The soybean cyst nematode (SCN), or Heterodera glycines, is the most damaging pathogen to soybean production in North America and current annual yield losses are estimated at more than $1.2 billion. Though SCN-resistant soybean varieties are available to minimize yield loss, producers are faced with limited options for rotation once virulent SCN populations have developed in their fields. The widespread lack of diversity for SCN resistance genes utilized and available for farmers in commercial soybean varieties has significantly increased the prevalence of virulent SCN populations across the mid-west (mainly HG 1.2.5.7), 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.
• Nematologists need to 1) identify the SCN genes, and their functionality, required for the adaptation to reproduce on resistant varieties, 2) use these as molecular markers to monitor nematode population shifts in the field in real time, and 3) exploit this knowledge to help plant breeders identify the best resistance gene combinations for short- and long-term nematode management.
• Breeders need to increase the availability of genetically diverse SCN resistance in commercial soybean varieties and work with nematologists to determine the most effective rotation practices that preserve the efficacy of the known sources of SCN resistance.

Objective 1: Identify SCN virulence genes to better understand how the nematode adapts to reproduce on resistant varieties.
Sub-objective 1.1: Combine, compare, and catalogue the genomes that compromise the SCN pan-genome. (Hudson, Baum, Mitchum)

Sub-objective 1.2: Resequencing of the genomes and transcriptomes of virulent SCN populations and conduct comparative analyses. (Hudson, Mitchum, Baum)

Sub-objective 1.3: Validate and characterize genes associated with SCN virulence and evaluate their utility as novel resistance targets. (Mitchum, Baum)

Objective 2: Complete the evaluation of how rotations of various resistance gene combinations impact SCN field population densities and virulence profiles. (Diers, Scaboo, Tylka, Mitchum)

Objective 3: Translate the results of objectives 1 and 2 to the SCN Coalition to increase the profitability of soybean for producers and inform growers on effective rotation schemes designed to protect our resistant sources. (Tylka, Mitchum)

Objective 4: Organize tests of experimental lines developed by public breeders in the north central US states and Ontario. (Diers)

Objective 5: Diversify the genetic base of SCN resistance in soybean by developing and evaluating germplasm and varieties with new combinations of resistance genes in high-yielding backgrounds. (Diers, Scaboo)

Objective 1: Identify SCN virulence genes to better understand how the nematode adapts to reproduce on resistant varieties.
Sub-objective 1.1: Combine, compare, and catalogue the genomes that compromise the SCN pan-genome. (Hudson, Baum, Mitchum)
• Continuously update SCNBase with novel sequence data and also with a complete database of all known SCN effectors and variants
• Finish, annotate and publish all SCN genome sequencing projects started in phase II and analyze gene variants between HG types
• Establish the proximity labeling approach for use in our nematode effector studies and identify comprehensive interactomes of SCN effectors in planta
• Understand on a molecular level how SCN is able to inactivate certain soybean defense mechanisms
Sub-objective 1.2: Resequencing of the genomes and transcriptomes of virulent SCN populations and conduct comparative analyses. (Hudson, Mitchum, Baum)
• Sequence populations of SCN as virulence changes and analyze for selected genes
• Complete the analyses of early gland-expressed gene differences between virulent and avirulent SCN populations
• Generate and analyze later-stage gland transcriptomes of virulent and avirulent SCN populations
Sub-objective 1.3: Validate and characterize genes associated with SCN virulence and evaluate their utility as novel resistance targets. (Mitchum, Baum)
• Successfully perform the Pool-seq strategy and identify SCN genome regions conditioning virulence phenotypes
• Validate potential candidates for a correlation with virulence in field populations of known HG types using molecular-based assays
Objective 2: Complete the evaluation of how rotations of various resistance gene combinations impact SCN field population densities and virulence profiles. (Diers, Scaboo, Tylka, Mitchum)
• Upon completion of this project in 2024, we will have the ability to recommend specific rotation strategies to reduce SCN populations densities and combat shifting virulence in SCN populations due to the continuous use of PI 88788 type varieties
• These data are unique only to this project and will likely be a foundation for the long term management of SCN for farmers by precisely using genetic resistance in a rotation program beyond the traditional crop rotation
Objective 3: Translate the results of objectives 1-3 to the SCN Coalition to increase the profitability of soybean for producers and inform growers on effective rotation schemes designed to protect our resistant sources. (Tylka, Mitchum)
• The project will be described during interviews conducted by Mitchum and Tylka and the information will appear in print media, on the radio, and in presentations given at large farmer-oriented events such as Commodity Classic and the Farm Progress Show. Also, information and results from this project will be distributed to mass farmer audiences through the communication vehicles used by the SCN Coalition (videos on YouTube, videos on TheSCNCoalition.com, press releases, etc.)
Objective 4: Organize tests of experimental lines developed by public breeders in the north central US states and Ontario. (Diers)
• The data generated from this portion of the project is crucial for evaluation and release of new SCN resistant soybean varieties, and it is utilized by both public and private soybean breeders to request material for incorporation into their respective programs
Objective 5: Diversify the genetic base of SCN resistance in soybean by developing and evaluating germplasm and varieties with new combinations of resistance genes in high-yielding backgrounds. (Diers, Scaboo)
• Development and release of new germplasm and varieties with unique SCN resistance that will be transferred to private companies as well as other public and private soybean breeders and researchers
• These new germplasm and varieties will lead to improved productivity and profitability for farmers by maintaining yield potential in heavily infested fields

