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Background <p>Apple anthracnose, a disease complex that includes <i>Glomerella</i> leaf spot (GLS) and bitter rot caused by <i>Colletotrichum</i> 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.</p> Results <p>A total of 440 apple genotypes, including 411&#xa0;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&#xa0;Mb) associated with reduced anthracnose severity. This locus was distinct from the previously reported <i>Rgls/MdTNL1</i> region on chromosome 15 (~ 2–5&#xa0;Mb), suggesting the presence of a novel resistance-associated locus. In contrast, no genome-wide significant associations were detected from artificial inoculation datasets.</p> Conclusions <p>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.</p>

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

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年6月24日

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  • Dagyeong Kwon,
  • Baek Gyun Choi,
  • Jong Taek Park,
  • Seunghyun Ban,
  • Cheol Choi

摘要

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.