Genomic selection without own phenotypes exploits new mutational variance less than BLUP selection

Abstract

De novo mutations (DNM) create new genetic variance and are an important driver for long-term selection response. We hypothesized that genomic selection without own phenotypes exploits new mutational variance less than pedigree-based BLUP selection. The objectives were to compare GBLUP selection without own phenotype (GBLUP), GBLUP selection with own phenotype (GBLUP_OP) and pedigree-based BLUP selection with own phenotype for 20 generations using Monte Carlo simulation. GBLUP resulted in the lowest genetic variance (24.7% of total genetic variance) and response due to DNM after 20 generations (9.4% of total response). GBLUP_OP had the highest genetic variance due to new DNM (47.8% of total genetic variance) and selection response due to DNM (30% of total response), while BLUP was in between with 27.1% of genetic variance due to DNM and 21.9% of response due to DNM. However, GBLUP_OP caused a rapid decline in total genetic variance, because the genetic variance due to old QTL rapidly eroded. GBLUP had very little selection pressure on DNM and as a consequence, GBLUP had the highest number of DNM with negative effects that were still segregating 10 generations after a DNM arose. Due to the decline in genetic variance for all selection strategies, selection limits are foreseen and these selection limits are lower for GBLUP (11.2 phenotypic SD from the base population mean) and GBLUP_OP (10.7 phenotypic SD) than for BLUP selection (11.8 phenotypic SD). It can be concluded that genomic selection without own phenotypes exploits new mutational variance less than BLUP selection with own phenotypes, it increases the probability of DNM with negative effects and it lowers selection limits. Sustainable breeding strategies should consider optimal ways to exploit DNM.