1. Variety and germplasm development.
Each year we will develop a minimum of 100 new populations involving elite and exotic parents to produce new MG3 through 5 progeny to meet program objectives. Parents will be selected based on achieving the goals of producing progeny with competitive seed yield, increased genetic diversity in the US soybean gene pool, optimal seed composition, multiple pest resistance, high oleic oil and/or drought tolerance. Progeny will be advanced using winter nursery facilities in Puerto Rico to speed development. Each season 6,000 to 10,000 new F4-derived lines will be evaluated in progeny rows followed by replicated testing in Kansas and throughout the US in the Uniform Soybean Tests, the Northern Regional Soybean Cyst Nematode Tests, and the Diversity Cooperative Tests. Lines will be evaluated under both dryland and irrigation conditions in replicated plots in KS and the US to characterize performance over a wide range of environments. Lines will be evaluated for resistance to several pathogens, including soybean cyst nematode, Phytophthora root rot, soybean sudden death syndrome (SDS), and stem canker, depending upon the population. Seed composition will be measured using near infrared reflectance in our KSU lab, and in the USDA-ARS, National Center for Agricultural Utilization Research at Peoria, IL. Release decisions will generally be based on information from 30 to 50 environments. Time to complete one cycle of selection (from the time the crosses are made until release) will be about 8 years. Throughout these breeding activities we will continue to try and engage provate breeders in collaborative activities to help them develop new materials for the farmer.

2. Implement and evaluate breeding technologies.
Through support from the North Central Soybean Research Program (NCRSP), a genomic selection model has been developed by the Univ. of Minnesota soybean breeder, Aaron Lorenz. We will use this model to implement selection of genotypes. This process will involve intermating a population of F1 genotypes to produce 100 to 130 new F1s per generation. Genomic selection will identify progeny to use in intermating. This process will be repeated 3 times per year (once in the summer, once in the fall greenhouse, and once in the spring greenhouse). Evaluation of this selection and intermating process will be accomplished by producing F4 derived lines from each generation for evaluation in replicated yield trials in 2022 and later. We will also continue our efforts to use remote sensing technology to improve the speed and accuracy of identifying superior breeding material. We will focus this project in using remote sensing during the progeny row stage when selection is generally based on visual evaluations. Selections based on thermal and spectral data will be compared in replicated tests with visual and random selections from progeny rows to determine if gain from selection has been improved using this technology.

3. Screen for Dectes stem borer resistance.
Initially screen 500 accessions for stem breakage on a 1-5 scale, presence of stem girdling and presence of stem borer larva in year one (2020) after plant maturity. Screening will be conducted at one location (Manhattan) in replicated (2 reps) short-row plots where incidence of plants infested with stem borer often exceeds 60%. About 25% of the lines evaluated in year one will be advanced for further evaluation in year two in a three replicate test. Antixenosis and antibiosis screening will be conducted at one location in replicated (4 reps) short-row plots. Characterizing antixenosis and antibiosis is labor intensive and time consuming, so we will limit screening to 20 accessions at a time for evaluation. Three to five plants per plot will be scored for oviposition punctures and the number of live larvae in the stem as described by Niide et al. (2012). In the second year a new set of 20 accessions will be screened using the same procedures.

4. Breed transgenic events into elite breeding lines.
Transgenic lines will be crossed into elite varieties with and without traditional sources of resistance. Currently we are incorporating the transgenes into KS4117Ns, and early MG4 variety with excellent yield potential and conventional resistance to SCN, and K12-2333, another MG4 line with excellent yield potential but susceptible to SCN. Based on screening results for 2019, additional parents will be selected to incorporate the transgene(s). 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. Breed valuable maturity group (MG) 3, 4 and 5 commodity and specialty soybean varieties for use as genetic resources for companies and other public programs that develop varieties and for direct on-farm production.

2. Implement and evaluate breeding technologies.

3. Screen diverse soybean germplasm for resistance to Dectes stem borer stem breakage, girdling and oviposition punctures.

4. Breed transgenic events into elite breeding lines.

• Varieties and germplasm in MG 3–5 developed from this program can be used by private 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.

• 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.

• Web pages used to disseminate information on new releases and germplasm.

• Improved recommendations for appropriate management strategies.

• Peer reviewed publications.

• Trained graduate students.

Update:
During the summer of 2022, experimental lines in maturity groups III-V will be tested at eight breeding nurseries located throughout Kansas.

We are evaluating 60 Conventional K-lines in the National Regional trials this year in maturity groups III through V.

We are increasing four conventional varieties (MG IV) for possible release in 2023. All lines have SCN resistance and three lines possess STS resistance.

The Spring greenhouse F1 of backcross populations was harvested and seeds incorporated into the summer crossing block which was planted in June.

The F1 generation in the Puerto Rico winter nursery was harvested, and the F2 generation was returned to Kansas and the F3 generation planted in June.

Our field trials currently involve the evaluation of about 3200 experimental K-lines and another 3200 experimental lines/plant introductions from cooperative trials in over 20,000 plots.

Planting dates of our sites included:

On 6/14 planted tests at Salina consisting of: 40 entries for a commercial drought resistance trial in 275 plots; 50 genotypes in 1379 plots from breeding programs across the Midwest to evaluate performance under drought; and 175 KA entries in 442 plots.

On 6/15 planted tests at Manhattan irrigated Field T consisting of: 620 Kansas Preliminary (KP) yield plots; 8000 progeny rows; and 1600 experimental and germplasm lines in 3200 plots.

On 6/16 replanted tests at Ottawa consisting of: 175 KA entries in 350 plots; 86 UT entries in 222 plots; and 726 Kansas Preliminary (KP) yield plots.

