Breeding with Major and Minor Genes: Genomic Selection for Quantitative Disease Resistance

Disease resistance in plants is mostly quantitative, with both major and minor genes controlling resistance. This research aimed to optimize genomic selection (GS) models for use in breeding programs that are needed to select both major and minor genes for resistance. In this study, stripe rust (Puccinia striiformis Westend. f. sp. tritici Erikss.) of wheat (Triticum aestivum L.) was used as a model for quantitative disease resistance. The quantitative nature of stripe rust is usually phenotyped with two disease traits, infection type (IT) and disease severity (SEV). We compared two types of training populations composed of 2,630 breeding lines (BLs) phenotyped in single-plot trials from 4 years (2016-2020) and 475 diversity panel (DP) lines from 4 years (2013-2016), both across two locations. We also compared the accuracy of models using four different major gene markers and genome-wide association study (GWAS) markers as fixed effects. The prediction models used 31,975 markers that are replicated 50 times using a 5-fold cross-validation. We then compared GS models using a marker-assisted selection (MAS) to compare the prediction accuracy of the markers alone and in combination. GS models had higher accuracies than MAS and reached an accuracy of 0.72 for disease SEV. The major gene and GWAS markers had only a small to nil increase in the prediction accuracy more than the base GS model, with the highest accuracy increase of 0.03 for the major markers and 0.06 for the GWAS markers. There was a statistical increase in the accuracy using the disease SEV trait, BLs, population type, and combining years. There was also a statistical increase in the accuracy using the major markers in the validation sets as the mean accuracy decreased. The inclusion of fixed effects in low prediction scenarios increased the accuracy up to 0.06 for GS models using significant GWAS markers. Our results indicate that GS can accurately predict quantitative disease resistance in the presence of major and minor genes.