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Sample Design: Evaluating DNA methylation of experimentally reared spring Chinook
  • ID: 16995
  • State: Finalized
  • Owner: Hayley Nuetzel
  • Spatial Design Category: Census: Full
  • Version History: v1.0 Finalized (1/11/2024)

The details of this Sample Design, including all the parameters used to generate it, are included below. Sample designs must belong to a Study Plan.


This study is designed to assess 1) how rearing density affects methylation patterns, and 2) if methylation could be associated with precocial maturation. The goal of this study is to improve our understanding of how hatchery conditions impact fitness at a molecular level, and to then use that understanding to suggest alterations to hatchery management to optimize fitness. 

Beginning in fall of 2024, approximately 5,000 fertilized eggs will be collected from a partner hatchery. The dams and sires will be sampled, as well as their gametes prior to fertilization. We intend to take a random sample of fertilized eggs from each of the family groups designated for this experiment. Eggs will either be incubated at the hatchery, or at the Fish Performance and Genetics Lab in Corvallis, pending facility space. 

In March of 2025, swim-up fry will be transferred to the Aquatic Animal Health Lab (AAHL) at Oregon State University (Corvallis, OR). Fry will be transferred into nine, 380L tanks. Each treatment will occur in triplicate: 3 tanks replicating density levels from a typical conservation hatchery, 3 tanks replicating density levels from a typical production hatchery, and 3 tanks with an experimentally low density, more reminiscent of natural conditions. Fish from each family group will be equally, but randomly distributed across these nine tanks. 

Study fish will be subsampled at regular intervals throughout the study - from swim-up to smolt. In Spring 2026 (smolt stage), all remaining study fish will be lethally sampled. We intend to collect, at least, liver, heart and muscle tissue from each individual. Blood will be taken from a subset of samples to evaluate markers of maturation (11-KT assay). Weight and length measurements will also be taken at this time.

Samples will be stored in RNAlater and transferred to the Hagerman Genetics Laboratory (Hagerman, ID). Parentage analyses will then be conducted to determine family structure. An equal number of fish will be chosen from each family group and then processed for whole genome bisulfite sequencing.


Start Year


End Year


Study Plan

Investigating Epigenetic Markers of Hatchery Rearing v1.0

Data Repositories





Area of Inference


AOI Notes


Sample Sites
These are the unique sites that are participating in this sample design over the time period covered by the design.

Map of Sites


Sampling Schedule
This section describes which sites are scheduled to be sampled in any given year, and (if applicable) the panel and stratum that the sample site belongs to.

Plan Description

Fall 2024 - begin experiment with BY2024

Fall 2024 - Spring 2026: rear study fish at the AAHL/OHRC

Spring 2026: end experiment, collect final samples

Spring - Summer 2026: Extract samples, bisulfite library prep

Summer 2026 - Winter 2026: Sequencing 

2027: Data analysis & summation

2028: Publication

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