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

Genetic selection has been applied for many generations in animal, plant, and experimental populations. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allelic architecture are different for the recently introduced technique genomic selection compared to traditional selection methods and whether they depend on the genetic architectures of traits. Here we investigate the allele frequency changes of old and new causal loci under fifty generations of phenotypic, pedigree, and genomic selection, for a trait controlled by either additive, additive and dominance, or additive, dominance and epistatic effects. Genomic selection resulted in slightly larger and faster changes in allele frequencies of causal loci than pedigree selection. For each locus, allele frequency change per generation was not only influenced by its statistical additive effect, but also for a large extent by the linkage phase with other loci and its allele frequency. Selection fixed a large number of loci, and five times more unfavorable alleles became fixed with genomic and pedigree selection than with phenotypic selection. For pedigree selection, this was mainly a result of increased genetic drift, while genetic hitchhiking had a larger effect with genomic selection. When epistasis was present, the average allele frequency change was smaller (∼15% lower) and a lower number of loci became fixed for all selection methods. We conclude that for long-term genetic improvement using genomic selection, it is important to consider hitchhiking and to limit the loss of favorable alleles.