Changes to evaluation system (April
Revisions to genomic
By Paul VanRaden and George Wiggans
The order of calculations for genomic evaluations was changed so that new lactation records
received between January and April could be included in April genomic evaluations.
Thus, traditional April evaluations for domestic bulls and January multitrait
across-country evaluations (MACE) for foreign bulls were the input data for estimating the effects of single-nucleotide polymorphisms (SNPs). Current MACE evaluations still are official for bulls with
foreign daughters rather than using the previous MACE evaluation plus genomic information. Although new
programs to combine genomic information with current MACE evaluations are ready, they
were not introduced because the April genotype file was received by the Animal Improvement Programs Laboratory 1 week
later than expected, which did not allow adequate time to check results of the
new blending procedure.
Approximate genomic reliabilities replaced exact reliabilities because
of insufficient time for matrix inversion and multiplication due to the delay in receipt of genotype data. The
total number of animals genotyped now exceeds 25,000, and the time required for
exact reliability calculations increases with the cube of that number. Computation of exact
reliabilities would have required about 2 days, whereas approximate reliabilities require
only about 2 minutes. With the matrix inversion used previously, the number of
daughter equivalents from genomic information differed for each animal
depending on how many close relatives were genotyped. The new approximate
formula adds the same number of daughter equivalents for each genotyped animal.
The sum of traditional reliabilities minus parent-average reliabilities for all
genotyped animals in a breed is divided by a constant chosen to make exact and
approximate daughter equivalents equal on average. Both the exact and
approximate methods are multiplied by 0.6 to match reliabilities observed in
data cutoff studies. As a result of switching to the approximation, genomic
reliabilities for individual animals with many or few genotyped relatives
decreased or increased slightly in April as compared with January. The
approximate reliabilities could be improved, or exact reliabilities could be calculated
in the future if adequate time is available. Use of the approximate
procedure for Holsteins is expected to continue as the number of genotyped animals increases.