Progress 07/15/10 to 07/14/13
Outputs
Target Audience: The target audience for the Soybean Disease and Biotechnology Center (SDBC) has been U.S. soybean farmers, soybean and soy product consumers such as swine producers and feedmillers, as well as soybean breeders and others researching soybean genetics and soy production. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? The SDBC funding support has initiated very early genomic, next generation sequencing projects, creating a core of expertise within the University that has grown ever since. How have the results been disseminated to communities of interest? The results have been shared with the reserach community including soybean geneticists, pathologists, and nematologists. Findings have also been communicated to soybean farmers, agronomists, animal nutritionists, swine producers, and feedmillers. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Some highlights from the most recent accomplishments are included below. The selection of the soybean miRNAs and siRNAs to use for testing in the microring resonators was achieved from new sequencing small RNA sequencing data generated in our laboratory (Zabala et al., BMC Plant Biology 2012). Conditions for the microring resonators to measure the small RNAs were adapted and modified for plant tissues from those previously used in the Bailey lab for animal systems. A genomic census of protein domains in the genomes of 492 organisms, including many basiodiomycetes, revealed the centrality of metabolic functions for rust fungi and a tendency to evolve via genome expansion mechanisms. Fungal proteomes showed limited functional diversity that was comparable to plants and the development of complex protein structures wiht specialized functions, some of which act as pathogenicity determinants. The soybean gene expression database has been updated to allow comparision of RNA-Seq experiments, in addition to microarray experiments. We have also updated the gene annotations using the latest release of the soybean genome. Comparative transcriptomic analysis using mRNA sequencing (RNA-Seq) revealed significant differences in transcriptional responses of legumes to elevated ozone concentrations, and a putative ozone tolerance strategy that could be employeed in soybean biotechnological improvement efforts. The impact of abiotic stress, including drought, elevated ozone and temperature stress, on the ability of the seed coat to maintain sink strength during the soybean pod fill identified stress-responsive genes that are also know to be involved with regulating disease resistance. The SDBC research has led to papers, including one published in Science, patents, and elucidation of nematode and aphid resistance genetics in cultivated soybean and leveraged funding from several different sources. Fermentation of soybean meal results in a soybean meal that contains more protein and amino acids, but less phytate and oligosaccharides, and has a greater digestibility of phosphorus than conventional soybean meal. Because of these changes, fermented soybean meal can be included in diets fed to weanling pigs as a replacement for fish meal or other animal proteins that are usually used in diets fed to weanling pigs.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2012
Citation:
Zabala, G., Campos, E., Varala, K.K., Bloomfield, S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M., and Vodkin, L.O. Divergent patterns of endogenous small RNA populations from seed and vegetable tissues of Glycine max. BMC Plant Biology 12:177.
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Progress 07/15/11 to 07/14/12
Outputs
OUTPUTS: For Comparative and Functional Genomic Analysis of Soybean Rust Fungi, protein domains are compact, recurrent, and independent folding units of proteins also considered evolutionary units and the basis for several protein structure classification schemes; SCOP and CATH are accepted as gold standards. We annotated the distribution of domains in proteomes, their molecular functions, and the structural architectural designs; and generated phylogenomic trees and timelines of evolutionary history from 492 sequenced genomes, including basidiomycete fungi many of which belong to rust fungi. For Identification of Genes Involved in Ozone Tolerance in Soybean, results from the research were presented at Monsanto Co. in Chesterfield, MO, the 2nd University of Illinois Postdoctoral Research Symposium in Urbana, IL, the Graduate Students in Ecology and Evolutionary Biology Symposium at the University of Illinois in Urbana, IL, the Biology of Plants meeting at Cold Spring Harbor Lab, and the annual meeting of the American Society of Plant Biologists in Austin, TX. For Characterization and Evaluation of Soybean Cyst Nematode Viruses, we developed five different TaqMan assays, one for each SCN virus, that can be used to monitor the presence of the virus in any developmental stage of the nematode. The assay is rapid, sensitive and can detect viruses in a single nematode in both laboratory and field populations of the nematode. For Molecular Cloning and Sequencing of the Rhg1 Locus for Cyst Nematode Resistance, a postdoc and graduate student were employed on a project that successfully found a new mechanism