CHINOOK AND STEELHEAD GENOTYPING FOR GENETIC STOCK IDENTIFICATION AT LOWER

GRANITE DAM

ANNUAL PROGRESS REPORT January 1, 2014 December 31, 2014

Prepared by:

Ninh Vu, Fisheries Research Biologist Michael W. Ackerman, Fisheries Research Biologist

Matthew R. Campbell, Fisheries Genetics Program Coordinator

IDFG Report Number 15-02 January 2015

CHINOOK AND STEELHEAD GENOTYPING FOR GENETIC STOCK IDENTIFICATION AT LOWER GRANITE DAM

Project Progress Report

2014 Annual Report

By

Ninh V. Vu Michael W. Ackerman

Kristin K. Wright Jesse McCane

Matthew R. Campbell

Idaho Department of Fish and Game 600 South Walnut Street

P.O. Box 25 Boise, ID 83707

and

Jon E. Hess

Shawn R. Narum

Columbia River Inter-Tribal Fish Commission Hagerman Fish Culture Experiment Station

3059-F National Fish Hatchery Road Hagerman, ID 83332

Project Number 2010-026-00 Contract Number 65455

IDFG Report Number 15-02 January 2015

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TABLE OF CONTENTS Page

ABSTRACT ................................................................................................................................. 7 INTRODUCTION ........................................................................................................................ 8 REPORT STRUCTURE .............................................................................................................. 9 SECTION 1: EVALUATE AND MAINTAIN SNP MARKER PANELS ......................................... 10 INTRODUCTION ...................................................................................................................... 10 METHODS ................................................................................................................................ 10

SNP Standardization .............................................................................................................. 10 SNP Documentation .............................................................................................................. 11 SNP Evaluation ...................................................................................................................... 11

RESULTS ................................................................................................................................. 11 SNP Standardization .............................................................................................................. 11 SNP Documentation .............................................................................................................. 12 SNP Evaluation ...................................................................................................................... 12

DISCUSSION............................................................................................................................ 12 SNP Standardization .............................................................................................................. 12 SNP Documentation .............................................................................................................. 12 SNP Evaluation ...................................................................................................................... 12

SECTION 2: UPDATE, MAINTAIN, AND TEST SNP BASELINES FOR STEELHEAD AND CHINOOK SALMON IN THE SNAKE RIVER .............................................................. 14

INTRODUCTION ...................................................................................................................... 14 METHODS ................................................................................................................................ 14

Sample Collection .................................................................................................................. 15 Laboratory Protocol ................................................................................................................ 15 Statistical Analyses ................................................................................................................ 16

RESULTS ................................................................................................................................. 17 Steelhead Genetic Stock Identification ................................................................................... 18 Chinook salmon Genetic Stock Identification ......................................................................... 19

DISCUSSION............................................................................................................................ 19 SECTION 3. IMPLEMENT GSI METHODS TO ESTIMATE PROPORTIONS AND

BIOLOGICAL PARAMETERS OF WILD STOCKS AT LOWER GRANITE DAM ................. 21 METHODS ................................................................................................................................ 21

Sampling at Lower Granite Dam ............................................................................................ 21 Adult Trap Operations ......................................................................................................... 21 Juvenile Trap Operations .................................................................................................... 22 Fish Handling Protocols (Adults and Juveniles) ................................................................... 22 Scale Aging Protocol ........................................................................................................... 22 Genetics Laboratory Protocol .............................................................................................. 23 Parentage-Based Tagging................................................................................................... 23 Genetic Stock Identification ................................................................................................. 23

RESULTS ................................................................................................................................. 24 SY2013 Steelhead Adults ................................................................................................... 24 MY2013 Steelhead Juveniles .............................................................................................. 24

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SY2013 Chinook Adults ...................................................................................................... 25 MY2013 Chinook Juveniles ................................................................................................. 25

DISCUSSION............................................................................................................................ 25 ACKNOWLEDGEMENTS ......................................................................................................... 27 LITERATURE CITED ................................................................................................................ 28 TABLES .................................................................................................................................... 34 FIGURES .................................................................................................................................. 58

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LIST OF TABLES Page

Table 1. Summary of 185 SNPs (Appendix A and Hess et al. 2013) screened

among 68 steelhead collections in Snake River baseline v3.0. SNPs designated as PBT are used for both the PBT (BPA Project #2010-031-00, Steele et al. 2012) and GSI projects. SNPs designated as GSI are used primarily for GSI applications. Summary statistics include minor-allele frequency (MAF) range, expected heterozygosity (HE), mean of Weir and Cockerham (1984) FST, HWE designates the number of populations that a SNP deviated from Hardy-Weinberg expectation (deficient or in excess) for any SNP that deviated in greater than 10% of collections and LD signifies SNPs that exhibit linkage disequilibrium in more than half of the collections. ........................................................................ 35

Table 2. Summary of 191 SNPs (Appendix B and Hess et al. 2013) screened across 54 stream-type Chinook salmon collections in Snake River baseline v3.0. (Note: fall Chinook collections were excluded from analyses below.) SNPs designated as PBT are used for both PBT (BPA Project #2010-031-00, Steele et al. 2012) and GSI projects. SNPs designated as GSI are used primarily for GSI applications. Summary statistics include minor-allele frequency (MAF) range, expected heterozygosity (HE), mean Weir and Cockerham (1984) FST, HWE designates the number of collections that a SNP deviated from Hardy-Weinberg expectation (deficient or in excess) for any SNP that deviated in greater than 10% of collections. LD signifies SNPs that exhibit linkage disequilibrium in more than half of all collections. ............................................... 39

Table 3. Sixty-eight collections of Snake River basin steelhead (Oncorhynchus mykiss) screened with the PBT and GSI SNP panels for baseline v3.0. Each collection is identified by its TRT population, genetic stock, major population group (MPG), sample size (n), year collected, genotyping agency, baseline version in which it first appeared, latitude, longitude, life stage, expected heterozygosity (HE), mean pairwise fixation indices (FST), and number of loci out of HardyWeinberg expectation (deficient or excess in 10% of SNPs). Map # corresponds to numbers in Figure 1. Agency indicates the laboratory where samples were genotyped. Life stage codes are A adult and J Juvenile. All collections are summer-run, inland lineage, natural origin, and p