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

Abstract

Genomic selection has become the dominant tool for genetic improvement in livestock and plants. Therefore, its sustainability is essential for global food production. Selection changes the allelic architecture of traits to create genetic gain. It remains unknown whether the changes in allele architecture are different for genomic selection and whether they depend on the genetic architectures of traits. Here we investigate the allele frequency changes of loci and new causal mutations 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 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 large 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, it is very important to be able to minimize the impact of hitchhiking and to limit the loss of favorable alleles more that current genomic selection methods do.