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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVING GENETIC PREDICTIONS FOR DAIRY ANIMALS USING PHENOTYPIC AND GENOMIC INFORMATION Title: Genomic Evaluations: Past, Present, Future

Author
item Wiggans, George

Submitted to: Dairy Cattle Reproduction Council Proceedings
Publication Type: Proceedings
Publication Acceptance Date: November 11, 2010
Publication Date: November 11, 2010
Repository URL: http://aipl.arsusda.gov/publish/other/2010/DCRC2010_grw.pdf
Citation: Wiggans, G.R. 2010. Genomic Evaluations: Past, Present, Future. Dairy Cattle Reproduction Council Proceedings. St. Paul, MN, Nov. 11-12, pp. 45-52.

Interpretive Summary: Genomic evaluation has been implemented in dairy cattle causing profound changes in dairy cattle breeding. Genomic evaluations using Single Nucleotide Polymorphism (SNP) genotypes generated by the Illumina BovineSNP50™ Bead chip resulted from an international consortium including government, university and industry participants. A steady increase in accuracy of evaluations has resulted from including an increasing number of bulls with genotypes and traditional evaluations. Exchange of genotypes with other countries has added predictor bulls and continued collaboration is expected. Illumina has introduced two new chips, the 3K chip with 2900 SNP and the high density (HD) chip with 777,962 SNP. The 3K chip is expected to greatly increase the number of animals genotyped and to replace microsatellites in parentage verification. The HD chip can provide more accurate genomic evaluations by better tracking the loci responsible for genetic differences. To integrate multiple chips, a method to impute missing genotypes was developed based on splitting each genotype into its maternal and paternal haplotypes, and tracing their inheritance. This technique also is used to impute genotypes of ungenotyped dams based on their genotyped progeny and mates. The reliability of resulting evaluations is appropriately discounted to reflect the errors inherent in this process. Accuracy of evaluations is expected to continue to increase and the large population of existing genotypes may be applied to new traits.

Technical Abstract: Genomic evaluation has been implemented in dairy cattle causing profound changes in dairy cattle breeding. All young bulls purchased by major AI organizations are selected based on genomic evaluations. The reliability of these evaluations reaches the mid seventies for yield traits and is adequate to widely market semen on bulls as two year olds. The shortening of the generation interval from using these evaluations is the most important factor in increasing the rate of genetic improvement. Genomic evaluations are based on the over 50,000 Single Nucleotide Polymorphism (SNP) genotypes generated by the Illumina BovineSNP50™ Bead chip. This chip, which resulted from an international consortium including government, university and industry participants, became available in December 2007 and the first unofficial evaluations based on it were released in April 2008. Genomic evaluations became official for Holstein and Jersey in January 2009 and for Brown Swiss in August 2009. A steady increase in accuracy of evaluations has resulted from including an increasing number of bulls with genotypes and traditional evaluations. Much of this increase occurs automatically as bulls genotyped as young bulls receive a traditional evaluation when 5 years old. Cow evaluations also contribute. Their evaluations are adjusted to give them the same mean and variance as bull evaluations which increases their contribution. This adjustment in most cases reduces the evaluation. The full integration of the genotype database with Canada provided a critical source of genotypes to achieve acceptable accuracy initially and the cooperation provides continuing benefits to both countries. Exchange of genotypes with other countries has added predictor bulls for Brown Swiss and collaboration for other breeds is expected. In July 2010, Illumina shipped two new chips, the 3K chip with 2900 SNP and the high density (HD) chip with 777,962 SNP. The 3K chip is expected to greatly increase the number of animals genotyped and to replace microsatellites in parentage verification. The HD chip can provide more accurate genomic evaluations by better tracking the loci responsible for genetic differences. To integrate multiple chips, a method to impute missing genotypes was developed. It is based on splitting each genotype into its maternal and paternal haplotypes, and tracing their inheritance. This technique also is used to impute genotypes of ungenotyped dams based on their genotyped progeny and mates. The reliability of resulting evaluations is appropriately discounted to reflect the errors inherent in this process. Accuracy of evaluations is expected to continue to increase by adding predictor animals and increasing the number of SNP. The large population of existing genotypes can be applied to new traits; however, the challenge is to measure the new traits on enough animals to estimate the SNP effects with sufficient accuracy that they can be usefully applied to the general population.

Last Modified: 8/27/2014
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