REVISED SOW-Parentage Assignments updated.pdf

Single Nucleotide Polymorphism Low-Density Array Genotyping and Parentage Assignment Services in Rainbow Trout

Statement of Work: The USDA ARS National Center for Cool and Cold Water Aquaculture requires parentage assignments services for rainbow trout from 168 full-sib individual families, including 310 parents genotyped in duplicate and 5,880 offspring. The service includes DNA extractions and single nucleotide polymorphism (SNP) genotyping of 6,500 rainbow trout DNA samples using low-density (LD) assays of 96 SNPs or more and high confidence assignment of at least 95% of the offspring. Deliverables will include the results of the parentage assignment analysis and the genotyping raw data for all the samples in Excel file or in flat files. Unused tissue samples and DNA samples will be sent back to the government. Contractor shall provide all services, supplies, equipment and facilities necessary to provide the deliverable specified in accordance with the terms, conditions, and specifications contained in this document.

The government will provide the tissue samples (fin clips in ethanol) for DNA extractions and genotyping, including samples from the parents of the fish and pedigree information of the specific crosses made. The following performance elements and benchmarks are required:

1. Amount of DNA per sample required is at least 200 ng of total rainbow trout genome DNA;

2. Passing samples have SNP call rates greater than or equal to 90%;

3. Minimum offspring sample pass rate of 95% and 100% for the parents;

4. Vendor must have a fully integrated LIMS (Laboratory Information Management System) for sample tracking to ensure that there are no errors in matching the genotypes to the samples;

5. Vendor must have barcodes or barcoded plates for the DNA samples;

6. Vendor must have in place a series of quality control (QC) steps during the SNP genotype processing;

7. Completion and return of required data is required within 90 days of samples receipt.

8. Sending back of remaining tissue samples in ethanol and unused DNA samples upon completion of the project.

Schedule of Line Items:

Line Item 01 – DNA extractions and SNP genotyping of 6,500 rainbow trout DNA samples All government samples will be provided before December 30, 2021.

Line Item 02 – Parentage analysis results and assignments for each individual sample with high confidence assignment of at least 95% of the offspring

Line Item 03 – Return shipping of all unused tissue samples in ethanol and DNA samples

Deliverable will include the genotyping data for all the samples, and the parentage analysis results, and shipping back of all unused tissue samples in ethanol and DNA samples. All data must be provided via secure portal download or in external hard drives delivered FOB Destination to POC will be given once awarded. Completion and return of deliverable is required within 90 days after receipt of all Government provided samples. The order number shall be included on all documentation and shipments.