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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: The genome of black raspberry (Rubus occidentalis)

Author
item Vanburen, Robert - Michigan State University
item Bryant, Doug - Danforth Plant Science Center
item Bushakra, Jill
item Vining, Kelly - Oregon State University
item Edger, Patrick - Michigan State University
item Rowley, Erik - Danforth Plant Science Center
item Priest, Henry - Danforth Plant Science Center
item Michael, Todd - Ibis Biosciences
item Lyons, Eric - University Of Arizona
item Filichkin, Sergei - Oregon State University
item Dossett, Michael - British Columbia Blueberry Council
item Finn, Chad
item Bassil, Nahla
item Mockler, Todd - Danforth Plant Science Center

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/12/2016
Publication Date: 9/30/2016
Citation: Vanburen, R., Bryant, D., Bushakra, J., Vining, K.J., Edger, P.P., Rowley, E.R., Priest, H.D., Michael, T.P., Lyons, E., Filichkin, S., Dossett, M., Finn, C.E., Bassil, N.V., Mockler, T.C. 2016. The genome of black raspberry (Rubus occidentalis). Plant Journal. 87(6):535-547. doi: 10.1111/tpj.13215.

Interpretive Summary: Black raspberry is an important specialty crop in the US Pacific Northwest. This chapter describes the available genomic resources for black raspberry, including the recently released draft genome sequence. These resources will expedite marker assisted improvement of raspberry with applications across the Rose family. WHen comparing the black raspberry genome sequence with the genomes of strawberry and peach, we found sumilarities in gene order across the chromosomes. This information will be valuable for breeders of crops in this economically important family.

Technical Abstract: The US Pacific Northwest is the primary production region of black raspberry, and this high-value specialty crop has been underutilized for several decades. Black raspberries contain high levels of anthocyanins and other bioactive compounds, which has sparked a renewed interest in breeding programs and cultivation. Despite this potential, black raspberry stands have seen a marked decline that many attribute to disease pressures and only three new cultivars have been released over the last 20 years. Here we discuss the available genomic resources for black raspberry, including the recently released draft genome. These resources will expedite marker assisted improvement of raspberry with applications across the Rosaceae family. The 243 Mb black raspberry genome was sequenced using an Illumina based whole genome shotgun sequencing approach and a chromosome scale assembly was generated using a high density genetic map. Black raspberry is the sixth genome to be sequenced in the Rosaceae facilitating in depth comparative genomics across the family. Black raspberry and the diploid wild strawberry (Fragaria vesca) are largely collinear with some lineage-specific structural rearrangements. The genome has 28,005 genes which is comparable to other Rosaceae species and includes a number of recently duplicated genes which may be related to domestication. Gene expression atlases during fruit ripening and Verticillium inoculation provide insights into ripening and disease resistance respectively. Together the resources discussed here will provide tools for the improved understanding and breeding of Rosaceae crops.