Comments on anatomy and temporal ontologies
Pankaj Jaiswal
pj37 at cornell.edu
Sun May 19 18:51:20 EDT 2002
Based on the discussion in the last conference call and subsequent e mails from
Leszek and Tanya, here are my comments. The new growth stage ontology files are
attached.
Tanya Berardini wrote:
>
> I have summarized specific comments from the TAIR group below. As you will
> see, they are quite extensive yet arise from only a partial review of the
> ontologies. We find that there are many problems that need to be resolved
> before the ontologies can be made public. It would be helpful if we can
> discuss the content issues by email: discussions of definitions, what
> should be term synonyms, the goal of a generic temporal framework that can
> accomodate all plants, etc.
>
> What should our next step be? What are your opinions on going back to
> the basics vs. trying to fix the current ontology?
>
> Tanya
>
Thanks Tanya for going through the files I sent earlier. I will work on the
anatomy files now.
> TEMPORAL FILES:
>
> (1) We should try to not divide these by monocot and dicot but instead,
> like Leonore suggested, by actual stages:
>
> sporophytic(new)
> embryonic
> vegetative
> reproductive
> senesence (new)
> gametophytic(which would overlap with sporophytic reproductive stages,
> e.g. ovule developmental stages)
>
> This will help achieve our goal of using single terms to describe common
> processes.
>
> (2) Duplications and definitions (again): There are DBXrefs for terms
> like germination PO:0007051 but NO text. So there is germination
> PO:0000391 (Arabidopsis- also undefined), PO:0007053 and probably
> more. Can we define germination broadly as including imbibition,
> through radicle emergence and then make sensu terms. We can have a
> generic germination and then stages according to the organism ... but
> they should be developmental stages- NOT processes that are being
> defined.
>
In the attached file I have tried to bring all the growth stages from cereals
Maize, Sorghum, barley, rice and oat, under higher order terms
reproductive stage PO:0007140
vegetaive stages PO:0007139
embryonic stage PO:0007002
I have not placed them under the similar stages defined by arabidopsis, because
I want TAIR to have a look at both the vesions and try to bring in the terms
defined for arabidopsis, by either moving the instances of
reproductive stage PO:0007140
vegetaive stages PO:0007139
embryonic stage PO:0007002
into their version or the vice versa. TAIR has to decide where to place them,
because we in cereals definitely do not recognize most of the growth stages they
have defined. However, there are some similarities, where Arabidopsis calls
"stage 1 flower " is panicle initiation in rice/tassel initiation in Maize.
"stage 2 flower " is panicle differentiation is rice
Some of the ovule development stages defined by Maize may overlap with that of
arabidopsis.
My concers were
Calling a term(s) "stage 1-18 flower" gives a wrong impression to the user. They
are all stages of inflorescence development with the flower as an underlying
entity, where the changes are observed. In a generic way it should be called as
"inflorescence development stage 1-18" and "stage 1-18 flower" can go as
synonym.
definitions for "flower development TAIRPO: 0000004" such as "stages of flower
development in Arabidopsis" should be changed.
DBXref like "principal growth stage-1.0" should be replaced with "Arabidopsis
growth stage-1.0"
Terms like
"12 rosette stage" PO?TAIR:0000415, can be replaced with "12 leaf stage" as a generic one with
"12 rosette stage" and "Arabidopsis growth stage 1.12" as synonyms
followed by definition part from existing term "12 rosette stage"
PO?TAIR:0000415
definition: stage at which the first 12 leaves have reached more than 1mm
length.
replaced by saying
Comment: For arabidopsis: stage at which the first 12 leaves have reached more
than 1mm length.
The reason for asking this is because if we agree to do something like this then
a person from Maize can also use the same term with a comment for maize.
Same has been done for all the similar terms from cereals. The terms like
booting stage
milk stage
dough stage
heading stage
Example:
term: booting stage (sensu Poaceae)
goid: PO:0007148
definition: This stage is characterized by a swelling of the flag leaf sheath,
caused by an increase in the size of the panicle/tassel as it grows up the leaf
sheath.
definition_reference: GR:pj37
definition_reference: web:http
//www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
comment: For Barley, Wheat and Oat: Zadok scale-40.
For Sorghum, leaf collars of all leaves are now visible. Sorghum head is
enclosed in the flag leaf sheath. Peduncle (stalk supporting the head) is
beginning to elongate
(I have not included DBXref from MaizeDB, since Leszek needs to work on this)
With the comments from respective crops which may suggest how they identify the
stage or when does this stage appears in teh particular crop. Mean how many days
after pollination, or after days to heading. There is no difference in
definition of these stages with one exception of when this stage appears in
different crops/plants, and if there are any other underlying events, then they
all go as commets from that crop/plant.
conflicts with
reproductive stage PO:0007140
Stages from inflorescence initiation or formation of inflorescence primordia to
flowering (GR:pj37).
Comment: A greater part of vegetative stage in Poaceae overlap the reprdutive
stage.
Everyone knows that the stage should be defined by the time reproduction is
occurring which includes the development of gametes. In case of the Poaceae
family members, this stage of development starts almost at the same time stem
elongation stage begins (this is about the same time when 5th leaf has emerged).
So its not only temporal but also spatial.
Vs
reproductive: TAIR/PO: 0000306
stages of development that between flowering and death of the plant. (TAIR:lr)
In most of the cereal crops, the plant does not die. Its harvested for forage
(on e may call it an unnatural death). However in some of maize and rice
varieties (atleast I know about these two), there is a new growth cycle
"ratooning stage PO:0007145", which "Produces new tillers from nodes after
harvest". There is no question of plant dyeing. There are stay green varieties
of sorghum which does not follow the pattern of undergoing natural death.
I am afraid of using the word death in the definition "stages of development
that occur between flowering and death of the plant. (TAIR:lr)". since the plant
may be perennial (ratooning variety of rice/maize or the tree species)
I would rather say "Stages from inflorescence initiation or formation of
inflorescence primordia or flower initial (in cases of plants having solitary
flower) to flowering. Includes fertilization (GR:pj37)". and in the comments I
will say
"The mid vegetative and vegetative lag phase may overalp with the reproductive
stage".
I believe, we need to redefine the definitions for
"vegetaive stages"PO/TAIR:0000305 and PO:0007139 (chose either)
"stages of development that occur from seed germination up to flowering" from
PO/TAIR:0000305
or
"Stages from germination to inflorescence initiation or formation of flower
initial in plants with solitary flowers (without inflorescence)." from
PO:0007139
with comments saying "The mid vegetative and vegetative lag phase may overalp
with the reproductive stage".
Conflict with the term germination.
Although its the same process but the type of gerination differ, epigeal Vs
hypogeal. I have not said anything about in the present file. However a person
can understand from looking at the terms
hypocotyl and cotyledon emergence PO?TAIR:0000396
and
coleoptile emergence from seed (sensu Poaceae) PO:0007006
Do we need to mention about the germination types?
Leszek, Could you please look at the following and try to fix it.
linear grain-filling (sensu Zea) PO:0007029. and its instances
blister stage PO:0007030 its instances
coleoptilar stage PO:0007031
embryo-1 PO:0007032
early dough stage (sensu Zea)PO:0007034
late dough stage (sensu Zea)PO:0007035
milk stage (sensu Zea)PO:0007033
I believe, except
linear grain-filling (sensu Zea) PO:0007029. and its instance
blister stage PO:0007030
rest all can go in as general for sensu Poaceae.
