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Research article - Peer-reviewed, 2021

qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)

Christie, Nanette; Mannapperuma, Chanaka; Ployet, Raphael; van der Merwe, Karen; Mahler, Niklas; Delhomme, Nicolas; Naidoo, Sanushka; Mizrachi, Eshchar; Street, Nathaniel R.; Myburg, Alexander A.


Background: 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. 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 ( ) 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.Results: We have developed 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.Conclusions: qtlXplorer 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.


qtlXplorer; Eucalyptus; EucGenIE; Systems genetics; eQTL; Co-expression; 'Omics integration; Online resource; Database; Genome browser

Published in

BMC Bioinformatics
2021, volume: 22, number: 1, article number: 595
Publisher: BMC

Authors' information

Christie, Nanette
University of Pretoria
Mannapperuma, Chanaka
Umea University
Ployet, Raphael
University of Pretoria
van der Merwe, Karen
University of Pretoria
Mahler, Niklas
Umea University
Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology
Naidoo, Sanushka
University of Pretoria
Mizrachi, Eshchar
University of Pretoria
Street, Nathaniel R.
Umea University
Myburg, Alexander A.
University of Pretoria

UKÄ Subject classification

Plant Biotechnology

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