Progress 05/09/08 to 02/28/13
Outputs
Progress Report 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. 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. We distributed 193,000 seed samples from the USDA Soybean Germplasm Collection and grew 9757 plots to replace seeds in the Collection. We sent 3329 back-up samples to the National Center for Genetic Resources Preservation and 13,457 accessions to the Svalbard Arctic Seed Vault. We released 4 high yielding germplasm lines derived from 9 exotic accessions. LG004-6000 significantly exceeded the yield of the best check in the USDA Uniform IV test for two consecutive years. We made available to commercial soybean breeders 1234 high yielding experimental lines derived from over 50 exotic soybean accessions. We did general field evaluations for 1214 germplasm accessions. We identified soybean lines with differential responses to increased ozone concentration. The most sensitive lines had yield decreases of 14% while the less sensitive lines declined only 5%. Increase CO2 concentration increased yield in some varieties by as much as 24% and some varieties showed no yield increases. We identified accessions that are resistant to Asian soybean rust and genetically mapped the resistance in two accessions. We established a core collection of 1685 accessions for the G. max accessions using both qualitative and quantitative data. We identified and mapped the location of three chromosomal regions where the genes from exotic germplasm increased yield. We determined small RNA production in response to several pathogens. We analyzed soybean response to Sclerotinia sclerotiorum and its main virulence factor oxalic acid (OA) with transcriptomic studies involving purified OA, a transgenic soybean that degrades OA, and an OA mutant. We identified over 2000 genes that were either increased or decreased in response to Sclerotinia and/or OA. The gene expression patterns support that OA is affecting physiology related to iron, benefitting the pathogen by providing for its iron needs, and affecting the plant's ability to defend against the pathogen. Several genes were selected as being candidate defense-associated genes. These defense-associated genes were selected for studies involving the reduction of the expression of these genes by RNA interference (RNAi) or Virus Induced Gene Silencing (VIGS). We generated RNAi transgenics that reduce expression of 3 candidate defense genes, and preliminary studies indicate that all three of these genes are providing enhanced defense. We designed at least 20 VIGS constructs, however we were not able to obtain clear results with the VIGS system for our studies. We identified candidates for Rpp1 and rpp5, genes providing resistance to certain isolates of soybean rust. We designed VIGS constructs to silence these candidates, but again, VIGS results were not clear. One of the genes selected as a candidate defense gene was a 14-3-3, and we showed that this gene is also involved in establishing nodulation, as soybean roots transformed with a construct that silences the gene were severely inhibited in nodule formation. This work was published. We continued to improve our soybean gene expression database, allowing us and the public researchers to cross compare how soybean genes responded to different pathogens and other treatments.
Impacts
(N/A)
Publications
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report 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. 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. 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. Significant Activities that Support Special Target Populations: Participated in the University of Illinois Research Apprentice Program program this year, a program that gives high-school students from under- represented communities exposure to research in agricultural sciences. In the summer of 2012, we explained to the students how plant transformation works using Agrobacterium tumefaciens, and included a hands-on demo of how one can transform Arabdipsis thaliana, a plant that is easily transformed. We also showed the steps involved in our wide hybridization project of developing lines from crosses between soybean and G. tomentella including the initial crosses, culturing immature seeds, and developing plants from callus tissue. Accomplishments 01 The 14-3-3 proteins are a family of molecules expressed in all eukaryoti cells that are important in many regulatory processes. Although 14-3-3 proteins are ubiquitous in organisms, few 14-3-3 proteins have been show 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 formati 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 o first gene expression studies, which examined soybean root response to t nodulation inducing bacterium Bradyrhizobium japonicum. From approximate 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.
Impacts
(N/A)
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.
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Progress 10/01/10 to 09/30/11
Outputs
Progress Report 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. 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. 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. Accomplishments 01 The genetic base of soybean varieties grown in the U.S. is largely deriv 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 locat in Urbana, Illinois are in the process of releasing for research purpose 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 ou best soybean varieties. 02 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 these genes reflect the physiological and biochemical changes taking pla 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.
Impacts
(N/A)
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.
