Opportunity Information: Apply for R13AP30003
Apply for R13AP30003
- The Bureau of Reclamation Lower Colorado Region in the natural resources sector is offering a public funding opportunity titled "Development and Characterization of Microsatellite PCR Primers for Bonytail Chub" and is now available to receive applicants.
- Interested and eligible applicants and submit their applications by referencing the CFDA number(s): 15.517 Fish and Wildlife Coordination Act.
- This funding opportunity was created on Feb 26, 2013 and posted on Feb 26, 2013.
- Applicants must submit their applications by Mar 12, 2013. (Agency may still review applications by suitable applicants for the remaining/unused allocated funding in 2026.)
- The funding agency has allocated a total of $34,392.00 to eligible and selected applicants.
- Each selected applicant is eligible to receive up to $34,392.00 in funding.
- The number of recipients for this funding is limited to 1 candidate(s).
- Eligible applicants include: Others (see text field entitled Additional Information on Eligibility for clarification).
- This is a Notice of Intent to Award, no competition is being sought.
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Opportunity Summary:
The grant opportunity titled "Development and Characterization of Microsatellite PCR Primers for Bonytail Chub" focuses on a very specific conservation genetics problem tied to recovery efforts for the endangered bonytail chub (Gila elegans), a native fish that historically ranged widely across the Colorado River basin but is now extremely rare in the wild. Because wild populations are so scarce, recovery has depended heavily on hatchery production and repatriation. A major complication is that the species has very low genetic diversity due to a historical bottleneck, and the current broodstock traces back largely to a small number of founders collected from Lake Mohave in 1981. Although 11 fish (5 males and 6 females) were captured to establish the initial broodstock, later genetic work indicated that fewer than eight individuals actually contributed genetically to that founding year class. Attempts to bring additional Lake Mohave fish into the broodstock have not succeeded, which leaves managers with a genetically depauperate population that is vulnerable to inbreeding and associated reductions in fitness.
The scientific and management need driving this award is the risk that, even when many offspring are produced, only a small number of parents may account for most of the juveniles that survive and are ultimately stocked back into the river. Bonytail chub are long-lived and iteroparous (they can spawn multiple times across their lives), and females can produce thousands of eggs in a single spawn. That high fecundity can be a demographic advantage when conditions support recruitment, but genetically it can be a drawback if reproduction is skewed toward a few successful breeders. In that scenario, hatchery or backwater-reared cohorts may represent only a narrow slice of the already limited genetic variation, accelerating inbreeding over time. For this reason, managers need reliable genetic tools that can (1) distinguish individuals unambiguously, and (2) assign parentage so they can estimate how many adults are contributing to each cohort and whether rearing practices are maintaining as much remaining diversity as possible.
The core purpose of the project is to expand and validate microsatellite-based genetic markers for bonytail chub by testing PCR primers that were originally developed for other closely related Gila species (specifically Gila nigrescens and Gila nigra) and determining whether those primers amplify reliably and produce useful, polymorphic microsatellite loci in bonytail chub. Roughly 20 microsatellite markers had already been developed for bonytail and related chubs, but the announcement states that additional markers, on the order of 5 to 10 depending on how polymorphic they are, are needed to make individual identification and parentage analysis robust and unambiguous. A key rationale is that even species with low genetic variability, like Gila nigrescens (which has also experienced bottlenecks), can still yield a workable set of microsatellite loci; in this case, nine loci had been identified that amplified reliably in that species. The project aims to leverage that prior work, adapt it to bonytail chub, and optimize existing primer sets so they are suitable for analyzing reproductive success in backwater or off-channel habitats where spawning and rearing may occur.
On the recipient side, the work is straightforward molecular genetics: using standard laboratory procedures to characterize microsatellite loci, optimize PCR conditions, and evaluate marker performance. Importantly, the opportunity specifies that the recipient will test the microsatellite markers on known parents and their progeny produced at the Dexter National Fish Hatchery and Technology Center. Using known pedigrees allows the recipient to verify that the markers are reliable for parentage assignment (for example, that allele inheritance patterns make sense, amplification is consistent, and error rates are low enough for confident assignments). The end product is expected to be a set of validated and optimized microsatellite PCR primers and loci that can be used routinely to track genetic diversity and quantify reproductive contribution among broodstock and offspring destined for repatriation.
The Bureau of Reclamation (Lower Colorado Region) is the sponsoring federal agency, but the announcement notes that Reclamation does not anticipate substantial programmatic involvement beyond normal federal stewardship. In practical terms, that means routine grant oversight, monitoring performance, and providing technical assistance if requested, rather than active collaboration or day-to-day project direction.
Administratively, this was a discretionary grant under the Natural Resources activity category, tied to CFDA 15.517 (Fish and Wildlife Coordination Act). It was issued as a Notice of Intent to Award with no competition, meaning the agency planned to make the award to a specific recipient rather than solicit proposals broadly. The posting and creation date were February 26, 2013, with a closing date of March 12, 2013, and an archive date of April 11, 2013. The funding amount was fixed: estimated total funding of $34,392, with the award ceiling and floor both listed as $34,392, and the expectation of a single award. No cost sharing or matching requirement was indicated. Contact for access issues was the Grants Officer, Shawna Thompson, at the Bureau of Reclamation (phone 702-293-8570; email smthompson@usbr.gov).
Frequently Asked Questions (FAQs)
What is the title of this grant opportunity?
The opportunity is titled "Development and Characterization of Microsatellite PCR Primers for Bonytail Chub."
What conservation problem is this grant trying to address?
