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

Dagyeong Kwon·Baek Gyun Choi·Jong Taek Park·Seunghyun Ban·Cheol Choi
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Abstract

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.

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MalusPlant DiseasesColletotrichumGenome-Wide Association StudyQuantitative Trait LociDisease ResistancePhenotypeGenotypeMalus × domesticaAnthracnoseArtificial inoculationDisease resistanceField phenotypingGenome-wide association studyGenotype-by-environment interactionJournal Article

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Dagyeong Kwon, Baek Gyun Choi, Jong Taek Park, Seunghyun Ban, Cheol Choi. 2026-06-24. Genome-wide association study combined with multi-assay phenotyping identifies a novel anthracnose resistance locus in apple.. https://doi.org/10.1186/s12870-026-09198-y

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