Genome Haplotype Phasing and Comparison of Eastern Filbert Blight Resistance Sources in European Hazelnut (Corylus avellana)

The European hazelnut (Corylus avellana) is grown in the Oregon Willamette Valley, representing 99% of United States hazelnut production. Eastern Filbert Blight, (EFB), a fungal disease caused by Anisogramma anomala, reduces yield and ultimately results in plant death. The threat from emerging variants of EFB in the US threatens to overwhelm current qualitative resistance in commercial cultivars released by Oregon State University (OSU). The EFB resistant cultivar ‘Jefferson’ has been the focus of ongoing genome resource development. In an effort to genetically characterize additional sources of EFB resistance, we have generated PacBio Sequel IIe-based genome assemblies. We now have integrated Illumina reads of the ‘Jefferson’ parents and produced a haplotype-resolved assembly. High quality HiFi-based assemblies have been generated for ‘Tonda di Giffoni’ and ‘Sacajawea’, which have quantitative resistance expressed as fewer, smaller cankers. Additionally, we have produced draft genome assemblies for five trios of more recently identified, additional sources of EFB resistance: ‘OSU1540.052’, ‘OSU1541.086’, ‘OSU1582.018’, ‘OSU1692.055’  and ‘Somerset’. Preliminary gene prediction of ‘Jefferson’ V4 by BRAKER show 28,413 predicted genes, with BUSCO embryophyta10 results being 96.8% complete BUSCOs for version 4 haplotype 1. BLAST comparisons between ‘Jefferson’ V3 and V4 gene annotations showed high similarity for 79% of V4 annotations. Pairwise scaffold alignments show high synteny between version 3 ‘Jefferson’ and version 4 assemblies at the EFB R-gene cluster. These genome analyses have allowed us to compare parental contributions at the chromosomal and gene levels, narrowing down candidate genes at each of the mapped resistance loci. We have differentiated homologous chromosomes using haplotype phasing and identified the allelic contributions of elite EFB-resistant hazelnut accessions. Genome comparisons are helping to validate resistance gene annotations and develop markers to improve marker based selection in the breeding program.