Development and validation of KASP markers for powdery mildew resistance in Korean naked barley using QTL-seq

Powdery mildew (PM), caused by Blumeria graminis f. sp. hordei, is a destructive fungal disease affecting barley (Hordeum vulgare L.), particularly under warm and humid conditions. Developing resistant cultivars through molecular marker-assisted selection (MAS) represents an eco-friendly and sustainable strategy for disease control. However, validated molecular markers for PM resistance in naked barley remain limited. In this study, quantitative trait locus-sequencing (QTL-seq) was conducted using two independent parental combinations, Nurichal (susceptible) and Jeonju144 (resistant), to identify genomic regions associated with PM resistance in Korean naked barley. A consistent QTL region was detected on chromosome 1 H, within which 40 Kompetitive Allele-Specific PCR (KASP) markers were developed based on gene-associated sequence variants. Stepwise validation using an F₂ segregating population (n = 244) identified two markers, NPM32 and NPM43, that showed strong and consistent associations with PM resistance. Among them, NPM43 exhibited complete concordance between genotype and phenotype in the evaluated population, indicating its high diagnostic reliability. The associated sequence variant was located within an uncharacterized gene in the barley reference genome. Validation of the KASP marker NPM43 revealed stable performance and a strong association with PM resistance, highlighting its potential utility for MAS in breeding PM-resistant naked barley. This study provides useful genomic resources for marker-based breeding and supports the development of precision breeding strategies for disease resistance in barley.

The online version contains supplementary material available at 10.1007/s11032-026-01649-6.