Soybean cyst nematode (SCN) is a persistent threat to growers throughout Minnesota. Fields infested with SCN are more susceptible to other disease, pest, and environmental stresses. Moreover, some parts of Minnesota have seen a breakdown in varietal resistance, with the appearance of new SCN races capable of overcoming the widely grown 88788-source of resistance. Developing new germplasm with alternative forms of resistance to combat resistance breakdown for long-term success is an important function of the public sector breeding efforts. With this in mind, our overall objective is to advance the development of SCN-resistant soybean varieties as well as provide accurate and unbiased sources of information on the resistance of commercial soybean varieties. Our specific aims are to: 1) Enhance the efficiency and efficacy of breeding for SCN resistance through the deployment of DNA markers linked to major genes conferring SCN resistance; 2) Advance new sources of SCN resistance and expand the use of these new sources for crossing in the breeding program; 3) Conduct SCN bioassays on commercial varieties entering the 2022 UMN Variety Trials, as well as all non-88788 commercial SCN varieties available to Minnesota growers.

Goals 1. Continue to efficiently produce new SCN-resistant germplasm and varieties and thus expand availability of SCN resistance across all maturity groups grown in Minnesota.
Objective 1. Deploy DNA markers linked to genes conferring SCN resistance to enhance the efficiency and efficacy of breeding for SCN resistance.

Goals 2. Create elite soybean germplasm with non-88788 sources of SCN resistance so that future soybean growers have more tools in their toolbox to compete with this evolving major pest of soybean.
Objective 2. Advance new sources (non-88788) of SCN resistance and expand the use of these new sources as parents for crossing in the breeding program
Goals 3. Provide an unbiased source of information to growers on the level of SCN resistance in 88788-type commercially available varieties as well as those that have non-88788 sources of resistance.
Objective 3. Conduct SCN bioassays on commercial varieties entering the 2022 UMN Variety Trials using race 3, and conduct bioassays on commercially available non-88788 SCN varieties using races 3 and 14.

1) Public and licensed SCN-resistant varieties, particularly ones carrying the non-88788 source of resistance such as Peking and 567516C; 2) An unbiased source of information on the actual SCN resistance of currently available 88788-type resistant varieties to race 3 (HG Type 0); and 3) An unbiased source of information on the resistance of advertised non-88788 resistant varieties to SCN race 1 (HG Type 2.5.7).
Background
Soybean cyst nematode (SCN) is a persistent threat to growers throughout the state of Minnesota. Fields infested with SCN are lower yielding and more susceptible to other disease and pest pressures. Moreover, new SCN isolates increasingly overcome existing resistant varieties. Therefore, novel resistant cultivars are needed to control SCN and provide growers with greater yield stability. A primary objective of the University of Minnesota breeding program continues to be the development of northern-adapted soybeans with robust SCN resistance.
The research in this proposal will enhance SCN resistance in Minnesota germplasm by building on a long and successful record of traditional plant breeding and DNA marker-assisted selection. A robust and high-throughput marker lab helps to increase soybean profitability through better resistant varieties and disease management strategies. Our breeding and genetics work will also result in resistant “pre-breeding” germplasm that can be utilized by the broader public and private breeding communities.
This proposal specifically targets the use of novel sources of SCN resistance for future crosses and variety development. While novel resistance sources have been part of the program for years, this area of research and breeding work will continue to be expanded upon. For example, a series of promising breeding lines originated from crosses made in 2010 with a new source of SCN resistance – PI 567516C – discovered by Co-PI Dr. Senyu Chen. Breeding lines originating from these crosses were advanced to regional trials and performed relatively well in those trials. The Soybean Breeding Program has expanded the use of these lines as parents to develop new germplasm, target progenies coming from these crosses for advancement, as well as search for better markers that can tag the novel alleles donated from these new sources. Dr. Senyu Chen is continuing his work in discovering new sources of SCN resistance. His laboratory is the only one at UMN with the expertise to phenotype for SCN resistance on a large scale. As co-investigators on this project, Drs. Chen and Lorenz will continue to work together to discover new sources and integrate them into the breeding program. The breeding program is also actively working with the Peking-source of resistance, and will be creating foundation seed for two new public Peking varieties in 2022. One of these Peking-type varieties, with strong resistance to the HG Type 2.5.7, is of relative maturity 0.8, making it only one of two available Peking-type varieties in MG 0.
Beyond discovery and development, soybean producers need reliable and unbiased information on SCN resistance and performance of currently available commercial and public soybean varieties. The UMN Soybean Variety Trials are conducted each year and consist of ~120 commercial and public varieties evaluated in common tests across four maturity zones in Minnesota. Within the Variety Trials, a special SCN Trial is conducted where entered varieties are evaluated at sites confirmed to be infested with SCN. In addition to the yield trials, entered varieties are also tested for resistance to SCN race 3 using greenhouse bioassays. The cost of the greenhouse bioassay raises the entrance fee for the SCN trial to nearly twice that of the entrance fee for the normal variety trial. Because of this increased fee, seed companies have been reluctant to enter varieties into the SCN variety trial. Nevertheless, growers want an unbiased source of information about the SCN resistance of the varieties they are purchasing, and in the past the Council has funded the entrance of commercial varieties into the SCN test.
As interest in non-88788 SCN varieties increases, it is also important to provide unbiased information on the actual effectiveness of these sources to races that can overcome 88788. Dr. Greg Tylka at Iowa State University and Bruce Potter at the UMN Southwest Research and Outreach Center annually compile lists of all commercially available non-88788 SCN resistant soybean varieties. These lists, however, are simply based on claims of the seed companies and no verification of their actual resistance has been reported. We feel it is important to do the hard work and actually test these varieties for their resistance to multiple races of SCN. We successfully did this in 2021, and would like to repeat this activity in 2022-23. This report (link here) was written and posted online. We only listed the varieties confirmed to be resistant to a HG Type 2.5.7 isolate, but we did find commercial varieties claiming Peking resistance that in fact were not resistant, verifying the importance of this independent screening.

