Alfalfa Genome Assembly

Sources Sought Notification for Alfalfa Genome Assembly

This is a Sources Sought Announcement issued by the United States Department of Agriculture (USDA) for informational and planning purposes only. This is NOT a solicitation, nor is it an announcement for a forthcoming solicitation. Submission of any information in response to this notification is purely voluntary. The Government assumes no financial responsibility for any costs incurred in providing a response.

The USDA has a requirement for a Omni-C analysis of eight alfalfa genomes for long-range mapping in accordance with the attachment 1: Statement of Work.

Responses to this notification will help to determine the acquisition strategy for any future solicitation.

Submission Instructions: Interested vendors are invited to submit a response to this Sources Sought notification by 11:00 a.m. CT on April 22, 2024, to the attention of Tiffany Reval, Contracts Specialist, at tiffany.reval@usda.gov . All questions are asked to be submitted in writing to the Primary Point of Contract and will be addressed accordingly.

Responses should be no more than 10 pages and include the following information:

1. Organization Name;
2. Contact Name, e-mail address and phone number;
3. Organizations UEI number;
4. Business size status for the applicable NAICS code;
5. A statement of interest in any forthcoming acquisition.
6. A statement of capability to perform details of the requirement to include all requirements outlined in SOW.

Interested vendors are instructed to provide only the data requested. No proprietary classified confidential or sensitive information should be included in your response. The Government reserves the right to use any nonproprietary technical information in any resultant solicitation(s). Any additional information will not be reviewed by the USDA.

1. Scope of Work:  

The service provider will perform Dovetail® Omni-C® Assays from alfalfa leaf samples provided by the Plant Science Research Unit located at the University of Minnesota, St. Paul, MN. The goal of the ARS project is to obtain long range mapping data to accurately assemble the four haplotypes of the alfalfa genome for eight unique alfalfa genotypes. 

2.0    Background:  

Developing genomic resources for alfalfa has lagged behind other crop species. One goal of this project is to assemble the genomes of diverse alfalfa plants and carry out comparisons to identify key genes responsible for agronomic traits important to alfalfa farmers. The highly heterogeneous and tetraploid nature of alfalfa makes assembly of genomes very complex. Long range mapping by Omni-C is required to accurately assemble genomes.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks: 

Young leaf material from eight plants will be shipped to the service provider on dry ice. The service provider will perform these specific tasks:

1. Construct a sufficient number of Omni-C libraries to generate 15x coverage per haplotype of genome.
2. Sequence each Omni-C library to a target depth of 15X per haplotype of PE150 reads.
3. Deliver the results files to the Customer electronically via secure FTP. The Results shall consist of:  QC report  and Raw ILMN data from deep sequencing the Omni-C library

Delivery schedule: 7 weeks from the receipt of samples.

4. Government Furnished:

The service provider is solely responsible for the entire service.  There will be no support or use of federal facility by the service provider.  The service provider will submit a report to end user at the end of the completion of the service.

5. Deliverables / Schedule: 

All data generated by the vendor will be submitted to Deborah Samac at debby.samac@usda.gov. 

6. Travel:  

No Travel requirements

7. Contractor’s Key Personnel: 

Not applicable

8. Security Requirements:  

Not applicable

9. Data Rights:  

All the data generated by the vendor belongs to the government.

10. Section 508 – Electronic and Information Technology Standards:

Not applicable.