The research in our lab is devoted to the analysis of epigenetic and genetic regulation of plant genome stability under normal and stressful conditions. We are investigating how plants are able to acclimatize to constantly changing environments. Further knowledge of how plants respond to stress will allow the generation of better, hardier plants. In our lab, we analyze a particular component of a plant's response to stress; DNA repair machinery. We are trying to decipher what genetic and epigenetic regulations exist in plants that allow them to tolerate abiotic and biotic stressors. Our recent research has indicated that there are substantial epigenetic changes that occur in the progeny of plants exposed to stress (Kovalchuk et al., 2003, Nature; Boyko et al., 2007, NAR).
Our recent work shows that exposure to abiotic and biotic stress results in heritable changes in the genome stability (homologous recombination), methylation and stress tolerance. Analysis of methylation in the progeny of stressed plants using Nimblgen technology allowed to identify many loci with changes in methylation pattern. Moreover, microchip analysis identified over 100 genes that changed their expression in the progeny. Analysis of changes in various mutants impaired in small RNA biogenesis suggested that small RNAs play an important role in the process. In the future, we plan to perform detailed analysis of epigenetic changes that occur in the progeny of stressed plants.

Since double strand break (DSB) repair enzymes are involved in the integration of foreign (transgenic) DNA into genome, we also analyze whether it is possible to manipulate the endogenous repair machinery to influence the integration of transgenes. Recent plant regeneration and plant transformation technologies developed in our laboratory allowed us to launch pre-commercial application and to obtain the funds for the start-up of the biotechnology company "Plantbiosis".

Genetic and epigenetic regulation of plant genome stability
The NSERC Discovery Grant (2006-2011) and recent Alberta Agriculture Research Institute Grant (2009-2013) will support research aimed at analyzing the mechanisms of plant adaptation to stress including plant DNA repair mechanisms. We will attempt to answer the following questions: Do all stresses, abiotic and biotic in nature, trigger similar kinds of epigenetic responses or is there a signature response for each individual stress? Which DNA repair components or lack there of, have the most profound effect on chromatin remodelling? How stable are changes in methylation patterns over numerous generations?

Somatic and transgenerational effects of the pathogen infection in plants
Response to pathogen stress is also one of the key components of our research. Under the framework of the Human Frontiers Science Program (HFSP; 2006-2009), we plan to investigate plants' responses to pathogenic stress. In particular, we are interested in the specific mechanisms of plant adaptation. This is a joint grant application that brought together scientists from four different countries and disciplines; Profs. Manfred Heinlein, University of Strasbourg, France; Martin Kuiper, Flanders Interuniversity Institute for Biotechnology, The Netherlands; Scott Peck, University of Missouri-Columbia, USA; and our lab. It is known that plants lacking the gene of resistance to a pathogen are not able to mount the hypersensitive response but are apparently still capable of generating short wave of oxidative bursts possibly involved in signalling. Under the scope of this program, we plan to study the mechanisms of compatible pathogen interaction, including the epigenetic mechanisms of the development of the stress signal. Our main contribution to this program will be the generation of crosses between various pathogen response mutants and our recombination reporter plants as well as analysis of the regulation of small interfering RNAs, using mi- and si-microchips.
Previously, our laboratory found a special type of signal that is generated in plants infected with a compatible pathogen. This signal could travel faster than the virus and could promote rearrangements in plant genome (Kovalchuk, et al., 2003, Nature). We suggested the signal was epigenetic in nature and as such represents a novel "bystander" effect - the response of cells to stress that were not directly treated with stress.

Analysis of the mechanisms of DNA integration in plants
There are several differently successful methods of DNA delivery to plants but the specific mechanism of integration of foreign DNA into the plant genome remains unclear. We believe that transgenic DNA interacts with plant factors prior to integration. Thus, manipulation with these factors should allow better control over such a random process. Recent results in the lab suggest that shifting the balance in strand break repair results in over 2-fold increase in the number of primary transformants. Recently obtained NSERC Strateigc Grant and AARI grants will allow to develop new techniques for plant transformation and gene targeting. To understand the mechanism that allows the shift in the balance of the NHEJ and HR DNA repair pathways we will use the transformation of ku80 mutant Arabidopsis plant impaired in one of the mechanisms of the strand break repair. These plants should have a higher proportion of precise integration events. Despite the fact that this is a fundamental research, it has the potential, in the future to contribute to Canadian biotechnology efforts. Recently we also identified several plant mutants impaired in chromatin stability that have high frequency of transformation. Currently our lab is exploring the possibilities of transient inactivation of such components in commercial plants in order to increase the transformation frequency.
Our recent activity resulted in obtaining several important grants, from NSERC, AARI, HFSP and AVAC, totalling the annual lab budget to close to $500,000. Recent grant from AVAC is especially important since it allows us to start up a biotechnology company that will focus on the development of new efficient methods of plant transformation. These techniques will allow multiple transgene stacking and production of effective plant bioproduct models.