solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

BMC Bioinformatics

Database

Isaak Y Tecle¹  Naama Menda¹  Lukas A Mueller¹  Robert M Buels¹  Esther van der Knaap² 

[1] Boyce Thompson Institute for Plant Research, Tower Rd, 14853, Ithaca, NY, USA;Department of Horticulture and Crop Science, The Ohio State University/OARDC, 44691, Wooster, OH, USA;

关键词: Quantitative Trait Locus;    Quantitative Trait Locus Mapping;    Quantitative Trait Locus Region;    Peak Quantitative Trait Locus;    Quantitative Trait Nucleotide;   

DOI  :  10.1186/1471-2105-11-525

 received in 2010-07-21, accepted in 2010-10-21,  发布年份 2010

来源: Springer

【 摘 要 】

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.DescriptionThe 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.

【 授权许可】

Unknown   
© Tecle et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.