Genomic selection in the presence of major and minor genes

Arron H. Carter and Lance F. Merrick.

**Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA

ahcarter@wsu.edu

Abstract

Many traits in plants are quantitative in nature and under control of both major and minor genes. This research aimed to optimize genomic selection (GS) models for use in breeding programs needing to select both major and minor genes. In this experiment, stripe rust (Puccinia striiformis Westend. f. sp. tritici Erikss.) of wheat (Triticum aestivum L.) was used as a model for quantitative disease resistance. Two traits of stripe rust, infection type and disease severity, were used as the phenotype. Two types of training populations were compared, one composed of 2,630 breeding lines phenotyped in unreplicated trials between 2016 and 2020, and a diversity panel with 472 lines from 2013 to 2016, both across two locations. The accuracy of models with four different major gene markers and genome-wide association (GWAS) markers as fixed effects were used. The prediction models included 31,975 markers replicated 50 times using 5-fold cross-validation. Genomic selection models were compared with marker-assisted selection to evaluate the prediction accuracy of the markers alone and in combination. The GS models had higher accuracies than marker-assisted selection and reached an accuracy of 0.72 for disease severity. The major gene and GWAS markers had only a small to zero increase in prediction accuracy over the base GS model, with the highest accuracy increase of 0.03 for major markers and 0.06 for GWAS markers. There was a statistical increase in accuracy by using the breeding lines, population type, major markers, and by combing years. The inclusion of fixed effects in low prediction scenarios increased 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. This method should be useful for other traits in which breeding program have already heavily selected for the presence of major and minor genes within the program.

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Keywords: Genomic selection, Wheat, Disease resistance, Major and minor genes.

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