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

Christie, Nanette and Mannapperuma, Chanaka and Ployet, Raphael and van der Merwe, Karen and Mahler, Niklas and Delhomme, Nicolas and Naidoo, Sanushka and Mizrachi, Eshchar and Street, Nathaniel R. and Myburg, Alexander A. (2021). qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE). BMC Bioinformatics. 22 , 595
[Research article]

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Abstract

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 (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.Results: We 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.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.

Authors/Creators:Christie, Nanette and Mannapperuma, Chanaka and Ployet, Raphael and van der Merwe, Karen and Mahler, Niklas and Delhomme, Nicolas and Naidoo, Sanushka and Mizrachi, Eshchar and Street, Nathaniel R. and Myburg, Alexander A.
Title:qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
Series Name/Journal:BMC Bioinformatics
Year of publishing :2021
Volume:22
Article number:595
Number of Pages:21
Publisher:BMC
ISSN:1471-2105
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 4 Agricultural Sciences > 404 Agricultural Biotechnology > Plant Biotechnology
Keywords:qtlXplorer, Eucalyptus, EucGenIE, Systems genetics, eQTL, Co-expression, 'Omics integration, Online resource, Database, Genome browser
URN:NBN:urn:nbn:se:slu:epsilon-p-115058
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-115058
Additional ID:
Type of IDID
DOI10.1186/s12859-021-04514-9
Web of Science (WoS)000730565000001
ID Code:26608
Faculty:S - Faculty of Forest Sciences
Department:(S) > Dept. of Forest Genetics and Plant Physiology
Deposited By: SLUpub Connector
Deposited On:27 Dec 2021 07:26
Metadata Last Modified:27 Dec 2021 07:31

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