Approach
1. Continue to develop and deploy DNA markers for SCN resistance.

In 2022, we will continue SCN resistance breeding at roughly the same level of intensity as in past years. This will include at least 50 new crosses between parents with SCN resistance and other desirable traits, and in making the 2022 crosses, we will specifically emphasize parents carrying novel resistance sources distinct from PI 88788.
In addition to variety breeding, we will continue to pursue “parent building” because some of the novel resistant parents are simply too exotic to be used directly in variety development. As a result, we hope to create semi-adapted SCN resistant lines that are stable and promising – and in this way – useful for subsequent crosses by us and other breeding programs.
Based on crosses made in earlier years, we will examine lines that reach the F4 generation for the presence of target SCN resistance genes through the use of proven DNA marker technology. Plants that are selected will be planted into “plant rows” where agronomic traits and yield begin to be systematically screened. We expect to screen approximately 4000 F4 plants using DNA markers. As we have in the past, we will continue to increase the efficiency of this screen. In 2020, we moved to single-plant screening using a more efficient marker assay. Will continue to build upon this advancement in 2022.

2. Advance and expand new sources of SCN resistance

Nearly all resistance sources carry the major gene Rhg1 – though different resistant parents carry different versions of this critical gene. PI 88788 is by far the most common source of one version of this resistance gene. Our current DNA marker technology successfully differentiates these different versions of the Rhg1 gene from one another. At the same time, an exciting novel resistance source, PI 567516C, carries a second SCN resistance gene on a separate chromosome and we have previously created a DNA marker system to follow the inheritance of this second important gene.

We will continue to advance non-88788 SCN resistant germplasm through the pipeline by routinely crossing to these sources and tracking inheritance of resistance using molecular markers in the breeding pipeline. Once the best performing breeding lines are advanced to regional trials, they will be screened for resistance to HG Type 2.5.7, the type of SCN that typically breaks down the 88788 source of resistance.

Two new varieties have recently been disclosed and foundation seed of these varieties will be made in 2022. These varieties have confirmed Peking-type SCN resistance, making them resistant to SCN populations that are virulent on 88788-type varieties. These varieties have superior yield, with one being a 0.8 RM and the other being a 1.6 RM. These varieties will also be used as parents in building up the Peking-type resistance germplasm in our program.

3. Conduct SCN testing on commercial varieties in UMN Variety Trials.

Each year the UMN Soybean Breeding Program conducts the MN Statewide Variety Trials (soybeans.umn.edu). This year we will test all newly entered commercial soybean varieties for resistance. Last year only 27 commercial varieties were entered into the SCN trials, but years past suggests this number can range up to 100. We will budget for screening 50 entries and fill entries from other tests if necessary. Bioassays are conducted using an HG Type 0 (Race 3) SCN population. Each container is inoculated with 4000 SCN eggs. Female index values are scored after 30 days. Results from these trials are reported in the Soybean Field Crop Trials Results published by the Minnesota Ag Experiment Station and provide an unbiased source of information allowing growers to evaluate the level of SCN resistance in their varieties.