of pathogen resistance in plants. For Label-free and Real Time Quantitation of Soybean Small RNAs Using Microring Resonators, the selection of the soybean miRNAs and siRNAs to use for testing in the microring resonators is completed from small RNA sequencing data generated in our laboratory (Zabala et al., BMC Plant Biology 2012). We selected those that are produced in low, mid and high abundance by the sequence counts. For Carbon Nanotubes for Bigger and Better Soybeans - A Pilot Study, safety protocols have been established at the University of Illinois carbon nanotubes and artificial growth media, the experimental design is finalized, and facilities for the experiment has been set up, materials have been ordered, and soybean seeds are available. For Nutritional Effects of Macrochanges in Soybean Quality, results of the project provided values for the apparent and standardized ideal digestibility of amino acids, values for the digestible and metabolizable energy, and values for the apparent and standardized total tract digestibility of phosphorus in fermented soybean meal, conventional soybean meal and fish meal. Data for growth performance of pigs fed diets containing fermented soybean meal were also generated and data for these diets were compared with those of pigs fed fish meal, poultry by product meal, or chicken meal. For VIPS and Industry Communications, VIPS continues to ensure soybean production research findings are available to the soybean industry using multi-media outlets and web-based tools available at www.nsrl.illinois.edu. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Marketing personnel in the soybean industry, molecular biologists, genomicists, population biologists, evolutionary biologists, plant pathologists, the general public, bioinformaticists, abiotic stress physiologists, climate change scientists, molecular breeders, nutritionists in the feed industry, independent swine nutrition consultants, and pork producers. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
For Comparative and Functional Genomic Analysis of Soybean Rust Fungi, CATH definitions allow better annotation of topological features of molecular structure than SCOP and permit better understanding of the evolution and distribution of structures and associated functions in genomes. In fungi, some of these complex structures adopt specialized functions and become pathogenicity determinants. Structural trends reveal a unique structural sharing between archaeal microbes and eukaryotic organisms such as fungi that involves domains of relatively recent origin. For Identification of Genes Involved in Ozone Tolerance in Soybean, an RNA-Seq analysis protocol was developed to assist a bench scientist beginning to perform the bioinformatics analysis associated with determining differentially expressed genes using RNA-Seq. This paper has general applications to RNA-Seq analysis beyond the scope of soybean and has been highly accessed online since publication. For Characterization and Evaluation of Soybean Cyst Nematode Viruses, the full length SCN virus genome was assembled, shown to be replicating in the nematode and turned out to be new viruses never before identified in any organism. The viruses were very common (50-100%) in laboratory greenhouse cultures and were present to a lesser extent in wild SCN populations. The nematode populations containing viruses grow at a much slower rate suggesting the viruses may be useful as biological control agents. Since the SCN viruses are common in laboratory cultures, they may also be interfering in greenhouse tests done to assess soybean plants for resistance to SCN by making plants appear more resistant than they really are. For Molecular Cloning and Sequencing of the Rhg1 Locus for Cyst Nematode Resistance, we have identified the molecular nature of the locus responsible for the most useful nematode resistance in soybean, making possible new research and resistance breeding methods. For Label-free and Real Time Quantitation of Soybean Small RNAs Using Microring Resonators, finding a method to measure small RNA molecules from plant tissues would allow us to determine the function and fluctuation of small RNAs during soybean development. For Nutritional Effects of Macrochanges in Soybean Quality, data generated from this work enable nutritionists to formulate diets for weanling pigs that contain fermented soybean meal rather than fish meal or other protein sources. Results also demonstrate that pig performance can be maintained if fermented soybean meal is used rather than animal protein sources. This will contribute to an increase in the usage of soybean meal. For VIPS and Industry Communications, promotes rapid dissemination of research using multi-media venues allowing soybean producers and associated agribusinesses to be first adopters of new research and technologies.
Publications
- Bekal, S., Niblack, T., Domier, L. and Lambert, K.N. 2011. Discovery and initial analysis of novel viral genomes in the soybean cyst nematode. Journal of General Virology 92:1870-1879.
- Bukhari, A.S. and G. Caetano-Anolles. 2012. Origin and evolution of protein fold designs inferred from phylogenomic analysis of CATH domain structures in proteomes. PLoS Comput. Biol. (In Press).
