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Legume terms

submitted by Austin Mast

Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)

See agenda for 7-05-2011.

Remaining:

phyllode

At an earlier meeting, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.

Background:

Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:

"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."

The main reference people cite for phyllodes is: D.R. Kaplan 1980, Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.

Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."

Some more contemporary uses of the term phyllode:

Gardner et al. 2005 (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):

"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles."

and later in the paper:

"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.

"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."

Leroy and Heuret 2007 (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by a type of foliar organ called a phyllode." and "...the different transitional forms range from pinnate leaves to phyllodes..."

See fig. 1 in this paper. They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.

Yang et al. 2008 (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.

Forster and Bonser 2009, Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."

RW did not find any contemporary papers that said that a phyllode is a petiole.

Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.

Unifacial leaf as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311).

Proposed terms and definitions:

vascular leaf

>unifacial leaf

>>terete leaf (round in cross section)

>>ensiform leaf (flat in cross section)

>>>phyllode

unifacial leaf: A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to absence of the opposite surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia, most monocots?). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface.

RW: need to check and add references for all of these

terete leaf: A unifacial leaf that is round in cross section throughout all of part of the length of the leaf. (ref.: xxx)

Comment: The surface of a terete leaf corresponds to either the adaxial or abaxial surface of a normal leaf.

ensiform leaf: A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.(ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)

Comment: Common in many monocots and some dicots. Both surfaces of an ensiform leaf correspond to only one of either the adaxial or abaxial surface of a normal leaf. In some leaves, the petiole may twist, giving the appearance that the lamina is ensiform, but it is not.

RW: Maybe phyllode should just be a narrow synonym of ensiform leaf?

phyllode: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in develop.

Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, phyllode-type transition leaf). Phyllodes are generally xeromorphic.

is_a ensiform leaf, is_a adult leaf

phyllode-type transition leaf: A transitional vascular leaf in which the basal portion of the leaf has unifacial lamina development in a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.

Comment: Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.

is_a transitional leaf, is_a ensiform leaf

bristle

(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)

Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.

We have the term stipule spine. Could also add the term stipule bristle: A stipule that has a brush-like appearance.

A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).

There are two meanings for bristled:

!. Stiff and sharp (e.g., a bristled trichome)

2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)

Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):

1. bristle-like:

This is a combination of two PATO descriptors:

Something describing the shape:

PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.

or

PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.

and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.

and something describing a quality of a substance:

PATO has:

PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)

PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)

A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.

PATO:

quality of a substance (existing)

>flexibility (existing)

>>flexible (existing)

>>inflexible (existing)

>rigidity (new)

>>rigid (new)

>>flacid (new)

2. bristle-bearing: A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.

is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)

Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).

To describe legume stipules, we may also need a term brush-like: A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.

Then if we want to, we could add terms like brush-like stipule (is_a stipule) or bristle-like stipule (is_a stipule) or bristle-bearing stipule, or users could post-compose these terms on their own.

TraitNet requests

podarium

Comment from Traitnet: is synonym to tubercle

Rebman and Pinkava, Florida Entemologist (2001) describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:

"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."

Beentje's definition of podarium: (in cacti or other succulents): a modified leaf base functioning as the photosynthetic organ.

Beentje's definition of tubercle: (in ball- or barrel- shaped cacti), cone-shaped protuberances that are enlarged modified leaf bases fused with adjacent stem tissue (also lists two other definitions for tubercle).

proposed def. podarium or tubercle (based on Rebman and Pankava): A conical shaped collective organ part structure that consists of a swollen leaf base and part of a shoot axis fused together.

Comment: Found in cacti and other succulents. May elongate and swell, as in species of pincushion cacti (Mammillaria spp.). If the raised podaria align vertically around the stem they can coalesce with those directly above and below to form ribs, as in saguaro (Carnegiea).

has_part leaf base

synoyms: tubercle, podaria (plural)

cladode and phylloclade

Suggest we also add these terms for use in cacti.

