84045 REL 30: Rev 1: WE P: Work Element Summary

Work Element Summary PDF

Select a work element:

Basics

Contract Number:

84045 REL 30

Contract Title:

2010-031-00 EXP SNAKE RIVER CHINOOK AND STEELHEAD RM&E

Contract Start Date:

7/1/2024

Contract End Date:

6/30/2025

WE ID:

157. Collect/Generate/Validate Field and Lab Data

Work Element Usage Report

Title:

P: 157 - OBJ 3: PBT Baseline maintenance

Description:

Sample genotyping (IDFG): All samples will be genotyped with standardized panels of SNP and/or Microhaplotype loci.

WE Agreement Type:

Contracted

Deliverable Specification:

All sample metadata and genotype data stored on local Progeny database, duplicated external hard drives and Amazon Cloud.

WSE Effective Budget:

$225,000

% of Total WSE Effective Budget:

12.10%

WSE Start:

07/01/2024

WSE End:

06/28/2025

WSE Completion:

WSE Progress:

In Progress

WSE ID Continued From:

n/a

WSE ID Continued To:

n/a

Finite or Recurring:

Recurring

Budget History

SOWRevision	Planned	Updated	Contractor Comments (optional)	BPA Comments (optional)
Work Element Budget (Current Performance Period)	$225,000	$225,000

Milestones

4 Milestones

Sort	Type	Title	Start	End	Status	Modified By	Modified Date
A	EC	Environmental compliance requirements complete	7/1/2024	7/3/2024	Concluded	Martin Allen	3/17/2024 4:10:01 PM
		Description: On-the-ground work associated with this work element cannot proceed until this milestone is complete. Milestone is complete when final documentation is received from BPA environmental compliance staff.
B	PUBPROTOCOL	Review, revise, and finalize study plan sample design protocol and methods in MonitoringResouces.org	7/3/2024	12/29/2024	Concluded	Martin Allen	3/17/2024 4:10:46 PM
		Description: The Study Plan's Sample Design, Protocol and Methods for this work element are stored at MonitoringResources.org.
C		Genotype Backend Hatchery samples	7/1/2024	6/28/2025	Active	Martin Allen	3/17/2024 4:10:46 PM
		Description: Hatchery samples of steelhead and Chinook Salmon will be genotyped with a standardized set of SNP loci. All genotyping will be quality controlled by utilizing positive (known genotype) and negative (without DNA) controls in each run. Repetitive genotyping of randomly selected individuals will be completed to ensure repeatability of genotyping results.
D	DELIV	Produce accessible, error-checked datasets		6/28/2025	Active	Martin Allen	5/6/2024 2:40:53 PM
		Description: All sample metadata and genotype data stored on local Progeny database, duplicated external hard drives and Amazon Cloud.

Metrics

Implementation Metrics

Metric	Planned	Actual	Contractor Comments	Measures	HLIs
1464. Primary R, M, and E Focal Strategy [Population Status, Hydrosystem, Tributary Habitat, Estuary/Ocean, Harvest, Hatchery, Predation, Multiple Strategies]	Population Status
1472. Primary R, M, and E Type [Status and Trend Monitoring, Action Effectiveness Research, Uncertainties Research, Project Implementation/ Compliance Monitoring]	Status and Trend Monitoring
1478. Secondary R, M, and E Type [Status and Trend Monitoring, Action Effectiveness Research, Uncertainties Research, Project Implementation/ Compliance Monitoring]	Uncertainty Research
1495. Secondary R, M, and E Focal Strategy [Population Status, Hydrosystem, Tributary Habitat, Estuary/Ocean, Harvest, Hatchery, Predation, Multiple Strategies]	Multiple Strategies

Location

Work Site ID	Latitude	Longitude	State	County	Province	Subbasin
71058	43.67769	-116.40596	Idaho	Ada	Middle Snake	Boise
71109	42.761351	-114.858828	Idaho	Gooding	Upper Snake	Snake Upper

Focal Species

Primary Focal Species:

Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened); Chinook (O. tshawytscha) - Snake River Spring/Summer (not listed); Steelhead (O. mykiss) - Snake River DPS (Threatened)

Secondary Focal Species:

None

Environmental Compliance

None

RM&E Metadata

Data Repositories:

Title	Link
FishGen	http://www.fishgen.net/
Idaho Fish and Wildlife Information System	https://fishandgame.idaho.gov/ifwis/portal/
IDFG Fisheries Technical Reports	https://collaboration.idfg.idaho.gov/FisheriesTechnicalReports/Forms/AllItems.aspx

