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 Crop Production and Pest Control Research: West Lafayette, IN
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ARS Home Midwest Area West Lafayette, Indiana Crop Production and Pest Control Research Research





- Hudson, Karen
- Cai, Guohong
- 2023
- 2022
- 2021
- 2020
- 2019
- Publications
- Plant Genetic Resources, Genomics and Genetic Improvement (301)
- Plant Diseases (303)

Research Project: Genetic Enhancement of Seed Quality and Plant Health Traits, and Designing Soybeans with Improved Functionality **Location:
                            Crop Production and Pest Control Research** 2020 Annual Report **Objectives**
                                

Objective 1: Identify genetic loci involved in seed oil, protein, and carbohydrate content using forward and reverse genetic approaches, and create genetic combinations that serve as new variability for selection in breeding programs.

Subobjective 1A: Identification of genes implicated in control of seed protein/oil levels.
Subobjective 1B: Alteration of carbohydrate partitioning in soybean seeds. 
Subobjective 1C: Combining genes identified by this project to form a basis for improved soybean germplasm.

Objective 2: Evaluate newly identified sources of resistance against Phytophthora sojae, identify candidate Avr gene(s) in the pathogen that are recognized by the new resistance, and design strategies to maintain resistance.

Objective 3: Characterize population structure of Fusarium virguliforme, determine the role of root endophyte community in SDS (soybean Sudden Death Syndrome) resistance, identify key endophytes that can be used for development of new control strategies, and create a SDS genome-wide molecular marker database as a resource for research.  

Objective 4: Construct, coordinate, and publish the results of a relevant regional and national variety testing program for soybean that provides timely phenotypic information useful for selection. **Approach**
                                

Objective 1: Genes regulating carbohydrate, protein, and fatty acid levels of soybean seeds will be identified using a combination of forward and reverse genetic approaches. Mutants will be evaluated by NIR, GC, and HPLC analysis for multiple aspects of seed composition. Conventional and sequence-enabled mapping techniques will be used to determine gene positions. qRT-PCR will be used to measure the expression of candidate genes during seed development. The best candidate genes will be validated through transformation assays to determine gene impact on seed phenotype.
Objective 2: The performance of resistance genes, including several recently identified, will be evaluated against a large collection of Phytophthora sojae isolates. The best gene pyramiding combination will be recommended for soybean breeding efforts. Genomes and transcriptomes of a subset of isolates will be sequenced to determine how P. sojae evades gene-mediated host resistance, and to identify candidates for uncharacterized Avr genes. 
Objective 3: A genome-wide informative microsatellite marker database will be constructed for Fusarium virguliforme using a comparative genomics approach. Identified microsatellite markers will be used to investigate global population structure of F. virguliforme. Prokaryotic and eukaryotic root endobiome of soybean lines susceptible or highly resistant to sudden death syndrome will be characterized using culture and high-throughput sequencing approaches. Endophytic groups associated with SDS resistance will be identified. 
Objective 4: Public soybean breeders submit their soybean breeding lines for evaluation of agronomic performance, disease resistance and quality traits. Entries are separated by maturity group and assigned to either the ‘Preliminary Tests’ or the ‘Uniform Tests’. Seeds of each entry, along with those of the standard reference varieties, are packaged and distributed to collaborators throughout the U.S. and Canada for evaluation. In addition, entries will be evaluated at multiple locations in Indiana. Harvested seeds will also be tested for quality traits. Collaborators submit performance data from their locations to ARS after harvest. This data is compiled and analyzed by this research group following established protocols. The results will be published in an annual report book and online. **Progress Report**
                                

Objective 1. With the goal of identifying genetic map positions for elevated protein and oil genes, twelve mapping populations (generated from 2018 crosses) were grown in the field in 2019 and measured for seed protein and oil content in the fall and winter of 2019. Eight populations were selected for mapping based on clear segregation of elevated protein or oil traits, and DNA was extracted for genetic mapping in the summer or fall of 2020. For the 2020 field season, 118 protein /oil mutant lines were planted in the field. Thirty-six mapping populations were planted, and 68 backcross populations were planted. Map positions will enable further study of the genes involved in protein and oil content. 
To combine favorable seed oil traits with low raffinose/stachyose meal traits, in 2020 we will select individuals with ultra-low RFOs and high oleic and/or low linolenic traits using molecular markers from a population of 2000 F2 individuals. F3 seed will be increased in the greenhouse to enable multilocation studies with recombinant inbred lines in 2021-2022.
Objective 2. Due to harsh harvesting conditions in 2018, differential seeds had low germinating rates. All differentials were increased again in 2019. High purity and quality differential seeds are now available. Pathotyping of all Phytophthora sojae isolates against the differentials were completed. We are beginning data analysis. A subset of isolates were identified for genome and transcriptome sequencing in preparation for 36-month milestone.
Objective 3. The fungus Fusarium virguliforme causes soybean Sudden Death Syndrome. Understanding its population structure is important for disease management and breeding for resistance. Population characterization of F. virguliforme using the microsatellite markers were completed. Preliminary data analysis has been completed. Based on our preliminary results, we plan to expand the research beyond what we described in the project plan. We are requesting additional isolates from South America.
 Objective 4. An ARS scientist in West Lafayette, Indiana, organized the 2019 Northern Uniform Soybean Tests and is organizing the 2020 tests. In 2019 tests, 538 soybean breeding lines and checks in maturity groups 00 to IV were evaluated and the tests were conducted at 41 sites in 10 Midwest states in the United States and two provinces in Canada. These soybean lines were evaluated for yield and other agronomic characteristics including seed quality, lodging, and shattering, etc. They were also evaluated for disease resistance including soybean cyst nematode and Phytophthora root and stem rot. Soybean lines bred for seed quality traits (oil and protein content, amino acid, high oleic acid) were also evaluated for their target traits. These breeding lines were submitted by public breeders in the Unites States and Canada. The ARS scientist in West Lafayette, Indiana, directly evaluated lines at two sites in Indiana, and evaluated all lines for resistance to Phytophthora root rot, which is a significant disease of soybeans, under greenhouse conditions. The ARS scientist in West Lafayette, Indiana, collected data from collaborators, analyzed the data, and published the results in the book “THE UNIFORM SOYBEAN TESTS NORTHERN REGION 2019”.  The hard copy was delivered to participants and interested stake holders. The electronic copy of the book is freely available online. Twenty-four high quality soybean breeding lines were publicly released or licensed in 2019. The 2020 tests are underway. **Accomplishments**
                                

1. New gene markers for improved soybean meal composition. Soybean is the top global source of protein meal for animal feed, however soybean seeds contain carbohydrate compounds called raffinose family oligosaccharides (RFOs) that prevent the complete digestion of soybean meal in non-ruminant animals.  To combat this problem, ARS scientists in West Lafayette sought to identify and incorporate new genes to reduce or eliminate RFOs in soybean meal. A randomly mutagenized soybean population was screened via a targeted molecular approach to detect damaging changes in specific genes in the RFO biosynthesis pathway. The method took advantage of high throughput DNA sequencing and can be applied to any crop. A new mutant was recovered from this screen that was demonstrated to reduce RFOs from 5-6% of total carbohydrates to below detectable levels when used in combination with other soybean genes.  This combination of genes can be deployed widely in soybean breeding programs to generate soybean with improved meal characteristics. Low-RFO soybean meal has been demonstrated to improve the growth and nutrition of poultry. 2. Publication of the book “THE UNIFORM SOYBEAN TESTS NORTHERN REGION 2019”. The ARS lab in West Lafayette, Indiana, organizes the Northern Uniform Soybean Tests yearly. The tests evaluate soybean breeding lines for agronomic performance, disease resistance and seed quality traits in Northcentral states in the United States and provinces in Canada. The soybean lines are those developed by public breeders in the United States and Canada that are suitable for planting in these regions. In addition to performing tests at multiple sites in Indiana, the ARS lab in West Lafayette, Indiana, coordinated the project, collected seeds from collaborators, designed the field maps, distributed seeds to collaborators, collected data from collaborators, analyzed the data, and published the 2019 test results in this book. The hard copy was delivered to collaborators and interested stake holders. The electronic copy of the book is freely available online. This book is used as primary evidence by breeders when making the decision to further advance their lines or release their lines to the public. Twenty-four high quality soybean breeding lines were publicly released or privately licensed in 2019. 3. Mitochondrial genome of Phytophthora sansomeana. P. sansomeana causes root rot of soybean. Its incidence and geographic range have been increasing in recent years. The ARS lab in West Lafayette, Indiana, sequenced and annotated its mitochondrial genome. We also compared it with mitochondrial genomes of other Phytophthora species and identified shared and unique features. **Review Publications**
                            *Hagely, K., Jo, H., Kim, J., Hudson, K.A., Bilyeu, K. 2020. Molecular-assisted breeding for improved carbohydrate profiles in soybean seed. Theoretical and Applied Genetics. 133:1189-1200. https://doi.org/10.1007/s00122-020-03541-z.*
                                *Thapa, R., Carrero-Colon, M., Rainey, K.M., Hudson, K.A. 2019. TILLING by Sequencing: A successful approach to identify rare alleles in soybean populations. Genes 2019. 10(12):1003. https://doi.org/10.3390/genes10121003.*
                                *Cai, G., Fry, W.E., Hillman, B.I. 2019. PiRV-2 stimulates sporulation in Phytophthora infestans. Virus Research. 271:197674. https://doi.org/10.1016/j.virusres.2019.197674.*


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