Genome-wide association study combined with multi-assay phenotyping identifies a novel anthracnose resistance locus in apple

Background Apple anthracnose, a disease complex that includes Glomerella leaf spot (GLS) and bitter rot caused by Colletotrichum species, is a major disease affecting apple production worldwide. In this study, we combined multi-year field evaluations with controlled inoculation assays to identify genomic regions associated with anthracnose resistance in apple. Results A total of 440 apple genotypes, including 411 F₁ progenies derived from six parental crosses and 29 cultivars, were evaluated under natural orchard conditions and through artificial fruit and leaf inoculation assays using wound and non-wound methods. Disease severity varied substantially between years, particularly under contrasting environmental conditions, indicating strong genotype-by-environment interactions. Genome-wide association analysis (GWAS) using field-derived disease severity scores from 2019 identified a significant quantitative trait locus (QTL) on chromosome 15 (~ 31.8 Mb) associated with reduced anthracnose severity. This locus was distinct from the previously reported Rgls/MdTNL1 region on chromosome 15 (~ 2–5 Mb), suggesting the presence of a novel resistance-associated locus. In contrast, no genome-wide significant associations were detected from artificial inoculation datasets. Conclusions These findings demonstrate the importance of field-based, multi-environment phenotyping for detecting field-relevant resistance loci and improving understanding of the genetic architecture underlying anthracnose resistance in apple.