C04c_Attachment 1 Statement of Work.pdf

US Department of Agriculture (USDA)

Statement of Work

Contents Project General Information

1.0 Scope of Work

2.0 Background

Contractor Requirements

3.0 Technical Requirements / Tasks

4.0 Government Furnished

5.0 Deliverables / Schedule

6.0 Optional Tasks for Future Expansion

7.0 Travel

8.0 Contractor’s Key Personnel

9.0 Security Requirements

10.0 Data Rights

11.0 Section 508 – Electronic and Information Technology Standards Attachment .............................................................................................................. Error! Bookmark not defined.

Project Genetic Sampling for pine species that are difficult to reliably identify in the field.

General Information

1.0 Scope of Work

The scope of work is to provide genetic testing services to accurately identify tree tissue samples of whitebark pine (Pinus albicaulis) and limber pine (Pinus flexilis). This work supports the USDA Forest Inventory and Analysis (FIA) program by improving species data accuracy for these morphologically similar trees, which are impossible to distinguish in the field when cones are absent.

Period of Performance:

Base year will be Award Date – May 14th, 2027 Option Year 1 will be May 15th, 2027 – May 14th, 2028 Option Year 2 will be May 15th, 2028 – May 14th, 2029 Option Year 3 will be May 15th, 2029 – May 14th, 2030 Option Year 4 will be May 15th, 2030 – May 14th, 2031

Deliverable items will have specific timelines for submission listed under 5.0 Deliverables / Schedule section 5.2.

2.0 Background

The accurate identification of whitebark pine (Pinus albicaulis) and limber pine (Pinus flexilis) presents a significant challenge for the USDA Forest Inventory and Analysis (FIA) program. Whitebark pine was listed as a threatened species under the Endangered Species Act in December 2022, which elevates the need for precise and defensible species data.

The similarity in the needles, bark, and overall morphology of these two species makes them impossible to distinguish through field observation unless cones are present. However, cones are rarely a reliable diagnostic tool. They are frequently absent because whitebark pines do not produce them for up to the first 80 years of life, and cones on mature trees are a highly sought-after food source for wildlife.

A pilot study conducted by RMRS-FIA confirmed the unreliability of field identification. Results showed that field identifications in areas of species overlap were correct only 83% of the time, with limber pine identification being correct in just 60% of cases. These accuracy rates fall well below the nationally standardized Measurement Quality Objective (MQO) of 95% for correct tree species identification. Consequently, genetic analysis is the only viable method to achieve the data quality required for monitoring these critical species.

White pine blister rust (Cronartium ribicola), a non-native pathogen, is a primary driver of decline in both target species and a central reason whitebark pine was listed as threatened. Genetic resistance to the rust is uncommon and varies widely across the landscape (for example, the limber pine Cr4 resistance allele occurs at roughly five percent overall, ranging locally from zero to nearly fourteen percent), and the frequency and distribution of that resistance will largely determine restoration success under the National Whitebark Pine Restoration Plan. Because FIA plots are the only systematic, statistically designed sample of these species across their range, an assay that also returns blister-rust-resistance (CR gene) information would convert the same tissue samples into a landscape-scale estimate of resistance-allele frequency, directly usable for seed-zone and core-area restoration prioritization. This added genetic information therefore carries program value well beyond species identification alone.

Contractor Requirements

3.0 Technical Requirements / Tasks

3.1 Overall Scope:

The contractor shall provide all necessary personnel, equipment, facilities, and materials to perform genetic species identification on tree tissue samples provided by the government. The contractor is responsible for the entire workflow, from sample processing to the delivery of a final data in spreadsheet format.

This contract may include up to three phases. Contractors who already possess a validated and published genetic assay for the target species (e.g., the chloroplast restriction-site method of Alongi et al. 2019) may propose to waive Phases I and II and proceed directly to Phase III production-level testing. Contractors proposing a new or unvalidated assay shall include Phases I and II in their proposal.

Estimated Quantity and Ordering. The estimated production volume is approximately 1,000 samples per performance year, and the Government may order up to a maximum of 1,350 samples per performance year at its discretion. The applicable firm-fixed per-sample price applies to the actual number of samples ordered and accepted; these figures are estimates and do not obligate the Government to any minimum or maximum order. Samples may originate from RMRS- FIA and, at the Government's option, from other FIA units, and the contractor shall accept and process samples from these sources under the same terms without a change to the contract scope.

Phase I: Feasibility and Panel Design. The contractor shall conduct a technical and cost feasibility study to develop a genetic identification assay for whitebark pine and limber pine using DNA genotyping methodologies. This includes reviewing existing scientific literature, identifying discriminating genetic markers, and designing and manufacturing reagents (e.g., primers, probes, or SNP panels). The deliverable for Phase I is a report detailing the validated method and a list of markers that can be included in the genotyping assay. Taxonomically validated reference materials will be provided by the Government (see Section 4.4).

