Simulations of multiple breeding strategy scenarios in common bean for
assessing genomic selection accuracy and model updating
Abstract
Genomic prediction allows breeders to make selections based on the
genomic estimated breeding value (GEBV) of selection candidates. GEBVs
are assigned using a prediction model trained with genotypes and
phenotypes from a training population. For this reason, the
effectiveness of genomic selection is strongly tied to the prediction
accuracy of the model used to estimate breeding values and the training
population used to inform the model. The aim of this study was to
evaluate the accuracy of the ridge regression best linear unbiased
prediction (rrBLUP) model across different traits, parent population
sizes, and breeding strategies when estimating breeding values in
Phaseolus vulgaris. The model was trained on a simulated population
genotyped for 1010 SNP markers including 38 known QTLs identified in the
literature (Lin, 2022). Simulation results revealed that realized
accuracies fluctuate depending on the factors investigated: trait
genetic architecture, breeding strategy, and the number of initial
parents involved in the breeding program. Trait architecture and
breeding strategy appeared to have a larger impact on accuracy than the
initial number of parents. Generally, maximum accuracies were achieved
under a mass selection strategy followed by pedigree and single-seed
descent methods. This study also investigated model updating, which
involves re-training the prediction model with a more relevant set of
genotypes and phenotypes. While it has been repeatedly shown that model
updating generally improves prediction accuracy, it benefitted some
breeding strategies more than others. For low heritability traits (e.g.,
yield) conventional phenotype-based selection methods showed consistent
rates of genetic gain, but genetic gain under genomic selection reached
a plateau in after fewer cycles.