Difference between revisions of "POC Conf. Call 12-13-11"

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(Created page with ''''POC meeting, Webex Conference Call; Date: Tuesday Dec 13th, 2011 10am (PST)''' In attendance: POC members: Absent: Collaborators: none Any changes or corrections (a…')
 
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=PDSO Revisions: Plant structure development stages=
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==Whole plant development stages==
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===[https://sourceforge.net/tracker/?func=detail&aid=3435050&group_id=76834&atid=835555 gametophyte/sporophyte dormant stage]===
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====GO terms====
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GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.
 +
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'''dormancy process (GO:0022611):''' The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity. (They also have a term for seed dormancy.)
 +
 +
'''proposed new definition for dormancy process:'''  A developmental process in which a dormant state is induced, maintained or broken.
 +
 +
Comment: A dormant state is characterized by a suspension of most physiological activity, and, in plants, by a suspension of growth.
 +
 +
 +
'''seed dormancy (GO:0010162):''' The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated.
 +
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'''proposed new definition for seed dormancy:'''  A dormancy process that has as participant a seed.
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comment: Seed dormancy is characterized by a suspension of physiological activity that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.(''work on comment'')
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'''organism dormancy (new term):''' A dormancy process that has as participant a whole organism.
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====PO terms====
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'''sporophyte dormant stage (PO:0007132):''' A sporophyte development stage during which a sporophyte participates in an organism dormancy process (GO:xxxx).
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 +
comment: This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure, although a sporophyte dormant stage involves the formation of dormant buds. These may be above ground (in woody plants), at ground level (in herbaceous plants), or underground (in plants with tubers, bulbs, corms, or perennating rhizomes). Dormancy may be preceded by the senescence of other plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of dormancy is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, even though environmental stimuli may not be necessary for the onset of dormancy.
 +
 +
'''gametophyte dormant stage (PO:0025342):''' A gametophyte development stage during which a gametophyte participates in a dormancy process (GO:0022611).
 +
 +
comment: This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures.  The dormant stage is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, even though environmental stimuli may not be necessary for the onset of dormancy.
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References:
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[http://www.annualreviews.org/doi/abs/10.1146/annurev.pp.15.060164.001153 Vegis; Dormancy in Higher Plants ARPP 1964]
 +
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[http://www.jstor.org/stable/3244383 paper on sporophyte dormancy in a bryophyte]
 +
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Dormancy of gemmae in a liverwort: DOI: 10.1034/j.1600-0706.2001.940314.x. In this case, the gemma is a whole plant.
 +
 +
Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3432979&group_id=76834&atid=835555 gametophyte/sporophyte senescent stage]===
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Work on these terms is ongoing. Will present new definitions and GO proposal for senescence at a future meeting.
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===[https://sourceforge.net/tracker/?func=detail&aid=3439459&group_id=76834&atid=835555 embryo stage] and [https://sourceforge.net/tracker/?func=detail&aid=2982384&group_id=76834&atid=835555 plant embryo]===
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====embryo stage====
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We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed '''embryo stage''' and made is_a sporophyte vegetative stage.
 +
 +
proposed def.:
 +
 +
'''embryo stage (PO:0007631):''' A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.
 +
 +
Comment: The embryo stage generally starts after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.
 +
 +
====plant embryo====
 +
Now that we have a working term for embryo stage, we can define '''plant embryo''' in terms of the stage.
 +
 +
'''existing def. plant embryo (PO:0009009):''' A whole plant in the early part of a sporophytic phase after the first cell division.
 +
 +
'''proposed def. plant embryo (PO:0009009):''' A whole plant that participates in the embryo stage (PO:0025369).
 +
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comment (basically the same as existing comment): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.
 +
 +
-change from participates_in sporophyte development stage to participates_in embryo stage
 +
 +
''We had a discussion a few weeks ago whether is better to define stages in terms of structures in terms of stages. In general, it is better to define stages in terms of structures. This works well for terms like trichome development stage. However, in the case of embryo stage, the structure is really a whole plant that is undergoing certain processes, and the stage is a more fundamental term.''
 +
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===[https://sourceforge.net/tracker/?func=detail&aid=3439450&group_id=76834&atid=835555 zygote stage]===
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We already have a term "A zygotic stage" (PO:0001097), is_a embryo stage. This was renamed '''zygote stage''' and made is_a sporophyte development stage.
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 +
'''proposed def. zygote stage (PO:0001097):'''A sporophyte development stage that occurs during the interval between syngamy and the first cell division.
  
  

Revision as of 15:32, 6 December 2011

POC meeting, Webex Conference Call; Date: Tuesday Dec 13th, 2011 10am (PST)

In attendance:

POC members:

Absent:


Collaborators: none


Any changes or corrections (additions/deletions, etc) needed in the minutes from the POC_Conf._Call_12-6-11?