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 setm or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.

proposed definitions:

cladode: An internode that is flattened and laterally expanded.

comment: Has an increased area for photosyntheses, and may function similar to a leaf in plants that have no leaves or small leaves, such as cacti. A cladode consists of a single internode while a phylloclade consists of several nodes and internodes.

phylloclade: A shoot axis that is flattened and laterally expanded.

comment: Has an increased area for photosyntheses, and may function similar to a leaf in plants that have no leaves or small leaves, such as cacti. A phylloclade consists of several contiguous nodes and internodes while a cladode consists of a single internode.

corm

proposed def: A short, enlarged stem in which the internodes do not elongate.

Comment: May serve as a storage organ. Usually underground.

child of stem (PO:0009047).

pneumatophore

definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves

proposed def: A root that is erect and protrudes above the soil.

Comment: Pneumatophores are found in trees that live in flooded habitats such as mangroves. May provide oxygen to below ground roots growing in flooded soils.

tendril

Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.

tendrils can be (evolutionarily) derived from multiple types of structures. Suggest we make separate terms:

branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.

leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaflet tendril (child of leaflet): A leaflet that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.

leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.

Can add other types of tendrils if they come up or users need them.

This is the way we defined spine (no parent class spine, only leaf spine and stipule spine with is_a relations to leaf and stipule).

Alternative is to create a parent 'tendril'(is_a plant structure) with children that are part_of the other structures:

tendril: A plant structure that is slender and coiling. Comment: Aids plant in climbing.

branch tendril is_a tendril part_of branch

leaf tendril is_a tendril part_of leaf

leaflet tendril is_a leaf tendril part_of leaflet

leaf apex tendril is_a leaf tendril part_of leaf apex

The part_of relations are technically correct (not proper part), but I'm not sure it conveys the proper meaning.

sorus

from Crum (2001): a cluster of fern sporangia

from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.

Proposed definition: A collective plant structure composed of a cluster of two or more adjacent sporagia on the surface of a leaf.

Comment: Found in ferns. May be enclosed by an indusium.

Part_of vascular leaf, has_part sporangium

cone

Synonym of strobilus (PO:0025083) or child?

proposed def: A strobilus that is woody?

diaspore

definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.

We could add this term as a kind of upper level bin term (similar to trichome)

root terms

Submitted by Rich Zobel (Nov 2009).

Still need to work on definitions for these terms.

New children of calyptra perianth

This item is on the agenda for POC_Conf._Call_9-20-11.

User requests still open on Source Forge; PGDSO

coleoptile emergence

This was dealt with at the NYBG Meeting, on Sunday_Sept_11th,_2011

We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed. (rather than above ground)

This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.

At the POC meeting on Sunday_Sept_11th,_2011, we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.

current structure:

Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.

Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.

current and proposed terms and definitions

All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.

Comment: This terms is used only for seed plants.

proposed: shoot emergence from seed coat development stage (new number): A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.

Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.

current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence from growth medium development stage (PO:0007045): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???

Comment: This terms is used only for seed plants.

proposed: coleoptile emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???

Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.

current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence from growth medium development stage (PO:0007049): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

proposed: cotyledon emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.

current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence from growth medium development stage (PO:0007054): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.

proposed: epicotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???

Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.

current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence from growth medium development stage (PO:0007043): A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

proposed: hypocotyl emergence from seed coat development stage (new number): A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.

Could also add terms for feeder emergence for some gymnosperms.

For all of the above terms, need to check existing synonyms and move or copy them as needed.

5 fruit formation; FF.00 fruit size 10%

Initial Comment from MS:

"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view. Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size. For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."

current def'n:FF.00 fruit size 10% (PO:0007032): The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]

Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green

All the other sizes are defined similarly.

proposed def'n.: (based on Mary's suggestion): A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.

Comment: This stage can only be used when the final size of the fruit is known.

At the POC meeting on 9-11-11, we agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.

RW: When does formation of a fruit occur? Should we say fertilization of an ovary instead?

new proposed: FF.00 fruit size up to 10% (PO:0007032): A fruit formation stage that begins with fertilization of an ovary and ends when the fruit has reached 10% of its final size.

Comment: A fruit development stage may begin without fertilization in cases of parthenocarpy, apomixis, or other hormone-induced conditions.

