C04-12444726Q0077 SOW.pdf
PDF 72 KB Posted
- Attached to
- Sole Source-Genotyping Tropical Derived Corn Lines Federal contract opportunity
- Solicitation number
- 12444726Q0077
- Issued by
- Department of Agriculture Forest Service
About this file
This is a Statement of Work for genotyping tropical derived corn lines under the USDA Germplasm Enhancement of Maize (GEM) Project located at the North Central Regional Plant Introduction Station in Ames, Iowa.
The contractor must perform genotyping services using target sequencing with probe-in-solution target enrichment methodology. Technical requirements include: kernel chipping capability for corn seeds; DNA extraction with quality control measures; DNA library preparation encompassing fragmentation, end repair, A-tail addition, adapter ligation, and barcode amplification with qPCR quantification; two marker panels targeting approximately 45,000 SNPs (capturing over 250,000 multiple SNP clusters) and 10,000 SNPs (capturing over 50,000 multiple SNP clusters, as a subset of the 45k panel), evenly distributed across 10 corn chromosomes and developed from temperate, subtropical, and tropical germplasm using consistent SNP sets for historical comparisons; quality-controlled sequencing with trimming; and bioinformatics analysis with a user-friendly interface for reference sequence comparative analysis, sequencing depth and coverage statistics, and detection and annotation of variation loci including SNPs, indels, and STRs/SSRs. The government will furnish corn seeds for genotyping by December 31, 2026, and the contractor must complete all work within 180 days of seed receipt. Evaluation criteria include technical capability, price, and delivery availability. Generated data will be owned by the USDA and made available upon request. The technical point of contact is Adam Vanous at 515-231-3517 or adam.vanous@usda.gov.
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| File | Type | Posted |
|---|---|---|
| C04-12444726Q0077_RFQ.pdf |
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Text version
Statement of Work
Project: Genotyping tropical derived corn lines
GENERAL INFORMATION
1.0 Scope of Work: The USDA Germplasm Enhancement of Maize (GEM) Project, located at the North Central Regional Plant Introduction Station in Ames, IA, is conducting a study with the objective of determining genomic contributions of exotic maize and how this is affected when using genomic selection.
2.0 Background: The Germplasm Enhancement of Maize Project adapts exotic maize germplasm from around the world to the U.S. Corn-Belt. Temperate corn lacks diversity for many key traits: disease resistance, drought tolerance, and pest resistance. Exotic maize possesses the diversity to increase tolerances and resistances; however, the GEM corn lines are predominately temperate maize.
Genotyping GEM material would allow for the quantification of exotic maize contributions and allow for a more focus approach to breeding for these tolerances and resistances. These genotypes would also allow for the development of a scheme that would allow for the implementation of genomic selection to speed up the breeding cycles, all while maintaining genetic diversity.
CONTRACTOR REQUIREMENTS
3.0 Technical Requirements/Tasks:
Methodology: Genotyping by target sequencing utilizing probe-in-solution target enrichment.
Plant material: Capable of kernel chipping corn seeds.
DNA: DNA extraction from kernel chipping. DNA quality control measures must be practiced, ensuring genotyping quality.
Library Construction: Must be able to provide DNA library preparation: 1) DNA fragmentation, 2) end repair and A-tail addition, 3) adapter ligation, and 4) library amplification with barcode primers. Library quality checks should be performed via qPCR to quantify concentration.
Marker Panel: Marker panel capable of targeting ~45,000 SNPs and capturing over 250,000 multiple SNP clusters. A second marker panel targeting ~10,000 SNPs and over 50,000 multiple SNP clusters that is a subset of the 45k SNP panel. Marker panel must be evenly distributed across the 10 corn chromosomes. Marker panel should be developed and tested from diverse corn germplasm consisting of temperate, subtropical, and tropical germplasm. Marker panel should consist of the same SNPs that were used in the past to ensure direct comparisons between genotyped materials.
Sequencing: Quality control for sequence reads must be practiced. Sequence trimming to ensure quality is a must.
Bioinformatics: Bioinformatics analysis must be included. Interface should include a user-friendly interface for reference sequence comparative analysis, sequencing depth and coverage statistics, detection and annotation of variation loci, including SNPs, indels, STRs/SSRs.
4.0 Government Furnished: Corn seeds for genotyping by December 31, 2026.
5.0 Deliverable/Schedule: Work should be completed within 180 days of receiving corn seeds.
6.0 Evaluate Factors: Bids will be evaluated on technical capability outlined in Section 3.0, price, and delivery availability.
7.0 Data Rights: Generated data will be owned by the USDA and will be made available as requested.
8.0 Technical Point of Contact: Adam Vanous, 515-231-3517, adam.vanous@usda.gov
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