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 | |
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 |