Phase II: Validation and Panel Verification. The contractor shall validate the genetic identification assay using positive control DNAs for each species. Verification shall include DNA quality control and compatibility checks, testing of genetic markers for reproducibility and species diagnosability, and determination of whether contaminants co-isolated in DNA preparations inhibit the genotyping method. The deliverable for Phase II is a report detailing DNA quality, performance of the genotyping reaction, and a firm per-sample price for production-level testing.

Phase III: Production-Level Testing. If the Government accepts the Phase II report (or if Phases I and II are waived), the contractor shall perform routine DNA-based species identification for unknown five-needle pine samples at the per-sample price established in Phase II or proposed in the bid. The deliverable for Phase III is a data report as described in Section 5.1.

3.2 Technical Tasks:

The contractor shall perform the following:

• 3.2.1 Sample Receipt and Preparation: Receive shipments of tree needle samples. The contractor shall verify received samples.

• 3.2.2 DNA Extraction: Extract high-quality genomic DNA from each sample suitable for downstream genetic analysis.

• 3.2.3 Genetic Species Identification: Perform a validated genetic assay to reliably distinguish between whitebark pine (Pinus albicaulis) and limber pine (Pinus flexilis). The government's required performance standard is an assay that achieves results equivalent to, or better than, those described in Alongi et al. (2019)). Assays that can also reliably identify potential hybrids (e.g., P. albicaulis x P. flexilis ) are highly desirable and will be considered preferable to methods that identify only the pollen or seed parent .

3.3 Preferred and Evaluated Enhanced Capability:

Value-Added Data (Desirable): Value-Added Data - Blister Rust Resistance (CR Gene) Detection and Hybrid Resolution:

The government has a secondary interest in identifying the presence of the major gene for blister rust resistance (e.g., CR1 for sugar pine; CR2 for western white pine; CR4 for limber pine). Quoters are encouraged to propose technical solutions that provide both species identification and CR gene detection, provided this does not significantly increase the per-sample cost. Proposed solutions offering this additional data may be considered more technically advantageous.

An assay that provides this blister-rust-resistance (CR gene) information, or that resolves hybrids and introgressants between the target species (for example, through chloroplast and nuclear marker congruence or discordance), constitutes a Preferred Enhanced Capability under this contract. Species identification remains the minimum requirement that every offeror must meet. For the reasons stated in Section 2.0, however, the Government considers the enhanced capability a material technical advantage, and the solicitation's evaluation criteria will treat it as such: the Government intends to make award on a best-value basis and may select a higher-priced offer providing the enhanced capability over a lower-priced offer providing species identification alone. Offerors that provide the enhanced capability shall price it as a separate contract line item so its added value can be evaluated against its cost.

This enhanced capability favors an assay that reads multiple independent chloroplast and nuclear markers over a single-organelle method (e.g., chloroplast-only restriction-site test or KASP assay) because methods based solely on the chloroplast genome only report the identity of the pollen parent. Since only one parent is revealed, hybrids and introgressants cannot be detected, which is a goal of this program. A multi-locus assay targeting two organelles (e.g., chloroplast and nucleus) significantly improves accuracy on the core species-identification requirement, not merely the volume of data. Such an assay also yields reusable, multi-locus genotype data for each sample that the Government may retain for characterization of genetic diversity and population structure across FIA plots, a benefit beyond binary species identification that the Government will consider as additional technical merit. Extension of a multi-locus panel to additional five-needle (subgenus Strobus) pines is addressed as an optional task in Section 6.0 and is not required under the base scope.

3.4 Quality Assurance and Process Control:

The contractor shall maintain a robust Quality Assurance/Quality Control (QA/QC) program to ensure the accuracy and repeatability of results. The contractor's process shall include:

• 3.4.1 Contractor-Provided Process Controls: For every analysis plate, the contractor shall be responsible for including positive controls (known P. albicaulis and P. flexilis DNA or synthetic equivalents) and a negative template control. Positive control samples may be provided by the US Forest Service’s Dorena Genetic Resource Center. If a sample internal controls fails, the contractor shall re-analyze each failed sample one additional time at no cost to the government.

• 3.4.2 Blind Duplicate Analysis: The government will provide a subset of samples (approximately 5%) as "blind duplicates" under unique sample identifiers. These duplicates may be included within the same sample shipment or in subsequent shipments. The contractor is responsible for processing these samples as part of the standard workflow, with no knowledge of their duplicate status. The government will perform the final concordance analysis to measure reproducibility.