This grant targets a conservation genetics challenge affecting recovery efforts for the endangered bonytail chub (Gila elegans). Because the species is now extremely rare in the wild, recovery relies heavily on hatchery production and repatriation. The core issue is very low genetic diversity caused by a historical bottleneck, which increases the risk of inbreeding and reduced fitness over time.
Why is genetic diversity such a concern for bonytail chub recovery?
The current broodstock largely traces back to a small number of founders collected from Lake Mohave in 1981. Although 11 fish (5 males and 6 females) were captured to establish the initial broodstock, later genetic work suggested fewer than eight individuals actually contributed genetically to that founding year class. Attempts to add additional Lake Mohave fish to the broodstock have not succeeded, leaving managers with a genetically depauperate population that is more vulnerable to inbreeding and related fitness impacts.
What management risk does the grant highlight about hatchery or backwater-reared cohorts?
The grant notes the risk that even if many offspring are produced, only a small number of parents may account for most juveniles that survive and are eventually stocked back into the river. If reproduction is highly skewed toward a few successful breeders, cohorts could represent only a narrow slice of the already limited genetic variation, which can accelerate inbreeding over time.
How do bonytail chub life history traits relate to the genetics problem described?
Bonytail chub are long-lived and iteroparous, meaning individuals can spawn multiple times across their lives. Females can produce thousands of eggs in a single spawn. While high fecundity can help demographically when conditions support recruitment, it can be genetically problematic if only a few breeders contribute disproportionately to the surviving offspring.
What genetic tools do managers need, according to the opportunity?
The opportunity states managers need reliable genetic tools that can: (1) distinguish individuals unambiguously, and (2) assign parentage. These tools are needed to estimate how many adults are contributing to each cohort and to evaluate whether rearing practices are maintaining as much remaining genetic diversity as possible.
What is the main scientific purpose of the funded project?
The core purpose is to expand and validate microsatellite-based genetic markers for bonytail chub by testing PCR primers originally developed for closely related Gila species (specifically Gila nigrescens and Gila nigra) and determining whether those primers amplify reliably and produce useful, polymorphic microsatellite loci in bonytail chub.
Why are primers from other Gila species being considered for bonytail chub?
The project is designed to leverage prior work from closely related species and assess cross-amplification in bonytail chub. The announcement points out that even a low-variability species like Gila nigrescens (which has also experienced bottlenecks) still produced a workable set of microsatellite loci, with nine loci identified that amplified reliably in that species. The grant aims to adapt similar primer sets for bonytail chub.
How many microsatellite markers are already available, and how many more are needed?
The announcement indicates that roughly 20 microsatellite markers had already been developed for bonytail and related chubs. However, additional markers are needed, on the order of 5 to 10 (depending on how polymorphic they are), to make individual identification and parentage analysis robust and unambiguous.
What does "polymorphic" mean in the context of the markers mentioned?
In this opportunity, "polymorphic" refers to microsatellite loci that show enough genetic variation to be informative. The more informative (polymorphic) the loci are, the fewer may be needed to reliably distinguish individuals and assign parentage.
What types of laboratory work is the recipient expected to perform?
The recipient is expected to use standard molecular genetics laboratory procedures to characterize microsatellite loci, optimize PCR conditions, and evaluate marker performance for bonytail chub.
How will the project validate that the markers work for parentage assignment?
The opportunity specifies that the recipient will test the microsatellite markers on known parents and their progeny produced at the Dexter National Fish Hatchery and Technology Center. Because the pedigrees are known, the recipient can verify parentage performance by checking that allele inheritance patterns are consistent, amplification is reliable, and error rates are low enough for confident assignments.
What is the expected end product or deliverable?
The expected end product is a set of validated and optimized microsatellite PCR primers and loci that can be used routinely to track genetic diversity and quantify reproductive contribution among broodstock and offspring destined for repatriation.
Where are the known parents and progeny for testing expected to come from?
They are expected to come from fish produced at the Dexter National Fish Hatchery and Technology Center, as specified in the opportunity.
What habitats or management settings are specifically mentioned as an application for these tools?
The announcement mentions application to analyzing reproductive success in backwater or off-channel habitats where spawning and rearing may occur, in addition to broader hatchery and repatriation contexts.
Which federal agency is sponsoring this grant?
The sponsoring federal agency is the Bureau of Reclamation, Lower Colorado Region.
Will the Bureau of Reclamation have substantial involvement in the project?
The opportunity states that Reclamation does not anticipate substantial programmatic involvement beyond normal federal stewardship. This is described as routine grant oversight, performance monitoring, and technical assistance if requested, rather than active collaboration or day-to-day project direction.
What type of grant was this, and what activity category does it fall under?
This was a discretionary grant under the Natural Resources activity category.
What CFDA number is associated with this opportunity?
The opportunity is tied to CFDA 15.517, Fish and Wildlife Coordination Act.
Was this opportunity competitive?
No. It was issued as a Notice of Intent to Award with no competition, meaning the agency planned to make the award to a specific recipient rather than solicit proposals broadly.
What were the key dates for the opportunity?
The posting/creation date was February 26, 2013. The closing date was March 12, 2013. The archive date was April 11, 2013.
How much funding was available?
The estimated total funding was $34,392. The award ceiling and award floor were both listed as $34,392, and the opportunity anticipated a single award.
Is cost sharing or matching required?
No cost sharing or matching requirement was indicated in the opportunity description provided.
Who should be contacted for access issues related to this grant?
The contact listed for access issues was the Grants Officer, Shawna Thompson, Bureau of Reclamation. Phone: 702-293-8570. Email: smthompson@usbr.gov.
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