HudsonAlpha’s genetic recipe for a new breed of Alabama farm crops

HudsonAlpha is working with genetic sequencing to produce new crop varieties with enhanced traits

Harvesting barley during field trials.

A team of scientists at the HudsonAlpha Institute for Biotechnology’s Genomic Sequencing Center in Huntsville is breaking farming tradition by introducing genomic sequencing technology to Alabama farmers.

The new approach is a faster, more targeted means for improving profitable farming seasons in Alabama and accelerates the production of new crop varieties. This helps farmers produce more crops with lower inputs like fertilizer and pesticides, decreasing costs on downstream processes like harvesting and food processing.

For generations, farmers selected plants based on measurable characteristics like color, size, health, weatherability and thousands of years of trackable production to domesticate and increase the efficiency of crop production, a process called phenotyping. Now, genetic sequencing can produce similar results much more quickly and accurately.

“The point of genetic sequencing is to accelerate the production of new crop varieties and then rapidly introduce those traits into an existing coltivirus as opposed to phenotyping, which takes a long time,” says Jeremy Schmutz, co-director of the HudsonAlpha’s Genomic Sequencing Center. “In the genetic world, a breeder can introduce a genetic trait like cold tolerance or disease resistance and put it immediately into any inbreeding pipeline.”

Prior to genetic technology, farmers selected plants for domestication and didn’t worry about what other traits came along for the ride.

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“A lot of modern crops have been severely bottlenecked because they have lost or reduced the amount of genetic variation,” Schmutz says. “That’s good because we were trying to improve certain traits, but at the same time, we also brought along some traits that were not desirable on the genetic side, and we lost traits in past breeding cycles.

“Genetic-based breeding allows you to do both. It lets you capture and keep that genetic variation but accelerate towards an entirely different set of traits at the same time.”

Dr. Josh Clevenger, faculty investigator over HudsonAlpha’s Wiregrass Peanut Project, compares genetic sequencing technology to an advanced Lego Kit.

“Lego Kits are complicated, but they tell you exactly what to do at each step,” he says. “There are a lot of steps in building something and a thousand weird looking pieces involved, but you have a picture and instructions to guide you.

“Now imagine you have 1,000 Lego pieces but you do not have a picture of what you are building, and you do not have any instructions.

“That is what genomic sequencing is — identifying a set of instructions to help us figure out how to breed perfect plants based on needs and environment. It’s about getting a desirable end product,” Clevenger says.

HudsonAlpha currently has three main breeding programs for food crops: peanuts and pecans, two of Alabama’s best producing food crops; and the reinstatement of barley as an important Alabama-grown crop.

Bringing Barley Back to Bama

More than 100 years ago, Alabama farmers surrendered growing barley to northern regions because they faced fewer climate challenges there. Now, with the ability to pinpoint genetic traits related to cold and heat resistance in the barley genome, scientists believe it is possible to reinstate barley as an Alabama food crop.

The HudsonAlpha barley project, funded by the Alabama Department of Economic and Community Affairs and supported by Alabama A&M University and Auburn University, has breeding programs with two successful barley producers — North Dakota State University and Virginia Polytechnic Institute. Both schools have provided the GSC with startup summer and winter barley.

Jeremy Schmutz shows off their first barley crop grown in Alabama in 120 years.

The breeding program so far exemplifies the challenges farmers face in Alabama.

“The first year, we planted over 30 different varieties of spring barley sent to us from North Dakota State in October and November as an overwinter crop,” says Schmutz. “Barley makes an excellent cover crop that reduces the erosion of soil over winter months, but it leafs out in the spring to be harvested between April and June.”

Schmutz says they were excited after the first year because of its success.

“But the second year, we had a couple of days of prolonged cold weather, and it died over the winter and didn’t come back in the spring,” he says, causing the loss of several varieties and genotypes.

They planted it again the third year but backcrossed barley varieties from Virginia Tech that had genetic cold tolerance traits with surviving NDS varieties. Some varieties survived, but Schmutz says it wasn’t the quality or quantity of production they got from Virginia Tech.

“While the goal of most genetic sequencing is to increase yield, some have decoupled traits underlying yield to maximize production. The producer’s goals, however, are not always to produce more, but to produce a more reliable product.

“Winter barley requires the cold tolerance trait or it’s not going to produce every year and farmers depend on reliability.”

One goal is malted local barley, which is used for beer production. When heated and put in water to make it sprout, barley growers are introducing the technology of agronomy — producing and using plants for food and other purposes.

Local sprouted barley, dried down again and put in beer, was a big hit last fall when Mobile’s Braided River Brewing Co. released Alabama’s first barley malt beer grown and brewed in Alabama.

That barley/malt production is an economic advantage for the state. Local farmers, Auburn and Alabama A&M formed a supply chain selling Alabama malt to Alabama breweries, keeping the economics in Alabama.

Wiregrass Peanut Project

What goes best with a cold glass of Alabama beer? Wiregrass peanuts!

According to the Alabama Farmers Federation, Dothan — and the 100-mile radius surrounding it known as the Wiregrass region —  is the Peanut Capital of the World. From there, an average of more than 400 million pounds of peanuts are grown per year representing about half the peanut production in the U.S.

Dr. Josh Clevenger, left, tends to peanut plants as part of the Wiregrass Peanut Project.

Led by Clevenger, HudsonAlpha’s peanut-breeding project currently partners with a dozen local high schools to serve as a hands-on classroom-based study of the genetics of agriculture with a focus on breeding better peanut plants.

The “peanut gallery” begins with each student receiving a peanut.

“I take each peanut seed into my lab, shave a little off and put it in a well to extract DNA,” Clevenger says. “A peanut’s DNA is as unique to another peanut as the DNA of people standing in Times Square.”

He used the DNA to sequence the peanut’s genetic traits and, with the students, analyzed the sequence to give them a complete genetic profile of each peanut, identifying the attributes that will produce specific variations in the peanut.

“We have serious discussions about what attributes we want when they nominate the peanut worthy of moving ahead in the development process,” Clevenger says.

The chosen peanut is backcrossed, transferring a good trait from one variety to the favored genetic background of another. Within a couple of years, they will breed a great peanut with resistance to diseases, a trait that will contribute to the economic bottom line of the producer.

“This is important because fungal diseases are a major concern in south Alabama due to heat and humidity,” Clevenger says. “The average farmer will require seven or eight fungicidal treatments during a growing season.”

The cost of those treatments comes straight from the farmer’s profits.

The Pecan Project

Nowhere are the benefits of genetic sequencing over traditional phenotyping better demonstrated than with Jeremy Schmutz’ pecan project.

Pecan growers also benefit from research being done by HudsonAlpha.

The common phenotypic selection for breeding pecan trees is very slow. It takes seven years for a pecan tree to produce its first nut and 10 more years before it produces its first full harvest, used to measure the pecan’s production for its 30-year lifecycle. That pecan tree must survive in that spot, remain healthy and produce nuts for decades.

With genetic sequencing, the breeder selects the most desirable pecan varieties and within two years, can move into a more rapid breeding cycle by backcrossing and creating offspring. The process is accelerated by chopping off a healthy desirable root stock and grafting it onto a tree with a desired trait like disease or drought resistance.

“We go back into the breeding program and transition some of them away from the phenotypic base and hopefully accelerate the production of new varieties,” says Schmutz. “We are focused on minimizing inputs going in, and hopefully optimize on the other side, the plant’s ability to live in that environment.”

Kimberly Ballard is a Huntsville-based freelance contributor to Business Alabama.

This article appears in the January 2024 issue of Business Alabama.

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