Using the ARS-UCD1.2 reference genome in U.S. evaluations.

The U.S. genomic evaluation began using a new reference map in December 2018 to improve genotype imputation and lethal carrier detection. Additional selected markers and gene tests also were included at the same time to improve reliability of genomic predictions. After edits removed some markers from both the old and new maps that were potentially mismapped, haplotype inheritance was better with the new map for all five breeds tested. The new map and the inclusion of more gene tests detected more carrier animals for 18 of the 24 individual variants tracked, thereby improving the accuracy of imputing carrier status. A further benefit of using the new map for national genetic evaluation was to allow simpler merging with international sequence data from run 7 of the 1000 Bull Genomes Project that also aligned variants to the new map.