Mutation breeding for quantitative traits in the era of genomic selection

Mutation breeding creates new genetic variation by inducing random mutations and screening for mutants with desirable phenotypes, whereas selective breeding exploits variants that already segregate in breeding populations. The two approaches have rarely been combined, and whether genomic selection (GS) can capture polygenic variation induced by mutagenesis has not been tested. We evaluated GS in two public panels of advanced mutants (190 wheat and 74 tomato lines) and in simulated biparental and multiparental populations derived from mutants. In both panels, predictive abilities (up to 0.39 in wheat and 0.45 in tomato) came entirely from variants shared among lines, which in wheat formed chromosome segments segregating from the parental cultivar. Variants private to single lines, where induced mutations lie, carried no predictive signal. In simulated crosses in which mutations segregate, GS outperformed marker-assisted selection (MAS) of the largest mutation when mutations were numerous and their effects balanced (genetic value 2.84 vs 0.45 after two cycles), but not when unfavorable mutations dominated. In simulated multiparental populations, mutant founders increased genetic gain over five cycles of GS by 1.3- to 6.8-fold when mutational variance was large, but by only 4-5% when it was small relative to standing variation. Induced polygenic variation therefore becomes accessible to GS once mutations are shared among relatives through crossing, which offers a route to integrate mutation breeding into pre-breeding programmes.