Building the Genomic Infrastructure in Black Raspberry

Cultivar improvement of black raspberry (Rubus occidentalis L.) has been stagnant for the past 75 years, with only a handful of new releases to date. The most commonly grown elite cultivars are susceptible to aphid-transmitted viruses and soil-borne pathogens that lead to a rapid decline in plant health necessitating frequent stand replacement by the growers. Recent research supporting the anti-cancer effects of black raspberries has led to a resurgence of interest in this fruit and a renewal of breeding efforts. Genomic tools we are developing will be applied to the identification of quantitative trait loci and alleles important for breeding objectives regionally and nationally. We applied high-throughput genome sequencing of a highly homozygous accession to generate 2,200 scaffolds of approximately 240 Mbp, with 353 kbp N50, and 0.06% per-basepair variation. We employed genotyping by sequencing on the full-sibling population ORUS 4305 (115 progeny) to generate more than 900 single nucleotide polymorphic (SNP) markers to construct a linkage map. The consensus linkage map consists of seven linkage groups spanning 613.1 cM with the longest group spanning 101.7 cM with 103 markers (G1) and the shortest spanning 77.6 cM with 61 markers (G7). The linkage map was used to place over 50% of the genomic sequence into linkage groups. In addition, RNA-seq data from seven replicated libraries of five tissue types were assembled by de novo and reference-guided approaches, forming the basis for our empirically-based structural annotation (~26,000 transcription units). The ORUS 4305 population and a second population (ORUS 4304, 192 progeny) are being evaluated across production regions for a number of economically important traits. The genomic data and the phenotype information will be used to develop markers to assist plant breeders in parent selection with the goal of developing cultivars that satisfy the demands of the growers and the marketplace, adding to the sustainability and profitability of the industry.