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United States Department of Agriculture

Agricultural Research Service

Research Project: CURATION AND DEVELOPMENT OF THE SOYBEAN BREEDER'S TOOLBOX AND ITS INTEGRATION WITH OTHER PLANT GENOME DATABASES
2011 Annual Report


1a.Objectives (from AD-416)
Objective 1: Implement web-accessible computational and visualization tools, including semantic web technologies, to enable comparison and transfer of agronomically important genetic information among soybean and other legume and related dicot species. Objective 2: Continue to curate and enhance SoyBase and the Soybean Breeder’s Toolbox (SBT), more fully integrating the genetic, phenotypic, physical map, and whole-genome sequence data from soybean and other legumes. Objective 3: Coordinate the quality assembly and annotation of the soybean whole-genome sequence.


1b.Approach (from AD-416)
Soybean ontologies will be prepared to describe selected data types from the Soybean Breeders Toolbox (SBT). Data exchange descriptions (“RDF graphs”) will be developed to allow integration of the data into the Virtual Plant Information Network (VPIN). To let researchers transparently find, retrieve, or apply analytical methods to data contained in the SBT, web services will be developed to make these services accessible through a single portal. Soybase and the SBT will be maintained and updated with new data classes as needed. The Williams 82 physical map and the soybean whole genome sequence, new sequence-based data types in SoyBase, and comparative data from other legume will be integrated and displayed. The project works closely with DOE-JGI to enhance the quality of the soybean whole-genome sequence assembly. This will include analysis of sequence-based genetic markers, comparative analyses with other genomes, and various informatic analyses.


3.Progress Report
SoyBase staff developed screen views that show how genetic features (genetic markers, specifically) are related among nine legume species and the genomes of three species with sequenced genomes: soybean, Medicago truncatula and Lotus japonicus. This fulfilled Sub-objective 1.A of the parent project; annotation of existing data with soybean trait ontology terms and ID numbers. We also added references to external ontology terms to Soybean Breeders Toolbox (SBT) data. Several on-line tools have been added at SoyBase and the Legume Information System (LIS) to link large amounts of genetic data with visual and agronomic traits. One of these tools is for virtual representation of patterns of gene expression in 12 different tissues or stages of development. The “RNA-Seq Atlas of Glycine max,” at http://soybase.org/soyseq/, offers a way for researchers to explore the activities of sets of genes as they change between different tissues and conditions. Development has also continued in the Legume Information System (http://comparative-legumes.org/), with redesigned navigation to focus on typical tasks of researchers; and with a powerful new search tool (http://search.comparative-legumes.org) that integrates results from three reference legume species and from other genomic resources. These additions to the web interfaces provide tools to help scientists and plant breeders develop improved varieties. Project members established that the origin of nitrogen-fixing legume nodules must have predated a genome doubling that occurred in the ancestor of these species. If nodules and nitrogen fixation was able to evolve in this “simpler” ancestral plant (a plant with many fewer genes than in modern crop legumes), then it may eventually be feasible to induce other crop plants outside the legumes to fix nitrogen – and ultimately, to rely less on expensive industrial sources of nitrogen fertilizer. Pulse crops in the bean and pea family provide the majority of protein for a large proportion of the world’s population; yet many of these crop species have received little attention using modern breeding methods. The Ames, Iowa group, working with researchers in India, identified and reported the majority of gene sequences in pigeonpea and chickpea, two important pulse crops providing the majority of protein for a large portion of the world’s population, and described the locations of these genes with respect to the chromosomes of soybean and Medicago truncatula (a genetic model species). The locations of these genes, and new genetic markers for these species, have been added to the genome browsers in SoyBase and the Legume Information System.


4.Accomplishments
1. Powerful new web-based tools available for geneticists and breeders to improve legume crops. A major challenge in plant genetic research is to link the large amounts of new genetic data with concrete breeding objectives and traits of interest. Several on-line tools have been added at SoyBase (the USDA's genetic database for soybean research) and the Legume Information System (LIS: the USDA-sponsored legume-wide genetic database) to meet this challenge. The “RNA-Seq Atlas of Glycine max” offers a way for researchers to explore the activities of sets of genes as they change between different tissues and conditions. Development has also continued in the LIS with redesigned navigation to focus on typical tasks of researchers; and with a powerful new search tool that integrates results from three reference legume species and from other genomic resources. These additions to the web interfaces provide tools to help scientists and plant breeders expedite the development of improved crop varieties. SoyBase alone in accessed by more than 2,000 unique visitors per month and LIS has even greater visitation.

