Plant growth stage review page
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Objectives of POC for developing an ontology for whole plant growth stages:
- To capture the biological concept and transcend the differences in growth stage terminology and arrive at comparable growth stages in different species.
- Standardize plant growth stage nomenclature.
- Integrate monocot and dicot growth stages.
- To enable querying of comparable growth stages across plant species, to find homologies in gene or phenotype expression profiles and any functional similarity..
- To enable annotation of various experimental materials to growth stages of plants from a common platform.
Introduction:
Growth is a complex process with different organs developing, growing and dying in overlapping sequences. Understanding the orderly succession of changes leading from the simple structure of the embryo to the highly complex organization of the mature plant, presents some of the most fascinating and challenging problems of biology today. The succession of changes can be assessed as a series of growth stages to describe what is known about the processes underlying and controlling plant development. Growth stages help to track and demarcate the observable changes that occur during the life cycle of a plant, from germination to fruiting and senescence.
In order to accomplish this goal of having an integrated version which is robust and can be used across the monocot/dicot divide, we referred to the BBCH scale publication. BBCH is the only system that has attempted to integrate the growth stages of different crops. In addition it is the same scale used by Boyes et. al. (2001) to draw equivalences from Arabidopsis to cereal plant growth stages for phenotypic evaluation. Thus there is already a foundation for correlating growth stages across crops and much of the initial work of extracting and integrating ideas from published literature has already been accomplished by this system. It is based on Zadoks scale meant for the cereal crop plants, therefore it brings the two systems together. Zadoks scale is the most widely used scale for cereals in the United States by agronomists.
- Recognizable morphological landmark events of a growing plant are treated as identifiers to indicate the underlying biology of growth (physiology, major biochemical pathways, genes and gene interactions).
- Thus making it possible to accurately and reliably estimate the growth stage of a particular plant model.
- This allows one to leverage information available from this model to study a similar mechanism in another species.
- While providing only a coarse level of resolution, agreement on objective criteria for classifying crop growth stages assures that different people evaluating the same or even different plant material/model will recognize the same or equivalent growth stages.
Reviewers section
In order to help in the review process, please open the following web pages or links.
* The stages for maize were replicated from the stages defined by MaizeGDB. They used Ritchie’s growth staging system.
- You can browse the plant growth stages by vising the online ontology browser.
In order to get you started we have created a couple of following sample queries.
These queries are dependent on the species specific terms that were recorded as synonyms and not the actual term name. The actual term name you see is a generic concept (e.g. inflorescence emegence stage as compared to heading in cereal plants.For help on browser click here or visit the bottom of ontology browser page and look for "help".
- Sample query-1: search for all growth stages in Arabidopsis.
- Sample query-2: search for all growth stages in rice.
- Sample query-3: search for rosette growth in Arabidopsis.
- Sample query-4: search for search for late whorl stage in maize.
- Sample query-5: search for the stage at which tassel emergence occurs in maize.
- Sample query-6: search for the stage at which ear initiation occurs in maize.
- Sample query-7: search for heading stages.
- Sample query-8: search for the stage at which panicle initiation occurs in rice.
- You must look at the GROWTH STAGE DOCUMENT for more details on this ontology (download in PDF format or MS-word format)
- How the species specific growth stages were mapped
- Refences links
- BBCH growth staging document: Download the PDF file from source website.
- Rice, maize*, wheat, barley, oat and sorghum: browse growth stage ontology at Gramene database.
- Arabidopsis: consult Boyes et al (2001) or browse growth stage ontology at TAIR
- Zadok, Feeks and Haun scales: browse the website http://weeds.montana.edu/crop/Growth_stages_book/p22_23.htm
- Questionnaire
- Please fill out the questionnaire after you have reviewd the ontologies and send it to Anuradha Pujar.
Reviewers
We acknoweldge the following researchers for their valuable feedback and many thanks for accepting our request to review the growth stage ontology.
Please feel free to contact Anuradha Pujar if you have questions.
1. Greg McMaster, ARS USDA, USA
2. Sarah Hake, U.C. Berkeley, USA
3. Tinker Nicholas, Agriculture and Agri-Food Canada
4. Simon Jupp, NASC, Nottingham, UK
5. Alice Clara Augustine, Monsanto, India
6. Lukas Mueller, SGN and Cornell University, USA
7. Victoria Carollo, GrainGenes and USDA
8. Tom Blake, University of Montana, USA
9. Paul Counce, University of Arkansas, USA
10. Marty Sachs, UIUC, Illinois, USA
11. Taba Suketoshi, CIMMYT-CGIAR, Mexico
12. Thomas Brutnell, Boyce Thompson Inst. and Cornell University, USA
13. Thomas Bjorkman, NYSAES and Cornell University, USA
14. Scott Poethig, University of Pennsylvania, USA
15. Richard Bruskiewich, IRRI-CGIAR, Philippines
16. Diane Mather, University of Adelaide, Australia
17. Dave Matthews, GrainGenes and Cornell University, USA
18. Selinger Dave, Dupont Pioneer Hi-Bred, USA
19. Ed Coe, University of Missouri Columbia, USA
20. Yukiko Yamazaki, Oryzabase, Japan
21. Junjian Ni, Gramene database and Cornell University, USA
21. Immanuel Yap, Gramene database and Cornell University, USA
22. Margarita Garcia Hernandez, TAIR and Carnegie Institution, Stanford, USA