2013 Annual Report
1a.Objectives (from AD-416):
1) Assess critical needs and determine gaps in various ARS Glycine sub-collections of national importance and of ARS programmatic priority, and acquire the appropriate cultivated and/or wild accessions to fill those gaps or increase numbers where necessary;.
2)For all maturity groups, conduct nationally-coordinated baseline evaluations for morphological classifications, other valuable traits, or genes of interest, as well as conserve and distribute available accessions in the soybean collection; 2a) Evaluate annual accessions for basic agronomic, descriptive and seed composition traits; 2b) Conserve, regenerate, and distribute genetic resources and associated information;.
3)Identify useful genomic regions in soybeans and other Glycine species or find rare alleles for selection during introgression to improve traits such as yield, nutritional quality, stress tolerance, and pest resistance; 3a) Develop genetically diverse, high yielding experimental soybean lines that can expand the genetic base of the commercially used gene pool; 3b) Transfer economically important genetic traits from Glycine soja to soybean; 3c) Characterize an alternative gene pool used for increasing U.S. soybean yield; 3d) Transfer economically important genetic traits from Glycine tomentella to soybean; and,.
4)Facilitate functional evaluation of candidate genes, determine gene identity of known soybean defense-associated candidate genes, identify genes for resistance to Sclerotinia and sudden death syndrome or other diseases, and apply marker technologies to incorporate them into improved soybean lines; 4a) Use high-throughput gene expression analysis to identify candidate defense-associated genes from the germplasm collection; and, 4b) Generate transgenic Arabidopsis and soybean for functional analyses of candidate defense associated genes.
1b.Approach (from AD-416):
We will continue to expand the holdings of the USDA Soybean Germplasm Collection by acquiring accessions from underrepresented areas of Asia and other relevant accessions through exchange and exploration. We will collect data on descriptive and agronomic traits to facilitate the use of the Collection. High quality seeds will be maintained and distributed. We will use available breeding, genetic, and genomic tools to exploit the diversity of the Collection to increase seed yield and improved disease or pest resistance. Exotic accessions not in the commercially used gene pool will be used to develop high yielding experimental lines and populations to expand the genetic base of soybean production in the U.S. and identify new alleles from exotic germplasm that increase seed yield. Mining of gene expression data will lead to identification of candidate defense-associated genes, and the genes will be isolated by RT-PCR cDNA cloning. Candidate defense genes will be over and under expressed in Arabidopsis and/or soybean, and plants assayed for changes in disease responses.
665 accessions in maturity groups V through VIII were evaluated in Stoneville, MS; 459 accessions in maturity groups I through IV were evaluated in Urbana, IL; and 90 accessions in maturity groups 000 through I were evaluated in Rosemont, MN. Data were collected for at least 20 traits including seed yield. For each accession grown at Urbana, pictures of a leaf, leaf surface showing pubescence orientation, pulvinus, mature plants, pods, and seeds were recorded and were added to Germplasm Resources Information Network (GRIN).
We distributed 33,737 seed lots from 14,157 accessions from the USDA Soybean Germplasm Collection in response to 703 requests from 395 individuals. This is the second highest annual distribution in the history of the USDA Soybean Germplasm Collection. This is the eleventh year in a row and 15 of the past 18 years in which we have distributed more seed lots than total accessions in the Collection. We are the only collection in the National Plant Germplasm System with a distribution number to collection size ratio that is over 1. We also sent backup seeds of 315 accessions to the National Center for Genetic Resources Preservation and 1,103 accessions for storage in the Svalbard Arctic Seed Vault. We have sent 10,351 accessions to Svalbard.
In the USDA Uniform Preliminary IIA test, LG10-1562, with a pedigree that is 31% exotic germplasm derived from 8 exotic lines, was 0.4 bu/a below the yield of IA2102, the best check. In USDA Uniform Preliminary IIIB test, LG09-7163 was 1.2 bu/a below IA4005, the highest yielding check, and has a pedigree that is 50% exotic germplasm. In USDA Uniform Preliminary IV test, three of our experimental lines exceeded the yield of all the checks. LG10-2695 was the highest yielding entry and exceeded the best check (IA4004) by 3.8 bu/a. LG09-7167 and LG09-8519 exceeded IA4004 by 0.7 bu/a. There are 13 exotic accessions in the parentages of these three lines.
The best G. tomentella-derived lines of similar maturity to the recurrent soybean parent yielded 15% more than the recurrent parent when averaged over two locations of testing. G. tomentella-derived lines that were 8 days later than the recurrent parent yielded 26% more than the recurrent parent. The magnitude of the yield increases has not been previously reported with the use of wild Glycine germplasm in soybean breeding. We have also tentatively identified lines with resistance to soybean rust and several biotypes of soybean cyst nematode.
We investigated the role of iron in soybean/Sclerotinia interactions by analyzing expression of iron-related genes and effect of iron added or removed from the disease process. Transgenics were brought up to T2 or T3 stage, and homozygous lines have been obtained for RNAi against GPCR and 14-3-3. The RNAi against MMP will be checked for homozygousity. New RNAi vectors have been constructed to allow controlled induction of the RNAi construct, and new constructs have been made to target multiple MMPs. Preliminary data supports that all three of these genes are required for maximum defense to pathogens.
Use of wild soybean germplasm in soybean breeding. The wild soybean is a very diverse source of germplasm that has not been exploited for increasing soybean yield because of its many negative attributes. ARS researchers at Urbana, IL crossed soybean varieties with five wild soybean lines and created 30 experimental lines that yielded as much as the soybean parents. These lines are unique because based on 1546 DNA markers some of the high yielding lines contained more than 30% of the genes from wild soybean. Based on the procedure used to develop these lines, it was expected that much fewer than 12% of the genes should have come from wild soybean. For the first time we have high yielding experimental lines that contain much of the genetic diversity from 5 wild soybeans. These lines are important parents for expanding the genetic diversity and increasing yield in future U.S. varieties.
Kim, K., Diers, B., Hyten, D., Mian, R.M., Shannon, J., Nelson, R.L. 2012. Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations. Journal of Theoretical and Applied Genetics. 125(6):1353-1369.
Song, Q., Hyten, D., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., Cregan, P.B. 2013. Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS Genetics. 8(1):e54985.
Betzelberger, A.M., Yendrek, C.R., Sun, J., Leisner, C.P., Nelson, R.L., Ort, D.R., Ainsworth, E.A. 2012. Ozone exposure response for U.S. soybean cultivars: linear reductions in photosynthetic potential, biomass and yield. Plant Physiology. 160(4):1827-1839.
Mengistu, A., Bond, J., Nelson, R.L., Rupe, J., Shannon, G., Arelli, P.R., Wrather, A. 2013. Identification of soybean accessions resistant to macrophomina phaseolina by field screening and laboratory validation. Online. Plant Health Progress. 10.1094/PHP-2013-0318-01-RS.
Radwan, O., Wu, X., Govindarajulu, M., Libault, M., Neece, D.J., Berg, H.R., Stacey, G., Taylor, C.G., Huber, S.C., Clough, S.J. 2012. 14-3-3 Proteins SGF14c and SGF14l play critical roles during soybean nodulation. Plant Physiology. 160:2125-2136.
Zabala, G., Campos, E., Varala, K.K., Bloomfield, S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M., Vodkin, L.O. 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. Biomed Central (BMC) Plant Biology. 12:177.