Dustin Moss, PhD Oceanic Institute of Hawaii Pacific University · 2019-09-25 · IHHNV AHPND (EMS)...
Transcript of Dustin Moss, PhD Oceanic Institute of Hawaii Pacific University · 2019-09-25 · IHHNV AHPND (EMS)...
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Breeding for Disease Resistance in Penaeid Shrimp
Dustin Moss, PhD Oceanic Institute of Hawaii Pacific University
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Aquaculture Breeding Programs
Goal – Improve production of target species and profitability of farming
How – Genetic improvement of traits that are economically important
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What are the “most” important traits?
• Growth • Shortened culture period • Larger harvest size • Growth is growth is growth!
• Survival • Higher survival = higher biomass/production • What is survival?
– Pathogen resistance? Which pathogen(s)? – Tolerance of low/fluctuating salinity? – Tolerance of fluctuating pH? – Tolerance of low oxygen? – Interaction of factors?
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How to improve survival?
• What survival related traits should be selected for? • Depends of situation • All of them? • Environment specific conditions?
• Selection for pathogen resistance? • Which pathogen(s)? • Is resistance heritable? • Is there genetic variation? • Evaluation strategy(ies)? • Accuracy of selection? • Other effective measures? • Effects on other traits?
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Other approaches to disease mitigation
• Specific Pathogen Free (SPF) • Unrelated to genetic quality • Not coddled • Sib-selection
• Biosecurity • Reduce/eliminate pathogen load
• Probiotics • Competitive exclusion • Improve environmental conditions
• Immune stimulants?
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Has selective breeding for pathogen
resistance been effective?
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History of Shrimp Breeding• Late 1980s/early 1990s: Captive breeding and SPF stock
development (in response to IHHNV) • First formal breeding program established in 1995 at OI (in
response to TSV) • SPF • Family-based
• CENIAQUA first formal breeding program in Central America (family based)
• Mid 2000s - present: breeding programs in Asia begin • Mid 2000s - present: mass selection programs in C. Am.
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History of Shrimp Breeding
• Traits: – Growth
• Generally considered the most important trait • Selection response is good and consistent
– Growout survival • Selection response is mixed, inconsistent • Difficult to define farming environment
– Pathogen resistance • Taura syndrome virus (TSV) • White spot syndrome virus (WSSV)
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Selection for TSV resistance
• h2 estimates ~ 0.2 (low - moderate) • Good selection response (>10% per generation) • Resistance stocks have been distributed globally
Shrimp families0
20
40
60
80
1000
20
40
60
80
100
Mean = 84%CV = 13.6%
Mean = 44%CV = 43.3%
Generation 7
Generation 2
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Selection for WSSV resistance
• h2 estimates typically < 0.1 (very low) • Low genetic diversity; rare alleles/mutation(s) • Family-based breeding largely unsuccessful • Mass selection has had moderate/good success
WSSV virion mean size = 275 nm
Family Treatment Survival
LP-1 Negative control 49 of 50 (98%)
LP-2 Negative control 91 of 96 (95%)
LP-3 Negative control 68 of 68 (100%)
Kona WSSV positive control
0 of 20 (0%)
LP-1 (2 tanks) WSSV challenge 24 of 104 (23%)
LP-2 (2 tanks) WSSV challenge 74 of 129 (57%)
LP-3 (2 tanks) WSSV challenge 34 of 130 (26%)
Modified from Cuéllar-Anjel et al. 2012
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Difficulty with breeding for
pathogen resistance
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So many pathogens, so little time (money)
VIRUSES PROCARYOTESTSV EHP
WSSV NHPYHV, GAV, LOV RLB-MHD
IHHNV AHPND (EMS)SHIV*
MBV, BP, BMN PROTOZOAIMNV MicrosporidiansHPV HaplosporidiansPvNV GregarinesMoV WFS
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Challenges with Multi-trait Selection
• Breeding can’t do everything!
• Some challenges better addressed through management (e.g. feeds, probiotics, biosecurity measures, etc.)
• Traits of interest:
• Variable environment – Physical environment (rainfall, temp, salinity, pathogens) – Management (pond size, biosecurity, stocking density) – Economics
Maturation Hatchery Nursery Growout
Spawn Freq Spawn Size Hatch Rate
Survival Growth
Survival Growth
Survival Growth
Processing
Size Size Dist.
Tail : Body Color
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Challenges with Multi-trait Selection
• Always tradeoffs when adding trait(s) to a selection program!
Stewart et al. 1999
• Few traits – rapid improvement possible
• Many traits – slower improvement
• Multiple pathogen resistance?
