Items In Progress

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Please include the date when the item was added; topics will move off of here as they are dealt with.

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Open trackers: To be fixed:

archegonium egg cell

archegonium egg cell (PO:0025122): A plant egg cell that is produced by and located in an archegonium.

PO:0025126: archegonium: A plant gametangium that produces an archegonium egg cell that is located in it.

proposed revised def'n: archegonium (PO:0025126): A plant gametangium (PO:0025124) that produces and contains an archegonium egg cell (PO:0025122).

Link to SF for archegonium

plant gametangium (PO:0025124): A plant organ (PO:ID) that produces and contains one or more gametes (PO:0025006) that are located in it and is part of a whole plant (PO:ID) in the gametophytic phase(PO:ID).

root tuber

Currently: We have PO:0025476 tuberous root: A radially enlarged root (PO:0009005).

existing: Comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuber root may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuber roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuber root is attached. A tuber root usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).

Propose new term: tuberous root: A root (PO:0009005) that is radially enlarged relative to other lateral or shoot-borne roots on the same plant but not as enlarged as a tuberous root tuber.

comment: A tuberous root, as found in Cassava, may develop through further enlargement into a tuberour root tuber.

proposed rename (PO:0025476): new name: tuberous root tuber: A tuber (PO:0004543) that develops from a tuberous root (PO:0009005)and is further radially enlarged.

add: develops from relationship

old: comment: Functions in storage. This term should be used for tubers derived from roots, as found in Cassava, not for tubers derived from branches (PO:0025073), as found in potatoes and yams. Use the term tuber (PO:0004543), aerial tuber (PO:0004548), or subterranean tuber (PO:0004547) for tubers derived from branches. A tuberous root may be distinguished from a tuber that is derived from a branch by the presence of a root cap (PO:0020123) early in development, or the presence of lateral roots (PO:0020121) or their remnants. Sometimes tuberous roots bear vegetative buds (PO:0000058) like a tuber derived from a branch, but these arise from adventitious buds or are derived from the stem (PO:0009047) to which the tuberous root is attached. A tuberous root usually develops from a shoot-borne root (PO:0000042) or a lateral root (PO:0020121).

Add "root tuber" and "tuber root" as exact synonym.

old notes:

On further investigation, it seems that not only primary growth is involved in the formation of root tubers. There is secondary thickening from irregular growth from the vascular cambium, as well as thickening due to cell division in the cortex. Need to look into it more.

Also, it seems there are both tuberous roots (enlarged roots that form tubers along part of their length), and tubers, that form within those roots (see http://aob.oxfordjournals.org/content/38/2/307.full.pdf+html and hortsci.ashspublications.org/content/44/3/651.full.pdf)

Tuber

Currently: tuber: PO:0004543: A shoot axis (PO:0025029) that is radially enlarged and develops from a branch (PO:0025073)

Propose new parent term: Tuber: (new PO ID): A plant axis (PO:0025004) that is radially enlarged and develops from a branch (PO:0025073) or a root (PO ID).

Synonyms: need to tweak

narrow: shoot axis branch tuber, exact: tuber branch

broad: diaspore

proposed: rename existing tuber term: Shoot axis tuber (PO:0004543): A tuber that is a radially enlarged shoot axis (PO:0025029) and develops from a branch (PO:0025073)

Existing Comment: Functions in storage of photosynthate metabolites. This term should be used for tubers derived from branches, as found in Solanum spp. (e.g. potato) or Dioscorea spp. (e.g. yam) and other species. Use the term tuberous root (PO:0025476) for tubers derived from roots, such as those found in Cassava, Ipomoea, or Hemerocallis.

tuber growth and development stages

This item has been open on SF since 6/2009

From Naama Menda: I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).

Suggested stages:

-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)

-tuber initiation

-tuber growth

-tuber maturation

How we work these in will depend on restructuring of PSDS

l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926

generative cell (PO:0020097) and related terms

generative cell (PO:0020097) and related terms

We need to fix this definition, as it currently only includes angiosperms:

Current def'n: propose change (PO:0020097) to a spermatogenous cell and make generative cell a synonym of it

generative cell (PO:0020097): A cell of the male gametophyte of angiosperms that divides to produce two male gametes or sperm cells. [source: APweb:Glossary]

Proposed def'n: A plant cell (PO:0009002) of the microgametophyte (PO:0025280) of seed plants that divides to produce two plant sperm cells (PO:0000084).

Need to add to PO: spermatogenous cell (PO:xxxxxxx)

Good idea. Note that spermatogenous cells also occur in non-seed plants.

should be: part_of the microgametophyte (PO:0025280)

suggest making it part_of pollen (PO:0025281) -- only found in seed plants

Definition from Raven 5th ed: generative cell: 1. In gymnosperms, the cell of the male gametophyte that divides to form the sterile and spermatogenous cells

2. In angiosperms, the cell of the male gametophyte that divides to form two sperm

proposed definition: spermatogenous cell: raven: the cell of the male gametophyte or pollen grain of gymnosperms, which divides to form 2 sperm cells

Probably should also have the prothallial cell- part of the gymnosperm pollen grain: Definition from Raven 5th ed: The sterile cell or cells found in the male gametophytes, or microgametophytes of vascular plants other than angiosperms; believed to be the remnants of the vegetative tissue of the male gametophyte.

Generative cells can occur in both angiosperms and gymnosperms. They are the same thing, even though they develop into something else. Need to look at Singh's book on gymnosperm embryology.

Existing:

plant sperm cell (PO:0000084)

---

From Pankaj:

Please add the following anatomy term required for the rice gene expression data I am annotating http://www.ncbi.nlm.nih.gov/pubmed/22046259

PO:0020097 : generative cell

--IS_A--pollen generative cell (NEW-suggested)<--[ please add]

--DEVELOPS_FROM-- PO:0025121 : pollen sperm cell [please add this relationship]

Generative cell is not found outside pollen-bearing plants. Suggest just adding this term as a synonym. Special class would be redundant, as there is no non-pollen generative cell.

Agree to add pollen sperm cell develops_from generative cell. BUT only in angiosperms

May need to add new term for pollen sperm cell in angiosperms, which develops from generative cell and pollen sperm cell in gymnos, which develops from pollen spermatogenous cell.

We need these synonyms:

• body cell (of generative cell)

• central cell
• prothallial cell
• stalk cell (of sterile cell)
• antheridial inital
• antheridial cell
• tube cell
• male gametes

have:

• microspore (PO:0020048)

fruit ripening stage and sub-classes

New terms are needed to describe the stages of ripening for individual fruits. Have a revised parent term; need the sub-classes.

Proposed name and def'n:

fruit ripening stage (PO:0025502): A fruit development stage (PO:0001002) during which a fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).

Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).

fruit ripening (GO:0009835): An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.

related synonyms: fruit maturation; fruit senescence

whole plant fruit ripening stage

whole plant fruit ripening stage (PO:0007010): A whole plant fruit development stage (PO:0025500) that begins when the first 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 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: Succeeds a whole plant fruit formation stage (PO:0007042). 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 fruit ripening (GO:0009835), which is a type of senescence, during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages 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 formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of synonyms like "10-dough stage in sorghum" properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.

Proposed Revisions to sub-classes:

Comment from RW: 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.

need to open tracker for this set:

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

whole plant beginning of fruit ripening stage (PO:0007036):

current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.

proposed def'n: 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 synonyms:

• BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour
• grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison

whole plant early fruit ripening stage (PO:0007001)

current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening

proposed def'n: 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 synonyms:

• middle of veraison
• BBCH principal growth stage 83

whole plant mid fruit ripening stage (PO:0007031):

current name and def'n: FR.02 mid stage of fruit ripening (PO:0007031) The stage when fruit ripening is midway.

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

proposed 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.

whole plant late fruit ripening stage (PO:0007050)

current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.

proposed new def'n: 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.

whole plant fruit ripening complete stage (PO:0007038):

current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.

Proposed Def'n: 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 term 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 synonyms:

• BBCH principal growth stage 89
• grape E-L stage: 38; Berries ripe for harvest

From 10-10-12 skype meeting

common primordium

This request was made by Elena Kramer during the beta review: , I wondered if there was some way to incorporate ...the phenomenon of common primordia (...would only apply to the development ontology)

"During floral development (at least in peas, maybe others), petals and stamens (and maybe other floral organs) may share a common primordium before development of a distinct petal or stamen primordia. We may want to add this to the flower developmental stage branch of the PGDSO."

This could be a structure in the PAE branch, and we can consider adding it as a stage when we work on flower development stages.

