Project Details:

Integrating Germplasm Evaluation, Genetic Engineering, Breeding and High-Throughput Phenotyping to Improve Sustainability of Soybean Production

Parent Project: Integrating Germplasm Evaluation, Genetic Engineering, Breeding and High-Throughput Phenotyping to Improve Sustainability of Soybean Production
Checkoff Organization:Kansas Soybean Commission
Categories:Breeding & genetics
Organization Project Code:1930
Project Year:2019
Lead Principal Investigator:William Schapaugh (Kansas State University)
Co-Principal Investigators:
Tim C. Todd (Kansas State University)
Harold Trick (Kansas State University)
Keywords: Breeding, genetic diversity, genetic gain, Remote Sensing, Soybean

Contributing Organizations

Funding Institutions

Information and Results

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Project Summary

This project will develop new soybean germplasm with superior traits or unique combinations of traits. Superior genetics represent the foundation for increasing yield and protecting yield from abiotic and biotic stresses. We will focus on the development of Kansas adapted germplasm in conventional (non-gmo) backgrounds to minimize intellectual property rights issues, but we will also develop and evaluate transgenic material with potential to provide unique solutions for biotic stress resistance.

Advances in genomics and high-throughput phenotyping can improve the speed and accuracy of identifying superior breeding material and permit the selection of traits that have not been evaluated on a widespread basis. However, to utilize this technology robust models must be developed. This project will produce new genotypes and evaluate those genotypes in field evaluations to collect agronomic data used in the development of genomic and remote sensing selection tools. Evaluations will consist of experimental breeding lines, exotic germplasm, elite breeding lines, and advanced lines in the Uniform Soybean Performance Tests. In-season soybean canopy thermal and spectral profiles will be collected on breeding plots with a small unmanned aircraft system (sUAS). Genotypes possessing extremes in phenotypes (such as yield potential, disease resistance, wilting and canopy temperature) will be included in the evaluations. Genotypic selections for relative seed yield, relative maturity, and wilting scores based on the spectral and thermal data will be evaluated for effectiveness to increase genetic gain.

Limited genetic variation is present in the commercial soybean gene pool. Without adequate levels of “good” genetic variation, progress from selection can slow, or even stop. Searching the germplasm collection for beneficial genetic variation will help maintain, or enhance improvements made through breeding. In an attempt to broaden the genetic base of soybean, we will screen hundreds of different germplasm accessions (exotic germplasm) not contributing to the genetic diversity of US soybean varieties for seed yield, maturity, lodging, shattering, seed composition, and stress response. Genotypic data is also being collected on these accessions in support of Objective 1. The best exotic germplasm will be used as parents to create new populations and varieties for evaluation.

Over the last 85 years, protein levels in soybean have decreased about two percentage points. This trend will likely continue and negatively impact the value of soybean meal unless better efforts are made to focus on composition while improving seed yield. Through support of a USB project we are utilizing exotic sources to develop breeding lines with increased protein and yield with the goal of developing varieties capable of producing 48% protein meal and about 11 pounds of oil per bushel.

High oleic soybean represents a value-added commodity for some soybean producers. Conventional germplasm owned jointly by the USDA and the Missouri Soybean Merchandizing Council is available with high oleic acid. We are using this germplasm to incorporate the high-oleic trait into Kansas adapted material through backcrossing and forward crosses.

In previous funding from KSC, NCSRP, and USB we have produced stable transgenic lines showing enhanced resistance to SCN. Current KSC research is evaluating alternative methods for SDS, SCN and RKN resistance. Together with stable lines already produced, we will move these traits to elite breeding lines that have traditional resistances and evaluate the new genotypes in field evaluations for effectiveness to limit SCN reproduction.

SDS, caused by Fusarium virguliforme, consistently ranks within the top-five yield reducing soybean diseases. Even with the development of a recent seed treatment that reduces disease severity, higher levels of resistance are needed for effective management and maximum seed yields. SDS resistance is most effective when combined with SCN resistance. Using SDS resistant lines identified from previous NCSRP supported breeding efforts we will develop varieties with SDS and SCN resistance.

Project Objectives

1. Provide high quality germplasm and phenotypic data for development of genome selection tools
2. Identify new sources of germplasm (exotic) and genes that improve yield and seed composition of elite U.S. soybean varieties
3. Develop superior varieties and germplasm using new sources of germplasm with improved yield under the extreme range of environmental conditions in KS
4. Develop high yielding varieties and germplasm lines with desirable levels of protein and oil
5. Develop non-GMO, high oleic soybean varieties and germplasm lines
6. Breed transgenic events into elite breeding lines
7. Develop superior SDS resistant varieties and germplasm lines using new sources of resistance
8. Develop soybean varieties and germplasm with stacked traits, including SCN and SDS resistance, optimal protein and oil concentrations, and stress tolerance
9. Develop enhanced high throughput technology to rapidly identify genotypes which have the desired disease resistance, yield potential, drought resistance or heat stress characteristics

Project Deliverables

Varieties and germplasm in maturity groups III through V developed.

