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Title: Building the genomic infrastructure in black raspberry

item BRYANT, DOUG - Danforth Plant Science Center
item Bushakra, Jill
item DOSSETT, MICHAEL - Pacific Agri-Food Research Center
item VINING, KELLY - Oregon State University
item FILICHKIN, SERGEI - Oregon State University
item Weiland, Gerald - Jerry
item Lee, Jungmin
item Finn, Chad
item Bassil, Nahla
item MOCKLER, TODD - Danforth Plant Science Center

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/20/2014
Publication Date: 4/20/2014
Citation: Bryant, D., Bushakra, J., Dossett, M., Vining, K., Filichkin, S., Weiland, G.E., Lee, J., Finn, C.E., Bassil, N.V., Mockler, T. 2014. Building the genomic infrastructure in black raspberry [abstract]. American Society for Horticultural Science Annual Conference.

Interpretive Summary: A concerted effort is being conducted to breed improved cultivars of black raspberry. We are using a variety of genomic and genetic tools to sequence the genome and construct a linkage map that is a representation of the chromosomes. We have identified specific DNA sequences that we will test to determine if they are associated with the expression of important traits. This information will be used to assist breeders in parent selection to develop cultivars that satisfy the demands of the growers and the marketplace, adding to the profitability and sustainability of the industry.

Technical Abstract: 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). ORUS 4305 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.