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. 2006 Jun 5:7:283.
doi: 10.1186/1471-2105-7-283.

The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

Pavana Polineni  1 , Prathyusha Aragonda, Suresh R Xavier, Richard Furuta, David L Adelson
Affiliations

The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci

Pavana Polineni et al. BMC Bioinformatics. .

Abstract

Background: Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been integrated into a genomic context. Without such integration application of these data to agricultural enterprises will remain slow and inefficient. Our goal was to populate a genomic database with data mined from the bovine quantitative trait literature and to make these data available in a genomic context to researchers via a user friendly query interface.

Description: The QTL (Quantitative Trait Locus) data and related information for bovine QTL are gathered from published work and from existing databases. An integrated database schema was designed and the database (MySQL) populated with the gathered data. The bovine QTL Viewer was developed for the integration of QTL data available for cattle. The tool consists of an integrated database of bovine QTL and the QTL viewer to display QTL and their chromosomal position.

Conclusion: We present a web accessible, integrated database of bovine (dairy and beef cattle) QTL for use by animal geneticists. The viewer and database are of general applicability to any livestock species for which there are public QTL data. The viewer can be accessed at http://bovineqtl.tamu.edu.

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Figures

Figure 1
Figure 1
QTL viewer description. This is a diagrammatic view describing the inputs and outputs from the database and viewer. QTL and marker information are assembled from the literature or web sites and entered into the linked, discrete marker and QTL databases. The integrated marker/QTL database serves as the back end for queries emanating from the user interface (viewer). The viewer will display different views depending on user choices which can ultimately be resolved to single QTL details with links to literature and markers.
Figure 2
Figure 2
Genome view of multiple QTL. This screen shot shows the result of a query for QTL for carcass quality, carcass yield, milk yield and milk fat traits. The QTL regions are color coded and for ease of viewing multiple, overlapping QTL for any single trait are collapsed into a single color coded line. By selecting a single QTL line with the mouse, the user is able to transition to the single chromosome view, where all individual QTL are displayed (see Figure 3).
Figure 3
Figure 3
Detailed view of QTL. The critical interval of the QTL is shown along with peak marker location. QTL summary data such as QTL ID, statistical signficance, family structure and statistical methods are presented. Links to the USDA marker database are provided, along with links to references used. When a fully functional genome browser becomes available a link to that site will be provided here.
Figure 4
Figure 4
Entity-Relationship diagram of the integrated database. The integrated database consists of two major, linked divisions, the marker database, which is independent from the QTL database. This allows easy updating of either component of the database or potentially allowing the QTL database to be linked to multiple maps. QTL are characterized in terms of trait types, allowing QTL for similar phenotypes originally described with different terms to be linked by a single category. The markers can be linked to external databases such as NCBI via STS accessions. This will allow eventual direct browsing of genome annotations within QTL regions using Gbrowse.
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