Location: Crop Production and Pest Control Research
2022 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.
This year we continued population development and study of composition in a collection of protein and oil mutants isolated from our mutant population. We instituted a two-tier approach to mutant mapping. In the first growing season we perform a “mini-map” experiment to assign mutant loci to a chromosome arm, and in subsequent seasons we pursue interesting mutants by fine mapping in larger, expanded populations with more individuals. In collaboration with ARS researchers in Beltsville, Maryland, we genotyped four populations this year for mini-mapping, and tentatively identified quantitative trait locus on chromosome 10 associated with elevated seed protein in three populations. We also identified linkage to locations on chromosomes 4, 11, and 19 that were each unique to specific populations, suggesting that these loci could be associated with novel genes affecting seed protein levels. Currently we are validating these results with polymerase chain reaction-based markers and progeny testing the F2 lines that demonstrated linkage to the peaks. In FY22 we planted 46 backcrossed populations to analyze inheritance patterns (dominant/recessive) of additional protein and oil mutants, as well as six populations for mini-mapping and seven populations for fine mapping. In previous years we made genetic combinations (crosses) to combine traits isolated in our programs that add value with both improved soybean oil composition and enhanced nutritional energy in soybean meal. We successfully isolated high-oleic (HO), low linolenic (LL), ultra-low RFO (ulRFO) individuals by genotyping a segregating population in FY21 (this combination stacks six independent mutations). We also isolated high oleic ulRFO (HO-RFO) individuals and low linolenic uLRFO (LL-RFO) individuals from these populations. These genotypes will form the basis of a multi-year study examining the interaction of fatty acid and carbohydrate composition traits both in the field and on a molecular basis. Analysis of fatty acid composition from these individuals suggests that the HOLL trait is not negatively affected by the addition of the ulRFO trait. We are awaiting results of RFO quantification (carbohydrate composition) and protein composition in the lines. We planted replicated plots in FY22 to repeat the composition analysis and increase seed for analysis in future growing seasons.
Objective 2:
After completing pathotyping of over 600 isolates of Phytophthora sojae using a set of 18 soybean differentials each carrying one of the following genes: rps, Rps 1a, Rps1b, Rps1c, Rps1d, Rps1k, Rps2, Rps3a, Rps3b, Rps3d, Rps4, Rps5, Rps6, Rps7, Rps8, RpsUN1, RpsUN2 andRps11, in previous years, we selected a set of 100 isolates for genome and transcriptome sequencing. There were multiple isolates virulent or avirulent to each Rps gene. Genomic DNA was extracted from these isolates. These isolates were inoculated on universal susceptible soybean cultivar Williams and samples were collected 24 hours after inoculation from active growing lesions. RNA were extracted from these samples for transcriptome sequencing.
Objective 3:
Three soybean lines that are susceptible to soybean Sudden Death Syndrome (SDS) and three lines that are partially resistant to SDS were planted with three plots each. We are preparing to collect root samples.
Objective 4:
Organized the 2021 Northern Uniform Soybean Tests and are currently organizing the 2022 tests. In 2021 tests, over 500 soybean breeding lines and checks in maturity groups 00 to IV were evaluated and the tests were conducted at 42 sites in 10 northcentral states in the United States and three 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 from both countries.
Directly evaluated lines at three sites in Indiana, and evaluated all lines for resistance to Phytophthora root rot under greenhouse conditions. Collected data from collaborators, analyzed the data, and published the results in the book “The Uniform Soybean Tests Northern Region 2021”. The hard copy was delivered to collaborators and interested stake holders. The electronic copy of the book is freely available online. The 2022 tests are underway. Organized the annual coordination meeting, designed field maps, collected and distributed seeds to cooperators and planted trials in three locations in Indiana.
Accomplishments
1. Published the book “THE UNIFORM SOYBEAN TESTS NORTHERN REGION 2021”. An ARS researcher in West Lafayette, Indiana, organizes the Northern Uniform Soybean Tests yearly. The tests evaluate soybean breeding lines developed by public breeders for agronomic performance, disease resistance and seed quality traits in northcentral states in the United States and provinces in Canada. The hard copies of this report were delivered to collaborators and interested stake holders. The electronic copy of the book is freely available online. This program addresses the bottleneck collectively faced by soybean breeders in the public sectors: lack of resources to conduct field trials in many locations and environments. Annual reports from this program are the primary data source for public soybean breeders to determine the merit of their breeding lines. In 2021, 35 soybean germplasm/cultivars tested in this program have been publicly released or licensed to commercial companies.
2. Developed soybean germplasm that reduces mature seed damages and maximizes profits for producers.. An ARS researcher in West Lafayette, Indiana, collaborated with ARS scientists in Stoneville, Mississippi, and Jackson, Tennessee, to develop the soybean germplasm DS31-243. It’s an early maturity group IV germplasm line with reduced mature seed damage (visual mold, stink bug feeding, discoloration, green seed, etc.) when subjected to hot humid conditions during plant maturation and dry down. Tolerance to mature seed damage was derived principally from Huang mao bai shui dou (PI 587982A), a soybean accession from Sichuan, China. This germplasm is resistant to multiple diseases, including frogeye leaf spot, races 1, 3, 4 and 7 of Phytophthora root and stem rot caused by Phytophthora sojae, and stem canker. Mature seed damage results in price discounts when grain is sold and can cause economic loss to producers in the southern United States, as well as in other hot humid production environments. This is the first improved U.S. soybean germplasm release that addresses this problem.
Review Publications
Wang, W., Chen, L., Fengler, K., Bolar, J., Llaca, V., Wang, X., Clark, C.B., Fleury, T.J., Myrvold, J., Oneal, D., Van Dyk, D., Hudson, A., Munkvold, J., Baumgarten, A., Thompson, J., Cai, G., Crasta, O., Aggarwal, R., Ma, J. 2021. A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean. Nature Communications. 12:6263. https://doi.org/10.1038/s41467-021-26554-8.
Chen, L., Wang, W., Ping, J., Fitzgerald, J.C., Cai, G., Clark, C., Aggarwal, R., Ma, J. 2021. Identification and molecular mapping of Rps14, a gene conferring broad-spectrum resistance to Phytophthora sojae in soybean. Journal of Theoretical and Applied Genetics. https://doi.org/10.1007/s00122-021-03933-9.
Carrero-Colon, M., Hudson, K.A. 2022. Reduced palmitic acid content in soybean seed as a result of mutation in FATb1a. PLoS ONE. 17(3): e0262327. https://doi.org/10.1371/journal.pone.0262327.
