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Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa
Department of Cell and Molecular Biology, Göteborg University, Box 462, 403 20 Göteborg, Sweden.
University of Skövde, School of Humanities and Informatics.
Department of Cell and Molecular Biology, Göteborg University, Box 462, 403 20 Göteborg, Sweden.
Department of Cell and Molecular Biology, Göteborg University, Box 462, 403 20 Göteborg, Sweden.
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2005 (English)In: BMC Plant Biology, ISSN 1471-2229, Vol. 5, 18- p.Article in journal (Refereed) Published
Abstract [en]

Background

Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required.

Results

From an oat cDNA library 9792 single-pass EST sequences were obtained. The library was prepared from pooled RNA samples isolated from leaves of four-week old Avena sativa (oat) plants incubated at +4°C for 4, 8, 16 and 32 hours. Exclusion of sequences shorter than 100 bp resulted in 8508 high-quality ESTs with a mean length of 710.7 bp. Clustering and assembly identified a set of 2800 different transcripts denoted the Avena sativa cold induced UniGene set (AsCIUniGene set). Taking advantage of various tools and databases, putative functions were assigned to 1620 (58%) of these genes. Of the remaining 1180 unclassified sequences, 427 appeared to be oat-specific since they lacked any significant sequence similarity (Blast E values > 10-10) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX E values ≤ 10-10) to genes previously reported to be involved in cold stress related processes. 107 novel oat transcription factors were also identified, out of which 51 were similar to genes previously shown to be cold induced. The CBF transcription factors have a major role in regulating cold acclimation. Four oat CBF sequences were found, belonging to the monocot cluster of DREB family ERF/AP2 domain proteins. Finally in the total EST sequence data (5.3 Mbp) approximately 400 potential SSRs were found, a frequency similar to what has previously been identified in Arabidopsis ESTs.

Conclusion

The AsCIUniGene set will now be used to fabricate an oat biochip, to perform various expression studies with different oat cultivars incubated at varying temperatures, to generate molecular markers and provide tools for various genetic transformation experiments in oat. This will lead to a better understanding of the cellular biology of this important crop and will open up new ways to improve its agronomical properties.

Place, publisher, year, edition, pages
BioMed Central, 2005. Vol. 5, 18- p.
National Category
Natural Sciences
Research subject
Natural sciences
Identifiers
URN: urn:nbn:se:his:diva-1693DOI: 10.1186/1471-2229-5-18ISI: 000202936500001PubMedID: 16137325Scopus ID: 2-s2.0-25844512589OAI: oai:DiVA.org:his-1693DiVA: diva2:31969
Available from: 2007-08-13 Created: 2007-08-13 Last updated: 2014-02-07Bibliographically approved

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CiteExportLink to record
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Citation style
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