I already have similar terms
dough stage (sensu Poaceae)PO:0007042
hard dough stage PO:0007154
soft dough stage PO:0007152
milk stage (sensu Poaceae)PO:0007046
I hope now TAIR will work on this file to organize rest of the part. I am
freezing the work on this file from my side. I have not touched the TAIR part
since its them who will have to work on it. Please make the necessary
corrections or updates.
Another thing, I am not willing to accept this ontology as a "plant temporal
ontology", because its not based on time frames. There is an element of spatial
variation in it because of overlapping vegetative and reproductive stages. The
best is to call it a "plant growth stage ontology" PO:0007040
I might be wrong in interpreting some of the concepts, so please correct me.
Pankaj
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!autogenerated-by: DAG-Edit version 1.306-beta-1
!saved-by: pj37
!date: Sun May 19 18:10:46 EDT 2002
!version: $Revision: 1.3 $
!Editors: Pankaj Jaiswal (Gramene), Leonore Reiser, Jonathan Clarke (TAIR)
!Disclaimer: Copyright 2002 Plant Ontology Consortium
!Title: Plant Anatomy and Temporal Ontology
!This is a draft version and should not be implemented in the database
$plant ontology ; PO:0080001
%plant growth stage ontology ; PO:0007040
%developmental stages of arabidopsis ; PO:0007138
%embryonic ; PO:0000374
%curled cotyledon stage ; PO:0000320
%dermatogen stage ; PO:0000369 ; synonym:early globular stage ; synonym:sixteen cell stage
%eight-celled stage ; PO:0000180 ; synonym:octant stage embryo
%heart stage ; PO:0000186
%late globular stage ; PO:0000185 ; synonym:64-cell embryo
%mature ; PO:0000368
%mid-globular stage ; PO:0000184 ; synonym:16-cell embryo
%torpedo stage ; PO:0000187
%two-celled stage ; PO:0000177
%zygote ; PO:0000423 ; synonym:one cell stage
%reproductive ; PO:0000306
%first open flower ; PO:0000421 ; synonym:principal growth stage 6.00
%flower development ; PO:0000004
%stage 1 flower ; PO:0000375
%stage 10 flower ; PO:0000384
%stage 11 flower ; PO:0000385
%stage 12 flower ; PO:0000386
%stage 13 flower ; PO:0000388 ; synonym:anthesis
%stage 14 flower ; PO:0000389 ; synonym:Zero hours after flowering ; synonym:zero hours HAF
%stage 15 flower ; PO:0000390
%stage 16 flower ; PO:0000391
%stage 17 flower ; PO:0000392
%stage 18 flower ; PO:0000422
%stage 2 flower ; PO:0000376
%stage 3 flower ; PO:0000377
%stage 4 flower ; PO:0000378
%stage 5 flower ; PO:0000379
%stage 6 flower ; PO:0000380
%stage 7 flower ; PO:0000381
%stage 8 flower ; PO:0000382
%stage 9 flower ; PO:0000383
%ovule development ; PO:0000005
%ovule stage 1-I ; PO:0000006
%ovule stage 1-II ; PO:0000007
%ovule stage 2-I ; PO:0000008
%ovule stage 2-II ; PO:0000009
%ovule stage 2-III ; PO:0000010
%ovule stage 2-IV ; PO:0000011
%ovule stage 2-V ; PO:0000012
%ovule stage 3-I ; PO:0000013
%ovule stage 3-II ; PO:0000014
%ovule stage 3-III ; PO:0000015
%ovule stage 3-IV ; PO:0000016
%ovule stage 3-V ; PO:0000017
%ovule stage 3-VI ; PO:0000018
%visible flower buds ; PO:0000420 ; synonym:principal growth stage 5.10
%vegetative ; PO:0000305
%10 rosette leaf ; PO:0000413 ; synonym:principal growth stage 1.10
%11 rosette leaf ; PO:0000414 ; synonym:principal growth stage 1.11
%12 rosette stage ; PO:0000415 ; synonym:principal growth stage 1.12
%13 rosette leaf ; PO:0000416 ; synonym:principal growth stage 1.13
%14 rosette leaf ; PO:0000417 ; synonym:principal growth stage 1.14
%2 rosette leaf ; PO:0000398 ; synonym:principal growth stage 1.02
%3 rosette leaf ; PO:0000407 ; synonym:principal growth stage 1.03
%4 rosette leaf ; PO:0000399 ; synonym:principal growth stage 1.04
%5 rosette leaf ; PO:0000408 ; synonym:principal growth stage 1.05
%6 rosette leaf ; PO:0000409 ; synonym:principal growth stage 1.06
%7 rosette leaf ; PO:0000410 ; synonym:principal growth stage 1.07
%8 rosette leaf ; PO:0000411 ; synonym:principal growth stage 1.08
%9 rosette leaf ; PO:0000412 ; synonym:principal growth stage 1.09
%complete rosette ; PO:0000418 ; synonym:principal growth stage 3.90
%cotyledons fully open ; PO:0000397 ; synonym:principal growth stage 1.0
%germination ; PO:0000393 ; synonym:principal growth stage 0
%hypocotyl and cotyledon emergence ; PO:0000396 ; synonym:principal growth stage 0.7
%radicle emergence ; PO:0000395 ; synonym:principal growth stage 0.7
%imbibition ; PO:0000394 ; synonym:principal growth stage 0.10
%post-germination ; PO:0000267
%embryonic stage ; PO:0007002
%dough stage (sensu Poaceae) ; PO:0007042 ; synonym:rice growth stage-8
%early dough stage (sensu Zea) ; PO:0007034 ; synonym:R4 ; synonym:dough stage ; synonym:embryo stage 3 ; synonym:embryo-3 ; synonym:maize growth stage-7.3 % linear grain-filling (sensu Zea) ; PO:0007029
%hard dough stage ; PO:0007154 ; synonym:late dough ; synonym:late dough grain ; synonym:late dough stage ; synonym:rice growth stage-8.2 ; synonym:sorghum growth stage-10
%late dough stage (sensu Zea) ; PO:0007035 ; synonym:embryo stage 4 ; synonym:embryo-4 ; synonym:maize growth stage-7.4 % linear grain-filling (sensu Zea) ; PO:0007029
%soft dough stage ; PO:0007152 ; synonym:early dough ; synonym:early dough grain ; synonym:early dough stage ; synonym:embryo stage 3 (sensu Zea) ; synonym:embryo-3 ; synonym:rice growth stage-8.1 ; synonym:sorghum growth stage-9
%leveling off of grain-filling (sensu Zea) ; PO:0007036 ; synonym:R5 ; synonym:attenuative ; synonym:dent stage ; synonym:embryo stage 5 ; synonym:embryo-5 ; synonym:levling off of dry matter accumulation ; synonym:maize growth stage-8
%linear grain-filling (sensu Zea) ; PO:0007029 ; synonym:effective filling period ; synonym:grain filling ; synonym:maize growth stage-7
%blister stage ; PO:0007030 ; synonym:R2 ; synonym:maize growth stage-7.1
%coleoptilar stage ; PO:0007031 ; synonym:embryo coleoptilar stage ; synonym:maize growth stage-7.1.1
%embryo-1 ; PO:0007032 ; synonym:embryo stage 1 ; synonym:maize growth stage-7.1.2
%early dough stage (sensu Zea) ; PO:0007034 ; synonym:R4 ; synonym:dough stage ; synonym:embryo stage 3 ; synonym:embryo-3 ; synonym:maize growth stage-7.3 % dough stage (sensu Poaceae) ; PO:0007042
%late dough stage (sensu Zea) ; PO:0007035 ; synonym:embryo stage 4 ; synonym:embryo-4 ; synonym:maize growth stage-7.4 % dough stage (sensu Poaceae) ; PO:0007042
%milk stage (sensu Zea) ; PO:0007033 ; synonym:R3 ; synonym:embryo stage 2 ; synonym:embryo-2 ; synonym:maize growth stage-7.2 % milk stage (sensu Poaceae) ; PO:0007046
%milk stage (sensu Poaceae) ; PO:0007046 ; synonym:milk development ; synonym:milk grain ; synonym:rice growth stage-7
%early milk ; PO:0007107
%kernel watery ripe ; PO:0007106
%late milk ; PO:0007109
%medium milk ; PO:0007108
