A partnership is blossoming between the Arkansas High Performance Computing Center and the University of Arkansas System Division of Agriculture’s fruit breeding program.
In 2015, the fruit breeding program reported a dozen significant findings in fruit quality and disease resistance traits using phenotypic and genotypic data. The researchers generated the results in conjunction with staff at the computing center.
“This connection with the Arkansas High Performance Computing Center is allowing us to evaluate DNA sequencing to parallel classical phenotypic observation – what we see in that tree,” said John Clark, University Professor of horticulture who leads the fruit breeding program. “This is providing us accuracy of knowing what that genotype is to clearly help us manage the development of superior phenotypes.”
John Clark, University Professor of horticulture | Fred Miller, Division of Agriculture communications
Collaborating with the computing center also accelerated work that usually takes many years through classical breeding techniques.
“A fruit variety can take 10 to 20 years to develop,” Clark said. “Using the new molecular technology can not only increase the efficiency of the process but potentially shorten the interval from idea to product.”
Several of these findings have already been developed into DNA tests that include genetic markers that serve as signposts to indicate desirable genetic traits in a plant’s DNA. A marker may indicate a plant has resistance to a particular disease or that its fruit will be sweet or suitable for storage and shipping.
These DNA tests can be used to apply genetic marker-assisted breeding as a tool in a traditional breeding program to increase efficiency and decrease operating costs by reducing seedlings with undesirable genetics. Genetic markers serve as signposts that indicate desirable genetic traits in a plant’s DNA.
The collaboration began three years ago when graduate students Terrence Frett and Alejandra Salgado consulted with Pawel Wolinski, senior administrator at the Arkansas High Performance Computing Center, on how to run a software program known as FlexQTL on the center’s supercomputers.
Pawel Wolinski | Matt Reynolds, University of Arkansas
Their work is part of RosBREED, a research initiative to apply genetic marker technology to fruit crop breeding programs around the country.
Frett, who recently completed his doctorate at the U of A, tried FlexQTL as a master’s degree student at Clemson University.
“I was about zero for a couple thousand using my own laptop,” he said. “I never got it to work. A few of my colleagues told me it is essential to be using a supercomputer for this.”
When Frett enrolled at the U of A for his doctoral studies, he joined Salgado in identifying the genetic control of multiple breeding-relevant traits in peaches in the fruit-breeding program.
“Most everything you do in bioinformatics requires long run times and large chunks of memory,” said Jeff Pummill, co-director of the Arkansas High Performance Computing Center. “The software is not a classical supercomputer code, but we had been working on genome assembly with some of our biologists, so it was certainly worth trying.”
The Division of Agriculture is one of the 22 fruit breeding programs funded by RosBREED, a $10 million project funded by the U.S. Department of Agriculture to adapt and demonstrate new DNA-based tools. The division’s RosBREED research focuses on the peach and the blackberry. The fruit breeding program has released more than 60 varieties since its initiation in 1964, and has activities based in Arkansas but also with cooperators in various states and countries.
Terrence Frett (left) describes physical and other characteristics of peaches at the Division of Agriculture Fruit Research Station in Clarksville. | Fred Miller, Division of Agriculture Communications
“The goal of the project,” Clark said, “is to implement the use of DNA-based tools to complement the traditional breeding process by increasing the efficiency of breeding new peach and blackberry varieties with both superior product quality and disease resistance.”
Clark said the Division of Agriculture was included in the RosBREED project because the project leaders recognize the quality of the Arkansas fruit breeding program. As a result, the program will be able to bring a host of new tools to the job of serving Arkansas fruit growers and consumers.
“All these tools help us get down the road to more efficient fruit breeding,” Clark said. “Producers will have more options to sustainably protect their crops, while consumers and the entire supply chain will directly benefit from products with better taste, nutrition, keeping ability, and appearance.”
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