Justification:
1. Variety and germplasm development.
Combining resistances to important pathogens, optimizing seed composition (high oleic oil), enhancing genetic diversity and improving abiotic stress (drought and heat) resistance will help enable public and private breeding programs to sustain improvement of resilient soybean varieties able to meet the production and quality of soybean products needed in the marketplace. Elite as well as potentially “good” diverse germplasm will be used as parents to develop new progeny to help bridge the gap in performance between exotic germplasm and elite varieties. High oleic, low linolenic soybean represents a value-added commodity. There is also a need to produce high-protein soybean meal, and increase the amount of soybean oil produced per acre to help meet the demand for soybean oil in such produces as biofuels. We will continue to incorporate these traits into KS adapted varieties. Resistance to SCN continues to be dominanted by the PI 88788 source in both public and private soybean varieties, despite the fact that HG Type 2 SCN populations, which reproduce well on this source of resistance, now dominate the North Central Region, including Kansas. Several recent releases by the KSU Soybean Breeding Program have utilized sources of resistance other than PI 88788 that have proven to be resistant to diverse HG Type 2 populations from across Kansas. Additionally, novel sources of resistance, including resistance gene stacks are being developed by soybean breeders, and these new resistances need to be incorporated into Kansas soybean germplasm to provide more durable resistance in the future.

2. Evaluate and implement breeding technologies.
Focusing on the development and use of new technologies will help improve genetic gain across public and private breeding programs. Advances in genomics have made genotyping cost effective, but robust models must be capable of predicting phenotypic performance. We are working with the soybean breeders and geneticists in the North Central US to test the effectiveness of recurrent selection of F1 progeny in soybean using genomic selection to predict progeny performance. This method has the potential to improve selection accuracy, reduce the time required to develop new varieties and increase the performance of the progeny relative to current breeding methods. Here we propose to further develop our genomic selection capabilities and combine traditional phenotypic selection with genomic selection and remote sensing to help develop robust genomic selection methods for soybean breeding based on Kansas environments and Kansas germplasm. Also, we will use and validate marker assisted selection to compliment phenotyping of traits such as Soybean Cyst Nematode resistance.

3. Drought and heat tolerance.
Soybean is perceived as a relatively drought and heat-tolerant crop. However, high temperatures and drought conditions during the seed-filling or seed development can dramatically reduce seed yield and modify seed composition. Therefore, maintaining soybean yield and a balanced seed composition under high temperature and drought stress is a major objective of the program with the long-term goal of helping to develop improved post-flowering drought and heat-stress resilient varieties and strengthen the improvement pipeline between untapped soybean germplasm and commercial soybean varieties. Development of soybean varieties and identifying stable and effective molecular markers available to the wider soybean community will help mitigate the negative impacts of drought and heat stress across major soybean growing regions of the US and elsewhere.

4. Breed transgenic events into elite breeding lines.
Field tests demonstrated lines expressing transgenes targeting nematode fitness decreased SCN cyst and egg numbers compared to non-transgenic controls. Breeding these lines with elite lines containing conventional sources of resistances would be important to determine if there is a synergistic effect by stacking resistance traits. Providing breeding programs with novel modes of resistance against both SCN and Fusarium virguliforme should help reduce the economic impact of these two organisms.

Procedures:
1. Variety and germplasm development.
Each year we will: hybridize selected parents in the fall and winter greenhouses, and summer growing seasons to produce progeny for this project; advance populations and lines lines for evaluation; plant and maintain field plots; collect agronomic, environmental, genomic and spatial data throughout the growing season; harvest plots in the fall; summarize and analyze data; plant and maintain fall and winter greenhouses and utilize winter nursery facilities to advance and increase populations and lines; and build training populations to discover new genes (markers), and optimize genomic and phenotypic selection models. Parents will be selected based on achieving the goals of producing progeny that will contribute to the genetic gain for soybean seed yield, increased genetic diversity in the US soybean gene pool, optimizing seed composition, and enhancing pest resistance and drought and heat tolerance. Breeding lines will be screened for resistance to multiple SCN populations representing the virulence diversity existing across Kansas. Throughout these breeding activities we will continue to stive to engage private breeders in collaborative activities to help them develop new materials for the farmer.

