Accelerating Solutions to Root Rot in Peas and Lentils Using a Multifaceted and Integrative Approach 

Principal Investigator — Dr. Syama Chatterton, pulse pathology research scientist with Agriculture and Agri-Food Canada (AAFC) Lethbridge Research and Development Centre 

Root rot in peas and lentils poses a significant threat to production and rotations across the Canadian Prairies. Addressing this challenge on behalf of pulse growers requires a multifaceted approach. Dr. Syama Chatterton and her colleagues are adopting an integrative strategy—combining breeding, biology, and agronomy—to combat the disease and boost yields for farmers. The team is building upon previous cluster research by initiating these new activities in genetics, biology, and agronomy.  

The Pulse Science Cluster (the Cluster) is a cost-shared initiative under the federal government’s Sustainable Canadian Agricultural Partnership. Through the Cluster, research is funded that aims to advance the profitability and resilience of pulse growers by addressing key challenges in pulse production and developing new variety options.  

“Effective management strategies will require a multi-pronged approach based on a foundation of soil testing, crop rotation, and the deployment of partially-resistant cultivars, coupled with the best pest management practices to support the longevity of resistance – all functioning within a dynamic feedback loop,” says Dr. Chatterton. 

Breeding Genetic Resistance Traits  

Developing a gene-editing platform in peas and lentils will help evaluate which genes may act as susceptibility or resistance factors for root rot. In Lethbridge, Alta. Dr. Stacy Singer is working to create novel pea and lentil germplasm with enhanced genetic variability to explore innovative resistance traits. An effective pea-transformation protocol has been established. Gene-edited plants are growing in the greenhouse, and a CRISPR/Cas-based gene-editing platform for peas is under development.  

The previously published method for genetically improving lentils hasn’t worked as expected in the tested varieties. While the cells are growing (forming callus), they’re not developing into new plantlets (shoots). Researchers are currently troubleshooting different methods and lentil varieties to achieve successful genetic transformation. “We’ve successfully optimized a pea-transformation protocol and are in the final stages of developing an efficient lentil protocol,” adds Dr. Chatterton.  

Haplo-genomic markers identify groups of alleles (gene variants) inherited from a single parent, helping researchers trace lineage, understand genetic diversity, and select for genetic combinations that contribute to disease resistance. At the National Research Council of Canada in Saskatoon, Dr. Wentao Zhang is developing consistent, cost-effective haplogenomic markers for rapid screening of root rot resistance traits in peas.  

Assessing many pea lines by creating a genetic map will enable more precise breeding targets and markers for selecting for resistance traits in large populations. A high-resolution database has been constructed by integrating 110 million high-quality genetic variants identified from the reference sequence and resequencing 300 pea lines from root rot genetic resistance resources.  

“This database enables the development of high-resolution genetic maps, achieving an accuracy of 99.6%,” says Dr. Chatterton. “Additionally, it has facilitated the identification of novel resistance genes within our established pea root rot genetic resources. ”  

Biology  

By studying and harnessing the microbial communities in soils that naturally suppress plant diseases, researchers can unlock the potential for biocontrol strategies. Microbiome characteristics from soils were meticulously collected from 60 fields across Alberta, Saskatchewan, and Manitoba. At the AAFC Lethbridge Research and Development Center, Dr. Monika Gorzelak has spearheaded the compilation of the first comprehensive set of soil- and pea-rhizosphere metagenomic data—genetic insights obtained from microbial communities in the soil region surrounding plant roots.  

Additionally, she is creating an extensive library of mycorrhizal fungi, which form symbiotic relationships with plant roots. These fungi will be matched to various pulse crops and tested for their effectiveness against plant diseases. 

Dr. Chatterton is leading greenhouse trials in sterile soil using lentil and pea Aphanomyces euteiches isolates, a pathogen responsible for root rot, to compare infection dynamics in peas and lentils. Understanding the concentration thresholds of A. euteiches oospores, the soilborne inoculum that initiates infection, under different soil conditions, can significantly enhance root rot prediction and diagnostics. Although the lentil isolate was slightly less aggressive than the pea isolate, both required the same inoculum level of 100 oospores per gram of soil to cause disease.  

Previously undetermined for lentils, these findings confirm that the inoculum threshold is consistent with that of peas. Upcoming greenhouse trials will further investigate lentil and pea disease dynamics and inoculum thresholds under varying moisture and temperature conditions. 

Agronomy 

Collecting long-term data on root rot incidence and severity across the Prairie provinces increases understanding of the risk factors underlying root rot development. In 2023 and 2024, provincial partners collaborated to perform field surveys in Alberta, Saskatchewan, and Manitoba. Roots were tested for various pathogens, and data is matched with soil zones and precipitation to determine long-term trends. The results from the 2023 samples are shown in Table 1. 

Root samples from 2024 are being analyzed from 100 pea fields in Alberta, 40 lentil fields and 40 pea fields in Saskatchewan, and 50 pea fields in Manitoba.  

In 2024, Dr. Jeff Schoenau at the University of Saskatchewan led field trials examining the efficacy of copper sulphate and monoammonium phosphate treatments across seven sites in Saskatchewan, Alberta, and Manitoba. Preliminary data from the AAFC Swift Current research site suggests copper sulphate application may slightly reduce root rot. Building on this work, Dr. Michelle Hubbard at AAFC Swift Current and Dr. Chris Yost at the University of Regina evaluated biocontrol agents in 2025 field trials, leveraging insights from previously funded research. 

Conclusion 

This research activity addresses all the essential aspects required for an integrated, practical management approach using genetics, biology, and agronomy to combat pea and lentil root rot. Traditional products and practices, such as seed treatments, chemical applications, tillage, intercropping, liming, and crop rotations, have not been shown to reduce disease severity or improve yields significantly.  

Dr. Chatterton and her dedicated team are conducting rigorous research across fields, greenhouses, and laboratories in Western Canada to prevent and mitigate root rot damage in peas and lentils. Their integrative approach holds great promise, ensuring the long-term sustainability and productivity of pea and lentil crops for Western Canadian farmers.  

“Root rot of peas and lentils has plagued pulse growers for over 10 years,” says Dr. Chatterton. “Research is a slow process, but with projects like these, we make the incremental changes needed to devise multi-pronged solutions. ”