Thornless blackberry breakthrough

Researchers have discovered the genetic region responsible for blackberries’ deploying of a type of pointy self-protection: thorns.

Thorns can scratch pickers and damage fruit, making thornless blackberry varieties the preferred option in the U.S. market. Now, a team of researchers has pinpointed the genetic location behind the trait, paving the way for plant breeders to speed up development of thornless varieties.

Margaret Worthington, associate professor of fruit breeding and genetics for the Arkansas Agricultural Experiment Station — the research arm of the University of Arkansas (UA) System Division of Agriculture and UA’s Dale Bumpers College of Agricultural, Food and Life Sciences — supervised the project.

Worthington said blackberry breeders have long lacked the genetic information needed to understand why some plants are thornless. All fresh-market blackberry varieties are tetraploids, meaning they have four copies of every chromosome rather than humans’ two. The extra copies make genetic analysis more difficult.

Prickly conundrum

No one knew the genetic locus — the location of a gene on a chromosome — for the prickly trait, making it an obvious target for Worthington, who began working on it in 2016.

The resulting study, “Genetic control of prickles in tetraploid blackberry,” was published in G3: Genes, Genomes, Genetics.

To Worthington’s knowledge, the findings reveal the “first diagnostic marker for any trait that’s been developed and published in blackberry.”

Ellen Thompson, study co-author and global director of breeding for Hortifrut Genetics, highlighted the significance of the breakthrough.

“These are the world’s first publicly available markers developed for freshmarket and processing blackberries,” she said. “Markers save time and money, allowing breeders to make decisions faster before seedlings are planted in the field.

“Though Hortifrut Genetics’ blackberry breeding program is already 100% thornless — something many other companies are trying to achieve — using these markers to screen seedlings in a high-throughput manner allows us to incorporate diverse and rustic traits of thorny germplasm, study segregation ratios more quickly and identify the associated desirable prickle-free phenotypes at a very early stage,” Thompson said.

Worthington hopes future research can move beyond identifying the locus and pinpoint the causal gene itself. A locus describes where a gene is found, while a causal gene is more specific and directly responsible for an organism’s trait.

Determining genetic makeup

The research team used a genomewide association study — an analysis of a plant’s complete set of genetic information — to identify the locus responsible for the thornless trait.

Researchers gathered DNA from 374 blackberry varieties, both prickly and thornless. They analyzed the DNA samples through genotyping, scanning for variations known as singlenucleotide polymorphisms (SNPs) that may influence the trait. When SNPs are strongly linked to a physical characteristic, they signal a gene in that region may be influencing it.

Use of genetic markers is relatively new in blackberry and raspberry breeding, though it is well established in row crops like rice and soybeans.

“Genetic markers are used widely in row crops to select for things like disease resistance, cutting or flowering date, and other traits of interest,” Worthington said.

Double-edged sword

Another key finding is the lack of genetic variation around chromosome Ra04, resulting in a “linkage disequilibrium block,” where genetic markers are more likely to be inherited together than by chance, Worthington said.

For the thornless gene within this block, that means it is often passed on from parent plant to child plant along with other genes, including undesirable traits like high acidity, low cold tolerance and canes that don’t grow upright unless supported.

Worthington said that by selecting so strongly for thornlessness, breeders have unintentionally narrowed variation around the locus and carried forward negative traits. Crossing with prickly plants could restore that variation.

The discovery of the thornless locus will allow breeders to avoid “waiting years to phenotype mature canes, which reduces breeding cycle length … and improves selection efficiency for thornless blackberries,” said study co-author Hudson Ashrafi, associate professor of horticultural science at North Carolina State University.

The process of phenotyping involves measuring observable traits and selecting the plants with desirable characteristics for future breeding.

The study’s lead author, Carmen Johns, is an assistant fruit breeder working with Worthington. Other coauthors include UA’s Alexander Silva, Thomas Mason Chizk, Lacy Nelson, John Clark (a distinguished professor emeritus of horticulture), Rishi Aryal (a former NC State postdoctoral research associate) and Michael Hardigan (a USDA plant geneticist.)

The work was supported in part through the Specialty Crop Research Initiative and through the Agriculture and Food Research Initiative, both from the USDA’s National Institute of Food and Agriculture. Hatch Project ARK02846 provided additional funding.

Maddie Johnson is with the University of Arkansas System Division of Agriculture’s Arkansas Agricultural Experiment Station.

— Maddie Johnson, University of Arkansas System Division of Agriculture

Above photo: Scientists’ pinpointing of the genetic locus for blackberry’s thorny trait is a step toward more efficient selection for thornlessness. Photo courtesy of Ellen Thompson.