Activating genomics to accelerate climate-smart crop delivery

The four-year (2023–2026) University of Saskatchewan (USask) ACTIVATE project was designed to contribute to Canada’s greenhouse gas (GHG) reduction targets and develop new and improved climate-smart wheat and lentil cultivars and microbiomes. In combination, it also aims to improve on-farm crop-rotation management options.

New genomics-assisted plant crosses and the genomic strategies used to manage them will assist in reducing synthetic fertilizer use and provide substantial economic benefits to farmers when combined with optimized crop rotations.

The project’s multi-species breeding strategy targets crosses to plant lines carrying genes, reducing losses resulting from soil nitrogen cycling and microbiome interactions. Their integration, especially in lentil-wheat crop rotations, ensures less nitrogen is lost and more remains available.  

The ACTIVATE team of GHG, microbiome, and socio-economic experts, plus numerous graduate students, are led by USask researchers in the College of Agriculture and Bioresources (AgBio), Dr. Kirstin Bett (PhD) in the Department of Plant Sciences, and Dr. Curtis Pozniak (PhD), director of the Crop Development Centre (CDC). Both researchers offer extensive experience and expertise in pulse and cereal crop research.

Nearly half the $6.15-million project value is coming from Genome Canada with matching funds contributed by the Saskatchewan Pulse Growers, Saskatchewan Wheat Development Commission, Manitoba Crop Alliance, Alberta’s Results Driven Agricultural Research, Western Grains Research Foundation, and Saskatchewan’s Agriculture Development Fund.

Field trials are being meticulously managed, a prerequisite for the delicate experiment’s success.

Bett and Pozniak focused on nitrogen and crop rotations designed to confirm a lentils-to-wheat transition gain.

“The real premise behind the project is to determine how to maximize producer productivity and yield while reducing nitrogen losses from production systems,” said Pozniak. “We’re verifying what lentil varieties do well in producing nitrogen for durum and which durum varieties take optimal advantage.”

“Pulses are known for their nitrogen-fixing abilities so we’re confident of reducing synthetic nitrogen while letting inoculants work to their capacity,” said Bett. “We want to access the underlying genetics to assess how nitrogen is transferred from a pulse to a cereal, plus manage it efficiently along with the soil microbiome.”

The pattern of specific durum varieties benefiting from nitrogen fixation in the previous pulse crop is inherent to individual plant genetics. Using current genomic technologies, genome sequencing can begin with precise experiments identifying the genome parts responsible for improved fixation and uptake.

“Once we gain this genomic fingerprint, we can start selecting more efficiently for this signature in our breeding programs,” Pozniak said.

The project’s intent is early proof of concept regarding breeding for crop rotations. Using lentils and durum wheat made sense as plenty of genomic information representing 20 years of work was already available.

Traditionally, plant breeders tend to focus on individual crops in isolation, and challenges such as enhancing climate resiliency and adaptation, yields, and productivity through crop rotation make the proof of concept an exciting and novel idea for the team.

“In Western Canada, the rotation isn’t only lentil and durum wheat but a variety of other combinations,” Pozniak said. “Before we dive into those complicated layers, we wanted to tackle something with more background information. Plant variety interaction is real. We need to detect and confirm these genetic fingerprints to verify which ones will do well in rotation.”

Bett explained their plant breeding and rotation results should offer crop-agnostic tools displaying broad applications outside the two designated crops.

“The beauty of this project is we’re hitting the ground running using existing breeding material. Once we show how it’s accomplished, we’ll be able to point to new, already superior varieties,” she said.

Of course, a farmer’s concern typically revolves around yield and profitability.

“Producers want, and understandably need high-yielding varieties,” Bett stressed. “Selections must be high-performing and contribute to multi-season profitability. Paying a premium to grow and rotate these new reduced-emissions products needs incentivization, which is an issue AgBio assistant professor (Dr.) Nicholas Tyack (PhD) is addressing.”

One year into the project, the initial seeds have been produced, and the first 100 lentil lines are currently established with 100 durum lines designated for the next growing season providing the equivalent of 1,000 combinations.

Pozniak believes the project’s extensive data management, cross-cutting, and crop-agnostic decision support systems will be a key to the project’s legacy.

“Data management is a huge component of today’s science as so much is being generated,” he said. “When we think of a single wheat genome sequence, it's 16 billion base pairs of information.”

Information must be stored, accessed, analyzed, and necessary portions extracted to help plant breeders and producers make climate-smart decisions. These resources will ensure genomic data, developed germplasm, microbial samples, analyses, and decision support tools are available and accessible to other research projects and diverse end-users, an aspect database developer Lacey Sanderson in the Department of Plant Sciences at USask is overseeing.

“We’re excited about expanding the work from lentils to barley, oats, canary seed, flax, and all other crops we work on at the CDC,” Pozniak said. “Taking advantage of this support is paramount as often it’s a lost piece of the puzzle.”

Even though it is early in the project’s experiments, the team is pleasantly surprised to discover a high level of plant genetic variabilities, essential for progressive plant breeding.  

The future hope sparked by the project is once improved genomic signatures are in place, breeders will voluntarily begin selecting for them, leading to a variety of development programs.

“Like any strong research, when we answer one question, it creates 10 more,” Bett said. “We’re already starting to see this in our data. Experiments interconnected with breeding systems cause knowledge to flow and our connections will continue this curiosity-driven research around the interesting data and questions we’re starting to see.”

The team believes its climate-smart cultivars and microbiomes could reduce fertilizer use, creating cost savings of more than $1.2 billion over the next 20 years (2024–2043) while lowering fertilizer-related emissions between 2-3 metric tons. Additionally, productivity gains from improved crop rotations and varietal improvements could yield another $1 billion in benefits to farmers over the same period.

 

Agknowledge, Fall 2024