Aerial view of forest

FastPheno Project One of Ten to Receive Funding from Genome Canada

Tanya Rohrmoser


Professor Ingo Ensminger

Biology’s Ingo Ensminger was recently awarded $4.7 million in funding for his FastPheno project by Genome Canada, a non-profit organization funded by the Government of Canada and co-funding partners. Genome Canada’s Genomic Applications Partnership Program (GAPP) brings new applied genomics solutions to issues facing Canadians, and supports collaborations in forestry, agrifood, the environment, and health.

The challenge? Canada has 328 million hectares of forest, but with climate change impacting tree health and productivity, sustainable forest management is essential; the trees planted today need to withstand future climates. Genomic resources can be used to accelerate breeding cycles and select genotypes that are better adapted and more resilient; however, large-scale phenotyping is needed to assess adaptive traits in breeding populations of thousands of trees

Enter Ensminger’s lab: he studies plant-environment interactions and the impact of climate change on metabolism and photosynthesis of plants from molecular to leaf, species, and ecosystem level. Ensminger and his team have developed a drone-based technology that remotely assesses photosynthetic phenology and plant fitness.

Most people who use drones in trees and forests try to measure height and the size of the canopy, they use drones for inventories,” he says. “Our goal is different, we try to assess health and fitness, and overall performance as indicated by the ability of vegetation to remove CO2 from the atmosphere when they photosynthesize and produce biomass.”

The unique technology enables them to distinguish performance of thousands of trees, and researchers can use the approach to detect drought stress control on photosynthesis in natural forests.

“All this is based on the optical fingerprint of vegetation,” Ensminger explains. “This fingerprint is derived by measurements of leaf spectral reflectance. Leaf spectral reflectance is highly variable, and it can be used as a plant health indicator, because it changes upon exposure to drought stress or heat stress.” The fingerprint is also species specific, and hence future work in Ensminger’s lab will also explore how species can be distinguished to monitor biodiversity

When it comes to tree breeding and forest conservation, the ability to distinguish trees that perform well during drought and heat is incredibly useful—complementing genomic selection with adaptive traits could help produce trees resilient to future climate in Canada. Simply put, it could transform our forest sector.

“Outcomes have been very promising,” Ensminger reports. “We can distinguish trees that are water stressed from well-watered trees, we can assess how photosynthetic activity varies over the course of the year, and in large forest stands we can identify trees that perform well and distinguish those from unhealthy trees or trees that are stressed.”

Ensminger’s technology is fast, reliable, and cost-effective compared to vegetation monitoring that relies on visual inspections and manual measurements. New research enabled through FastPheno now aims to apply the drone-based phenotyping approach at large scale and explore how reliably it can be used across forests in Ontario and Quebec to monitor the health and fitness of individual trees. If successful, FastPheno could create cost savings of $540 million per year and reduce assessment times from a matter of weeks to hours—and it can be transferred from forest vegetation to applications in agriculture, conservation, and biodiversity studies.

“It is very rewarding to receive funding to develop and implement tools that will hopefully be used to help tree breeders and forest practitioners to identify trees that are resilient to climate change,” says Ensminger, who anticipates they’ll be used for tree improvement programs or be targets for forest conservation and management.


researchers in cherry picker monitoring drone

What’s next for his team? During their drone flights, they’re collecting an enormous amount of data—and now it’s a matter of processing and analyzing it. They’re collaborating with robotics experts to improve field data collection and will be developing tools to automate the process of image analysis and pixel classification using machine learning and AI technologies.

“We also aim to develop software and web-interfaces that provide users access so that not just researchers, but a wide range of end-users have access to the data produced through this approach,” he says.

Earlier this month, the Minister of Innovation, Science and Industry announced $13.8 million in federal support to innovative research and development projects through GAPP which—combined with funding from co-partners—represents a $41.4 million investment that will apply genomics research and innovation in three priority areas: sustainable resources and nature-based solutions for climate change; advancement of climate smart agriculture and agrifood; and precision health.

“This is an exhilarating time for genomics,” noted Genome Canada President and CEO, Dr. Rob Annan following the federal announcement. “The knowledge, tools and technologies it is generating are driving innovation in traditional sectors and helping them achieve green growth, as well as improving the health and quality of life of Canadians.” 

Ensminger’s project will complement the genomic selection research and operational programs of Natural Resources Canada and Ministère des Forêts, de la Faune et des Parcs du Québec.

*St. Casimir experimental forest in Quebec, a field site where Ensminger and his team do a lot of their drone work. The white spruce forest is operated by their collaborators, including Nathalie Isabel, from Natural Resources Canada, Laurentian Forestry Centre and Julie Godbout, from Ministère des Forêts, de la Faune et des Parcs, Québec.