Search

Supplemental tables for the manuscript Sallam et al. (2022):Across-countries genomic prediction using national breeding values or multitrait across-countries evaluation breeding valuesM. Sallam, H. Benhajali, S. Savoia, D. J. de Koning, and E. Strandberg** Manuscript in Journal of Dairy Science

Additional file 1: Figure S1. Predicted porcine PRDM9 binding site from the amino acid sequence, with reverse complement and the canonical PRDM9 motif for comparison. The sequence logos were generated with the online predictor of [45].

BackgroundIn this paper, we simulate deleterious load in an animal breeding program, and compare the efficiency of genome editing and selection for decreasing load. Deleterious variants can be identified by bioinformatics screening methods that use sequence conservation and biological prior information about protein function. Once deleterious variants have been identified, how can they be used in breeding?ResultsWe simulated a closed animal breeding population subject to both natural selection against deleterious load and artificial selection for a quantitative trait representing the breeding goal. Deleterious load was polygenic and due to either codominant or recessive variants. We compared strategies for removal of deleterious alleles by genome editing (RAGE) to selection against carriers. Each strategy varied in how animals and variants were prioritized for editing or selection.ConclusionsGenome editing of deleterious alleles reduces deleterious load, but requires simultaneous editing of multiple deleterious variants in the same sire to be effective when deleterious variants are recessive. In the short term, selection against carriers is a possible alternative to genome editing when variants are recessive. The dominance of deleterious variants affects both the efficiency of genome editing and selection against carriers, and which variant prioritization strategy is the most efficient. Our results suggest that in the future, there is the potential to use RAGE against deleterious load in animal breeding.