Project Details:

Title:
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
NCSRP, USB, QSSB Project Code:1830
Project Year:2018
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

In support of an NCSRP project, we will use this project to 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 exotic germplasm, elite breeding lines, and advanced lines in the Uniform Soybean Performance Tests.

In an attempt to broaden the genetic base of soybean, we are screening hundreds of different germplasm (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 for evaluate. Each year, we will develop approximately 40 populations involving exotic parents or lines derived from exotic germplasm with high yielding, elite varieties. These progeny will be evaluated in both dryland and irrigation field conditions in KS and the US and characterize resistance to soybean cyst nematode (SCN) and Soybean Sudden Death Syndrome (SDS).

Through a USB project we are utilizing exotic sources to breed for increased protein and yield. We will also target oil concentrations in our work in KS to develop high yielding soybean varieties with desirable levels of protein and oil. Each year, we will develop approximately 15 populations involving exotic parents or lines derived from exotic germplasm with high yielding, elite varieties. These progeny will be evaluated in both dryland and irrigation field conditions in KS and the US and characterize resistance to SCN and SDS.

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 KS 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.

Using SDS resistant lines identified from a previous NCSRP SDS breeding project to combine SDS and SCN resistance, we will develop approximately 15 populations each year involving exotic parents or lines derived from exotic germplasm with high yielding, elite varieties. These progeny will be evaluated in both dryland and irrigation field conditions in KS and the US and characterize resistance to SCN and SDS.

Each year, soybean lines exhibiting a wide range of desirable traits, including pest resistance, yield stability, and seed quality will be used to develop new populations to produce progeny with combinations of the most desirable traits for Kansas soybean producers, with the ultimate goal of developing varieties with broad pest resistance and yield stability that can be used by farmers directly, or by other breeding programs as parents in crosses to form new populations.

We will continue to record in-season soybean canopy thermal and spectral profiles with a small unmanned aircraft system (sUAS) at irrigated and dryland research plots. Genotypes possessing extremes in phenotypes (such as disease resistance, wilting and canopy temperature) will be included in the evaluations. Effectiveness of the system will be assessed by correlating thermal and spectral canopy profiles with relative seed yield, relative maturity, and wilting scores. This phenotypic data will be used to support gene mapping.

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 3 through 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.

Improved techniques to develop 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.

Progress of Work

Updated June 21, 2018:
KANSAS SOYBEAN COMMISSION QUARTERLY REPORT OF PROGRESS

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

We completed the release and licensing of the new soybean variety KS5518 this quarter.

During the summer of 2018, experimental lines in maturity groups III-V will be tested at eleven breeding nurseries located throughout Kansas.

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

We will be increasing three conventional group 5 varieties and one glyphosate resistant group IV variety for possible release in 2019.

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

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 7800 experimental K-lines and another 600+ experimental lines/plant introductions from cooperative trials in over 10,000 plots. To date, nine of our eleven sites have been planted, including:

On 5/7 planted tests at Rossville for SDS evaluations consisting of 111 commercial varieties and experimental lines in 444 plots.

On 5/8 planted yield trials at Colby consisting of 26 commercial varieties and experimental lines in 104 plots.

On 5/10 and 5/11 planted tests at Onaga consisting of: 120 Kansas Advanced (KA) entries in 240 plots; 1440 Kansas Preliminary (KP) yield plots; 75 Uniform Test (UT) entries in 180 plots and 1 Soybean Variety Performance Test (SVPT) entries in 124 plots.

On 5/15 planted tests at Ottawa consisting of: 190 KA entries in 380 plots; 75 UT entries in 180 plots; and 1440 Kansas Preliminary (KP) yield plots.

On 5/17 and 5/18 planted tests at Manhattan irrigated Field B consisting of: 120 KA entries in 240 plots; 1564 Kansas Preliminary (KP) yield plots; 6720 progeny rows containing K-lines; 220 UT entries in 525 plots; and 257 Diversity entries in 514 plots.

