Genotyping of Soybeans

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in Subpart 12.6, as supplemented with additional information included in this notice. This announcement constitutes the only solicitation; quotes are being requested and a written solicitation will NOT be issued. Solicitation number 12505B22Q0163 is issued as a request for quote (RFQ). The solicitation document and incorporated FAR provisions and clauses are those in effect through Federal Acquisition Circular 2022-06. This solicitation will be a 100% Total Small Business Set-Aside. The associated NAICS code is 541714, Research and Development in Biotechnology (except Nanobiotechnology), with a small business size standard of 1,000 employees and the PSC code is B504. The United States Department of Agriculture - Agricultural Research Services (USDA- ARS) has the need for the following service(s): 0001) Whole Genome Genotyping of Soybean Samples (Minimum 1,050 SNP Positions; ALL Major Haplotype Blocks Across ALL 20 Chromosomes) WITH Bioinformatic Analyses 0002) Genome Genotyping of 54 Specific User-Provided Single Nucleotide Polymorphisms (SPNs) of Soybean Sample WITH Bioinformatic Analyses 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 for two subprojects. Genotypic data must have high fidelity (~?80% call rate for each SNP for at ?80% samples). The request is organized around two subprojects: Subproject One is a requirement to provide genotypic data provided for each of 1,700 lyophilized soybean tissues samples provided by USDA-ARS. A minimum of 1,050 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. Subproject Two is a requirement to provide genotypic data provided for each of 2,100 lyophilized soybean tissues samples provided by USDA-ARS. Genotypic data to be provided for Subproject Two is a set of 54 specific SNP positions for each sample. Details on the 54 SNP positions (sequences, polymorphisms expected, relative ratios, etc.) will be provided by USDA-ARS. Background: Modern soybean breeding requires application of genetic markers, typically in the form of Single Nucleotide Polymorphisms (SNPs) to make time critical decisions. Two subprojects detailed below are part of two running genomic selection experiments at USDA-ARS. Subproject one requires whole genome coverage of at least 1,050 SNPs covering all major haplotype blocks of the twenty chromosomes of soybean, for 1,700 samples. Subproject two requires 54 SNP genotypic information for highly valuable genetic loci for selection among segregating populations, for 2,100 samples. Technical Requirements: Vendor service tasks include, but are not limited to: Vendor will receive lyophilized plant tissue samples from USDA-ARS. USDA-ARS plans to ship samples between 6-8 weeks prior to September 30, 2022 (USDA-ARS is dependent on planting date and plant growth conditions for timing). Vendor will perform DNA isolation, DNA quality control, DNA normalization and all other steps to permit downstream genotyping. Vendor will perform all steps needed to accurately call (~?80% call rate) genotypes for at least 1,050 SNPs covering all major haplotype blocks across the 20 chromosomes of soybean, for 1,700 soybean plant samples provided by USDA-ARS. USDA-ARS can provide appropriate SNP positions; or an existing method that meets minimum requirements is acceptable Perform all steps need to accurately call (~?80% call rate) genotypes for 54 user-provided SNP positions for 2,100 soybean samples (~?80% call rate) provided by USDA-ARS. If applicable to the method, quote must include all bioinformatic analyses – raw sequencing data (e.g. FASTQ files) are not acceptable on their own. If relevant, raw sequencing data is requested (but not required) in addition to genotypic data provided in either excel tabular format or hapmap file format. Data must be provided in either hapmap or excel file format electronically submitted by email to Jason D. Gillman of the USDA-ARS at [email protected] by no later than September 30, 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. Government Furnished: USDA-ARS researcher will provide 1,700 lyophilized soybean leaf tissue samples for subproject one and 2,100 soybean leaf tissue samples for subproject two. 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. Data Rights: USDA-ARS will retain all rights to genotypic information for the all provided samples. All of the SNP information provided will be drawn from the public domain. Key Deliverables: Whole Genome Genotyping of Soybean Samples (Minimum 1,050 SNP Positions; ALL Major Haplotype Blocks Across ALL 20 Chromosomes) WITH Bioinformatic Analyses; Quantity: 1,700 samples. Genome Genotyping of 54 Specific User-Provided Single Nucleotide Polymorphisms (SPNs) of Soybean Sample WITH Bioinformatic Analyses; Quantity: 2,100 samples. All data must be provided in either excel tabular format (genotype x SNP position) or hapmap file format. Delivery: All data generated by the vendor must be submitted by email (in excel tabular format OR hapmap file format) to Jason D. Gillman of the USDA-ARS at [email protected] by no later than September 30, 2022 (to permit time-critical breeding decisions). The Government anticipates award of a Firm Fixed Price contract. Evaluation Factors: The basis for award will be Lowest Price, Technically acceptable. The Government intends to make a single firm-fixed price award based on the lowest price technically acceptable (LPTA) quote received. "LPTA" means the best value is expected to result from selection of the technically acceptable quote with the lowest evaluated price. Pursuant to FAR 52.212-2, the criteria for evaluation are: (1) Price; (2) Technical Requirements. The lowest priced quote will be evaluated first; if NOT found acceptable, the next lowest priced quote will be evaluated, and so on until a technically acceptable quote is identified. The government will NOT review higher priced quotes if the lowest priced quote is determined to be technically acceptable. For quoted services to be considered technically acceptable, they must meet ALL of the technical requirements identified in this solicitation. Submitting a Quote: Offerors responding to this announcement shall submit their quote in accordance with FAR 52.212-1. The applicable FAR clauses and provisions that apply to this acquisition are included with the attached quote submission form (SF1449). The Government anticipates award of one Firm Fixed Price Contract. To be eligible for an award, all contractors must be registered in the System for Award Management (SAM) with a current and active registration. A contractor can contact SAM by calling 1-866-606-8220 or e-mail at www.sam.gov. NO EXCEPTIONS. A Unique Entity Identifier (UEI) number is required in order to register. Vendor must also include their UEI# on their quote. The submission and payment of invoices on the resulting contract will be made through the Invoice Processing Platform (IPP). As such, contractors must be currently registered or register in IPP in order to be able to submit and receive payment on invoices for the resulting award. Offerors responding to this announcement shall submit their quote on the SF1449 (see attached) and provide a written Quality Assurance Plan (or QAP, in response to the QASP) as well as completed FAR clauses and provisions. The quoted price(s) should include all fees, delivery charges, and/or surcharges. This will be a tax-exempt purchase. Failure to demonstrate compliance will constitute sufficient cause to reject a quote without further discussions. All responsible sources may submit a quote which will be put into considered for award. Questions in regards to this combined synopsis/solicitation must be submitted through email (NO calls with questions will be accepted) and are due by NO later than 5:00 PM CT on Wednesday, August 3, 2022. Answers to any questions received by that time will be posted as an amendment to this combined synopsis/solicitation. No questions will be answered after this date unless determined to be in the best interest of the Government. Only electronic submissions made via email will be accepted (NO phone calls or quotes submitted by USPS mail will be accepted). Please email all quotes in writing on the SF1449 with a completed QAP and FAR clauses/provisions to [email protected] by NO later than Tuesday, August 9, 2022 at 12:00 PM Central Time (CT). Note: Be absolutely certain to reference the RFQ number “12505B22Q0163” and/or title of the solicitation “Genotyping of Soybeans” in the subject, body, and/or attachments on your quote submission email to ensure your submission can be located and attributed to this solicitation. Failure to do so could potentially result in your submission being deemed “unresponsive” and as a result your quote may NOT be put into consideration for award (as your quote may NOT be located when searching the recipients email to ensure all responses to the solicitation have been logged before making an award determination).