A Livestock Database for Long Term Storage and Use of Genomic and Other Associated Information

As more livestock are genotyped the need for long term and secure storage of genotypic information becomes necessary for public and private sector interests. The National Animal Germplasm Program has developed a second generation database (Animal-GRIN) which stores phenotypic, management, environmental and gene bank repository information for samples in the repository. This database can be queried via the internet. Due to the comprehensive nature of the Animal-GRIN database it provides a framework amenable to the addition of a component to store, view and retrieve genomic data. An ARS, CSU and EMBRAPA team was formed to develop this new component. By using Animal-GRIN and bovine SNP-chip data as the framework, software development proceeded by adding a series of database tables to accommodate SNP: chip type, identification, reference number, file format, and uploading formats. Actual storage of genomic information is on a separate storage system and not part of the database per se. Future users will be able to access information on the animals stored within Animal-GRIN (access genotypic, phenotypic, managerial, and environmental information) via the internet. Additionally, users will be able to query, request and receive various types of information for their analysis. Facilitating speed of transfer will be made possible by linking Animal-GRIN to the new ARS initiative that involves development of a high speed internet 2 system with public interfacing capabilities. The genomics element of Animal-GRIN is a mechanism to facilitate the secure storage and future use of livestock genomic data for breed associations and the research community.