The control of prickle formation in <i>Rubus</i>
Prickles on blackberry and raspberry canes make pruning, harvesting, and handling more difficult and can increase labor costs for growers. The trait has been challenging to improve in these clonal crops because it is recessive and linked to undesirable agronomic traits. In blackberry and red raspberry, breeding programs have used recessive mutants at the <i>S</i> locus to generate prickleless cultivars for the last century. In this study, we identified independent loss-of-function mutations in a WUSCHEL-LIKE HOMEOBOX transcription factor, <i>WOX1</i>, as the genetic basis of the prickleless <i>S</i> locus in both blackberry and red raspberry. We mapped the <i>S</i> locus using integrated genome-wide association, bulked segregant analysis, and identity-by-descent analyses informed by breeding pedigrees. Additionally, we generated a genome sequence from Luther Burbank's prickleless blackberry variety Burbank Thornless that contained an additional allele of <i>WOX1</i>. To verify the gene's role, we used gene editing to knock out <i>WOX1</i> in an elite prickled commercial blackberry line. All edited plants were prickleless and lacked glandular trichomes, confirming that <i>WOX1</i> controls a joint developmental pathway. Other plant traits were unchanged, indicating <i>WOX1</i> is a specific and safe target for improvement. Gene editing can enable breeders to remove prickles directly from elite varieties, reducing the need for extensive breeding cycles and delivering safer, easier-to-harvest cultivars to growers.
Authors
- Alexander Silva
- Erez Lieberman Aiden (ORCID: https://orcid.org/0000-0003-0634-6486)
- Shai J. Lawit (ORCID: https://orcid.org/0000-0002-3261-1696)
- Olga Dudchenko (ORCID: https://orcid.org/0000-0001-9163-9544)
- Brian St. Aubin (ORCID: https://orcid.org/0000-0002-6656-1826)
- Rishi Aryal (ORCID: https://orcid.org/0000-0001-5297-1528)
- Daniel G. Mead (ORCID: https://orcid.org/0000-0001-7717-4330)
- David Weisz (ORCID: https://orcid.org/0000-0001-5868-6672)
- Margaret Worthington (ORCID: https://orcid.org/0000-0001-8019-165X)
- Melanie Pham (ORCID: https://orcid.org/0000-0002-6083-271X)
- Cherie Ochsenfeld
- Lauren E. Redpath
- Matteo Buti (ORCID: https://orcid.org/0000-0002-1430-7826)
- Tomáš Brůna (ORCID: https://orcid.org/0000-0001-9811-5532)
- Andrew S. Fister (ORCID: https://orcid.org/0000-0001-8468-489X)
- Eric Déan
- Nahla V. Bassil
- Pradeep Marri
- Allie Sandra Castillo
- Joel Reiner
- Hudson Ashrafi
- Nat Graham
- Tom Poorten
- Gina Pham
- Warner Lowry
- Deepika Chauhan
- Daniel James Sargent
- Brian CW Crawford
Institutions
- North Carolina State University (US)
- National Institute of Agricultural Botany (GB)
- Baylor College of Medicine (US)
- Joint Genome Institute (US)
- Wellcome Sanger Institute (GB)
- National Clonal Germplasm Repository (US)
- Healthwise (US)
- Center for Theoretical Biological Physics (US)
- Owlstone Medical (United Kingdom) (GB)
- University of Florence (IT)
- The University of Texas Medical Branch at Galveston (US)
- Rice University (US)
- University of Arkansas at Fayetteville (US)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2025-12-23
- DOI
- https://doi.org/10.64898/2025.12.22.695586
- Citations
- 1
- Primary Topic
- Berry genetics and cultivation research
- Type
- article
- Field-Weighted Citation Impact
- 1.75
Funders
- National Science Foundation
- U.S. Department of Energy
- U.S. Department of Agriculture
- North Carolina State University
- Joint Genome Institute
- National Institutes of Health
- National Institute of Food and Agriculture
- Agricultural Research Service
- Division of Biological Infrastructure