Inclusion of cow records in genomic evaluations and impact on bias due to preferential treatment

Abstract

Abstract Background Today, genomic evaluations are an essential feature of dairy cattle breeding. Initially, genomic evaluation targeted young bulls but recently, a rapidly increasing number of females (both heifers and cows) are being genotyped. A rising issue is whether and how own performance of genotyped cows should be included in genomic evaluations. The purpose of this study was to assess the impact of including yield deviations, i.e. own performance of cows, in genomic evaluations. Methods Two different genomic evaluations were performed: one including only reliable daughter yield deviations of proven bulls based on their non-genotyped daughters, and one including both daughter yield deviations for males and own yield deviations for genotyped females. Milk yield, the trait most prone to preferential treatment, and somatic cell count, for which such a bias is very unlikely, were studied. Data consisted of two groups of animals from the three main dairy breeds in France: 11 884 elite females genotyped by breeding companies and 7032 cows genotyped for a research project (and considered as randomly selected from the commercial population). Results For several measures that could be related to preferential treatment bias, the elite group presented a different pattern of estimated breeding values for milk yield compared to the other combinations of trait and group: for instance, for milk yield, the average difference between estimated breeding values with or without own yield deviations was significantly different from 0 for this group. Correlations between estimated breeding values with or without yield deviations were lower for elite females than for randomly selected cows for milk yield but were very similar for somatic cell count. Conclusions This study demonstrated that including own milk performance of elite females leads to biased (over-estimated) genomic evaluations. Thus, milk production records of elite cows require specific treatment in genomic evaluation.