On 6/17 planted tests at Manhattan dryland Field B consisting of: 275 KA entries in 550 plots; 1400 Kansas Preliminary (KP) yield plots; and 385 K-lines and lines from other programs 918 plots.

On 6/20 replanted heat evaluation trials at Manhattan consisting of 20 germplasm and elite lines for evaluation under heat tents.

On 6/21 planted tests at Manhattan dryland Field F consisting of: KP entries in 620 plots; our F3, F4 populations and crossing block.

On 6/22 planted tests at McCune Field consisting of: 100 KA entries in 200 plots; 540 Kansas Preliminary (KP) yield plots; and 130 UT entries in 410 plots.

On 6/23 panted tests at Pittsburg dryland Field consisting of: 205 KA entries in 410 plots; 1056 Kansas Preliminary (KP) yield plots; and 130 UT entries in 410 plots.

Since July, we have captured spectral reflectance data on over 1900 yield plots in three environments to produce models that accurately predict relative seed yield, relative maturity and drought stress response. We have used spectral reflectance data to characterize plant population and plant stand, and throughout August captured spectral reflectance data to compare with our leaf wilting scores observed in the dryland plots near Manhattan.

Rainfall totals were above average through June, but July and August rainfall was well below normal at most locations. Because of these conditions drought stress began to appear at our test sites. We have been able to capture 10 dates of wilting ratings on entries in maturity groups III through V. In total, we have collected over 15,000 visual wilting ratings on 1500 genotypes. During the evaluations growth stages ranged from late vegetative to R5 depending on the date of evaluation and maturity of the entry. Severe wilting was noted in several entries with most with some entries experiencing severe stress and premature senescence.

We completed our 2022 crossing season with over 80 different populations created. A detailed list of the populations will be included in the final report after the successful crosses are harvested.

SCN screening activities:
• 300 advanced breeding lines have been screened against three HG Types.
• Recent KAES soybean germplasm releases have been screened against six HG Type 2 populations.
• 60 Kansas Soybean Performance Test entries are being screened against two HG Types in replicated trials.

Update:

View uploaded report

“Develop valuable soybean varieties and germplasm for use as genetic resources for companies and for direct on-farm production”

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 23

Variety development
This project enabled the development of over 80 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 10,000 genotypes were evaluated in over 21,000 plots in Kansas in 2022. Over 1600 K-lines were evaluated in our preliminary trials. Over 292 K-lines were evaluated in our KS advanced yield trials. Over 550 (including 59 K-lines) breeding lines from programs across the country were evaluated in USDA Uniform and other cooperative yield. Over 1,500 genotypes, (experimental breeding lines and plant introductions) were evaluated in our drought, remote sensing, and diversity yield trials.

Funding from this project enabled the development and release of KS4323NS and KS4423N from the Kansas Agricultural Experiment Station. These are high-yield, early maturity group IV varieties. The lines are being licensed for commercial production and for use in breeding.

SCN resistance
Breeding lines: Soybean resistance to SCN was evaluated in replicated screening trials for 275 breeding lines in 2022. Approximately 50% of 2022 lines were rated as resistant or moderately resistant to the HG Type 7 SCN screening population, while 9% were rated as resistant or moderately resistant to the HG Type 2.5.7 SCN screening population. Three soybean lines were resistant to both SCN populations, while 17 lines were moderately resistant to both SCN populations. Kansas Soybean Performance Test: Soybean resistance to SCN was evaluated in replicated screening trials for 25 KAES entries and 28 non-KAES entries in the Kansas Soybean Variety Performance Test (KSVPT). Evaluations involved SCN populations that varied in their virulence to the common resistance source PI 88788. Six KAES entries and 10 non-KAES entries were resistant (FI < 10) or moderately resistant (FI = 30) to the HG Type 7 population, while only three KAES entries and one non-KAES entry were resistant or moderately resistant to the GH Type 2.5.7 population. Female indices for the HG Type 7 population were strongly predictive of FI for the HG Type 2.5.7 population, confirming that most KSVPT entries shared a common source of resistance (PI 88788). Female indices for the HG Type 7 population were similarly predictive of FI for the HG Type 1.2.3.5.6.7 population for non-KAES entries but not for KAES entries, reflecting the greater prevalence of resistance sources other than PI 88788 (e.g. Peking) in the KAES entries. No entry had a FI = 30 for all three HG Type 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 for seed yield, maturity, lodging, plant height, and seed protein and oil. These progeny will be evaluated again in 2023 at three locations. Results of these field trials will be used in 2023 and 2024 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 in progeny rows in 2023, with plans to evaluate the progeny in replicated field trials in 2024.

Opportunities for training and professional development
Four undergraduate students completed internships with the breeding project during the summer of 2022. One graduate student working on objectives related to this project has completed her M.S. degree requirements and will receive her diploma in May 2023. One post-doc on this project completed work on a manuscript, which was published, and moved to a position in private industry. One additional post-doctoral scientist has joined the team to focus on the applying remote sensing and genomic selection technology to our breeding project.

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 2022 included:

Alencar Xavier, William Beavis, James Specht, Brian Diers, Rouf Mian, Reka Howard, George Graef, Randall Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah McHale, Perry Cregan, Qijian Song, Miguel Lopez, William Muir, Katy Rainey. (2022). Soybean Nested Association Mapping Dataset. https://scholar.google.com/scholar?oi=bibs&cluster=5938341747497625123&btnI=1&hl=en.

Ayalew, H., Schapaugh, W., Vuong, T., & Nguyen, H. T. (2022). Genome-wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments. The Plant Genome, 15, e20268. https://doi.org/10.1002/tpg2.20268.