Project Details:

The effect of rotations of host resistance genes (Rps) on pathogen avirulence genes (Avr) in the soybean P, sojae pathosystem

Parent Project: The effect of rotations of host resistance genes (Rps) on pathogen avirulence genes (Avr) in the soybean Phytophthora sojae pathosystem
Checkoff Organization:Iowa Soybean Association
Categories:Soybean diseases, Breeding & genetics
Organization Project Code:
Project Year:2015
Lead Principal Investigator:Alison Robertson (Iowa State University)
Co-Principal Investigators:
Andrew Severin ((not specified))
Keywords: Pathogenicity Studies, Phytophtora Root Rot

Contributing Organizations

Funding Institutions

Information and Results

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Project Summary

The proposed project is novel in that a unique population of P. sojae that were recovered from a carefully controlled study in which different sources of resistance to P. sojae were used to impose selection pressure on a known population of P. sojae will be utilized in this study. The data from this proposal will extend the current state of knowledge of (i) genetic changes that occur in Avr genes that enable them to cause disease on P. sojae resistant cultivars and (ii) the impact of Rps genes on Avr gene evolution. Our short-term goal is to improve our understanding of Avr gene evolution. Our long-term goal is to reduce losses to P. sojae through an improved understanding of the Rps-Avr interaction.

Project Objectives

1. Characterize avirulence genes in isolates of P. sojae collected from the soybean cultivar rotation microplot study.
2. Determine changes in avirulence genes in P. sojae under controlled conditions.

Project Deliverables

Research and extension presentations and publications (scientific papers, newsletter articles, blogs, tweets) summarizing the project progress and documenting new information that will expand the knowledge of producers, industry and researchers regarding Phytophthora root rot of soybeans.

Progress of Work

The presence or absence of Avr1a, 1c, 1d and 3b in isolates recovered from a microplot rotation study that were virulent on the respective Rps genes varied as determined by PCR using specific primers. Similarly, transcripts of the genes also varied among isolates.

Pathotype differences were detected in PR1 (race 1 of P. sojae.; virulent of Rps7 only) in a culture that was grown in the lab on dV8 agar for 33 generations.

Similarly pathotype differences were detected among three generations of single zoospore isolates recovered from PR1. These data indicate that changes in virulence can occur in the absence of selection pressure by Rps genes;

Three rotations of soybean have been planted in the greenhouse. A fourth rotation is in progress.

PacBio sequencing of P. sojae isolate PR1 from Iowa has been completed and we have obtained a new version of the P. sojae genome. Comparative analysis of the new genome with existing P. sojae P6497 genome revealed an additional 2Mb bases in the newly assembled genome. Annotation of the PR1 genome is in progress.

In the meantime, we have been using the data we have to start to compare Avr genes between PR1 and P6497. We have discovered that the PR1 assembly is missing the Avr1d gene, which is consistent with reported data from Gijzen’s lab (Canada). Preliminary analysis of the missing region surrounding Ar1d gene, however, differs between PR1 and P6497. Preliminary analysis suggests a ‘jumping gene’ may be responsible and consequently suggests a possible mechanism for pathogen to escape detection by Rps genes in soybean.

We have identified representative isolates from each of the three populations we are investigating. Currently we are pathotyping each isolate (since it is possible for virulence of the isolate to change during storage) and extracting DNA for sequencing. These isolates vary in pathotype and consequently in virulence on various Rps genes. By looking at these isolates we will be able to determine what changes in the corresponding Avr gene resulted in virulence. Are the changes the same? Do they differ between populations? We also received check strains from Dr. Brett Tyler’s lab at Oregon State University.

Drs. Clarice Smidt and Usha Muppirala attended the Oomycete Molecular Genetics Meeting in Asilomar, California in March 2015. Dr. Muppirala was awarded a travel grant to attend the meeting.

Final Project Results

Benefit to Soybean Farmers

Stewart, S., Robertson, A.E. Wickramasinghe, D, Michel, A. and Dorrance A.E. XXXX. Population structure among and within Iowa, Missouri, Ohio and South Dakota populations of Phytophthora sojae. Plant Disease (submitted)
Dorrance, A.E., Kurle, J., Robertson, A.E., Bradley, C., Giesler, L. and Wise, K. XXXX. Pathotype diversity of Phytophthora sojae in ten states in the United States. Plant Disease (submitted)
Matthiesen, R. and Robertson, A.E. 2014. Pathotype diversity in single zoospore isolates from a race 1 isolate of Phytophthora sojae. Phytopathology 103(Suppl.) (in press)

Extension web resource
Sandall, L., Lee, D. and Robertson, A.E. 2014. Oomycete Learning Community. Plant and Soil Sciences eLibrary (

Performance Metrics

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