Progress 10/01/06 to 09/30/07
Outputs
Progress Report Objectives (from AD-416) The overall objective of this research is to 'anchor' the physical map of the soybean genome to the genetic map. The specific objectives to accomplish the overall objective are 1) to identify genetic markers that will serve as anchors to the genetic map, 2)to identify bacterial artificial chromosome (BAC) clones in which these markers reside, and 3) to develop and map additional genetic markers as needed to anchor any remaining contigs of BAC clones that are not anchored to the genetic map. Approach (from AD-416) The DNA sequence of clones that contain simple sequence repeat (SSR) motifs from which SSR markers were developed and mapped on the soybean genetic map will be used as a source of DNA sequence to develop overgo (OVERlapping oliGOnucleotides) probes. The overgo probes will be hybridized to membranes containing more than 90,000 BAC clones. The clones identified in this manner will serve as anchors to the genetic map. In another project the same 90,000 BAC clones will be fingerprinted and assembled into contigs. Those contigs that are not anchored to the genetic map (floating contigs) will be identified. The DNA sequence of the ends of four to six BAC clones from each floating BAC contig will be determined. Sequence based genetic markers, referral to a single nucleotide polymorphisms (SNPs) will be developed from the sequence information. The SNPs will then be used as genetic markers to map the floating BAC contigs to the genetic map using the single base extension SNP detection system. Significant Activities that Support Special Target Populations This report serves to document research under a reimbursable agreement between ARS and the United Soybean Board (Project #4239) and supports the objectives of project 1275-21000-164-00D. Additional details of the research can be found in the report for the parent project 1275-21000-164- 00D (A Single Nucleotide Polymorphism-based Map of Soybean and Applications to Gene Discovery in Germplasm). The work is conducted in collaboration with researchers at Purdue University. The objective of this work is to anchor the physical map of the soybean genome to the genetic map. This is being accomplished by 1) the identification of bacterial artificial chromosomes (BAC) clones that contain DNA sequences that are already positioned on the soybean genetic map 2) the screening of soybean BAC libraries with �overgo� probes developed from sequence tagged sites that are being genetically mapped via the presence of SNPs they contain and 3) the development of single nucleotide polymorphism (SNP) DNA markers from end-sequences of BAC clones that are located at the ends of BAC contigs that have not been positioned on the genetic map. These are so-called �floating contigs�. The SNP markers developed from the BAC-end sequences were genetically mapped on the existing soybean genetic map using the Minsoy x Noir 1, Minsoy x Archer, and/or Evans x Peking recombinant inbred line (RIL) mapping populations. During the reporting period research centered on the third approach listed above. Progress was made in discovering new SNP DNA markers in DNA sequences of BAC-ends that are in present in 450 different BAC contigs on the physical map that have not as yet been anchored to the soybean genetic map. These SNPs and the BAC clone and BAC contig in which they reside were genetically mapped using the Illumina Bead Station which is a high throughput SNP analysis system recently purchased by the Beltsville Agricultural Research Center. The Illumina BeadStation was used to genetically map these SNPs in one or more of the soybean RIL mapping populations. Progress is monitored via quarterly written reports and by periodic meetings with the collaborator at Purdue University as well as continuous contact with the collaborator via e-mail.
Impacts
(N/A)
Publications
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Progress 02/01/04 to 02/28/07
Outputs
Progress Report Objectives (from AD-416) The overall objective of this research is to 'anchor' the physical map of the soybean genome to the genetic map. The specific objectives to accomplish the overall objective are 1) to identify genetic markers that will serve as anchors to the genetic map, 2)to identify bacterial artificial chromosome (BAC) clones in which these markers reside, and 3) to develop and map additional genetic markers as needed to anchor any remaining contigs of BAC clones that are not anchored to the genetic map. Approach (from AD-416) The DNA sequence of clones that contain simple sequence repeat (SSR) motifs from which SSR markers were developed and mapped on the soybean genetic map will be used as a source of DNA sequence to develop overgo (OVERlapping oliGOnucleotides) probes. The overgo probes will be hybridized to membranes containing more than 90,000 BAC clones. The clones identified in this manner will serve as anchors to the genetic map. In another project the same 90,000 BAC clones will be fingerprinted and assembled into contigs. Those contigs that are not anchored to the genetic map (floating contigs) will be identified. The DNA sequence of the ends of four to six BAC clones from each floating BAC contig will be determined. Sequence based genetic markers, referral to a single nucleotide polymorphisms (SNPs) will be developed from the sequence information. The SNPs will then be used as genetic markers to map the floating BAC contigs to the genetic map using the single base extension SNP detection system. Significant Activities that Support Special Target Populations Funds from the United Soybean Board were provided as part of Project #4239 entitled �Anchoring the Soybean Physical Map to the Soybean Genetic Map�. The work was conducted in collaboration with researchers at Purdue University. The objective of this work was to anchor the physical map of the soybean genome to the genetic map. This was accomplished by 1) the identification of bacterial artificial chromosomes (BAC) clones that contain DNA sequences that were already positioned on the soybean genetic map 2) the screening of soybean BAC libraries with �overgo� probes developed from sequence tagged sites that were being genetically mapped via the presence of SNPs they contained and 3) the development of single nucleotide polymorphism (SNP) DNA markers from end-sequences of BAC clones that are located at the ends of BAC contigs that had not been positioned on the genetic map. These were so-called �floating contigs�. As a result of the availability of the Illumina BeadStation and the success of the Illumina GoldenGate assay which is analyzed on the BeadStation, SNPs were mapped using the GoldenGate assay as well as with the Luminex Flow Cytometer. A total of 1213 BAC-ends, which included 227 + 292 BAC-ends mapped with the Luminex flow cytometer plus 694 mapped using the Illumina GoldenGate assay system were genetically mapped. Once the mapping data were obtained it was used to synthesize an updated version of the Consensus Soybean Genome Map. The new map, as well as all of the underlying DNA sequence data used to design each genotyping assay were forwarded to the USDA, Ames. The expanded version of the map was quite useful not only in anchoring the physical map (based upon fingerprinted BAC clones) to the genetic map, but it was very helpful in anchoring and ordering the supercontigs in the developing sequence of the soybean genome that is being completed by the Department of Energy, Joint Genome Institute in Walnut Creek, CA. Progress was monitored via quarterly written reports and by periodic meetings with the collaborator at Purdue University as well as continuous contact with the collaborator via e-mail.
