Early Dialogue Critical for Plant Breeding Innovations

May 14, 2018

By Chris Crawford • From Spring 2018 American Soybean Magazine

Photo courtesy of Calyxt


New plant breeding techniques, which can include genome editing and epigenetic modifications, are being used to expand traditional plant breeding tools and introduce new plant traits more rapidly and precisely.

Michael Gregoire, associate administrator for the U.S. Department of Agriculture’s (USDA) Animal and Plant Health Inspection Service (APHIS), said the agency likes to use the term “plant breeding innovation” (PBI) to describe gene editing techniques that essentially mimic what can be done in the greenhouse through traditional plant breeding.

“The term refers to a suite of new techniques—such as CRISPR and TALEN—that are increasingly being deployed by plant breeders to produce new plant varieties,” he said.

It’s important to note that as rapidly as these techniques are being developed, so is a unified effort to make sure consumers fully understand the difference between PBIs and genetically modified organisms (GMOs), and the far-reaching benefits PBIs can bring to the table.

“They have the potential to solve specific challenges facing U.S. agriculture, benefit global food security and contribute to environmental sustainability by improving crop quality, increasing yields and improving nutritional value,” Gregoire said.

The USDA’s APHIS currently reviews inquiries of new PBI developers on a case-by-case basis through its “Am I Regulated Under 7 CFR part 340” process.

“If there was not a plant pest involved, we’ve determined them not to be regulated,” Gregoire said. “The ‘Am I Regulated’ process was established for developers wanting to better understand if their biotechnology products fall under the agency’s regulatory oversight. We will have more to say about this in the future.”

Bernice Slutsky, Ph.D., senior vice president of domestic and international policy for the American Seed Trade Association (ASTA), said one of the latest and most versatile methods used for gene editing is CRISPR-Cas9.

According to a genetics resource from the U.S. National Library of Medicine, CRISPR-Cas9 stands for “clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9.”

The resource said CRISPR-Cas9 has become a popular genome editing method because it’s faster, cheaper, more accurate and more efficient than other current methods.

“CRISPR-Cas9 was adapted from a naturally occurring genome editing system in bacteria,” it said. “The bacteria capture snippets of DNA from invading viruses and use them to create DNA segments known as CRISPR arrays.”

These CRISPR arrays let the bacteria remember the viruses, and if the viruses attack again, the bacteria produce RNA segments from the arrays to target the viruses’ DNA.

“The bacteria then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus,” according to the U.S. National Library of Medicine resource.

For example, Slutsky said CRISPR-Cas9 can allow soybean breeders to silence a gene that makes the plant sensitive to a disease.

“This gene deletion would mean the plant was no longer sensitive to that disease,” she said.

Slutsky said it’s also important to mention that this process doesn’t introduce foreign DNA into a plant; it uses the plant’s own DNA to do the work.

“We’re saying these are breeding tools,” she said, “Doing much the same thing breeders have since farmers started selecting the best crops in their fields hundreds of years ago.”

Differentiating PBIs from GMOs

PBIs are different from GMOs, which are transgenic organisms that have been altered by adding genetic material from an unrelated organism.

Renee Munasifi, Washington representative for the American Soybean Association (ASA), who specializes in biotechnology, said this differentiation needs to start by how PBIs are described.

“I think generally, producers have a great story to tell,” she said. “They need to tell it better—why we use techniques, biotech or plant breeding techniques. They can be better stewards of environment while making safe, affordable products.”

Gregoire said USDA’s APHIS recognizes the need to better communicate with consumers about biotechnology.

In fact, he said Congress recently appropriated $3 million to fund the Agricultural Biotechnology Education and Outreach Initiative, which calls on the USDA and Food and Drug Administration (FDA) to collaborate to provide education and outreach to the public on agricultural biotechnology, and food and animal feed ingredients derived from biotechnology.

“The goal of this initiative is to provide consumer outreach and education through publication and distribution of science-based educational information on the environmental, nutritional, food safety, economic and humanitarian impacts of agricultural biotechnology,” Gregoire said.

Interesting PBI applications

Jack Bobo, chief communications office and senior vice president for bioengineering company Intrexon Corp., said his company has been using genetic engineering in many agricultural applications.

For example, Intrexon’s subsidiary Okanagan Specialty Fruits has used gene silencing of polyphenol oxidase in apples to tell the plants not to rot.

Okanagan Specialty Fruits has used gene silencing of polyphenol oxidase in apples to tell the plants not to brown or rot. Gene silencing was used on the apple on the right. Photo Credit: Okanagan Specialty Fruits Inc.


“This is great if you want to keep fruit from bruising,” Bobo said. “If the apple is dropped, it will have some indentation but won’t bruise. This means there will be less finger bruising for growers, less bruising at retail and less browning when slicing the apples for kids.”

