Determining the current Phytophthora sojae population and the status of variety resistance in Minnesota using improved methods
Sustainable Production
Biotic stressCrop protectionField management Pest
Parent Project:
This is the first year of this project.
Lead Principal Investigator:
Megan McCaghey, University of Minnesota
Co-Principal Investigators:
Project Code:
Contributing Organization (Checkoff):
Institution Funded:
Brief Project Summary:
The purpose of this work is to determine the current population of Phytophthora sojae causing soybean root and stem rot. To avoid Phytophthora root and stem rot, growers plant soybean varieties that carry resistance genes. Unless the varietal resistance genes align with the specific P. sojae pathotype in the field, resistant varieties will remain ineffective. It is crucial to determine the specific P. sojae pathotype present so the most effective soybean varieties can be deployed. The goal is to survey for the current P. sojae population, as the last survey was 10 years ago and P. sojae’s adaptation to resistance shifts over time.
Key Beneficiaries:
#agronomists, #breeders, #farmers, #pathologists
Unique Keywords:
#insects and pests, #Phytopthora, #root rot, #soybean diseases
Information And Results
Project Summary

In 2022, cool wet conditions followed planting, exacerbating an intermittent problem that has been observed in Minnesota, seedling emergence issues, damping off, and higher incidence of root and stem rots (personal communication with Angie Peltier, Brett Arenz of the Plant Disease Diagnostics Clinic, and David Kee). Compacted soils, such as those in northwestern Minnesota, can become waterlogged and are especially prone to seedling diseases and root rots. When present, yield losses from these diseases can be significant, and symptoms are caused by a variety of pathogens including Phytophthora sojae. Planting varieties with genetic resistance to P. sojae is one of the best management options for P. sojae-associated diseases. However, resistance genes in the variety must align with the specific pathogen pathotype present in a grower’s field.

Phytophthora root and stem rot (PRSR) is caused primarily by the pathogen P. sojae (Dorrance et al., 2007). P. sojae is not a true fungus but is a member of a group of organisms called oomycetes that are more closely related to algae. While they do have a fungal-like growth habit, they produce motile spores (zoospores) that can ‘swim’ in films of water in the soil. Thus, organisms like P. sojae are often referred to as water-molds and are problems generally in water-logged or abnormally wet soils. There is also a second Phytophthora species that can cause PRSR and is known as Phytophthora sansomeana. Dean Malvick has previously identified and surveyed this species in Illinois (Malvick et al., 2004). Although it is present in Minnesota, the current distribution and potential contribution of this species to PRSR in the state is not known.

There are more than 50 pathotype s of Phytophthora sojae known in the U.S. (Dorrance et al. 2008). The main method of managing this pathogen with so many pathotypes is to use either pathotype - specific soybean resistance genes (Rps genes) or soybean varieties with incomplete resistance (partial resistance) or even varieties with both forms of resistance (Matthiesen et al., 2021). Despite the use of Rps genes and/or incomplete resistance, Phytophthora sojae can develop resistance and eventually overcome the soybean-host resistance deployed. Therefore, it is important to understand the pathogen population in a particular field, region, or state to be better able to deploy appropriate Rps genes and varieties with high levels of partial resistance. Interestingly, Rps genes are not effective on other species of Phytophthora such as Phytophthora sansomeana. In addition to understanding the Phytophthora sojae pathotype profile, understanding the Phytophthora species profile is also important in fields where soybean is planted.

In Minnesota, all forms of resistance have been deployed in modern soybean varieties. Phytophthora sojae population profiling has not been done recently. It has been approximately 10 years (2012 and 2013) since surveys were conducted understand the pathotype profiles of Phytophthora sojae in the state. At that time, Anne Dorrance suggested that many fields in Minnesota, were infested with Phytophthora sojae pathotype s that could be managed using the Rps 8 or 3a genes with the Rps 6 gene also being somewhat effective (2016), although commercial varieties with these resistance genes were new or uncommon at the time of previous study.
Research by Anne Dorrance et al. (2016) showed increasing virulence on lines containing Rps 1 genes, and research in Iowa and Nebraska indicated that over 70% of isolates collected during the 2016-2018 field seasons were virulent on soybean varieties deployed with Rps 1c or Rps 1k genes (Matthiesen et al., 2021). Varieties grown and screened in Minnesota most commonly contain genes from the Rps 1 locus (Lorenz et al. 2022 Variety Trials). Many of the soybean varieties being commercially sold, therefore, do not contain Rps genes that match the current Phytophthora sojae pathogen population.

