Using Genomic Data to Improve Dairy Cattle Genetic Evaluations

Genomic data Genotypes for about 40,000 single nucleotide polymorphisms (SNP) now act as a third source of data for national genetic evaluations of dairy cattle, in addition to phenotypes and pedigrees that were the basis of selection for the previous 100 years. Rapid developments in genotyping tools have lowered the cost of obtaining this genomic data to just over $200 per animal. The Illumina BovineSNP50 BeadChip (Matukumalli et al., 2008), developed in cooperation with USDA's Bovine Functional Genomics Laboratory (Beltsville, MD) and the University of Missouri (Columbia, MO), has been used to genotype >15,000 dairy animals in North America already during the first year of sale. This same chip is being used worldwide by dairy cattle breeders, with rapid adoption across Europe and in Oceania. Advances in genomic technology in recent years were driven primarily by human DNA sequencing and genotyping projects. The human sequence was completed in 2001, the cattle sequence in 2004, and the pig sequence is now being constructed. Design of the cattle SNP chip required obtaining equally spaced SNP that are highly polymorphic across many dairy and beef breeds (Van Tassell et al., 2008) so that the BovineSNP50 chip could be used for Bos taurus breeds and also for Bos indicus breeds, with possible use for buffalo, bison, yak, etc. Future advances in genomic technology may be driven more by commercial applications to animal breeding programs, with an emphasis on low cost chips applied to large populations. Quality of genomic data is very high (Wiggans et al., 2008). Most SNP have <1% missing genotypes, and error rates are <0.05%. Missing genotypes can be filled in and errors corrected by comparing SNP of closely related animals. About 10,000 of the 50,000 SNP that were polymorphic across breeds had minor allele frequencies <2% in Holsteins and were not used in genomic evaluation. Seven different laboratories provided data, including BFGL, U. Missouri, U. Alberta, GeneSeek, Genetics and IVF Institute, Genetic Visions, and Illumina.