%milk stage (sensu Zea) ; PO:0007033 ; synonym:R3 ; synonym:embryo stage 2 ; synonym:embryo-2 ; synonym:maize growth stage-7.2 % linear grain-filling (sensu Zea) ; PO:0007029
%post-flowering (sensu Zea) ; PO:0007025 ; synonym:R1 ; synonym:lag phase ; synonym:maize growth stage-6 ; synonym:proembryo
%dilatory ; PO:0007026 ; synonym:free nuclear ; synonym:maize growth stage-6.1
%exponential ; PO:0007027 ; synonym:maize growth stage-6.2
%transition stage ; PO:0007028 ; synonym:endoreduplication ; synonym:maize growth stage-6.2.1
%ripening stage (sensu Poaceae) ; PO:0007114 ; synonym:maize growth stage-9 ; synonym:maturity stage ; synonym:senescence
%kernel hard ; PO:0007116
%kernel loosening in daytime ; PO:0007117
%kernel medium hard ; PO:0007115
%mature grain ; PO:0007045 ; synonym:black layer ; synonym:dry kernel ; synonym:dry seed ; synonym:maize growth stage-9.2 ; synonym:physiological maturity ; synonym:rice growth stage-9 ; synonym:sorghum growth stage-11 ; synonym:storage maturity
%physiological maturity stage (sensu Sorghum) ; PO:0007135 ; synonym:black layer ; synonym:sorghum growth stage-11
%physiological maturity stage (sensu Zea) ; PO:0007038 ; synonym:R6 ; synonym:black layer ; synonym:embryo stage 6 ; synonym:embryo-6 ; synonym:maize growth stage-9.1
%secondary dormancy induced ; PO:0007122
%secondary dormancy lost ; PO:0007123
%seed dormant ; PO:0007119
%seed not dormant ; PO:0007121
%viable seed germination ; PO:0007120
%reproductive stage ; PO:0007140
%booting stage (sensu Poaceae) ; PO:0007148 ; synonym:rice growth stage-5 ; synonym:sorghum growth stage-6
%early booting stage ; PO:0007149 ; synonym:rice growth stage-5.1
%boots just swollen ; PO:0007092
%flag leaf sheath extending ; PO:0007091
%late booting stage ; PO:0007150 ; synonym:rice growth stage-5.2
%first awns visible ; PO:0007094
%flag leaf sheath opening ; PO:0007093
%flag leaf visible (sensu Sorghum) ; PO:0007129 ; synonym:sorghum growth stage-5
%ear initiation (sensu Zea) ; PO:0007013 ; synonym:6 leaf ; synonym:6-8 leaf ; synonym:7 leaf ; synonym:8 leaf ; synonym:V6 ; synonym:V7 ; synonym:V8 ; synonym:maize growth stage-3.1 ; synonym:mid-whorl stage
%flowering stage ; PO:0007151 ; synonym:anthesis ; synonym:anthesis stage ; synonym:rice growth stage-6.1 ; synonym:sorghum growth stage-8
%anthesis ; PO:0007021 ; synonym:VT ; synonym:maize growth stage-5.1
%fertilization ; PO:0007024 ; synonym:double fecundation ; synonym:double fertilization ; synonym:fecundation ; synonym:maize growth stage-5.4
%pollination ; PO:0007023 ; synonym:Pollen shed ; synonym:Pollen shedding ; synonym:maize growth stage-5.3
%silking (sensu Zea) ; PO:0007022 ; synonym:R1 ; synonym:maize growth stage-5.2 ; synonym:silk emergence
%gametophyte development ; PO:0007017 ; synonym:gametogenesis ; synonym:maize growth stage-4
%embryo sac development ; PO:0007019 ; synonym:female gametophyte development ; synonym:maize growth stage-4.2 ; synonym:megagametogenesis ; synonym:megaspore development ; synonym:megasporogenesis
%pollen development ; PO:0007018 ; synonym:maize growth stage-4.1 ; synonym:male gametophyte development ; synonym:microspore development ; synonym:microsporogenesis % mid-vegetative stage (sensu Zea) ; PO:0007015
%heading stage (sensu Poaceae) ; PO:0007044 ; synonym:inflorescence emergence ; synonym:rice growth stage-6
%early heading stage ; PO:0007050 ; synonym:rice growth stage-6.1
%first spikelet emergence (sensu Triticum) ; PO:0007096
%late heading stage ; PO:0007090 ; synonym:rice growth stage-6.3
%complete inflorescence emrgence ; PO:0007100
%mid heading stage ; PO:0007105 ; synonym:half-bloom ; synonym:heading date ; synonym:rice growth stage-6 ; synonym:rice growth stage-6.2 ; synonym:sorghum growth stage-7
%panicle differentiation stage (sensu Oryza) ; PO:0007041 ; synonym:PD ; synonym:rice growth stage-4.2
%panicle initiation stage (sensu Oryza) ; PO:0007147 ; synonym:PI ; synonym:green ring stage ; synonym:rice growth stage-4.1
%tassel initiation stage (sensu Zea) ; PO:0007011 ; synonym:4-6 leaf stage ; synonym:early whorl stage ; synonym:maize growth stage-2 ; synonym:tassel differentiation
%vegetative stage ; PO:0007139
%germination stage ; PO:0007043 ; synonym:maize growth stage-0 ; synonym:rice growth stage-1
%coleoptile emergence from seed (sensu Poaceae) ; PO:0007006 ; synonym:maize growth stage-0.3 ; synonym:seedling emergence ; synonym:sorghum growth stage-0
%imbibition ; PO:0007004 ; synonym:maize growth stage-0.1
%radicle emergence from seed ; PO:0007005 ; synonym:maize growth stage-0.2
%mid-vegetative stage (sensu Zea) ; PO:0007015 ; synonym:V12 ; synonym:V13 ; synonym:V14 ; synonym:maize growth stage-3.3
%pollen development ; PO:0007018 ; synonym:maize growth stage-4.1 ; synonym:male gametophyte development ; synonym:microspore development ; synonym:microsporogenesis % gametophyte development ; PO:0007017
%ratooning stage (sensu Poaceae) ; PO:0007145 ; synonym:rice growth stage-3A
%seedling stage ; PO:0007047 ; synonym:maize growth stage-1 ; synonym:pre-tillering ; synonym:rice growth stage-2 ; synonym:seedling growth
%1-2 leaf stage ; PO:0007111 ; synonym:maize growth stage-1.2 ; synonym:rice growth stage-2.1
%3 leaf stage ; PO:0007126 ; synonym:maize growth stage-1.3 ; synonym:rice growth stage-2.2 ; synonym:sorghum growth stage-1
%4 leaf stage ; PO:0007143 ; synonym:maize growth stage-1.3 ; synonym:rice growth stage-2.3 ; synonym:sorghum growth stage-2
%5 leaf stage ; PO:0007127 ; synonym:rice growth stage-2.4 ; synonym:sorghum growth stage-3
%seedling emergence ; PO:0007008 ; synonym:maize growth stage-1.1
%stem elongation stage (sensu Poaceae) ; PO:0007048 ; synonym:internode elongation ; synonym:jointing stage ; synonym:maize growth stage-3 ; synonym:mid-whorl stage ; synonym:rapid stem elongation ; synonym:rice growth stage-4 ; synonym:telescoping
%growing point differentiation stage (sensu Sorghum) ; PO:0007128 ; synonym:sorghum growth stage-4
%late whorl stage (sensu Zea) ; PO:0007014 ; synonym:1-11 leaf ; synonym:10-leaf ; synonym:11-leaf ; synonym:9-leaf ; synonym:V-11 ; synonym:V10 ; synonym:V9 ; synonym:maize growth stage-3.2
%tillering stage (sensu Poaceae) ; PO:0007049 ; synonym:rice growth stage-3
%maximum tillering ; PO:0007144 ; synonym:rice growth stage-3.1
%vegetative lag stage (sensu Poaceae) ; PO:0007146 ; synonym:rice growth stage-4.3 ; synonym:vegetative lag phase
%vegetative lag stage (sensu Zea) ; PO:0007016 ; synonym:V15 ; synonym:V16 ; synonym:V17 ; synonym:V18 ; synonym:V19 ; synonym:V20 ; synonym:late vegetative ; synonym:maize growth stage-3.4
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!version: $Revision: 1.3 $
!date: Sun May 19 16:48:11 EDT 2002
!saved-by: pj37
!autogenerated-by: DAG-Edit version 1.306-beta-1
!
