Improving Genomic Prediction of Late Blight Resistance in Potato by Incorporating Indirect Genetic Effects and Foliage Maturity–Corrected Breeding Values

Abstract Late blight of potato ( Phytophthora infestans ) remains a persistent threat to global potato production. Due to the pathogen’s ability to rapidly overcome race-specific resistance genes, modern potato breeding must focus on durable quantitative resistance, including the use of genomic selection approaches. In this study, several genomic prediction models for late blight resistance were evaluated, differing in their treatment of spatial effects and incorporation of indirect genetic effects (IGEs) from neighbors. The optimal model was subsequently extended to a bivariate formulation to derive maturity-corrected genomic breeding values, effectively removing the confounding influence of foliage maturity on late blight resistance. Our results showed that additive genetic variance for late blight resistance accounted for a substantial proportion of total variance (h² = 0.32±0.02) and IGEs from neighboring plots were significant based on a standard likelihood ratio test. Although IGEs explained only a small portion of total variances, their inclusion markedly improved model prediction accuracy. We also observed a relatively high genetic correlation between foliage maturity and late blight score (0.56± 0.09), indicating that late-maturing lines tend to exhibit higher levels of durable resistance to late blight. After correcting for the confounding influence of foliage maturity, the narrow-sense heritability of the residual breeding value remained moderate (h² = 0.26), suggesting that meaningful genetic gain through selection is still possible. From a breeder’s perspective, selection based on total late blight resistance could unintentionally favor late-maturing genotypes, due to the positive genetic correlation between two traits. However, with residual breeding value, it is possible to get a response to selection for late blight resistance without affecting foliage maturity type.