For over 75 years the United States black raspberry industry has been in steady decline due in large part to a lack of adapted and disease resistant cultivars. Recently, potential health benefits associated with black raspberry’s high concentration of bioactive compounds have sharply increased interest in breeding and production of new cultivars. To facilitate and enhance breeding efforts, we have developed a wide set of genomic resources based on deep sequencing of the black raspberry genome and broad sampling of the transcriptome. Further, we have performed reduced representation genotyping-by-sequencing (GBS) for the ORUS 4305 mapping population that was propagated and planted in growers’ and research fields across five US production areas. A high-quality genome assembly was generated through high-throughput genome sequencing of a highly homozygous accession (~2200 scaffolds, ~240 Mbp, ~353kb N50, 0.06% SNP). Over 50% of the genomic sequence was placed onto linkage groups based on our GBS analyses. RNA-seq data from seven replicated libraries were assembled by de novo and reference-guided approaches, forming the basis for our empirically-based structural annotation (~30,000 transcription units). Associated functional predictions are in progress. These broad genomic resources are poised to enable marker-assisted breeding efforts and lead to development of improved black raspberry cultivars.
