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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

Location: Corn Insects and Crop Genetics Research

2012 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:
Ontologies have been converted into Open Biological Ontologies (OBO) format and are accessible over the web using the Genetic Model Organism Database (GMOD) AmiGO viewer. This program displays and allows free text searches of the SoyBase ontologies. It is accessible at the SoyBase web site at http://soybase.org/ontology.php. In addition, the SoyBase ontologies were also made viewable and searchable at the OBO Foundry website, BioPortal (http://bioportal.bioontology.org/ontologies/47150?p=terms) and at the Generation Challenge Program Crop Ontology website (http://www.cropontology.org/ontology/SOY/SoyBase Soybean Trait Ontology). The existing SoyBase Simple Semantic Web Architechture and Protocol (SSWAP) services have been upgraded and were incorporated into the iPlant Collaborative’s Semantic Discovery Environment. SoyBase staff curated 44 Quantitative Trait Locus (QTL) references from the literature, representing 844 new QTL records added to the Soybean Breeders Toolbox and to the Soybean Composite Genetic map. This increases the resolution of QTL regions facilitating the discovery of genes responsible for agronomically important traits. Added Williams82 minimum tiling path Bacterial Artificial Chromosome (BAC) clones to the SoyBase genome sequence browser. This allows users to relate a phenotypic character to a BAC clone for further sequence analysis. The SoyBase genome viewer was updated with newly annotated soybean genes. SoyBase staff also added 50,574 National Center for Biotechnology Information (NCBI) RefSeq gene models to the SoyBase genome viewer. These gene models were predicted using a different algorithm and provide additional support to some Joint Genome Institute (JGI) gene models as well as indicate regions of the genomic sequence that need focused attention. Compared the soybean genome against the genome sequence of common bean, for improvement of both genomes. Locations for improvement of soybean for the next round of genome assembly were identified. SoyBase and Legume Information System (LIS) personnel worked with Department of Energy-Joint Genome Institute (DOE-JGI) to revise the soybean gene annotations. In the allied LIS, added features for whole-genome searches and comparisons among each of the sequenced legume genomes: soybean, pigeonpea, Medicago truncatula, and Lotus japonicus. Sequence-search matches to soybean lead to the SoyBase GBrowse viewer for close-up exploration. For improved performance and features, the genome browser software was updated from GBrowse 1 to GBrowse 2. In the genome browser, added these data sets: whole-genome comparisons with pigeonpea; gene sequences and genetic markers from pigeonpea; RNA-Seq gene expression data from a soybean/pathogen experiment; a new set of gene predictions from NCBI. For improved performance and features, updated the genome browser software from GBrowse 1 to GBrowse 2. Worked with DOE-JGI and other soybean researchers to evaluate a revised set of soybean gene predictions. Promoted approximately 1,300 gene models into the revised set, which would not have been included without our review.


4.Accomplishments
1. Gene sequencing and genetic markers for chickpea and pigeonpea, toward improved drought tolerance. Global food security requires crops that are nutritious, versatile, and capable of growing in a wide range of challenging growing environments. ARS researchers in Ames, IA working with the SoyBase and Legume Information System have partnered with scientists at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) in India to determine essentially all of the gene sequences for chickpea and pigeonpea, and to design genetic markers for plant breeding work. This work has been used to assist breeders to develop more drought-tolerant crop varieties. Chickpea is grown worldwide, from India to the northern U.S. and Canada, and has a large domestic and international market. Pigeonpea, a protein-rich and highly drought-tolerant relative of soybean, is widely used in India and the Caribbean, and may be suitable as a crop in the southern U.S.

