SOW - Genotyping Service.pdf

Statement of Work (SOW)

Whole genome and User Specified SNP Genotyping Service for soybean plant samples

GENERAL INFORMATION

1.0 Scope of Work: Contractor will receive lyophilized soybean tissue samples provided by USDA-ARS. Contractor will then extract genomic DNA for each sample and carry out all necessary steps to provide usable genotypic Single Nucleotide Polymorphism (SNP) information for each sample. Genotypic data must have high fidelity (~≥80% call rate for each SNP for at ≥80% samples). The request is for:

1) Project is a requirement to provide genotypic data provided for each of 1,200 lyophilized soybean tissues samples provided by USDA-ARS. A minimum of 1050 SNP positions, covering all major haplotype blocks across all 20 chromosomes of the soybean genome. USDA-ARS can supply appropriate sequence position information if requested or an existing method may be applicable if it can meet the minimum requirements listed here.

2.0 Background: Modern soybean breeding requires application of genetic markers, typically in the form of Single Nucleotide Polymorphisms (SNPs) to make time critical decisions. Project is detailed below are part of two running genomic selection experiments at USDA-ARS.

The project goals require whole genome coverage of at least 1050 SNPs covering all major haplotype blocks of the twenty chromosomes of soybean, for 1,200 samples.

CONTRACTOR REQUIREMENTS

3.0 Technical Requirements/Tasks:

Vendor service tasks include, but are not limited to:

1) Vendor will receive lyophilized plant tissue samples from USDA-ARS.

ARS plans to ship samples between July 1 and August 10 2022 (ARS is dependent on planting date and plant growth conditions for timing).

2) Vendor will perform DNA isolation, DNA quality control, DNA normalization and all other steps to permit downstream genotyping.

3) Vendor will perform all steps needed to accurately call (~≥80% call rate) genotypes for at least 1050 SNPs covering all major haplotype blocks across the 20 chromosomes of soybean, for 1,200 soybean plant samples provided by ARS. USDA-ARS can provide appropriate SNP positions; or an existing method that meets minimum requirements is acceptable

4) Data must be provided in either hapmap or excel file format electronically submitted by email to ARS no later than September 31st, 2022 to permit time-critical breeding decisions. Data must be a minimum 80% complete on average in regard to each of the genotype x SNP combinations.

4.0 Government Furnished: USDA-ARS researcher will provide 1200 lyophilized soybean leaf tissue samples. The service provider is solely responsible for the entire service. The service provider will submit a report to end user at the end of the completion of the service.

5.0 Deliverables / Schedule: All data generated by the vendor will be submitted to the

ARS within 60 calendar days from date of receipt.

Key Deliverables Item No.

Deliverable

Objective

Due

1 Provide to USDA-ARS genotypic information for ≥1050 SNPs covering all major haplotype blocks across 20 chromosomes, for 1,200 soybean tissue samples

Isolate DNA from lyophilized leaf tissue and perform all steps necessary to provide USDA-ARS genotypic data for 1,200 samples for at least 1050 SNPs. SNPs must cover all major haplotype blocks across all 20 chromosomes in soybean.

Genotyping data must be provided in either excel tabular format (genotype x SNP position) or hapmap file format (~≥80% call rate averaged across SNPs and across samples)

Genotypic data must be provided to USDA-ARS no later than September 30, 2023 to permit time-critical breeding decisions.

6.0 Travel: Not applicable

7.0 Contractor’s Key Personnel: Not applicable.

8.0 Security Requirements: Not applicable.

9.0 Data Rights: USDA-ARS will retain all rights to genotypic information for all provided samples. All of the SNP information provided will be drawn from the public domain.

10.0 Section 508 – Electronic and Information Technology Standards: Not applicable.