Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it>
<p>Abstract</p> <p>Background</p> <p>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 toleranc...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2005-09-01
|
| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/5/18 |
| _version_ | 1818001571292643328 |
|---|---|
| author | Olsson Björn Gharti-Chhetri Gokarna Zakhrabekova Shakhira Lindlöf Angelica Bräutigam Marcus Olsson Olof |
| author_facet | Olsson Björn Gharti-Chhetri Gokarna Zakhrabekova Shakhira Lindlöf Angelica Bräutigam Marcus Olsson Olof |
| author_sort | Olsson Björn |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Avena sativa </it>(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 <it>Avena sativa </it>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 <it>E </it>values > 10<sup>-10</sup>) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX <it>E </it>values ≤ 10<sup>-10</sup>) 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 <it>Arabidopsis </it>ESTs.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-04-14T03:36:10Z |
| format | Article |
| id | doaj.art-b102c579a5644dd5ba85eb4b96ff1ae1 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-04-14T03:36:10Z |
| publishDate | 2005-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-b102c579a5644dd5ba85eb4b96ff1ae12022-12-22T02:14:46ZengBMCBMC Plant Biology1471-22292005-09-01511810.1186/1471-2229-5-18Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it>Olsson BjörnGharti-Chhetri GokarnaZakhrabekova ShakhiraLindlöf AngelicaBräutigam MarcusOlsson Olof<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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 <it>Avena sativa </it>(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 <it>Avena sativa </it>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 <it>E </it>values > 10<sup>-10</sup>) to any sequence available in the public databases. Of the 2800 UniGene sequences, 398 displayed significant homology (BlastX <it>E </it>values ≤ 10<sup>-10</sup>) 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 <it>Arabidopsis </it>ESTs.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2229/5/18 |
| spellingShingle | Olsson Björn Gharti-Chhetri Gokarna Zakhrabekova Shakhira Lindlöf Angelica Bräutigam Marcus Olsson Olof Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it> BMC Plant Biology |
| title | Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it> |
| title_full | Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it> |
| title_fullStr | Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it> |
| title_full_unstemmed | Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it> |
| title_short | Generation and analysis of 9792 EST sequences from cold acclimated oat, <it>Avena sativa</it> |
| title_sort | generation and analysis of 9792 est sequences from cold acclimated oat it avena sativa it |
| url | http://www.biomedcentral.com/1471-2229/5/18 |
| work_keys_str_mv | AT olssonbjorn generationandanalysisof9792estsequencesfromcoldacclimatedoatitavenasativait AT ghartichhetrigokarna generationandanalysisof9792estsequencesfromcoldacclimatedoatitavenasativait AT zakhrabekovashakhira generationandanalysisof9792estsequencesfromcoldacclimatedoatitavenasativait AT lindlofangelica generationandanalysisof9792estsequencesfromcoldacclimatedoatitavenasativait AT brautigammarcus generationandanalysisof9792estsequencesfromcoldacclimatedoatitavenasativait AT olssonolof generationandanalysisof9792estsequencesfromcoldacclimatedoatitavenasativait |