Project Details:

Title:
An integrated approach to enhance durability of SCN resistance for long term strategic SCN management

Parent Project: This is the first year of this project.
Checkoff Organization:North Central Soybean Research Program
Categories:Insects and pests, Insects and pests, Nematodes
Organization Project Code:459-44-04
Project Year:2016
Lead Principal Investigator:Thomas Baum (Iowa State University)
Co-Principal Investigators:
Andrew Severin ((not specified))
Thomas Baum (Iowa State University)
Gregory Tylka (Iowa State University)
Brian Diers (University of Illinois at Urbana-Champaign)
Matthew Hudson (University of Illinois at Urbana-Champaign)
Melissa Mitchum (University of Missouri)
Henry Nguyen (University of Missouri)
Andrew Scaboo (University of Missouri)
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Keywords: SCN management, Genome assembly, Effectors, Resistance breeding

Contributing Organizations

Funding Institutions

Information and Results

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Project Summary

The soybean cyst nematode (SCN) or Heterodera glycines is the most damaging pathogen to soybean production in North America. Current annual yield losses are estimated at more than $1.2 billion. Though SCN-resistant soybean varieties frequently are available to minimize yield loss, producers are faced with limited options for rotation once virulent SCN populations develop in their fields. The widespread lack of genetic diversity in SCN resistance in soybean has significantly increased the prevalence of virulent SCN populations and reduced the effectiveness of current sources of resistance. Thus, we have two major research challenges that, when successfully achieved, will enable us to develop more efficient management practices for this pest in the future.
1. Plant breeders need to increase the genetic diversity of SCN resistance in commercially available SCN-resistant soybean cultivars and work with nematologists to determine the most effective rotation practices that preserve these sources.
2. Nematologists need to complete the SCN genome (genetic blueprint of the nematode) assembly to facilitate the identification of nematode genes required for the adaptation to reproduce on resistant cultivars, use these as markers to monitor nematode population shifts in the field, and exploit this knowledge to help plant breeders identify novel sources of resistance.
To address these issues we are proposing a state-of-the-art opportunity for farmers and the soybean industry through an integrated, collaborative, and multi-state proposal among plant breeders, molecular biologists, bioinformaticists, nematologists, and extension specialists. Our proposed objectives specifically address performance measures under Goals 1 (1.1, 1.2, 1.3), 3 (3.1, 3.2), 4 (4.6), and 5 (5.1) of the 2015-2020 SCN-Soybean Research Program Strategic Plan and complement funding from federal agencies and the United Soybean Board. The genetic resources developed and knowledge gained from this project will not only provide immediate benefit to NC soybean researchers and producers, but can be adopted nationwide. We plan to achieve the following objectives during the funding cycle:

Project Objectives

Objective 1. Diversify the genetic base of SCN resistance in soybean
Objective 1.1: Develop and evaluate germplasm with new combinations of resistance genes in high yielding backgrounds. (Diers, Nguyen, Scaboo).
Objective 1.2: Determine resistance gene copy number in the experimental lines for more effective breeding. (Diers, Nguyen, Scaboo).
Objective 2. Identify SCN virulence factors and better understand how the nematode adapts to resistance
Objective 2.1: Refine SCN genome assembly and its accessibility.
Objective 2.1.1: Improve genome assembly. (Hudson)
Objective 2.1.2: Genome curation and annotation. (Baum, Severin).
Objective 2.2: Conduct comparative population studies to identify genes associated with SCN virulence and evaluate utility as novel resistance targets. (Mitchum, Baum)
Objective 2.3: Determine unique resistance gene stacks that would be beneficial in rotations to enhance durability of SCN resistance. (Diers, Nguyen, Scaboo, Mitchum)
Objective 3. Translate the results of objectives 1 and 2 to increase the profitability of soybean for producers (Tylka)
Objective 3.1: Educate growers on how SCN adapts to grow on resistant soybeans.
Objective 3.2: Inform growers on effective rotation schemes designed to protect our resistant sources.

