Comparison of Models and Whole‐Genome Profiling Approaches for Genomic‐Enabled Prediction of Septoria Tritici Blotch, Stagonospora Nodorum Blotch, and Tan Spot Resistance in Wheat

Abstract

The leaf spotting diseases in wheat that include Septoria tritici blotch (STB) caused by Zymoseptoria tritici , Stagonospora nodorum blotch (SNB) caused by Parastagonospora nodorum , and tan spot (TS) caused by Pyrenophora tritici‐repentis pose challenges to breeding programs in selecting for resistance. A promising approach that could enable selection prior to phenotyping is genomic selection that uses genome‐wide markers to estimate breeding values (BVs) for quantitative traits. To evaluate this approach for seedling and/or adult plant resistance (APR) to STB, SNB, and TS, we compared the predictive ability of least‐squares (LS) approach with genomic‐enabled prediction models including genomic best linear unbiased predictor (GBLUP), Bayesian ridge regression (BRR), Bayes A (BA), Bayes B (BB), Bayes Cπ (BC), Bayesian least absolute shrinkage and selection operator (BL), and reproducing kernel Hilbert spaces markers (RKHS‐M), a pedigree‐based model (RKHS‐P) and RKHS markers and pedigree (RKHS‐MP). We observed that LS gave the lowest prediction accuracies and RKHS‐MP, the highest. The genomic‐enabled prediction models and RKHS‐P gave similar accuracies. The increase in accuracy using genomic prediction models over LS was 48%. The mean genomic prediction accuracies were 0.45 for STB (APR), 0.55 for SNB (seedling), 0.66 for TS (seedling) and 0.48 for TS (APR). We also compared markers from two whole‐genome profiling approaches: genotyping by sequencing (GBS) and diversity arrays technology sequencing (DArTseq) for prediction. While, GBS markers performed slightly better than DArTseq, combining markers from the two approaches did not improve accuracies. We conclude that implementing GS in breeding for these diseases would help to achieve higher accuracies and rapid gains from selection.