2. Understanding the evolution of nitrogen fixation in legumes could lead to its use in other crops. Nitrogen is a growth and production limiting nutrient for most crops, but is available to legumes such as soybeans, field beans, and peas, via an association with specialized nitrogen-fixing soil bacteria, in legume root nodules. An understanding of the way in which this association evolved is needed before this capacity can be extended to other crops. ARS researchers in Ames, IA established that the origin of nitrogen-fixing legume nodules must have predated an evolutionary event in which the numbers of chromosomes doubled in the ancestors of these species. If nodules and nitrogen fixation were able to evolve in this simpler ancestral plant (a plant with many fewer genes than in modern crop legumes), then it may eventually be feasible to induce other crop plants outside the legumes to fix nitrogen and ultimately, to rely less on expensive industrial sources of nitrogen fertilizer.

3. Bringing modern gene science techniques to pigeonpea and chickpea improvement. Pulse crops in the bean and pea family provide the majority of protein for a large proportion of the world’s population; yet many of these crop species have received little attention using modern breeding methods. ARS scientists in Ames, IA, working with researchers in India, identified and reported the majority of gene sequences in pigeonpea and chickpea, and described the locations of these genes with respect to the chromosomes of soybean and Medicago truncatula (a genetic model species). The locations of these genes, and new genetic markers for these species, have been added to SoyBase, the USDA soybean genetic database, and the Legume Information System, a USDA-sponsored legume genetic database. These databases make the information available freely and worldwide. Pigeonpea is an important protein-rich pulse crop used in the Caribbean and south Asia, and chickpea is used worldwide as a versatile pulse crop. Both are important for global food security, and chickpea is a significant crop in the Northern Great Plains.


Review Publications
Hiremath, P.J., Farmer, A., Woodward, J., Cannon, S.B., Kudapa, H., Tuteja, R., Kumar, A., Varshney, R.K. 2011. Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa. Plant Biotechnology Journal. 9:922-931.

Dubey, A., Farmer, A., Schlueter, J., Cannon, S.B., Abernathy, B., Tuteja, R., Woodward, J., Varshney, R.K. 2011. Defining the transcriptome assembly and its use for genome dynamics and transcriptome profiling studies in pigeonpea (Cajanus cajan L.). DNA Research. 18(3):153-164.

Cannon, S.B., Ilut, D., Farmer, A.D., Maki, S.L., May, G.D., Singer, S.R., Doyle, J.J. 2010. Nodule evolution did not depend on early polyploidy in the legumes. PLoS One. 5(7):e11630.

Findley, S.D., Cannon, S.B., Varala, K., Du, J., Ma, J., Hudson, M.E., Birchler, J., Stacey, G. 2010. A Fluorescence In Situ Hybridization System for Karyotyping Soybean. Genetics. 185:727-744.

Bolon, Y.E., Haun, W.J., Xu, W.W., Grant, D.M., Stacey, M.G., Nelson, R., Gerhardt, D.J., Jeddeloh, J.A., Stacey, G., Muehlbauer, G.J., Orf, J.H., Naeve, S.L., Stupar, R.M., Vance, C.P. 2011. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiology. 156(1):240-253.

Peto, M.F., Grant, D.M., Shoemaker, R.C., Cannon, S.B. 2010. Applying small-scale DNA signatures as an aid in assembling soybean chromosome sequences. Advances in Bioinformatics. DOI:10.1155/2010/976792.

Du, J., Tian, S., Hans, C., Jackson, S., Cannon, S.B., Shoemaker, R.C., Ma, J. 2010. Evolutionary conservation, diversity and specificity of LTR retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison. Plant Journal. 63(4):584-598.

Song, Q., Jia, G., Zhu, Y., Hwang, E., Hyten, D.L., Cregan, P.B., Grant, D.M., Nelson, R. 2010. Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Science. 50:1950-1960.

Bolon, Y.E., Joseph, B., Cannon, S.B., Graham, M.A., Diers, B.W., Farmer, A.D., May, G.D., Muehlbauer, G.J., Specht, J.E., Tu, Z., Weeks, N.T., Xu, W.W., Shoemaker, R.C., Vance, C.P. 2010. Complementary Genetic and Genomic Approaches Help Characterize the Linkage Group I Seed Protein QTL in Soybean. Biomed Central (BMC) Plant Biology. 10:41. Available: http://www.biomedcentral.com/1471-2229/10/41.

Last Modified: 12/18/2014
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