We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.

nucellar projections

The current definition of nucellar projection (PO:0008007) is: A portion of plant tissue that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis. part_of nucellus.

This definition is specific to grasses, and should be rephrased, so it is more general.

Actually, I can't find any references to this outside grasses, so perhaps it is fine as is. Does anyone know of an example of this outside grasses? Maybe in other monocots?

No one know of an example outside grasses, so it is okay, but we can rephrase slightly to make it more braod.

proposed def.: A portion of plant tissue (PO:0009007) that is a morphologically distinct part of a nucellus (PO:0020020) overlying the vascular bundles (PO:0005020).

comment: Found a caryopsis in Poaceae.

part_of nucellus

rosette leaf and cauline leaf

The definitions for these terms need revision, especially cauline leaf. Rosette leaf is okay, but should be converted to genus-differentia form.

Current definitions:

rosette leaf (PO:0000014): One of multiple leaves borne in a rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes.

comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.

cauline leaf (PO:0000013): Leaf or pairs/whorls of leaves borne on the stem. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

Perhaps we should use the appropriate growth stages in their definitions, e.g., PO:0007113 rosette growth, and PO:0007089 stem elongation. However, stem elongation is defined as a vegetative growth stage, so it doesn't really apply to plants that are bolting

proposed definitions

rosette leaf: A vascular leaf (PO:0009025) that is part of a collective leaf structure (PO:0025022) in which the leaves are borne on a stem base (PO:0008039) that has very short stem internodes (PO:0020142).

comment: In many species, including Arabidopsis thaliana, the sporophyte vegetative stage (PO:0007134) is characterized by the production of the rosette leaves.

cauline leaf (PO:0000013): A vascular leaf (PO:0009025) that is borne on a stem (PO:0009047) or branch (PO:0025073) that has elongated shoot internodes (PO:0005005).

comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.

Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?

Links from Lol:

http://www.arabidopsis.org/portals/education/growth.jsp

http://www.jstor.org/stable/2656849

non-vascular rosette leaves?

At the POC meeting on 6/7/11, PJ suggested that we make new general terms for rosette leaf and cauline leaf, is_a children of leaf. Then we could make specific terms for vascular rosette leaf and vascular cauline leaf.

However, I don't know if the terms rosette leaf and cauline leaf are ever used for non-vascular plants. Certainly leaves occur on a stem in mosses and liverworts, but it is not the case that the leaves first form during a rosette stage then the stem elongates. Instead, leaves are formed from the stem apex as it elongates.

If rosette leaf and cauline leaf only have one child each (vascular rosette leaf or vascular cauline leaf), is there really a point in making the general category?

Don't need these

sporocyte

Existing definitions:

sporocyte (PO:0006204): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.

microsporocyte (PO:0020047): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]

synonyms: microspore mother cell, PMC, pollen mother cell

megasporocyte (PO:0000431): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]

synonyms: megaspore mother cell, MMC

At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.

Already have:

megasporocyte develops_from female archesporial cell

microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell

Proposed definitions:

sporocyte (PO:0006204): A plant cell (PO:0009002) that develops from an archesporial cell (PO:0030056) and undergoes meiosis (GO:0007126) to produces four plant spores (PO:0025017).

Add: sporocyte develops_from archesporial cell

Should we add spore develops_from sporocyte? yes

meiosis (GO:0007126)

microsporocyte (PO:0020047): A sporocyte (PO:0006204) that develops from a primary sporogenous celll (PO:0006088) and undergoes meiosis (GO:0007126) to produces four microspores (PO:0020048). [source: ISBN:0878934030]

synonyms: microspore mother cell, PMC, pollen mother cell

Should we add microspore develops_from microsporocyte?

male meiosis (GO:0007140)

Better to use meiosis, rather than male meiosis.

megasporocyte (PO:0000431): A sporocyte (PO:0006204) that develops from a female archesporial cell (PO:0006015) and undergoes meiosis (GO:0007126) to produces four megaspores (PO:0020019). [source: ISBN:0471245208]

synonyms: megaspore mother cell, MMC

female meiosis (GO:0007143)

Better to use meiosis, rather than female meiosis.