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Progress 10/01/09 to 09/30/10
Outputs
Progress Report 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. 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. Nearly 250 lines derived from exotic germplasm were tested with soybean breeders in five planting breeding companies. These lines ranged from 7 to 100% exotic germplasm. Thirteen lines numerically exceeded the yield of the check cultivar including one derived from two backcrosses to wild soybean. Twenty lines derived from 27 soybean introductions were entered into the USDA Uniform (UT) and Preliminary (PT) Tests. In UT III, LG05-2359 was only 0.9 bu/a less than the highest yielding entry, IA4004, and exceeded the other checks by more than 5 bu/a. In PT IIIB, LG06-2354, with 38% exotic germplasm, was the highest yielding of 40 entries exceeding IA4004 by 2.2 bu/a. We had 5 additional entries that yielded more than the second highest yielding check (IA3023). Averaged over two years in UT IV, LG04-5372 (38% exotic) and LG04-5190 (50% exotic) were within 0.5 bu/a of the highest yielding entry. LG04-4866 (25% exotic) was equal to second highest yielding check. In PT IV, LG06-5920 (50% exotic) was the highest yielding entry exceeding the best check by 0.7 bu/a. It has a pedigree that is 50% exotic germplasm. We were able to confirm 4 of 13 putative QTL that increase seed yield where the favorable allele is derived from exotic germplasm. The yield increases associated with these QTL range from 1 to over 4 bushels per acre. We successively produced over 2000 fertile progeny from G. max (soybean) by G. tomentella crosses. We have transferred resistance to Phytophthora rot and sudden death syndrome from G. tomentella to G. max. 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. We requested improved constructs of the bean pod mottle virus for viral- induced gene silencing (VIGS). We have selected 8 SDS defense-associated candidate genes that Iowa State is analyzing via VIGS. We have screened Arabidopsis mutants for a G-protein coupled receptor protein (GPCRP), but the mutants were all heterozygotes so we are screening the next generation for homozygousity of the T-DNA mutation; nine other Arabidopsis T-DNA transgenics are also being screened to determine a possible defense role of these genes. This GPCRP gene, and a 14-3-3 gene, will be analyzed by stable transformation in collaboration with the lab of our cooperator in AgCanada. Significant Activities that Support Special Target Populations We participated once again in the University of Illinois RAPII program that gives high-school students from under-represented communities exposure to research in agricultural sciences. In the summer of 2009, we had a high-school student in the lab for 7 weeks. The student did a small gene expression study using soybean microarrays, and presented her work in the form of a poster, a written report, and as an oral presentation. Accomplishments 01 Identification of an important soybean gene. The type of stem terminatio is a difference between soybean varieties grown in northern (indetermina or southern (determinate) U.S. A single gene controls this major effect on plant type. In cooperation with scientists from Purdue University, we used the sequence of a regulatory gene encoding a signaling protein of shoot meristems in Arabidopsis to locate similar sequences in the soybea genome. From the four possible genes identified, the most likely candida causing determinate stem termination was selected based on known chromosomal location. We were able to determine that this was the gene causing determinate stem termination by inserting that gene into Arabidopsis and soybean, and documenting the predicted response. In a survey of diverse soybean and wild soybean germplasm, we found four variations in the sequence of this gene. Three of the variations could b associated with known phenotypic variations that had been previously described but those differences often cannot be distinguished because of effects of the genetic background in which the genes occur. No variation was found among the gene sequence in wild soybean. The variations were found extensively in primitive soybean germplasm indicating that human selection for determinacy took place at early stages of landrace development. This research demonstrates the power of selection for diversity at the level of gene sequence that will become more common now that the sequence of total soybean genome is available. (PNAS 107: 8563- 8568). 02 Number genes in selected gene families is highly variable. Many genes in plants occur in large families in which the genes share some common structure and often have similar functions. Working with scientists at Texas A & M University, we evaluated the numbers of genes in two large gene families: the nucleotide-binding site-encoding gene family and receptor-like kinase family. Genes in both families are often involved resistance to diseases. Data from 187 lines selected from 57 species of rice, soybean and cotton showed that the number genes in each family varied by several fold both among and within species. Differences betwee modern soybean cultivars were shown to vary by three fold for each gene family and that was as great as any difference among exotic accessions. The variation in these two gene families was generally correlated so increases or decreases in one family were reflected in similar changes i the other. We also showed that the changes in the size of the gene families are regulated by several factors, including natural selection, artificial selection and the size of the genome. These results indicate that the changes in gene family size provide an important source of genetic variation. The exact mechanisms that produce these changes are n known but understanding the processes will be an important step in understanding variation among and evolution of these important agricultu species. (Nucleic Acids Research doi: 10.1093/nar/gkq524).
Impacts
(N/A)
Publications
- Shannon, J.G., Nelson, R.L., Lee, J.D., Wrather, J.A. 2010. Registration of LG04-6863 Soybean Germplasm Line with Diverse Pedigree. Journal of Plant Registrations. 4:70-72.
