Comparing the Potential of Marker-Assisted Selection and Genomic Prediction for Improving Rust Resistance in Hybrid Wheat

Abstract

Improving leaf rust and stripe rust resistance is a central goal in wheat breeding. The objectives of this study were to (1) elucidate the genetic basis of leaf rust and stripe rust resistance in a hybrid wheat population, (2) compare the findings using a previously published hybrid wheat data set, and (3) contrast the prediction accuracy with those of genome-wide prediction. The hybrid wheat population included 1,744 single crosses from 236 parental lines. The genotypes were fingerprinted using a 15k SNP array and evaluated for leaf rust and stripe rust resistance in multi-location field trials. We observed a high congruency of putative quantitative trait loci (QTL) for leaf rust resistance between both populations. This was not the case for stripe rust resistance. Accordingly, prediction accuracy of the detected QTL was moderate for leaf rust but low for stripe rust resistance. Genome-wide selection increased the prediction accuracy slightly for stripe rust albeit at a low level but not for leaf rust. Thus, our findings suggest that marker-assisted selection seems to be a robust and efficient tool to improve leaf rust resistance in European wheat hybrids.

Keywords: genome-wide selection; leaf rust (Puccinia triticina); marker-assisted selection; resistance breeding; stripe rust (Puccinia striiformis Westend).

FIGURE 1

Result of principal component analysis (PCoA) observing the relationship and aggregation of parental lines and check varieties based on Rogers’ distances calculated using genome-wide marker data.

FIGURE 2

Manhattan plots of the genome-wide association scans for additive and dominance effects on leaf rust (A) and stripe rust resistance (B). The horizontal line symbolizes the significant threshold of P < 0.05 applying Bonferroni correction. The hexaploid genome of bread wheat consists of 42 chromosomes combining the complete chromosomal sets of three different wild grasses, which are differentiated by the letters A, B, and D. The x-axis shows chromosomal location of the corresponding markers, while UM are unmapped markers.

FIGURE 3

BLUEs representing leaf rust and stripe rust resistance of 11 check varieties, used in field trials of a previous study realized during field seasons in 2016 and 2017 in comparison to the field trial of 2018 belonging to this study.

FIGURE 4

Venn diagram showing numbers of detected and overlapping QTLs for leaf rust (A) and stripe rust resistance (B) comparing results of the present study with a previous published study by Beukert et al. (2020) (previous study).