Also need to address:

primary sporogenous cell (PO:0006088), current def.: It is formed by the division of the male archesporial initial. After several mitotic divisions these cells differentiate into pollen mother cells.

proposed def.: A plant cell (PO:0009002) that develops from a male archesporial cell (PO:0006014) and, after several mitotic divisions, develops into microsporocytes (PO:0020047).

okay

Note: external ontology ids should go in both the definition and as a Dbxref, because they don't work as links otherwise. They work as links okay in the comments.

spikelet

At the POC meeting on 8-30-11, we decided that this definition needs some work.

Current def.: Ultimate and congested inflorescence branch of the grasses. [source: APWeb:Glossary] Comment: It consists of one to many closely-packed flowers and associated glumes etc.

Should make it more general, because spikelets are found throughout the Poales (close relatives of grasses).

Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.

Comment: Part of a spike type inflorescence as found in grasses and other Poales.

From Ale:

spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards

spikelet: a small spike or secondary spike; the ultimate flower cluster of grasses and sedges, consisting of one to may flowers subtended by two bracts (glumes)

Flower, fruit, and inflorescence development stages

We currently have terms for:

• flower development stage (PO:0021004) five subclasses
• fruit development stage (PO:0001002) no subclasses
• inflorescence development stage (PO:0021004) - has two subclasses

The last two, in particular, are poorly developed (few specific subclasses)

It is far too easy to confuse these terms with:

• 4 flowering stage (PO:0007016)
• 5 fruit formation stage (PO:0007042)
• 3 inflorescence detectable stage (PO:0007047)

all of which are subclasses of sporophyte reproductive state (PO:00071300), meaning that they should only be used to describe the development state of a whole plant.

The first and easiest step to be taken would be to change the names of the whole plant development stages to make it clear that they apply to whole plants. For example, 4 flowering stage could be renamed flowering whole plant development stage. The definitions should probably be tweaked accordingly.

Flower development stage (PO:0021004) needs some work, but at least there is a good selection of terms for annotators to pick from.

For fruit development stage and Inflorescence development stage we need to develop at least some basic subclasses. For example, the plant phenotype pilot project needs terms for fruit development stages such as milk stage (as synonym for more general term) and mature or dry stage. These stages could (should?) parallel the stages for whole plants.

Flower development stage (PO:0021004) and subclasses

current def.: Stages of development of a flower defined by characteristic morphological, structural, histological or other visible features.

Proposed def.: A collective plant organ structure development stage (PO:new) that has as primary participant a flower (PO:0009046).

comment: (from original def.) Defined by characteristic morphological, structural, histological or other visible features. May have as parts the development stages of floral parts such as a gynoecium development stage (PO:0007606) or a corolla development stage (PO:0007604).

flower organ development stage

Should be an inferred class (like floral organ), and the subclasses should move to their proper parent. For example, gynoecium development stage and corolla development stage should be collective plant organ structure development stages and palea development stage should be a phyllome development stage. These classes should be part_of flower development stage, not is_a.

1 flower meristem visible stage (PO:0007601)

Current def.: Stage of flower development marked by the emergence of the floral meristem on the flank of the inflorescence meristem.

Needs to refer to apical meristem, not inflorescence meristem (same for the rest of them).

From 10-17-12 skype meeting

lamina areole

Propose new definitions:

phyllome lamina areole (PO:0025391): A cardinal organ part (PO:0025001) that is part of a phyllome lamina (PO:0025396) and is completely surrounded by phyllome lamina veins (PO:0025348) and cannot be divided into any smaller parts that are completely surrounded by phyllome lamina veins.

Comment: Any order of phyllome lamina vein can form the sides of a phyllome lamina areole. Taken together, the phyllome lamina areoles form a contiguous field of polygons over the area of a phyllome lamina. part_of phyllome lamina

leaf lamina areole (PO:0025392): A phyllome lamina areole (PO:0025391) that is part of a leaf lamina (PO:0020039) and is completely surrounded by leaf lamina veins (PO:0020138) and cannot be divided into any smaller parts that are completely surrounded by leaf lamina veins.

Comment: Any order of leaf lamina vein can form the sides of a leaf lamina areole. Taken together, the leaf lamina areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina

ovuliferous scale

New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).

"Ovuliferous scale" seems to be the more commonly used name.

proposed def., ovuliferous scale: A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).

Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().

ovulate cone, new term: A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).

synonym: female cone (related)

Move more specific synonyms form strobilus to these terms.

microsporangiate cone, new term: A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).

seed-scale complex: A reproductive shoot system (PO:0025082) that is part of an ovulate cone (PO:0025083) and has as parts a ovuliferous scale () and a ovuliferous scale sterile bract ().

ovuliferous scale sterile bract: A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().

Definitions of megasporophyll and microsporophyll

move part about angiosperms to the comment

Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.

Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.

pericarp and seed coat

What is the problem with pericarp?

pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.

Synonyms related: fruit peel, fruit rind

New def.: A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.

comment: Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.

endocarp ; PO:0009086, synonym inner epidermis of pericarp

exocarp ; PO:0009085 synonyms outer epidermis of pericarp,

seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.

Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed.

develops_from integument

Get rid of "usually" in def. of integument.

http://en.wikipedia.org/wiki/Caryopsis

is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.

The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.

The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.

link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251

we also have the term:

caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]

ovary and the like

An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.

The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).

ovary wall: Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.

style: (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.

If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.

stigma: Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.

anther and filament

Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this cool picture).

It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).

Cacti terms:

spinule: word for when the spines are stipules – synonym of stipule spine

In Beentje, spinule is defined as a small spine.

Add "spinule" as narrow synonym for stipule spine and as related synonym for other kinds of spines.

cladode and phylloclade

From Beentje:

cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf

phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.

FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.

proposed definition:

cladode: A shoot axis that is flattened and expanded.

comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.

synonyms: phylloclade, cladophyll

Dennis said: A shoot axis that is flattened. expanded is redundant. What about cholla? This does not work. The comment also does not work. Similarily the synonyms are not so much synonyms as they are subsets.

I don't know what the problem is with Cholla. As far as I know, it does not have cladodes or phylloclades, because the axes are round.

Recent interesting paper on cladodes in Asparagus:

Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. The Plant Cell Online, 24, 929 –940.

PMID:22415273

In Asparagus, some cladodes have re-evolved a rounded shape. Are they still cladodes, or just shoot axes again at that point (given that the PO is not based on homology)?

rib

Should also add 'rib' for cacti and other plants.

Definition:

-caryopsis new child of fruit

-adventitious root nodule

other things to fix

• ovary wall should not be a cardinal organ part as ovary is not an organ See Items_for_future_meetings#ovary_and_the_like below.
• pappus element should not be a COP, as a pappus is not an organ- collective organ part structure. Each pappus element is a part of some organ (although there is some debate about which organ it is part of), thus pappus element is a cardinal organ part. The pappus is a collection of pappus elements, and therefor a collective organ part structure. I think the classification is correct.
• egg apparatus- should not be a COP, as it part_of embryo sac which is_a megagametophyte which is_a whole plant This was classified back when we were looser with putting things under COP. Need to propose an alternative classification. Maybe a portion of plant tissue?
• there are a number of parts of fruit such as the fruit septum (PO:0025268), fruit locule, fruit valve that should have dual parentage- e.g. fruit septum is_a septum (is_a col. organ part structure) and should also be is_a cardinal part of a multi-tissue plant structure.

Wood ontology terms

See separate page: Wood Ontology PO and GO Term Development

Open items from older agendas and user requests

root terms

Submitted by Rich Zobel (Nov 2009).

Still need to work on definitions for these terms.

Leaf development stages

Current structure:

This seems pretty good, overall. Need to look into non-vascular leaf development and see if it applies there as well, or if we will need separate terms for vascular and non-vascular leaves.

new parent term

phyllome development stage, proposed def.: A plant organ development stage that has as primary participant a phyllome (PO:0006001).

Comment: Includes stages for the intitiation, expansion, and sensecence of a phyllome such as a leaf, lemma, or stamen.

lemma development stage (PO:0001047), lodicule development stage (PO:0001049), and palea development stage (PO:0001048), currently under flower development stage, should go here, and instead be part_of flower development stage.

Will also need a new term "bract development stage", parent to lemma and palea development stage.

leaf development stage

leaf development stage (PO:0001050), current def.: Stages of development of a leaf defined by characteristic morphological, structural, histological or other visible features.

proposed def.: A phyllome development stage (PO:id) that has as primary participant a leaf (PO:0025034).

Growth forms

From Daniel Hiss: "IMHO plant growth/life forms should be best integrated as an extension to PO. "

Also need acrocarpous and pleurocarpous moss (these could be growth forms).