Optimizing Bovine SNP discovery efforts

Cow genome sequencing is underway at Baylor College of Medicine (BCM) sequencing center and will be completed in the next few months. A recent white paper indicated a goal to identify 100,000 SNP for use in identification and mapping of QTL regions [1]. In September 2004, the preliminary assembly of the cow (Btau_1.0), Hereford breed, using whole genome shotgun (WGS) reads with an average of three fold coverage was released. BCM predicted 15,000 in silico SNP by comparing the Hereford preliminary assembly with traces from other breeds. Those SNP are currently being validated at the U.S. Meat Animal Research Center (MARC), ARS-USDA. The SNP discovery efforts by the consortia are currently randomized in the assembly and are optimized only for maximizing the experimental SNP confirmation.