Project Details:

Confirmation, Characterization and Deployment of the Perfect Markers and Developing Germplasm for Resistance to Phytophthora Sojae, Pythium Spp., and Fusarium Graminearum in Soybean (1920-172-0110)

Parent Project: This is the first year of this project.
Checkoff Organization:United Soybean Board
Categories:Soybean diseases, Breeding & genetics
Organization Project Code:1920-172-0110
Project Year:2019
Lead Principal Investigator:Anne Dorrance (The Ohio State University)
Co-Principal Investigators:
Alison Robertson (Iowa State University)
Dechun Wang (Michigan State University)
Pengyin Chen (University of Missouri)
Michelle Graham (USDA/ARS-Iowa State University)
M A Saghai Maroof (Virginia Tech)
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Keywords: Phytophthora root and stem rot, Fusarium root rot, Pythium, seedling disease, 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. We have identified numerous sources of resistance to these soybean pathogens, many of the resistance loci have been mapped and a few candidate genes identified. 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. Our secondary goal is to understand how this resistance works to provide a better overall framework for companies to select for resistance.

Project Objectives

Overall our activities are focused on germplasm development across Maturity Groups 1-6 with yield tests, verify markers, and verify candidate resistance genes for a complete product. Continue to screen mapping and breeding populations for response to different pathogens, collect the data, and fine map resistance genes with the newly developed linked markers to narrow the genomic regions important for resistance. Establish field studies to collect yield data on the developed lines.

1. Identify key markers associated with Rps genes for Phytophthora sojae and resistance QTL for all three pathogens (Phytophthora, Pythium and Fusarium). Additional targeted sequencing of key regions, either through an RNAseq approach or through long-range amplification and sequencing of target DNA, or both to assist in the identification of the candidate genes associated with the resistance will continue to be a top priority. Bioinformatic approaches can be used to overlay genes onto the genome and related QTL. Once genes are verified through gene silencing or gene editing approaches, we will develop markers targeted to each gene in the region. For the Rps genes, most are associated with the NB-LRR type of resistance genes. The difficulty will be separating the 10 to 20 of NB-LRRs within the Rps regions. For the QTL, we have had to partition our approaches to focus on specific genetic mechanisms. For example, in the Conrad x Sloan population our eQTL approach identified targets associated with our mapped QTL, in addition to targets which are not physically linked to the QTL.

2. Advance earlier populations and continue to combine the different resistance QTL into elite adapted germplasm, testing 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 correct combination of markers we can efficiently move multiple resistance loci into elite germplasm.

3. Utilize the silencing vectors and procedures that we have developed for cotyledon hairy root transformation, ALSV and BPMV. The next step is to continue identifying the best silencing approaches for our targeted genes and evaluate the response to infection with the pathogens. RNA-seq of silenced and control plants infected with the appropriate pathogen will determine resistance mechanisms. This data will be released through presentations at conferences and through published manuscripts to expedite delivery to seed companies.

4. Finally, a selected set of high confidence candidate genes will be disrupted with the CRISPR/Cas9 technology and the phenotypic changes of the resulting knock-out mutants will be assessed to determine how these genes confer disease resistance.

Project Deliverables

• Release of adapted germplasm with resistance to multiple soil-borne pathogens in a range of maturity groups.
• Rps gene sequences from novel sources in 2019, 2020, and 2021 – a goal is 2 per year.
• Functional analysis of the candidate genes for PI 567301B with resistance to F. graminearum will be reported – 2020
• Identify the candidate genes and potential mechanisms of resistance that map to the quantitative trait loci associated with resistance to Pythium spp.
o Fine mapping of QDRL for Pythium spp. (both ISU & OSU) NAM series publish summer 2019. Develop additional populations for fine mapping.
• Candidate gene identification for resistance to these pathogens will be ongoing and reported in USB quarterly reports and sequences provided to the group to develop silencing vectors.
o Identify key candidate genes in PI 427106, PI 427105B, V71-370 (chr. 18) for a major QTL for P. sojae. (USB Fellow Stephanie Karhoff).
o Candidate genes from the cultivar Conrad with resistance towards P. sojae
o Novel R-genes and putative mechanisms
• Coordinate genotyping system for introgression of five QTLs for resistance to soil borne pathogens into high yielding adapted germplasm.

