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Taking the lab to the field

High-throughput phenotyping provides powerful new tool for plant breeders

periodiCALS, Vol. 8, Issue 1, 2018

Research support specialist Nicholas Kaczmar prepares a drone for takeoff at Musgrave Research Farm. Photo: Matt Hayes

New technology is changing the game for plant breeders. Before long, drones could become like farmworkers, scouting crops for disease and helping farmers react with the right fungicide or pesticide, before an outbreak of disease spreads out of control.

As DNA sequencing technology has become smarter, faster and cheaper, scientists have benefited from an abundance of genetic information at their disposal. But DNA is not everything. Understanding of phenotypes—the way that the genetic code interacts with the environment to express an organism’s actual characteristics—is just as important, but is currently far more difficult and time-consuming to achieve. 

This problem of genetic/phenotypic data imbalance is particularly troubling for plant breeders, who are in the business of choosing the best individual organism among a large group of the same species; in other words, the plant with the best phenotypes, or traits. 

“Around 2010, when DNA sequencing technology got to a very low price point, the field of plant sciences really began turning its attention to how to solve the problem of collecting a lot of phenotypic data, large volumes of it, at low cost with less labor,” said Michael Gore, associate professor of plant breeding and genetics in the School of Integrative Plant Science. “People were trying to figure out how to take the lab to the field.”

"We are in an era of rapid change in agriculture."
-Michael Gore, associate professor of plant breeding and genetics

The result is a method called “high-throughput phenotyping.” It refers to almost any approach that gathers and analyzes large amounts of physical data. In plants, it can be everything from crop height to protein expression, spectral reflectance to seed metabolites. 

Gore is developing technology that harnesses the power of this method. He is using aerial drones trained to spot disease across acres of corn, smartphone apps that can tell African farmers what’s infecting or infesting their cassava, and ground vehicles that can take the temperature of thousands of cotton plants. 

In the cotton project, Gore and his team are looking at transpiration—the water that plants emit in hot temperatures to cool their canopies and prevent heat stress. For more than 50 years, cotton breeders have been selecting for plants with high transpiration rates in hot, arid environments that are heavily irrigated. But with climate change increasing the probability and severity of droughts and freshwater shortages, breeders are now placing more value on plants that use less water, while still being resilient in the heat. 

“Canopy temperature is a very time-sensitive phenotype; you often only have a two-hour window to try to robustly phenotype those plants, based on the changing solar angle, air temperature, soil water content and vapor pressure deficit,” Gore said. “Imagine having a ground vehicle driving through with an infrared radiometer: it could quickly and precisely measure the canopy temperature of each of those thousands of plants in the field.”

While technology cannot replace the more nuanced decision making that breeders and farmers must engage in to ensure crop health, Gore said this new method of phenotyping marks a huge breakthrough in how they approach those decisions.

“We are in an era of rapid change in agriculture,” Gore said. “Technology is transforming what we grow and how we grow it, and the result is more nutritious and resilient crops.”