Umeå University's logo

umu.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, South Africa.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0003-1589-9138
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, South Africa.
Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Pretoria, South Africa.
Show others and affiliations
2021 (English)In: BMC Bioinformatics, E-ISSN 1471-2105, Vol. 22, no 1, article id 595Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
BioMed Central, 2021. Vol. 22, no 1, article id 595
Keywords [en]
Co-expression, Database, eQTL, Eucalyptus, EucGenIE, Genome browser, Online resource, qtlXplorer, Systems genetics, ‘Omics integration
National Category
Genetics Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:umu:diva-190864DOI: 10.1186/s12859-021-04514-9ISI: 000730565000001PubMedID: 34911434Scopus ID: 2-s2.0-85121369417OAI: oai:DiVA.org:umu-190864DiVA, id: diva2:1623474
Available from: 2021-12-29 Created: 2021-12-29 Last updated: 2024-01-17Bibliographically approved

Open Access in DiVA

fulltext(4995 kB)135 downloads
File information
File name FULLTEXT01.pdfFile size 4995 kBChecksum SHA-512
6c2ad600ced814956eec2f9f9e1f095f0e3bcc6f739a9f19b6e6ec5ceb4f668bbce6fb1fd3be5990abc8ffc9cbe67d5a6f9915dcf29e67282e52a4f276e0ac0e
Type fulltextMimetype application/pdf

Other links

Publisher's full textPubMedScopus

Authority records

Mannapperuma, ChanakaMähler, NiklasStreet, Nathaniel

Search in DiVA

By author/editor
Mannapperuma, ChanakaMähler, NiklasStreet, Nathaniel
By organisation
Department of Plant PhysiologyUmeå Plant Science Centre (UPSC)
In the same journal
BMC Bioinformatics
GeneticsBioinformatics and Systems Biology

Search outside of DiVA

GoogleGoogle Scholar
Total: 135 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 374 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf