Fruits and Nuts
NPGS Blackberries – Prickleless Canes
USDA NPGS GERMPLASM IDENTIFIES THE GENE FOR PRICKLELESS BLACKBERRIES AND RASPBERRIES
Brian Crawford; Margaret Worthington; and Nahla V. Bassil
Pairwise, 807 E. Main St. Suite 4 100, Durham, North Carolina 27701.
University of Arkansas, Department of Horticulture, 316 Plant Sciences Building, 495 N Campus Walk, Fayetteville, Arkansas 72701.
USDA-ARS National Clonal Germplasm Repository, 33447 Peoria Rd, Corvallis, Oregon 97333.
Corresponding author: nahla.bassil@usda.gov
OUTLINE
- Summary
- Problems addressed
- Solutions developed
- Impact
- Germplasm
- Additional resources
- References
- Chapter information
1. SUMMARY
From 2018 to 2025, a large research team led by scientists at the Pairwise company collaborated to uncover the genes responsible for “prickleless” (also called “thornless”) canes (another name for “stems”) in caneberries (raspberries, blackberries, etc.). Extensive morphological analyses, genome sequencing, and analyses of these data for more than 500 diverse germplasm accessions from the USDA-ARS National Plant Germplasm System (NPGS) National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon uncovered the causal factors for prickleless canes in caneberries were the genes encoding the WOX1 protein. This finding, confirmed through gene editing, represents a major advance for blackberry and raspberry genetic improvement because it can enable precise breeding and gene editing to deliver prickleless cultivars.
The goal of this project was to identify the genetic mechanism controlling prickleless canes in blackberries and raspberries to enable efficient breeding of prickle-free caneberry cultivars.
Download a printable fact sheet by clicking the image below.
2. PROBLEMS ADDRESSED
Prickles (often called thorns) on blackberry and raspberry canes complicate pruning, harvesting, handling and add labor costs. Although naturally prickleless plants exist, the trait is genetically recessive and has been thought to be linked to undesirable characteristics such as winter injury, canes that trail on the ground, or poor fruit quality, complicating the efficient incorporation of the prickleless trait in breeding programs. Prior research suggested that the same gene(s) governed the prickleless trait in both raspberry and blackberry and that it was located within a long sequence on chromosome 4, but the specific causal gene for this trait had never been identified. Finding the exact gene(s) and mutation(s) controlling this valuable trait was essential for enabling precise breeding and gene editing to deliver prickleless cultivars.
3. SOLUTIONS DEVELOPED
Prickle in blackberry on the left (indicated by the arrow). Absence of prickles caused by gene-edited mutant Ruwox1-4 genetic variant on the right. Photos by Brian Crawford.Several different genomic, statistical, genetic, and sequence analyses of 268 blackberry and raspberry germplasm accessions from the NPGS NCGR collection pinpointed the location of the prickleless gene to a small length of Chromosome 4. Additional analyses that made use of the genome assemblies of the R. argutus cv. ‘Hillquist’ (PI 553951) and the prickleless R. ulmifolius accession ‘Burbank Thornless’ (PI 554060) from the NCGR identified the gene WOX1 that encoded a protein named WOX1 as the key gene active during prickle formation. Comparative genome analyses revealed that prickleless raspberries and blackberries independently carry natural loss-of-function mutations of WOX1. Gene editing of WOX1 in a prickled tetraploid blackberry cultivar confirmed that gene’s essential role, as all gene-edited plants were prickleless.
