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SGN Database: From QTLs to Genomes

Isaak Y. Tecle¹, Naama Menda¹, Robert Buels¹ & Lukas Mueller¹

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1. Boyce Thompson Institute for Plant Research, Tower Rd, Ithaca, NY 14853

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Document Type:

Poster

Date:

Received 23 April 2009 14:11 UTC; Posted 23 April 2009

Subjects:

Genetics & Genomics, Bioinformatics, Plant Biology

Tags:

• QTL analysis
• Solanaceae Genomics Network
• QTL databases
• genotype data
• genomic database
• Quantitative trait loci
• genome
• phenotype
• R/QTL
• sgn
• biocuration

Abstract:

Quantitative trait loci (QTL) analysis is used to dissect the genetic basis underlying polygenic traits. Several public databases have been storing and making QTL data available to research communities. To our knowledge, current QTL databases rely on manual curation where curators read literature and extract relevant QTL information to store in databases. Evidently, this approach is expensive in terms of expert manpower and time use and limits the type of data that can be curated. At the Solanaceae Genomics Network (SGN) (http://sgn.cornell.edu), we have developed a database to store raw phenotype and genotype data from QTL studies, perform, on the fly, QTL analysis using R/QTL statistical software (http://www.rqtl.org) and visualize QTLs on a genetic map. Users can identify peak, and flanking markers for QTLs of traits of interest. The QTL database is integrated with other SGN databases (eg. Marker, BACs, and Unigenes), and analysis tools such as the Comparative Map Viewer. Using the comparative map viewer, users can compare chromosome with QTL regions to genetic maps of interest from the same or different Solanaceae species. As the tomato genome sequencing advances, users can also identify corresponding BAC sequences or locations on the tomato physical map, which can be suggestive of candidate genes for a trait of interest.

Furthermore at SGN, images, quantitative phenotype and genotype data, publications, genetic maps generated by QTL studies are displayed and available for download. Currently, data from three F2 and two backcross population QTL studies on fruit morphology traits (18 – 46 traits per population) is available at the SGN website for viewing at population, accession, and trait levels. Traits are described using ontology terms. Phenotype data is presented in tabular and graphical formats such as frequency distributions with basic descriptive statistics. Mapping data showing location of parental alleles on individual accession genetic maps is also available.

SGN is a public database hosted at Boyce Thomson Institute, Cornell University, and funded by USDA CSREES and NSF.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

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License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Tecle, Isaak , Menda, Naama, Buels, Robert, and Mueller, Lukas. SGN Database: From QTLs to Genomes. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3160.1> (2009)

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