The Impact of Genetic Relationship Information on Genome-Assisted Breeding Values

TLDR

Genomic selection’s success hinges on accurately predicting genome‑assisted breeding values (GEBVs) over generations without additional phenotyping, a goal that requires sufficient linkage disequilibrium (LD) between markers and quantitative trait loci. The study proposes strategies to validate the accuracy of GEBVs that arise from LD. These strategies involve evaluating GEBV accuracy across generations using simulations and practical data. Simulations reveal that marker‑based GEBV accuracies are nonzero without LD, decline rapidly as LD decays, yet a persistent component remains that can be modeled; RR‑BLUP is most affected, Bayes‑B performs best, FR‑LS merits further study, and RR‑BLUP is not recommended, highlighting the need to analyze multiple generations to assess LD effects.

Abstract

The success of genomic selection depends on the potential to predict genome-assisted breeding values (GEBVs) with high accuracy over several generations without additional phenotyping after estimating marker effects. Results from both simulations and practical applications have to be evaluated for this potential, which requires linkage disequilibrium (LD) between markers and QTL. This study shows that markers can capture genetic relationships among genotyped animals, thereby affecting accuracies of GEBVs. Strategies to validate the accuracy of GEBVs due to LD are given. Simulations were used to show that accuracies of GEBVs obtained by fixed regression–least squares (FR–LS), random regression–best linear unbiased prediction (RR–BLUP), and Bayes-B are nonzero even without LD. When LD was present, accuracies decrease rapidly in generations after estimation due to the decay of genetic relationships. However, there is a persistent accuracy due to LD, which can be estimated by modeling the decay of genetic relationships and the decay of LD. The impact of genetic relationships was greatest for RR–BLUP. The accuracy of GEBVs can result entirely from genetic relationships captured by markers, and to validate the potential of genomic selection, several generations have to be analyzed to estimate the accuracy due to LD. The method of choice was Bayes-B; FR–LS should be investigated further, whereas RR–BLUP cannot be recommended.