On 5/12 and 5/23 planted tests at Manhattan irrigated Field T consisting of: 190 KA entries in 380 plots; 1564 Kansas Preliminary (KP) yield plots; 448 entries in a shattering test; over 550 plant introductions for observation; and all our F4 populations for single plant selection.

On 5/24 planted tests at Salina consisting of: 75 entries for a commercial drought resistance trial in 300 plots; 682 genotypes in 2120 plots from breeding programs in MO, NC, SC, AR, GA and KS for evaluation to drought; and 190 KA entries in 380 plots.

On 6/5 planted tests at Pittsburg consisting of: 70 KA entries in 140 plots; 306 Kansas Preliminary (KP) yield plots; and 138 UT entries in 327 plots.

On 6/6 planted tests at McCune consisting of: 70 KA entries in 140 plots; 306 Kansas Preliminary (KP) yield plots; 138 UT entries in 327 plots; and 31 SVPT entries in 124 plots.

We will finish packeting tests, and populations in June once all seed has been returned from our Puerto Rico winter nursery.

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

Updated September 14, 2018:
KANSAS SOYBEAN COMMISSION QUARTERLY REPORT OF PROGRESS

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

A soybean cyst nematode field study containing several lines of transgenic soybean was planted at the Kansas River Valley Experimental Field Station near Topeka Kansas on May 22nd, 2018. A randomized complete block design was employed with seven different transgenic lines and three background controls. Random samples from soybean rows at flowering revealed extremely low numbers of cysts forming on roots, making statistical analysis between treatments infeasible. Plants are being grown to seed to aid in future experiments.

On 6/18 planted our double-crop trial consisting of 30 entries in 120 plots near Pittsburg.

On 6/28 planted seed increases, F3 populations and high oleic germplasm lines from seed returned from our winter nursery in Puerto Rico.

Since July we have captured thermal and spectral reflectance data about every 14 days using a drone on multiple days throughout vegetative and early reproductive work for our trials at Salina, Manhattan, Onaga and Topeka to produce models that accurately predict relative seed yield, relative maturity and SDS resistance.

In July and early August, all our dryland trials experienced significant drought and heat stress, not only at our drought prone site near Salina, in central KS, but also at our locations in Northeast, East Central and Southeast, KS. We took advantage of this environmental stress and evaluated wilting response in commercial yield trials at five locations. The number of commercial entries ranged from 29 near Pittsburg, to 75 near Salina. Depending upon the location we captured from 1 to 4 wilting ratings at each location, at growth stages ranging from R2 to R5.8. In addition to the commercial entries, we had Uniform Test trials at four of the five locations, and took wilting ratings on the maturity groups 3, 4, 4s and 5 trials near Onaga, Ottawa, McCune and Pittsburg, KS. Unfortunately, our Salina trials were damaged by dicamba drift in June, so we focused on the Xtend soybean varieties (over ½ of the entries at our commercial trial at Salina were Xtend genotypes) at this location initially in the ratings, until the susceptible plants had an opportunity to recover. It took several weeks, but by the end of August, most of the maturity group 5 and later entries at Salina had grown out of the dicamba damage and the upper canopy leaf structure looked normal. We took advantage of hot, dry conditions at the end of August at Salina and on 8/31 and 9/1 we took about 2500 wilting ratings on the genotypes at that location. Along with seed yield and maturity data, this information will be useful to quantify drought response both in commercial varieties, in germplasm and out breeding material.

We completed our 2018 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.

We have completed the Race 3 SCN screening tests for our breeding material and commercial varieties and now are evaluating resistance to a Race 4 population. Initial SDS ratings have been taken on breeding material and commercial varieties at the Rossville disease nurseries. Final rating will be completed in September.

