Jun 5, 2023

University of Arkansas leads blackberry genome project

An international team of scientists has assembled the first complete sequence of the blackberry genome, creating a genetic tool that will help guide fruit breeders to develop new varieties with improved flavor, hardiness and other desired characteristics.

Margaret Worthington, associate professor and fruit breeder for the Arkansas Agricultural Experiment Station, the research arm of the University of Arkansas System Division of Agriculture, said this project yielded the first chromosome-length assembly and annotation of the blackberry genome.

Choice berry

Worthington collaborated with a team of 26 researchers from seven countries, including institutions in seven U.S. states. Together they assembled the genome of Hillquist, a wild blackberry with a unique fruiting habit discovered in 1949 by H.L. Hillquist, a gardener in Ashland, Virginia. It is the only known source of primocane-fruiting genetics and is the parent of every primocane-fruiting variety developed by public and private breeding programs.

Blackberry plants are perennial plants with biennial canes, or stems, that live for two years. The stems are known as primocanes in the first year and floricanes in the second year. Most blackberries only produce fruit on the floricanes.

Primocane-fruiting blackberries flower and fruit on floricanes in the early summer and on primocanes in the late summer.

The University of Arkansas System Division of Agriculture released the first primocane-fruiting varieties, Prime-Jim and Prime-Jan, in 2004. Six of the division’s 21 blackberry releases are primocane-fruiting varieties.

Americans spent more than $656 million on blackberries in 2020, according to data from the 2022 Produce Market Guide cited in the research paper.

Putting it all together

Worthington pieced together the international team of scientists who used multiple advanced genetic tools to sequence and annotate the blackberry genome with high accuracy.

The group sequenced Hillquist blackberry and assembled the pieces into complete chromosomes. The scientists then examined the genome to build an accurate structural annotation — identification of the precise location of every DNA sequence that comprises a gene. They also developed a function annotation — a description of the likely function of each gene based on the roles of similar genes in other plants that were used as models.

A research paper about the genome project, titled “A chromosome-length genome assembly and annotation of blackberry,” was published in the February issue of G3, a genetics research journal published by Oxford University Press.

The completed genome has already proven helpful in the university’s breeding program.

“We have used the genome for a lot of things since then,” Worthington said. “We have several research papers already in progress that draw from this assembly.”
The blackberry assembly gave Worthington’s research group a starting point from which they were able to develop thousands of molecular markers and perform a genome-wide association study for the first time in blackberries, she said.

A genome-wide association study is an observational analysis of the genetic variants in huge numbers of individuals of the same species. The aim is to identify genes that are statistically associated with specific traits. The resulting information has a wide range of applications, including estimating the heritability of desirable traits in plants.

Worthington said this effort yielded diagnostic genetic markers for primocane-fruiting that the Arkansas fruit breeding team is using for the first time this year.

“Fieldwork will always be our bread and butter,” she said. “But it would be a mistake not to use modern tools to advance our program, to streamline it and make it more efficient.”

To learn more about Division of Agriculture research, visit the Arkansas Agricultural Experiment Station website.

Fred Miller, University of Arkansas System Division of Agriculture

Photo: The Arkansas Agricultural Experiment Station led an international team that assembled the first complete sequence of the blackberry genome. Photo by Fred Miller.