2. Develop, evaluate and implement breeding technologies.
We are currently testing a genomic selection model developed at the Univ. of Minnesota. This research involves developing lines and populations, build training sets and optimize models for Kansas growing conditions. Remote sensing technology will be combined with genomic selection to improve the speed and accuracy of identifying superior breeding material for both yield and seed composition.

3. Drought and heat tolerance.
We will evaluate commercial varieties and germplasm for response to drought and heat stress with a focus on seed yield and seed composition. Specific populations will be developed involving drought resistant parents to give rise to lines that will be evaluated in replicated field plots under dryland and irrigated conditions both in KS and regional trials. These efforts involve the discovery of new genes (markers) that can facilitate the incorporation on newly discovered genes into high-yielding backgrounds.

4. Transfer transgenic events into elite breeding lines.
For SCN resistant events, we will focus on incorporating transgenic traits into early MG4 lines with high yield potential from the KSU breeding program. Incorporating the transgenic traits into elite varieties with and without traditional sources of SCN resistance may help determine if there is any synergistic effect of multiple sources of SCN resistance. As events from the Dectes stem borer and the SDS resistance project are identified they will also be incorporated into appropriate elite varieties Presence of the transgene(s) in progeny will be determined using molecular markers. Lines will be rescreened for SCN resistance in greenhouse and field bioassays.

1. Develop soybean varieties and germplasm (Maturity groups 3, 4 and 5) for on-farm production and use as genetic resources for other breeders with public or private breeding programs, focusing on traits including:
a. seed yield
b. high oleic and low linolenic soybean oil,
c. desirable levels of protein and oil, and
d. stacked traits, including Soybean Cyst Nematode and Soybean Sudden Death Syndrome resistance, optimal protein and oil composition, and abiotic stress tolerance.
2. Improve genetic gain through the development, evaluation and implementation of breeding technologies including marker assisted selection, genomic selection and phenomics.
3. Evaluate, identify and develop germplasm with improved drought and heat tolerance.
4. Transfer desirable transgenic events into elite breeding lines.

• Varieties and germplasm in MGs 3 through 5 developed from this program can be used by private and public soybean breeders to develop new varieties. Some releases can be used directly by farmers for commercial production.
• Germplasm exchange with private and public breeding programs.
• Genomic information and improved techniques to develop improved soybean varieties.
• Extension publications, news releases, and experiment station reports, field days, extension meetings and tours will be used to share the results of this project with stakeholders.
• Web pages used to disseminate information on new releases and germplasm.
• Improved recommendations for appropriate management strategies.
• Peer reviewed publications or patents.
• Trained undergraduate, graduate and post-doctoral students.

Update:
September 2024 Progress report

We completed the release and licensing of two new soybean varieties, KS4323NS and KS4423NS.

During the summer of 2023, experimental lines in maturity groups III-V are being tested at six breeding nurseries located throughout Kansas.

We are evaluating 27 Conventional K-lines in National Regional trials, Uniform Tests (UT), this year in maturity groups III through V.

We are increasing two conventional varieties (early MG IV) for possible release in 2024.

The Spring greenhouse F1s from backcross populations were harvested in June and seeds incorporated into the summer crossing block which was planted in May through June.

Our field trials involve the evaluation of more than 7000 experimental K-lines and another 900+ experimental lines/plant introductions from cooperative trials in over 13,000 plots.

On 5/22 planted tests at Manhattan on dryland Field HO consisting of: elite breeding lines in 275 plots; 16 entries in a commercial variety test in 64 plots; and 45 K-lines in seed increase plots.

On 5/23 planted tests at Manhattan on dryland Field F1 consisting of: 240 KA entries in 480 plots; 1320 Kansas Preliminary (KP) yield plots; 5700 progeny rows; 280 elite breeding lines in 677 plots; 230 plant introductions in 690 yield plots and elite breeding lines in 275 plots.

On 5/24 planted tests at Ottawa consisting of: 130 KA entries in 260 plots; and 135 UT entries in 330 plots.

On 6/5 planted tests at McCune consisting of: 85 KA entries in 170 plots; 137 UT entries in 327 plots; and 546 Kansas Preliminary (KP) yield plots.

On 6/6 planted tests at Pittsburg consisting of: 110 KA entries in 220 plots; and 180 UT entries in 327 plots; and 546 Kansas Preliminary (KP) yield plots.

