Prediction of additive, epistatic, and dominance effects using models accounting for incomplete inbreeding in parental lines of hybrid rye and sugar beet

Genomic models for prediction of additive and non-additive effects within and across different heterotic groups are lacking for breeding of hybrid crops. In this study, genomic prediction models accounting for incomplete inbreeding in parental lines from two different heterotic groups were developed and evaluated. The models can be used for prediction of general combining ability (GCA) of parental lines from each heterotic group as well as specific combining ability (SCA) of all realized and potential crosses. Here, GCA was estimated as the sum of additive genetic effects and within-group epistasis due to high degree of inbreeding in parental lines. SCA was estimated as the sum of across-group epistasis and dominance effects. Three models were compared. In model 1, it was assumed that each hybrid was produced from two completely inbred parental lines. Model 1 was extended to include three-way hybrids from parental lines with arbitrary levels of inbreeding: In model 2, parents of the three-way hybrids could have any levels of inbreeding, while the grandparents of the maternal parent were assumed completely inbred. In model 3, all parental components could have any levels of inbreeding. Data from commercial breeding programs for hybrid rye and sugar beet was used to evaluate the models. The traits grain yield and root yield were analyzed for rye and sugar beet, respectively. Additive genetic variances were larger than epistatic and dominance variances. The models' predictive abilities for total genetic value, for GCA of each parental line and for SCA were evaluated based on different cross-validation strategies. Predictive abilities were highest for total genetic values and lowest for SCA. Predictive abilities for SCA and for GCA of maternal lines were higher for model 2 and model 3 than for model 1. The implementation of the genomic prediction models in hybrid breeding programs can potentially lead to increased genetic gain in two different ways: I) by facilitating the selection of crossing parents with high GCA within heterotic groups and II) by prediction of SCA of all realized and potential combinations of parental lines to produce hybrids with high total genetic values.