The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci
© Polineni et al; licensee BioMed Central Ltd. 2006
Received: 05 April 2006
Accepted: 05 June 2006
Published: 05 June 2006
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.
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.
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.
Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. While significant information regarding the mode of inheritance of these traits is available, most of this information is not integrated into a genomic context. As large amounts of genomic sequence data become available (estimated completion time of the bovine genome sequence is early 2006), they require livestock genome researchers to integrate sequence data not only with existing gene maps, but more importantly with Quantitative Trait Locus (QTL) and phenotype data. Without integration, application of these data to agricultural enterprise productivity will remain slow and inefficient. In order to facilitate this overall integration, there is a requirement for an integrated database of QTL of cattle and an analytical tool for this database such as a visualization component.
While there are livestock genetic map viewers [1, 2] and at least one QTL database , to the best of our knowledge there is only one other bovine QTL viewer available , but it is not dynamic and is restricted to one meta-analysis of dairy QTL data . Our inspiration for this effort was RatMap , but our code and database schema differ substantially from theirs. We have created a web accessible, integrated database of bovine QTL that will be extended to link to genome sequence data as it becomes available. Our QTL viewer is able to show the contents of the database in a manner suitable for both novice and expert users.
Construction and content
The ER diagram consists of these entities:
QTL information, including all the details of each QTL
Marker information, including all the details of each marker
References, including the complete list of references
Trait information, including the details of the traits of the cattle
Category information, which gives details about the categories into which traits are divided
Chromosome information, which has the length of each of chromosome measured in linkage units (Morgans).
The database is modeled such that each trait can fall under multiple categories. In addition, each QTL and marker record can have more than one reference. Finally, the QTL information and marker information are not linked directly. These data are linked dynamically by the QTL Viewer based on the position of the marker and the position of the QTL on the chromosome. This provides flexibility when the database is updated, allowing marker information and QTL information to be updated independently of each other.
Data can be added or edited using a set of web based tools that simplify database administration. Database administrators can add single QTL or easily modify QTL attributes without resorting to the command line. This makes updating the database possible by less skilled individuals such as students or technicians who may not have the training to mine the data out of the literature or have admin access to MySQL. Security settings are such that it is possible to assign users limited admin privileges over their own data, enabling them to submit and edit data but not delete QTL entries. User submitted data can be kept private and not accessible to other users until a user is ready to divulge the data for public access. This feature has been implemented to allow users to directly submit data prior to publication, allowing them to view their data in the context of public data in a genomic context.
Utility and discussion
By ensuring the QTL records and the map information are not linked directly we make it easy to migrate the viewer to additional maps (integrated maps with arbitrary map units or RH maps) that also include map information for the QTL markers of interest. This can provide genomic visualization free from distortions caused by recombination hotspots (in the case of linkage maps) but more importantly allow QTL regions to be viewed on the best possible map, not just the map the QTL were identified from.
The QTL literature is constantly being added to, so a strategy to keep the QTL database is a necessity. At present we have settled on manual, periodic literature searches to identify new publications that we can mine for QTL data. It would be advantageous if journals that publish significant numbers of bovine QTL studies could be persuaded to require submission to our database a requirement as is done for GenBank. We hope that as our site becomes more widely used, that journals will require or at least strongly encourage authors to submit their QTL data directly to us.
While there are a number of livestock genomics web sites, there is only one other site that incorporates a dynamic, genome wide display of QTL data . We have concentrated on bovine QTL, but there is no reason why this viewer/database cannot be easily altered to accommodate genomes from other species with QTL data. The honey bee community has plans to adopt our database and viewer for their needs (C. Elsik, personal communication). For the bovine (or any other livestock species) genome sequence to be fully and efficiently exploited by animal scientists and biomedical researchers, map based genome coordinates must be converted from Morgans and Rays to base pairs. Therefore, as soon as the final bovine assembly is released, we expect to link the existing linkage markers to the bovine sequence using STS coordinates of the USDA markers from the map, and display the resulting QTL regions using Gbrowse. In this fashion livestock genomics researchers should be able to dispense with lengthy positional cloning exercises associated with QTL mapping. This should significantly speed up the identification and testing of candidate genes.
Availability and requirements
Hardware requirement, any UNIX/LINUX/OSX server. Software required includes Apache, MySQL and PHP. The database and viewer code are available upon request.
Thanks to Per Johnson of Ratmap and John Keele of USDA-MARC for providing the data model and bovine marker data respectively. The authors would like to thank Kelli Key, Clare Gill and members of her lab, and Loren Skow and members of his lab for user feedback and beta testing.
- Kappes SM, Keele JW, Stone RT, Sonstegard TS, Smith TPL, McGraw RA, LopezCorrales NL, Beattie CW: A second-generation linkage map of the bovine genome. Genome Res 1997, 7(3):235–249.View ArticlePubMed
- Hu J, Mungall C, Law A, Papworth R, Nelson JP, Brown A, Simpson I, Leckie S, Burt DW, Hillyard AL, Archibald AL: The ARKdb: genome databases for farmed and other animals. Nucleic Acids Res 2001, 29(1):106–110. 10.1093/nar/29.1.106PubMed CentralView ArticlePubMed
- Weiss B, Piry S, Steinbach D, Samson F, Eggen A: Bovmap database.[http://locus.jouy.inra.fr/cgi-bin/bovmap/intro2.pl]
- Khatkar MS, Thomson PC, Tammen I, Costa F, Raadsma HW: Online Combined QTL Map of Dairy Cattle Traits.[http://www.vetsci.usyd.edu.au/reprogen/QTL_Map/]
- Khatkar MS, Thomson PC, Tammen I, Raadsma HW: Quantitative trait loci mapping in dairy cattle: review and meta-analysis. Genet Sel Evol 2004, 36(2):163–190. 10.1051/gse:2003057PubMed CentralView ArticlePubMed
- Petersen G, Johnson P, Andersson L, Klinga-Levan K, Gomez-Fabre PM, Stahl F: RatMap--rat genome tools and data. Nucleic Acids Res 2005, 33(Database issue):D492–4. 10.1093/nar/gki125PubMed CentralView ArticlePubMed
- Hu ZL, Dracheva S, Jang W, Maglott D, Bastiaansen J, Rothschild MF, Reecy JM: A QTL resource and comparison tool for pigs: PigQTLDB. Mamm Genome 2005, 16(10):792–800. 10.1007/s00335-005-0060-9View ArticlePubMed
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