Efficiency Under Epistasis of Haplotype-Based Genomic Selection for Pure Line Breeding

The haplotype-based approach is considered a more efficient alternative for genomic selection under epistasis. In this simulation-based study, we evaluated the efficacy of haplotype-based genomic selection under seven digenic epistasis types and the significance of including additive x additive (AxA) effect in selection, in pure line breeding. We simulated a genome comprised of 10 chromosomes of 100 cM, including 1000 genes and 49825 SNPs. We assumed positive dominance and 30% of epistatic genes. We performed haplotype-based genomic selection, using haplotypes of sizes 3, 6, and 9. The training set included all F2 individuals and 18% of the F3 to F7 individuals. Selection efficacy was assessed using realized total genetic gain. We also evaluated the correlation between prediction accuracy and realized genetic gain and the decrease in the genotypic variance. Regardless of the epistasis type, genomic selection is an efficient procedure to develop superior pure lines. There was no haplotype size effect on the genomic selection efficacy. Under no selection, the AxA genetic value showed no significant negative correlation with the number of favorable genes. Under selection, the inclusion of the predicted AxA value for selection did not increase the selection efficacy. Haplotype- and SNP-based genomic selection were equally efficient. Epistasis can decrease the total genetic gain in pure line breeding, compared to traits determined only by additive and dominance gene effects. Under epistasis, there was a highly positive correlation between genetic gain and prediction accuracy. There is no difference between genomic selection procedures regarding the decrease in the genotypic variance.