Genome-wide association mapping revealed a major QTL for Septoria tritici blotch resistance in wheat

• GWAS of 318 diverse wheat accessions identified 14 QTLs for Septoria tritici blotch resistance. • Three stable QTLs ( qSTB-3B.1 , qSTB-4A.2 , and qSTB-6B ) were consistently detected across environments. • The qSTB-4A.2 allele reduced disease scores from 5.4 to 3.9, and it acted additively with qSTB-6B for enhanced resistance. Septoria tritici blotch (STB), caused by the fungal pathogen Zymoseptoria tritici , poses a major threat to global wheat production, adversely affecting both yield and grain quality. To identify the genetic loci controlling STB resistance, a genome-wide association study (GWAS) was conducted using 13,098 high-quality SNPs across a diverse panel of 318 wheat accessions including Australian commercial varieties, Australian Grains Genebank, Chinese commercial varieties, and Chinese landraces. Disease resistance was evaluated over two consecutive years under field conditions. Population structure and principal component analyses revealed distinct genetic differentiation between Chinese landraces and other groups. Notably, Chinese landraces exhibited the highest proportion of resistant accessions. We identified a total of 14 quantitative trait loci (QTLs) associated with STB resistance. Notably, three QTLs ( qSTB-3B.1 , qSTB-4A.2 , and qSTB-6B ) were consistently detected across all environments, with qSTB-4A.2 as a major resistance locus. Selection for the qSTB-4A.2 allele reduced the average disease score from 5.4 to 3.9. Furthermore, an additive effect was observed, where accessions carrying resistance alleles at both qSTB-4A.2 and qSTB-6B exhibited significantly lower disease scores than those with only the qSTB-4A.2 allele. Candidate gene analysis within these stable QTLs identified 27 promising genes including homologs of known disease resistance-related genes such as Lr34 / Yr18 / Pm38 , and OsWAK1 . These findings enhance our understanding of STB resistance genetics and provide robust markers and candidate genes for marker-assisted selection in breeding durable and disease-resistant wheat cultivars.