Response to selection from using identified genes and quadratic indices in two-traits breeding goals

Abstract

Benefits from the use of optimised selection for maximising genetic gain while constraining the rate of inbreeding were evaluated through stochastic simulation for scenarios where the breeding goal includes two negatively correlated traits. One of the traits was controlled only by polygenes and had a heritability of 0.3 while the other trait was controlled by an identified additive biallelic QTL (with an initial allele frequency of 0.15) and by polygenes and had a polygenic heritability of 0.1. Optimised selection was compared to standard truncation selection both when the information on the QTL was used and when it was ignored. Extra gains in the breeding goal were observed throughout the 10 simulated generations from the combined use of optimised contributions and QTL information although, as expected, this scheme was not the most effective for improving individual traits. By generation ten, the gain in the aggregate breeding value with optimised selection was about 12% higher than with truncation selection. Optimised selection allowed extra polygenic responses in both traits but these extra responses were negative for the trait under mixed inheritance. The use of the QTL allowed not only positive gains in the trait with the lowest heritability, but also avoided the loss of the favourable allele. The effect of selecting for the QTL on each trait depended on its relative weight in the selection index and not exclusively on the inheritance model.