As last year, we will work with Bruce Potter to identify all non-88788 SCN varieties currently on the market and test them with a bioassay using multiple SCN races to determine whether these varieties truly have broad resistance. We will obtain seed from as many of these varieties as we can and bioassay them using SCN race 3 (HG Type 0) and race 1 (HG Type 2.5.7). Results will be made available on www.soybeans.umn.edu as well as through MinnLine. Last year’s report is published here. We received some attention from seed company agronomists and crop consultants, and are confident that we can expand the number of varieties tested next year.

Update:
Progress this quarter for each objective is as follows:
Objective 1. Continue to develop and deploy DNA markers for SCN resistance

The stage at which we deploy molecular markers to help select for SCN resistance is at the F4 plant stage. This allows us to determine which single plants need to be harvested for advancement to the more costly “plant row” stage of evaluation. Over the years, we have been able to use markers at the F4 stage to reduce the cost of our plant row trials.
This past summer in our F4 population nursery we staked, tagged, and sampled tissue from 5264 plants. Tissue was sent to a private service provider to extract DNA and genotype each plant for 25 molecular markers. The economy of scale that this private lab can leverage makes it more inexpensive to genotype there than in our own lab when such a large number of samples is genotyped. The 25 molecular markers include markers tagging 88788 SCN resistance, Peking SCN resistance, and 567516C SCN resistance. We expect data back in September when we can use it to make selections to enhance SCN resistance in more advanced breeding stages.

Objective 2. Advance and expand new sources of SCN resistance

Foundation seed is being created of two new Peking-type public varieties: M13-250056 (RM 0.8) and M13-250046 (RM 1.5). These varieties are in regional and state wide yield trials once again, and their release is contingent upon 2022 performance.
Further into the yield trial pipeline, we are testing 272 new breeding lines with novel forms of SCN resistance in their pedigrees for yield and basic agronomics in preliminary yield trials (two locations, two replications). All parents chosen to create these lines were resistant to HG Types 2.5.7. Some progenies were derived from PI567516C, which has a novel QTL on chromosome 10. Twenty-two breeding lines are being tested in advanced yield trials (three MN locations, two replications). Most of these lines derived from 324-1BA1-472, which carries resistance to many HG Types and has QTL from PI 567516C. We are hopeful that some of these lines are good enough to advance to regional trials. Lines that have SCN resistance but to not make the cut for advancement will be considered for parent recycling.
In the breeding nursery, we planted and managed 19 F2 populations containing novel SCN resistance for generational advancement. Likewise, we advanced four F4 populations (crossing was greatly reduced in 2020 because of COVID). In 2022 we made 22 new crosses involving at least one parent with a novel source of SCN resistance. Successful attempts will be counted at harvest time.

Objective 3. Conduct SCN testing on commercial varieties in UMN Variety Trials.


In the spring we solicited entries for the UMN State Soybean Variety Trials (https://varietytrials.umn.edu/soybean). We planted all varieties in yield trials, and sent seed down the Waseca SCN lab for resistance testing against race 3. The test is currently in progress but we expect to have results in time for the report in the fall.

Additionally, we combed through all seed catalogues and identified non-88788-type soybean varieties adapted to MN. We requested seed for testing of all those varieties that were not tested in 2021 to add to our list. Unfortunately we found only three additional varieties for which we could access seed. A major supplier of non-88788 type soybean varieties for MN has not agreed to let us test their seeds. We are still working with them to see if we can agree on terms for testing. The three varieties are currently being tested in laboratory and we expect results during the next quarter.

Update:
The major activity this past quarter was harvest.

Objective 1. Continue to develop and deploy DNA markers for SCN resistance

The data described in the Q1 report was received on time and we harvested the single plants in our breeding populations that carry SCN resistance according to our molecular markers. These plants are being stored and threshed currently.


Objective 2. Advance and expand new sources of SCN resistance

Foundation seed of the two Peking-type lines was successfully harvested and officially released through the UMN Crop Variety Review Committee. All other lines were harvested and data analysis is underway. Seed from breeding populations described in Q1 report was harvested and sent to Chile winter nursery for generational advancement.


Objective 3. Conduct SCN testing on commercial varieties in UMN Variety Trials.


The trials were successfully harvested and data analysis is underway.

Update:
The main activity this past quarter was data analysis and yield trial report preparation

Objective 1. Continue to develop and deploy DNA markers for SCN resistance

Single plants selected by the molecular markers were threshed, and are currently being organized into plant rows for the 2023 planting. We are still quantifying the number of plants successfully saved.


Objective 2. Advance and expand new sources of SCN resistance

Selections are being made and advancements into regional trials and advanced trials are being made at the time.
As mentioned in the last report, the Peking-type varieties we developed were officially released by the CVRC. We are currently trying to work with at least one private company to license this line. We have sent it to two other private companies for crossing rights.