Progress of Work

Updated February 26, 2020:

Final Project Results

Updated February 26, 2020:
Chen Lab:
Released lines: We have released 12 high yielding lines with resistance/tolerance to Phytophthora root rot from 2016-19 (S13-10590, S13-10592, S13-1955, S15-10434, S11-16653, S12-4718, S11-20242, S13-2743, S13-3851, S14-15146, S14-9017, S14-15138). Among those, three lines (S13-2743, S13-3851, S14-9017) carry Rps-1 alleles and eight of them have been licensed to private companies for commercialization.

Advanced lines: In the 2019 USDA Uniform Tests, four of our lines (S15-3772RY, S16-16641R, S16-11651C, S15-17812C) were found to carry Rps 1a resistance gene while another (S15-3847RY) was found to carry Rps 1c gene in hypocotyl and layer tests conducted in Dorrance Lab in 2019. These lines also showed high yield performance (S15-3847RY = 63 b/a, 113% of checks; S16-11651C = 62 b/a, 112% of checks; S15-17812C = 60 b/a, 102% of checks; S15-3772RY = 59 b/a, 101% of checks; and S16-16641R = 55 b/a, 98% of checks) across multiple locations.

In the 2019 USDA Uniform Prelim Tests, two lines (S09-13608C and S17-19874R) were found to carry Rps 1a gene while another line, S16-14161C carries Rps 1c gene. S16-14161C had yield of 69 b/a and ranked 1st among 16 test entries. Lines S09-13608C and S17-1984 had yield of 63 b/a and 59 b/a, respectively and ranked 5 and 12, respectively.

A total of 40 new high yielding lines have been selected for 2020 USDA Uniform tests and will be screened for resistance in hypocotyl and layer tests conducted in Dorrance Lab in 2020.

Breeding lines in the pipeline: A total of 64 crosses were made in 2018 involving 5 high-yielding lines carrying Rps genes are now under generation advance in winter nurseries in Costa Rica and Puerto Rico. F4:5 lines will be tested in progeny rows in 2020 for selection of promising lines. Nine RILs carrying different novel Rps genes and breeding lines S13-2743C, S15-3772RY, S15-17812C and S15-3847RY carrying Rps genes, were used in crossing with elite lines in 2019 season. A total of 22 new crosses were made and the F1 are being under light in the winter nurseries for generation advance, and the F4:5 lines are expected to return home station in 2021 for evaluation.

Wang Lab: In spring 2019, a total of six crosses were made in the greenhouse between two resistance lines, carrying the QDRLs identified in Dr. Anne Dorrance’s group and three high yielding lines, E14077, LD02-4485, and LD10-10198. The F1s were grown in the MSU research farm in summer of 2019 and the F2 seeds were harvested and were planted in the greenhouse in the fall of 2019. The populations will be advanced for two generations in 2019-2020 winter to F3:4. Molecular markers developed by Anne Dorrance’s group will be used to screen the F3 plants for individuals carrying the resistance QDRLs. The selected F3:4 will then be planted in our single-row plots in 2020 for initial field evaluations.
In the summer of 2019, additional seven crosses between seven new resistance lines from Dr. Anne Dorrance and an MSU high yielding line, E15339, were made. These F1 seeds will be planted in 2020.

Maroof and Robertson Labs. A major QDRL to P. sylvaticum, P. irregulare, and P. torulosum was identified on chromosome 8 in an advanced RIL population developed in the Maroof lab. In addition, several minor QDRL to P. sylvaticum, P. irregulare, and P. torulosum were identified in 4 advanced RIL populations developed in the Maroof lab and the soybean NAM resource. These are the first QDRL to be identified for resistance to P. oopapillum, and P. torulosum.

Dorrance and McHale Labs. Select RILs with novel resistance to one or more soilborne pathogen were provided to the breeders for germplasm and variety development in 2019. Based on new maps and markers, another set of RILs will be provided to the collaborators for additional crosses in 2020.

Benefit to Soybean Farmers

Growers will benefit with varieties which contain new and improved types of resistance to overcome the race shifts occurring for Phytophthora and have new (not currently available in the industry) sources of resistance for several Pythium species and for Fusarium graminearum.

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 provide durable protection to 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 to 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, thereby achieving higher yields and less dependence on fungicides and pesticides.

Project Years