Project Deliverables

Objective 1:
1.1 A population segregating for Rhg1 from PI 88788, two resistance genes from G. soja, and the chromosome 10 gene from PI 567516C will be yield evaluated in two locations to test for the presence of yield drag associated with these genes. Breeding will be done to incorporate new combinations of resistance genes into high yielding genetic backgrounds.
1.2 From 200-300 experimental lines in the Northern Regional Soybean Cyst Nematode Tests and the Northern Uniform Test that were tested and shown to have SCN resistance will be tested for Rhg1 copy number. Lines that may carry Rhg4 will be tested for this gene.
Objective 2:
2.1.1 Inbreed nematodes, extract DNA, begin sequencing, begin cell culture experiments
2.1.2 Create SCN-SoyBase cyberinfrastructure, GBrowse, tracks, and integrating with Soybase using existing draft assembly and available SNP data/transcript data. This pipeline will be created in a species generic fashion to enable the reuse of this pipeline for other soybean pest species.
2.2 RNAseq data generated from sequencing whole nematodes representing the early parasitic stages of SCN populations differing in virulence on resistant soybean will be mapped to the draft SCN genome to facilitate annotation. In addition, various computational analyses will be conducted to compare and identify differences among the populations to identify genes that may correlate with SCN virulence on resistant soybean. All data will be integrated into the SCN-SoyBase website.
2.3 A series of greenhouse selection experiments will be undertaken on genetic material developed by the plant breeders with new combinations of SCN resistance genes to evaluate different rotation schemes for effectiveness at reducing the selection pressure on the nematode population.
Objective 3: A survey of extension and outreach educational materials about SCN biology and management in the NCSRP states will be conducted.
Objective 1:
1.1 The population segregating for Rhg1 from PI 88788, two resistance genes from G. soja, and the chromosome 10 gene from PI 567516C will be yield evaluated in three locations to test for the presence of yield drag associated with these genes. A second population segregating for Rhg1 and Rhg4 from PI 437654, two resistance genes from G. soja, and the chromosome 10 gene from PI 567516C will be yield evaluated in two locations to test for the presence of yield drag associated with these genes. Breeding will be done to incorporate new combinations of resistance genes into high yielding genetic backgrounds.
1.2 From 200-300 experimental lines in the Northern Regional Soybean Cyst Nematode Tests and the Northern Uniform Test that were tested and shown to have SCN resistance will be tested for Rhg1 copy number. Lines that may carry Rhg4 will be tested for this gene.
Objective 2:
2.1.1 Complete first phase of sequencing, begin genome assembly and produce first drafts, evaluate cell culture and extract DNA if working.
2.1.2 Create gene models from latest assembly from Object 2.1.1 using RNASeq data from Objective 2.2. Provide functional annotation for gene models based on best BLAST to human curated databases and using the literature.
2.2 Genes identified as putative virulence genes in year 1 will be further characterized using molecular, biochemical and/or genetic analysis. Additionally, genetic differences that correlate with virulence will be exploited for marker development.
2.3 A series of greenhouse selection experiments will be undertaken on genetic material developed by the plant breeders with new combinations of SCN resistance genes to evaluate different rotation schemes for effectiveness at reducing the selection pressure on the nematode population.
Objective 3: Create traditional and innovative information materials to further educate and increase awareness of SCN-related topics.
Objective 1:
1.1 The population segregating for Rhg1 and Rhg4 from PI 437654, two resistance genes from G. soja, and the chromosome 10 gene from PI 567516C will be yield evaluated in three locations to test for the presence of yield drag associated with these genes. Breeding will be done to incorporate new combinations of resistance genes into high yielding genetic backgrounds.
1.2 From 200-300 experimental lines in the Northern Regional Soybean Cyst Nematode Tests and the Northern Uniform Test that were tested and shown to have SCN resistance will be tested for Rhg1 copy number. Lines that may carry Rhg4 will be tested for this gene.
Objective 2:
2.1.1 Complete all sequencing, complete cell culture evaluation, complete genome assembly.
2.1.2 SCNBase will be updated with the final assembly and annotation.
Final data from this project will be curated into SCN-SoyBase: Genetic Markers and copy number variation identified in Soybean from Objective 1.2, SNPs and markers spanning 200-300 lines identified in Objective 1.1. Link SCN genes to soybean genes for easy cross reference of databases.
2.2 Genes identified as putative virulence genes in year 1 will be further characterized using molecular, biochemical and/or genetic analysis. Additionally, genetic differences that correlate with virulence will be exploited for marker development.
2.3 A series of greenhouse selection experiments will be undertaken on genetic material developed by the plant breeders with new combinations of SCN resistance genes to evaluate different rotation schemes for effectiveness at reducing the selection pressure on the nematode population.
Objective 3: Create traditional and innovative information materials to further educate and increase awareness of SCN-related topics.

Progress of Work

Update:
See attached document.

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Final Project Results

Benefit to Soybean Farmers

Performance Metrics

Project Years