Objective 3. Conduct SCN testing on commercial varieties in UMN Variety Trials.

The analysis of the SCN data was completed and published at https://varietytrials.umn.edu/soybean. We solicited seed of non-88788 varieties for testing with SCN HG Types that defeat the 88788 source of resistance. We had a hard time getting seed, but were able to get a few new ones to add to the table. See attached document.

View uploaded report

Update:
Annual Progress Report, 2022
Advancing Varietal Resistance to Soybean Cyst Nematode in Minnesota
PIs: Aaron Lorenz and Senyu Young

Objectives

The objectives of this project and related accomplishments were as follows:

Goals 1. Continue to efficiently produce new SCN-resistant germplasm and varieties and thus expand availability of SCN resistance across all maturity groups grown in Minnesota.

Objective 1. Deploy DNA markers linked to genes conferring SCN resistance to enhance the efficiency and efficacy of breeding for SCN resistance.

During the summer of 2022,40 new breeding crosses that included at least one parented specifically targeted for SCN resistance were made. All crosses were successfully made and F1 seed was sent to Chile. F2 seeds were returned in time for planting.

F2, F3, and F4 breeding populations previously targeted for SCN resistance were advanced successfully using winter and summer nurseries per standard operating procedures.

In 2022, we genotyped 5264 plants for SCN resistance and found that 2229 were homozygous resistance. These plants were targeted for harvest and we harvested each selected plant individually. The seeds from these plants are growing in plant rows this year. Using molecular markers to select which individual plants have SCN resistance greatly enriches our breeding pipeline for SCN resistance. Without this funding to use these markers, we would have a much harder time breeding for SCN resistance.

This is evidenced by the number of SCN resistant breeding lines we enter into regional trials. In 2022, we entered 23 advanced breeding lines. All but one of these lines was determined to in fact have resistant according to a greenhouse bioassay, indicating the effectiveness of our marker program. Many of the resistant lines performed well in terms of yield and overall agronomics. For example, M13-118036 and M13-250056 were the highest yielding lines in the MG 0 test. M13-118036 is undergoing purification in 2021. Another highlight is M14-122031 which was the highest yielding line in the test and carries solid SCN resistance and beat the check variety closest in maturity by 3.5 bushels yet. Breeder’s seed as produced for this variety in 2022 and it has been sent to private companies for testing.

We are also striving to integrate SCN resistance into our specialty and food type varieties. For example, natto varieties have not typically carried SCN resistance, but with increased SCN pressure in natto growing regions, there has been more interest in this trait. One line, M13-171089, has done well and we are making foundation seed for this line and it has been sent to several companies for testing. It has good yield, quality, and SCN resistance. There are 121 food-type breeding lines in our program with SCN resistance.





Goals 2. Create elite soybean germplasm with non-88788 sources of SCN resistance so that future soybean growers have more tools in their toolbox to compete with this evolving major pest of soybean.

Objective 2. Advance new sources (non-88788) of SCN resistance and expand the use of these new sources as parents for crossing in the breeding program

During the summer of 2022, 22 successful crosses were made between adapted soybean varieties and breeding lines or exotic accessions carrying putative novel SCN resistance genes. New sources ranged from Peking sources, as well as some new sources from the germplasm collection that appear to be novel. The F1 seeds resulting from these crosses were sent to Chile for generational advancement. F2 populations were successfully generated from these crosses and have been returned from Chile and planted in the St. Paul breeding nurseries for generation advancement. Additionally, we have advanced 19 F2 populations and 4 F4 populations segregating for new sources of SCN resistance. The F2 populations were harvested last summer, sent to Chile for generational advancement, and now we have 19 F4 populations. The F4 populations were harvested as single plants based on genotype data, threshed, and planted in 2023 as plant rows. We have 604 plant rows being grown in 2023 with novel SCN resistance as a result of this project.

Breeding lines developed from crosses with novel sources of resistance back in 2017 have been advanced to multi-location yield testing. From 719 plant rows with novel resistance planted in 2022, we selected and harvested 90 for preliminary yield testing in 2023. Of the 160 tested in preliminary yield tests in 2022, 66 were advanced to a second year of testing at three locations in 2023. One new lines with 567516-type resistance was advanced to regional trials.

Most importantly, advanced breeding lines carrying Peking resistance were again tested regional trials in 2022. These lines continued to perform well and therefore we decided to release these new varieties and create foundation seed. The UMN Crop Variety Review Committee decided to release these varieties as ‘MN0812CN-P’ (M13-250056) and ‘MN1614CN-P’ (M13-250046). The ‘-P’ indicates Peking-type resistance and these are the first Peking-type varieties released from the UMN program.

