Sequencing of the bovine (Hereford) genome consumed a large part of 2004-06 BCM-HGSC resources. The project was staged to produce an initial 3x WGS assembly followed by a second 6x WGS assembly to allow gene predictions for preliminary annotation, and a final assembly including BAC sequences for improved local assembly refinement. The 3x assembly was used by Ensembl to test their pipeline on low coverage genome assemblies. The 6x WGS assembly was released and gene predictions from Ensembl and NCBI have been made public. The final assembly has been completed using the Atlas assembler and BAC data from equal numbers of BACs sequenced individually or by the CAPSS clone pooling strategy.
WGS samples from six other breeds were sequenced to identify SNPs for genetic studies. A panel of 10,000 SNPs were mined at the HGSC from this interbreed dataset and genotyping reagents were developed. 227 animals representing 9 breeds were genotyped and analyzed. An expanded set of markers (32,000) was applied to a more extensive group of animals (449). The results form the basis of a Bovine HapMap Project. Affymetrix now markets a bovine genotyping chip based on this work, allowing broader translation of the genome project into applications.
A meeting of sixty bovine researchers in Houston in March 2005 began coordination for overall genome analysis and the future of bovine research. A working group for annotation selected themes for analysis (Global analyses; Muscle, Immune function; Lactation; Energy partitioning, Metabolism, Rumen function; Reproduction, Endocrinology, Sex determination, Development; Imprinted genes, HDACs, Methyl transferases; Bovine models of human diseases; Non-coding RNA; Genetics/Genotyping; Behavior, Maternal nurturing; Prion protein). The Bovine Genome Project leveraged NHGRI funds with funds from other sources. This allowed the utility of the sequence to be enhanced by genetic analysis, outside the scope of the standard basic genome project deliverables.