McGill Plant Phenomics Platform (MP3) Ramp Up in the Value-directed Evolutionary Genomics Initiative (VEGI)

VEGI (Value-directed Evolutionary Genomics Initiative; funding through Genome Canada and Genome Quebec) intends to reveal and characterize functional non-coding DNA sequences by employing a strategy that combines comparative, population and functional genomics approaches. The Brassicaceae plant family has been targeted as it includes not only the model plant, Arabidopsis thaliana, but also several important crop plants to the Canadian economy, such as canola. Our strategy involves not only bioinformatics approaches but also genome sequencing, expression profiling, and agriculturally-relevant functional assessment through detailed phenotype characterization of disrupted targets. Key to our strategy is using comparative and population genomics methodologies that uncover conserved non-coding DNA sequences that evolve under selection. However, a rate limiting step in our validation pipeline is phenotyping at high-throughput. To this end, we applied (Feb. 2011; Canadian Foundation for Innovation or CFI) and received funding (Aug. 2011) for the LemnaTec HTS and 3D systems as part of the planned McGill Plant Phenomics Platform (or MP3). The HTS system was only recently installed in our plant growth chamber facility and is currently being optimized for integration into the VEGI pipeline. The 3D system will be installed into our rooftop greenhouse facility in November 2012 and fully operation in the spring/summer of 2013.

In order to identify controls, optimize abiotic trait assays, and assess logistical bottlenecks, a pilot study of a subset of conserved targets was conducted and prior to the installation of the LemnaTec facility. The study included the selection of 223 targets, processing 411 Arabidopsis thaliana T-DNA mutant lines through a genotyping pipeline, identifying 240 homozygous lines used in three trait assays for nitrogen use efficiency, freezing tolerance, and salt tolerance. The majority of targets were so-called domesticated transposable elements (DTEs) and candidate protein-coding control genes underlying each of the traits. DTEs are derived from transposons but are no longer mobile. Instead they have been co-opted to presumably perform, largely unknown, host specific functions. Our pilot study has uncovered the functional potential of DTEs and hint to possible agricultural relevancy. We look forward to exploiting the MP3 to further pursue the functional role of DTEs and other non-coding DNA targets revealed by VEGI.