Impacts
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Publications
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Progress 10/01/05 to 09/30/06
Outputs
Progress Report 4d Progress report. This report serves to document research under a reimbursable agreement between ARS and the United Soybean Board (Grant #4239) and supports the objectives of parent project 1275-21000-164-00D. Additional details of the research can be found in the report for the parent project 1275-21000- 164-00D (A Single Nucleotide Polymorphism-based Map of Soybean and Applications to Gene Discovery in Germplasm). The work is conducted in collaboration with researchers at Purdue University. The objective of this work is to anchor the physical map of the soybean genome to the genetic map. This is being accomplished by 1) the identification of bacterial artificial chromosomes (BAC) clones that contain genetic marker DNA sequences that are already positioned on the soybean genetic map 2) the screening of soybean BAC libraries with overgo probes developed from sequence tagged sites that are being genetically mapped via the presence of SNPs they
contain and 3) the development of single nucleotide polymorphism (SNP) DNA markers from end-sequences of BAC clones that are located at the ends of BAC contigs that have not been positioned on the genetic map. These are so-called floating contigs. The SNP markers developed from the BAC-end sequences will be genetically mapped on the existing soybean genetic map using the Minsoy x Noir 1, Minsoy x Archer, and/or Evans x Peking recombinant inbred line (RIL) mapping populations. During the reporting period research centered on the third approach listed above. Progress was made in discovering new SNP DNA markers in DNA sequences of BAC-ends that are in present in 450 different BAC contigs on the physical map that have not as yet been anchored to the soybean genetic map. These SNPs and the BAC clone and BAC contig in which they reside are being genetically mapped using the Illumina Bead Station which is a high throughput SNP analysis system recently purchased by the Beltsville
Agricultural Research Center. An Illumina Bead Array was designed to permit the mapping of these SNPs in one or more of soybean RIL mapping populations.
Impacts
(N/A)
Publications
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Progress 10/01/04 to 09/30/05
Outputs
4d Progress report. This report serves to document research under a reimbursable agreement with the United Soybean Board (Grant #4239) and supports the objectives of project 1275-21000-164-00D. Additional details of the research can be found in the report for the parent project 1275-21000-164-00D (A Single Nucleotide Polymorphism-based Map of Soybean and Applications to Gene Discovery in Germplasm). The work is conducted in collaboration with researchers at Purdue University; the USDA/Iowa State University; and the University of Georgia, Athens. The objective of this work is to anchor the physical map of the soybean to the genetic map. This is being accomplished by 1) the identification of bacterial artificial chromosomes (BAC) clones that contain genetic marker DNA sequences that are already positioned on the soybean genetic map 2) the screening of soybean BAC libraries with "overgo" probes developed from sequence tagged sites that are being genetically mapped
via the presence of SNPs they contain and 3) the development of single nucleotide polymorphism (SNP) DNA markers from end-sequences of BAC clones that are located at the ends of BAC contigs that have not been positioned on the genetic map. The SNP markers developed from the BAC-end sequences will be genetically mapped on the existing soybean genetic map using the Univ. of Utah Minsoy x Noir 1 or Minsoy x Archer mapping populations. Progress was made in developing SNP- containing STS from soybean unigenes. Information on the DNA sequence of more than 1000 such STS was forwarded to collaborator at Purdue University.
Impacts
(N/A)
Publications
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Progress 10/01/03 to 09/30/04
Outputs
4. What were the most significant accomplishments this past year? This report serves to document research under a reimbursable agreement with the United Soybean Board (Grant #4239) and supports the objectives of project 1275-21000-164-00D. Additional details of the research can be found in the report for the parent project 1275-21000-164-00D (A Single Nucleotide Polymorphism-based Map of Soybean and Applications to Gene Discovery in Germplasm). The work is conducted in collaboration with researchers at Purdue University; the USDA/Iowa State University; and the University of Georgia, Athens. The objective of this work is to anchor the physical map of the soybean to the genetic map. This is being accomplished by 1) the identification of bacterial artificial chromosomes (BAC) clones that contain genetic marker DNA sequences that are already positioned on the soybean genetic map and 2) by the development of single nucleotide polymorphism (SNP) DNA markers from
end-sequences of BAC clones that are located at the ends of BAC contigs that have not been positioned on the genetic map. The SNP markers developed from the BAC- end sequences will be genetically mapped on the existing soybean genetic map using the Univ. of Utah Minsoy x Noir 1 mapping population. Markers that are not polymorphic in the Minsoy x Noir 1 mapping population will be mapped on the Univ. of Utah Minsoy x Archer recombinant inbred line mapping population.
Impacts
(N/A)
Publications
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