Study Plan:

Study Plan Name	Study Plan Owner	Protocol State	Sample Design Name
Parentage Based Tagging for hatchery Chinook salmon and steelhead in the Snake River basin (2010-031-00) v1.0	Matthew Campbell	Finalized	Obj. 3, Genotyping (Backend sampling) - Idaho Department of Fish and Game (IDFG) v1.0

Methods:

ID	Name	Type	Optional	Customized Based On	Status
1352	Assessing genetic population structure using fixation indices v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1345	Estimating Genetic Diversity v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1340	Genetic Sex Marker for O. mykiss and O. tshawytscha v1.0	Data Collection	No	N/A	Finalized
1339	Nexttec 96-Well Tray DNA Extraction Kit Protocol v1.0	Data Collection	No	N/A	Finalized
1356	O. mykiss and O. tshawytscha SNP marker sets for PBT and GSI use in the Columbia River basin v1.0	Data Collection	No	N/A	Finalized
1362	Obtaining genetic samples from juvenile steelhead and Chinook salmon v1.0	Data Collection	No	N/A	Finalized
1341	Parentage assignments using SNPPIT software v1.0	Data Analysis/Interpretation	No	N/A	Finalized
1332	SNP genotyping on Fluidigm platform v1.0	Data Collection	No	N/A	Finalized
1432	Tissue sampling for Parentage Based Tagging v1.0	Data Collection	No	N/A	Finalized

Metrics:

Title	Category	Subcategory	Subcategory focus 1	Subcategory focus 2
Annual stock abundance over Lower Granite Dam	Fish	Abundance of Fish (ID: 46)	Fish Life Stage: Adult - Returner	Fish Origin: Hatchery
Age structure of Snake River hatchery adults	Fish	Age Structure: Fish (ID: 49)	Fish Life Stage: Adult - Returner	NA
Determining stock proportion within harvest	Fish	Harvest Abundance (ID: 52)	Fish Life Stage: Adult - Returner	Fish Origin: Hatchery
Effective population size of Snake R. hatchery stocks	Fish	Effective Population Size (ID: 65)	NA	NA
Genetic Diversity of Hatchery Stocks	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Hatchery	NA
Temporal estimates of genetic diversity in hatchery stocks	Fish	Genetics: Fish Diversity, Fitness or Variation (ID: 72)	Fish Origin: Hatchery	NA
Annual estimates of length at age for hatchery stocks	Fish	Length: Fish Species (ID: 75)	Fish Life Stage: Adult - Returner	NA
Length of hatchery adults sampled at LGR Dam	Fish	Length: Fish Species (ID: 75)	Fish Life Stage: Adult Fish	NA
Estimate of PIT tag retention in returning hatchery adults	Fish	Mark Retention (ID: 76)	Fish Life Stage: Adult - Returner	NA
Progeny-per-Parent Ratio of Snake River hatchery broodstock	Fish	Progeny-per-Parent Ratio (P:P) (Productivity) (ID: 86)	Fish Life Stage: Adult - Spawner	NA
RRS of hatchery and wild adults in integrated programs	Fish	Relative Reproductive Success (RRS) (ID: 88)	Fish Origin: Both	NA
Variance in reproductive success of hatchery broodstock	Fish	Reproductive Success (Nb/N) (ID: 89)	Fish Origin: Hatchery	NA
Sex ratio of hatchery stocks returning over LGR dam	Fish	Sex Ratio: Fish (ID: 92)	Fish Life Stage: Adult - Returner	Fish Origin: Hatchery
Annual phenotype error rate estimation of unmarked adults	Fish	Stock Identity (ID: 95)	Fish Life Stage: Adult - Returner	NA
Stock proportion of hatchery adults returning over LGR Dam	Fish	Stock Identity (ID: 95)	Fish Life Stage: Adult - Returner	NA
Genetic tagging of all Snake River hatchery stocks	Fish	Mark/Tag Application (ID: 201)	NA	NA
Stock origin of hatchery adults	Fish	Origin (ID: 202)	NA	NA
Stock origin of hatchery adults straying into wild spawning area	Fish	Origin (ID: 202)	NA	NA
Stock origin of hatchery juveniles implanted w/acoustic tags	Fish	Origin (ID: 202)	NA	NA
Stock origin of hatchery kelts capture at LGR dam	Fish	Origin (ID: 202)	NA	NA
Stock origin of returning hatchery adults via PBT tagging	Fish	Mark/Tag Recovery or Detection (ID: 381)	NA	NA

Please correct the errors noted below.

Implementation Metrics