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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