Can Study of Epigenetics and Alternate Splicing Uncover Novel Methods to Increase Drought Productivity in Rice?

Supervisors: Professor Adam Price, Dr Tyler Stevenson and Dr Craig Simpson (James Hutton Institute)

Background: The need for increased quality and yield of rice plants has significant implications for world food security. A large proportion of rice plants are grown in environmentally stressful conditions such as drought or high soil arsenic conditions. It is becoming clear that external environmental factors can have rapid and lasting effects on rice plant growth and development. It is hypothesised that epigenetic modifications induced by the environment might have a significant impact on rice growth. Drought has been shown to produce heritable epigenetic effects on rice (Li et al. 2012). Examining recent published transcriptomic studies conducted in Aberdeen has identified key epigenetic markers are regulated by environmental conditions such as drought and arsenic treatment. However, the mechanisms that drive epigenetic modifications (such as DNA methylation) in rice growth and the functional outcomes are not known. This studentship will aim to identify how epigenetic modifications are induced by environmental conditions and the downstream effects of altered epigenetic enzymatic activity. It will also examine the hypothesis that epigenetic changes alter alternative splice site choice in pre-mRNA transcripts (as suggested by Luco et al. 2014)). These studies will give insights into the regulation of gene expression by the environment through the interaction of epigenetic and post-transcriptional processes. Our increased understanding of this process will offer opportunities for plant genetic manipulation. Using a range of laboratory and wild grown rice plants, the studentship will uncover novel means to increase productivity under water stressed conditions and therefore contribute directly to enhancing food security fields both nationally and internationally.

Approach: This project will require a multi-disciplinary and integrative project that will take advantage of the international collaborations in rice research maintained by the PI Dr. Adam Price as well as the epigenetic expertise provided by co-PI Dr. Tyler Stevenson and on alternative splicing provided by Dr Craig Simpson. It is expected that this PhD studentship will require several studies divided into progressive steps. This could involve use of chemical moderators of methylation and ChIP-Sequencing techniques. An important approach will involve RNAseq analysis on plants that show altered expression which correlate to different epigenetic marker genes.
Training: Students will receive extensive training in plant care. Specific laboratory techniques will include RNA extraction, DNA synthesis, quantitative PCR and western blotting. Methods that are specific to epigenetic analyses will involve ELISA assays for methylation, sodium bisulfite sequencing, methylation sensitive restriction enzyme PCR and methyltransferase, acetyltransferase expression assays and bioinformatics analysis of sequencing data. Functional studies will require students to administer various epigenetic compounds to assess effect of epigenetic agents on rice growth. Moreover, studies will also require the examination of growth dynamics in wild type and target knockout rice plants. The student will take the lead role in data collection, interpretation and drafting manuscripts. Students will also be encouraged to engage other scientists at the University of Aberdeen and James Hutton Institute to foster their own collaborations. Lastly, the student will attend and present their findings at several UK meetings as well as international conferences.