Clotilde Patry

Evidence of biases in genetic evaluations due to genomic preselection in dairy cattle

A genomic preselection step of young sires is now often included in dairy cattle breeding schemes. Young sires are selected based on their genomic breeding values. They have better Mendelian sampling contribution so that the assumption of random Mendelian sampling term in genetic evaluations is clearly violated. When these sires and their progeny are evaluated using BLUP, it is feared that estimated breeding values are biased. The effect of genomic selection on genetic evaluations was studied through simulations keeping the structure of the Holstein population in France. The quality of genetic evaluations was assessed by computing bias and accuracy from the difference and correlation between true and estimated breeding values, respectively, and also the mean square error of prediction. Different levels of heritability, selection intensity, and accuracy of genomic evaluation were tested. After only one generation and whatever the scenario, breeding values of preselected young sires and their daughters were significantly underestimated and their accuracy was decreased. Genomic preselection needs to be accounted for in genetic evaluation models.

Accounting for genomic pre-selection in national BLUP evaluations in dairy cattle.

BackgroundIn future Best Linear Unbiased Prediction (BLUP) evaluations of dairy cattle, genomic selection of young sires will cause evaluation biases and loss of accuracy once the selected ones get progeny.MethodsTo avoid such bias in the estimation of breeding values, we propose to include information on all genotyped bulls, including the culled ones, in BLUP evaluations. Estimated breeding values based on genomic information were converted into genomic pseudo-performances and then analyzed simultaneously with actual performances. Using simulations based on actual data from the French Holstein population, bias and accuracy of BLUP evaluations were computed for young sires undergoing progeny testing or genomic pre-selection. For bulls pre-selected based on their genomic profile, three different types of information can be included in the BLUP evaluations: (1) data from pre-selected genotyped candidate bulls with actual performances on their daughters, (2) data from bulls with both actual and genomic pseudo-performances, or (3) data from all the genotyped candidates with genomic pseudo-performances. The effects of different levels of heritability, genomic pre-selection intensity and accuracy of genomic evaluation were considered.ResultsIncluding information from all the genotyped candidates, i.e. genomic pseudo-performances for both selected and culled candidates, removed bias from genetic evaluation and increased accuracy. This approach was effective regardless of the magnitude of the initial bias and as long as the accuracy of the genomic evaluations was sufficiently high.ConclusionsThe proposed method can be easily and quickly implemented in BLUP evaluations at the national level, although some improvement is necessary to more accurately propagate genomic information from genotyped to non-genotyped animals. In addition, it is a convenient method to combine direct genomic, phenotypic and pedigree-based information in a multiple-step procedure.

Effects of a national genomic preselection on the international genetic evaluations

Genomic preselection of young bulls is now widely implemented in dairy breeding schemes, especially in the Holstein breed. However, if this step is not accounted for in genetic evaluation models, the national breeding values of bulls retained by a genomic preselection and of their progeny are estimated with bias. It follows that countries participating in international genetic evaluations will provide a selected and possibly biased set of data to the Interbull Centre (Swedish University of Agricultural Sciences, Uppsala, Sweden). The objective of the study was to show evidence of bias at the international level due to a genomic preselection step in national breeding schemes. The consequence of a genomic preselection for the international evaluations (i.e., using selected and biased national estimated breeding values) was simulated using actual national estimated breeding values as a proxy for genomically enhanced breeding values. Data were provided for 3 countries with a large population of Holstein bulls. International breeding values from simulated scenarios were compared with international breeding values using all available data, assumed to be complete and unbiased. Bias was measured among young bulls retained by a genomic preselection and their contemporaries in other countries. The results were analyzed by traits measured within each country and by country of origin of the young bulls. It turned out that sending preselected data, though based on genomic information, created bias in international evaluations, penalizing young bulls from the country sending the incorrect data. It also had an effect on the young bulls from the other countries. Sending biased data further affected the quality of international evaluations. This study underlines the importance of accounting for genomic preselection at the national level first. Moreover, submitting all available data appeared essential to maintain the quality of the international genetic evaluations after implementation of a genomic preselection step.