Project Details:

Increasing Soybean Yield with Exotic Germplasm (Year 1 of 1420-532-5650)

Parent Project: This is the first year of this project.
Checkoff Organization:United Soybean Board
Categories:Breeding & genetics
Organization Project Code:1420-532-5650
Project Year:2014
Lead Principal Investigator:Randall Nelson (University of Illinois at Urbana-Champaign)
Co-Principal Investigators:
Blair Buckley (Louisiana State University)
Thomas E Carter Jr (North Carolina State University)
E. Tallercio (North Carolina State University)
Zenglu Li (University of Georgia)
Brian Diers (University of Illinois at Urbana-Champaign)
James Orf (University of Minnesota)
Pengyin Chen (University of Missouri)
Andrew Scaboo (University of Missouri)
Grover Shannon (University of Missouri)
George Graef (University of Nebraska)
Rouf Mian (USDA/ARS-Ohio State University)
Rusty Smith (USDA/ARS-University of Illinois)
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Keywords: Soybean Gene Expression, Soybean Genetic Diversity, Soybean Genomics

Contributing Organizations

Funding Institutions

Information and Results

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Project Summary

The narrow genetic base in U.S. soybean breeding is a major limitation to the rate of yield improvement. With USB support we have developed high yielding lines and varieties from exotic germplasm that commercial companies are using. We will add new soybean germplasm to that high yielding pool and identify the genetic control of those yield increases. We will develop new procedures to effectively select among the thousands of exotic accessions not yet used. We will also build upon exciting preliminary results that show that wild soybean and perennial Glycine are important sources of new genes for high yield.

Project Objectives

1. Add new soybean germplasm to the pool of high yielding soybean lines.
2. Identify the genetic control of those yield increases.
3. Develop new procedures to effectively select among the thousands of exotic accessions not yet used.
4. Continue to explore wild soybean and perennial Glycine as sources of new genes for high yield.

Project Deliverables

• Identify genes and genomic region for yield and mine new yield alleles from exotic PIs.
• Develop a set of near isogenic lines for yield to confirm the yield QTL.
• Develop genome-wide selection models for yield selection.
• Understand the genomic regions that affect yields and develop a novel breeding strategy for selection of PIs for future germplasm enhancement.
• Transfer of new genetic materials with exotic pedigree and high yield to commercial breeders via MTAs.
• Release of new genetic materials with exotic pedigree and high yield potential.
• Germplasm and data will be made available for use by soybean breeders.
• Genomic selection evaluations will be useful in testing the effectiveness of this procedure when applied to exotic sources of genetic diversity. In addition, experimental lines that are high yielding and genetically diverse could potentially be released as varieties or experimental lines.
• High-quality, multi-environment yield and other agronomic performance data for 500 accessions in the USDA Soybean Germplasm Collection. Data will be entered into the GRIN database.
• Based on two years of field data and the 50K SNP genotype data, we will develop models to predict yield of germplasm accessions based on DNA marker data.
• Release of first high yield lines derived from G. tomentella.
• Germplasm well adapted to the early soybean production system to produce high yield and seeds with high germination.
• QTL for soybean yield improvement from wild and/or domesticated Japanese soybean.
• Validation of QTL from Japanese germplasm for soybean yield improvement.
• Develop SNP markers for the yield QTL from Japanese germplasm.
• Understand the regions under breeding selection from Japanese germplasm.
• Determine efficacy of yield QTL from Japanese germplasm across a range of maturity groups and genetic backgrounds.
• Determine the potential to combine yield alleles from Japanese soybean and wild soybean.
• Develop improved method for production of adapted breeding lines from wild soybean.
• Determine the proportion of the wild soybean genome transferred to adapted soybean breeding lines from the hybridization of soybean N7103 and wild soybean PI 366122.
• Understand factors that control soybean yield enhancement.
• Publications describing results from USB supported research.
• Discover new sources of genetic variation in wild soybean that have the potential to enhance soybean yield.
• Identify and develop novel strategies that enhance soybean yield potential using wild soybean.
• Identify a core collection of 30 or fewer breeding lines from each soybean x wild soybean population that in the aggregate carry all SNP markers that can be identified in wild soybean.
• Convince public and private breeders to use these materials in their applied and basic breeding research.