- Zhu, J., Patzoldt, W.L., Shealy, R.T., Vodkin, L.O., Clough, S.J., Tranel, P.J. 2008. Transcriptome response to glyphosate in sensitive and resistant soybean. Journal of Agricultural and Food Chemistry. 56:6355-6363.
- Mikel, M.A., Diers, B.W., Nelson, R.L., Smith, H.H. 2010. Genetic Diversity and Agronomic Improvement of North American Soybean Germplasm. Crop Science. 50:1219-1229.
- Bilgin, D.D., Zavala, J.A., Zhu, J., Clough, S.J., Ort, D.R., Delucia, E.H. 2010. Biotic Stress Globally Down-Regulates Photosynthesis Genes. Plant Cell and Environment. doi: 10.1111/j.1365-3040.2010.02167.x.
- Tian, Z., Wang, X., Lee, R., Li, Y., Specht, J.E., Nelson, R.L., McClean, P.E., Qiu, I., Ma, J. 2010. Artificial Selection for Determinate Growth Habit in Soybean. In: Proceedings of the National Academy of Sciences. PNAS 107(19):8563-8568. Available: www.pnas.org/cgi/doi/10.1073/pnas. 1000088107.
- Zhang, M., Wu, Y., Lee, M., Liu, Y., Rong, Y., Santos, T.S., Wu, C., Xie, F., Nelson, R.L., Zhang, H. 2010. Numbers of Genes in the NBS and RLK Families Vary by More than Four-Fold Within a Plant Species and are Regulated by Multiple Factors. Nucleic Acids Research. Available: doi:10. 1093/nar/gkq524.
- Betzelberger, A.M., Gillespie, K.M., Mcgrath, J.M., Koester, R.P., Nelson, R.L., Ainsworth, E.A. 2010. Effects of Chronic Elevated Ozone Concentration on Antioxidant Capacity, Photosynthesis and Seed Yield of 10 Soybean Cultivars. Plant Cell and Environment. 33(9):1569-1581. Available: doi: 10.1111/j.1365-3040.2010.02165.x.
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Progress 10/01/08 to 09/30/09
Outputs
Progress Report 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. 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. Significant Activities that Support Special Target Populations Over 3200 plots were planted for seed replacement for the USDA Soybean Germplasm Collection. During the first 6 months of 2009 we distributed over 40,000 seed samples in response to 558 requests. Over 3700 four-row yield plots are being grown to identify yield genes from exotic soybean germplasm or to confirm genes tentatively identified in previous research. The objective is to find yield enhancing genes from exotic germplasm that can improve the yield of U.S. commercial varieties. Over 100 accessions from the USDA Soybean Germplasm Collection are being planted at 6 locations to confirm resistance to soybean rust identified in previous research. Nearly 2400 four-row yield plots and 3800 one-row yield plots were planted to identify high yielding experimental lines derived from exotic germplasm. These lines have pedigrees that range from 13 to 100% exotic germplasm. Two hundred fifty one advanced experimental lines are being cooperatively tested with soybean breeders in private industry. Over 1800 experimental lines were analyzed to select for high oil concentration, and 1100 lines were analyzed for high protein concentration, and 100 lines were analyzed to select for high or low isoflavone concentration. Genome expression in roots responding to Fusarium virguliforme was analyzed for 3 biological replicates for both resistant and susceptible genotypes. Determined that 2500 of the 38,000 genes analyzed were significantly changing in expression level during these interactions at 5 and 7 days post inoculation. Finished analysis of experiments designed to determine soybean responses to specific type- three-secretion-system effectors released by plant-invasive bacteria. Identified over 6630 significantly changing genes out of 38,000 in the soybean leaf response to Psuedomonas syringae and 3050 changing in response to Bradyrhizobium japonicum. qRT-PCR has been performed on 20 genes to verify the B. japonicum data. RNA has been purified from an additional time point to be used for verification of the P. syringae study. Completed and published our Sclerotinia stem infection study. The final analysis was the mapping of genes that were differentially expressed during the resistance response and determining their location relative to known Sclerotinia resistance QTL. Six of these genes were within 500 kb of a known resistance QTL. We conducted third microarray replication of soybean leaves infiltrated with the Sclerotinia virulence factor, oxalic acid. We obtained RNA of 3 biological replicates for qRT- PCR verification of our microarray study involving the oxalate oxidase transgenic and have begun the qRT-PCR analysis of 17 genes. Conducted analysis of D1 subunit of photosystem II during pathogen attack. Conducted qRT-PCR on this and 14 other chloroplast genes from leaves inoculated with P. syringae and conducted western blots using a D1- specific antibody on proteins extracted from similarly infected leaves. Implementing functional analysis tools for our lab to allow RNAi studies in soybean roots and leaves. We successfully made RNAi constructs to 6 defense-candidate genes. These constructs were transformed in soybean roots