Genomic resource development in hazelnut breeding

J.W. Snelling, V.R. Sathuvalli, B.C. Colburn, G. Bhattarai, E.R. Rowley, T.C. Mockler, C.A. Saski, D. Copetti, S.A. Mehlenbacher
Genomic resources are being developed by Oregon State University (OSU) and used in breeding new hazelnut cultivars with excellent kernel quality and resistance to eastern filbert blight (EFB). A bacterial artificial chromosome (BAC) library with 12× coverage of the ‘Jefferson’ genome (~385 Mb/1C) was used for high information content fingerprinting (HICF), resulting in a physical map with a minimum tiling path (MTP) of 5232 clones. BAC ends of the MTP were Sanger sequenced. The library was probed using markers for the ‘Gasaway’ EFB resistance and incompatibility loci, and fine-mapping of each region was begun. BACs associated with resistance were Illumina sequenced and the de novo assemblies used for gene prediction and marker development. Fine mapping narrowed the resistance locus to a single BAC and five candidate genes were identified. The transcriptome and genome of ‘Jefferson’ were also Illumina sequenced and assembled de novo, resulting in 28,255 and 36,641 contigs, respectively. 23,652 full gene models were annotated and placed on the ‘Jefferson’ genome. Concurrently, the genomes of seven additional cultivars were Illumina sequenced at ~20× coverage and aligned with the reference ‘Jefferson’ to identify polymorphic simple sequence repeats (SSRs). An ApeKI genotyping-by-sequencing (GBS) library was constructed and 4,164 new single nucleotide polymorphism (SNP) markers added to the maps of the parents of the reference population OSU252.146 × OSU414.062, which now also includes ~470 SSR markers. The draft genome of ‘Jefferson’ from Illumina sequences is highly fragmented. Long-read Pacific Biosciences technology was used to sequence the ‘Jefferson’ genome, giving 1865 high confidence contigs. Current efforts will integrate the genome sequence, physical map MTP, and genetic maps. When unified, these resources will increase fidelity to the large-scale genomic representation, and the genome sequence will be an indispensable reference for hazelnut researchers.
Snelling, J.W., Sathuvalli, V.R., Colburn, B.C., Bhattarai, G., Rowley, E.R., Mockler, T.C., Saski, C.A., Copetti, D. and Mehlenbacher, S.A. (2018). Genomic resource development in hazelnut breeding. Acta Hortic. 1226, 39-46
DOI: 10.17660/ActaHortic.2018.1226.5
Corylus avellana, filbert, transcriptome, marker-assisted selection, linkage map

Acta Horticulturae