!Gene Ontology definitions
!
term: 1-2 leaf stage
goid: PO:0007111
definition: The emergence of first (embryonic) and second leaf. First or second leaf collar visible.
definition_reference: GR:pj37
definition_reference: MaizeDB:67353
comment: Starts with the emergence of coleoptile in grasses until the second leaf emerges. #For Barley, Wheat and Oat: Zadok scale-11 to 12; Haun scale-1.+
term: 10 rosette leaf
goid: PO:0000413
definition: stage at which the first 10 leaves have reached more than 1mm length.
definition_reference: PMID:11449047
term: 11 rosette leaf
goid: PO:0000414
definition: stage at which the first 11 leaves have reached more than 1 mm length.
definition_reference: PMID:11449047
term: 12 rosette stage
goid: PO:0000415
definition: stage at which the first 12 leaves have reached more than 1mm length.
definition_reference: PMID:11449047
term: 13 rosette leaf
goid: PO:0000416
definition: stage at which the first 13 leaves have reached more than 1mm length.
definition_reference: PMID:11449047
term: 14 rosette leaf
goid: PO:0000417
definition: stage at which the first 14 leaves have reached more than 1mm length.
definition_reference: PMID:11449047
term: 2 rosette leaf
goid: PO:0000398
definition: stage at which the first two rosette leaves have reached more than 1 mm in length.
definition_reference: PMID:11449047
term: 3 leaf stage
goid: PO:0007126
definition: Collar of 3rd leaf is visible
definition_reference: GR:pj37
definition_reference: web:http //primera.tamu.edu/ir4/sor-stage.pdf
definition_reference: MaizeDB:25331
comment: In sorghum, this stage will occur approximately 10 days after emergence, depending on soil temperature, moisture, planting depth, etc.#For Barley, Wheat and Oat: Zadok scale-13; Haun scale-2.+
term: 3 rosette leaf
goid: PO:0000407
definition: stage at which the first 3 rosette leaves have reached more than 1 mm in length.
definition_reference: PMID:11449047
term: 4 leaf stage
goid: PO:0007143
definition: Collar of 4th leaf is visible.
definition_reference: web:http //primera.tamu.edu/ir4/sor-stage.pdf
definition_reference: GR:pj37
definition_reference: MaizeDB:25331
comment: In sorghum, occurs approximately 15 days after emergence. #For Barley, Wheat and Oat: Zadok scale-14; Haun scale-3.+
term: 4 rosette leaf
goid: PO:0000399
definition: stage at which the first 4 rosette leaves have reached more than 1mm in length.
definition_reference: PMID:11449047
term: 5 leaf stage
goid: PO:0007127
definition: Collar of 5th leaf is visible
definition_reference: GR:pj37
definition_reference: web:http //primera.tamu.edu/ir4/sor-stage.pdf
comment: In sorghum, occurs approximately 20 days after emergence. May have lost 1st leaf (coleoptile) by this time.#For Barley, Wheat and Oat: Zadok scale-15; Haun scale-4.+
term: 5 rosette leaf
goid: PO:0000408
definition: stage at which the first 5 leaves have reached more than 1 mm length.
definition_reference: PMID:11449047
term: 6 rosette leaf
goid: PO:0000409
definition: stage at which the first 6 leaves have reached more than 1 mm in length.
definition_reference: PMID:11449047
term: 7 rosette leaf
goid: PO:0000410
definition: stage at which the first 7 leaves have reached more than 1 mm length.
definition_reference: PMID:11449047
term: 8 rosette leaf
goid: PO:0000411
definition: stage at which the first 8 leaves have reached more than 1 mm length.
definition_reference: PMID:11449047
term: 9 rosette leaf
goid: PO:0000412
definition: stage at which the first 9 leaves have reached more than 1 mm length.
definition_reference: PMID:11449047
term: anthesis
goid: PO:0007021
definition: Opening of the flower or bloom
definition_reference: GR:pj37
definition_reference: MaizeDB:67361
comment: For Barley, Wheat and Oat: Zadok scale-60 to 69; Feekes scale-10.51; Haun scale-11.4 to 11.6
term: blister stage
goid: PO:0007030
definition: This stage is initiated when significant starch accumulation begins, approximately 12-17 days after pollination (dap). Kernels appear white and translucent; endosperm and its inner fluid are clear. Endoreduplication, an increase in DNA content in endosperm cells, which began in the transition stage, peaks about 16-18 dap
definition_reference: GR:pj37
definition_reference: MaizeDB:67372
comment: (dap) is days after pollination
term: booting stage (sensu Poaceae)
goid: PO:0007148
definition: This stage is characterized by a swelling of the flag leaf sheath, caused by an increase in the size of the panicle/tassel as it grows up the leaf sheath.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
comment: For Barley, Wheat and Oat: Zadok scale-40# For Sorghum, feaf collars of all leaves are now visible. Sorghum head is enclosed in the flag leaf sheath. Peduncle (stalk supporting the head) is beginning to elongate
term: boots just swollen
goid: PO:0007092
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: Zadok scale-45; Feekes scale-10; Haun scale-9.2
term: coleoptilar stage
goid: PO:0007031
definition: In the coleoptilar stage, the embryo develops a prominent shoot apical meristem surrounded by the coleoptilar ring, and backed by the flattened, spade-shaped scutellum; it occurs about 12-14 days after pollination
definition_reference: GR:pj37
definition_reference: MaizeDB:67376
term: coleoptile emergence from seed (sensu Poaceae)
goid: PO:0007006
definition: The coleoptile, enclosing the plumule or embryonic shoot, pushes through the pericarp
definition_reference: GR:pj37
definition_reference: MaizeDB:67352
comment: For Barley, Wheat and Oat: Zadok scale-7
term: complete inflorescence emrgence
goid: PO:0007100
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: Zadok scale-59; Feekes scale-10.5; Haun scale-11
term: complete rosette
goid: PO:0000418
definition: stage at whichleaf growth has ceased and the rosette no longer increases in size.
