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A Primo Berry Genome!

Caneberries, including blackberries (Rubus subgenus Rubus) and raspberries (R. idaeus), are botanically unique in that they have perennial root systems and crowns and biennial canes. Typically, first-year vegetative canes (primocanes) must overwinter and accumulate chilling hours before flowering and fruiting in their second year after becoming floricanes (Clark et al., 2007). The development and adoption of primocane-fruiting raspberry and blackberry cultivars that fruit on first year canes has revolutionized the caneberry industry. Now growers can produce a summer crop on floricanes and a second fall crop on primocanes, extending the growing season and producing two crops in one year!

Tetraploid primocane-fruiting breeding selection from the University of Arkansas fruit breeding program that has Hillquist blackberry is in the pedigree! Photo by Margaret Worthington.

Today, we share the chromosome-length genome assembly for the diploid blackberry ‘Hillquist’ (R. argutus, PI 553951), generated using plants donated by the USDA-ARS National Clonal Germplasm Repository in Corvallis, OR.

‘Hillquist’ was chosen for the assembly because it is the source of the recessive allele for primocane-fruiting used in modern blackberry breeding programs (Clark, 2008; Lopez Medina et al., 2000). ‘Hillquist’ was originally discovered in Ashland, VA by L.G. Hillquist, who noticed that some of the wild blackberries growing in his backyard had an unusual fruiting habit. His wife later donated the plants to the New York State Agricultural Experiment Station in 1949. Jim Moore, the founder of the University of Arkansas System Division of Agriculture fruit breeding program, first crossed ‘Brazos,’ a tetraploid, floricane-fruiting blackberry cultivar, to ‘Hillquist’ in 1967, but the first primocane-fruiting cultivars, ‘Prime-Jim’ ® and ‘Prime-Jan’® were not released until 2004, nearly 40 years later (Clark, 2008). Since then, primocane fruiting cultivars have transformed the blackberry industry and ‘Hillquist’ is now represented in the pedigree of much public and private blackberry breeding germplasm around the world.

This work is part of a collaborative effort between DNA Zoo, the University of Arkansas, USDA-ARS, North Carolina State University, NIAB-EMR, Pairwise Plants, and the Wellcome Sanger Institute. The assembly was generated using PacBio and Hi-C sequencing data. The PacBio data was assembled using FALCON software. The Falcon assembly was phased into haplotypes using FALCON-Unzip (see Chin, Peluso et al., 2016), with error correction on the phased assembly performed using Arrow. The Hi-C scaffolding was performed using the standard DNA Zoo workflow, based on in situ Hi-C (Rao, Huntley et al., 2014) prepared from fresh leaf samples. The tools used for Hi-C data processing included Juicer (Durand, Shamim et al., 2016), 3D-DNA (Dudchenko et al., 2017), and Juicebox Assembly Tools (Dudchenko et al., 2018).

See below the whole-genome alignment plots that compare the Hillquist genome to the Burbank Thornless (R. ulmifolius), available here at the DNA Zoo, black raspberry (R. occidentalis V. 3, VanBuren et al., 2018), and woodland strawberry (Fragaria vesca V. 4, Edger et al., 2017) genomes. All four genomes are highly collinear. (Note that inversions on chromosomes 4 and 6 in R. occidentalis likely represent errors in the chromosome-scale assembly of R. occidentalis.)

Whole-genome alignment plots between the new genome assembly for ‘Hillquist’ blackberry (Hillquist_HiC) and the chromosome-scale assemblies of R. ulmifolius ‘Burbank Thornless’ (Burbank_HiC) blackberry, woodland strawberry (Fragaria vesca v.4, from Edger et al., 2017) and black raspberry (R. occidentalis v.3, from VanBuren et al., 2018). The ‘Burbank Thornless’ (Burbank_HiC) genome assembly is available on DNAzoo ( and both woodland strawberry and black raspberry genomes are publicly available at the Genome Database for Rosaceae (

All the following people contributed to the project: Erez Aiden, Rishi Aryal, Hamid Ashrafi, Nahla Bassil, Mario Caccamo, Brian Crawford, Michael Dossett, Olga Dudchenko, Felicidad Fernandez-Fernandez, Gina Fernandez, Dan Mead, Cherie Ochsenfeld, Gina Pham, Melanie Pham, Tom Poorten, Dan Sargent, Aabid Shariff, David Weisz, Margaret Worthington, Xiaoyu Zhang


Clark, J.R. (2008). Primocane-fruiting blackberry breeding. HortScience 43, 1637–1639.

Clark, J.R., Stafne, E.T., Hall, H.K., Region, N., and Finn, C.E. (2007). Blackberry breeding and genetics. Plant Breed. Rev. 29, 19–144.

Lopez-Medina, J., Moore, J.N. and McNew, R.W.. 2000. A proposed model for inheritance of primocane fruiting in tetraploid erect blackberry. J. Am. Soc. Hortic. Sci. 125, 217–221.

Edger, P.P., VanBuren, R., Colle, M., Poorten, T.J., Wai, C.M., Niederhuth, C.E., Alger, E.I., Ou, S., Acharya, C.B., Wang, J., et al. (2017). Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity. Gigascience 7, 1–7.

VanBuren, R., Wai, C.M., Colle, M., Wang, J., Sullivan, S., Bushakra, J.M., Liachko, I., Vining, K.J., Dossett, M., Finn, C.E., et al. (2018). A near complete, chromosome-scale assembly of the black raspberry (Rubus occidentalis) genome. Gigascience 7, 1–9.


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