On 6/20 and 6/21 planted tests at Manhattan Field W consisting of: 2460 Kansas Preliminary (KP) yield plots; 205 KA entries in 410 plots; 1300 elite and drought germplasm in 3000 plots; and F4 populations for single plant selection.

Remote sensing projects to produce models that accurately predict relative seed yield, relative maturity and leaf wilting continue this summer. Drone flights began at V4, with one or two flights scheduled every week. Through August, over 165,000 data points for reflectance and canopy temperature have been collected on yield plots at three locations.

We completed our 2023 crossing season with over 100 different populations created. A detailed list of the populations will be included in the final report after the successful crosses are harvested.

We continue to screen our breeding material and the entries in the Kansas Soybean Variety Performance Tests to Race 3 and Race 4 SCN populations. Results of the evaluations will be available at the end of the growing season. Two hundred forty soybean breeding lines have been screened in replicated trials for resistance to three SCN populations. A total of 1,440 plants have been evaluated so far. Screening of soybean performance test entries is in progress. SCN populations include HG Type 7, which does not reproduce on PI 88788 or Peking resistance sources, HG Type 2.5.7, which reproduces on the PI 88788 resistance source, and HG Type 1.2.3.5.6.7, which reproduces on both resistance sources.

Updated April 17, 2024:

View uploaded report

“Breeding soybean to improve climate and disease resilience and compositional quality”

Principal Investigators: Schapaugh, W. - Agronomy
Todd, T. - Plant Pathology
Harold Trick – Plant Pathology
Kansas State University, Manhattan, KS

Outcomes of research on variety development, SCN resistance, genetic gain, drought, and high-throughput phenotyping, FY 24

Variety development and Germplasm Development
This project enabled the development of over 100 new breeding populations, and advancement of over 300 populations in the F1, F2, F3, F4 and F4:5 generations. Parents used to create these populations were selected for their yield potential, drought tolerance, herbicide resistance (Roundup Ready 1 and STS), seed protein content, oil composition, disease resistance (primarily SCN and Soybean Sudden Death Syndrome), and genetic diversity.

Nearly 9,000 genotypes were evaluated in over 16,000 plots in Kansas in 2023. Over 1200 K-lines were evaluated in our preliminary trials. Over 232 K-lines were evaluated in our KS advanced yield trials. Over 460 (including 25 K-lines) breeding lines from programs across the country were evaluated in USDA Uniform and other cooperative yield. Over 1,200 genotypes, (experimental breeding lines and plant introductions) were evaluated in our drought, remote sensing, and diversity yield trials.

Funding from this project did not result in releases of any new varieties or germplasm in 2024, but several varieties and germplasm are under increase for possible release in 2024 and 2025.

Germplasm
Cooperative work with the Univ. of Arkansas, Univ. of Georgia and the USDA continued in the development of a set of several maturity group IV non-nodulating isolines and the nodulating recurrent parent. A release manuscript for publication in the Journal of Plant Registrations is under development, with the first releases occurring in 2024. Information of this work has been shared at national meetings and we have supplied preliminary releases to a number of researchers throughout the US to study nitrogen fixation in soybean.

SCN resistance
Breeding lines: Soybean resistance to SCN was evaluated in replicated screening trials for 240 Kansas Agricultural Experiment Station (KAES) breeding lines in 2023. Among early-maturing MG III-IV cultivars, 28% and 22% of lines were rated as resistant or moderately resistant to the HG Type 7 and HG Type 2.5.7 SCN screening populations, respectively, while only 3% were rated as resistant or moderately resistant to the HG Type 1.2.3.5.6.7 SCN screening population. Among later-maturing MG IV-V cultivars, 61% of lines were rated as resistant or moderately resistant to the HG Type 7 SCN screening population, while 22% and 17% were rated as resistant or moderately resistant to the HG Type 2.5.7 and HG Type 1.2.3.5.6.7 SCN screening populations, respectively. Female indices on breeding lines that were resistant or moderately resistant to the HG Type 7 population averaged 47 for the HG Type 2.5.7 and HG Type 1.2.3.5.6.7 populations.
Genetic gain
Following three generations of selection where we used genomic predictions for yield, genetic variation, and seed composition to select, intermate and rapidly cycle F1 plants, progeny from the initial base population and the rapid cycling generations were evaluated at three locations in 2022 and 2023 for seed yield, maturity, lodging, plant height, and seed protein and oil. We plan to evaluate the selections in 2024 and then use the three years of data to characterize the effectiveness of the genomic selection and rapid cycling methodology. We also used the same genomic prediction model to create populations from elite public breeding lines that are predicted to produce superior progeny and have a negligible negative correlation between seed yield and seed protein content. The progeny of these crosses will be evaluated for seed yield in replicated field trials in 2024.

