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Researchers have discovered the genetic region responsible for blackberries' deployment 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 them, paving the way for plant breeders to speed up the development of thornless varieties.

The work is in the journal G3: Genes, Genomes, Genetics.

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

Worthington said blackberry breeders have not had the necessary genetic information to identify why some plants lack what are technically known as prickles but are commonly called thorns.

All fresh-market blackberry varieties are tetraploids, meaning they have four copies of every chromosome, as opposed to humans' two copies. The higher number of copies makes genetic analysis more difficult.

No one knew the genetic locus, or the location of a gene on a chromosome, for the prickly trait, making it "an obvious target to work on" in Worthington's eyes. She's been doing so since 2016.

Worthington said that to her knowledge, the results reveal the "first diagnostic marker for any trait that's been developed and published in blackberry."

Ellen Thompson, co-author of the study and Global Rubus Breeding and Development Director for Hortifrut Genetics, also highlighted the significance of the work.

"These are the world's first publicly available markers developed for fresh-market 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's 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," she said.

Worthington said she hopes future research can go beyond identifying the locus and pinpoint the thorny trait's causal gene itself.

Determining genetic makeup

The research team used a genome-wide association study to determine the locus responsible for the thornless trait. A genome refers to the blackberry plant's complete set of genetic information. Researchers gathered DNA from a total of 374 blackberry varieties, some with the prickly trait and some without.

These DNA samples were then analyzed through genotyping, a highly precise process that involves scanning for and identifying variations in the genetic code that could influence the prickly trait. If these variations, known as single-nucleotide polymorphisms (SNPs) are significantly associated with the trait, it suggests a gene in that area could be influencing the trait.

These SNPs, also referred to as markers, are what point to the region associated with the trait in question.

Worthington said that the use of genetic markers is more recently being adopted for blackberries and raspberries, but this type of development is more advanced when it comes to row crops like rice and soybeans.

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

Double-edged sword

Worthington said another key finding of the study was the lack of genetic variation around chromosome Ra04, leading to a "linkage disequilibrium block," or a region where genetic markers are more likely to be inherited together than by happenstance.

For the thornless gene included in this block, this means it is often passed on from parent plant to child plant with many other genes—including undesirable traits like high acidity, lack of cold tolerance and canes that don't grow upright unless supported.

Worthington explained that in selecting so specifically for thornless plants, these negative traits have been brought in and variation around the locus has been lost. She said conducting crosses with prickly plants could help bring the variation back.

The study's lead author, Carmen A. Johns, is an assistant fruit breeder working with Worthington, and the project served as her master's thesis.

Worthington noted that collaborators in the "Tools for Genomics-Assisted Breeding of Polyploids: Development of a Community Resource" Specialty Crop Research Initiative project helped develop the bioinformatic and genetic analysis tools that made the project possible.

Co-authors Alexander Silva and Thomas Chizk were especially involved in the bioinformatics work behind the study.

Researcher Hudson Ashrafi said the study's finding of a thornless locus enables breeders to avoid "waiting years to phenotype mature canes, which reduces breeding cycle length … and improves selection efficiency for thornless blackberries."

The process of phenotyping involves measuring observable traits of a plant and then selecting the organisms with the desirable trait for future breeding.