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Title: Developing black raspberry genetic and genomic resources

item Bushakra, Jill
item BRYANT, DOUG - Danforth Plant Science Center
item DOSSETT, MICHAEL - Agriculture And Agri-Food Canada
item VINING, KELLY - Oregon State University
item VANBUREN, ROBERT - Danforth Plant Science Center
item Gilmore, Barbara
item FILICHKIN, SERGEI - Oregon State University
item Weiland, Jerry
item Peterson, Mary
item BRADISH, CHRISTINE - North Carolina State University
item FERNANDEZ, GINA - North Carolina State University
item Lewers, Kimberly
item GRAHAM, JULIE - The James Hutton Institute
item Lee, Jungmin
item MOCKLER, TODD - Danforth Plant Science Center
item Bassil, Nahla
item Finn, Chad

Submitted to: International Rubus Ribes Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2015
Publication Date: 3/1/2015
Citation: Bushakra, J., Bryant, D., Dossett, M., Vining, K., Vanburen, R., Gilmore, B.S., Filichkin, S., Weiland, G.E., Peterson, M.E., Bradish, C.M., Fernandez, G., Lewers, K.S., Graham, J., Lee, J., Mockler, T., Bassil, N.V., Finn, C.E. 2015. Developing black raspberry genetic and genomic resources [abstract]. International Rubus and Ribes Symposium.

Interpretive Summary: Since the early 1900s, the black raspberry industry in the United States has steadily declined due to lack of cultivars that are adapted to a range of environments and that have disease resistance. Interest in developing new cultivars has been fueled by by news regarding the potential health benefits of black raspberry compounds. We are developing methods to study the genetics of black raspberry that will benefit both black and red raspberry U.S. breeding programs. We used a new method to determine the genetic diversity of a black raspberry population. Using this new method, we detected differences that will aid in determining the inheritance of important horticultural traits such as resistance to feeding aphids and fungal diseases, and plant growth characteristics.

Technical Abstract: This study incorporates field and laboratory components to advance and streamline identification of a variety of traits of economic interest and to develop molecular markers for marker assisted breeding of black raspberry (Rubus occidentalis). A lack of adapted, disease resistant cultivars has led to a steady decline of the black raspberry (BR) industry in the US. Interest in production and breeding new cultivars has been fueled by news regarding the potential health benefits of black raspberry bioactive compounds. To accomplish our goals, we are using two related full-sibling populations that have been replicated and planted at five production sites (OR, WA, OH, NC, NY). We are taking detailed measurements on traits including primocane vigor, flowering and fruiting, disease and aphid tolerance, and plant architecture to assess the influence of environment on genotype (GxE). Initial analysis of (GxE) on primocane vigor indicated that individual genotypes showed significant variation among sites. We are also developing, and making available, genomic tools including molecular markers for construction of linkage and physical maps, and a draft genome assembly. Markers are being developed by sequencing and analyzing libraries generated by genotyping by sequencing (GBS). Initial analysis through a custom data pipeline identified over 23,000 single nucleotide polymorphic/insertion-deletion (SNP/indel) loci. Preliminary results indicate that GBS is appropriate for SNP detection in this highly-homozygous species. A densely populated genetic linkage map will be used to improve the draft genome assembly, for quantitative trait locus (QTL) mapping, and comparative genomic studies with other Rosaceae.