Advanced bovine genome assembly, genetic resources released: Cow genome project heads for home

HOUSTON -- (August 14, 2006) -- Researchers from the Bovine Genome Sequencing Project recently announced the release of a comprehensive set of genome resources into freely available public databases. These new assets for bovine researchers include the most complete and accurate genome sequence to date, an upgraded genetic map, and a new set of two million DNA base differences for use as DNA sequence polymorphisms.

Contributors to the $53 million international effort to sequence the genome of the cow (Bos taurus) include: the National Human Genome Research Institute, which is part of the National Institutes of Health; the U.S. Department of Agriculture's Agricultural Research Service and Cooperative State Research, Education, and Extension Service; the state of Texas; Genome Canada via Genome British Columbia, The Commonwealth Scientific and Industrial Research Organization of Australia; Agritech Investments Ltd., Dairy Insight, Inc. and AgResearch Ltd., all of New Zealand; the Kleberg Foundation; and the National, Texas and South Dakota Beef Check-off Funds.

The sequencing of the bovine genome was conducted at the Baylor College of Medicine Human Genome Sequencing Center in Houston. The new genome sequence is 2.9 billion DNA base pairs, similar to the human and other mammalian genomes. It incorporates about one-third more data than earlier versions. The new information comes from sequencing 20,000 clones containing large pieces of bovine DNA (BACs), created at the BACPAC Resource Center at Children's Hospital Oakland Research Institute in Oakland, Calif. and mapped at the Michael Smith Genome Sciences Centre at the British Columbia Cancer Agency in Vancouver.

The use of the BAC data allows a more structured assembly of DNA sequences into a complete genome, more effectively addressing challenges posed by repeated sequences. New techniques developed at the BCM-HGSC allowed the BACs to be sequenced in groups rather than individually, reducing cost and effort. The new high-quality bovine sequence, which covers 95 percent of the genome, will enable researchers to make accurate gene predictions and evolutionary comparisons for this important animal.

The Hereford breed was selected for the bulk of the sequencing project. Although an inbred animal was used, heterozygosity in the sequence was detectable. The sequence data was analyzed to identify likely single nucleotide polymorphisms (SNPs), representing positions where members of each chromosome pair of the diploid animal differ in DNA sequence. About two million SNPs were found, and will be of great utility for high-resolution studies of the differences between breeds and relating associated traits to the genome.

DNA sequencing to sample other breeds to detect genetic differences was also performed on Holstein, Angus, Jersey, Limousin, Norwegian Red and Brahman animals. DNA differences between these breeds will expand the discovery of traits for better meat and milk production and to model human disease.

The genome sequence was also used to order over 50,000 genetic markers, creating the most dense and complete genetic map of the bovine genome to date. This genetic map will be invaluable in identifying heritable traits and conditions of interest in agriculture and medicine. About 17,000 of the markers were contributed by several groups within the BGSP and combined at the U.S. Department of Agriculture’s Meat Animal Research Center in Clay Center, Nebraska before being integrated with the genome sequence to contribute to the map. Another 35,000 markers were selected from the SNP collection, and from ESTs previously aligned to the genome. Mapping reagents for about 9,000 of these are already commercially available and are being used in bovine genetic studies around the world.

Sequencing of the bovine genome began in December 2003. With the release of these new data, the project now heads into the final analysis phase. The bovine genome sequence will aid agricultural researchers to improve health and disease management of cattle and enhance the nutritional value of beef and dairy products. Medical researchers will also use the bovine information to interpret the human genome and thereby develop better ways of treating and preventing disease.

Researchers can access the sequence data through the following public databases:

Baylor College of Medicine Human Genome Sequencing Center (www.hgsc.bcm.tmc.edu)
GenBank (www.ncbi.nih.gov/Genbank) at NIH's National Center for Biotechnology Information
EMBL Bank (www.ebi.ac.uk/embl/index.html) at the European Molecular Biology Laboratory's Nucleotide Sequence Database
DNA Data Bank of Japan (www.ddbj.nig.ac.jp)

The data will also be viewable through NCBI's Map Viewer (www.ncbi.nlm.nih.gov), UCSC Genome Browser (www.genome.ucsc.edu) at the University of California at Santa Cruz, and the Ensembl Genome Browser (www.ensembl.org) at the Wellcome Trust Sanger Institute in Cambridge, England.