Short communication: Improving accuracy of Jersey genomic evaluations in the United States and Denmark by sharing reference population bulls

Abstract

The effect on prediction accuracy for Jersey genomic evaluations of Danish and US bulls from using a larger reference population was assessed. Each country contributed genotypes from 1,157 Jersey bulls to the reference population of the other. Data were separated into reference (US only, Danish only, and combined US-Danish) and validation (US only and Danish only) populations. Depending on trait (milk, fat, and protein yields and component percentages; productive life; somatic cell score; daughter pregnancy rate; 14 conformation traits; and net merit), the US reference population included 2,720 to 4,772 bulls and cows with traditional evaluations as of August 2009; the Danish reference population included 635 to 996 bulls. The US validation population included 442 to 712 bulls that gained a traditional evaluation between August 2009 and December 2013; the Danish validation population included 105 to 196 bulls with multitrait across-country evaluations on the US scale by December 2013. Genomic predicted transmitting abilities (GPTA) were calculated on the US scale using a selection index that combined direct genomic predictions with either traditional predicted transmitting ability for the reference population or traditional parent averages (PA) for the validation population and a traditional evaluation based only on genotyped animals. Reliability for GPTA was estimated from the reference population and August 2009 traditional PA and PA reliability. For prediction of December 2013 deregressed daughter deviations on the US scale, mean August 2009 GPTA reliability for Danish validation bulls was 0.10 higher when based on the combined US-Danish reference population than when the reference population included only Danish bulls; for US validation bulls, mean reliability increased by 0.02 when Danish bulls were added to the US reference population. Exchanging genotype data to increase the size of the reference population is an efficient approach to increasing the accuracy of genomic prediction when the reference population is small.