Identification of SNP Markers Associated With Pyrenophora Teres f. Maculata Resistance/susceptibility Loci in Barley (Hordeum vulgare L.)

Abstract Spot form of net blotch (SFNB), caused by the necrotrophic fungus Pyrenophora teres f. maculata (Ptm), is considered one of the emerging and devastating foliar diseases of barley. Deployment of host resistance against this pathogen remains one of the most effective strategies for its sustainable management. The SFNB resistance in a panel of 336 diverse barley genotypes (AM-2014) was evaluated against three isolates (FGO-Ptm [USA], SM4-2 [Morocco], and SM30-1 [Morocco]), at the seedling stage and under natural conditions in seven environments in Morocco at the adult-plant stage. We identified nine barley genotypes that confer high SFNB resistance in at least five distinct environments and against two isolates. The AM-2014 panel was genotyped with 9K single nucleotide polymorphism (SNP) using an Illumina Infinium select assay. Genome-wide association studies (GWAS) were carried out using mixed linear models accounting for population structure as covariates. Significant marker-trait associations were subject to false discovery rate (FDR) at q<0.05. At the seedling stage, we identified 23 isolate-specific loci associated with SFNB resistance/susceptibility. At the adult stage, 19 QTLs were detected. Fourteen of the identified QTL corresponded to previously mapped SFNB resistance QTL, including QRpts4, QRpt6, QRpt7, and SFNB-3H-58.64, while the remaining may represent novel loci. Together, the associated SNPs and resistance sources identified in this study will be useful resources for SFNB resistance breeding.