High-density single nucleotide polymorphisms (SNP) marker panel

Summary (Newest Update)

Background The United States Department of Agriculture (USDA) Horticultural Research Laboratory in Fort Pierce, Florida, is seeking a contractor to provide a high-density single nucleotide polymorphism (SNP) marker panel service for genotyping Florida Pompano (Trachinotus carolinus). This acquisition is set-aside for small business concerns, with the goal of enhancing genomic selection and genome-wide association studies by linking desired traits to specific genetic markers. Work Details The contractor will perform the following tasks: 1. Conduct pooled whole genome sequencing at 20x read depth from fin clips for 5 pools of 10 samples, which will take approximately 12 weeks after sample arrival. 2. Develop the SNP panel by aligning sequences to the reference genome, identifying between 30,000 and 60,000 polymorphic markers, and filtering these markers across the species' genome. This step will take about 4 months. 3. Validate the SNP panel design against actual performance using a genetically diverse set of validation samples over an additional period of 8 weeks after receiving new samples. The SNP panel must be delivered within 8 months after contract award. Period of Performance 08/01/2026 to 07/31/2027 Place of Performance USDA Facility at 2001 South Rock Road, Fort Pierce, FL, 34945, USA Bidder Requirements This opportunity is a Total Small Business Set-Aside. Bidders must demonstrate technical acceptability through a detailed explanation of their ability to perform the required services and provide past performance references that indicate their capability to meet contract requirements.