ArticleBMC bioinformatics2010
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Breedbase: a digital ecosystem for modern plant breeding.G3 (Bethesda, Md.) · 2022Article
- QTL Mapping and GWAS Reveal the Genetic Mechanism Controlling Soluble Solids Content inFoods (Basel, Switzerland) · 2021Article
- QTLTableMinerBMC bioinformatics · 2018Article
- The Sol Genomics Network (SGN)--from genotype to phenotype to breeding.Nucleic acids research · 2015Article
- solGS: a web-based tool for genomic selection.BMC bioinformatics · 2014Article
- The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.Database : the journal of biological databases and curation · 2011Article
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5 authors.
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Abstract
backgroundA common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases. DESCRIPTION: The Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application.
conclusionssolQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes underlying phenotypic variation and markers more closely linked to QTLs. solQTL is freely available on SGN and can be used in private or public mode.
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