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Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis through Comparative Analysis of Multiple EST sets
University of Skövde, School of Humanities and Informatics.
University of Skövde, School of Humanities and Informatics.
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2007 (English)In: Bioinformatics Research and Development: First International Conference, Springer Berlin/Heidelberg, 2007, 48-65 p.Conference paper, (Refereed)
Abstract [en]

Freezing tolerance in plants is obtained during a period of low non-freezing temperatures before the winter sets on, through a biological process known as cold acclimation. Cold is one of the major stress factors that limits the growth, productivity and distribution of plants, and understanding the mechanism of cold tolerance is therefore important for crop improvement. Expressed sequence tags (EST) analysis is a powerful, economical and time-efficient way of assembling information on the transcriptome. To date, several EST sets have been generated from cold-induced cDNA libraries from several different plant species. In this study we utilize the variation in the frequency of ESTs sampled from different cold-stressed plant libraries, in order to identify genes preferentially expressed in cold in comparison to a number of control sets. The species included in the comparative study are oat (Avena sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), rice (Oryza sativa) and Arabidopsis thaliana. However, in order to get comparable gene expression estimates across multiple species and data sets, we choose to compare the expression of tentative ortholog groups (TOGs) instead of single genes, as in the normal procedure. We consider TOGs as preferentially expressed if they are detected as differentially expressed by a test statistic and up-regulated in comparison to all control sets, and/or uniquely expressed during cold stress, i.e., not present in any of the control sets. The result of this analysis revealed a diverse representation of genes in the different species. In addition, the derived TOGs mainly represent genes that are long-term highly or moderately expressed in response to cold and/or other stresses.

Place, publisher, year, edition, pages
Springer Berlin/Heidelberg, 2007. 48-65 p.
Series
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), ISSN 0302-9743, 1611-3349 ; 4414 LNBI
Identifiers
URN: urn:nbn:se:his:diva-2013DOI: 10.1007/978-3-540-71233-6_5ISI: 000246237400005Scopus ID: 2-s2.0-34548078765ISBN: 978-3-540-71232-9 OAI: oai:DiVA.org:his-2013DiVA: diva2:32289
Available from: 2008-04-28 Created: 2008-04-28 Last updated: 2013-03-18

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Lindlöf, AngelicaOlsson, Björn
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CiteExportLink to record
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Cite
Citation style
  • apa
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