5 fruit formation; FF.00 fruit size 10%

These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 Sunday_Sept_11th,_2011

This item is on the agenda for POC_Conf._Call_9-20-11.

terms for seed trichome development stages

Open since 07-28-2010

Request

The following terms have been requested for cotton fiber development (their structure and defintions):

seed development stages PO: 0001170

---[part_of]Seed hair development stages

---[part_of]seed hair initiation stage: The earliest histological evidence of seed hair initiation, ie, a change in the orientation of cell division in the ovule epidermises occurs at or just before anthesis. (Ruan YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].

---[part_of]seed hair elongation stage: A period of rapid elongation of hair initials without cell division for 16-25 days. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources:PMID: 17905721, PMID: 12671090].

---[part_of] seed hair secondary wall biosynthesis stage: A phase of the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

---[part_of]seed hair maturation stage: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA). (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

Suggested terms and definitions:

Do we want to use stage or phase throughout PGDSO?

seed development stages (PO:0001170)

Current definition: Stages of seed development, from fertilization to the dry or quiescent state. [source: TAIR:ki]

Proposed name and definition: seed development stage: A plant structure development stage that begins with fertilization and ends with seed maturation.

Comment: Only used for seed plants. Some seeds may enter a period of dormancy after seed development is complete.

is_a plant structure development stage; part_of sporophyte phase; subset for gymnosperms and angiosperms; add relation: seed participates_in seed development stage

New terms and proposed definitions:

seed trichome development stage: A plant structure development stage that is part of a seed development stage during which one or more seed trichomes develop.

is_a plant structure development stage; part_of seed development stage; add seed trichome participates_in seed trichome development stage

synonym: seed hair development stage

seed trichome initiation stage: The earliest histological evidence of seed hair initiation, ie, a change in the orientation of cell division in the ovule epidermises occurs at or just before anthesis. (Ruan YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].

synonym: seed hair initiation stage

seed trichome elongation stage: A period of rapid elongation of hair initials without cell division for 16-25 days. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources:PMID: 17905721, PMID: 12671090].

synonym: seed hair elongation stage

seed trichome secondary wall biosynthesis stage: A phase of the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

synonym: seed hair secondary wall biosynthesis stage

seed trichome maturation stage: A period of seed hair maturation from 50 to 60 days post-anthesis (DPA). (Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].

synonym: seed hair maturation stage

tuber growth and development stages

This item has been open on SF since 6/2009

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 PGDSO

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

Conductive cells and tissues for vascular and non-vascular plants

THIS PART IS STILL UNDER CONSTRUCTION

conductive tissue for bryophytes and vascular plants

trace as possible name for category for veins, central strands, and costas

vascular tissue

For vascular plants, we have the class:

portion of vascular tissue (PO:0009015): A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]

Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.

part_of vascular bundle (which is part_of vascular system)

This is okay, but suggest that we make it a child of the new class portion of axial tissue (see below), and also change definition to include xylem or phloem.

Proposed definition: A portion of plant tissue that has as parts tracheary elements or sieve tube members.

Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or may occur as scattered vascular bundles. May include other types of tissue, such as fibers.

part_of vascular system (should add vascular system participates_in sporophytic phase)

currently part_of vascular bundle. Removed this relation, because it is not true for all plants. Also vascular bundle is now a portion of vascular tissue, so it can't be part_of.

children of vascular tissue:

hydathode (PO:0005660) - A structural modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis. [GR:pj, ISBN:0080374913]

Should be is_a cardinal organ part. Do hydathodes ever occur on stems or branches, or are they always part of phyllomes?

proposed definition: A cardinal organ part that releases water through a pore.

Comment: Usually found on leaves. Hydathodes may have one or more pores that appear to be incompletely developed stomata that lack the ability to open and close. Generally, hydathodes are located at the end of a minor vein. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.

leaf vein (PO:0005417) - see more below details below

phloem (PO:0005417): A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]

proposed definition: A portion of vascular tissue that has as parts sieve tube members.

Comment: Functions in the conduction of organic substances in vascular plants.

metaphloem (PO:0006076): Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

proposed definition: A portion of phloem tissue that is the part of a primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.

protophloem (PO:0006077): The first-formed elements of the primary phloem.

proposed definition: A portion of phloem tissue that has as parts the first-formed elements of the primary phloem.

tracheid bar (PO:0019026): A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]

-should be is_a xylem

xylem (PO:0005352): A portion of vascular tissue composed of (that has as parts) xylem elements.

vascular bundle (PO:0005020): A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]

This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.

proposed definition: A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.

