Project Details:

Identifying the Perfect Markers and Developing Germplasm for Resistance to Phytophthora Sojae, Pythium spp., and Fusarium Graminearum in Soybean (Year 1 of 1720-172-0125)

Parent Project: This is the first year of this project.
Checkoff Organization:United Soybean Board
Categories:Soybean diseases, Breeding & genetics
Organization Project Code:1720-172-0125
Project Year:2017
Lead Principal Investigator:Anne Dorrance (The Ohio State University)
Co-Principal Investigators:
Alison Robertson (Iowa State University)
Henry Nguyen (University of Missouri)
Grover Shannon (University of Missouri)
Michelle Graham (USDA/ARS-Iowa State University)
M A Saghai Maroof (Virginia Tech)
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Keywords: disease, Phytophthora root and seed rot, Fusarium, Pythium, genetic resistance

Contributing Organizations

Funding Institutions

Information and Results

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Project Summary

Companies that develop soybean cultivars lack information and markers for key disease resistance genes that target important soil-borne pathogens such as Phytophthora sojae, Pythium spp. and Fusarium graminearum which reduce stands and yield when environmental conditions favor infection. Combined losses for these three pathogens during the wet springs of 2013 and 2014 were estimated to be over 181 million bushels of soybean. Our primary goal is to provide industry with germplasm and the “perfect DNA markers” to expedite the incorporation of resistance into new cultivars to prevent any further losses to these important and widespread soybean pathogens.

Project Objectives

1. Complete germplasm development with yield tests, verify markers, and verify candidate resistance genes for a complete product.
Continue to screen the populations for their response to the different pathogens, collect the data, map the resistance with the BARCSOY6KSNP chip and add additional markers targeted to narrow down the genomic region that is important for resistance. Establish field studies to collect yield data on lines.
2. Identify key markers associated with the resistance for Rps for Phytophthora sojae and QTL resistance genes for all three pathogens. Additional sequencing of the key regions, either through RNA approach or long-range amplification of the target DNA and sequencing, or both to assist in the identification of the candidate genes associated with the resistance. Bioinformatic approaches can be used to overlay genes onto the genome and related QTL. Once the genes are verified then the process first begins to develop markers targeted to each gene in the region and then to target a mechanism. For the Rps genes this is fairly easy as to date these have been NB-LRR type of resistance genes, albeit there maybe 10 to 20 of them within the region. For the QTL, this is not as clear and we have had to partition our approaches on which genetic mechanisms to focus. For example in the Conrad x Sloan population there are 6 QTL, all minor, that each contribute towards the expression of resistance to one or two isolates of P. sojae. We have focused our attention towards the role of auxin (Chr. 19) and signaling genes (Chr. 18).
3. Advance earlier populations, and continue to combine the different resistance QTL into elite adapted germplasm and test earlier crosses with markers developed from earlier phases of the project. Several of our sources of resistance are effective towards more than one of the pathogens. With the combination of markers we can then move multiple resistance loci into elite germplasm
4. Develop silencing vectors, through Hairy Root or Virus. We will evaluate the function of the candidate genes involved in the resistance response through a series of experiments that modifies the expression of the targeted gene in the host and then follow how this gene responds after inoculation with the pathogen. Publish this data through presentations at conferences and manuscripts to expedite delivery to seed companies.

Project Deliverables

1. Release of adapted highly resistant germplasm in the different maturity groups
2. Rps gene sequences – manuscripts for Rps2, 3a, and 8, Spring 2017
3. Mapping of putative novel Rps genes (six), manuscripts and reports to USB in quarterly reports, and to soybean breeders during annual workshop (Feb 2017)
4. Candidate genes for PI 567301B and PI 567516C with resistance to F. graminearum will be reported – Summer 2017
5. Identify the quantitative trait loci associated with resistance to P. sojae, Pythium spp., and Fusarium graminearum in at least 10 populations.
• Initial mapping of QTL for Pythium spp. (ISU series) Summer 2017, develop additional populations for fine mapping.
• Initial mapping of QTL for Pythium spp. (OSU series) Winter/Spring – 2018, develop additional populations for fine mapping
6. Candidate Gene Identification for resistance to these pathogens will be ongoing and reported in USB quarterly reports and given to the group to develop silencing vectors.
• Identify key candidate genes in PI 427106, PI 427105B, V71-370 (chr. 18) for a major QTL for P. sojae. (USB Fellow Stephanie Verhoff).
• Identify key candidate genes in PI 561271 (Chr. 3 and 7) for 2 QTL for P. sojae. (MU)
• Complete transcript analysis of candidate genes in Conrad for P. sojae. Winter 2017.
7. Characterize the role of auxin related genes for partial resistance in Conrad – Winter 2017, (USB Fellow – Anna Stasko)
8. Characterize the role of auxin regulated genes for P. sojae partial resistance and its relationship to flooding tolerance in PI 561271 – Winter 2017, MU
9. Constructs for silencing candidate genes for both Rps genes and QTL will continue through both years of the study. Initially we are aiming for 20 Rps-related genes and more than 80 QTL related genes. This will also provide specific markers for marker assisted selection for the key genes.
10. Coordinate genotyping system for introgression of five QTLs for resistance to soil borne pathogens into high yielding adapted germplasm.

Progress of Work

Updated September 11, 2019:

Updated September 11, 2019:

Final Project Results

Updated December 4, 2018:
See Year 3 Project for Final Report (FY19)

See Year 2 Project for Final Results (FY19)

Benefit to Soybean Farmers

Farmers will benefit with resistant varieties to major diseases

Performance Metrics

Overall, the identification of sources of resistance, resistant genes, and their genetic markers will be utilized by public and private soybean breeders to incorporate resistance into elite high yielding varieties that afford inherent protection from three major diseases of soybean.

At least five material transfer agreements will be in place with public and private breeders for use of the germplasm that is developed in this study.

Early lines will be contributed and evaluated in the Public Breeders Soybean Uniform Trial tests. This data is publicly available to all private and public breeders

Farmers will begin to trial the adoption of varieties that offer increased protection against three major diseases of soybean that decrease early stand development and rob yield, by 2019.

Project Years