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 2021, experimental lines in maturity groups III-V will be tested at eight breeding nurseries located throughout Kansas.

We are evaluating 33 Conventional K-lines in the National Regional trials this year in maturity groups III through V.

We are increasing two conventional varieties (one late MG IV and one MG V) for possible release in 2021. Both lines have STS and SCN 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 1600 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 5/26 and 6/4 planted tests at Manhattan Field W consisting of: 46 Commercial and public entries in 184 plots, 1600 Diversity and drought entries in 2800 plots, 180 Kansas advanced (KA) entries in 360 plots, 1200 Kansas Preliminary (KP) yield plots, 160 Uniform Test (UT) entries in 390 plots, and our F3 and F4 populations and seed plots.

On 6/9 planted tests at Manhattan Field F1 consisting of: 8000 F4:5 line progeny rows, 770 plant introductions in 1500 plots for Dectes Stem Borer evaluations, 300 entries in a diversity panel for evaluating genotypic response to heat in 1500 plots, and the 2021 crossing block consisting of 53 different parents.

On 5/13 planted tests at Riley consisting of: 50 Commercial and public entries in 200 plots, 180 KA entries in 360 plots, 1200 KP yield plots, and 70 Diversity entries in 140 plots.

On 6/14 planted tests at Salina consisting of: 47 commercial and public entries in 188 plots.

On 6/10 planted tests at Ottawa consisting of: 120 KA entries in 240 plots, and 80 UT entries in 240 plots.

On 7/8 planted tests at Pittsburg consisting of: 44 commercial and public entries in 180 yield plots, 450 KA and KP entries in 600 plots and 100 UT entries in 280 plots.

On 6/16 planted tests at McCune consisting of: 39 commercial and public entries in 160 yield plots 450 KA and KP entries in 600 plots and 100 UT entries in 280 plots.

Since July, we have captured spectral reflectance data on over 8000 progeny rows and 300 yield plots at Manhattan and Riley 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 at Riley and Manhattan.

Rainfall totals were above average through July, but rainfall in August was well below normal at most locations. Because of these conditions drought stress began to appear at our test sites in August, especially at Manhattan. We have been able to capture 3 to 6 dates of wilting ratings on entries in maturity groups III through V. In total, we have collected over 10,000 visual wilting ratings on nearly 2000 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 2021 crossing season with over 90 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:
• 250 advanced breeding lines have been screened against three HG Types.
• Recent KAES soybean germplasm releases have been screened against six HG Type 2 populations.
• 81 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 22

Variety 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 11,000 genotypes were evaluated in over 19,000 plots in Kansas in 2021. Over 1400 K-lines were evaluated in our preliminary trials. Over 190 K-lines were evaluated in our KS advanced yield trials. Over 500 (including 20 K-lines) breeding lines from programs across the country were evaluated in our KS Uniform Tests and Uniform Preliminary yield trials. Over 8,900 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 KS4822NS (late maturity group (MG) IV, cyst nematode resistant, STS tolerant). This variety can be used for commercial production and as a parent by plant breeders for the development of new varieties.

SCN resistance
Breeding lines: Soybean resistance to HG Types 7, 2.5.7, and 1.2.3.5.6.7 was evaluated in replicated screening trials for ~240 preliminary and advanced breeding lines. Approximately 40% of breeding lines displayed moderate or better levels of resistance (FI = 30) to the HG Type 7 population, while only 3-8% of breeding lines displayed moderate or better levels of resistance (FI = 30) to HG Type 2 populations. Seven lines (~3%) were resistant or moderately resistant to all screening populations, and female indices for two of these averaged < 5. Kansas Soybean Performance Test: Soybean resistance to SCN was evaluated in replicated screening trials for 81 entries in the Kansas Soybean Variety Performance Test (KSVPT). Only 37% of KSVPT entries could be classified as resistant to moderately resistant to the HG Type 7 population, while only 5-10% could be classified as resistant or moderately resistant to the HG Type 2 populations. Four of the ten entries with the lowest female indices for the HG Type 7 population were KAES entries. No entries were resistant or moderately resistant to all SCN screening populations. Female indices for the HG Type 7 population were reasonably predictive of FI for the HG Type 2 populations, confirming that most KSVPT entries shared a common source of resistance (PI 88788).

Genetic gain
In 2021, we used genomic predictions for yield, genetic variation, and seed composition to select, intermate and rapidly cycle F1 plants to achieve three cycles of selection in one calendar year. Progeny from the initial base population and the rapid cycling generations are now being increased in a winter nursery to produce seed for planting in replicated field trials 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 compared with progeny produced from our standard selection process in the future.

High-throughput phenotyping to increase genetic gain and improve evaluations under drought stress
We continue to develop models utilizing canopy reflectance and canopy thermal properties to estimate relative soybean maturity, seed yield, drought stress, and disease resistance. Entries in our 2017, 2018 and 2019 progeny rows selected based on remote sensing criteria where slightly higher yielding than random selections in our 2018, 2019 and 2020 preliminary yield trials. This information is being summaried and will be submitted for publication.

In 2021, all trials experienced drought stress through August and September. Significant differences in wilting ratings in our breeding material were noted among the test entries. Phenotypic differences in wilting ratings will support the development of drought tolerance varieties and further our understanding of the genetic basis of drought stress. In additional to taking visual wilting ratings, efforts continue to refine techniques to characterize drought stress using high throughput phenotyping with drones.
Opportunities for training and professional development
One graduate student working on objectives related to this project in Agronomy completed his M.S. degree in 2020, and one additional student in Bio and Ag Engineering worked cooperatively using the field plots developed and evaluated through this project also completed an M.S. degree. Currently, one student in Agronomy is pursuing a Ph.D. degree focusing on the application of remote sensing technology in breeding and one M.S. student in Plant Pathology is evaluating the use of transgenic material for Dectes control.

Dissemination of results
Peer-reviewed publications, extension publications, news releases, and 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 are 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. Publications in 2021 included:

Aguirre-Rojas, L.M.; Buschman, L.L.; McCornack, B.; Schapaugh, W.T.; Scully, E.D.; Zhu, K.Y.; Trick, H.N.; Smith, C.M. 2021. Inheritance of Antibiosis Resistance to the Dectes Stem Borer, Dectes texanus, in Soybean PI165673. Agronomy 2021, 11, 738. https://doi.org/10.3390/agronomy11040738.

Walta, Dylan. 2021. Evaluation of drone imagery as a method for selection criteria in soybean breeding. M.S. Thesis, Kansas State University.

Singh, Asheesh K., Arti Singh, Soumik Sarkar, Baskar Ganapathysubramanian, William Schapaugh, Fernando E. Miguez, Clayton N. Carley et al. "High-Throughput Phenotyping in Soybean." In High-Throughput Crop Phenotyping, pp. 129-163. Springer, Cham, 2021.