Alternaria blotch, a major apple (Malus × domestica Borkh.) fungal disease in Japan, is caused by the Alternaria alternata apple pathotype that produces a host-selective toxin called AM-toxin. Although control of Alternaria blotch currently relies on spring-to-summer fungicide use, there is a growing need for sustainable agriculture practices that reduce chemical inputs in orchards. Therefore, breeding cultivars for resistance to Alternaria blotch is of particular interest. Given that ‘Golden Delicious’ (GD) and several of its offspring cultivars are moderately susceptible to the disease, a genetic analysis of their susceptibility was performed. Quantitative trait locus (QTL) analysis of the ‘Fuji’ × ‘GD’ population identified a single QTL on chromosome 11 in ‘GD’, which explained 48.7% of the phenotypic variation. This QTL was located in the same region as the previously identified susceptibility gene Alt derived from ‘Starking Delicious’. Therefore, we named it QTL Alt2, a putative allele of Alt (later renamed Alt1). Interaction analysis revealed that Alt1 was dominant over Alt2. A DNA marker set that simultaneously detects Alt1 and Alt2 was developed for breeding use. This marker shed light on the inheritance of the Alt locus in modern Japanese cultivars and selections. Moreover, Alt2 was less common than Alt1 in heirloom cultivars. These findings offer new insights into apple breeding for Alternaria blotch resistance and the interaction mechanism between apple and host-selective toxin-producing A. alternata.

链格孢斑病是日本的一种主要苹果 ( Malus × Domestica Borkh.) 真菌病害，是由链格孢(Alternaria alternata)苹果病型引起，该病型产生一种称为 AM 毒素的宿主选择性毒素。尽管目前对链格孢斑病的控制依赖于春季至夏季杀菌剂的使用，但人们越来越需要减少果园化学投入的可持续农业实践。因此，培育抗链格孢斑病的品种特别令人感兴趣。鉴于“金冠”（GD）及其几个后代品种对该病具有中度易感性，因此对其易感性进行了遗传分析。对'Fuji'×'GD'群体的数量性状位点（QTL）分析在'GD'中鉴定出11号染色体上的单个QTL，这解释了48.7%的表型变异。该QTL与先前鉴定的源自“Starking Delicious”的易感基因Alt位于同一区域。因此，我们将其命名为 QTL Alt2 ，这是Alt的假定等位基因（后来更名为Alt1）。交互分析表明Alt1优于Alt2。开发了同时检测Alt1和Alt2 的DNA 标记集，用于育种用途。该标记揭示了现代日本品种和选择中Alt基因座的遗传。此外，在传家宝品种中，Alt2不如Alt1常见。这些发现为苹果抗链格孢菌育种以及苹果与宿主选择性产生毒素的链格孢菌之间的相互作用机制提供了新的见解。