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Table 2 Summary of the long-term effects of genomic selection and associated mechanisms

From: The long-term effects of genomic selection: 1. Response to selection, additive genetic variance, and genetic architecture

Long-term effects of genomic selection on

Simulation results

Likely or proven mechanisms

Rate of genetic gain (Fig. 3)

Large drop in rate of genetic gain over generations

Loss in additive genetic variance and reduction in accuracy

Epistasis increased the drop in rate of genetic gain over generations

Epistasis reduced the informativeness of previous generations for breeding value estimation, and increased the level of inbreeding depression

Higher rate of genetic gain with genomic selection than with pedigree selection

Accuracy of breeding value estimation is higher with genomic selection than pedigree selection

Loss in additive genetic variance (Fig. 4)

First generations: large drop in additive genetic variance, smaller drop in additive genic variance

Bulmer effect, resulting in transient loss in additive genetic variance due to negative covariances between loci

Later generations: large drop in additive genetic and genic variance

Reduction in the number of segregating loci, because of fixation of alleles due to selection and losing rare favorable alleles as a result of shrinking estimated effects of rare loci towards zero. Moreover, the average heterozygosity level reduced due to selection

Epistasis reduced the loss in additive genetic variance

Epistasis resulted in fixing a lower number of loci, because the pressure and direction of selection at a locus can change over generations due to changing statistical additive effects

Similar loss in additive genetic variance with genomic selection than with pedigree selection

Genomic selection maintained more segregating loci, but each of them with a lower MAF than pedigree selection, probably because pedigree selection results in a stronger family selection

Change in genetic architecture of traits (Figs. 8, 9, 10)

Large change in genetic architecture

Selection changes the allele frequencies of causal loci, thereby changing the subset of segregating causal loci and their statistical additive effects

Epistasis reduced the change in subset of loci and allele frequencies, but increased the change in statistical additive effects

When epistasis was present, statistical additive effects of causal loci changed across generations, which lowered the change in allele frequency because the pressure and direction of selection at a locus changed across generations

Subtle differences in change in genetic architecture between pedigree and genomic selection

Genomic selection focused more on a subset of genes that change rapidly, but the average change in allele frequency was similar for genomic and pedigree selection