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United States Department of Agriculture

Agricultural Research Service

Research Project: SOYBEAN GENETIC MANAGEMENT AND UTILIZATION
2012 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 fifth-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.

The second year of a general germplasm evaluation of 1357 soybean accession was planted.

We distributed 26,785 seed lots from 15,196 in response to 594 requests from 336 individuals. This is the tenth year in a row in which we have distributed more seed lots than total accessions in the Collection and are the only collection in the National Plant Germplasm System (NPGS) to have ever done this. In data combined over 11 locations in the 2010 Uniform Preliminary IIIB Test - Northern Region and 18 locations in the 2011 Uniform III Test - Northern Region, LG08-1643 yielded 97% of the best check variety, IA 3048. By pedigree, LG08-1643 is 12% wild soybean.

Seeds of 256 experimental lines derived from 63 exotic parents were sent to soybean breeders in 6 commercial companies for testing and use. Over 9 locations, LG09-8166, derived solely from exotic germplasm equaled the yield of IA4005, the highest yielding cultivar. LG10-2699 yielded 6.1 bu/a more than IA4005 over 7 locations. It has 31% of its pedigree derived from 5 introductions.

We have tentatively identified soybean lines with rust resistance transferred from G. tomentella. We are growing for the first time soybean lines with G. tomentella cytoplasm.

Improved experimental lines were developed with seed isoflavone concentrations that range from 0.62 to 6.42 mg/gm.

We conducted viral-induced gene silencing (VIGS) on three MMP2 genes that are candidate pathogen-responsive genes, as well as 8 genes identified as being candidate defense genes against the disease sudden death syndrome (SDS). We had gene expression determined for 36 different disease or pest induced soybean samples, and have analyzed 20 of them. We have reduced expression via RNA-interference (RNAi) for a soybean G-protein coupled receptor protein (GPCRP) and have plants in the T2 stage, and we made constructs to use RNAi against an MPP2 gene as well as a 14-3-3 gene, and we have sent those to our collaborator at AgCanada for generation of stable transgenics. Arabidopsis T-DNA transgenics are also being screened to determine a possible defense role of 10 genes. We have identified 11 genes out of about 38,000 that showed pathogen-specific gene expression patterns, and we have cloned three of these into Agrobacterium for overexpression in Arabidopsis.


4.Accomplishments
1. The 14-3-3 proteins are a family of molecules expressed in all eukaryotic cells that are important in many regulatory processes. Although 14-3-3 proteins are ubiquitous in organisms, few 14-3-3 proteins have been shown to have a clear role in any plant species. ARS researchers at Urbana, Illinois were able to reduce expression of a gene that produces a 14-3-3 protein and show this 14-3-3 gene is essential for mature nodule formation. This research also confirms that our approach of mining gene expression data can successfully identify the functions of genes. In this case, we identified the 14-3-3 gene as being differentially expressed in one of our first gene expression studies, which examined soybean root response to the nodulation inducing bacterium Bradyrhizobium japonicum. From approximately 5000 genes initially identified, this gene was one of 10 chosen for further analysis based on its expression behavior in response to nodulation, as well as its response to pathogen infection.


Review Publications
Nelson, R.L., Johnson, E.O. 2012. Registration of high-yielding soybean germplasm line LG04-6000. Journal of Plant Registrations. 6:212-215.

Wang, D., Qi, M., Calla, B., Korban, S., Clough, S.J., Sudin, G.W., Toth, I., Cock, P.J., Zhao, Y. 2011. Genome-wide identification of genes regulated by the Rcs Phosphorelay system in Erwinia amylovora. Molecular Plant-Microbe Interactions. 25(1):6-17.

Panduranganl, S., Pajak, A., Molnar, S., Cober, E., Dhaubhadel, S., Hernandez-Sebastia, C., Kaiser, W.M., Nelson, R.L., Huber, S.C., Marsolais, F. 2012. Relationship between asparagine metabolism and protein concentration in soybean seed. Journal of Experimental Botany. 63(8):3173-3184.

Nelson, R.L., Johnson, E.O. 2011. Registration of Soybean Germplasm Line LG00-6313. Journal of Plant Registrations. 5:406-409.

Nelson, R.L., Johnson, E.O. 2011. Registration of Soybean Germplasm Line LG00-3372. Journal of Plant Registrations. 5:403-405.

Li, S., Smith, J.R., Nelson, R.L. 2011. Resistance to phomopsis seed decay identified in maturity group V soybean plant introductions. Crop Science. 51:2681-2688.

Burkey, K.O., Booker, F.L., Ainsworth, E.A., Nelson, R.L. 2012. Field assessment of a snap bean ozone bioindicator system under elevated ozone and carbon dioxide in a free air system. Environmental Pollution. 166:167-171.

Kim, K., Unfried, J.R., Hyten, D.L., Frederick, R.D., Hartman, G.L., Nelson, R.L., Song, Q., Diers, B.W. 2012. Molecular mapping of soybean rust resistance in soybean accession PI 561356 and SNP haplotype analysis of the Rpp1 region in diverse germplasm. Theoretical and Applied Genetics. 125:1339-1352.

Wang, D., Calla, B., Vimolmangkang, S., Korban, S.S., Wu, X., Huber, S.C., Clough, S.J., Zhao, Y. 2011. The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli. PLoS One. 6(9):e25293.

Last Modified: 12/21/2014
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