New genetic technology for the management of Columbia River salmon and steelhead

Parentage Based Tagging

Matthew CampbellIdaho Department of Fish and Game

LSRCP PRODUCTION MEETING AGENDAMARCH 16th, 2011

BOISE, IDAHO1

“by tying a ribbon or thread to the tails of young salmon which were swimming toward

salt water and catching them again when they came back to the same place upon their

return from the sea”

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In the Snake River basin, CWT recoveries are one of the primary tools used by managers in Oregon, Washington, and Idaho to: • Estimate the number of

hatchery salmon and steelhead contributing to fisheries in the Columbia River basin

• Estimate run-timing and harvest of individual hatchery stocks

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Despite its’ predominance in addressing these management questions, CWT technology has several limitations:

The process of physically tagging hundreds of thousands of juveniles from different hatchery stocks is

• logistically difficult

• labor intensive

• expensive

• potentially increases physiological stress

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Parentage-based genetic tagging - PBT(Anderson and Garza 2005)

Parentage-based tagging uses similar DNA techniques as those used in human parentage testing

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Parentage-based genetic tagging - PBT

• Every person receives a unique set of genetic information from their parents!

• If your parents have been genetically screened they can easily be identified from thousands of possible candidates! 6

Child

Genetic information can be obtained from all hatchery fish (broodstock) that are spawned

Sawtooth

Pahsimeroi

Oxbow

Dworshak/Clearwater

LookinglassWallowa

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Offspring from any of these parents (either collected as juveniles or returning adults), if genotyped, could be assigned back to their parents, thus identifying the hatchery they originated from and exact brood year they were produced in

Sawtooth BY2008

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• Any Snake River hatchery Chinook salmon or steelhead encountered in the basin (juvenile or adult) could be sampled, genotyped and its sex, exact age, and stock of origin could be determined

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Snake River ESU

Benefits of PBT

• Provides same information as CWTs (stock and cohort)

Run reconstruction (age, sex, stock of returning adults)

Harvest estimates

• Additionally, many issues associated with tagging studies all but go away

Tag lossTag detectabilityDifferential mortality

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Additional benefits of PBT

PROS:

• It is a passive mark (no handling of juveniles needed)

• “Tagged” fish can be non-lethally interrogated

Fin-clip

Scales

Biopsy hook

“The hollow stainless steel tip of the hook collects a small amount of tissue as the fish strikes, and a special rasp holds the sample in place while the hook is in the water”

“Genetag hook”

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Versatility of PBT

PROS:• Can potentially provide much more information

than stock and cohort of origin

• Host of other life history, ecological and quantitative genetic questions

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Versatility of PBT

• Hatchery reform (integrated programs)

What is the reproductive success of hatchery-origin/wild-origin spawners? (both in the wild and in the hatchery)

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Versatility of PBT

• Hatchery reform (segregated programs)

Concern that straying hatchery fish reduce the fitness of wild populations

Is it possible to manage a hatchery program so that it is truly “segregated” from wild populations?

PBT technology can identify where straying hatchery fish were released, their stock of origin, and age

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Versatility of PBT

• Heritability estimates

To what extent are physical or behavioral traits (e.g. size and age of returning adults) controlled by genetics, environment or interactions between the two?

Are hatchery spawning practices selecting for younger age at maturity in hatchery Chinook salmon populations

15Hankin et al (2009) recommended that in the hatchery male length ≥ female length

Versatility of PBT

• Origin of kelt steelhead

Thousands of kelt steelhead outmigrate past Lower Granite Dam each year (~50% hatchery origin)

Where are they from?How old are they?Is phenotypic sex correct?

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Versatility of PBT

• PBT program can easily be integrated into existing sampling/genetic programs at Bonneville Dam and in lower Columbia fisheries (CRITFC)

Bonneville Chinook weekly stock composition (2004-2006)

Collaborative Center for Applied Fish Science

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Easily integrated into IDFG’s GSI program at LGR dam

Genetic Stock Identification

Versatility of PBT

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PBT sounds great!!!....

However, it has been largely theoretical up to this point…

• Needs to be empirically tested and validated on a large scale

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Snake River ESU

These types of evaluations have been directly called for by both the Pacific Salmon Commission and the Independent Scientific Review Panel and Advisory Boards

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Snake River Chinook and Steelhead Parentage Based Tagging-Proposal #201003100

Perfect timing to conduct a large-scale test of this technology in the basin….