This spring, the company is adding non-browning Fuji apples to its offering of golden and Granny apples currently on the market. Bobo said 3 to 5 percent of new apple crops planted use Intrexon seeds.

Next up, the company is working to use its gene silencing technology to prevent browning in avocados and lettuces, he said.

Another of Intrexon’s subsidiaries, Oxitec has developed “Friendly Aedes” male mosquitos, which don’t bite or transmit diseases. When released, these Aedes aegypti mosquitos search for wild females to mate and their offspring inherit a self-limiting gene that causes them to die before reaching adulthood.

These mosquitos’ offspring also inherit a fluorescent marker that allows for better tracking and monitoring. They die along with their offspring so they don’t leave an ecological footprint.

“This technology is different from insecticides, which don’t allow for accurate tracking of population fluctuation,” Bobo said.

An additional product that uses Oxitec’s self-limiting technology and is of interest to soybean growers—an eco-friendly fall armyworm (FAW) solution—is being developed by Intrexon.

The self-limiting fall armyworm being developed contains a gene passed on by engineered males that specifically prevents female offspring from reaching adulthood, which reduces wild FAW populations and minimizes their ability to spread quickly across long distances.

Originally native to the Americas, fall armyworm invaded Africa in 2016 and rapidly spread to at least 28 countries, causing an estimated $13.8 billion in losses of corn, sorghum, rice and sugarcane, according to a report from the Center for Agriculture and Biosciences International.

Another interesting gene-editing project comes from majority-owned subsidiary of Intrexon, AquaBounty Technologies Inc. and the company’s AquAdvantage salmon.

Approved for sale by the FDA in November 2015, these genetically enhanced Atlantic salmon reach market size in half the time of conventionally farmed Atlantic salmon.

The U.S. currently imports more than 95 percent of the Atlantic salmon it consumes from Norway and Chile, Bobo said. Because AquAdvantage salmon are produced in the U.S., this reduces production costs and the carbon footprint associated with current salmon farming operations.

Bobo said AquAdvantage salmon will be available once the FDA finalizes its labeling guidance for the U.S. market on whether a product has been genetically engineered, which is expected by July. The company sold its first fish in Canada last year.

Salmon eggs pictured. AquaBounty Technologies Inc. uses gene editing to allow its AquAdvantage salmon to reach market size in half the time of conventionally farmed Atlantic salmon. Photo Credit: AquAdvantage


AquaBounty Technologies currently has a facility in Indiana that produces 1,200 metric tons of salmon.

Bobo envisions building a facility capable of producing 6,000 metric tons of salmon that could be an investment of $100-150 million and create tens of thousands of jobs.

The technology adds a gene from Pacific salmon, which grow year-round, in Atlantic salmon that usually only grow in the summer and winter, he said.

“These salmon grow twice as fast as traditionally farmed salmon and require 20 to 30 percent less feed,” Bobo said.

Bobo said Intrexon also is working on controlling traits in plants such as flowering. For example, the company has figured out how to turn the flowering of the Arabidopsis plant on and off and control flower color as well.

“Applications for this are interesting,” Bobo said. “It could be applied in alfalfa if you don’t want it to flower for harvesting. Also, alfalfa pollen can travel a long distance and organic growers could lose their certification if conventional pollen traveled onto their farms.”

Bobo said the company is also interested in drought-tolerant traits that can be easily activated and deactivated.

“Our technology would turn on drought tolerance only when needed during a drought,” he said. “That would be pretty exciting. And then you could spray the plants with an activator to turn this trait back off or on.”

This could be a breakthrough technology with 1.2 billion people living in areas with scare water resources.

Researchers at the Institute of Plant Biology at the University of Illinois announced a similar project in March, explaining they had modified a single tobacco plant gene that allowed the plant to use 25 percent less water with fairly normal yields.

That same month, another company, Calyxt, which specializes in gene editing for agricultural products, said it planned to launch a high oleic soybean variety later this year.

The company has contracted with 50 farmers in the Midwest, representing more than 10,000 acres planted of this new soybean. (Note from the Editor: Since publication of this article in the Spring 2018 issue of American Soybean magazine, Calyxt provided an update that it had ultimately contracted with 75 farmers in the Midwest, representing more than 16,000 acres of the new soybeans.)

The high oleic/low-saturated fat oil from this new variety of soybeans is designed to eliminate the need for hydrogenation. Because hydrogenation produces trans-fatty acids, the process needed to be changed, as the FDA said human food can no longer contain partially hydrogenated oils by June 18.