Updated December 14, 2018:
KANSAS SOYBEAN COMMISSION QUARTERLY REPORT OF PROGRESS

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

Over 80 new populations created this season were harvested, and the F1 generation has been advanced to the winter nursery in Puerto Rico. This generation has been planted and good stands were established. Over 40 F3 populations were advanced to the F4 generation during the summer of 2019.

We completed the 2018 harvest on 12/12 involving the evaluation of over 6000 experimental K-lines and another 400 elite experimental lines from other states field trials. Productivity and precision of the 2018 season was good but seed quality was poor. Data are being compiled for all K-lines and experimental lines from other experiment stations. Decisions on what lines to advance, increase, release or discard will be finalized next quarter.

Data from our evaluation of over 100 commercial soybean varieties for Soybean Cyst Nematode again three races in the greenhouse have been completed and analyzed. Results will be posted on the Agronomy Department’s Crop Performance Tests website.

Working with Shrada (BAE) we captured over 30,000 spectral images on breeding plots located at Onaga, Manhattan and Assaria. We analyzed those images from our progeny rows to select genotypes for evaluation in yields in 2019. Also, we are analyzing these images now to help characterize drought response, seed yield, plant maturity and resistance to Soybean Sudden Death Syndrome.

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, and seed yield 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.

From work partially supported by the Kansas Soybean Commission the following publications have been accepted or submitted.

Published in G3: Genome-wide analysis of grain yield stability and environmental interactions in a multi-parental soybean population. Brian Diers, James Specht, Katy Rainey, Perry Cregan, Qijian Song, Vishnu Ramasubramanian, George Graef, Randall Nelson, William Schapaugh, Dechun Wang, J Shannon, Leah McHale, Stella Kantartzi, Alencar Xavier, Rouf Mian, Robert Stupar, Jean-Michel Michno, Yong-Qiang An, Wolfgang Goettel, Russell Ward, Carolyn Fox, Alexander Lipka, David Hyten, Troy Cary, William Beavis

Submitted to Frontiers in Plant Science: Genome-Wide Association Analyses Reveal Genomic Regions Controlling Canopy Wilting in Soybean. Clinton J. Steketee, William T. Schapaugh, Thomas E. Carter Jr., Zenglu Li

Submitted to Crop Science: Genetic Gain for Seed Yield, Agronomic Traits and Seed Composition in Maturity Group V, VI, and VII U.S. Soybean Cultivars Measured Over 80 Years, Boehm, Jr., Jeffrey D.; Abdel-Haleem, Hussein; Schapaugh, William; Rainey, Katy Martin; Pantalone, Vincent Robert; Shannon, J. Grover; Carter, Tommy; Gillen, Anne M.; Chen, Pengyin; WEAVER, DAVID B.; Boerma, H. Roger; Li, Zenglu,

Submitted to Remote Sensing of Environment: Assessment of sudden death syndrome in soybean through broadband color infrared remote sensing, Nicholle Hatton, Ethan Menke, William Schapaugh, Deon Van Der Merwe, A.J. Shrada.

Updated April 15, 2019:

View uploaded report PDF file

Final Project Results

Outcomes of Research on Soybean Cyst Nematode Resistance (SCN), Genetic Diversity, Drought, Remote Sensing and Variety Development

SCN Breeding and Management
Our evaluations for SCN resistance have characterized the level of SCN resistance in soybean experimental lines and commercial varieties. This will assist soybean growers in making informed variety selection decisions that impact SCN management, and aid our breeding program in the selection and potential release the of the most resistant material in our program.

Genetic Diversity
We continue to evaluate plant introductions to identify new genetic variability for response to drought and heat stress, seed composition and improved yield potential. The past several seasons, we have conducted evaluations on over 2500 maturity groups 3 through 10 plant introductions. Data collected on these introductions included traits such as: maturity, lodging, height, seed yield, shattering, 100 seed weight, seed quality, seed protein and oil concentrations, and canopy wilting scores. Based on these evaluations we develop populations involving plant introductions that have not contributed to the genetic improvement of US soybean varieties. The goal of using these parents is to increase the genetic diversity of US germplasm to increase, or at least, maintain genetic gain.

