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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #366137

Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

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

Author
item Null, Daniel
item Vanraden, Paul
item Rosen, Benjamin
item O'CONNELL, JEFFREY - University Of Maryland School Of Medicine
item Bickhart, Derek

Submitted to: Interbull Annual Meeting Proceedings
Publication Type: Proceedings
Publication Acceptance Date: 11/13/2019
Publication Date: 11/13/2019
Citation: Null, D.J., Van Raden, P.M., Rosen, B.D., O'Connell, J.R., Bickhart, D.M. 2019. Using the ARS-UCD1.2 reference genome in U.S. evaluations. Interbull Bulletin. 55:30-34.

Interpretive Summary:

Technical Abstract: 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 5 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 run7 of the 1000 Bull Genomes Project that also aligned variants to the new map.