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Sequence and Analysis of the Black Raspberry (Rubus occidentalis) Genome

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The Genomes of Rosaceous Berries and Their Wild Relatives

Part of the book series: Compendium of Plant Genomes ((CPG))

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.

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Authors and Affiliations

  1. Department of Horticulture, Michigan State University, East Lansing, MI, 48823, USA

    Robert VanBuren & Patrick P. Edger

  2. Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA

    Robert VanBuren, Doug Bryant, Erik R. Rowley, Henry D. Priest & Todd C. Mockler

  3. United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, OR, 97333, USA

    Jill M. Bushakra & Nahla V. Bassil

  4. Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA

    Kelly J. Vining

  5. Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA

    Sergei Filichkin

  6. Ibis Biosciences, Carlsbad, CA, USA

    Todd P. Michael

  7. B.C. Blueberry Council (in Partnership with Agriculture and Agri-Food Canada), Pacific Agri-Food Research Centre, Abbotsford, BC, V0M 1A0, Canada

    Michael Dossett

  8. USDA-ARS Horticultural Crops Research Unit, Corvallis, OR, 97330, USA

    Chad E. Finn

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  1. Robert VanBuren
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  2. Doug Bryant
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  3. Jill M. Bushakra
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  7. Erik R. Rowley
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  8. Henry D. Priest
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  9. Todd P. Michael
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  10. Michael Dossett
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  11. Chad E. Finn
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  12. Nahla V. Bassil
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  13. Todd C. Mockler
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Correspondence to Nahla V. Bassil or Todd C. Mockler .

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Editors and Affiliations

  1. Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland

    Timo Hytönen

  2. Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom

    Julie Graham

  3. Genetics, Genomics and Breeding, NIAB EMR, East Malling, Kent, United Kingdom

    Richard Harrison

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VanBuren, R. et al. (2018). Sequence and Analysis of the Black Raspberry (Rubus occidentalis) Genome. In: Hytönen, T., Graham, J., Harrison, R. (eds) The Genomes of Rosaceous Berries and Their Wild Relatives. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-76020-9_13

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