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Research Project:
A STRATEGY FOR RESPONDING TO THE WHOLE-GENOME SHOTGUN SEQUENCE OF THE SOYBEAN GENOME
Location: Corn Insects and Crop Genetics Research
2007 Annual Report
1a.Objectives (from AD-416)
1) Assemble the DNA sequence and connect it to the soybean genetic 'road map'.
2) Additional SNP genetic markers will be developed and mapped.
1b.Approach (from AD-416)
Whole genome sequence (WGS) will be overlaid onto the physical and genetic map. Paired ends will be identified that indicate DNA clones span gaps in the genome sequence. BAC end sequences will be aligned to the WGS thus overlaying the sequence onto the physical map. Genome sequence from PI 468916 will be aligned with the WGS of Williams 82 and SNPS will be identified. Information will be provided to collaborators at USDA-ARS, Beltsville and SNP markers will be developed and mapped. A 200 SSR map infrastructure will be created in a cross population between Williams 82 and PI 468916. Approximately 4,000 SNPs will be mapped. The DNA sequence from which the SNPs were detected will be correlated with the WGS, thus anchoring the sequence map with the genetic map. Data will be entered into public soybean genome databases.
3.Progress Report
This report documents research conducted under a reimbursable agreement between ARS and the United Soybean Board. Additional details of research are in the report for the parent project 3625-21000-038-00D Curation and Development of SoyBase and its Integration with other Plant Genome Databases. This project is part of NP 301 Plant Genetic Resources, Genomics and Genetics Improvement, and fits within Action Plan Component II, Crop Informatics, Genomics and Genetic Analyses, Problem Statement 2A: Genome Database Stewardship and Informatics Tool Development, and 2B: Structural Comparison and Analysis of Crop Genomes. Progress on this project will be monitored through written progress reports, conference calls, email contact and personal visits. During the reporting period a new SCA with Purdue University was initiated and recruitment of an ARS post-doctoral was begun. An initial assessment of the 4X genome assembly was conducted using sequence-based genetic markers.
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Last Modified: 11/07/2008
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