Biotech traits
We have focused efforts on crossing two of our transgenic lines (hpRNAi-Y25 and hpRNAi-Prp17) for SCN resistance into Kansas adaptive lines that are both susceptible and moderately resistant to SCN Hg type 7 as well as crossing the two transgenes together. Currently we have F3 generations to test. We are also introducing hpRNAi-cytoP450 and hpRNAi-Lacc2 genes for Dectes Stem Borer tolerance in KS adaptive lines.

Abiotic stress
Data analysis continued on a field experiment conducted in 2020, 2021 and 2022 to evaluate the response of a diversity panel of over 300 genotypes to heat stress. Phenotypic data collected included: days to physiological maturity (R8), seed quality, seed yield (kg/ha), seed weight (100 seed weight in grams), lodging, plant height (cm), and seed composition (oil, protein linoleic, linolenic, palmitic, stearic, raffinose, and sucrose concentrations). Genome-Wide Association and Genomic Prediction studies were conducted to identify genomic regions responsible for the phenotypic traits with the goal of developing improved heat-tolerant germplasm. These analyses should be completed in 2024.

Opportunities for training and professional development
Five undergraduate students completed internships with the breeding project during the summer of 2023. Two graduate students worked on remote sensing and machine learning for research studies related to this project. Two post-docs on this project continued work on genomic evaluation and physiological response to stress.

Dissemination of results
Extension publications, news releases, radio interviews, experiment station reports, field days, extension meetings and tours are used to share the results of this project. Web pages have been developed to disseminate information on new releases and germplasm and pests. Distribution of results of genotype characterization for resistance published online. Distribution of SCN survey results to cliental will provide much-needed information for making informed decisions by producers regarding variety selections for SCN management and by soybean breeders for the development of varieties with improved levels of resistance. Effects of high temperature stress on soybean, and evaluations of host plant resistance were published at scientific conferences and published in peer-reviewed publications. Publications in 2023 included:

Journal articles
Menke, Ethan, Clinton J. Steketee, Qijian Song, William T. Schapaugh, Thomas E. Carter Jr., Benjamin Fallen, and Zenglu Li. 2024. Genetic mapping reveals the complex genetic architecture controlling of slow canopy wilting in soybean PI 471938. Theoretical and Applied Genetics https://doi.org/10.1007/s00122-024-04609-w

Jenny Koebernick, Anne M. Gillen, Robert Fett, Sejal Patel, Ben Fallen, Vince Pantalone, Grover Shannon, Zenglu Li, Andrew Scaboo, William Schapaugh, Rouf Mian, Quentin D. 2024. Soybean test weight in relation to genotype, environment, and genotype × environment interaction in the Southern United States. Agronomy J. https://doi.org/10.1002/agj2.21551

Abstract
U.C. Jha, S. Saffi, D. Chatti, W.T. Schapaugh, R. Welti, and P.V.V. Prasad. 2024. Transcriptome and Lipidome Dynamics of Soybean Floral Buds Under Heat Stress. American Society of Plant Biologists (ASPB) Midwest Section Meeting, March 16-17, 2024, at Purdue University in West Lafayette, Indiana

• Combining resistances to important pathogens, optimizing seed composition (high oleic oil), enhancing genetic diversity and improving abiotic stress (drought and heat) resistance will help enable public and private breeding programs to sustain improvement of resilient soybean varieties able to meet the production and quality of soybean products needed in the marketplace.
• Focusing on the development and use of new technologies will help improve genetic gain across public and private breeding programs.
• Maintaining soybean yield and a balanced seed composition under high temperature and drought stress will help develop improved post-flowering drought and heat-stress resilient varieties and strengthen the improvement pipeline between untapped soybean germplasm and commercial soybean varieties.
• Providing breeding programs with novel modes of resistance against both SCN and Fusarium virguliforme using transgenic approaches should help reduce the economic impact of these two organisms.