“The vast expansion of Calyxt’s high oleic soybean variety, along with our strong grower retention year-over-year, signifies important advancements in our product offering as we prepare for the commercial launch of the soybeans later this year,” said Federico Tripodi, Calyxt CEO, in a news release. “Calyxt is at the forefront of history when it comes to bringing to market crops with healthier characteristics and improved traceability that consumers want and need, and continuing to cultivate a dedicated, high-quality grower base in the upper Midwest region is key to our success.”

Calyxt, which specializes in gene editing for agricultural products, says it will launch a high oleic soybean variety later this year. Photo Credit: Calyxt


Advocating for PBIs

In the past year, USDA officials have traveled tens of thousands of miles to visit international trading partners and inform the U.S.’s approach to advanced breeding technologies, Gregoire said.

“The United States is joining other countries, such as Australia, Argentina, Brazil, Canada and Chile in refining regulatory approaches to new plant breeding techniques,” he said.

Additionally, Gregoire said the USDA’s Agricultural Marketing Service is working through the public rulemaking process required under the National Bioengineered Food Disclosure Law with the goal of increasing consumer confidence and understanding of the foods they buy, while avoiding regulatory ambiguity for producers.

Munasifi said the industry needs to be more proactive than reactive in telling the public about PBIs.

“With GMOs, anti-GMO groups were talking to consumers before the industry had a chance to explain why they were using GMOs in the first place,” she said.

In comparing PBIs with GMOs, Munasifi said, “We’re talking apples and oranges.”

Munasifi said it’s also important PBIs are embraced so that more food can be produced to feed the estimated 9 billion people that will be on Earth by 2050.

“PBIs allow growers to do more with less,” she said. “In soybeans, land for farm production hasn’t increased but output has increased. Higher yields from more targeted growing can happen with less water and pesticide use.”

She added that too stringent regulation of PBIs could limit developer competition to only the larger companies that can handle the expensive research and development required in the plant breeding process and squeeze out interested small businesses and universities.

Slutsky said that although there are no products of gene editing on the market today, ASTA has been actively reaching out to the food industry, discussing how to best communicate to consumers about PBIs.

She gave the example of researchers using CRISPR to develop low-gluten wheat, which would be incredibly useful for the growing number of people with gluten allergies.

Need leadership to promote PBIs

On April 25, 2017, President Donald Trump signed an executive order on “Promoting Agriculture and Rural Prosperity in America,” under which he established an Interagency Task Force on Agriculture and Rural Prosperity.

The task force formally presented its findings and recommendations to the president in January, which included increasing public acceptance of biotech products and developing a streamlined, science-based regulatory policy for biotechnology.

“These recommendations are part of the impetus for our international outreach outlined above, and include leveraging the tools of modern technology,” Gregoire said. “As part of the follow-up to the task force recommendations, the USDA will be looking into these issues.”

Gregoire said the USDA is working hard to engage with its trading partners.

“Our goal is to foster technological innovation and remove regulatory hurdles up front, encouraging domestic and international market acceptance to the benefit of U.S. farmers and trade,” he said. “Through international dialogue we will aim to avoid any undesirable trade outcomes and ensure that U.S. producers have certainty in the global marketplace.”

Munasifi said it’s important the USDA, FDA and Environmental Protection Agency, which have different authorities related to PBIs, coordinate their efforts and policies moving forward.

“We’ve seen very positive signals from the administration,” she said. “Now we need a statement of policy for plant breeding innovations and to get folks onboard internationally to have free flow of goods and technologies. There’s a great opportunity here to get regulation on this technology right and do a better job getting the message out to consumers to avoid the public relations issues we had with GMOs.”

Slutsky said the U.S. needs to take a leadership role in promoting PBIs, because like GMOs, they are considered an American technology—as the country is the biggest producer of biotech crops.

However, other countries are currently developing their own PBIs.

Take for instance Japan, which has poured substantial research dollars into gene editing for its popular food exports such as rice, tomatoes and tuna, Slutsky said.

Other areas busy researching plant gene editing include China, South America and South Korea.

Slutsky chairs an International Seed Federation working group on this topic, with all continents represented.

“Our main goal is to work towards science-based policies across all countries,” she said. “We don’t want country X to decide to regulate PBIs as GMOs and country Y does not. We think these applications are different from traditional GMOs.”

Currently, Slutsky said the only country that regulates PBIs as GMOs is New Zealand, and that stems from a court case requiring the government to do so.

“Many countries in South America are putting policies in place that if no foreign DNA is introduced, then they aren’t considered GMOs,” she said. “Australia has the same policy. So, lots of countries have stake in how PBIs are viewed compared to GMOs.”

If consumers are resistant to PBIs like they were with GMOs, Slutsky said the primary impact would be on plant breeders and losing an important tool in their innovation process. This will leave farmers without the widest range of varieties to plant.

“Hopefully, by the time lots of PBI products are on the market, we will have developed a good base of trust with consumers,” she concluded.