Exploiting Epigenetic Variation for Crop Improvement in the Emerging Oilseed Crop Camelina Sativa

Abstract

In the emerging oilseed crop Camelina sativa, breeding efforts have been focused on optimizing seed size and oil quality traits to improve its productivity for Canadian agriculture.Considering that epigenetic mechanisms, such as DNA methylation, undergo dynamic changes throughout seed development, we hypothesized that it may play an important regulatory role in seed traits. We successfully knocked out the epigenetic regulator DEFECTIVE IN RNA-DIRECTED DNA METHYLATION (DRD1) via CRISPR/Cas9 technology. Homozygous drd1 mutants showed a global reduction in DNA methylation predominantly within transposable elements in the upstream region of genes. Loss of DNA methylation in the drd1 seed was found to have a relatively small effect on the expression of genes. We did, however, detect transcriptional changes in 69 hypomethylated genes, of which two candidate genes, FRUCTOKINASE (FRK1) and ACYL CARRIER PROTEIN 2 (ACP2), are predicted to be involved in seed development. This study showcases the potential influence of epigenetic marks on gene expression and offers insights on the functional relevance of DNA methylation in seed development.iii Acknowledgements I would like to thank my mentor and supervisor, Jean-Sébastien Parent, for seeing potential in me as an undergraduate student and accepting me into your lab. I am thankful for all the guidance you have given me over the past 2 and a half years and for pushing me in every aspect of this experience to achieve my full potential. Thank you for your dedication in helping me grow in my research journey. I would also like to thank my lab mom, Elizabeth Routly, who fostered a healthy and comfortable lab environment and welcomed me with open arms. You were always willing to help me out in my experiments whenever possible, and because of you, I was able to gain the confidence I needed in the lab to succeed. You always believed in me and I will cherish all the funny lab memories we have together (like that one cursed DNA extraction where nothing went right). I would also like to thank Nathan Liang, you were the best help when it came to troubleshooting any of my problems. Your expertise in bioinformatics are unmatched, and I am so thankful that you took the time to prepare detailed user guides to better guide me through the difficult data analyses process. My RNA-seq analysis would not have gone so smoothly without your help. I would also like to thank Kasia Dadej and Sarah Martin as well as all of our AAFC collaborators, including Steve Robinson in Saskatoon, that have offered their expertise and guidance throughout my thesis. Lastly, I would like to express my deepest gratitude to my family for their unconditional support and love throughout this journey. iv Contributions This thesis examines the functional relevance of epigenetic regulation during seed development. I conducted the majority of the experiments outlined in this thesis under the supervision of Dr. Jean-Sébastien Parent, Ottawa Research and Development Centre, Agriculture and Agri-Food Canada and under the co-supe...