Development of a Genomics Database for the Cattle and Other Livestock
Plant And Animal Genetic Resources Preservation Research Unit
Project Number: 3012-31000-005-07
Specific Cooperative Agreement
Start Date: Sep 16, 2013
End Date: Sep 15, 2018
Develop a database capable of storing genomic data and facilitating the analysis of genetic inquiry. Such a database is necessary because there is a lack of long term data storage capabilities throughout the livestock research community and industry. Once operational genomic data derived from: animals in the ARS repository, Colorado State University herds, various ARS locations performing genomic research on livestock and aquatic species, plus the cattle industry. The genomic database will be constructed as a component of Animal-GRIN Version 2. This element of the Animal-GRIN database will serve as a long term storage location for such data. The data will be made available to researchers to improve the understanding of livestock genetics and to develop new genomic selection tools that industry requires. In addition, a genomic element in database will facilitate a greater understanding of the diversity captured in the ARS repository. Further more access and utilization of this information will facilitate the use of repository samples.
This project is currently developing a comprehensive database for the storage of germplasm and tissue samples in the repository. The existing database framework includes information on the samples, storage location, animals the samples were derived, breed, phenotypic performance, management system, and environmental conditions. Missing is a mechanism to enter, store and manipulate genomic information which can be in a variety of forms (varying length of SNP panels and/or microsatellite panels). Design, programming, testing, and validating a new genomics component will be performed as part of the software development. In addition, an advisory committee comprised of ARS, Colorado State University, industry, and other potential institutions will be form, convened on a regular basis. This group will provide guidance in the development of the software to insure the final product conforms to the community’s expectations.