A Systems Genetics Browser for Genome-Wide Expression Association Data in Forest Trees

Accessing and exploring large genomics data sets remains a significant challenge. The Plant Genome Integrative Explorer resource (http://plantgenie.org/), allows searching, visualizing and analysing genomics and transcriptomics data for plant species including poplar, spruce, Arabidopsis and recently Eucalyptus. It includes tools to visualise gene expression networks. To expand the current functionality to “omics” data from genome-wide association (e.g. eQTL or eGWAS) studies, and link such data to phenotypes, we are developing a suite of tools for querying and visualising large-scale systems genetics data. For example, starting from one or more phenotypic QTLs, it is possible to browse overlapping expression (e)QTLs using an interactive version of Circos, or explore underlying genes using Jbrowse. Integrating eQTL or eGWAS data with gene-wise correlation data allows the dissection of gene networks via the PlantGenIE exNet tool. To test this systems genetics browser, expression (eQTL), metabolite (mQTL) and phenotypic QTL data were analysed for two interspecific backcross populations of E. grandis x E. urophylla. Patterns of shared trans-eQTLs were visualized to identify the locations of polymorphisms affecting the expression of groups of co-regulated and functionally related genes. eQTL networks were constructed for expression modules involved in various aspects of xylem cell development. Our genetic variation module (qtlXplorer) provides a platform for systems genetics modelling and high-resolution dissection of the molecular basis of complex trait variation in plants. It will accommodate data from eQTL and eGWAS experiments, and together with the existing PlantGenIE tools, provide a means to formulate and test hypotheses from large-scale population genomics data.