Project Details:

Title:
Characterization and enhancement of soybean genetic resources for soilborne disease resistance

Parent Project: This is the first year of this project.
Checkoff Organization:North Central Soybean Research Program
Categories:Breeding & genetics, Soybean diseases
Organization Project Code:
Project Year:2015
Lead Principal Investigator:James Kurle (University of Minnesota)
Co-Principal Investigators:
Teresa Hughes (Purdue University)
Jianxin Ma (Purdue University)
Katy M Rainey (Purdue University)
James Orf (University of Minnesota)
Nevin Young (University of Minnesota)
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Keywords: Seedling Diseases, Soybean Genetic Mapping, Soybean Germplasm Screening

Contributing Organizations

Funding Institutions

Information and Results

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Project Summary

Soilborne diseases caused by various oomycete and fungal pathogens have been a major limitation to soybean production. Each year the U.S. soybean crop is attacked by several pathogens that cause estimated annual losses valued in the billions of dollars. Among these pathogens, Phytophthora sojae, Pythium ultimum, Pythium irregular, and Fusarium graminearum are the major culprits, particularly, in the North Cental Region.

The primary goals of this project are to characterize, identify, and/or isolate novel genes/QTLs conferring resistance or partial resistance to P. sojae, P. ultimum P. irregulare, and F. graminearum, and to deploy the new sources of resistance towards effective disease management in the entire North Central regions in coalition of the USB-funded soybean disease research project.

Project Objectives

1. Evaluate soybean germplasm for resistance or partial resistance to P. sojae, P. irregulare, P. ultimum and F. graminearum.
2. Identify QTLs underlying resistance to P. sojae, P. irregulare, P. ultimum and F. graminearum by association mapping.
3. Fine map, isolate and functionally verify two uncharacterized Rps genes conferring resistance to P. sojae.
4. Develop highly adapted soybean cultivars, or experimental lines, with major resistance QTLs and Rps genes by marker-assisted selection.

Project Deliverables

Minnesota: Screened 280 ancestral lines for resistance or partial resistance to P. sojae in duplicate runs of rice inoculum assay and F. graminearum in duplicate runs of rice inoculum and rolled towel assays.
Association mapping of phenotypic with genotypic data detected no significant marker trait associations for partial resistance to P. sojae. Population size and/or marker density combined with environmental error in measurement of traits possessed insufficient power to detect significant marker-trait associations. As alternative to association mapping, six crosses were made between diverse sources, resistant and susceptible lines, for use in biparental mapping of resistance to P. sojae. Grow out of seed from crosses will be conducted in South American location to make seed available for 2016 growing season.
In phenotyping for resistance to F. graminearum measures of resistance included reduced root necrosis score and maintenance of relative root weight and relative root length when inoculated plants are compared to uninoculated. Association mapping detected a significant marker associated with reduced root necrosis (1 marker on chromosome 8) and multiple markers (10 markers on multiple chromosomes) for maintenance of relative root dry weight and root length.

Purdue: Narrowed location of RpsUN1 to 81kb from original 1,300 kb and RpsUN2 to 64kb from original 430kb. Pinpointed the candidate gene for RpsUN2. Begun haplotype analysis by comparing this region between PI 567139B and other genotyped soybean accessions to deduce RpsUN1 and RpsUN2 region-unique SNPs for use as molecular markers. RpsUN1 and RpsUN2 are being introgressed into elite breeding lines.

Progress of Work

Update:
• Completed screening of 280 lines for partial resistance to P.sojae (6 reps.) Prepare inoculum of F. graminearum for screening, conduct preliminary run of screening protocol rates and inoculation method. P. irregulare isolates for inoculum production.
• Assembled data set from P.sojae screening for statistical analysis. Analyzing data for quality, indication of line performance, and transformation for use in association analysis.
• Defined 64-kb region within 430 kb previously associated with marker for RpsUN2. Conduct haplotype analysis comparing this region in source PI 567139B and other accessions. Begin analysis for unique SNPs useful as markers for RpsUN1 &RpsUN2.
• Initiated introgression of RpsUN1 and RpsUN2 to elite breeding lines.

