The identification of multiple SNP markers for scald resistance in spring barley through restriction-site associated sequencing

Leaf scald caused by Rhynchosporium commune (formerly R. secalis ) is an important fungal disease in barley ( Hordeum vulgare ) in western Canada. Pyramiding multiple scald resistance qualitative trait loci (QTL) is considered an effective strategy for breeding durable scald resistance into barley. The objective of this study was to map QTLs with restriction site-associated (RAD) markers and identify single nucleotide polymorphism (SNP) markers for scald resistance. Two recombinant inbred line (RIL) populations (crosses Harrington/Seebe and Seebe/Shyri) with good resistance to local scald isolates were genotyped by RAD sequencing (RADseq). A total of 4203 SNPs were obtained from the RADseq analysis of 162 F7 RILs. Inclusive composite interval mapping identified multiple major QTLs for scald resistance on chromosomes 3H, 4H, and 5H in Shyri, and 2H and 6H in Seebe. SNP markers from Shyri were located in the same region as the previously reported 3H QTL Rrs1. Several SNP markers from Seebe clustered on chromosome 6H near a major scald resistance QTL. The 6H QTL appeared effective for both adult plant resistance and seedling resistance, and explained up to 70.9% of the phenotypic variation among the sequenced lines. A tightly linked SNP for the major 6H QTL was converted into an allele specific PCR marker. The QTLs and their genetic markers found in this study will be useful in barley breeding for the selection of resistance to barley leaf scald.