Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/12/2026
Publication Date: 3/23/2026
Citation: Silva-Córdoba, A., Vaughn, I., Chizk, M., Nelson, L., John, C., Thompson, E., Bassil, N.V., Hardigan, M.A., Clark, J., Bruna, T., Mollinari, M., Worthington, M. 2026. A single genomic region controls primocane fruiting in tetraploid blackberry. Genetics. 233(2). Article iyag078. https://doi.org/10.1093/genetics/iyag078.
DOI: https://doi.org/10.1093/genetics/iyag078

Interpretive Summary: The fresh-market blackberry industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. In this study, two approaches were used to identify the chromosomal region contorlling this trait on chromosome 3. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved ‘Hillquist’ genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory variation in the upstream region in the zinc finger homolog. Two diagnostic DNA markers (PF1 and PF2), predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify strong candidate genes for flowering regulation in the Rubus genus, and deliver diagnostic markers that can be immediately deployed in breeding programs.

Technical Abstract: The fresh-market blackberry (Rubus subgenus rubusRubus) industry has expanded dramatically in the past two decades, driven in part by improved cultivars. Introgression of the primocane-fruiting (PF; annual flowering) trait into elite germplasm has enabled dual cropping in a single year, season extension, and cultivation in tropical and subtropical regions. Despite its economic performance, the genetic basis of PF is not well understood. It has been proposed that the PF trait is controlled by a major recessive locus, but its genomic location is unclear. Here, a genome-wide association study (GWAS) of 365 tetraploid blackberry genotypes identified a single genomic region on chromosome Ra03 (~33 Mb) strongly associated with PF. Genetic linkage analysis in a biparental population confirmed that the same interval (32-35 Mb) was linked to the PF phenotype. Ten putative candidate genes were identified in this region. Allele mining using whole-genome resequencing of 17 genotypes highlighted two high-priority candidates: a CCCH-type zinc finger gene and a ubiquitin-specific protease gene. Use of an improved Rubus argutus ‘Hillquist’ genome annotation (v1.2) enabled refined variant interpretation, including identification of regulatory 3'UTR polymorphisms in the zinc finger homolog. Two diagnostic KASP markers (PF1 and PF2), designed from peak GWAS SNPs, predicted the PF phenotype with over 96% accuracy in a validation panel of 494 tetraploid blackberries from multiple breeding programs. Together, these results provide the first high-resolution mapping of the PF locus in blackberry, identify strong candidate genes for flowering regulation in Rubus, and deliver diagnostic markers that can be immediately deployed in breeding programs.