and restricted nodulation. Significant Activities that Support Special Target Populations We participated in the University of Illinois Research Apprentice Program II (RAPII) and hosted a high school student from June 14 to August 1, 2009. The RAP program is designed to expose high-school students from under-represented communities to Agriculture-related research. An African- American high-school student from Chicago, participated in a project involving the genetic analysis of a soybean mutant. She did some work in the field (collect leaf discs and phenotypic data from a segregating population) as well as work in the lab (RNA extractions, small gene expression study, and a chemical assay). At the end of the program, she presented a research paper, a poster and gave a 12 minute PowerPoint presentation. She was one of several students to win awards for �Outstanding Scholarship� and �Outstanding Presentation�. Technology Transfer Number of New/Active MTAs(providing only): 2 Number of New Germplasm Releases: 1 Number of Web Sites managed: 1 Number of Other Technology Transfer: 7
Impacts
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Publications
- Bilgin, D.D., Delucia, E.H., Clough, S.J. 2009. A Robust Plant RNA Isolation Method for Affymetrix Genechip� Analysis and Quantitative Real- Time RT-PCR. Nature Protocols. 4:333-340.
- Wang, W., Dia, V.P., Vasconez, M., Nelson, R.L., De Mejia, E.G. 2008. Analysis of Soybean Protein- Derived Peptides and the Effect of Cultivar, Environmental Conditions, and Processing on Lunasin Concentration in Soybean and Soy Products. Journal of Association of Official Analytical Chemists International. 91:936-946.
- Calla, B., Vuong, T., Radwan, O., Hartman, G.L., Clough, S.J. 2009. Gene Expression Profiling Soybean Stem Tissue Early Response to Sclerotinia sclerotiorum and in Silico Mapping in Relation to Resistance Markers. The Plant Genome. 2:149-166.
- Zhu, J., Patzoldt, W.L., Radwan, O., Tranel, P.J., Clough, S.J. 2009. Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome. The Plant Genome. 2:191-205.
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Progress 10/01/07 to 09/30/08
Outputs
Progress Report 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. 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. Significant Activities that Support Special Target Populations Determined soybean gene expression response to Fusarium virguliforme and verified the results using qRT-PCR. Determined the expression of genes in plants naturally infected. We expanded our original study over 6 time points. This addresses NP301 National Program Action Plan Problem Statement 1B: Assess the Systemic Relationships and Genetic Diversity of Crop Genetic Resources and NP303 National Program Action Plan Problem Statement 3A: Mechanisms of Plant Resistance. Added an additional replicate to our Sclerotinia stem infection study. We conducted additional array studies related to effect of virulence factor oxalic acid. This addresses NP301 National Program Action Plan Problem Statement 1B: Assess the Systemic Relationships and Genetic Diversity of Crop Genetic Resources and NP303 National Program Action Plan Problem Statement 3A: Mechanisms of Plant Resistance. Over 1,400 plots have been planted for seed replacement for the USDA Soybean Germplasm Collection. We received and planted 214 new introductions from northern Vietnam. During the first 6 months of 2008 we have already distributed nearly 16,000 seed samples in response to 391 seed requests. This addresses National Program Action Plan Problem Statement 1A: Efficiently and Effectively Manage Plant and Microbial Genetic Resources. Nearly 3200 four-row yield plots are being grown to identify yield genes from exotic soybean germplasm or to confirm genes already tentatively identified in previous research. The objective is to find yield enhancing genes from exotic germplasm that can improve the yield of U.S. commercial varieties. This addresses National Program Action Plan Problem Statement 2C: Genetic Analyses and Mapping of Important Traits. Over 90 accessions from the USDA Soybean Germplasm Collection are being planted at 7 locations to confirm resistance to soybean rust that has been identified in previous research. This addresses National Program Action Plan Problem Statement 3B: Capitalizing on Untapped Genetic Diversity Nearly 2400 four-row yield plots and 4200 one-row yield plots were planted to identify high yielding experimental lines derived from exotic germplasm. These lines have pedigrees that range from 13 to 100% exotic germplasm. Two hundred thirty advanced experimental lines are being cooperatively tested with soybean breeders in private industry. This addresses National Program Action Plan Problem Statement 3C: Germplasm Enhancement/Release of Improved Genetic Resources and Varieties.
Impacts
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Publications
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