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dc.contributor.authorBräutigam, Marcus
dc.date.accessioned2009-02-27T10:23:47Z
dc.date.available2009-02-27T10:23:47Z
dc.date.issued2009-02-27T10:23:47Z
dc.identifier.isbn978-91-628-7683-8
dc.identifier.urihttp://hdl.handle.net/2077/19495
dc.description.abstractCold acclimation protects plants from temperate regions of the world from the deleterious effects of low and freezing temperatures. This is through a series of transcriptional, regulatory and metabolic changes that enable continued growth and survival. The focus in this thesis is to increase our understanding of the cold acclimation process and there by open the door to development of cold hardy oat (Avena sativa) varieties for the Nordic climate conditions. We started by sequencing 9,792 oat ESTs from a cDNA library prepared from pooled total RNA extracted from cold induced oat plants. These sequences were assembled into a UniGene ser of 2,800 sequences, 398 displayed homology to genes previously reported to be involved in cold acclimation. The CBF factor family have a key regulatory role during cold acclimation and in our UniGene set we found four oat CBF sequences. To infer regulatory networks we developed a rule-based method, which combined data from microarrays with promoter sequences and known cis¬-elements. The method was tested on the cold acclimation process in Arabidopsis and could indentify both known and novel network connections. We also performed a comparative transcriptome study between rice and Arabidopsis during low temperature stress to explore the molecular differences between chilling sensitive and freezing tolerant plants. Interesting observations were that the dynamics of the response of key genes appears to be higher in Arabidopsis than in rice. Several important downstream genes encoding proteins with freezing protective activities in Arabidopsis are not present in rice or important cis-elements. Also stress mediated hormone signalling seem to be absent in rice. Together these observations partly explain why rice is unable to cold acclimate to the same extent as Arabidopsis. Finally we developed a TILLING (Targeting Induced Local Lesions IN Genomes) population in the oat consisting of 2,600 independent events. By random sequencing of two genes involved in the lignin (AsPAL1) and ß-glucan (AsClsF6) synthesis we estimated the mutation frequency in the population to be approximately 1 per 26,000 bp. This means that each gene is mutated ca 250 times looking at the entire population and assuming an average gene size of 2 kb. This TILLING population will now be an important tool for both breeding and genetic studies in oats.en
dc.language.isoengen
dc.relation.haspartI. Bräutigam, M., Lindlöf, A., Zakhrabetkova, S., Gharti-Chhetri, G., Olsson, B. and Olsson, O. (2005) Generation and analysis of 9792 EST sequences from cold acclimated oat, Avena sativa. BMC Plant Biology 5:18.::doi::10.1186/1471-2229-5-18en
dc.relation.haspartII. Chawade A, Brautigam M, Lindlof A, Olsson O, Olsson B (2007) Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors. BMC Genomics 8: 304.::doi::10.1186/1471-2164-8-304en
dc.relation.haspartIII. Bräutigam, M., Lindlöf, A., Chawade, A., Gharti-Chhetri, G., Olsson, B. and Olsson, O. (2008) Transcriptional profiling of cold stress response in rice and comparative analysis to Arabidopsis thaliana (manuscript).en
dc.relation.haspartIV. Chawade, A., Sikora, P., Bräutigam, M., Larsson, M., All Nakash, M., Chen, T. and Olsson, O. (2008) Development and characterisation of an Oat TILLING population and identification of mutations in lignin and ß-glucan biosynthesis genes. (manuscript).en
dc.subjectcold acclimationen
dc.subjectoaten
dc.subjectESTen
dc.subjectmicroarrayen
dc.subjecttranscriptomeen
dc.subjectchillingen
dc.subjectfreezingen
dc.subjectriceen
dc.subjectArabidopsisen
dc.subjectTILLINGen
dc.subjectmutationen
dc.titleCold Acclimation in oats and other plants: Dissecting low temperature responses using a comparative genomic approach.en
dc.typeText
dc.type.svepDoctoral thesiseng
dc.gup.mailmarcus.brautigam@cmb.gu.seen
dc.type.degreeDoctor of Philosophyen
dc.gup.originGöteborgs universitet. Naturvetenskapliga fakultetenen
dc.gup.departmentDepartment of Cell and Molecular Biology ; Institutionen för cell- och molekylärbiologien
dc.gup.defenceplaceFredagen den 20 mars 2009, kl. 10.00, Hörsal Åke Göransson, Medicinaregatan 11en
dc.gup.defencedate2009-03-20
dc.gup.dissdb-fakultetMNF


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