definition_reference: PMID:11449047
term: curled cotyledon stage
goid: PO:0000320
definition: The stage at which the cotyledons curvedown towards the suspensor. At this time protein deposition in the cotyledons begins.
definition_reference: ISBN:0387940898
term: dermatogen stage
goid: PO:0000369
definition: The stage at which the embryo has undergone three mitotic divisions and contains sixteen cells. The outer protodermal cells will give rise to the epidermis through a series of anticlinal divisions. Development of the suspensor is complete at this stage.
definition_reference: ISBN:0387094898
term: dilatory
goid: PO:0007026
definition: This phase is the initial few days following fertilization, during which time very slow dry matter accumulation occurs in the kernel. In the endosperm, the primary endosperm nucleus divides 2-4 hours after fertilization, followed by rapid synchronous divisions to produce a free nuclear tissue. The fertilized egg undergoes its first division about 10-12 hours after fertilization, and by the end of this stage will have developed into the proembryo with about 12-24 cells
definition_reference: GR:pj37
definition_reference: MaizeDB:67371
term: dough stage (sensu Poaceae)
goid: PO:0007042
definition: One of the ripening stage when endosperm starts hardening.
definition_reference: GR:pj37
term: ear initiation (sensu Zea)
goid: PO:0007013
definition: Elongation of apical dome of axillary meristem corresponding to top ear, followed by appearance of spikelet primordia.
definition_reference: GR:pj37
definition_reference: MaizeDB:67356
comment: Typically, in adapted materials in the US Corn Belt, 6-8 leaf collars are visible, but this depends on genotype and environmental conditions.
term: early booting stage
goid: PO:0007149
definition: In this stage meiosis occurs. Panicle/tassel/spike continues to grow
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
definition_reference: GR:pj37
term: early dough stage (sensu Zea)
goid: PO:0007034
definition: Endosperm fluid has changed to a pasty or soft dough-like consistency; kernels have about 70% moisture; occurs about 22-28 days after pollination. Embryo is at stage 3: third leaf primordium forms; radicle is recognizable within the coleorhiza; embryo is about 3 mm long
definition_reference: GR:pj37
definition_reference: MaizeDB:67374
term: early heading stage
goid: PO:0007050
definition: About 25 percent of inflorescence emegred in grasses
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-1; Feekes scale-10.3; Haun scale-10.5
term: early milk
goid: PO:0007107
definition:
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: Zadok scale-73; Haun scale-13
term: eight-celled stage
goid: PO:0000180
definition: An embryo comprised of eight cell. The mitotic divisions leading to this stage do not cause a significant increase in size.
definition_reference: ISBN:0387094898
term: embryo sac development
goid: PO:0007019
definition: Includes megasporogenesis (female meiosis) and megagametogenesis (beginning with mitotic division of the meiotic products through maturation of the embryo sac)
definition_reference: GR:pj37
definition_reference: MaizeDB:67384
term: embryo-1
goid: PO:0007032
definition: Embryo stage 1 is defined by the appearance of first leaf primordium from the shoot apical meristem; it occurs about 14-18 days after pollination, when embryo is slightly more than 1 mm long
definition_reference: GR:pj37
definition_reference: MaizeDB:67377
comment: Stage 1 embryos are often used to initiate embryonic callus in tissue culture experiments
term: embryonic
goid: PO:0000374
definition: Stages of development that occur after fertilization and before germination.
definition_reference: TAIR:lr
comment: In cereal crops light intensity is very important during this interval since 60 percent or more of the carbohydrates used in grain filling are photosynthesized during this time interval. High temperatures tend to reduce the grain filling period and may reduce grain weight. Low temperatures tend to lengthen the time required for grain fill and ripening.
term: embryonic stage
goid: PO:0007002
definition: Growth stages from fertilization, embryo formation to ripening and maturation
definition_reference: GR:pj37
term: exponential
goid: PO:0007027
definition: The phase with increased metabolic activity and rapid kernel development that links the dilatory phase with the linear grain-filling period. It occurs approximately 5-12 days after pollination (dap). In the endosperm, cell walls are laid down beginning about 5 dap, changing the free nuclear tissue into a cellular one. The embryo continues in the proembryo stage through about 10 dap. Maizedb includes a substage
definition_reference: GR:pj37
definition_reference: MaizeDB:67369
term: fertilization
goid: PO:0007024
definition: Fusion of one sperm cell with the egg to form the diploid zygote
definition_reference: GR:pj37
definition_reference: MAizeDB:67365
comment: In Maize it occurs 16-24 hours after pollination. It consists of the simultaneous fusion of 1 sperm cell with the egg to form the diploid zygote, and the other sperm cell with 2 polar nuclei to form the triploid primary endosperm nucleus.
term: first awns visible
goid: PO:0007094
definition: The first aws become visible.
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-49; Haun scale-10.1
term: first open flower
goid: PO:0000421
definition: whole plant stage at which the first flower has reached stage 13 (fully open, pollen dehiscence).
definition_reference: PMID:11449047
term: first spikelet emergence (sensu Triticum)
goid: PO:0007096
definition: When the first spikelet is visible
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-50; Feekes scale-10.1; Haun scale-10.2
term: flag leaf sheath extending
goid: PO:0007091
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: Zadok scale-41; Haun scale-8 to 9
term: flag leaf sheath opening
goid: PO:0007093
definition: The flag leaf has completely extended
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-47
term: flag leaf visible (sensu Sorghum)
goid: PO:0007129
definition: Tip of the flag leaf (last leaf) is visible in the whorl.
definition_reference: GR:pj37
definition_reference: web:http //primera.tamu.edu/ir4/sor-stage.pdf
comment: The last 3 to 4 leaves may not be fully expanded (collars not visible).
term: flower development
goid: PO:0000004
definition: stages of flower development in Arabidopsis
definition_reference: ISBN:0387940898
term: flowering stage
goid: PO:0007151
definition: Occurs when 50% of the plants in the field are in some stage of bloom
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
comment: The events occurring in this stage are: (a). The tips of the lemma and palea (hulls) open. #(b) The filaments elongate.# (c). The anthers exsert from the lemma and palea. #(d). As the lemma and palea open further, the tips of the feathery stigma become visible. #(e). The filaments elongate past the tips of lemma and palea. #(f). The spikelet closes, leaving the anther outside. Anther dehiscence (pollen shed) usually occurs just prior to or at the time the lemma and palea open (step a).
term: gametophyte development
goid: PO:0007017
definition: Includes both male (pollen) and female (embryo sac) gametophyte development, which are substages of this stage
definition_reference: GR:pj37
definition_reference: MAizeDB:67385
term: germination stage
goid: PO:0007043
definition: Stages from imbibition to coleoptile or hypocotyl and cotyledon emergence
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Vegetative.asp
definition_reference: MaizeDB:64055
comment: For rice under dry-seeded or aerobic conditions, the radicle emerges before the coleoptile, whereas, under water-seeded or reduced oxygen (anaerobic) conditions, the coleoptile may emerge before the root. #For Barley, Wheat and Oat: Zadok scale-0 to 9
term: growing point differentiation stage (sensu Sorghum)
goid: PO:0007128
definition: Growing point visible above the soil surface.
definition_reference: web:http //primera.tamu.edu/ir4/sor-stage.pdf
definition_reference: GR:pj37
comment: Occurs approximately 30 to 35 days after emergence. Generally corresponds with the 7 to 8 leaf stage. May have lost 1 to 3 leaves from the bottom of the plant.
term: hard dough stage
goid: PO:0007154
definition: The whole grain is firm during this stage and almost ready for harvest. The moisture content is still above 22 percent.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Ripening.asp
comment: For Barley, Wheat and Oat: Zadok scale-87; Haun scale-15#For Sorghum three-fourths of grain dry weight has accumulated
term: heading stage (sensu Poaceae)
goid: PO:0007044
definition: is the time when the panicle begins to exsert from the boot.
