The long-term effects of genomic selection: 2. Changes in allele frequencies of causal loci and new mutations.

This article investigates the long-term effects of different selection methods—phenotypic, pedigree-based best linear unbiased prediction (PBLUP), and genomic best linear unbiased prediction (GBLUP)—on allele frequency changes at causal loci and new mutations over 50 generations in simulated livestock populations. The study compares traits controlled by additive, additive plus dominance, and additive plus dominance plus epistatic genetic architectures. Results show that genomic selection (GBLUP) induces slightly larger and faster allele frequency changes and fixes more loci, including a higher number of unfavorable alleles due to genetic hitchhiking, compared to pedigree selection and phenotypic selection. The presence of nonadditive effects, especially epistasis, reduces allele frequency changes by altering selection pressure and direction over time. Additionally, phenotypic selection maintains more new mutational variance than genomic or pedigree selection, highlighting the importance of own performance records in exploiting new mutations for long-term genetic gain. The findings emphasize the need to manage hitchhiking effects in genomic breeding programs to preserve favorable alleles critical for sustained improvement.