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United States Department of Agriculture

Agricultural Research Service

Research Project: SOYBEAN GENETIC MANAGEMENT AND UTILIZATION
2010 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
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.


4.Accomplishments
1. Identification of an important soybean gene. The type of stem termination is a difference between soybean varieties grown in northern (indeterminate) 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 soybean genome. From the four possible genes identified, the most likely candidate 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 be 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).

2. 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 in 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 between 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 in 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 not known but understanding the processes will be an important step in understanding variation among and evolution of these important agriculture species. (Nucleic Acids Research doi: 10.1093/nar/gkq524).


5.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.


Review 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.

Last Modified: 12/21/2014
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