Upweighting rare favourable alleles increases long-term genetic gain in genomic selection programs

The short-term impact of using different genomic prediction (GP) models in genomic selection has been intensively studied, but their long-term impact is poorly understood. Furthermore, long-term genetic gain of genomic selection is expected to improve by using Jannink's weighting (JW) method, in which rare favourable marker alleles are upweighted in the selection criterion. In this paper, we extend the JW method by including an additional parameter to decrease the emphasis on rare favourable alleles over the time horizon, with the purpose of further improving the long-term genetic gain. We call this new method dynamic weighting (DW). The paper explores the long-term impact of different GP models with or without weighting methods.

Different selection criteria were tested by simulating a population of 500 animals with truncation selection of five males and 50 females. Selection criteria included unweighted and weighted genomic estimated breeding values using the JW or DW methods, for which ridge regression (RR) and Bayesian lasso (BL) were used to estimate marker effects. The impacts of these selection criteria were compared under three genetic architectures, i.e. varying numbers of QTL for the trait and for two time horizons of 15 (TH15) or 40 (TH40) generations.

For unweighted GP, BL resulted in up to 21.4% higher long-term genetic gain and 23.5% lower rate of inbreeding under TH40 than RR. For weighted GP, DW resulted in 1.3 to 5.5% higher long-term gain compared to unweighted GP. JW, however, showed a 6.8% lower long-term genetic gain relative to unweighted GP when BL was used to estimate the marker effects. Under TH40, both DW and JW obtained significantly higher genetic gain than unweighted GP. With DW, the long-term genetic gain was increased by up to 30.8% relative to unweighted GP, and also increased by 8% relative to JW, although at the expense of a lower short-term gain.

Irrespective of the number of QTL simulated, BL is superior to RR in maintaining genetic variance and therefore results in higher long-term genetic gain. Moreover, DW is a promising method with which high long-term genetic gain can be expected within a fixed time frame.