Abstract
BackgroundAffordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.ResultsWe have developed qtlXplorer (https://eucgenie.org/QTLXplorer) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases.ConclusionsqtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.
Highlights
Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits
To illustrate the features and capability of qtlXplorer within EucGenIE, we present a case study investigating the roles of laccases and peroxidases in biotic stress response and wood formation in Eucalyptus
Construction and content We developed qtlXplorer as the first population genomics tool in the PlantGenIE.org environment. qtlXplorer is available as a tool to browse Eucalyptus systems genetic data in EucGenIE, which is one of the four species-specific subdomains of the online
Summary
Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. Online genomics resources have been developed to cope with the large amounts of ‘omics data available for many plant species and to provide researchers access to web-based tools for online analysis and visualization of increasingly complex ‘omics datasets [4] Online platforms such as Phytozome [5], Ensembl Plants [6], Gramene [7] and PLAZA [8] provide broad taxonomic coverage, while others such as The Arabidopsis Information Resource (TAIR) [9] and the Maize Genetics and Genomics Database (MaizeGDB) [10] provide access to deep genomics and genetics information for individual model species. Genevestigator [15], is an online transcriptome analysis resource that is highly curated and commercialized, while PlaNet [16] was designed to transfer knowledge across species via conserved co-expression networks and sequence relationships
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