Phytophthora stem and root rot (PSRR), caused by Phytophthora sojae, is a soilborne oomycete pathogen that ranks among the top five pathogens causing economic losses of soybean annually in the United States (Allen et al. 2017). Reducing losses to PSRR relies on single resistance (Rps) genes that are deployed in commercial soybean varieties. In Iowa, the most commonly deployed Rps genes are Rps 1c and Rps 1k; while less than 10% of commercial varieties have Rps 1a and less than 5% have Rps 3a (Matthiesen et al. 2021). However, P. sojae can naturally change overtime to cause disease on Rps genes (Dorrance et al. 2003). Consequently, incorporating Rps genes together with partial resistance has been encouraged (Dorrance et al. 2016). Partial resistance has no Rps genes, is multigenic and is effective against all pathotypes of the pathogen (Schmitthenner 1985). Recently Matthiesen et al. (2021) reported the population of P. sojae in Iowa continues to gain virulence on varieties with Rps genes. Furthermore, pathotype complexity (the number of Rps genes an isolate was virulent on) of the isolates had increased since previous surveys. Traditionally it has been postulated that deploying Rps genes exerts selective pressure on the pathogen population so the number of pathotypes within a population increases and/or becomes more complex. In the past 10 years, however, there has been little change in the Rps genes that are deployed in commercial soybean (Matthiesen et al. 2021) and yet the population continues to evolve. Why?
Slusher and St Claire (1973) reported the cultivars with partial resistance to P. sojae had more root mass but as many oospores as the roots of a susceptible cultivar, while the roots of a cultivar with a Rps gene had considerably less oospores. Oospores are sexual thick-walled spores that overwinter in the soil. Thus, planting varieties with partial resistance may be contributing to a buildup of inoculum in the field. More importantly however, sexual reproduction increases genetic diversity within a population.
Stewart et al. (2016) recovered more pathotypes of P. sojae from rotations of soybean that included a cultivar with partial resistance compared to rotations in which cultivars with only Rps genes were grown. Thus, planting varieties with partial resistance may be contributing to increased pathotype diversity of P. sojae in Iowa. We hypothesize that partial resistance exerts as much or more selection pressure on the population than Rps resistance and is responsible for the increased pathotype complexity in P. sojae reported across the Midwest. Our proposed research will test this hypothesis under controlled conditions. An improved understanding of how resistance in soybean affects P. sojae is crucial to breeders and pathologists to enable improved management of PSRR.

Objective 1: To compare the number of oospores produced on soybean varieties with different types of resistance to P. sojae.
Objective 2: To pathotype oospores of P. sojae recovered from soybean varieties with different types of resistance to P. sojae.

• Improved understanding of contribution of resistance to inoculum levels in the soil.
• Knowledge of the effect of resistance in soybean on pathotype diversity in P. sojae.
• Guidance for soybean breeders developing PSRR resistant cultivars.

Update:
We are continuing to work on optimizing the hydroponic method to inoculate soybean with P. sojae. We are still struggling to get infection after V1. If we want to evaluate the role of partial resistance in shaping the diversity of P. sojae, we need to consistently get infection after V1.

We have also been evaluating a molecular assay based on discriminant mutations leading to genetic variations associated with seven Avr genes that was recently published. The assay accurately predicted virulence of Canadian isolates of P. sojae on Harosoy differentials based on the presence or absence of each Avr gene amplicon. We'd like to use this assay to pathotype oospores we recover from our infected soybeans. We evaluated the assay with P. sojae isolates from the United States (US) pathotyped on Harasoy and Williams differentials. Strain P6497 was used as a positive control to compare our results with the published assay. While virulence was predicted correctly for some Avr genes of some isolates, inconsistencies were also observed. For some isolates virulence varied between backgrounds for the same Rps gene, suggesting a different Rps allele or a linked Rps gene may have been incorporated on each background. Virulence on a differential did not always correspond with absence of the associated amplicon, suggesting Avr mutations present in the US population of P. sojae differ from those occurring in the Canadian population.

An abstract for a poster describing our work on the molecular assay was submitted to the annual APS meeting that will be help in Denver in August 2023.

Update:
We continue to work on developing a modified hydroponic method to inoculate soybean with zoospores of P. sojae which simulates natural infection better than inoculating the hypocotyl with a slurry of mycelium. We have successfully caused infection of soybean seedlings and will use this method to study the effect of DNA methylation on the soybean-P. sojae interaction (see leveraged funding). We plan to test this method on V1 soybean, which is the growth stage at which partial resistance is activated.

We are finishing up our work comparing a molecular assay for pathotyping with the standard hypocotyl assay. We have evaluated approximately 30 isolates of P. sojae, some of which were used to develop the molecular assay. As our initial work suggest, there were inconsistencies between the two methods. Moreover, there were inconsistencies among the differentials used in the hypocotyl test. We plan to follow up with some sequencing work to identify if different mutations are present in the Avr loci of the isolates we have been evaluating compared to the isolates used to develop the molecular pathotyping test.

• Improved resistant varieties for soybean farmers.
• Reduced losses to PSRR and improved profitability for farmers. From 2010-2020, PSRR losses for Iowa were estimated at $0.73 per acre (Crop Protection Network). Preventing losses to PSRR on half of the soybean acres on Iowa would equate to approximately $3.6 million return on the soybean checkoff investment of $65,673.