Comparison of linear and semi-parametric models incorporating genomic, pedigree, and associated loci information for the prediction of resistance to stripe rust in an Austrian winter wheat breeding program

KEY MESSAGE: We used a historical dataset on stripe rust resistance across 11 years in an Austrian winter wheat breeding program to evaluate genomic and pedigree-based linear and semi-parametric prediction methods. ABSTRACT: Stripe rust (yellow rust) is an economically important foliar disease of wheat (Triticum aestivum L.) caused by the fungus Puccinia striiformis f. sp. tritici. Resistance to stripe rust is controlled by both qualitative (R-genes) and quantitative (small- to medium-effect quantitative trait loci, QTL) mechanisms. Genomic and pedigree-based prediction methods can accelerate selection for quantitative traits such as stripe rust resistance. Here we tested linear and semi-parametric models incorporating genomic, pedigree, and QTL information for cross-validated, forward, and pairwise prediction of adult plant resistance to stripe rust across 11 years (2008–2018) in an Austrian winter wheat breeding program. Semi-parametric genomic modeling had the greatest predictive ability and genetic variance overall, but differences between models were small. Including QTL as covariates improved predictive ability in some years where highly significant QTL had been detected via genome-wide association analysis. Predictive ability was moderate within years (cross-validated) but poor in cross-year frameworks. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00122-023-04249-6.