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In the quest for a cold tolerant variety: gene expression profile analysis of cold stressed oat and rice
University of Skövde, The Systems Biology Research Centre. University of Skövde, School of Life Sciences.
2008 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cold acclimation is a process which increases the freezing tolerance of an organism, after exposure to low, non-freezing temperatures. The acclimation ensures that cold tolerant species can endure harsh winter conditions, by preparing them to sub-zero temperatures. Cold-sensitive plants such as oat and rice have limited abilities to cold acclimate and are therefore easily damaged during winter time.

 

The development of more tolerant varieties by using biotechnological methods is desirable, since the yields are expected to improve due to a prolonged vegetation period. However, in order to apply such methods, more knowledge about the underlying mechanisms regulating the cold tolerance and acclimation is required. One step in this direction is to analyze gene expression data generated from cold stressed oat (Part I) and rice plants (Part II).

 

The focus of this thesis is, consequently, analysis of expression profiling data, which was generated using the EST sequencing and cDNA microarray technologies. The results show that both oat and rice are cold responsive,with many of the previously identified cold regulated genes having a counterpart in these species. In rice, however, the response is less dynamic than in the model organism Arabidopsis thaliana and this may explain its inability to fully cold acclimate.

 

 

 

Additionally, the work in this thesis focuses on evaluating if small-scale EST sets can be used for ‘digital-Northern’, in order to identify genes that are involved in the regulation of the cold stress response. The results show that small-scaled EST sets are not optimal for such an analysis, since the method detected only a portion of cold responsive genes represented in the sets. This has to due with the inherent properties of EST data and limitations in the analysis steps of the sequences.

 

The work also concerns the identification of cis-elements coupled to transcription factors prominent in the regulation of the response. Since cold acclimation is a quantitative trait the response and regulation of cold stress is under combinatorial control of several transcription factors and the results show that this should be taken into account when identifying binding sites.

Place, publisher, year, edition, pages
Göteborgs universitet , 2008. , 78 p.
Keyword [en]
cold tolerance, oat, rice, bioinformatics analysis
National Category
Bioinformatics and Systems Biology
Research subject
Technology
Identifiers
URN: urn:nbn:se:his:diva-2713ISBN: 978-91-628-7200-7 OAI: oai:DiVA.org:his-2713DiVA: diva2:159673
Public defence
(English)
Note

List of Papers: I. Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. Bräutigam, M., Lindlöf, A., Zakhrabetkova, S., Gharti-Chhetri, G., Olsson, B., and Olsson, O. BMC Plant Biology. (2005), 5:18 II. Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis through Comparative Analysis of Multiple EST sets. Lindlöf, A., Bräutigam, M., Chawade, A., Olsson, B., and Olsson, O. Bioinformatics Research and Development - First International Conference, BIRD '07. (2007), LNBI 4414: 48-65 III. Evaluation of combining several statistical methods with a flexible cut-off for identifying differentially expressed genes in pairwise comparison of EST sets. Lindlöf, A., Bräutigam, M., Chawade, A., Olsson, O., and Olsson, B. Biology and Bioinformatics Insight. (2008), 2: 215-237 IV. Transcriptional profiling of cold stress response in rice and comparative analysis to Arabidopsis thaliana. Bräutigam, M., Lindlöf, A., Chawade, A., Gharti-Chhetri, G., Olsson, B., and Olsson, O. Manuscript V. In silico analysis of promoter regions from cold-induced CBFs in rice (Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control. Lindlöf, A., Bräutigam, M., Chawade, A., Gharti-Chhetri, G., Olsson, B., and Olsson, O. Manuscript

Available from: 2010-04-09 Created: 2009-02-09 Last updated: 2013-04-16Bibliographically approved

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http://hdl.handle.net/2077/18308

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