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Challenges with Multi-trait SelectionSpecies # Breeding
ProgramsFamilies per
ProgramAverage # Traits
Common Carp 8 76 2.0Tilapia (Nile) 20 229 3.6Tilapia (Blue) 2 90 2.0Tilapia (Red) 4 125 4.0
Atlantic Salmon 13 280 5.4Chinook Salmon 2 100 1.5
Coho Salmon 4 133 2.7Rainbow Trout 13 206 5.2Atlantic Cod 3 110 4.0
European Seabass 3 100 5Sea Bream 4 100 6
Oysters 3 48 4.3P. monodon 3 212 ---P. vannamei 4 197 2.0
modified from Gjedrem et al. 2012
Species # Breeding Programs
Families per Program
Average # Traits
Common Carp 8 76 2.0Tilapia (Nile) 20 229 3.6Tilapia (Blue) 2 90 2.0Tilapia (Red) 4 125 4.0
Atlantic Salmon 13 280 5.4Chinook Salmon 2 100 1.5
Coho Salmon 4 133 2.7Rainbow Trout 13 206 5.2Atlantic Cod 3 110 4.0
European Seabass 3 100 5Sea Bream 4 100 6
Oysters 3 48 4.3P. monodon 3 ~200 ~2
P. vannamei ~10 >100 ~4
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Challenges with Multi-trait Selection
• TSV not correlated with other commercially important traits
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Trait USTX95 BZ01 TH04 VZ05
USTX95 0.26 ± 0.05
BZ01 0.90 ± 0.31** 0.16 ± 0.04
TH04 0.56 ± 0.25* 0.35 ± 0.23 0.33 ± 0.07
VE05 0.87 ± 0.29** 0.99 ± 0.26** 0.50 ± 0.24* 0.27 ± 0.06
* p ≤ 0.05 ** p ≤ 0.005
Viral Mutation Adds Difficulty
Moss et al., (2013)
• Among TSV Isolates
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Inbreeding
➢ Can negatively affect important traits (inbreeding depression)
Trait Inbreeding Depression (%)
Hatch Rate -13Survival – Hatchery -11Survival – Growout <-4Survival – TSV-AG -9Survival – TSV-BG -31Survival – WSSV -40Growth – Growout <-4
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Types of Shrimp Breeding Programs
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Mass Selection Programs
• Can be simple • Relatively cheap to implement and operate • Traits measured on live breeding candidates (e.g. growth) –
breeders selected from farms • Large-scale commercial evaluations/feedback • Effective for binary traits (dead or alive) in where desired
phenotype is in low frequency (e.g. WSSV survival) • Poor selection accuracy for traits with low heritability • Can be difficult to monitor/control inbreeding • Cannot select for destructive traits (e.g. carcass) • Selected stocks can carry pathogens (non-SPF)
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Mass Selection in Americas
2013 2014 2015 20162017 From João Rocha
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From João Rocha
Mass Selection in Americas
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Family-based Breeding Programs
• Majority of aquaculture programs use this approach • Breeders selected based on family performance (or performance of
siblings) • Can select for all types of traits • Costly to implement and operate • Can have complicated designs, unique facilities • Pedigree data is needed • Sophisticated statistical analyses • Increased selection accuracy (low-moderate heritability) • Control of inbreeding
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Family Breeding Program Structure
Complicated, but powerful ▪ Provides SPF
broodstock to CH
▪ On-farm evaluations
▪ Multiplication / in-country breeding center
▪ Potential for locally developed lines / line breeding
▪ Increased commercial feedback
NBC
Commercial Hatcheries
CH CH
Commercial Farms
CF CF CF CF
Family/Line Evaluations
Sele
ctio
n D
ata
LBC
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Family Selection in Asia
Cohort Harvest Date
# Families
# Shrimp
Harvest Size
Growth (g/day)
Survival (%) Notes
1 Jan-2013 50 2,612 18.7 0.273 92 Luminescent bacteria2 July-2013 48 3,106 28.3 0.301 533 Oct-2013 50 4,025 22.7 0.389 80 Cyclone, severe flooding4 Aug-2014 49 4,139 19.3 0.311 555 Mar-2015 50 3,693 14.3 0.168 87 WSSV, premature harvest6 Jun-2015 50 4,799 21.5 0.421 87 WSSV7 Oct-2015 50 4,735 8.5 0.300 79 WSSV, premature harvest8 Jun-2016 50 4,469 13.2 0.197 62 EHP/WSSV, premature harv.9 July-2016 20 2,479 18.2 0.314 86 WSSV10 Dec-2016 50 3,379 22.8 0.385 9211 Dec-2016 22 2,003 19.6 0.340 94
Total 489 37,436 Overall 18.8 0.309 79
Means Premature harvests 12.0 0.222 76 Full evaluations 21.4 0.342 80
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Family Selection in Asia
Gro
wth
(g/d
ay)
0.10
0.20
0.30
0.40
0.50
Dec-12 Dec-13 Dec-14 Dec-15 Dec-16
0.17
0.3
0.2
0.2730.301
0.389
0.311
0.421
0.314
0.3850.400
Premature harvests
+5% per year
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Which type is “best” for shrimp?
Many factors must be considered: • Traits – How many? Heritability? Correlations? • Level of biosecurity • Clients – self, local, international • SPF? • Capital investment / existing facilities • Available staff • Farming system • Farming environment • Founder stocks – diversity, disease status, pedigree • How to prevent inbreeding? Costs?
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Thank You!