Update:
Completed screening of 280 lines for partial resistance to P.sojae (6 reps.) Prepare inoculum of F. graminearum for screening, conduct prelim. run of screening protocol rates and inoculation method. P. irregulare isolates for inoculum production.

Assembled data set from P.sojae screening for statistical analysis. Analyzing data for quality, indication of line performance, and transformation for use in association analysis
.
Defined 64-kb region within 430 kb previously associated with marker for RpsUN2. Conduct haplotype analysis comparing this region in source PI 567139B and other accessions. Begin analysis for unique SNPs useful as markers for RpsUN1 &RpsUN2.

Initiated introgression of RpsUN1 and RpsUN2 to elite breeding lines.

Final Project Results

During this project year tests of multiple methods of inoculation with F. graminearum were conducted to validate the methodology, effectiveness, and consistency of the method used to conduct screening for resistance to seed, seedling, and root rot caused by F. graminearum. Based on these tests, the rolled towel assay and rice inoculum method were selected as the most reliable screening methods for assessing root rot and root development.
Utilizing these methods, rolled towel and rice inoculum assay, we completed phenotyping and association mapping of results obtained from multiple phenotyping assays of 280 ancestral lines for resistance or partial resistance to P. sojae and F. graminearum.
Association mapping performed on results obtained in P. sojae and F. graminearum phenotyping indicating the location of markers for partial resistance to F. graminearum. In 280 ancestral lines two categories of marker were identified that indicated resistance to F. graminearum, one marker located on chromosome 8 indicating resistance to root necrosis and 10 markers distributed on multiple chromosomes associated with resistance to loss of root mass. These markers may also be good targets for genomic selection for root rot resistance. Association mapping of phenotypic data for P. sojae partial resistance did not detect significant marker- trait associations for resistance to P. sojae although phenotyping indicated that 280 lines differed widely in response to P. sojae inoculation. To examine this phenomenon more closely we have elected to examine the results of biparental crosses between cultivars exhibiting a wide divergence of resistance to P. sojae inoculation. For this reason we completed six crosses of lines with divergent resistance characteristics, resistant and susceptible, for use in biparental mapping of resistance and partial resistance to P. sojae.
First run consisting of one rep of evaluation of 280 lines for resistance or partial resistance to P. ultimum is underway.
Pinpointed location of RpsUN1 and RpsUN2, identified RpsUN2 candidate gene, and began haplotype analysis to identify SNP markers associated with RpsUN1 and RpsUN2. Introgressed RpsUN1 and RpsUN2 into prebreeding lines and elite breeding lines.

Benefit to Soybean Farmers

The goal of this research is to capitalize on molecular methods for identifying novel resistance to seed and seedling rot pathogens. The potential impact of this research would add to the options available to soybean farmers for managing these diseases. The potential benefit for American soybean farmers would be an increase in yield of as much as 10% based on estimates of yield lost to P. sojae and the complex of seedling diseases that include Fusarium and Pythium species.
The research is necessitated by changing patterns in the occurrence of diseases common in the corn-soybean cropping system. Identification of additional highly effective Rps genes is a necessity because of the appearance of new and complex P. sojae pathotypes capable of overcoming currently available resistance genes. Resistance to F. graminearum is necessitated by the increased prevalence of this fungus as a pathogen of soybeans grown in rotation with corn. Resistance to Pythium species is increasingly important as the prevalence of Pythium species that infect both corn and soybean become more common with planting of sequences consisting of only these two crops. Because resistance would be available as a varietal trait, the benefit would be available at the lowest cost. In addition, effective control of seed and seedling rots would protect the value of seed, currently the largest single expense in soybean production. In combination with seed treatment fungicides and management practices, varietal resistance would enhance the ability of these tactics to limit losses caused by seed, seedling, and root rots.

Performance Metrics

The success of this project would be indicated by 1) identification of markers for partial resistance to P. sojae, F. graminearum, P. ultimum, and P. irregulare; 2) their incorporation into breeding lines and utilization in breeding programs and 3) adoption of RpsUN1 and RpsUN2 as effective genes for protection against P. sojae.

Project Years