Measuring genomic pre-selection in theory and in practice

Authors: Vanraden, Paul; Wright, Janice

Submitted to: Interbull Annual Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 9/13/2013
Publication Date: 9/13/2013
Citation: Van Raden, P.M., Wright, J.R. 2013. Measuring genomic pre-selection in theory and in practice. Interbull Annual Meeting Proceedings. Interbull Bulletin 47:147–150.

Interpretive Summary: Genomic selection now occurring in dairy cattle may cause biases in traditional genetic evaluations. Size of biases from genomic pre-selection were estimated using mating patterns for two groups of US Holstein bulls: the top 50 bulls with daughters, mostly selected prior to genomics, and the top 50 bulls without daughters, selected after genomic evaluations were available. Differences between mates’ genomic evaluation and traditional evaluations were small in both groups. The younger bulls had more opportunity for bias, but only 6 of the 50 bulls had >50% of mates genotyped. Biases from mate pre-selection will increase as more animals are genotyped. In addition to bias from mates, future bias from dams of highly pre-selected sons was estimated and found to be larger than that from mates. Some bias can be removed using deregression and the current evaluation method, but a change to single step methods, where all sources of information are used simultaneously, would be better. To continue improvement in traits of economic interest to dairy producers, methods to reduce genomic pre-selection bias are critical and should be implemented soon.

Technical Abstract: Potential biases from genomic pre-selection were estimated from actual selection and mating patterns of US Holsteins. Traditional models using only phenotypes and pedigrees do not adjust for average genomic merit of an animal’s parents, progeny, mates, or contemporaries. Positive assortative mating of elite young bulls to elite genotyped females and dams of highly selected sons will become primary sources of bias in the next few years unless methods of adjustment are introduced. However, deregression can remove some biases such as by crediting the dam for only her own records and not for those of her selected progeny. Diagonals of genomic and pedigree relationship matrices, their inverses, and their differences were examined. The animal’s own genotype provides a fourth source of information along with traditional information from parents, progeny, and own phenotype.