Progress of Work

Final Project Results

This project was initiated preceding the incorporation and standardization of KPIs. The progress of objectives are as follows:
Achieving objectives:
• Soybean breeders in commercial companies are using lines from this project as parents and lines from those crosses are now in their more advanced yield tests, over 300 lines were transferred in 2013. More than 15 experimental lines have been used as parents by companies.
• Lines containing diverse germplasm did exceptionally well in both the 2014 Northern and Southern Uniform Tests. Over 110 lines, derived from over 70 exotic parents, were entered in the tests from this project this year. Additional lines were entered by public breeders not involved directly in the project, but whose lines contain exotic germplasm originally from the project. This is an incredible amount of diversity when contrasted to the knowledge that current soybean varieties have over 95% of their genes derived from only 35 ancestral lines. In the Northern Test, 25 lines derived from 29 exotic ancestors exceeded checks by 1-13%. In the Southern Test, 5 lines exceeded the checks from 1-16%. Some of these lines may derive their advantage to later maturity, which needs to continue to be monitored.
• High yielding lines are being advanced in each of the state programs.
• Many of the best yielding lines have genes derived from PI416937. The researchers believe there are two yield alleles or QTL responsible for these increases. They are termed Yld1 and Yld2. These alleles confer improvement in several but not all backgrounds. Work is ongoing to understand these genetic regions better.
• Last fall over 60 attendees participated in the 2nd Annual Wild Soybean Farmer-Finder Pick Your Bean Tour at Rocky Mount, NC where 1.5 million offspring (F3 plants) from wild x domesticated hybridizations (~30 acres) were grown. Hundreds of plants were selected by attendees. Attendees included from representatives USB, NC Soybean Producers Association, growers, breeders from Monsanto, Bayer, and Pioneer. A film crew from Osborn and Barr filed the event to prepare a magazine article and video.
• Genomic selection is being applied to Soybean Asian Germplasm Evaluation (SAGE) data that was collected in 1998 and 1999, to see if yield prediction can be modeled and/or if yield QTL can be mapped. Genomic selection is also being applied to the NAM breeding populations that include exotic germplasm.
• A dominant gene responsible for the impermeable seed coat, a problem for the early soybean production system in the south, was identified. Manipulation of the gene has potential for the early soybean production system and also for reducing seed damage caused by weathering and mold. Unusually good weather in Stoneville led to a relatively stress free growing season. Yields of DS65-1, the line containing the impermeable seed coat gene, did not yield as well as other checks, but was superior to all in terms of seed quality and germination.
• The researchers are pursuing continued use of the 6K SNP chip rather than developing a new 3K chip. Illumina has agreed to lower the price if enough chips are ordered.
• A set of G. max x G. soja (N7103 x PI366122) crosses was generated, creating lines that segregate for all of the SNP alleles. Analysis of the lines is ongoing, but the set of lines are expected to be released in 2015.
• Work to transfer large portions of the wild soybean genome from 35 diverse accessions to agronomically adapted soybean breeding lines is ongoing in several. Lines were advanced in the fields this summer and the data is being collected and analyzed. In North Carolina, F4, F3, F2 and F1 plants were generated. In Missouri and Illinois F3 plants were progressed.
• Assessment of the core and mini-core collections of wild soybean is ongoing. Seventy two wild soybean accessions were sequenced using Illumina HiSeq resulting almost 200,000 SNPs present in over 50 accessions and 8.6 million SNPS in more than 4 accessions. The collections area also being evaluated for a second year for seed traits, including root architecture, and seed composition. GWAS will be developed for this data. New data will be added in 2015.
• High yielding lines from G. tomentella x soybean crosses are being advanced. Some lines continue to yield better than the soybean parent, in several cases the yield increases may be due to later maturity, but others seem to yield better at the same maturity.
Not Achieving objectives:
•None at this time.

Benefit to Soybean Farmers

Performance Metrics

This project was initiated preceding the incorporation and standardization of KPIs. The goals of the project are as follows:

1. How the high yielding and diverse germplasm lines available to the public and private soybean breeders for soybean variety development are used.
2. The use of DNA markers that associated with the yield will be available to public and private breeders to be used in their breeding programs.
3. The use of the result from multi-family-based and SAGE-based genomic selection.
4. Acceptance of scientific results will be presented in the soybean community meetings, and published in the international journals.
5. Transfer of new genetic materials with exotic pedigree and high yield to commercial breeders via MTAs
etc. The main KPI that is being targeted is to increase the rate of yield improvement in breeding programs through the use of genomic and phenotypic information in selections and through the release of improved germplasm derived from exotic sources. The project will be successful when we can show these methods work and the breeding community uses the methods and the germplasm that we release.
Use of yield and other agronomic data collected in this experimental by soybean breeders.
Successful application of the predictive model to select soybean germplasm accessions.
Use of germplasm that is well adapted to the early soybean production system.
The use of high yield germplasm derived from G. tomentella by soybean breeders.
The use of QTL and genome segments associated with yield enhancement by soybean breeders.
Show that soybean yield QTL from Japanese materials function across maturity groups and genetic backgrounds, share results with industry.
Transfer to industry improved breeding methods for producing adapted breeding lines.
Convince public and private breeders to use experimental lines derived from wild soybean in their applied and basic breeding research.

Project Years