Remote Sensing
Canopy reflectance represents a high-throughput opportunity for phenotyping in soybean breeding. We continue to develop models utilizing canopy reflectance and canopy thermal properties to estimate relative soybean maturity, seed yield, maturity, drought stress, and disease resistance. The focus on 2017 and 2018 was obtaining remote sensing data on SDS screening trials, on our progeny rows and on germplasm and varieties evaluated for drought stress. All spectral data collected in 2017 and 2018 was accomplished using unmanned aerial vehicles (UAVs). Selections based on data collected using the UAVs were made in 2017 and 2018 and are being evaluated in replicated yield trials to characterize the benefits of using this technology to improve selection efficiency.

Slow wilting QTL analysis
Our assessment of slow wilting in genotypes under drought stress may help improve drought tolerance in soybean. In work with the Univ. of Arkansas, we characterized canopy wilting of 373 maturity group (MG) IV soybean genotypes to identify new and previously reported QTLs for canopy wilting. Over 60, environment-specific significant SNP – canopy wilting associations were identified. Some of the associations were located near previously reported chromosomal regions associated with canopy wilting, and other associations were new. This information will be important for pyramiding beneficial genes into the same genotype, and identifying parents to use in developing populations with improved drought tolerance.

Commercial wilting trials
Seventy-five maturity group 4 and 5 soybean genotypes, consisting of commercial varieties and checks, were evaluated for wilting in replicated trials at Salina KS in 2018. These evaluations included several of the new Roundup Ready Xtend soybean varieties. Between two to four wilting scores were taken on each plot during late vegetative and early reproductive growth. In addition to the wilting ratings, seed yield, maturity, lodging and plant height were collected on all plots. The plants experienced severe drought and heat stress during late vegetative and early reproductive growth. Cultivar wilting scores ranged from near 0 to 65 across rating times. A score of 0 indicated no wilting present and a score of 25 indicated moderate wilting and rolling of leaves in the top of the canopy. Wilting scores of the slow-wilting checks ranged from 0 to 5, while wilting scores of the fast-wilting checks averaged from 40 to 50. The most severe rating of a cultivar on any day was 65, indicating severe leaf rolling throughout the canopy. Most of the commercial soybean varieties possessed wilting ratings similar to, or more severe, than the fast wilting checks, which possessed average wilting scores around 20. However, one commercial group 4 variety, and 2 commercial group 5 varieties possessed wilting scores similar to the slow wilting checks. Out of these 3 commercial varieties which exhibited slow-wilting characteristics in KS, the yield of the group 4 variety, and one of the group 5 varieties were similar in seed yield to the highest yielding entries across the two locations. Commercial Wilting Trials were evaluated in Missouri, Arkansas, South Carolina, Georgia and North Carolina. Data from these trials will be used to develop a robust assessment of the wilting and drought resistant characteristics of currently available commercial experimental soybean varieties and help guide our breeding activities.

Variety Development/Genetics
This project enabled the development of 90 new breeding populations, and advance over 300 populations in the F1, F2, F3, F4 and F4:5 generations. Parents used to create these populations in 2018 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.

This project enabled the evaluation of about 5000 genotypes in over 16,000 plots in Kansas. Over 1600 K-lines were evaluated in our preliminary trials. Over 180 K-lines were evaluated in our KS advanced yield trials. Over 600 (including 28 K-lines) breeding lines from programs across the country were evaluated in our KS Uniform Tests and Uniform Preliminary yield trials. Over 700 genotypes, (experimental breeding lines and plant introductions) were evaluated in our drought, remote sensing, and diversity yield trials.

This project enabled the release by The Kansas Agricultural Experiment Station of KS4949N, a late group 4 variety. This is a conventional variety that can be used for commercial production, and as a parent by other plant breeders for the development of new varieties.

