Mapping Quantitative Trait Loci Associated with Spot Form Net Blotch of Barley

The leaf spot disease spot form net blotch (SFNB) caused by the necrotrophic fungus Pyrenophora teres f. maculata has emerged as a major disease in barley producing regions worldwide. Deployment of adequate host resistance is a challenge because the virulence of P. teres f. maculata is highly variable and resistance is quantitative. A worldwide collection of 1,947 barley lines were phenotyped in the greenhouse with four diverse P. teres f. maculata isolates collected from Fargo, ND (FGOB10ptm-1), New Zealand (NZKF2), Australia (SG1) and Denmark (DEN2.6). A subset of 6,575 SNP markers with MAF >0.05 was used to identify the association between markers and SFNB resistance. The best model among six different regression models for each isolate was identified and association analysis was performed separately for each isolate.  A total of 5, 8, and 3 highly significant markers associated with SFNB resistance were obtained for the FGOB10ptm-1, NZKF2, and DEN 2.6 isolates respectively at FDR <0.05 threshold. No significant markers were found for the SG1 isolate at both FDR < 0.05 or < 0.01. Common QTL were also investigated at a P-value threshold of < 0.05 for all isolates and were found on chromosome 1H, 3H, 4H, 6H and 7H. Several unique QTLs specific to one or more isolates were also found on all seven chromosomes. The identified markers will be used in a marker assisted selection scheme to deploy these resistance QTLs into elite barley varieties.