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
definition_reference: GR:pj37
comment: In rice, heading may take over 10 to 14 days due to variations within tillers on the same plant and between plants in the field. #Agronomically, ?heading date? is defined as the time when 50 percent of the panicles/spikelets/tassel have at least partially exserted from the boot.
term: heart stage
goid: PO:0000186
definition: Embryonic stage at which the cotyledon primordia have enlarged enough to form two mounds on either side of the apical meristem.
definition_reference: ISBN:03870940898
definition_reference: TAIR:lr
term: imbibition
goid: PO:0007004
definition: Adsorption of water by colloidal materials of the seed, leading to seed swelling and increased metabolic activity in the initial stages of germination.
definition_reference: GR:pj37
definition_reference: MaizeDB:64054
comment: For Barley, Wheat and Oat: Zadok scale-1 to 3
term: kernel hard
goid: PO:0007116
definition: Kernel no longer dented with thumbnail.
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-92; Feekes scale-11.4; Haun scale-16
term: kernel loosening in daytime
goid: PO:0007117
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: For Barley, Wheat and Oat: Zadok scale-93
term: kernel medium hard
goid: PO:0007115
definition: Difficult to divide with thumbnail.
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: For Barley, Wheat and Oat: Zadok scale-91; Feekes scale-11.3
term: kernel watery ripe
goid: PO:0007106
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: Zadok scale-71; Feekes scale-10.54; Haun scale-12.1
term: late booting stage
goid: PO:0007150
definition: In this stage the flag leaf has completely extended.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
comment: In rice it occurs about 6 days prior to heading.
term: late dough stage (sensu Zea)
goid: PO:0007035
definition: Endosperm consistency is a firmer dough than in the previous stage. Towards end of this stage, in dent genotypes, kernels begin to dent on top; occurs about 28-35 days after pollination. Embryo is at stage 4: fourth leaf primordium has formed; embryo is 5-6 mm long
definition_reference: GR:pj37
definition_reference: MaizeDB:67379
term: late globular stage
goid: PO:0000185
definition: At this stage the protoderm, procambium, hyposeal cell are present and the endosperm begins to cellularize.
definition_reference: ISBN:03870940898
term: late heading stage
goid: PO:0007090
definition: From 50-100 percent inflorescence emegred in grasses
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-57; Feekes scale-10.4; Haun scale-10.7
term: late milk
goid: PO:0007109
definition:
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: Zadok scale-77
term: late whorl stage (sensu Zea)
goid: PO:0007014
definition: In adapted materials in the US Corn Belt, the collars of leaves 9-11 are visible (some of the lowest leaves may already have degenerated by this stage). By 10-leaf stage, new leaves appear every 2-3 days. Tassel development accelerates, and rapid stem elongation continues.
definition_reference: GR:pj37
definition_reference: MaizeDB:67357
term: leveling off of grain-filling (sensu Zea)
goid: PO:0007036
definition: Embryo is at stage 5, fifth leaf primordium has formed and lateral seminal root primordia can be observed
definition_reference: GR:pj37
definition_reference: MaizeDB:67382
comment: Rate of dry matter accumulation in kernel diminishes as endosperm transfer cells are crushed. All or nearly all kernels are dented (in a dent genotype); kernels are about 50-55% moisture; husk has begun to dry rapidly; occurs about 35-42 days after pollination.
term: linear grain-filling (sensu Zea)
goid: PO:0007029
definition: Stage of rapid, nearly linear increase in kernel dry matter, that begins about 2 weeks after pollination and lasts almost until physiological maturity
definition_reference: GR:pj37
definition_reference: MaizeDB:64632
term: mature
goid: PO:0000368
definition: Stage at which the embryo has ceased to divide.
definition_reference: ISBN:0387940898
term: mature grain
goid: PO:0007045
definition: The whole grain is hard and ready for harvest. This stage is reached at approximately 15-20 percent moisture
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Ripening.asp
definition_reference: MaizeDB:67381
comment: For Barley, Wheat and Oat: Zadok scale-94
term: maximum tillering
goid: PO:0007144
definition: Tillering is complete
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Vegetative.asp
comment: After maximum tillering has occurred, no more effective tillers are produced. A portion of the late tillers will generally die due to competition effects
term: medium milk
goid: PO:0007108
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: Zadok scale-75; Feekes scale-11.1
term: mid heading stage
goid: PO:0007105
definition: About 50 percent of inflorescence emegred in grasses
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-55; Feekes scale-10.3; Haun scale-10.5
term: mid-globular stage
goid: PO:0000184
definition: Stage at which the embryo under goes mitotic divisions to produce a 32 then 64- celled embryo.
