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United States Department of Agriculture

Agricultural Research Service

Research Project: SOYBEAN GENETIC MANAGEMENT AND UTILIZATION
2011 Annual Report


1a.Objectives (from AD-416)
1. Strategically expand the USDA Soybean Germplasm Collection, conserve and distribute available genetic diversity in genus Glycine, and evaluate genetic resources in the collection. 2. Develop experimental lines derived from exotic germplasm with high yield and/or modified seed composition and map the loci associated with these traits. 3. Elucidate genetic mechanisms of resistance to sudden death syndrome, white mold, and soybean rust in diverse soybean germplasm.


1b.Approach (from AD-416)
Identify genes associated with defense to various pathogens such as Fusarium solani, Sclerotinia sclerotiorum, and Phakopsora pachyrhizi by comparing genomic mRNA levels between resistant and susceptible lines. Candidate genes related to defense will be characterized by functional molecular studies and will be located on the physical map to determine if gene is from a region of the genome associated with any known QTLs for resistance to the specific disease. Analyze soybean interactions with Sclerotinia by analyzing effects of oxalic acid on soybean. Examine physiological conditions that might enhance soybean susceptibility to rust disease caused by Phakopsora pachyrhizi. Strategically expand the USDA Soybean Germplasm Collection to better represent the diversity of the genus Glycine. Conserve, evaluate and distribute available genetic diversity in genus Glycine. Develop experimental lines derived from exotic germplasm with high yield, high protein concentration and/or high oil concentration. Map and confirm quantitative trait loci for yield, and protein and oil concentration with the positive allele coming from exotic germplasm.


3.Progress Report
This is the fourth-year report for the project 3611-21000-023-00D. The research plan has been followed, except for a few minor adjustments and good progress is being made.

Seeds of 256 experimental lines in maturity groups II to IV derived from exotic germplasm were sent to soybean breeders in 6 commercial companies for testing and use in their variety development programs. The pedigrees of these lines include 63 exotic accessions including three wild soybean accessions and by pedigree, these line range from 12 to 100% exotic germplasm.

In the Northern Uniform Tests, 8 lines that had yields at least 100% of the best commercial varieties. Three lines were in the Preliminary Test II but were 5 to 7 days later than the group II commercial varieties. Two lines were equal to the best commercial variety in Preliminary III Test and similar in maturity. One of those lines is LG06-2284 which has 6 introductions that contribute 50% of the pedigree. The other line is LG07-2309 which has a pedigree that is 12% wild soybean. Three lines in Uniform Test IV were equal or better than the best commercial variety. LG06-5798 and LG06-5920 have the same pedigree which is 50% exotic germplasm. LG06-5798 yielded a statistically significant 7% more than the highest yielding check and is being released. LG07-9814, that was equal to the highest yielding commercial variety, also has a pedigree with 50% exotic pedigree from four introductions. We successively produced over 2500 fertile progeny from G. max (soybean) by G. tomentella crosses. We have transferred resistance to Phytophthora rot and sudden death syndrome (SDS) from G. tomentella to G. max. We have tentatively identified transferred resistance to soybean rust and soybean cyst nematode. In addition to the fertile progeny with the same number of chromosomes as soybean (2n=40), we have identified numerous self-fertile, genetically stable 2n=42 lines that have a pair of chromosomes from G. tomentella.

Our research strategy of conducting gene expression studies to identify defense-associated genes is progressing well. We published on the gene expression response in soybean roots to SDS, and have started to prepare a manuscript on the response in soybean leaves to SDS toxin. From these studies we have identified over 2000 genes that were pathogen and/or toxin responsive and have started to conduct virus-induced gene silencing assays to verify function of the most promising defense-associated genes from the lists. Likewise, we have identified candidate defense-associated genes from our Sclerotinia studies and are developing transgenic plants (in collaboration with AgCanada) of RNAi lines to test the importance of these candidate defense genes. We also have good candidate genes for Rpp1 and rpp5 and are conducting VIGS assays for those genes. We have used the gene expression database that we developed to see how genes are being expressed across many disease and stress experiments, and from that analysis found about 20 genes that were strongly induced in a pathogen-specific manner. These genes will be candidates for future functional characterization.


4.Accomplishments
1. The genetic base of soybean varieties grown in the U.S. is largely derived from fewer than 10 ancestral lines. This may be a factor in the limited rate of yield improvement in U.S. soybean breeding. ARS scientists located in Urbana, Illinois are in the process of releasing for research purposes the high-yielding soybean line LG06-5798. The parents of LG06-5798 are LG00-3372 and LD00-3309. LG00-3372, released by ARS scientists and the University of Illinois in 2005, was developed by crossing PI 561319A and PI 574477. PI 561319A was received from the Institute of Crop Germplasm, Chinese Academy of Agricultural Sciences, Beijing, China in 1991. PI 574477 is Fen dou 31 released in Shanxi province in 1990 and introduced into the United States in 1992. In regional testing at 15 locations in 2010, LG06-5798 was significantly higher yielding than all of the commercial varieties in the test including LD00-3309, one of its parents. This demonstrates that genes from previously unused germplasm from the USDA Soybean Germplasm Collection can be used to improve the yield of our best soybean varieties.

2. An important disease of soybean that is spreading across the Midwest is Sudden Death Syndrome, caused by the fungus Fusarium virguliforme. ARS researchers at Urbana, Illinois used high-throughput gene expression profiling to identify about 2,500 genes and 800 small RNA that change in expression levels in response to this pathogen. The expression patterns of these genes reflect the physiological and biochemical changes taking place inside the plants during infection and provide geneticists and molecular biologist with candidate defense genes to target for marker development and development of defense strategies.


Review Publications
Krishnan, H.B., Nelson, R.L. 2011. Proteomic analysis of high protein soybean (Glycine max) accessions demonstrates the contribution of novel glycinin subunits. Journal of Agricultural and Food Chemistry. 59:2432-2439.

Libault, M., Farmer, A., Brechenmacher, L., Franck, W.L., Drnevich, J., Langley, R.J., Bilgin, D.D., Radwan, O., Neece, D.J., Clough, S.J., May, G., Stacey, G. 2009. Complete Transcriptome of the Soybean Root Hair Cell, a Single Cell Model, and its Alteration in Response to Bradyrhizobium japonicum Infection. Plant Physiology. 152: 541-552.

Lee, J., Vuong, T.D., Moon, H., Yu, J., Nelson, R.L., Nguyen, H.T., Shannon, J.G. 2011. Genetic diversity and population structure of Korean and Chinese soybean [Glycine max (L.) Merr.] accessions. Crop Science. 51:1080-1088.

Nelson, R.L. 2011. Managing self-pollinated germplasm collections to maximize utilization. Plant Genetic Resources. 9:123-133.

Oliveira, M.F., Nelson, R.L., Geraldi, I.O., Cruz, C.D., Toledo, J.F. 2010. Establishing a soybean germplasm core collection. Field Crops Research. 119:277-289.

Radwan, O., Liu, Y., Clough, S.J. 2011. Transcriptional analysis of soybean roots response to Fusarium virguliforme, the causal agent of sudden death syndrome. Molecular Plant-Microbe Interactions. 24:958-972.

Last Modified: 11/21/2014
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