Comparison of long-term effects of genomic selection index and genomic selection using different Bayesian methods

Aggregate genotype in selection programs commonly includes multiple traits, and response to individual traits have importance in addition to their inclusion in the aggregate genotype. The availability of the effect of all markers on genomic selection is an opportunity to select animals based on the desired marker alleles that affect different traits. Genomic selection index (GSI) method divides markers into different groups based on their effects on different traits. It combines and weighs the genomic breeding value of each marker group into an overall index such that maximize response in the aggregate genotype. The primary purpose of this study was to evaluate the long-term effect of GSI compared to genomic selection on genetic progress of a two-trait aggregate genotype and its constituent traits using different Bayesian methods. The results showed that when the correlation between traits was negative, the GSI method yielded higher gain than the genomic selection for the low heritable trait and the aggregate genotype. However, the GSI superiority was decreased as the correlation between the traits increased and a similar response to the genomic selection was obtained for the correlation of 0.5. A higher reduction in genetic variance was observed for scenarios that cause a more significant response to selection. The inbreeding rate was relatively low in all scenarios. The results of this study suggest the use of GSI rather than genomic selection, especially when traits with low heritability are present in the aggregate genotype, and have a negative correlation with other high heritability traits.