definition_reference: ISBN:03870940898
term: mid-vegetative stage (sensu Zea)
goid: PO:0007015
definition: Rapid stem eleongation continues. In adapted materials in the US Corn Belt, 12-14 leaf collars are visible. Number of ovules (potential kernels) is being determined. Male meiosis begins about this time
definition_reference: MaizeDB:67359
definition_reference: GR:pj37
term: milk stage (sensu Poaceae)
goid: PO:0007046
definition: At this stage, the developing starch grains in the kernel are soft, and the interior of the kernel is filled with a white liquid resembling milk.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Ripening.asp
comment: For Barley, Wheat and Oat: Zadok scale-70
term: milk stage (sensu Zea)
goid: PO:0007033
definition: Endosperm fluid has changed from clear to a milky white, more viscous substance due to accumulating starch; kernels are about 80% moisture; aleurone color characteristic of the genotype appears; occurs about 18-22 days after pollination
definition_reference: GR:pj37
definition_reference: MaizeDB:67373
comment: The embryo is at stage 2: second leaf primordium is formed, and embryo length is approx. 2 mm
term: ovule development
goid: PO:0000005
definition: stages of ovule and megagametophyte development
definition_reference: PMID:9118807
term: ovule stage 1-I
goid: PO:0000006
definition: ovule primordia arise
definition_reference: TAIR:publicaton 11808
term: ovule stage 1-II
goid: PO:0000007
definition: ovule primordium elongate
definition_reference: TAIR:publicaton 11808
term: ovule stage 2-I
goid: PO:0000008
definition: megaspore mother cell enlarges
definition_reference: TAIR:publicaton 11808
term: ovule stage 2-II
goid: PO:0000009
definition: inner integument initiates
definition_reference: TAIR:publicaton 11808
term: ovule stage 2-III
goid: PO:0000010
definition: outer integument intitiates, chalazal nucellus divides
definition_reference: TAIR:publicaton 11808
term: ovule stage 2-IV
goid: PO:0000011
definition: megaspore meiosis occurs
definition_reference: TAIR:publicaton 11808
term: ovule stage 2-V
goid: PO:0000012
definition: tetrad of megaspores formed, integuments elongate towards apex of the nucellus
definition_reference: TAIR:publicaton 11808
term: ovule stage 3-I
goid: PO:0000013
definition: non-functional megaspores degenerate, outer integument envelops the nucellus and inner integument, funiculus and nucellus begin to curve
definition_reference: TAIR:publicaton 11808
term: ovule stage 3-II
goid: PO:0000014
definition: two nucleate megagametophyte stage, outer integument surrounds nucellus, micropylar end points more than 90 degrees away from funiculus, differential growth of integuments
definition_reference: TAIR:publicaton 11808
term: ovule stage 3-III
goid: PO:0000015
definition: megagametophyte develops large central vacuole, micropylar end of ovule at 90 degree angle from funiculus
definition_reference: TAIR:publicaton 11808
term: ovule stage 3-IV
goid: PO:0000016
definition: four-nucleate megagametophyte , inner integument surrounds nucellus, endothelium differentiates
definition_reference: TAIR:publicaton 11808
term: ovule stage 3-V
goid: PO:0000017
definition: eight nucleate megagametophyte
definition_reference: TAIR:publicaton 11808
term: ovule stage 3-VI
goid: PO:0000018
definition: central cell nuclei fuse, antipodal cells degenerate, additional cell layer forms in inner integument
definition_reference: TAIR:publicaton 11808
term: panicle differentiation stage (sensu Oryza)
goid: PO:0007041
definition: At this point, the panicle is 1 to 2 mm in length and the branching of the panicle is visible
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
definition_reference: GR:pj37
comment: In parallel the stem elongation is continuing
term: panicle initiation stage (sensu Oryza)
goid: PO:0007147
definition: Is the time when the panicle premordia initiate the production of a panicle in the uppermost node of the culm
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
comment: A thin green band is visible just above the top node, and represents the very beginning of internode elongation (stem elongation stage) and is evident for only a couple of days
term: physiological maturity stage (sensu Sorghum)
goid: PO:0007135
definition: This stage is identified by the dark spot on the tip of the kernel. Grain will contain 25 to 35% moisture.
definition_reference: GR:pj37
definition_reference: web:http //primera.tamu.edu/ir4/sor-stage.pdf
comment: Maximum total dry weight has been achieved
term: physiological maturity stage (sensu Zea)
goid: PO:0007038
definition: Occurs when grain dry matter accumulation ceases and a black abscission layer forms at the base of the kernel, approx. 50-65 days after pollination; grain moisture is about 30-35%. Embryo is at stage 6: a sixth leaf primordium may have formed, although many genotypes form only 5 embryonic leaves; dormancy occurs after massive hydration of embryo cells
definition_reference: GR:pj37
definition_reference: MaizeDB:67380
term: pollen development
goid: PO:0007018
definition: Microsporogenesis, or pollen development, includes all stages from microsporocyte meiosis through the mature pollen grain
definition_reference: GR:pj37
definition_reference: MaizeDB:67383
term: pollination
goid: PO:0007023
definition: Shedding of pollen from the anthers
definition_reference: GR:pj37
definition_reference: MaizeDB:67364
term: post-flowering (sensu Zea)
goid: PO:0007025
definition: The period of slow kernel growth between fertilization and the beginning of linear grain-filling, lasting roughly 10-12 days. Some workers divides this period into dilatory and exponential phases, which approximately coincide with the endosperm's free nuclear and mitotic stages, respectively. From about 4-10 days after pollination, the embryo is in the proembryo stage, a club-shaped mass of cells with little differentiation except for a basal suspensor region, and an apical region of smaller cells, the embryo proper
definition_reference: GR:pj37
definition_reference: MaizeDB:67370
term: radicle emergence from seed
goid: PO:0007005
definition: The radicle and its enclosing sheath, the coleorhiza, break through the pericarp
definition_reference: GR:pj37
definition_reference: MaizeDB:67351
comment: For Barley, Wheat and Oat: Zadok scale-5
term: ratooning stage (sensu Poaceae)
goid: PO:0007145
definition: Producing new tillers from nodes after harvest
definition_reference: GR:pj37 , JCL
comment: Excluding germination and early seedling stages, it begins a fresh cycle producing new tillers from nodes post-harvest. It may or may not be considered as a growth stage by other, howvever, Gramene is proposing it to be included as one of the new growth stage.
term: reproductive
goid: PO:0000306
definition: stages of development that between flowering and death of the plant.
definition_reference: TAIR:lr
term: reproductive stage
goid: PO:0007140
definition: Stages from panicle initiation to heading
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Reproductive.asp
term: ripening stage (sensu Poaceae)
goid: PO:0007114
definition: Grain undergoing maturation phase.
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: MaizeDB:11088
comment: The stage begins at physiological maturity (when the kernel has approximately 30-35% moisture) and continues through dry kernel (15% moisture or less). #For Barley, Wheat and Oat: Zadok scale-90
term: secondary dormancy induced
goid: PO:0007122
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: For Barley, Wheat and Oat: Zadok scale-98
term: secondary dormancy lost
goid: PO:0007123
definition:
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-99
term: seed dormant
goid: PO:0007119
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: For Barley, Wheat and Oat: Zadok scale-95
term: seed not dormant
goid: PO:0007121
definition:
definition_reference: GR:pj37
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For Barley, Wheat and Oat: Zadok scale-97
term: seedling emergence
goid: PO:0007008
definition: Coleoptile appears above the soil surface. Nodal roots begin to develop.
definition_reference: MaizeDB:64057
term: seedling stage
goid: PO:0007047
definition: The period from development of the first to fourth or fifth leaf stage. Alternatively until tillering starts
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Vegetative.asp
definition_reference: MaizeDB:1863
term: silking (sensu Zea)
goid: PO:0007022
definition: Silks (styles) emerge from the husks at the ear tip. Normally the first silks appear slightly after anthesis begins, but this interval can be delayed by drought or other stresses. Silks of spikelets at the base of the ear emerge prior to those from more apical spikelets
definition_reference: GR:pj37
definition_reference: MaizeDB:67362
term: soft dough stage
goid: PO:0007152
definition: The starch in the grain is beginning to become firm but is still soft
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Ripening.asp
comment: For Barley, Wheat and Oat: Zadok scale-83-85; Feekes scale-11.2; Haun scale-14. #InSorghum 8 to 12 functional leaves present. One half of grain dry weight has accumulated. #In Maize it occurs about 22-28 days after pollination. Embryo is at stage 3: third leaf primordium forms; radicle is recognizable within the coleorhiza; embryo is about 3 mm long
term: stage 1 flower
goid: PO:0000375
definition: stage of flower development marked by the emergence of the floral meristem on the flank of the inflorescene meristem.
definition_reference: ISBN:0387940898
term: stage 10 flower
goid: PO:0000384
definition: stage of flower development that begins when the petal height is level with the stamens.
definition_reference: ISBN:0387940898
term: stage 11 flower
goid: PO:0000385
definition: stage of flower development that begins when the stigmatic papillae appear.
definition_reference: ISBN:0387940898
term: stage 12 flower
goid: PO:0000386
definition: stage of flower development that begins when the petals are level with the long stamens.
definition_reference: ISBN:0387940898
term: stage 13 flower
goid: PO:0000388
definition: stage of flower development that begins when the floral bud opens and the petals are visible to the naked eye.
