Genome-wide association mapping and functional annotation of loci conferring resistance to Pyrenophora teres f. teres in barley
Net form net blotch (NFNB), caused by Pyrenophora teres f. teres ( Ptt ), is a major constraint to barley production. However, the genetic basis of adult plant resistance (APR) and seedling resistance remains incompletely understood. This study aimed to dissect the genetic architecture of NFNB resistance in a diverse panel of 273 spring barley accessions. APR was evaluated in two contrasting field environments in Kazakhstan, whereas seedling resistance was assessed under greenhouse conditions using two Ptt races. Genotyping with the 50K SNP array yielded 31,834 high-quality SNPs. Genome-wide association analyses were performed using four models – MLM, MLMM, FarmCPU, and BLINK – that accounted for population structure and kinship. Candidate genes within QTL intervals were prioritized using transcriptomic data from 16 barley tissues and co-expression network analysis. Substantial phenotypic variation was observed, with moderate heritability for APR ( h 2 = 50.6%) and seedling resistance ( h 2 = 41.3%), together with strong genotype × environment and genotype × race interactions. In total, 275 marker–trait associations were detected for APR and 48 for seedling resistance. These associations were consolidated into 57 genome-wide significant (P < 1.57E–6) or multi-model-supported QTLs across all seven barley chromosomes, including 39 APR and 18 seedling-resistance QTLs. Forty QTLs co-localized with known resistance genes ( Rpt1 , Rpt2 , Rpt3 , Rpt4 , Rpt6 , Rpt8 , Rpt9 , and SPN1 ) or previously reported net blotch QTLs, whereas 17 were potentially novel. Transcriptomic integration identified 87 highly expressed genes within APR QTL regions and 42 within seedling-resistance QTLs. The potentially novel QTLs Q_NB_1H.6 , Q_NB_2H.3 , and Q_NB_3H.1 harbored genes encoding proteins previously associated with pathogen resistance and stress responses. Co-expression analysis revealed stage-specific transcriptional patterns, with APR-associated genes enriched in regulatory functions and seedling-resistance genes enriched in metabolic and structural functions. The results demonstrate that NFNB resistance is polygenic and developmentally stage-dependent, with partly distinct mechanisms underlying adult plant and seedling resistance. The identified QTLs and prioritized candidate genes provide targets for independent validation, functional characterization, and the development of molecular markers to support breeding for durable NFNB resistance in barley.