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 large population of 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 15,463 SNPs. 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. FarmCPU identified additional associations on chromosomes 2H, 3H, and 4H. 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 QTL for disease resistance and agronomic traits. PLAIN LANGUAGE SUMMARYO_ST_ABSGenetic architecture of resistance to scald in winter malting barleyC_ST_ABSScald is an important foliar pathogen in winter malting barley, affecting both grain yield and quality. While resistance to scald is controlled by major and minor resistance genes, agronomic traits are also known to limit the spread of scald in barley. We determined the genetic architecture using a large multiparent population of winter malting barley. The FarmCPU genome-wide association model proved optimal for defining the resistance genes, with the major resistance gene, Rrs1, conferring 27% of the variation in this population. Fewer days to heading and taller plants contributed to plant avoidance of scald. Reduced canopy coverage in plants with low winter survival led to less scald severity. A region of the genome contributing a minor resistance effect was co-localized with a region for plant height, heading date and winter survival. Core IdeasO_LIResistance to scald in a large multiparent population was derived from a major resistance gene (Rrs1) and several smaller effect QTLs C_LIO_LIRrs1 resistance was derived from Lightning and is located within a large linkage block on Chromosome 3H C_LIO_LIFewer days to heading and taller plants were correlated with less disease in a large multiparent winter malting barley population in NY state C_LIO_LIA QTL for resistance to scald co-localized on chromosome 2H with winter survival, heading date, and plant height C_LIO_LIFarmCPU was an optimal model for association analysis for resistance to scald in the large unbalanced diallel population. C_LI