Development of Informatics Infrastructure to Support the use of High Throughput Genetic Data for Herd Management on Small and Mid-size Farms

The use of high throughput genetic data has transformed animal agriculture dramatically overthe last 15 years.Large breed associations and national breeding programs are collecting genomewide genotypes and implementing genomic selection to improve production phenotypes.Thesetechnologies have proven both powerful and transformative.They have also become inexpensive.Whole genome genotypes can be generated for cattle for $40/animal by a commercial provider.Unfortunately smaller breed associations farmers who wish to remain independent or farmersworking with species out of the mainstream cannot benefit from these technologies. Farmers thatwork with species such as Yak and Texas Longhorns require data management tools and analyticalsoftware sufficiently specialized as to be inaccessible on a limited budget.We are proposing a solution that would provide a web based data management system capableof inexpensively storing managing and analyzing high throughput data sets and providingrudimentary analyses such as DNA based meat/animal verification parentage testing andrudimentary marker based selection.Once these tools are in place we can subsequently build a companion database to storeproduction phenotype data allowing these smaller breed/species associations to work with geneticresearchers and identify genetic markers to improve or maintain production traits all the whilemonitoring and maintaining genetic diversity.The successful completion of this project will allow small farmers to produce manage and usewhole genome genotypes for their animals which in aggregate may subsequently be use in moresophisticated genome wide association studies aimed at improving or maintaining production traitsand efficiency.