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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

2008 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
We prepared a soybean trait ontology for traits described in the Germplasm Resources Information Network descriptors and SoyBase Trait Class. The soybean trait ontology was annotated (mapped) to Gramene trait ontology. A semantic ontology was prepared for the Soybean Breeders Toolbox (SBT) Quantitative Trait Loci (QTL) Class. A simple semantic web access protocol (SSWAP) was developed by collaborators at NCGR to provide ways to access the data remotely. The first experimentally confirmed QTL (cqQTL) have been added to the Soybean Breeders Toolbox. The first publicly available SNP markers have been positioned onto the Williams 82 physical map. Disease resistance gene families were mapped and characterized. A database for the retrieval of all sequences associated with soybean molecular markers has been developed. An evaluation and assessment of the 8X sequence assembly has begun. Several approaches were used to validate sequence scaffolds. We used a combination of markers, reciprocal syntenic comparisons between homoeologous regions, examination of clone-coverage depths and other scaffold-scaffold relationships, and genomic landmarks such as pericentromeric and telomeric sequences to confirm proper scaffold assembly. These evidence types were used in a "scaffold tracker" that records information about scaffolds in preliminary pseudomolecule sequences. We also assembled preliminary pseudomolecules by ordering and orienting each of the 296 genetically anchored scaffolds, and have compared all the resulting pseudomolecules against one another. With these comparisons, we checked for expected chromosomal synteny relationships, for centromeric and pericentromeric locations, and for potential scaffold mis-orientations. We checked all Bacterial Artificial Chromosome (BAC) end pairs that were not used in the assembly. Finally, we implemented a genome browser (Gbrowse) that is customized for quality control on the assembly. It displays clone coverage depths (BAC and fosmid), marker locations, and repeat densities. We used this and analysis of the markers to identify nine chimeric scaffolds. Updates are provided to DOE-JGI on a regular basis. This progress relates to NP 301 Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development, and Problem Statement 2B:Structural Comparison and Analysis of Crop Genomes because activities enhance the interoperability of plant databases and faciliates the physical and genetic mapping of the soybean genome, thus making it possible to compare genome structures.


4.Accomplishments
1. Prepared a semantic ontology for the SBT QTL class. Because of differences in nomenclature and data formatting from the various sources of information, automatic methods of collating data from diverse data sources is not impossible without human intervention. A simple semantic web access protocol (SSWAP) was developed to provide a way to identify similar data types regardless of file format or provider using a common semantic ontology. This protocol describes a uniform way to request and receive data from various heterogeneous data sources. This system allows researchers and programs to identify sources of data using the common ontology and a common way to retrieve data from the identified sources. This will greatly enhance the ability of researchers to draw upon diverse sources of data, thus speeding hypothesis driven research. This accomplishment addresses NP 301 Action Plan Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development.

2. Genetic dissection of resistance to anthracnose and powdery mildew. Despite the economic need to find novel disease resistance genes in legume crop plants such as soybean, pea, alfalfa, and red clover, only a few resistance genes have been isolated in this plant family. The location of anthracnose and powdery mildew resistance genes were mapped and characterized. Identifying major disease resistance genes and DNA markers associated with these genes will enable plant breeders to rapidly identify superior disease resistant plants and transfer the resistance into productive cultivated varieties, reducing reliance on fungicides and increasing plant productivity. This accomplishment relates to NP 301 Action Plan Component 2: Crop Informatics, Genomics, and Genetic Analyses, Problem Statement 2C: Genetic Analyses and Mapping of Important Traits.


5.Significant Activities that Support Special Target Populations
None.


6.Technology Transfer

None

Review Publications
Ameline-Torregrosal, C., Cazaux, M., Danesh, D., Chardon, F., Cannon, S.B., Esquerre-Tugaye, M., Dumas, B., Young, N.D., Samac, D.A., Huguet, T., Jacquet, C. 2008. Genetic dissection of resistance to anthracnose and powdery mildew in Medicago truncatula. Molecular Plant-Microbe Interactions. 21(1):61-69.

Last Modified: 4/15/2014
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