Genetic Architecture of Quantitative Disease Resistance Revealed By Genome-Wide Association Scan in Wheat

Understanding the genetic architecture of quantitative disease resistance in crops is critical for developing new cultivars resistant to shifts in pathogen populations. We applied reference genome-based analysis of high-density genotyping data generated using the genotyping-by-sequencing (GBS) approach and wheat 90K iSelect assay to investigate the genetic basis of adult plant resistance to three species of wheat rust. By using high-quality iSelect assay’s genotyping data as a framework for testing different imputation approaches aimed to compensate for the high rate of missing data in a GBS dataset, we showed an overall increase in the power of association mapping after genotype imputation and method-specific variation in imputation accuracy. Several mapping approaches based on single- and multi-locus association analysis have been utilized. Nearly 300 common SNP variants linked to both new and previously characterized loci showed a significant association with rust resistance phenotypes at FDR < 0.01. Among these loci we found genes conferring both species-specific and non-specific resistance to wheat rusts providing valuable targets for genomics-assited selection. Our study demonstrates the utility of reference-guided analysis of variation in the wheat genome and establishes a platform for dissecting the genomic architecture of complex trait variation in wheat.