Widely used methods for determining whether P. sojae isolates have overcome the plant resistance (pathotyping) are time consuming. It involves inoculating soybean lines with known Rps genes with an isolate of P. sojae and evaluating the isolate’s ability to infect the host to determine the Avr gene present (Dorrance, 2003 and Dussault-Benoit et al., 2020). In recent research, Avr genes were sequenced and primers were developed to amplify the specific Avr genes that are present in P. sojae isolates (Dussault-Benoit et al., 2020 and Tremblay et al., 2021). This method needs to be validated and can greatly increase the efficiency of pathotyping to predict whether soybean varieties will be resistant to field populations of P. sojae. Recently a private company using this method, AYOS, has started to offer pathotyping and variety recommendations to growers as a private service. However, this service has received few samples from Minnesota a validating the service as a decision making tool for growers may be useful for growers to make field-specific decisions about which resistant variety to deploy in their field.

Therefore, this proposal aims to provide guidance for soybean breeding programs and Minnesota farmers on Rps genes to manage PRSR and information on the potential risk of P. sansomeana as a yield limiting soilborne disease for which we do not have resistance tools.

Project Objectives

1. To understand the Phytophthora sojae pathotype diversity in Minnesota that is subject to selection by modern soybean varieties.
2. To understand how widespread Phytophthora sansomeana is in soybean fields in Minnesota.
3. To understand how recent commercial cultivar deployment has affected Phytophthora sojae
diversity in Minnesota.
4. To enhance the efficiency of pathotype identification
5. To validate a current P. sojae resistant variety recommendation service.
6. To develop improved management recommendations for Phytophthora species affecting soybean in Minnesota, including suggested Rps genes that should be deployed.

Project Deliverables

• Develop an improved understanding of the interaction of soybean Rps gene-mediated resistance and P. sojae populations in Minnesota soybean fields and how to manage potentially shifting populations.
• Improved Phytophthora stem and root rot management recommendations to soybean growers in Minnesota
• Improved understanding of which Rps genes should be deployed in Minnesota to mitigate losses due to Phytophthora root and stem rot
• Increased efficiency and accuracy for identification Phytophthora pathotypes
• Research-based information on how widespread P. sansomeana is in Minnesota and how likely this species is causing Phytophthora root and stem rot.
• Validation of a service that can provide ongoing recommendations for variety deployment in fields that have a history of P. sojae.
• Researchers and undergraduates trained in grower-driven agricultural research
• Peer-reviewed publications detailing the findings of this study
• Extension fact sheets summarizing the findings and offering management recommendations based on the results.

Progress Of Work
Final Project Results

Benefit To Soybean Farmers

This project will benefit growers by both confirming the presence of P. sojae and associated pathotypes and P. samoneana in their fields. A known pathogen population can lead to a change in practice in planting times, variety selection, or seed treatment. The project will also provide specific information on pathotypes and whether current varieties are likely to be effective. The presence of pathotypes complemented with annual variety trials conducted by researchers in the Department of Agronomy and Plant Genetics (which discloses Rps genes of evaluated lines) will allow growers to select lines with resistance genes that will be effective for the most common P. sojae pathotypes to reduced associated yield losses.
We will also validate a high throughput method that has the potential to provide pathotype information to growers in a matter of days versus weeks by using specific primers versus inoculating plants. This will allow information to be transferred to growers quicker. We will compare our findings with those provided by a service that uses a similar high throughput pathotyping method, AYOS. This private company provides field-specific information on pathotypes for the purpose of providing variety recommendations to growers. We will critically assess the utility of this service for growers to support their decision making.
The objectives described in our work will generate extension and outreach materials and information directly to growers via variety trial reporting, extension handouts, and meeting presentations. The overarching goal of the project will be to provide information that can reduce yield losses associated with Phytophthora species through the effective deployment of resistant varieties.

The United Soybean Research Retention policy will display final reports with the project once completed but working files will be purged after three years. And financial information after seven years. All pertinent information is in the final report or if you want more information, please contact the project lead at your state soybean organization or principal investigator listed on the project.