Alignment of pedigree and genomic information in a combined terminal sire and maternal sheep analysis

Recent efforts to combine the Sheep Genetics LAMBPLAN maternal and terminal sire analyses presented the opportunity to review the genomic model used in single-step genomic BLUP. This paper uses forward validation to examine the suitability of different genomic models, including metafounders, a genomic relationship matrix (GRM) constructed from a single set of allele frequencies and a breed-adjusted GRM using allele frequencies for each identified subpopulation. The metafounder model yielded slightly higher stability values and was slightly less biased than the other genomic models. Metafounders also largely resulted in higher within-breed stabilities. These results support the use of a metafounder model for the combined LAMBPLAN analysis.