Fruits and Nuts
Blackberry ‘Hillquist’ – Primocane Fruiting
DISCOVERY OF THE BLACKBERRY PRIMOCANE-FRUITING GENE ENABLED BY ‘HILLQUIST’ NPGS GERMPLASM
Alexander Silva; Margaret Worthington; Michael A. Hardigan; and Nahla V. Bassil
University of Arkansas, Department of Horticulture, 316 Plant Sciences Building, 495 N Campus Walk, Fayetteville, Arkansas 72701.
University of Arkansas, Department of Horticulture, 316 Plant Sciences Building, 495 N Campus Walk, Fayetteville, Arkansas 72701.
USDA-ARS Horticultural Crops Production and Genetic Improvement Research Unit, 3420 NW Orchard Ave, Corvallis, Oregon 97330.
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
Annual flowering, also known as primocane-fruiting (PF), is a valuable trait in blackberry and raspberry production. Although PF cultivars are widely grown, the genetic basis of the trait has remained unresolved. From 2021–2025, scientists at the University of Arkansas and the USDA National Plant Germplasm System (NPGS) National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon collaborated to uncover the genetic basis of the PF trait in blackberry. Analyzing genetic resources from the NCGR and diverse breeding germplasm, researchers identified a single interval of the blackberry genome associated with the PF trait and developed highly accurate genetic markers that breeding programs can use to expedite plant selection. Improved analysis of the genome sequence for the Rubus argutus ‘Hillquist’ (the NPGS accession PI 553951) enabled identification of different genetic variants associated with the PF trait.
The goal of this project was to precisely map the primocane-fruiting (PF) gene in blackberry and develop reliable diagnostic markers that breeding programs can use to identify seedlings with this valuable trait.
Download a printable fact sheet by clicking the image below.
2. PROBLEMS ADDRESSED
Primocane-fruiting cultivars offer substantial production advantages, including extended harvest periods, the ability to schedule fruiting through primocane management, reduced winter injury risk, and reliable production in warm regions where chilling is insufficient for optimal fruit yield. Primocane-fruiting can also reduce labor costs related to cane management due to erect architecture and the option to utilize production only from annual canes without overwintering. However, PF cultivars generally lag behind elite floricane-fruiting (FF) cultivars in fruit quality, necessitating repeated FF × PF crosses to improve the performance of PF germplasm and cultivars. Because PF is a genetically recessive trait in blackberry, only ~17% of seedlings from standard breeding crosses express the trait, greatly increasing space, labor, and time required for breeding. Reliable DNA tests for the PF trait could address this bottleneck by identifying FF parents that carry PF genetic variants, thus enabling early culling of seedlings with FF genetic variants, accelerating development of high-quality PF cultivars, and improving breeding efficiency.
3. SOLUTIONS DEVELOPED
Genomic analyses of 365 tetraploid blackberry germplasm accessions and cultivars identified a single region on chromosome Ra03 that is strongly associated with primocane fruiting (Silva et al., 2025). Linkage analysis confirmed this chromosomal location and supported the interpretation that the PF trait was controlled by a single recessive gene. Further analyses of the genome sequence of the NCGR Rubus argutus cv. ‘Hillquist’ accession (v1.2) facilitated gene discovery and genetic analyses. The team developed two diagnostic genetic markers that predicted the presence of the PF trait with over 96% accuracy across a validation panel of 494 plants from multiple breeding programs.
Collaborators involved in developing solution:
- Isabella Vaughn, T. Mason Chizk, Lacy Nelson, Carmen Johns, John Clark: University of Arkansas System Division of Agriculture, Department of Horticulture, Fayetteville, Arkansas, USA
- Ellen Thompson: Hortifrut Genetics Ltd., Freedom, California, USA
- Tomáš Brůna: U.S. Dept. of Energy Joint Genome Institute, Lawrence Berkeley National Lab, Berkeley, California, USA
- Marcelo Mollinari: North Carolina State University, Dept. of Horticultural Science, Raleigh, North Carolina, USA
4. IMPACT
This was the first high-resolution genetic mapping of the primocane-fruiting trait in blackberry and identified the chromosomal location controlling this economically important trait. The accompanying identification of causal genes and genetic variants, made possible by an improved ‘Hillquist’ genome analysis, creates a foundation for future research on flowering regulation in Rubus and other short-day length flowering Rosaceae crops. The PF1 and PF2 KASP genetic markers provide immediately deployable tools for marker-assisted plant selection, enabling breeders to identify plants with the PF trait, eliminate seedlings with the FF trait early, and better combine PF with other desirable fruit-quality traits. These advances will reduce breeding cycle length, improve research efficiency, and accelerate the development of next-generation PF cultivars for global blackberry markets.
5. GERMPLASM
The wild Rubus argutus NPGS accession ‘Hillquist’ (PI 553951), the original diploid source of primocane fruiting in blackberry, was discovered in Ashland, Virginia in 1949 and entered the NCGR collection in 1985. This accession served as the donor parent for the PF trait to the first tetraploid primocane-fruiting cultivars, which were released by the University of Arkansas in 2004, and remains foundational to all PF breeding. ‘Hillquist’ was also the source of the first chromosome-scale blackberry reference genome sequence, which was further refined in this study through an updated analysis (v1.2). The ‘Hillquist’ genome sequence served as the primary reference for alignment of resequencing data, enabling refined genetic variant interpretation and discovery of causal genes within the mapped location for the PF trait.
6. ADDITIONAL RESOURCES
Details about genome sequencing are available through the Joint Genome Institute’s Phytozome.
Datasets can be found on the Genome Database for Rosaceae (accessions 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
Silva A, Vaughn I, Chizk T, Nelson L, Johns C, Thompson E, Nassil N, Hardigan M, Clark J, Brůna T, Mollinari M, Worthington M. 2025. A single genomic region controls primocane fruiting in tetraploid blackberry. bioRxiv:12.15.694498. https://doi.org/10.64898/2025.12.15.694498
8. CHAPTER INFORMATION
Citation: Silva A, Worthington M, Hardigan M, Bassil N. 2026. Blackberry ‘Hillquist’ – Primocane Fruiting. 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/blackberry-hillquist-primocane-fruiting/
Content originally submitted: March 5, 2026
Date of publication: May 4, 2026
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