yet. Ideally, we could add both, but AmiGO can't handle it.

One problem is that sometimes the fruit doesn't ripen until well after the plant begins to senesce or go dormant. May need to put something this effect in the comment and point out that the individual fruits can still go on ripening afterwards.

We should mention in the comment that this stage begins when the fruit formation stage ends.

New fruit development stages

fruit development stage (PO:0001002)

def.: A plant structure development stage (PO:0009012) that has as primary participant a single fruit (PO:0009001).

comment: Defined by characteristic morphological, structural, histological or other visible features of a fruit. May have as part a seed development stage (PO:0001170). For development stages of a whole plant based on fruit development, use whole plant fruit development stage (PO:id) or its subclasses.

New proposed subclasses

under construction'

fruit formation stage

Proposed def.: A fruit development stage (PO:0001002) that being with fertilization (GO:id) and ends when process of fruit ripening (GO:id) begins.

comment: This stage applies to an individual fruit.

subclasses based on current whole plant stages

These are the stages that were developed for whole plants, but groups like SGN really need to apply them to individual fruits.

fruit initiation stage: A fruit formation stage (PO:id) that begins with the formation of a plant zygote and ends as soon as the fruit starts to grow.

fruit size up to 10% stage: A fruit formation stage (PO:id) that begins after the formation of a plant zygote as soon as the fruit starts to grow and ends when the fruit has reached 10% of its final size.

fruit size 10 to 30% stage: A fruit formation stage that spans the interval when a fruit has reached 10% to 30% of its final size.

etc.

fruit ripening stage

Proposed def.: A fruit development stage (PO:0001002) that

Subclasses of whole plant fruit formation stage (PO:0007042)

See SF tracker for FF.00 fruit size 10% and sibling terms

At the meeting on 9/4/12, we agreed to modify the names slightly to emphasize that they belong to whole plants, and to remove numbers. Definitions should be changed to use updated name of the parent term, and to make it clearer that they refer to whole plant stages.

What about plants with asynchronous fruit development? RW and MAG talked to Naama Menda about using these terms for tomato. She felt that these size classes were not useful for tomatoes, but in any case, they used the size classes only to describe individual fruits. They will need to go over all of there existing annotations and move them to fruit development stage and its new subtypes as necessary.

FF.00 fruit size up to 10% stage (PO:0007032)

current def.: A fruit formation stage that begins with the formation of a zygote and ends when the fruit has reached 10% of its final size.

comment: This fruit development stage may begin without fertilization or formation of a zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This term can only be used of the final size of the fruit is known.

proposed new name and definition:

whole plant fruit formation stage up to 10%: A whole plant fruit formation stage (PO:0007042) that begins with the formation of the first plant zygote (PO:0000423) of a growing season and ends when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% of final size.

comment: This stage may begin without fertilization or formation of a plant zygote in cases of parthenocarpy, apomixis, or other hormone-induced conditions. This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

FF.01 fruit size 10 to 30% stage (PO:0007009)

current def.: A fruit formation stage that spans the interval when a fruit has reached 10% to 30% of its final size.

comment: This term can only be used if the final size of the fruit is known.

proposed new name and definition:

whole plant fruit formation stage 10 to 30%: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 10% to 30% of final size.

comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

FF.02 fruit size 30 to 50% stage (PO:0007029)

current def.: A fruit formation stage that spans the interval when a fruit has reached 30% to 50% of its final size.

comment: This term can only be used if the final size of the fruit is known.

proposed new name and definition:

whole plant fruit formation stage 30 to 50%: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 30% to 50% of its final size.

comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

FF.03 fruit size 50 to 70% stage (PO:0007007)

current def.: A fruit formation stage that spans the interval when a fruit has reached 50% to 70% of its final size.

comment: This term can only be used if the final size of the fruit is known.

proposed new name and definition:

whole plant fruit formation stage 50 to 70%: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 50% to 70% of its final size.

comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

FF.04 fruit size 70% to final size stage (PO:0007027)

current def.: A fruit formation stage that spans the interval when a fruit has reached 70% of its final size to its final size.

comment: This term can only be used if the final size of the fruit is known.

proposed new name and definition:

whole plant fruit formation stage 70% to final size: A whole plant fruit formation stage (PO:0007042) that spans the interval when the average size of fruits (PO:0009001) on a whole plant (PO:0000003) has reached 70% of its final size to its final size.

comment: This terms is best used for plant with more or less synchronous fruit development and can only be used of the final size of the fruit is known. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

related synonyms: BBCH principal growth stage 75; BBCH principal growth stage 79

Add new synonyms for grapes

Add related synonym: BBCH principle growth stage 77; Berries beginning to touch

Add related synonym: grape E-L stage: 31 Berries pea-sized (7mm dia), bunches hang, (BBCH 75)

Add related synonym: grape E-L stage: 32 Beginning of bunch closure, berries touching (if bunches are tight), Berries beginning to touch (BBCH 77)

Add related synonym: grape E-L stage: 33 Berries still hard and green, Majority of berries touching, (BBCH 79)

Subclasses of whole plant fruit ripening stage (PO:0007010)

The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.

FR.00 beginning of fruit ripening stage (PO:0007036)

current def.: The stage at which fruit maturation begins.

proposed new name and definition:

whole plant beginning of fruit ripening stage: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

Add related synonym: BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour

Add related synonym: grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison

FR.01 early stage of fruit ripening (PO:0007001)

current def.: The early stage in fruit ripening

related synonym: BBCH principal growth stage 83

proposed new name and definition:

whole plant early fruit ripening stage: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

Add related synonym: middle of veraison

FR.02 mid stage of fruit ripening (PO:0007031)

current def.: The stage when fruit ripening is midway.

whole plant mid fruit ripening stage: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

FR.03 late stage of fruit ripening (PO:0007050)

current def.: The late stage of fruit ripening.

whole plant late fruit ripening stage: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

FR.04 fruit ripening complete stage (PO:0007038)

current def.: The stage at which fruit ripening is complete.

whole plant fruit ripening complete stage: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

related synonym: BBCH principal growth stage 89

Add related synonym: grape E-L stage: 38; Berries ripe for harvest

References for grape terms:

Coombe (1995) Growth Stages of the Grapevine: Adoption of a system for identifying grapevine growth stages. Australian Journal of Grape and Wine Research 1: 104–110 link

Lorenz et al (1995) Growth Stages of the Grapevine: Phenological growth stages of the grapevine (Vitis vinifera L. ssp. vinifera)—Codes and descriptions according to the extended BBCH scale†. Australian Journal of Grape and Wine Research 1: 100–103 link

BBCH grapes

Fruit development stage (PO:0001002) and subclasses

This term was a subtype of collective plant structure development stage, but has moved to be direct subtype of plant structure development stage.

current def.:

fruit development stage (PO:0001002): Stages of development of a fruit defined by characteristic morphological, structural, histological or other visible features.

proposed def.: A plant structure development stage (PO:0009012) that has as primary participant a fruit (PO:0009001).

comment: Defined by characteristic morphological, structural, histological or other visible features. May have as part a seed development stage (PO:0001170).

New sub-classes of fruit development stage

After last week's call, DWS suggested that we may be able to describe diverse types of fruit development by starting with the development of different parts of the fruit, like the mesocarp or endocarp, and then showing how development of different tissues leads to different types of fruits.

We could start with fertilization stage as a first stage in all fruit development (with parthenocarpy as an exception).

Should include a stage for fruit ripening, as this is common across all fruits.

Fertilization, expansion and differentiation, ripening and/or drying.