Abstract
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.
Highlights
In 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
In the CONTROL population, the Estimated Breeding Values (EBV) of young sires (YS) were unbiased since all the selection candidates were included in the BLUP evaluation (Table 3): both the mean Mendelian sampling estimate and the mean difference between true and estimated breeding values were not significantly different from zero
There is an urgent need to account for genomic preselection of young sires before their national EBV become biased
Summary
In 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. Including genotyped and non-genotyped animals in a single genetic analysis is necessary to properly account for biases due to selective genotyping [7] or phenotyping [4,6,8] The latter corresponds, for example, to young sires that are pre-selected based on genomic information: only sires with higher GEBV and with a higher Mendelian sampling term receive phenotypes from daughters a few years after pre-selection. One concern is that biased EBV and their corresponding daughter yield deviations (DYD) may impact the estimation of SNP effects in subsequent years This issue is relevant at the international level, since the trade of bull semen is based on EBV from Multiple Across Country Evaluations (MACE) that are computed assuming unbiased national EBV. With genomic pre-selection more and more widely implemented, accounting for such practices is becoming very important
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