Breeding for Disease Resistance in Penaeid Shrimp

Dustin Moss, PhD Oceanic Institute of Hawaii Pacific University

Aquaculture Breeding Programs

Goal – Improve production of target species and profitability of farming

How – Genetic improvement of traits that are economically important

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?

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?

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?

Has selective breeding for pathogen

resistance been effective?

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.

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)

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

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

Difficulty with breeding for

pathogen resistance

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

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

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?

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

Challenges with Multi-trait Selection

• TSV not correlated with other commercially important traits

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

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

Types of Shrimp Breeding Programs

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)

Mass Selection in Americas

2013 2014 2015 20162017 From João Rocha

From João Rocha

Mass Selection in Americas

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

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

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

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

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?

Thank You!