Research Article | Open Access

Volume 2019 |Article ID 3285904 | https://doi.org/10.34133/2019/3285904

Precision Phenotyping Reveals Novel Loci for Quantitative Resistance to Septoria Tritici Blotch

Steven YatesiD ,¹ Alexey Mikaberidze,² Simon G. Krattinger,³ Michael AbroukiD ,³ Andreas HundiD ,⁴ Kang YuiD ,⁴ Bruno Studer,¹ Simone Fouche,² Lukas Meile,² Danilo PereiraiD ,² Petteri KaristoiD ,² and Bruce A. McDonald iD ²

¹Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
²Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
³Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
⁴Crop Science, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland

Abstract

Accurate, high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant breeding. We developed an automated image analysis to measure quantitative resistance to septoria tritici blotch (STB), a globally important wheat disease, enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance. 335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen population. More than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the GWAS. We identified 26 chromosome intervals explaining 1.9-10.6% of the variance associated with four independent resistance traits. Sixteen of the intervals overlapped with known STB resistance intervals, suggesting that our phenotyping approach can identify simultaneously (i.e., in a single experiment) many previously defined STB resistance intervals. Seventeen of the intervals were less than 5 Mbp in size and encoded only 173 genes, including many genes associated with disease resistance. Five intervals contained four or fewer genes, providing high priority targets for functional validation. Ten chromosome intervals were not previously associated with STB resistance, perhaps representing resistance to pathogen strains that had not been tested in earlier experiments. The SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance genes. Our experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.