Varieties released to farmers for commercial production.

Varieties and germplasm for use by other public and private breeding programs.

Information on genomic selection and high-throughput phenotyping shared with the soybean breeding community.

Characterization of the effectiveness of new transgenic events to provide resistance to SCN.

Extension publications, news releases, and experiment station reports, field days, extension meetings and tours used to share the results of this project.

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

Peer reviewed publications.

Progress of Work

Updated July 12, 2019:

Principal Investigators: Schapaugh, W. - Agronomy
Todd, T. - Plant Pathology
Harold Trick – Plant Pathology

We completed the release and licensing of the new soybean variety KS4919N this quarter.

During the summer of 2019, experimental lines in maturity groups III-V will be tested at nine breeding nurseries located throughout Kansas.

We will be evaluating the 27 Conventional K-lines and one glyphosate line in the National Regional trials this year in maturity groups III through V.

We will be increasing three conventional varieties (one early MG IV, one late MG IV and one MG V) and one glyphosate resistant MG IV line for possible release in 2020. All four 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 is being harvested for return to Kansas, then planting the F3 generation in June.

Plans for our field trials currently involve the evaluation of more than 7200 experimental K-lines and another 600+ experimental lines/plant introductions from cooperative trials in over 10,000 plots. Planting was delayed this spring by wet weather and we did not begin planting until the end of May. To date, six of our nine sites have been planted including:

On 5/31 panted tests at Manhattan dryland Field W consisting of: 205 KA entries in 410 plots; 1056 Kansas Preliminary (KP) yield plots; and 4 drought tolerant germplasm entries in 20 plots.

On 6/3 planted tests at Ottawa consisting of: 90 KA entries in 180 plots; 139 UT entries in 328 plots; and 546 Kansas Preliminary (KP) yield plots.

On 6/4 planted tests at Riley consisting of: 115 Kansas Advanced (KA) entries in 230 plots; 1056 Kansas Preliminary (KP) yield plots; 70 Uniform Test (UT) entries in 185 plots and 25 Soybean Variety Performance Test (SVPT) entries in 100 plots.

On 6/5 planted tests at Manhattan irrigated Field V consisting of: 205 KA entries in 410 plots; 110 UT entries in 285 plots; 1056 Kansas Preliminary (KP) yield plots; 352 germplasm and high protein experimental lines in 704 plots; and some of our F4 populations for single plant selection.

On 6/7 planted tests at Salina consisting of: 77 entries for a commercial drought resistance trial in 308 plots; 670 genotypes in 1379 plots from breeding programs in MO, SC, AR, GA and KS for evaluation to drought; and 120 KA entries in 240 plots.

On 6/8 planted tests at Manhattan irrigated Field W/V consisting of: 6400 progeny rows.

On 6/10 planted tests at Manhattan dryland Field F consisting of: 120 KA entries in 240 plots; 100 KP entries in 300 plots; 571 UT entries in 637 plots; our F3 populations and some of our F4 populations.

We plan to continue our remote sensing projects this summer to produce models that accurately predict relative seed yield, relative maturity and leaf wilting.

Updated September 13, 2019:
We have conducted crossing and backcrossing from the RNAi transgenic lines to two Kansas cultivars, K11-2363B and K12-2333, respectively. So far we have completed 3 rounds of crossing and 1 round of backcrossing. The F2 seeds from crossing events (Prp17 X K11, Prp17 X K12, and Y25 X K12) have been increased and harvested. For K11XY25 and stacking two RNAi constructs (Y25 X Prp17, and Prp17 X Y25) into one transgenic line, we only have a few F1 seeds ready, and need to test these for the presence of the transgene. Seeds availability is shown in the following table:

Crossing (Female X pollinator) Crossing results
K11 X Y25 More F1 seeds to test
K11X Prp17 F2 available
K12 X Y25 F2 available
K12X Prp17 F2 available
Y25 X Prp17 More F1 seeds to test
Prp17 X Y25 More F1 seeds to test
* K11-2363B (mild resistance to SCN HG type7) and K12-2333 (mild tolerance)

We have done one round of backcrossing with either K11 or K12 as parent for positive F2 plants, and did get seed set. We need to grow these seeds and PCR test if the back cross was successful.

