Genomic Prediction of Pumpkin Hybrid Performance

Genomic prediction has become an increasingly popular tool for hybrid performance evaluation in plant breeding mainly because that it can reduce cost and accelerate a breeding program. In this study, we propose a systematic procedure to predict hybrid performance using a genomic selection (GS) model that takes both additive and dominance marker effects into account. We first demonstrate the advantage of the additive-dominance effects model over the only additive effects model through a simulation study. Based on the additive-dominance model, we predict genomic estimated breeding values (GEBVs) for individual hybrid combinations and their parental lines. The GEBV-based specific combining ability (SCA) for each hybrid and general combining ability (GCA) for its parental lines are then derived to quantify the degree of midparent heterosis (MPH) or better-parent heterosis (BPH) of the hybrid. Finally, we estimate the variance components resulting from additive and dominance gene action effects and heritability using a genomic best linear unbiased predictor (g-BLUP) model. These estimates are used to justify the results of the genomic prediction study. A pumpkin ( spp.) data set is given to illustrate the provided procedure. The data set consists of 320 parental lines with 61,179 collected single nucleotide polymorphism (SNP) markers; 119, 120, and 120 phenotypic values of hybrids on three quantitative traits within maxima Duchesne; and 89, 111, and 90 phenotypic values of hybrids on the same three quantitative traits within Dechesne.