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

Parentage Based TaggingMatthew CampbellIdaho Department of Fish and GameLSRCP PRODUCTION MEETING AGENDAMARCH 16th, 2011BOISE, IDAHO1

1by 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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Fishing enthusiasts have been using mechanical tags for the purpose of studying fish since as early as the mid-1650s. Izakk Walton wrote in The Complete Angler (1653) that homing was observed in Atlantic Salmon:

2In 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 3

3Despite 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 5

Parentage-based genetic tagging offered as an alternative to CWTs for the management of Pacific salmon fisheries.(Anderson and Garza 2005)-Theoretical Assessment

5Parentage-based genetic tagging - PBTEvery 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

ChildGenetic information can be obtained from all hatchery fish (broodstock) that are spawnedSawtoothPahsimeroiOxbowDworshak/ClearwaterLookinglassWallowa7

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 BY20088

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 determined9

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 mortality10

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 hookThe 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 waterGenetag hook11

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 questions12

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)13

13Versatility of PBT

Hatchery reform (segregated programs)

Concern that straying hatchery fish reduce the fitness of wild populationsIs 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 age14

14Versatility 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

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Hankin et al (2009) recommended that in the hatchery male length female lengthHankin et al 2009 recommended that in the hatchery male length female length.15Versatility 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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16Versatility 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 Science17

17Easily integrated into IDFGs GSI program at LGR dam Genetic Stock IdentificationVersatility of PBT18

18PBT 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 ESUThese types of evaluations have been directly called for by both the Pacific Salmon Commission and the Independent Scientific Review Panel and Advisory Boards20

Snake River Chinook and Steelhead Parentage Based Tagging-Proposal #201003100Perfect timing to conduct a large-scale test of this technology in the basin.21

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

22Advancements in genetic technology:

New genetic instruments and techniques allow more samples to be run at a quicker rate and for lower costs96 samples in one run!23

23Strong 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, IDDr. Shawn NarumDr. Jon Hess24

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

2525Total ColumbiaSnake RiverReleasesProportionSpring/Summer Chinook24,000,00010,000,00042%Summer Steelhead12,000,0008,000,00067%TOTALS36,000,00018,000,00050%26

This will effectively, permanently genetically tag ~18 million Snake River basin smolts, per yearMajor objectives over the next 3 years:Complete the first PBT broodstock baselines in the Columbia River basinMajor 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 data27Assessment of the stock composition and run timing of Snake River hatchery salmon and steelhead passing Bonneville Dam and harvested in mainstem Columbia River fisheriesAn assessment of the origin of straying hatchery steelhead in the Salmon River basinA 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?2828SNP development and testingIn collaboration with CRITFC we identified 96 robust SNP markers (includes sex marker)Genetically diverse (all MAF >.20)Robust (easy to score, high genotyping rate)

29SNP development and testing96 SNP set is accurate!!!High number of juveniles assigned (97.3%)100% accuracy to stock100% accuracy to parents (error from datasheets not genetics)Hatchery StockJuveniles GenotypedJuveniles Assigned% assigned correctly to stock# matching parents in cross records% matching parents in cross recordsSquaw Crk9292100.0%Sawtooth9391100.0%8593.4%*Dworshak9393100.0%93100.0%EF Salmon9488100.0%Pahsimeroi9388100.0%G.R. Cott.9391100.0%91100.0%Lyons Ferry930----30Broodstock genotypingCompleted steelhead hatchery broodstock from 2008 (~5500 samples)Will have steelhead broodstock from 2009 and Chinook broodstocks from 2008 and 2009 completed by June 30thParent Database31

Evaluations: Currently genotyping (N = 96) 1-0cean and (N = 96) 2-ocean CWT recovered adults (fall steelhead fisheries)CWTPBTDemonstrate accuracy of PBT in providing stock and age1-ocean fish should assign, 2-ocean fish should notResults by the end of this month!!!!!32

32Whats up next?

Sample and genotype kelts recovered at LGR this springComplete similar ground-truthing exercises on CWT-recovered Chinook (2011/2012)Genotype all hatchery broodstock sampled in 2011Continue to work with program managers on developing a strategy for transitioning from CWTs to PBT in the Snake River basinContinue to work with program managers on the development of the rearing and release module of the hatchery database.

3333Ultimate goal:Sawtooth Fish HatcheryDietDiseaseRearing densityTemperatureThis information could be available for all hatchery broodstock every year!SEX34http://www.flickr.com/photos/natekay/4319654380/sizes/o/

Questions???35