The fate of new mutations: genomic selection exploits new mutation variance to a much smaller degree than traditional selection

Abstract

New mutations create new genetic variance in populations and contribute to long-term response to selection. We hypothesize that genomic selection exploits new mutational variance much less than traditional selection methods, because new mutations are not in linkage disequilibrium with markers on the current SNP chips, while animals with a favourable mutation have a selective advantage with mass and pedigree-based BLUP selection. We used Monte Carlo simulation using real sequence data to generate the base generation to test this hypothesis. Genomic selection increased response to selection due to old QTL by 33% and 1% in generation 5 and 20 compared to mass selection, respectively, while response to selection from new mutations was 65-85% and 61% lower than with mass selection in generation 5 and 20, respectively. In genomic selection, genetic variance due to old QTL was much faster eroded, while new mutational variance did not increase much, resulting in a ~65% and ~43% lower total genetic variance in generation 20 with genomic selection, compared to mass and pedigree-based BLUP selection. In summary, we showed that genomic selection hardly exploits new mutational variance and erodes genetic variance much faster than mass and BLUP selection. Future research should focus on developing sustainable genomic selection strategies to optimize long-term response to selection, exploiting new mutational variance.