By John Lovett
University of Arkansas Division of Agriculture
FAYETTEVILLE, Ark. — Lifting a veil of uncertainty in blackberry genetics, a national team of horticulture scientists have discovered evidence pointing to the single genetic region that controls primocane-fruiting, or the ability to flower and fruit on first-year canes.
The primocane-fruiting trait has fueled the rapid growth of the fresh‑market blackberry industry over the past two decades, enabling fruit to be grown in warmer climates and to be produced outside the traditional harvest window. Still, scientists didn't fully understand its genetic basis, said Margaret Worthington, director of the Fruit Breeding Program for the University of Arkansas Division of Agriculture's research arm, the Arkansas Agricultural Experiment Station.
Published in the Genetics journal , the study by Worthington and her co-authors explains how genome-wide association identified a single genomic region on chromosome Ra03 that is strongly associated with primocane fruiting.
The new research can speed development of improved varieties with better yield, fruit quality and regional adaptability, she said.
"The world's first primocane-fruiting blackberries were developed here in the Arkansas Fruit Breeding Program, and we are continuing to breed new primocane-fruiting varieties with high yield potential, fruit quality and adaptation to the Southeast as part of our Prime-Ark® series," Worthington said. "So, it is gratifying that we are able to lead the charge to resolve some of the mysteries behind its genetic control and develop useful markers for the global blackberry community."
Worthington is also an associate professor in the department of horticulture for the Dale Bumpers College of Agriculture, Food and Life Sciences at the University of Arkansas.
To validate the result, the researchers conducted genetic linkage mapping in a separate biparental population, which independently confirmed that the same chromosomal region controls the trait.
Within the mapped region, the team identified 10 candidate genes potentially involved in flowering regulation. Follow‑up analysis narrowed the list to two high‑priority candidates that have known roles in plant developmental timing.
New DNA markers enable faster breeding
Beyond uncovering the genetics behind primocane fruiting in blackberries, the study delivered an immediate benefit for blackberry breeders. The researchers designed two DNA‑based markers, called PF1 and PF2, that reliably predict whether a blackberry plant will express primocane fruiting.
Tested across nearly 500 blackberry selections, the markers correctly identified the trait in more than 96 percent of cases, allowing breeders to screen seedlings long before they are mature enough to fruit.
Because primocane-fruiting blackberries tend to lag a little behind traditional floricane-fruiting blackberries in terms of fruit quality, Worthington said, breeders must make many crosses between elite floricane-fruiting material and primocane-fruiters to bring in flavor and firmness.
"But primocane-fruiting is recessively inherited, and these blackberries are autotetraploids, so for many of the crosses we make, we only expect one-sixth of the progeny to be primocane-fruiting," she explained.
Autotetraploids have four copies of each chromosome and offer breeding advantages, including increased genetic diversity, greater resilience to environmental stress and larger fruits and seeds than their diploid counterparts with only two copies of each chromosome.
Using the genetic markers, Worthington and her team can cull floricane-fruiting seedlings in segregating populations before planting, ensuring they have a chance to evaluate more primocane-fruiting seedlings.
"We have been using these markers in our applied breeding program for three years now and we are starting to see much more rapid progress on improving fruit quality in primocane-fruiters," Worthington said.
About the researchers and funding
The study's first author was Alexander Silva-Cordoba, a Ph.D. student in the department of horticulture. Co-authors included graduate student Isabella Vaughn, Mason Chizk, Ph.D., Lab Manager Lacy Nelson, Assistant Fruit Breeder Carmen Johns, Worthington and John Clark, Distinguished Professor emeritus of horticulture.
Other collaborators on the study included Ellen Thompson, Global Rubus Breeding and Development Director for Hortifrut Genetics; Nahla Bassil, molecular plant geneticist, and Michael Hardigan, plant geneticist, of the U.S. Department of Agriculture's Agricultural Research Service National Clonal Germplasm Repository in Corvalis, Oregon; Tomáš Brůna, a genome data scientist for the U.S. Department of Energy Joint Genome Institute at the Lawrence Berkeley National Laboratory in Berkeley, California; and Marcelo Mollinari, an assistant research professor in the department of horticultural science at North Carolina State University.
The research was funded by the U.S. Department of Agriculture's National Institute of Food and Agriculture Specialty Crop Research Initiative project "Tools for Genomics-Assisted Breeding of Polyploids: Development of a Community Resource," grant number 2020-51181-32156, and USDA-NIFA Agricultural and Food Research Initiative project "Genomic Breeding of Blackberry for Improved Firmness and Postharvest Quality," grant number 2019-67013-29196.
Hatch Project ARK02846 provided additional funding for the research. The work conducted by the Joint Genome Institute was supported by the Department of Energy's Office of Science under contract number DE-AC02-05CH11231.
To learn more about ag and food research in Arkansas, visit aaes.uada.edu