- Cook, D.E., T.G. Lee, X. Guo, S. Melito, K. Wang, A.M. Bayless, J. Wang, T.J. Hughes, D.K. Willis, T.E. Clemente, B.W. Diers, J. Jiang, M.E. Hudson, and A.F. Bent. 2012. Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science 30 November 338, 1206-1209.
- Nasir, A., A. Naeem, M.J. Kahn, H.D. Lopez Nicora and G. Caetano-Anolles. 2011. Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. Genes 2:869-911.
- Rojas, O.J. and H.H. Stein. 2012. Digestibility of phosphorus by weanling pigs of fermented and conventional soybean meal without and with microbial phytase. J. Anim. Sci. 90:1506-1512.
- Rojas, O.J. and H.H. Stein. 2011. Concentration of DE and ME in fermented soybean meal, conventional soybean meal, and fish meal fed to weanling pigs. J. Anim. Sci. 89(E-Suppl. 1):333 (Abstr.).
- Rojas, O.J. and H.H. Stein. 2011. Phosphorus and amino acid digestibility in fermented and conventional soybean meal fed to weanling pigs. J. Anim. Sci. 89(E-Suppl. 2):99 (Abstr.).
- Rojas, O.J. and H.H. Stein. 2010. Fermented soybean meal substitutes for fish meal. National Hog Farmer, December issue, 55:16.
- Rojas, O.J. 2011. Nutritional evaluation of fermented soybean meal fed to weanling pigs. Master of Science Thesis. Univ. of Illinois, Urbana-Champaign.
- Stein, H.H. 2012. Use of U.S. soybean meal. Whitepaper for the U.S. Soybean Export Council. Presented at the International Poultry Meeting in Atlanta, Jan. 2012.
- Yendrek, C.R., Ainsworth, E.A. and Thimmapuram, J. 2012. The bench scientists's guide to statistical analysis of RNA-Seq data. BMC Research Notes 5, 506.
- Zabala, G., Campos, E., Varala, K.K., Bloomfield, S., Jones, S.I., Win, H., Tuteja, J.H., Calla, B., Clough, S.J., Hudson, M. and Vodkin, L.O. 2012. Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biology 12:177.
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Progress 07/15/10 to 07/14/11
Outputs
OUTPUTS: For the project "Public Access to the Soybean Gene Expression Database", Dr. Steven Clough reports they updated the web-based Soybean Gene Expression Database (SGED) to be functional with latest version of Linux. They added gene IDs and annotations from the latest version of the soybean genome and added the ability to compare gene expression of data gathered from different expression platforms. For the project "Comparative and Functional Genomic Analysis of Soybean Rust Fungi", Dr. Gustavo Caetano-Anolles reports that the functional repertoire of a cell is largely embodied in its proteome. In a global comparative genomic exercise, we used hidden Markov models of structural recognition to infer protein domain structure at fold superfamily (FSF) level in 974 genomes, including 101 genomes of fungal origin. A total of 1,646 SCOP 1.73 FSF domains were identified, and their molecular functions were annotated using the SUPERFAMILY hierarchical scheme. For the project "Molecular Cloning and Sequencing of the Rhg1 Locus for Cyst Nematode Resistance", Dr. Matthew Hudson reports that data were presented in the plenary oral session at the Asilomar Legume Genomics meeting at Asilomar, CA, and at the Cambridge Healthtech Next Generation Genomics meeting in San Diego. For the project "Identification of Genes Involved in Ozone Tolerance in Soybean", Dr. Elizabeth Ainsworth reports that preliminary results were reported at the Model Legume Congress in Sainte Maxime, France. For the project "Characterization and Evaluation of Soybean Cyst Nematode Viruses", Dr. Kris Lambert reports that they verified that SCN contains four different RNA viruses and are working to confirm three others. Full-length sequences of the four virus genomes were obtained and confirmed to be present in all developmental stages and in many independent nematode isolates. SCN viruses appear similar to plant viruses but do not infect soybeans. For the project "Label-Free and Real Time Quantitation of Soybean Small RNAs Using Microring Resonators", Dr. Lila Vodkin reports they selected a range of soybean small RNAs for testing sensitivity of microring resonators developed by Ryan Bailey in the Chemistry department. The selection of the soybean miRNAs and siRNAs are derived from high throughput sequencing and those produced in low, mid, and high abundance were selected. Conditions for microring resonators have been adapted and modified for plant tissues. For project "Nutritional Effects of Macrochanges in Soybean Products", Dr. Hans Stein reports they completed three experiments to determine digestibility of energy, phosphorus, and amino acids in fermented and conventional soybean meal. Data were analyzed and written into final reports that will be published in peer-reviewed publications. They are completing the data analysis of three additional experiments on new diet formulations for weanling pigs. For project "Carbon Nanotubes for Bigger and Better Soybeans - A Pilot Study", Dr. Linda Kull reports that safety protocols and collaborations are in process to facilitate safe use of nanotubes and maintain sterile environment for transport of in vitro specimens between lab environments. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: The target audience includes other researchers in academic or agricultural industries, nutritionists in animal feed companies, swine producers, soybean breeders and molecular breeders, plant molecular biologist, plant physiologists, molecular biologists, genomicists, population biologists, evolutionary biologists, plant pathologists, bioinformaticists, climate change scientists, nematologists, soybean growers and the general public. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
For the project "Public Access to the Soybean Gene Expression Database", Dr. Steven Clough reports they used SGED and found 20 genes induced by multiple pathogens, which can identify common regulator features useful to discover pathogen inducible genes. For the project "Comparative and Functional Genomic Analysis of Soybean Rust Fungi", Dr. Gustavo Caetano-Anolles reports remarkable conservation in distribution of domains with most of the protein repertoire being spent in metabolic functions. Eukaryotic proteomes appear to evolve via genome expansion mechanisms directed towards innovating new domain structures for functions related to cellular processes (e.g., proteases, motility, cell adhesion) and regulation (e.g., receptors, signal transduction, kinases/phosphatases, nucleic acid binding). Fungal proteomes showed limited functional diversity comparable to plants. For the project "Molecular Cloning and Sequencing of the Rhg1 Locus for Cyst Nematode Resistance", Dr. Matthew Hudson reports they cloned most of the rhg1 locus from PI88788. This locus is a tandem duplication of a region of the soybean genome containing approximately three genes. This may represent a newly identified mechanism of plant resistance. We fine mapped the G. soja-derived nematode resistance locus. For the project "Identification of Genes Involved in Ozone Tolerance in Soybean", Dr. Elizabeth Ainsworth reports working closely with the KECK Center Bioinformatics Group and using transcriptome sequencing data to identify bioinformatic methods to analyze soybean RNAseq results in order to identify ozone responsive genes. For the project "Characterization and Evaluation of Soybean Cyst Nematode Viruses", Dr. Kris Lambert reports that nematode viruses present a potential new biological control agent for SCN. It was observed that greenhouse cultures of SCN had higher virus levels than field isolates, suggesting greenhouse conditions provide an excellent environment for the spread of nematodes. Preliminary observations that non-virulent nematodes had higher virus titers than virulent SCN indicates virus load may alter the virulence profile of nematodes. For the project "Label-Free and Real Time Quantitation of Soybean Small RNAs using Microring Resonators", Dr. Lila Vodkin reports using nanotechnology methods to quickly and sensitively measure small RNA molecules from plant tissues. If successful, a range of tests could determine the function and fluctuation of these molecules during soybean development and determine their involvement in disease response and resistance. For the project "Nutritional Effects of Macrochanges in Soybean Products", Dr. Hans Stein demonstrated that the energy and amino acid digestibility of fermented soybean meal is not changed compared with conventional soybean meal. However, fermentation increases the digestibility of phosphorus which may result in less phosphorus excreted in manure of pigs fed diets compared with conventional soybean meal. The nutritional value of fermented soybean meal is greater than the value of conventional soybean meal.
Publications
- Nasir, A., Naeem, A., Kahn, M.J., Lopez Nicora, H.D. and Caetano-Anolles, G. 2011. Annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. Genes (In Press).
- Rojas, O.J. and Stein, H.H. 2011. Digestibility of phosphorus by weanling pigs of fermented and conventional soybean meal without and with microbial phytase. Peer reviewed article submitted to Journal of Animal Science for publication. Accepted with revisions.
- Sadia Bekal, S., Domier, L.L., Niblack, T.L. and Lambert, K.N. 2011. Discovery and initial analysis of novel viral genomes in the soybean cyst nematode. Journal of General Virology (In Press).
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