Maize DNA Extraction and Sequencing

Questions & Answers / Clarifications

This document provides responses to vendor questions regarding the solicitation, clarifying requirements for sequencing methodology, data delivery, and sample specifications.

• Sequencing Methodology: Any methodology capable of sequencing fragmented genomic regions is acceptable. Bidders should refer to the attached SOW for further details.
• Data Delivery: Hard disk delivery is required for raw sequencing data and processed genotype data in VCF format. Uploading to a secure AWS bucket is not an alternative.
• Genome Size: The estimated genome size of Maize is 2.4 Gb.
• Shipping Date: Freeze-dried leaf tissue can be shipped approximately on 07/10/2026.
• Sample Amount: The amount of leaf tissue per sample that can be submitted is 0.1 gram.

This Q&A document clarifies specific technical requirements and logistical details, which bidders should consider when preparing their proposals. No changes to deadlines or submission rules are indicated.

Questions & Answers / Clarifications

This document provides responses to vendor questions regarding the Statement of Work (SOW) for an opportunity that involves providing raw sequencing data and processed genotype data.

• Data Delivery: The SOW requirement for "Provide both raw sequencing data and processed genotype data in VCF format on a hard disk" is clarified. Vendors may upload data into a secure AWS bucket for fast and safe transfer and storage, with security keys provided to approved collaborators. 90 days of free unlimited storage and transfer are included and can be extended.
• Maize Genome Size: The estimated genome size of Maize is 2.4 Gb.
• Shipping Date: The approximate date for shipping freeze-dried leaf tissue is 07/10/2026.
• Leaf Tissue Amount: The amount of leaf tissue per sample that can be submitted is 0.1 gram per sample.

This Q&A document clarifies data delivery methods and provides specific details on sample size, genome size, and shipping dates, which may impact proposal preparation and execution plans.

Statement of Work (SOW)

To provide DNA extraction and next-generation genotyping services for 384 maize leaf samples to support downstream genetic, breeding, diversity, and genome-wide association studies, contributing to the development of improved maize inbred lines.

• Extract high-quality genomic DNA from freeze-dried maize leaf tissue.

• Prepare genotyping libraries using an ApeKI restriction enzyme and a PCR-free method, including positive and negative controls.

• Perform Next Generation Sequencing using an Illumina NovaSeq X 10B or similar platform (2 x 150 Paired End reads, minimum 25x sequencing depth per sample).

• Analyze sequencing data to generate high-quality genotyping data with a minimum 95% call rate per sample, aligning to the B73 RefGen_v5 reference genome.

• Produce a minimum of 15,000 SNP markers with known chromosomal positions.

• Deliver user-friendly genotype data files and raw sequencing data in VCF format on a hard disk.

• Minimum 90% of samples must meet required DNA quality standards for genotyping.

• Minimum 95% call rate for successfully genotyped samples.

• Minimum 15,000 SNP markers produced.

• All processing activities to be completed within 15 weeks of sample receipt.

Not explicitly stated in the provided text, but implies processing of 384 samples.

• DNA quality-control (QC) metrics must be documented and provided.
• Samples that fail QC must be identified and reported.
• Data must be handled confidentially and released only to authorized project personnel.
• Regular status updates must be provided to the Government.

Solicitation / RFP / RFQ

This solicitation is for DNA extraction and sequencing services for 384 maize leaf samples. The USDA ARS Corn Host Plant Resistance Research Unit in Mississippi State, MS requires these services.

• DNA extraction and sequencing for 384 maize leaf samples.

• Services must be in accordance with the attached Statement of Work (SOW).

• Anticipated Award Type: Firm-Fixed price purchase order.

• Period of Performance: 15 weeks, from 06/15/2026 to 09/30/2026.

• Delivery: Required by 9/30/2026. Early deliveries are accepted.

• FOB Point: Destination.

• Offer Due Date: 06/05/2026 at 1700 CT.

• Offerors must submit pricing for all items to be considered responsive.

• Evaluation: Quotes will be evaluated based on Technical Approach, Price, and Past Performance.

  • Technical Approach: Assesses the offeror's ability to meet requirements and understanding of the SOW.
  • Price: Will be evaluated to determine if it is fair and reasonable.
  • Past Performance: Will be assessed as acceptable or neutral.

• Award will be made to the offeror whose proposal is determined to be the highest technically rated, provided the proposed price is fair and reasonable, and past performance is acceptable or neutral. Trade-offs will not be conducted.

• Offer Acceptance Period: Offerors agree to hold prices firm for 90 calendar days from the offer due date.

• NAICS Code: 541380

• Size Standard: $19 Million

• The acquisition is listed as "UNRESTRICTED" with no specific set-aside indicated.

• Questions are due no later than May 22, 2026, at 5:00 PM CDT.

• Submit questions via email to kerrie.hodges@usda.gov. Include the solicitation name and number in the subject line.

• This solicitation incorporates numerous FAR and AGAR clauses and provisions by reference. Full text is available upon request or at https://www.acquisition.gov/far-overhaul/far-part-deviation-guide/far-overhaul-part-52.

• The Statement of Work (SOW) is attached as Attachment 1.