If Plants Could Talk

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Agricultural and Agri-Food Canada Scientist Bernie Zebarth is studying gene expression in potato plants as a way to assess nutrient needs of crops. All photos AAFC.

[deck]Scientists at Agricultural and Agri-Food Canada’s Potato Research Centre hope to develop a handheld device that could one day tell farmers how their crops are doing.[/deck]

Imagine if you could walk into the field and have your potato plants tell you how they are doing. This groundbreaking technology is closer than you think.

Two Agriculture and Agri-Food Canada scientists at the Potato Research Centre in Fredericton, N.B., Bernie Zebarth and Helen Tai, are working on a method for collecting data from plants almost the same way as a car mechanic assesses your car’s engine. The researchers are looking at a process called ‘plant gene expression’ as an indicator of how plants are behaving and what they are sensing in their environment.

According to Zebarth, plants, like humans, carry a library of their genetic material. Not all genes are turned on all of the time, though. For example, he says, stress genes will only turn on when the plant experiences some kind of stressor such as nutrient deficiency, disease, cold temperatures or drought.

“The ‘active’ genes are copied into RNA, that is ribonucleic acid, in a process called gene expression,” says Tai. “At the molecular level, RNA plays a central role in the pathway from DNA to proteins, which are the workhorse of the plant cell carrying out critical biological functions. We extract RNA from plants and use it to query what genes are active, and from that, determine what stresses the plant is experiencing.”

Focus on Nutrient Needs

Specifically, Zebarth’s and Tai’s research focuses on nitrogen, phosphorus and potassium needs of potato plants. The goal, says Zebarth, is to develop a test capable of assessing the nutrient status of the crop as it grows in the field. In the future, the researchers would like to broaden the scope of their work to also look at more plant stressors.

“Identification of the best genes to use in order to quantify the plant status is the more challenging part of the process. We initially focused on genes that can be used to assess potato nitrogen status. While we have made good progress, we do not yet have a selection of genes that can be used reliably across all conditions,” Zebarth says.

“More recently, we have started focusing on phosphorus and potassium as well,” he continues. “Our long-term goal is to have a single assay that can detect multiple stresses.”

Tai is also working on a gene expression indicator for tubers that can guide the use of cold temperatures in storage. “There may be something we can detect in the potato leaves during the growing season that would tell us about the starches and sugars inside the potato tuber which are important in controlling potato quality and storage characteristics,” she says.

The project began a number of years ago, and the first results were published in 2010.

“Our first work was a small-scale study of plants in the greenhouse using reverse transcription-polymerase chain reaction (RT-PCR) technology to measure gene expression,” says Zebarth. “In 2010, plant material from the field was used and new technology was added to the lab including robotics-assisted processing of plant samples and new gene expression technology called nCounter from Nanostring.”

The new technology, he adds, allowed them to upscale the capacity for gene expression analysis and accommodate many more samples from multiple field trials across Canada in their study. Currently, this testing is done in the laboratory. However, the technology used to measure gene expression is advancing so rapidly, says Zebarth, that they could be measuring gene expression in the field using handheld devices within the next couple of years.

Bernie Zebarth is among the group of multi-disciplinary researchers that’s required for this kind of gene expression work.

Handheld Devices

As most growers know, in order to achieve optimum yields and quality, potato crops need high nutrient inputs. Optimal nutrient application rates can vary widely from field to field and from year to year. For this reason, a handheld device for evaluating a plant’s nutrient needs directly could be very beneficial for farmers.

“This can be an important tool for growers to make sure they supply enough nutrients to meet crop needs and achieve optimal yields, but not to apply more nutrients than are needed by the crop and which can then be lost,” says Zebarth.

“We can consider the plant gene expression to act like the ‘language’ of the plant, and tools like this can be used to let the plant tell us how it is doing in terms of nutrient status,” he continues.

There are added environmental benefits to the technology, which can help reduce leaching of fertilizers into the water supply. “By better matching nutrient applications to crop nutrient requirements, we can use nutrients more efficiently, and reduce any environmental nutrient losses,” Zebarth explains.

He adds there are also potential economic benefits for growers, since they’ll have a tool that tells them exactly what the crop needs at the right time. “With rising fertilizer costs, more efficient nutrient management can result in significant savings for growers,” says Zebarth.

Peter VanderZaag, a noted potato farmer and scientist in Alliston, Ont., believes agriculture represents a “new frontier” and is enthusiastic about the technology’s potential.

“This whole thing of measuring what’s going on inside a potato plant through a very simple app or a very simple tool is just, to me, so exciting,” he says, adding that the possibility of a user-friendly device like the one envisioned by Zebarth and Tai shows how sophisticated the technology is becoming.

“We live in a rapidly changing world,” he says “It’s a good time for young, educated and technologically astute people to be involved in farming because we’re living in very exciting times.”

VanderZaag believes a tool for measuring plant nutrient needs in the field could help farmers boost their productivity, efficiencies and returns on investment by “maybe one or two per cent,” and therefore shouldn’t be viewed as the “be-all and end-all” for potato producers.

“I think that this is just one more tool in the toolbox,” he explains. “The bottom line is that this is just one more way that a farmer can be efficient with the use of nutrients — not to waste, not to put too much on, but also to make sure we have enough on in the right balance.”

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Benefits of Potato Research Centre

Agriculture and Agri-Food scientists Bernie Zebarth and Helen Tai credit much of their research success to their surroundings as well as the AAFC’s national network of top-notch researchers.

Zebarth says the AAFC Potato Research Centre in Fredericton, N.B. is one of the few laboratories in the world that is applying plant gene expression to the development of tools for assessing nutrient needs in crops. He adds the research being conducted requires a combination of skills, including lab experience in molecular biology and expertise in soil science and agronomy.

“The Potato Research Centre houses a group of multi-disciplinary researchers that have the varied expertise needed for this research,” says Zebarth. “To apply gene expression to the development of crop nutrient status monitoring requires validation of candidate indicator genes across field trials at multiple sites. AAFC has the advantage of having multiple field sites across Canada for carrying out trials.”

The sites, he says, are staffed with experienced researchers and technicians who have access to the farm equipment needed for potato cultivation. “The development of gene expression indicators would not have been possible without this cross-Canada team of researchers and technicians,” Zebarth says.

On March 17, the federal government announced a $1.83 million investment in a new Canadian-led initiative aimed at giving potato farmers a technological edge in predicting and preventing yield losses in their fields and in storage.

Helen Tai will expand application of gene expression indicators to monitoring tuber quality in storage together with researchers from France and New Zealand and industry partners. The lead for the collaborative research effort is Claudia Goyer at the AAFC’s Potato Research Centre.

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