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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: Multibreed Genomic Evaluation of Dairy Cattle

Authors
item Olson, K -
item Vanraden, Paul

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: March 8, 2010
Publication Date: June 24, 2010
Citation: Olson, K.M., Van Raden, P.M. 2010. Multibreed Genomic Evaluation of Dairy Cattle. Journal of Dairy Science. 93(E-Suppl. 1):471(abstr. 438).

Technical Abstract: Multibreed models are currently used in traditional USDA dairy cattle genetic evaluations of yield and health traits, but within-breed models are used in genomic evaluations. Multibreed genomic models were developed and tested using all 19,686 genotyped bulls included in the official August 2009 USDA genomic evaluation. The data were divided into training and validation sets. The training data set were comprised of bulls that were proven (had daughter information) as of November 2004 and totaled 5,331, 1,361, and 506 Holstein, Jersey, and Brown Swiss, respectively. The validation data set had 2,477 Holstein, 410 Jersey, and 182 Brown Swiss bulls that were unproven (no daughter information) in November 2004 and proven by August 2009. A common set of 43,385 single nucleotide polymorphisms (SNP) were used for all breeds. Three methods of multibreed evaluation were investigated. Method 1 estimated SNP effects separately within-breed and was tested by multiple regressions to predict daughter deviations of bulls of another breed. Method 2 estimated a common set of SNP effects from combined genotypes and phenotypes of all breeds. Method 3 solved for correlated SNP effects within each breed estimated jointly using a multitrait model. Multiple regressions were used to test across-breed genomic predicted transmitting ability (GPTA) with within-breed GPTA and parent average (PA). A few effects were significant with method 1, mostly for Jerseys and Holsteins, but estimates were small compared with within-breed GPTA and PA. Across-breed GPTA from method 2 were significant for certain traits in some breeds; correlations between within-breed GPTA and across-breed GPTA ranged between 0.91 and 0.93. Results from method 3 were significant and adjusted coefficient of determinations for protein yield (the only trait tested for method 3) were highest of all methods for all breeds. However, compared with the current within-breed genomic model, method 3 increased the adjusted coefficient of determination by only 0.0097, 0.0042, and 0.0017 for Brown Swiss, Jerseys, and Holsteins, respectively.

Last Modified: 8/22/2014
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