To address these issues with SCN, we are proposing the second year of Phase III of an integrated, collaborative, and multi-state project among plant breeders, molecular biologists, bioinformaticians, and nematologists. Our proposed objectives specifically address the following key research area in the current RFP - Basic and applied research directed at soybean disease, nematode, insect pest and abiotic stress biology, management and yield loss mitigation, including new and emerging threats, of consistent or potentially significant economic impact across the North Central Region - and this proposed research complements funding from federal agencies, as well as respective state and United Soybean Board check-off support. The genetic resources developed and knowledge gained from this project will provide immediate and long-term benefit to soybean producers and researchers in both the private and public sector.

Objective 1: Identify SCN virulence genes to better understand how the nematode adapts to reproduce on resistant varieties.
Sub-objective 1.1: Combine, compare, and catalogue the genomes that compromise the SCN pan-genome. (Hudson, Baum, Mitchum)
• Continuously update SCNBase with novel sequence data and also with a complete database of all known SCN effectors and variants
• Finish, annotate and publish all SCN genome sequencing projects started in phase II and analyze gene variants between HG types
• Establish the proximity labeling approach for use in our nematode effector studies and identify comprehensive interactomes of SCN effectors in planta
• Understand on a molecular level how SCN is able to inactivate certain soybean defense mechanisms
Sub-objective 1.2: Resequencing of the genomes and transcriptomes of virulent SCN populations and conduct comparative analyses. (Hudson, Mitchum, Baum)
• Sequence populations of SCN as virulence changes and analyze for selected genes
• Complete the analyses of early gland-expressed gene differences between virulent and avirulent SCN populations
• Generate and analyze later-stage gland transcriptomes of virulent and avirulent SCN populations
Sub-objective 1.3: Validate and characterize genes associated with SCN virulence and evaluate their utility as novel resistance targets. (Mitchum, Baum)
• Successfully perform the Pool-seq strategy and identify SCN genome regions conditioning virulence phenotypes
• Validate potential candidates for a correlation with virulence in field populations of known HG types using molecular-based assays
Objective 2: Complete the evaluation of how rotations of various resistance gene combinations impact SCN field population densities and virulence profiles. (Diers, Scaboo, Tylka, Mitchum)
• Upon completion of this project in 2024, we will have the ability to recommend specific rotation strategies to reduce SCN populations densities and combat shifting virulence in SCN populations due to the continuous use of PI 88788 type varieties
• These data are unique only to this project and will likely be a foundation for the long term management of SCN for farmers by precisely using genetic resistance in a rotation program beyond the traditional crop rotation
Objective 3: Translate the results of objectives 1-3 to the SCN Coalition to increase the profitability of soybean for producers and inform growers on effective rotation schemes designed to protect our resistant sources. (Tylka, Mitchum)
• The project will be described during interviews conducted by Mitchum and Tylka and the information will appear in print media, on the radio, and in presentations given at large farmer-oriented events such as Commodity Classic and the Farm Progress Show. Also, information and results from this project will be distributed to mass farmer audiences through the communication vehicles used by the SCN Coalition (videos on YouTube, videos on TheSCNCoalition.com, press releases, etc.)
Objective 4: Organize tests of experimental lines developed by public breeders in the north central US states and Ontario. (Diers)
• The data generated from this portion of the project is crucial for evaluation and release of new SCN resistant soybean varieties, and it is utilized by both public and private soybean breeders to request material for incorporation into their respective programs
Objective 5: Diversify the genetic base of SCN resistance in soybean by developing and evaluating germplasm and varieties with new combinations of resistance genes in high-yielding backgrounds. (Diers, Scaboo)
• Development and release of new germplasm and varieties with unique SCN resistance that will be transferred to private companies as well as other public and private soybean breeders and researchers
• These new germplasm and varieties will lead to improved productivity and profitability for farmers by maintaining yield potential in heavily infested fields