Opportunities for Training and Professional Development
One graduate student worked on objectives related to this project in Agronomy, and two others in Bio and Ag Engineering utilized the field plots developed and evaluated through this project for research on remote sensing.

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 peer-reviewed publications in 2018 included:

Avjinder S. Kaler, Jeffery D. Ray, William T. Schapaugh, Antonio R. Asebedo, C. Andy King, E. E. Gbur, and Larry C. Purcell. 2018. Association mapping identifies loci for canopy temperature under drought in diverse soybean genotypes. Euphytica 214:135, https://doi.org/10.1007/s10681-018-2215-2.

Maduraimuthu Djanaguiraman, William Schapaugh, Felix Fritschi, Henry Nguyen and P.V. Vara Prasad. 2018. Reproductive success of soybean cultivars and exotic lines under high daytime temperature. Plant, Cell and Environment. https://doi.org/10.1111/pce.13421.

Diers B.W., Specht J., Rainey K.M., Cregan P., Song Q., Ramasubramanian V., Graef G., Nelson R., Schapaugh W., Wang D., Shannon G., Mchale L., Kantartzi S.K., Xavier A., Mian R., Stupar R.M., Michno J.-M., An Y.-Q.C., Goettel W., Ward R., Fox C., Lipka A.E., Hyten D., Cary T., Beavis W.D. 2018. Genetic architecture of soybean yield and agronomic traits. G3 8: 3367-3375.

Xavier A., Jarquin D., Howard R., Ramasubramanian V., Specht J.E., Graef G.L., Beavis W.D., Diers B.W., Song Q., Cregan P.B., Nelson R., Mian R., Grover Shannon J., McHale L., Wang D., Schapaugh W., Lorenz A.J., Xu S., Muir W.M., Rainey K.M. 2018. Genome-wide analysis of grain yield stability and environmental interactions in a multiparental soybean population. G3 8: 519-529.

Benefit to Soybean Farmers

Genomic selection. Advances in genomics have made whole-genome genotyping cost effective, but to utilize this information, robust models must be developed capable of predicting phenotype. We are assisting model development by providing high-quality phenotypic data required for model development.

Identify new sources of “good” germplasm. Limited genetic variation is present in the commercial 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.

Develop superior varieties using exotic germplasm. Potentially “good” germplasm will be used as parents to develop new progeny to help bridge the gap in performance between the exotic germplasm and elite varieties. This effort can result in the development of a new commercial product, or better enable the use of the exotic germplasm by private breeding programs. Additionally, there is a need for new and more effective sources of pest resistance, particularly for SCN. Private breeding programs primarily rely on a single source of resistance (PI 88788), which has become ineffective for many populations in Kansas and other North Central states.

Develop high yielding soybean varieties with desirable levels of protein and oil. 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.

Develop high oleic varieties. High oleic soybean represents a value-added commodity.

Breed transgenic events into elite breeding lines. Incorporating transgenic events into elite breeding lines offers novel traits for SDS, SCN and RKN resistance.

Develop SDS resistant varieties. Soybean sudden death syndrome (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. This resistance is most effective when combined with SCN resistance.

Develop soybean varieties and germplasm with stacked traits. The traits that will be focused on for stacking represent some of the most important and chronic issues for Kansas soybean producers. Germplasm with stacked traits for pest resistance and yield stability will be useful to both public and private breeding programs. Varieties developed with such stacked traits will be useful to producers precisely because of their yield stability across the diverse environmental and pest conditions in Kansas.

Develop high throughput technology. This technology, which can be applied in both the public and private sector, can improve the speed and accuracy of identifying superior breeding material, and permit the selection of traits that have never before been evaluated on a widespread basis.

Performance Metrics

At least one new variety, or germplasm line will be released every few years.

At least one peer-reviewed article will be published every other year that reports the results of germplasm evaluations or the effectiveness of using genomic or phenotypic techniques to evaluate genotypes.

Project Years