Goals 3. Provide an unbiased source of information to growers on the level of SCN resistance in 88788-type commercially available varieties as well as those that have non-88788 sources of resistance.
Objective 3. Conduct SCN bioassays on commercial varieties entering the 2022 UMN Variety Trials using race 3, and conduct bioassays on commercially available non-88788 SCN varieties using races 3 and 14.
Sixty-eight commercial varieties were entered into our 2022 SCN bioassay. Three of the 68 submitted varieties were found to be susceptible to race 3. Quantitative differences can be observed, with some varieties showing extremely high resistance (FI = 0), and others showing weather resistance (FI = 20). The results can be observed in Table 5 the Variety Trials Reports found at https://varietytrials.umn.edu/soybean.

Additionally, we all non-88788 SCN varieties currently on the market and test them with a bioassay using multiple SCN races to determine whether these varieties truly have broad spectrum resistance. We solicited seed of non-88788 varieties from seed companies. Only three new varieties were identified, but we tested them and included them in the table along with the 2021 entries. See blog post at
https://blog-crop-news.extension.umn.edu/2023/03/soybean-varieties-with-non-88788-scn.html

View uploaded report

View uploaded report 2

Advancing Varietal Resistance to Soybean Cyst Nematode in Minnesota
Aaron Lorenz and Senyu Chen, University of Minnesota

Soybean cyst nematode is the number one pest of soybean, causing large yield reductions wherever it is present in the soil. By far and away the best tool for ameliorating yield losses from SCN is to plant soybean varieties with genetic resistance. Development of varieties with strong resistance is not an easy task as SCN resistance screening is expensive and laborious. It is even possible that commercially available varieties claiming to have SCN resistance do not in fact have such resistance, or the resistance is only moderate. On top of all this, the most commonly deployed source of resistance – 88788-type resistance – has been in use for several decades. Reports of resistance breakdown have become increasingly common in Minnesota, and it is expected the situation will become rapidly worse. New sources of resistance are needed to sustain soybean production.

The research conducted as part of this proposal addresses all three of the above-mentioned issues. Firstly, this project funds the deployment of molecular markers that assist in the selection of SCN resistance. Each year, the UMN Soybean Breeding program screens 3000 – 5000 breeding line candidates for resistance, thus greatly enriching the probability an advanced variety has SCN resistance. During 2022, we made sure that all breeding crosses made contained SCN resistance, a scenario made possible only through these molecular markers. We are also converting many food-type varieties to having SCN resistance, and are having some success: new natto cultivars with SCN resistance have been advanced to foundation seed production and sent out to several potential commercial partners for evaluation.
An important component to the UMN Variety Trials partially made possibly by this project is the screening of commercial and public varieties for SCN resistance using a greenhouse bioassay. This was again conducted in 2022 by screening 68 commercially available varieties. As expected, the vast majority were indeed resistant or moderately resistant except for three, which were found to be susceptible. This result, and those in the past, highlight the need to independently screen commercial varieties for resistance to important pests such as SCN so growers are ensured they are getting what they are paying for. Results of this test are posted at soybeans.umn.edu and varietytrials.umn.edu/soybean. A couple of years ago we expanded this activity to testing non-88788 varieties for their resistance to other races that overcome the 88788-type of resistance.

The incorporation of new sources of resistance into elite varieties adapted to Minnesota is an ongoing long-term project. Nevertheless, it is an important endeavor to help assure that such varieties exist in the future. We have continued to make new breeding populations with new sources of SCN resistance, which will be important sources of new varieties in the future. These are currently progressing through our population developing and yield testing pipeline. We recently released two new public Peking-type varieties with good resistance to evolving populations of SCN. Foundation seed was produced in 2022, and seed was sent to potential commercial partners for licensing. One variety is a 0.8 RM, which will be useful for northwestern MN as very few non-88788 SCN resistant varieties are commercially available.

The proposed research addresses three areas targeted by the Production Action Team’s mission statement: (1) Plant breeding and genetics; (2) Molecular breeding and functional genomics; (3) Soybean cyst nematode (SCN). The work we propose aims to increase soybean yield and profit potential by providing growers with a broader range of variety options with stable or enhanced yield even in fields infested by SCN. To increase the utility of our work, we are introducing novel sources of resistance into Minnesota soybeans, combining SCN resistance with other marketable traits, and making our germplasm available to the broader community to catalyze additional variety development for the future benefit of Minnesota growers. We will also provide an unbiased source of information on the SCN resistance of commercially available varieties. This is particularly important for the non-88788 varieties, which have not been verified in this way before.