3.5 Contractor Experience and Qualifications

• The contractor's organization must demonstrate a proven track record of successfully performing high-throughput DNA extraction and genotyping from challenging plant tissues. Preference will be given to vendors who can provide references or case studies demonstrating specific experience with conifer species (particularly pines), or are using methods that have been validated for pines. Experience with non-plant materials (e.g., animals, fungi, bacteria) is not considered sufficient to meet this qualification. The contractor must demonstrate prior experience extracting DNA from pine needle tissue at production scale (hundreds to thousands of samples). DNA extraction from pines presents unique technical challenges due to high concentrations of polysaccharides, phenolics, and secondary metabolites that require species-specific methodological expertise.

4.0 Government Furnished

The Government will furnish the following items to the contractor for the performance of this work:

4.1 Tree Tissue Samples

The Government will provide collected tree tissue samples (typically pine needles) from suspected whitebark and limber pine trees. The samples will be prepared and delivered in one of two formats, specified by the government at the time of shipment:

• a) Individual Coin Envelopes: Each sample will be provided in a small, unsealed paper envelope marked with a unique Control Number (CN).

• b) 96-Well Plates: Samples may be provided as small tissue subsamples pre-loaded by government personnel into 96-well deep-well blocks. Each well will correspond to a unique Control Number (CN).

4.2 Electronic tracking spreadsheet (manifest)

With each sample shipment, the government will provide a corresponding electronic spreadsheet file (e.g., Microsoft Excel). This manifest will, at a minimum, list the unique Control Number (CN) for every sample included in the shipment.

4.3 Quality Control Samples

The sample shipments provided by the government will include blind duplicate samples for quality assurance purposes, as described in Section 3.5.2. These are to be processed by the contractor as standard samples.

4.4 Taxonomically Validated Reference Materials

The Government will provide taxonomically validated positive control samples (known species DNA or tissue) obtained from the USFS Dorena Genetic Resource Center (Dorena, OR) for use in assay validation (Phase II, if applicable) and as process controls during production testing (Phase III). The contractor shall not be responsible for sourcing its own taxonomic reference materials for species validation.

5.0 Deliverables / Schedule

5.1 Data Report

The final product shall be a data report delivered as an Excel spreadsheet (.xlsx) file via email. The report shall focus on the final results rather than intermediate technical data. The spreadsheet must contain, at a minimum, the following columns:

1. Control Number (CN): The unique sample identifier provided by the government for tracking purposes.

2. Genetic_Identification: The final species call determined by the contractor. This field shall be populated with one of three possible values: "albicaulis", "flexilis", or "Unknown". These values can be abbreviated if preferred (“albi”, “flex”, “unkn”).

3. Certainty: The contractor's assessment of the confidence in the result. This field shall be populated with one of two possible values: "High" or "Low".

4. Date_Analyzed: The date on which the genetic analysis for the sample was performed.

5. Lab_Comment: This field is for contractor notes. A comment is required in this field if the "Certainty" for a sample is "Low," explaining the reason for the uncertainty (e.g., "low DNA yield," "ambiguous signal"). The lab can add multiple comment fields if they are relevant to sample QA/QC metrics (e.g., number of per-sample sequence reads; number of mapped per-sample sequence reads or read depth) or species identification.

Sample spreadsheet as follows:

CN Genetic

_ID

Certainty Date_Analyzed Lab_comment

1 albicaulis high

3/11/2026 2 flexilis low 3/11/2026 Repeated test failure; likely poor DNA quality.

6. Alternative Information: If genetic analysis includes multiple independent chloroplast and nuclear markers, genetic identification can be made using each organelle. This makes it possible to assess the likelihood that trees are pure species (e.g., CP and NUC markers are fully congruent), hybrids (e.g., a subset of NUC markers are incongruent with CP) or introgressant (e.g., NUC markers fully incongruent with CP). An example spreadsheet is shown below:

When the enhanced capability described in Section 3.3 is provided, the data report shall also include, for each sample, a column reporting the blister-rust-resistance (CR gene) result and, where applicable, the hybrid or introgressant status.

CN CP_ID CP_cert NUC_ID NUC_cert HYB_prob Lab_comment Date_Analyzed

1 albi high albi high low Pure species 3/11/2026 2 albi high albi-flex high likely Likely hybrid (nuc markers segregating for albi & flex) 3/11/2026

3 albi high flex high likely Likely introgressant (nuc markers fixed for flex)

3/11/2026

5.2 Schedule and Turnaround Time

The contractor shall deliver final results for all tested samples on or before January 31st of each performance year, provided the samples were delivered on or before November 1st.

The January 31 deadline supports a federal mandate requiring FIA data publication within six months of field data collection. This deadline is non-negotiable.

