whole plant fruit ripening stage

[planteome-user]

The existing term 6 ripening stage (PO:0007010) is defined as "Maturation of the fruit. " There are two major problems with this definition: one, it describes a process, not a stage, and two, it refers to development of a fruit, rather than to the development of a whole plant.

After reviewing the history of the PO and discussing this term at the POC meetings on 9-4-12, we agreed that this term was originally created to describe a whole plant development stage during which fruit is ripening. We agreed to change the name and definition accordingly.

New proposed name: whole plant fruit ripening stage.

New proposed def.: A sporophyte reproductive stage (PO:0007130) during which a fruit (PO:0009001) on a whole plant (PO:0000003) is undergoing ripening (GO:0009835).

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 development stage (PO:0001002). An annual plant will only have one fruit ripening stage in its life, which is generally followed by a sporophyte senescent stage (PO:0007017), while a perennial may have one fruit ripening stage for each growing season. 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 has begun.

has_part fruit development stage (PO:0001002) (This could be made more specific, after we add specific types of fruit development stages.)

subset for angiosperms

The definition needs some work to clarify when this stage ends, particularly for perennials. We should also add a comment that ripening is a type of senescence and a comment to distinguish this stage from senescent stage of whole plant.We expect that this definition will change slightly as we work on the new and revised terms for fruit development stages.

Reported by: rlwalls2008

Original Ticket: obo/plant-ontology-po-term-requests/498

[planteome-user]

The sub-classes of this term also need work. Will open a separate tracker for them.

Original comment by: rlwalls2008

[planteome-user]

Modified proposed definition and comment:

A sporophyte reproductive stage (PO:0007130) that begins when a fruit (PO:0009001) on a whole plant (PO:0000003) is begins the process of ripening (GO:0009835) and ends when (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 development stage (PO:0001002). 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.

Original comment by: rlwalls2008

[planteome-user]

Also need to add some of the original comment to the proposed comment.

Original comment: Although the use of stages like dough or particular ripening stages properly refer to the development of an individual fruit, they are commonly used as here to extrapolate to a growth of a whole plant or a group of plants.

New proposed comment addition: 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.

I removed the word "commonly" and took out the clause about referring to a group of plants, which is inaccurate. This definition is intended for a single plant. If users need to refer to a group of plants, they should create proper ontology definitions that refer to a population or other group of organisms.

Original comment by: rlwalls2008