Genome-wide association analysis of resistance to scald in an adapted multiparent winter malting barley population.

Scald, caused by the fungus Rhynchosporium graminicola Heinsen 1897, is a major foliar disease in winter malting barley (Hordeum vulgare L). Resistance to scald in winter malting barley is controlled by major and minor resistance genes. We used a population of 377 lines derived from biparental crosses among five winter malting barley parents to analyze resistance to scald and associated agronomic traits. Increased winter survival and later heading dates were negatively correlated with increased resistance, whereas increased height was positively correlated with resistance. A genome-wide association study (GWAS) for resistance to scald was analyzed with multiple models, using 14,789 single nucleotide polymorphisms (SNPs) and 374 lines. The similarities and differences between the models were identified in SNP trait associations and phenotypic effect sizes. SNP associations identified a large region on chromosome 3H across models. Fixed and Random Model Circulating Probability Unification (FarmCPU) identified additional associations on chromosomes 2H, 3H, 4H, and 7H. Linkage disequilibrium on chromosome 3H and GWAS for resistance to scald using the Rrs1-linked marker, HVS3, as a covariate confirmed Rrs1 was segregating in this population. GWAS for winter survival, heading date, and plant height identified associations across the genome, with chromosome 2H showing SNP-trait colocalizations between resistance to scald, winter survival, heading date, and plant height. Breeding for durable resistance to scald in winter malting barley can include pyramiding major resistance loci, such as Rrs1, as well as quantitative trait locus for disease resistance and agronomic traits.