2. Genome sequencing of Medicago truncatula (Barrel medic). Medicago truncatula, a close relative of alfalfa and a more distant relative of soybean and other beans, is used as a biological model because of characteristics such as its small size, short generation time, and relatively simple genetics. ARS researchers in Ames, IA with the SoyBase and Legume Information System have worked with an international team to report the essentially complete genome sequence (the set of all DNA letters in the chromosomes) of M. truncatula. Analysis of the genome sequence and the contained genes shows that although the M. truncatula genome is less than half the size of the soybean genome, it nevertheless has nearly as many genes as soybean, and has accumulated many changes (large and small) since the two species diverged from their common ancestor. Analysis of genes involved in nitrogen fixation shows that this capacity probably evolved from older genes that were involved in plant-fungal interactions. The genome sequence and other findings are expected to have large impacts on the efforts of plant breeders and biotechnologists to develop crop varieties that are able to more efficiently "fix" atmospheric nitrogen to make their own fertilizer, rather than relying on supplemental nitrogen fertilizer which is expensive and can run-off into the environment.


Review Publications
Cannon, S.B., Crow, J.A., Grant, D.M. 2012. SoyBase and the legume information system: accessing information about the soybean and other legume genomes. In: Wilson, R. editor. Designing Soybeans for 21st Century Markets. Urbana, IL: AOCS Press. p. 53-66.

Young, N.D., Debelle, F., Oldroyd, G., Geurts, R., Cannon, S.B., Mayer, K.F., Gouzy, J., Van De Peer, Y., Schoof, H., Udvardi, M.K., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Proost, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Benedito, V.A., Murray, J.D., Naoumkina, M.A., Rosen, B., Silverstein, K.A., Tang, H., Rombauts, S., Zhao, P.X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Berges, H., Bidwell, S., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Doyle, J.J., Dudez, A., Farmer, A.D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Gonzalez, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S., Jeong, D., Jing, Y., Jocker, A., Kenton, S.M., Kim, D., Klee, K., Lai, H., Lang, C., Lin, S., Macmill, S.L., Magdelenat, G., Matthews, L., Mccorrison, J., Monaghan, E.L., Mun, J., Najar, F.Z., Nicholson, C., Noirot, C., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E.F., Riddle, C., Sallet, E., Samain, S., Samson, N., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Seigfried, M., Severin, A., Sherrier, J.D., Shi, R., Sims, S., Sinharoy, S., Sterck, L., Vasylenko, I., Viollet, A., Wang, K., Wang, B., Wang, X. 2011. The medicago genome provides insight into evolution of rhizobial symbiosis. Nature. 480(7378):520-524.

Ashfield, T., Egan, A.N., Pfeil, B.E., Chen, N.W., Ratnaparkhe, M.B., Ameline-Torregrosa, C., Denny, R., Cannon, S.B., Doyle, J.J., Geffroy, V., Roe, B.A., Maroof, M.S., Young, N.D., Innes, R.W. 2012. The impact of polyploidy on the evolution of a complex NB-LRR resistance gene cluster in soybean. Plant Physiology. DOI:10.1104/CS.112.195040.

Cannon, S.B., Shoemaker, R.C. 2012. Evolutionary and comparative analyses of the soybean genome. Journal of Breeding Science. 61(5):437-444.

Cannon, E.K., Cannon, S.B. 2011. CViT: “Chromosome Visualization Tool” – A whole-genome viewer. International Journal of Plant Genomics. DOI:10.1155/2011/373875.

Kudapa, H., Bharti, A.K., Cannon, S.B., Farmer, A.D., Deonovic, B., Kramer, R., Bohra, A., Weeks, N.T., Crow, J.A., Tuteja, R., Shah, T., Dutta, S., Gupta, D.K., Singh, A., Gaikwad, K., Sharma, T.R., May, G.D., Singh, N.K., Varshney, R.K. 2012. A comprehensive transcriptome assembly of pigeonpea (Cajanauscajan L.) using sanger and second-generation sequencing platforms. Molecular Plant. 5(5):1020-1028.

Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P.B., Ma, J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the Paleopolyploid Soybean. The Plant Cell. 24(1):21-32.

Last Modified: 7/25/2014
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