Comment: Usually contains both xylem or phloem. May also contain other types of tissue such as plant fibers or vascular cambium. May also contain portions of ground tissue.

part_of vascular system

New children of plant tissue:

hydrome: A portion of axial tissue that has as parts hyrdoids.

Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in water conduction and support, similar to xylem in vascular plants.

Synonyms: hydrom, leptoxylem (Hebant)

leptome: A portion of axial tissue that has as parts leptoids.

Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.

Synonyms: leptom, leptophloem (Hebant)

central strand: A unit strand of axial tissue that has as part hydrome or leptome.

Comment: Often contains both hydrome and leptome. Found in bryophytes located in the center of non-vascular shoot axes such as a gametophore axis or seta, or in the costa of a non-vascular leaf.

synonyms: conducting strand, central cylinder

stereome: A portion of axial tissue that has as parts stereids.

Comment: Found in bryophytes.

From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.

portion of plant fiber: Currently fibers are plant cell types, but they should also be a tissue type.

Proposed definition: A portion axial tissue that has as parts fiber cells.

Comment: Contains elongated, lignified fiber cells that are dead at maturity.

phloem fiber: A portion of plant fiber that has as parts phloem fiber cells.

xylem fiber: A portion of plant fiber that has as parts xylem fiber cells.

leaf vein, midrib, costa

• leaf vein (PO:0020138): A strand of vascular tissue in the leaf blade.

is_a portion of vascular tissue; part_of leaf vascular system

This term only applies to vascular leaves, and should be renamed vascular leaf vein.

proposed definition, vascular leaf vein (PO:0020138): A strand of vascular tissue that is part of a leaf lamina in a vascular leaf.

part_of leaf vascular system, part_of leaf lamina

• Suggest new term primary leaf vein: A vascular leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.

Comment: A leaf may have more than one primary vein. The central primary vein is the midvein.

• midvein (PO:0020139): The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]

Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ". Suggest we rename it vascular leaf midvein to distinguish it from costa.

proposed definition of vascular leaf midvein: A primary leaf vein that is the central vein of a leaf lamina in a vascular leaf.

Comment: Often the most prominent vein of a vascular leaf.

broad synonyms: mid rib, midrib, mid-rib

related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128

• Moss Ontology has requested the term midrib for bryophytes. It is often called a costa.

Proposed definition for costa:' A central strand that is part of a non-vascular leaf.

Comment: Found in bryophytes, especially mosses.

part_of non-vascular leaf

broad synonyms: mid rib, midrib, mid-rib

Refs:

Sperry 2003, IJPS; Hebant 1977;

conductive and related cell types for bryophytes and vascular plants

See also conducting cells for non-vascular plants.

Current parent: axial cell

axial cell (PO:0000081): A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]

Comment: These cells make up the axial system, also known as vertical or longitudinal system.

Existing descendents of axial cell:

sieve tube member (PO:0000289, alt: PO:0000286)

phloem fiber (PO:0004519)

xylem element (PO:0000273)

>tracheary element (PO:0000273)

>>tracheid (PO:0000301)

>>vessel member (PO:0002003)

>xylem fiber (PO:0000274)

>>fiber tracheid (PO:0000355)

>>libriform fiber (PO:0004520)

>>septate fiber (PO:0004521)

The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).

Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system

At the bryophyte term meeting on 4-25-2011 (RW and MAG present), we decided that axial cell was not the correct term to use to describe all of the elongated cells associated with conducting tissue in plants. They are different cell types and have different origins, so they should not all be grouped together.

New proposed hierarchy (children of plant cell):

plant cell

>hydroid

>leptoid

>vascular cell (new term)

>>sieve tube member

>>tracheary element

>>>tracheid

>>>vessel member

>>phloem fiber cell

>>xylem fiber cell

>>other kinds of fiber cells

>ground tissue cell (PO:0025030)

>>stereid

>>collenchyma cell

>>sclerenchyma cell (PO:0000077)

>>>fiber cell (new term)

>>>sclerid (new term)

Proposed definitions:

fiber cell:

vascular cell: