Location: Crop Production and Pest Control Research
2021 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. We analyzed protein and oil composition for 112 field plots of mutants for our multi-year study. Plants were advanced in the greenhouse from 5 mapping crosses and 14 backcrosses from the 2020 field. Combined with the seven mapping populations and 21 backcrosses advanced in the 2020 field, we have twelve mapping populations for high protein in the field this summer. DNA from last year’s mapping population was insufficient for mapping, so plants are being re-grown this year to make additional DNA. In the 2021 field, we will focus on crosses to test the additivity or complementation of the high protein trait with other known high protein loci.
Another goal of the project is to generate combinations of high oleic acid, low linolenic acid and reduced raffinose family oligosaccharides (RFOs) for more nutritious meal combined with high value soybean oil. In 2020 we selected individuals developed from several previous seasons of crossing carrying a combination of 6 mutant genes: rs2 rs3 fad2-1a fad2-1 fad3a and fad3c. This combination averaged 76% oleic acid, 2.7% linolenic acid and should be ultra-low RFO (we will measure this later in 2021). We increased seed for these individuals in the greenhouse in the winter of 2020-2021, and we have 26 plots in the field in summer 2021 for replicated composition testing.
Objective 2. Based on last year’s virulence screening results, we selected the Phytophthora sojae isolates for genomic and transcriptomics sequencing and verified their virulence. DNA extraction is substantially completed. RNA extraction is ongoing.
Objective 3. Population characterization of Fusarium virguliforme using the microsatellite markers were completed last year. We were planning to expand what we described in the project plan by including additional isolates from South America and other regions. Due to the pandemic, we did not obtain those isolates. Data analysis is in progress.
Objective 4. The 2020 Northern Uniform Soybean Test (NUST) was conducted, and the 2021 test is in progress. In the 2020 test, over 500 soybean breeding lines and checks in maturity groups 00 to IV were evaluated and the tests were conducted at 34 sites in nine Midwest states in the United States and two provinces in Canada. These soybean lines were evaluated for yield, disease resistance, seed nutritional composition and other agronomic traits. These breeding lines were submitted by public breeders in the Unites States and Canada. Two sites in Indiana, were grown and evaluated. Additionally, all the NUST lines were evaluated in West Lafayette for resistance to Phytophthora root rot under greenhouse conditions. All data was collected from collaborators, analyzed, and the analysis was published in the book “THE UNIFORM SOYBEAN TESTS NORTHERN REGION 2020”. The hard copy was delivered to collaborators and interested stake holders. The electronic copy of the book is freely available online. The 2021 tests are underway.
Accomplishments
1. Publication of the book “THE UNIFORM SOYBEAN TESTS NORTHERN REGION 2020”. Publication of the book “THE UNIFORM SOYBEAN TESTS NORTHERN REGION 2020”. The ARS researchers at West Lafayette, Indiana, organize 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 researchers 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 2020 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.
Review Publications
Gaskin, E.L., Carrero-Colon, M., Hudson, K.A. 2021. Combination of the elevated stearic acid trait with other fatty acid traits in soybean. Journal of the American Oil Chemists' Society (2021). 98:221-226. https://doi.org/10.1002/aocs.12446.
Hudson, K.A., Hudson, M.E. 2021. Genetic variation for seed oil biosynthesis in soybean. Plant Molecular Biology Reporter. https://doi.org/10.1007/s11105-020-01276-1.
Detranaltes, C., Cai, G. 2021. First report of Mycoleptodiscus terrestris causing root rot of soybean in Indiana. Plant Disease. 105:1194. https://doi.org/10.1094/PDIS-09-20-2023-PDN.
Detranaltes, C.E., Jones, C.R., Cai, G. 2021. First report of Fusarium fujikuroi causing root rot and seedling elongation of soybean in Indiana. Plant Disease. https://doi.org/10.1094/PDIS-03-21-0570-PDN.
