Fine-Mapping of the Vhc1 QTL for Apple Scab Resistance on Linkage Group 1 of ‘Honeycrisp’

Apple scab, caused by Venturia inaequalis, is the most economically important fungal disease impacting apple production globally. Most commercial apple cultivars are susceptible to scab, although several sources of genetic resistance have been identified. The availability of genetic markers tightly linked with the functional resistance alleles is one of the factors limiting the breeding of scab-resistant cultivars. ‘Honeycrisp’, one of the popular North American apple cultivars, is a source of Vhc1 scab resistance on linkage group 1, but the associated locus spans 12.6 cM and harbours over 200 genes. Here, we present the fine-mapping of the Vhc1 locus, the development of haplotype-specific simple sequence repeat (SSR) markers and the identification of candidate resistance alleles. Chromosome-level phased genome assemblies of the scab-resistant parent ‘Honeycrisp’ and scab-susceptible ‘Gala’ were used to design nine novel polymorphic markers, along with two previously reported markers, spanning the Vhc1 QTL region. An F₁ population derived from the two cultivars was developed and was evaluated for scab resistance across two consecutive years using the V. inaequalis isolate Vi-19-004 collected from Malus floribunda 821. Broad-sense heritability was estimated at 0.66 across experiments. Phenotype–genotype association analysis fine-mapped a moderate-effect apple scab resistance QTL, explaining 5.2%–11.8% of phenotypic variance, to a 4.2-cM genetic interval and a corresponding 0.85-Mb physical region. SSR markers mdCu_2500, mdCu_3000 and CH-Vf1 collocated with the Vhc1 QTL and can be used in future marker-assisted selection studies for Vhc1. Six LRR-encoding genes underlying the QTL region with enhanced expression upon inoculation with V. inaequalis were identified as scab resistance candidate alleles. These newly developed markers and candidate genes will accelerate the development of ‘Honeycrisp’ based scab-resistant cultivars.