Scientists at the University of Florida have generated the chromosome-scale genome assembly for the primocane-fruiting, thornless tetraploid blackberry BL1. Their results should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.
Blackberries. Image credit: Lin Animalart.
Blackberries belong to the genus Rubus subgenus Rubus (formerly subgenus Eubatus) within the family Rosaceae.
They are characterized by their dark purple to deep black color, compound fruit structure, and a combination of juicy, tart, and sweet flavors.
Blackberry fruits are an exceptional source of anthocyanins, antioxidants, and dietary fibers, offering significant health benefits to consumers.
Over the past two decades, a sharp increase in consumer demand has led to substantial expansion of the market for fresh and processed blackberries in the United States and other countries worldwide.
As the fourth most economically important berry crop in the United States, the country produced 16850 metric tons of processed and 1,360 metric tons of fresh blackberries in 2017.
In 2021, the USA imported 122,873 metric tons of fresh blackberries and 16,738 metric tons of frozen blackberries, valued at $519 million and $43 million, respectively.
The global production of blackberries is estimated to be over 900,000 metric tons, making it a substantial contributor to the international berry industry.
The ongoing development and introduction of new, improved cultivars has been instrumental in addressing consumer demands and increasing blackberry production across the globe.
“Overall, this new study not only advances our understanding of blackberry genetics, but it sets the stage for significant improvements in blackberry breeding techniques,” said Dr. Zhanao Deng, a researcher journal Horticulture Research.
“The end result could be better, more robust blackberry varieties that benefit both growers and consumers worldwide.”
Using a large collection of DNA sequences from an experimental blackberry BL1, Dr. Deng and colleagues computationally pieced them together, rebuilding the original sequence of the entire genome of this blackberry.
It starts with understanding that BL1 is a tetraploid fruit, one that comes from a plant with four copies of each chromosome in its cells.
That means it has twice the normal number of chromosomes as a typical diploid plant, like a raspberry.
“Working with a tetraploid is more complex than a diploid,” Dr. Deng said.
“The release of this tetraploid blackberry genome can contribute to more efficient and targeted breeding, ultimately leading to the development of new cultivars with enhanced fruit quality, and resistance to important diseases.”
“The reference genome created from this research can be a powerful tool for anyone working with blackberries.”
The genome assembly also uncovers the secrets behind key traits like growing blackberry plants with no thorns and the production of anthocyanin production, which affects the color and health benefits of the fruit.
“This finding can help us understand why blackberries develop their characteristic deep purple/black color over time and how to potentially enhance this process for more nutritious berries,” Dr. Deng said.
The team’s work was published in the journal Horticulture Research.
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Dev Paudel et al. 2025. A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson). Horticulture Research 12 (6): uhaf052; doi: 10.1093/hr/uhaf052
