Fine mapping, candidate gene identification and marker development for the apple scab resistance gene Rvi2

Breeding elite apple cultivars with scab resistance is a key global goal, as reliance on fungicides is unsustainable. Venturia inaequalis evolves rapidly, threatening single-gene-resistant cultivars. Since the 1980s, breeding programmes have introduced novel resistance sources via backcrossing. Here, we generated a haplotype-phased genome assembly of Russian apple R12740-7A and an Oxford Nanopore assembly of the Rvi2-resistant accession TSR34T15, enabling detailed dissection of the Rvi2 resistance locus. Fine-mapping using a ‘Royal Gala’ × TSR34T15 segregating family delimited Rvi2 to a narrow genomic interval, within which we identified a 10,041 bp long terminal repeat retrotransposon (LTR) insertion—an insert-based structural variant (SV) strongly linked with Rvi2. Notably, this LTR harbours an FPPS gene, a member of the farnesyl pyrophosphate/geranylgeranyl pyrophosphate (FPP/GGPP) synthase family, located 2 Kb from a key candidate defence gene. Although the FPPS gene exhibits stable expression, its integration within the retrotransposon suggests a cis-regulatory role, potentially priming adjacent defence genes for robust upregulation upon pathogen attack. We validated the marker derived from this SV in diverse germplasm and successfully implemented it in marker-assisted selection across extensive seedling cohorts. This marker will streamline the development of scab-resistant apple varieties.