definition_reference: ISBN:0387940898
term: stage 14 flower
goid: PO:0000389
definition: Stage of floral development when long anthers extend above the stigma.
definition_reference: ISBN:0387940898
term: stage 15 flower
goid: PO:0000390
definition: Stage of floral developement that begins when the stigma extends above the long anthers.
definition_reference: ISBN:0387940898
term: stage 16 flower
goid: PO:0000391
definition: Stage of floral development that begins when the petals and sepals begin to wither.
definition_reference: ISBN:0387940898
term: stage 17 flower
goid: PO:0000392
definition: Stage of floral development that begins when all of the floral organs have abscised and only the green silique remains.
definition_reference: ISBN:0387940898
term: stage 18 flower
goid: PO:0000422
definition: Stage of floral development that begins when the silique color changes from green to yellow.
definition_reference: ISBN:0387940898
term: stage 2 flower
goid: PO:0000376
definition: Stage of floral development that begins when the floral meristem becomes demarcated from the inflorescence meristem by a slight indentation.
definition_reference: ISBN:0387940898
term: stage 3 flower
goid: PO:0000377
definition: Stage of floral development that begins when the sepal primordia arise.
definition_reference: ISBN:038794898
term: stage 4 flower
goid: PO:0000378
definition: Stage of floral development that begins when the developing sepals overlie the floral meristem.
definition_reference: ISBN:0387940898
term: stage 5 flower
goid: PO:0000379
definition: Stage of floral development that begins when the petal and stamen primordia arise.
definition_reference: ISBN:038790898
term: stage 6 flower
goid: PO:0000380
definition: Stage of floral development that begins when the sepals enclose the floral bud.
definition_reference: ISBN:0387940898
term: stage 7 flower
goid: PO:0000381
definition: Stage of floral development that begins when the ling stamen primordia are stalked at the base.
definition_reference: ISBN:0387940898
term: stage 8 flower
goid: PO:0000382
definition: Stage of floral development that begins when thelocules appear on the long stamens.
definition_reference: ISBN:0387940898
term: stage 9 flower
goid: PO:0000383
definition: Stage of floral development that begins when the petal primordia are stalked at the base.
definition_reference: ISBN:0387940898
term: stem elongation stage (sensu Poaceae)
goid: PO:0007048
definition: Begins about the same time panicle initiation is occurring. It continues until full plant height is reached.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Vegetative.asp
definition_reference: MaizeDB:67358
comment: In rice the top five internodes may elongate. Stem internodes can be distinguished from root internodes by the green color in the stem wall. Overlaps the vegetative and reproductive stages. #For Barley, Wheat and Oat: Zadok scale-31 to 39; Feekes scale-6 to 9# In maize after tassel initiation, stem length begins to increase rapidly, through elongation of cells formed by the intercalary meristem at the base of above-ground internodes. The rate of elongation decreases prior to anthesis, but plant height may continue to increase until after flowering
term: tassel initiation stage (sensu Zea)
goid: PO:0007011
definition: Apical dome of shoot meristem elongates, followed by appearance of tassel branch primordia.
definition_reference: GR:pj37
definition_reference: MaizeDB:67306
comment: Under favorable conditions in adapted hybrids in the US Corn Belt, this may occur about 2-3 weeks after seedling emergence, when 4-6 leaf collars are visible. Stem growing point is at or near soil surface. Tassel initiation is very sensitive to photoperiod and temperature; maximal sensitivity to these factors occurs during a brief period with a duration equivalent to the emergence of two leaves, just before tassel initiation
term: tillering stage (sensu Poaceae)
goid: PO:0007049
definition: Emergence of tillers from the axils of 4-5th leaf and onwards. Involves primary, secondary and tertiary tillering.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Vegetative.asp
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
comment: For rice tillering begins at the fifth leaf stage when the first tiller is visible and emerges from the axillary bud of the second leaf on the culm. Tillering continues when the sixth leaf emerges, the second tiller comes from the axillary bud of the third leaf.In direct-seeded rice fields with a normal plant population (10 to 20 plants per square foot), rice plants generally produce 2 to 5 panicle bearing tillers per plant compared to 10 to 30 tillers per plant in transplanted rice where more space is available between plants. #For Barley, Wheat and Oat: Zadok scale-21 to 29; Feekes scale-2
term: torpedo stage
goid: PO:0000187
definition: During this stage the embryo elongates into the cellular endosperm and the internal layers of the hypocotyl and radicle differentiate to form the vascular tissue. Lipid deposition into the cotyledons begins at this stage. Organelle differentiation occurs leading to greening of the embryo.
definition_reference: ISBN:0387940898
term: transition stage
goid: PO:0007028
definition: Occurs when the ovoid, radially symmetrical proembryo elongates to form a cone-shaped structure, establishing the future shoot-root meristem axis; about 10-12 days after pollination.
definition_reference: GR:pj37
definition_reference: MaizeDB:67451
comment: In the endosperm, mitotic activity in the central region declines, and nuclear size and DNA content begin to increase (endoreduplication)
term: two-celled stage
goid: PO:0000177
definition: The embryo after the first mitotic division that produces a smaller apical cell and larger basal cell. The basal cell gives rise to the radicle and the suspensor. The apical cell gives rise all of the embryo except the root.
definition_reference: ISBN:0387940898
term: vegetative
goid: PO:0000305
definition: stages of development that occur from seed germination up to flowering
definition_reference: TAIR:lr
term: vegetative lag stage (sensu Poaceae)
goid: PO:0007146
definition: The period from the end of active tillering to the beginning of the reproductive stage.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development_Vegetative.asp
comment: For rice the length of this period is a function of the maturation period of the cultivar. For very-short season cultivars with 110-day maturity, this period may not be evident. In this situation, maximum tillering stage and the beginning of reproductive growth may overlap. In a 150-day rice cultivar, the lag phase period may last more than two weeks. The vegetative lag phase in midseason varieties is characterized by yellowing plants
term: vegetative lag stage (sensu Zea)
goid: PO:0007016
definition: Late vegetative stage, corresponding to the 15-leaf stage or later in adapted hybrids in the US Corn Belt, which normally have a total of about 20 leaves. Depending on genotype and environmental conditions, a corn plant may develop a total of 10-30 leaves. Ear is developing rapidly and silk elongation begins. Female meiosis begins when silks are approx. 2 mm long and ears approx. 2 cm long. Brace roots begin growing; a new leaf is added every 1-2 days
definition_reference: GR:pj37
definition_reference: MaizeDB:67360
term: vegetative stage
goid: PO:0007139
definition: Stages from germination to panicle initiation.
definition_reference: GR:pj37
definition_reference: web:http //www.uaex.edu/Other_Areas/publications/HTML/MP192/1_Rice_Growth_and_Development.asp#Vegetative
comment: The later stage (lag phase) may overalp with the reproductive stage
term: viable seed germination
goid: PO:0007120
definition:
definition_reference: web:http //weeds.montana.edu/crop/Growth_stages_book/p24_25_26_27.htm#top
definition_reference: GR:pj37
comment: For Barley, Wheat and Oat: Zadok scale-96
term: visible flower buds
goid: PO:0000420
definition: Whole plant developmental stage at which the first flower buds become visible to the naked eye
definition_reference: PMID:11449047
term: zygote
goid: PO:0000423
definition: The product of fusion of two gametes before mitosis or meiosis.
definition_reference: ISBN:0140514031
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