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Parental Genotyping to Evaluate Family Correlated Survival and Genetic Based Tagging Of a Small Hatchery Population. Andy Gray, Research Geneticist TSMRI, Juneau, AK. Presented to 23 rd Annual Alaska Salmon Hatchery Managers Meeting. Project Investigators. Principles:

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Parental Genotyping to Evaluate Family Correlated Survival and Genetic Based Tagging Of a Small Hatchery Population

Andy Gray, Research Geneticist

TSMRI, Juneau, AK

Presented to

23rd Annual Alaska Salmon Hatchery Managers Meeting


Project investigators
Project Investigators and Genetic Based Tagging Of a Small Hatchery Population

  • Principles:

  • Andy Gray, Research Geneticist, ABL, Juneau, AK

  • John E. Joyce, Fishery Research Biologist, ABL, Juneau, AK

  • Frank Thrower, Fishery Research Biologist, ABL, Juneau, AK

  • Adrian Celewycz, Fishery Research Biologist, ABL, Juneau, AK

  • Chuck Guthrie, Fishery Research Biologist, ABL, Juneau, AK

  • Collaborators:

  • Anthony J Gharrett, Professor, UAF, AK

  • Alex Wertheimer, Fishery Research Biologist, ABL, Juneau, AK

  • Ron Josephson, Fisheries Biologist, ADF&G, Juneau, AK

  • Bill Templin, Fisheries Geneticist, ADF&G, Anchorage, AK


Parentage Based Tagging (PBT) and Genetic Based Tagging Of a Small Hatchery PopulationGenetic tagging provides population and cohort information and does not require genetic differences between populations

  • Genotyping hatchery broodstock, you can create a data base of possible parent pairs and match recovered offspring genotypes against that, assigning offspring to parent pairs (and hence hatchery and cohort)

  • By genotyping two parents, you can effectively tag all their 1,000’s of offspring

  • Also provides scientifically interesting pedigree information


Project objectives
Project Objectives and Genetic Based Tagging Of a Small Hatchery Population

  • Evaluate the ability of microsatellites and SNPs to uniquely genotype all parents of a small brood of hatchery Chinook salmon.

  • Empirically test PBT methods in mixed stock fisheries using Coded Wire Tags as controls.

  • Examine the effect of family correlated survival on the performance of PBT method.

  • Define the impact family correlated survival has on effective population size in a closed broodstock hatchery.


Approach
Approach and Genetic Based Tagging Of a Small Hatchery Population

Phase I 2007-2009

  • Spawn adult Unuk and Release 2000 CWT individuals from each of 80 families

  • Genotype all parents used for broodstock

    • GAPS 13 microsatellite, ~75 SNPs

  • Parentage analysis of ≤2000 Vertical Raceway mortalities

    • Microsatellite panel


Approach1
Approach and Genetic Based Tagging Of a Small Hatchery Population

Phase II 2010-2014

  • Recover PBT Unuk brood samples from the troll fisheries via ADF&G tag lab and returns to LPW.

  • Test abilities of microsatellite and SNPs identify PBT Unuk brood troll caught fish.

  • Examine family correlated survival via parentage analysis on all PBT Unuk brood returning to LPW.


Lpw stock background
LPW Stock Background and Genetic Based Tagging Of a Small Hatchery Population

  • Unuk R. – Cripple Cr. Stock

    • Brought to LPW – 1976

    • Larger founder population (250)

    • Wild gametes (1976-81)

  • Hatchery lines 100% CWT

    • ~500 LPW Unuk stock CWT’s recovered by ADF&G tag lab annually


Progress phase i
Progress Phase I and Genetic Based Tagging Of a Small Hatchery Population

  • Spawning of 2007 Unuk Adults- 122 F, 61 M


Experimental design
Experimental Design and Genetic Based Tagging Of a Small Hatchery Population

  • Crossed 122 females, 61 males (2F x 1M)

    • Created 122 families, 61 halfsib pairs

  • Eyed stage selected 84 families, 42 halfsib pairs

  • Ponded 79 families, 39 halfsib pairs


Individual family data collected through incubation to ponding
Individual Family Data Collected and Genetic Based Tagging Of a Small Hatchery PopulationThrough Incubation to Ponding

Family Data

100

0.6

90

0.5

80

70

0.4

60

Grams

Percent Survival

50

0.3

40

0.2

30

20

0.1

10

0

0

Hatch

Avg. Weight


Ponding into micro vertical raceways
Ponding Into Micro Vertical Raceways and Genetic Based Tagging Of a Small Hatchery Population

Transfer

Genetic Sampling

Family 1

1100

1100


Ponding into micro vertical raceways1
Ponding Into Micro Vertical Raceways and Genetic Based Tagging Of a Small Hatchery Population

2200 fry from family split between Micro Arrays

1100 each


Data collected at transfer to vertical raceways

F50 and Genetic Based Tagging Of a Small Hatchery Population

Data CollectedAt transfer to Vertical Raceways

Micro Vertical Raceways

N=158

100

3.5

95

3

90

2.5

Grams

85

2

Percent

Survival

80

1.5

Weight

75

1

70

0.5

65

60

0

Avg. Survival

Avg. Weight


Transfer of families from micro vr s to large vr s
Transfer of Families from Micro-VR’s to large VR’s. and Genetic Based Tagging Of a Small Hatchery Population

Family1a

Family 1b

100

100


Transfer of families from micro vr s to large vr s1
Transfer of Families from Micro-VR’s to large VR’s. and Genetic Based Tagging Of a Small Hatchery Population

200

200

200

200

200

200

200

200

200

100

100


Collection of mortality s
Collection of Mortality’s and Genetic Based Tagging Of a Small Hatchery Population

  • Collect mortalities on weekly bases

  • Tissue sample each mortality and preserve

  • Total mortalities to date- 985


Tagging of juveniles in large vrs
Tagging of Juveniles in Large VRs and Genetic Based Tagging Of a Small Hatchery Population

  • Oct 2008 all 10 Vertical Raceways

  • Growth Data

  • Total number of tagged individuals


Growth data
Growth Data and Genetic Based Tagging Of a Small Hatchery Population


Number of cwt individuals
Number of CWT Individuals and Genetic Based Tagging Of a Small Hatchery Population


2009 field activities
2009 Field Activities and Genetic Based Tagging Of a Small Hatchery Population

  • Continue to monitor growth and survival

  • Evaluate CWT retention

  • Release smolts ~ May 15 2009

  • Collect mini-jacks July thru August


2009 laboratory activities
2009 Laboratory Activities and Genetic Based Tagging Of a Small Hatchery Population

  • Evaluate GAPS microsatellite and SNP for PBT

  • Parentage analysis of VR mortalities


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