Genome structural variation and gene regulation discovery in complex plant genomes using bioinformatics and microgenomics

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The genome, an amazing collection of tens of thousands of genes, orchestrated by different levels of regulation, leads to functional organisms adapted to their living conditions. My NSERC Discovery funded research program focuses on regulatory DNA motifs and plant gene regulation using an approach that integrates bioinformatics (computational methods) with genomics (molecular methods). The long-term objective is to understand different gene regulating mechanisms and how they contribute to plant functional anatomy. Plants in the Arctic have adapted to harsh weather conditions and sudden, extreme temperature fluctuations. During the growing season, roots and aerial parts are often exposed to a significant difference in temperatures, with soil temperatures below freezing, and above ground temperatures being 20 or more degrees higher. To be able to withstand the elements, arctic plants have assumed metabolic, phenological and anatomical adaptations, such as anti-freeze molecules, perennial slow growth, and thick hairs and low stature. This diversification is thought to partially be helped by polyploidization (doubling of the chromosome content), partial gene region duplications (increasing number of copies of key genes), as well as by several layers of gene regulation of key genes. The consensus is that arctic plants are prepared for stress through constitutive (constant) expression of specialized genes. However, with the changing climate more studies are urgently required to clarify the regulation of this gene expression, and what impact polyploidization may have on it. The proposed research pursues exciting findings on gene regulatory differences between arctic and temperate species in the Oxytropis genus (in the Fabaceae or legume family), assembling the first genome sequences for both diploid and polyploid Oxytropis species, developing a whole genome regulatory motif discovery bioinformatics tool and validation of motifs in planta. Embarking on this research into plants adapted to arctic conditions, and the molecular mechanisms that enable this adaptation, has invaluable impact: as an increase in knowledge of life in harsh conditions, an increase in our basic knowledge of plant development and function, a provider of potential innovations for biotechnology and crop improvement strategies, and a provider of better bioinformatics tools for plant sequence analysis. Maybe most importantly, we are in an excellent position to train Highly Qualified Personnel for a future in this exciting and rapidly expanding field. Highly Qualified Personnel trained in modern molecular genetics, genomics and bioinformatics through the proposed research will have publications in high impact journals, they will have in demand key skills, knowledge, scientific thinking, as well as a perspective on applications of crop improvement for resilience under a changing climate - traits which make them competitive in academia as well as industry in Canada and worldwide.