This summer we also have a field test for SCN with a few of our transgenic lines. We sampled a few plants in late July and found one line with a significant decrease (approximately 80%) in cysts compared to the non-transgenic control. We will be collecting seeds in the next quarter and test the progeny in greenhouse bioassays.

On 7/1 planted tests at Pittsburg consisting of: 85 KA entries in 170 plots; 137 UT entries in 327 plots; and 546 Kansas Preliminary (KP) yield plots.

On 7/5 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 7/15 planted our double-crop trial consisting of 33 entries in 132 plots near Pittsburg.

Since July we have captured thermal and spectral reflectance data on over 6000 progeny rows at Manhattan, and several thousand yield plots located at Ashland, Manhattan, Salina and Riley to produce models that accurately predict relative seed yield, relative maturity and drought stress response.

Rainfall totals have averaged about 50% greater than normal for most of the growing season. However, as pod-fill progressed, drought stress began to appear at our Salina location where we were able to capture one date of wilting ratings at R5.3 to R5.5 on the maturity groups III and IV commercial test and R2.0 to R3.0 on the maturity group V trial. Our dryland commercial trial near Manhattan of maturity groups III and IV has reached mid pod-fill, and has experienced mild drought stress with limited wilting observed. We will continue to take wilting ratings if the opportunity arises, and will follow through with collecting maturity, lodging, plant height and yield. Many of the varieties in this year’s tests were evaluated in 2018, so we should have contrasting environmental conditions to compare variety performance.

We completed our 2019 crossing season with over 250 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.

Updated December 12, 2019:

Principal Investigators: Schapaugh, W. - Agronomy
Todd, T. - Plant Pathology
Harold Trick – Plant Pathology

Progress Report: Third Quarter FY2020 (Sept 1 - November 30, 2019)

Over 300 new populations created this season were harvested. Most of these populations were advanced to the F1 generation currently growing in our winter nursery in Puerto Rico. About 100 of the populations were subjected to genomic prediction for intermating in our fall greenhouse. This is the first time in our program that genomic prediction has been used to help identify superior progeny for seed yield and high protein in the F1 generation. Further evaluation of this material will be made to evaluate the effectiveness of this breeding strategy. Over 50 F3 populations were advanced to the F4 generation during the summer of 2019.

We completed the 2019 harvest on 12/5 involving the evaluation of over 6000 experimental K-lines and another 600 elite experimental lines from other states field trials. Productivity and precision of the 2019 season was some locations were lost because of excessive rainfall. Data are being compiled for all K-lines and experimental lines from other experiment stations. Decisions on what lines to advance, increase, release, discard and use to create new populations will be finalized next quarter.

Data from our evaluation of over 100 commercial soybean varieties for Soybean Cyst Nematode (SCN) again two races in the greenhouse have been completed and analyzed. Results will be posted on the Agronomy Department’s Crop Performance Tests website. Over 1500 Kansas breeding lines have been screened for SCN resistance the past 6 months (Figure 1). A majority of our preliminary lines possessed resistance to SCN, while about 20% of our advanced lines possessed moderate to high levels of resistance. These results will be used to make decisions on selections for 2020.

Working with Shrada (BAE) we captured over 25,000 spectral images on breeding plots located near Manhattan and Salina. We analyzed those images from our progeny rows to select genotypes for evaluation in yield trials in 2020, and are analyzing images from yield trials to characterize drought response, seed yield, and plant maturity. Preliminary evaluation of the effectiveness of selections in progeny rows has shown that selections based on canopy coverage using spectral images, spectral reflectance and visual evaluations can identify higher yielding lines than random selection. We are continuing to evaluate this methodology in a robust manner.

About 140 plant introductions in MG’s 3 and 4 were grown in Manhattan, KS in replicated plots. Maturity, lodging, plant height, shattering, dates of R1, R3 and R3 growth stages, seed yield and spectral reflectance data were collected on the genotypes. Data will be summarized along with information from other states to identity unique germplasm which could benefit breeding efforts across the country.

Final Project Results

Benefit to Soybean Farmers

New varieties which can be used directly by farmers for commercial production.

New germplasm and varieties available to public and private breeding programs to develop new varieties, including new transgenic varieties.

Identification of unique germplasm accessions possessing beneficial traits which can be used by other public and private breeding programs to develop new varieties, including new transgenic varieties.

Advances in genomics and high-throughput phenotyping which can be utilized by other public and private breeding programs to increase genetic gain.

New transgenic germplasm which may provide a better solution to protect against biotic stress than can be achieved through alternative approaches.

Enhanced competitiveness of U.S. soybean producers.

Performance Metrics

Project Years