Gene regulatory networks for wheat genotype-dependent effects of cold temperatures

• Main Author: Giles, Tom
• Published: University of Nottingham 2012
• Subjects: 584.913
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.576493

Understanding and optimising the response of crops to climate change is of central importance in enhancing food security. A better understanding of how wheat genes influence traits is required to allow breeders to respond to socioeconomic issues. One aspect concerns adjusting flowering phenotypes to match predicted future climates. It is therefore crucial to understand this vernalisation process. The identification of the genes involved in the vernalisation response will be important for breeding crops able to cope with the effects of climate change. In this research project, bioinformatics methods were used to investigate the effects of decreasing temperatures and photoperiods on the transcriptomes of three different wheat varieties. The Affymetrix probe-sets associated with the known vernalisation genes and their expression profiles were characterised. Further analyses showed that gene expression varied significantly between wheat varieties. Genes involved in cold stress, cold acclimatisation, sugar / lipid metabolism and disease resistance have been identified. Probe-set Ta.17293.2.S1_at was a potential biomarker for vernalisation. In Arabidopsis, hundreds of vernalisation-related genes have been investigated. These were compaired to the probe-sets present on the Affymetrix wheat GeneChip® and a total of 184 putative wheat vernalisation-related genes were identified. As a step towards understanding the vernalisation process, a putative wheat network was constructed, of which several interactions were substantiated using co-expression correlation analysis. These results indicated that histone modification may be taking place, suggestive of an epigenetic switch. In addition, Artificial Neural Network inference was used to identify several novel candidate vernalisation genes. Of specific note was SPK1, a GTP binding protein. This was putatively associated with the expression of CDF2, a DOF-type transcription factor. In order to test the functions of CDF2 and SPK1, shRNAi constructs were developed to silence these genes in vivo. Transgenic wheat plants were analysed with T0 plants.