5.3 Invoicing

Upon delivery and government acceptance of the Data Report, the contractor shall submit a proper invoice electronically through the U.S. Treasury's Invoice Processing Platform (IPP). Each invoice must include all information required for processing, including:

The lab’s name, address, and telephone number U.S. Forest Service contract number Statement that the invoice is a request for payment.

Invoice date Performance dates of the work completed (start & end) Total invoice amount for the billing period Cumulative amount of all payments to date for the current fiscal year (October 1st through September 30th) Address for RMRS-FIA, which is as follows:

4919 S 1500 W Ste. 200 Riverdale, UT 84405

6.0 Optional Tasks for Future Expansion

The government may elect to fund the following optional tasks at its discretion during any performance period of this contract. Quoters shall describe their technical capability and provide separate pricing for these options in their proposal.

Optional Task 1: Addition of Western White Pine (Pinus monticola ) Identification Upon written notification from the Contracting Officer's Representative (COR), the contractor shall expand the genetic testing services to include the differentiation of whitebark pine (P. albicaulis ) from western white pine (P. monticola ).

• Technical Approach: It is anticipated that the same genetic assay used for the primary contract requirement can be used to fulfill this option. Quoters shall confirm this capability.

• Deliverable: The “Genetic_Identification” column in the data report shall be expanded to include "monticola " (or “mont”) as a possible value. As noted previously, if chloroplast and nuclear markers are used, it may be possible to identify whitebark x western white (or ‘albi x mont’) hybrids.

• Activation: This option may be exercised by the government on a per-shipment basis, with clear indication of which samples require this specific species comparison.

Optional Task 2: Feasibility Study and Validation for New Species Groups The government has a future interest in identifying other species, including (but not limited to) Southwestern white pine (Pinus strobiformis), various Pinus monophylla varieties, and species within the Alnus genus (e.g., A. rubra, A.

rhombifolia). In discussions with geneticists at the USFS PNW Research Station, data is available that clearly discriminates Alnus species; genetic data may also be available that discriminates P. strobiformis from P. flexilis. New information would need to be generated to evaluate DNA-based ID of P. monophyla varieties.

Upon written notification from the COR, the contractor shall perform a three-phased task for a new species group identified by the government. Contractors who already possess a validated assay for the target species group may propose to waive Phases I and II.

Phase I: Feasibility and Validation Study. The contractor shall conduct a technical and cost feasibility study to develop or validate a genetic assay for the new species group. This includes reviewing existing scientific literature, designing and testing primers/probes, and validating the assay's accuracy using reference samples. The deliverable for Phase I is a formal report detailing the validated method, its accuracy, and a firm per-sample price for production-level testing.

Phase II: Production-Level Testing. If the government accepts the Phase I report, it may elect to exercise Phase II, authorizing the contractor to perform routine identification for the new species group at the price established in Phase I.

Phase III: Production-Level Testing. If the Government accepts the Phase II report, it may elect to exercise Phase III, authorizing the contractor to perform routine DNA-based species identification for the new species group at the per-sample price established in Phase II.

7.0 Travel

No travel is expected for this project.

8.0 Contractor’s Key Personnel

Project Manager and Technical Capability The contractor shall designate one individual to serve as the Project Manager for this contract. This individual will be the primary point of contact for all communication with the government and will be responsible for ensuring all contract requirements, including technical performance and delivery schedules, are met. The Project Manager must have experience managing laboratory or similar technical projects and serving as a client liaison.

While the Project Manager is the key point of contact, the contractor's organization as a whole must possess the underlying scientific and technical expertise required to perform the work described herein. This includes the ability to validate assays, implement and interpret quality control measures, and troubleshoot analytical issues. The Project Manager will be responsible for leveraging this internal expertise to meet the contract requirements.

The individual designated as the Project Manager is considered essential to the successful execution of the work. The contractor agrees that this individual shall not be replaced without prior written notification to the Contracting Officer's Representative (COR).

9.0 Security Requirements

No security clearance is required for contractor personnel to perform the work under this contract. The Government will not provide the contractor with access to classified information or sensitive location data (e.g., FIA plot coordinates). All Government Furnished Information (GFI), including the sample Control Numbers (CNs), shall be handled by the contractor as proprietary information and must not be disclosed outside of the performance of this contract.

10.0 Data Rights

All data, results, and reports generated by the contractor in the performance of this contract shall be the sole and exclusive property of the U.S. Government. This is a fee-for-service agreement. The contractor shall not use, disclose, publish, or reproduce the data for any purpose other than the performance of work under this contract without prior, express written permission from the Contracting Officer's Representative (COR).

11.0 Section 508 – Electronic and Information Technology Standards

All electronic and information technology (EIT) deliverables provided under this contract must comply with the requirements of Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. § 794d).