Back to POC Meetings Minutes


PDSO Revisions: Plant structure development stages

Whole plant development stages

gametophyte/sporophyte dormant stage

GO terms

GO has terms for dormancy process and seed dormancy, but no term for whole organism dormancy.

dormancy process (GO:0022611): The process in which a dormant state is induced, maintained or broken. Dormancy is characterized by a suspension of physiological activity. (They also have a term for seed dormancy.)

proposed new definition for dormancy process: A developmental process in which a dormant state is induced, maintained or broken.

Comment: A dormant state is characterized by a suspension of most physiological activity, and, in plants, by a suspension of growth.


seed dormancy (GO:0010162): The process in which a dormant state is induced, maintained and broken in a seed. Dormancy is characterized by a suspension of physiological activity that can be reactivated.

proposed new definition for seed dormancy: A dormancy process that has as participant a seed.

comment: Seed dormancy is characterized by a suspension of physiological activity that can be reactivated. Often requires special conditions for reactivation such as specific temperature, scarification, or leeching of inhibitors.(work on comment)


organism dormancy (new term): A dormancy process that has as participant a whole organism.

PO terms

sporophyte dormant stage (PO:0007132): A sporophyte development stage during which a sporophyte participates in an organism dormancy process (GO:xxxx).

comment: This term only applies to a whole plant in the sporophyte stage, not to the dormant stage of a seed, bud, or other plant structure, although a sporophyte dormant stage involves the formation of dormant buds. These may be above ground (in woody plants), at ground level (in herbaceous plants), or underground (in plants with tubers, bulbs, corms, or perennating rhizomes). Dormancy may be preceded by the senescence of other plant parts such as leaves in woody plants or most of the shoot system herbaceous perennials. The end of dormancy is marked by resumed growth of buds and/or growth of vascular cambium. The dormant stage is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, even though environmental stimuli may not be necessary for the onset of dormancy.

gametophyte dormant stage (PO:0025342): A gametophyte development stage during which a gametophyte participates in a dormancy process (GO:0022611).

comment: This term only applies to a whole plant in the gametophyte stage, not to the dormant stage of other plant structures. The dormant stage is generally an evolved response to environmental conditions such as seasonality or extreme heat, drought, or cold, even though environmental stimuli may not be necessary for the onset of dormancy.


References:

Vegis; Dormancy in Higher Plants ARPP 1964

paper on sporophyte dormancy in a bryophyte

Dormancy of gemmae in a liverwort: DOI: 10.1034/j.1600-0706.2001.940314.x. In this case, the gemma is a whole plant.

Dessication tolerance in resurrection plants: DOI: 10.1080/07352680591008583. A kind of dormancy?

gametophyte/sporophyte senescent stage

Work on these terms is ongoing. Will present new definitions and GO proposal for senescence at a future meeting.

embryo stage and plant embryo

embryo stage

We already had a term PO:0007631, embryo development stages, is_a seed development stage. This term was renamed embryo stage and made is_a sporophyte vegetative stage.

proposed def.:

embryo stage (PO:0007631): A sporophyte vegetative stage that occurs during the interval between the first cell division and one of the following: germination in seed plants, formation of the first true leaf after the cotyledon(s) in pteridophytes, cessation of division of the apical cell and initiation of development of the sporangium in bryophytes, or the beginning of the formation of organs (roots, shoot axes, or leaves) in cultured plant embryos.

Comment: The embryo stage generally starts after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa.

plant embryo

Now that we have a working term for embryo stage, we can define plant embryo in terms of the stage.

existing def. plant embryo (PO:0009009): A whole plant in the early part of a sporophytic phase after the first cell division.

proposed def. plant embryo (PO:0009009): A whole plant that participates in the embryo stage (PO:0025369).

comment (basically the same as existing comment): An embryo is generally formed after the first division of a zygote, but in the case of adventitious embryos, somatic embryos, other embryos that arise through apogamy, and cultured haploid embryos, it is formed after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. In seed plants, the embryo stage ends with germination. In pteridophytes, the embryo stage ends with the formation of the first true leaf after the cotyledon(s). In bryophytes, the embryo stage ends when the apical cell stops dividing and the sporangium begins to develop. In cultured plant embryos, the embryo stage ends when organs (roots, shoot axes, or leaves) begin to form.

-change from participates_in sporophyte development stage to participates_in embryo stage

We had a discussion a few weeks ago whether is better to define stages in terms of structures in terms of stages. In general, it is better to define stages in terms of structures. This works well for terms like trichome development stage. However, in the case of embryo stage, the structure is really a whole plant that is undergoing certain processes, and the stage is a more fundamental term.

zygote stage

We already have a term "A zygotic stage" (PO:0001097), is_a embryo stage. This was renamed zygote stage and made is_a sporophyte development stage.

proposed def. zygote stage (PO:0001097):A sporophyte development stage that occurs during the interval between syngamy and the first cell division.



Next meeting scheduled for Tuesday, Dec. 20th, 2011 at 10am PST/1pm EST

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