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Cattle Genome Variation Mapped in Unprecedented Detail

By creating a global database, an international consortium of scientists has increased the detailed knowledge of the variation in the cattle genome by several orders of magnitude. The first generation of the new data resource, which will be open access, forms an essential tool for scientists working with cattle genetics and livestock history. The results are published in as the cover story (image) of the August 2014 issue of Nature Genetics. It's momentous, says one of the scientists behind the international effort, associate professor Dr. Bernt Guldbrandtsen from the Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Denmark. Scientists from Aarhus University – the only Danish university to participate – have been part of the consortium from the start and have contributed 15 percent of the data. The data used in the huge database are derived from key ancestor bulls. These bulls have produced millions of descendants and have had enormous influence on the genetic composition and characteristics of modern cattle breeds. For example, Holstein bulls in the database have fathered at least 6.3 million daughters worldwide. The data consist of sequenced genomes for a number of bulls and are based on new sequencing techniques. The article in Nature Genetics describes data from 232 bulls and 2 cows of the breeds Angus, Holstein, Jersey, and Fleckvieh. Because these animals are key ancestors, they carry most of the genetic variations present in the three races. Currently, the database contains genomes of more than 1,200 animals of different cattle breeds, but as more scientists from other countries gradually join the project, there is a continual influx of data. Key ancestor bulls have daughters all around the world, so it is a considerable strength of the project that such data are connected into one database. What makes the database so special is the level of detail of the data. Where previously only the location of the genes on the genome and some of the gene variants were known, a large part of the total variation has now been identified and the genetic types carried by new offspring can be predicted. These data can be linked to data on key attributes such as health, calving, fertility, milk yield, and growth allowing the identification of genetic variatiants that result in differences between animals. “In the past we had only mapped approximately two percent of the variation. Now we have knowledge of it all for a great number of key ancestors. If you use the analogy of a road map, we previously only had sufficient information to see the mileposts on the chromosomal roadmap, but now we can see the entire roadmap,” says Dr. Guldbrandtsen. He is supplemented by Professor Mogens Sandø Lund, Director of the Center for Quantitative Genetics and Genomics at the Department of Molecular Biology and Genetics, Aarhus University, who said, “Before we only knew about 700,000 markers. With the new and detailed database we have over 30 million markers to work with. We can predict the genotypes of all animals on the basis of the resource that we have created here. The scientists explain that the database will become the standard reference within bovine genetics. “It is a global resource that will be the basis for all bovine genetic studies for many years to come. It opens the doors for further studies of the genetic variation of different traits and for more information and studies on the history of cattle,” explains postdoc Dr. Rasmus Froberg Brøndum, also from the Center for Quantitative Genetics and Genomics. “When we have such detailed information to build on, we can more easily and effectively focus the breeding work for the benefit of livestock health, welfare, and production. We have already used data from the project to identify variations in genes that are associated with both embryo death, which is a major cause of reduced fertility in cattle, and milk yield,” says Dr. Guldbrandtsen. The article is entitled, "Whole-Genome Sequencing of 234 bulls Facilitates Mapping of Monogenic and Complex Traits in Cattle." [Press release] [Nature Genetics abstract] [Nature Genetics News & Views abstract]