Discovery, validation, and genotyping of single nucleotide polymorphisms in inconnu (Stenodus leucichthys). | Apply Online

Opportunity Summary:

The grant opportunity titled "Discovery, validation, and genotyping of single nucleotide polymorphisms in inconnu (Stenodus leucichthys)" is a small, targeted research award from the U.S. Fish and Wildlife Service focused on building a high-resolution genetic toolkit for inconnu (also known as sheefish) in Alaska. The project centers on generating a large panel of genetic markers called single nucleotide polymorphisms (SNPs). Specifically, the award supports the discovery, validation, and genotyping of roughly 10,000 SNPs from a sample of 200 inconnu collected in Alaska. The end product is intended to be an applied management resource rather than a purely academic dataset, designed so the Service can use these markers in routine fisheries and conservation decision-making.

The Service identifies two practical management objectives that the SNP panel must support. First, the markers will be used to conduct mixed stock analysis (MSA) for inconnu harvested in the winter subsistence fishery in Hotham Inlet, Alaska. Mixed stock analysis is a genetic approach used when fish caught in a single fishery may originate from multiple breeding populations; by comparing genotypes from the catch to a genetic baseline, managers can estimate the proportion of the harvest coming from each contributing stock. This matters for subsistence fisheries because it helps ensure that harvest levels do not disproportionately impact vulnerable or smaller populations, and it can inform in-season or long-term strategies that keep harvest sustainable while respecting subsistence needs.

Second, the SNPs will be used to describe and evaluate the genetic population structure of inconnu throughout Alaska. In practice, that means using the marker set to determine how many genetically distinct populations exist, how strongly separated they are, and how individuals and rivers or regions are related through gene flow. Understanding population structure is central to conservation and fisheries management because genetically distinct groups can respond differently to harvest pressure, habitat change, or environmental shifts. A clearer population map can influence how managers define stocks, set monitoring priorities, and interpret changes in abundance and distribution over time.

From a technical standpoint, the opportunity is geared toward applicants that can do modern next-generation sequencing and the bioinformatics needed to turn raw sequence reads into validated SNP assays. The announcement specifies that applicants must have laboratory capacity to conduct next-generation sequencing using a genome reduction method such as restriction site associated DNA (RAD) tag sequencing. RAD sequencing is commonly used for non-model species because it samples consistent portions of the genome across many individuals without needing a fully assembled reference genome, making it well-suited for discovering thousands of SNPs efficiently. Beyond sequencing, the applicant must also have the computational capacity and expertise to screen and analyze RAD tag data and deliver sufficient flanking sequence around each SNP so the Service can develop genotyping assays compatible with the Life Technologies QuantStudio PCR system. That requirement signals that the Service is not just seeking a discovery paper, but a deliverable marker panel that can be turned into a practical, repeatable genotyping workflow in a management lab.

Administratively, this was a discretionary funding opportunity offered as a cooperative agreement under the Fish and Wildlife Management Assistance program (CFDA 15.608). The funding amount was fixed: an estimated total of $12,000, with an award ceiling and floor both set at $12,000, and the agency expected to make a single award. There was no cost-sharing or matching requirement. Eligibility was described as unrestricted in general terms, but effectively limited by the technical qualifications laid out in the requirements, meaning only groups with appropriate sequencing and analytical infrastructure would realistically be competitive. The opportunity was posted on February 12, 2013, with a closing date of March 14, 2013, and it was archived on April 15, 2013.

For applicants or interested parties who could not access the full announcement online, the point of contact listed was Jeffery Olsen at the Conservation Genetics Laboratory (Fish and Wildlife Service), including a phone number and email address. The announcement also referenced an additional information link to the Conservation Genetics Laboratory webpage, suggesting the work would be closely aligned with the Service's genetics program and its operational needs for fisheries monitoring and stock assessment.

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