Simulation of pedigree vs. fully-informative marker based relationships matrices in a loblolly pine breeding population

Abstract

Computer simulations of breeding strategies are an essential resource for tree breeders because they allow exploratory analyses into potential long-term impacts on genetic gain and inbreeding consequences without bearing the cost, time, or resource requirements of field experiments. Previous work has modeled the potential long-term implications on inbreeding and genetic gain using random mating and phenotypic selection. Reduction in sequencing costs has enabled the use of DNA marker-based relationship matrices in addition to or in place of pedigree-based allele sharing estimates; this has been shown to provide a significant increase in the accuracy of progeny breeding value prediction. A potential pitfall of genomic selection using genetic relationship matrices is increased coancestry among selections, leading to the accumulation of deleterious alleles and inbreeding depression. We used simulation to compare the relative genetic gain and risk of inbreeding depression within a breeding program similar to loblolly pine, utilizing pedigree-based or marker-based relationships over ten generations. We saw a faster rate of purging deleterious alleles when using a genomic relationship matrix based on markers that track identity-by-descent of segments of the genome. Additionally, we observed an increase in the rate of genetic gain when using a genomic relationship matrix instead of a pedigree-based relationship matrix. While the genetic variance of populations decreased more rapidly when using genomic-based relationship matrices as opposed to pedigree-based, there appeared to be no long-term consequences on the accumulation of deleterious alleles within the simulated breeding strategy.