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Support from hatchery managers (ID, WA, OR):

• Sampled hatchery broodstock from all Snake River hatcheries (8 hatcheries, >45,000 samples in 2008, 2009 and 2010.

(Both species-steelhead and spring/summer Chinook salmon)

>45,000 samples !!!22

Advancements in genetic technology:

• New genetic instruments and techniques allow more samples to be run at a quicker rate and for lower costs

96 samples in one run!

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Strong collaboration among labs and the ability to standardize genetic marker sets:

• Allows multiple labs to process samples and share data

Collaborative Center for Applied Fish ScienceHagerman, ID

Dr. Shawn Narum

Dr. Jon Hess 24

Major objectives over the next 3 years:

• Continue with 100% PBT sampling at all Snake River hatcheries for spring/summer Chinook and steelhead.

• Complete transition from microsatellite DNA markers to “single nucleotide polymorphic” markers (SNPs)Identify a set of SNP markers that can achieve high

parental assignment accuracy even when tens of thousands of potential parents are involved and when parentage involves hatchery populations that are very similar genetically due to shared ancestry or in situations where the broodstock contains closely related individuals

Why?• Low genotyping error rate• Allele calls (nomenclature) are easily standardized between labs• Amenable to high-throughput / low-cost genotyping

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Total Columbia

Snake River

Releases

Proportion

Spring/Summer Chinook

24,000,000 10,000,000 42%

Summer Steelhead 12,000,000 8,000,000 67%

TOTALS 36,000,000 18,000,000 50%

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• This will effectively, permanently genetically “tag” ~18 million Snake River basin smolts, per year

Major objectives over the next 3 years:• Complete the first PBT broodstock baselines in the Columbia

River basin

Major objectives over the next 3 years:

• We intend to demonstrate the applications of this technology through three sampling/genotype projects that will provide evaluations of both the accuracy and relative costs of PBT technology in providing equivalent CWT recovery data

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1. Assessment of the stock composition and run timing of Snake River hatchery salmon and steelhead passing Bonneville Dam and harvested in mainstem Columbia River fisheries

2. An assessment of the origin of straying hatchery steelhead in the Salmon River basin

3. A paired CWT and PBT recovery experiment as part of existing LSRCP hatchery evaluations in Idaho

What progress have we made thus far on our objectives?

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SNP development and testing

• In collaboration with CRITFC we identified 96 robust SNP markers (includes sex marker)Genetically diverse (all MAF >.20)Robust (easy to score, high genotyping rate)

SNP development and testing• 96 SNP set is accurate!!!High number of juveniles assigned (97.3%)100% accuracy to stock100% accuracy to parents (error from datasheets

not genetics)

Hatchery Stock

Juveniles Genotyped

Juveniles Assigned

% assigned correctly to

stock

# matching parents in

cross records

% matching parents in cross

records

Squaw Crk 92 92 100.0%

Sawtooth 93 91 100.0% 85 93.4%*

Dworshak 93 93 100.0% 93 100.0%

EF Salmon 94 88 100.0%

Pahsimeroi 93 88 100.0%

G.R. Cott. 93 91 100.0% 91 100.0%

Lyons Ferry 93 0 ----

Broodstock genotyping• Completed steelhead hatchery broodstock from 2008 (~5500

samples)• Will have steelhead broodstock from 2009 and Chinook

broodstocks from 2008 and 2009 completed by June 30th

Parent Database

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Evaluations: Currently genotyping (N = 96) 1-0cean and (N = 96) 2-ocean CWT recovered adults (fall steelhead fisheries)

CWT

PBT

• Demonstrate accuracy of PBT in providing stock and age• 1-ocean fish should assign, 2-ocean fish should not• Results by the end of this month!!!!!

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What’s up next?

• Sample and genotype kelts recovered at LGR this spring

• Complete similar “ground-truthing” exercises on CWT-recovered Chinook (2011/2012)

• Genotype all hatchery broodstock sampled in 2011• Continue to work with program managers on

developing a strategy for transitioning from CWTs to PBT in the Snake River basin

• Continue to work with program managers on the development of the “rearing and release” module of the hatchery database.

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Identify parents

Stock and age

Where it incubate

d

Where it reared

Where and

when it was

released

Ultimate goal:

Sawtooth Fish Hatchery

DietDiseaseRearing densityTemperature

This information could be available for all hatchery broodstock every year!

SEX

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http://www.flickr.com/photos/natekay/4319654380/sizes/o/

Questions???

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