Haplotype-resolved Jefferson Hazelnut reveals EFB resistance inheritance

European hazelnut (Corylus avellana L.) is an important tree nut crop. Hazelnut production in North America is currently limited in scalability due to Anisogramma anomala, a fungal pathogen that causes Eastern Filbert Blight (EFB) disease in hazelnut. Successful deployment of EFB resistant cultivars has been limited to the state of Oregon, where the breeding program at Oregon State University (OSU) has released cultivars with a dominant allele at a single resistance locus identified by classical breeding, linkage mapping, and molecular markers. Jefferson is resistant to the predominant EFB biotype in Oregon and has been selected by the OSU breeding program as a model for hazelnut genetic and genomic research. Here, we present a near complete, haplotype-resolved chromosome-level hazelnut genome assembly for C. avellana Jefferson. Using parental reads, of a resistant parent OSU414.062 and a susceptible parent OSU252.146, analysis of genomic regions linked to EFB resistance and self-incompatibility confirmed haplotype splitting. This work contributes to the identification of gene candidates that are essential for downstream molecular marker development, thereby facilitating breeding efforts.