Collaborators involved in developing solution:
- Brian St. Aubin, Tom Poorten, Andrew Fister, Cherie Ochsenfeld, Joel Reiner, Nat Graham, Deepika Chauhan, Eric Dean, Warner Lowry, Lauren Redpath, Pradeep Marri, Shai Lawit, Gina Pham: Pairwise, Durham, North Carolina, USA
- Rishi Aryal, Hudson Ashrafi: North Carolina State University, Dept. of Horticultural Science, Raleigh, North Carolina, USA
- Tomáš Brůna: U.S. Dept. of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, California, USA
- Olga Dudchenko, Erez Lieberman Aiden: The Center for Genome Architecture, Baylor College of Medicine, Houston, Texas, and Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, Texas, USA
- Melanie Pham, David Weisz: The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Daniel James Sargent: Department of Genetics, Genomics and Breeding, NIAB-EMR, East Malling, Kent, and Natural Resources Institute, University of Greenwich, Medway Campus, Chatham Maritime, Kent, UK
- Daniel Mead: Wellcome Sanger Institute, Hinxton, Cambridge, and Owlstone Medical Ltd, Cambridge, UK
- Matteo Buti: Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
- Alexander Silva: University of Arkansas, Department of Horticulture, Fayetteville, Arkansas, USA
4. IMPACT
Gene-edited caneberry lines showed no changes in plant growth or fruiting other than the targeted loss of prickles and glandular trichomes, indicating that gene-editing WOX1 is a safe and targeted breeding approach. This discovery enables breeders to edit the gene to remove prickles directly from elite cultivars without years of crossing or the risk of bringing along undesirable traits linked to the prickleless gene. Because the chromosomal region surrounding the prickleless locus has a long history of selection and reduced diversity, gene editing offers a pathway to bypass what is termed “linkage drag” entirely. The ability to rapidly develop prickle-free blackberry and raspberry cultivars could reduce labor costs, improve worker safety, and accelerate the release of improved cultivars for growers.
5. GERMPLASM
The prickled Rubus argutus NPGS accession ‘Hillquist’ (PI 553951) was originally discovered by L. G. Hillquist of Ashland, Virginia and donated to the New York State Experiment Station in 1949 before being added to the NPGS NCGR collection in 1985. ‘Hillquist’ served as the source material for the first chromosome-scale blackberry reference genome, released in 2023, which provided critical information for this research. In the present study, the genome sequence of this accession was used as the primary reference for alignment of whole-genome resequencing data from 268 Rubus accessions and for comparative analyses with the Rubus occidentalis v3 and Rubus idaeus ‘Anitra’ genomes.
The diploid prickleless Rubus ulmifolius accession ‘Burbank Thornless’ (PI 554060) is a historical cultivar developed by Luther Burbank as an easier-to-handle alternative to prickled blackberry types. Although the genetic contribution of Burbank’s material to the prickleless gene used in the development of ‘Merton Thornless’ and other modern prickleless cultivars is unclear, ‘Burbank Thornless’ represents a classic diploid, naturally prickleless genotype. To clarify the genetic basis of prickliness in Burbank’s material and its relation to other genetic sources of prickleless, the research generated a chromosome-scale genome sequence and analysis for this accession. This genome sequence served as a comparative reference for chromosomal structural and gene sequence analyses within the prickleless gene on Chromosome 4 and revealed two independent WOX1-disrupting gene variants.
6. ADDITIONAL RESOURCES
Details about R. ulmifolius genome sequencing and R. argutus genome sequencing are available through the Joint Genome Institute’s Phytozome.
Datasets can be found on the Genome Database for Rosaceae (accessions tfGDR1091, tfGDR1090, tfGDR1056).
7. REFERENCES
Brůna T, Aryal R, Dudchenko O, Sargent DJ, Mead D, Buti M, Cavallini A, Hytonen T, Andres J, Pham M, Weisz D, Mascagni F, Usai G, Natali L, Bassil N, Fernandez GE, Lomsadze A, Armour M, Olukolu B, Poorten T, Britton C, Davik J, Ashrafi H, Aiden EL, Borodovsky M, Worthington M. 2022. A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. ‘Hillquist’). G3 Genes|Genomes|Genetics 13:jkac289. https://doi.org/10.1093/g3journal/jkac289
8. CHAPTER INFORMATION
Citation: Crawford B, Worthington M, Bassil N. 2026. NPGS Blackberries – Prickleless Canes. In: Volk GM, Chen KY, Byrne PF, Bretting PK (Eds.) Plant Genetic Resources: Success Stories. Fort Collins, Colorado: Colorado State University. Date accessed. Available from https://colostate.pressbooks.pub/pgrsuccessstories/chapter/npgs-blackberries-prickleless-canes/
Content originally submitted: March 5, 2026
Date of publication: May 4, 2026
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