Download Genetic and Genomic Approaches for Improving Disease

Genetic and Genomic Approaches for Improving
Disease Resistance in Farmed Salmon
Almas A Gheyas PhD
Prof. Ron Roberts PhD FRCVS FRSE
Alan E Tinch PhD
Impact Through Bioscience conference
18-19 Oct 2010
Scottish Salmon Industry
„ Salmon Industry has grown since
Global Atlantic Salmon Production.
1980 to 2008. (FAO)
1,600,000
Scotland
1,400,000
Chile
1,200,000
Norway
Rest of World
1,000,000
800,000
600,000
400,000
200,000
year
2008
2006
2004
2002
2000
1998
1996
1994
1992
1990
1988
1986
1984
1982
0
1980
tonnes
1990
„ Today 90% of marketed salmon
comes from farming
„ Scotland is the 2nd largest salmon
producer
„ Salmon industry has become of
higher value than beef & sheep
industry combined by 2009
Landcatch
„ Established in 1979
„ Part of Lithgow Group
„ Produces salmon eggs, smolts &
table fish
„ Landcatch stocks were derived
from Norwegian and Scottish wild
stocks
„ Modern breeding techniques are
being applied since 1996
Landcatch Natural Selection (LNS)
„ A new company established to
„
apply standard quantitative
genetic techniques for selection
„
establish pedigrees and
„
apply molecular genetic analysis
„ THIS IS NOT IN ANY WAY GM
Our business in a nutshell
‰Products
‰ Salmon eggs
‰ Salmon smolts
‰ Table fish
‰ Genetic services
¾ Parentage & relatedness
analysis
¾ Breeding programme
management
¾ Selective breeding & markerassisted selection
Products sold in:
‰ Australia
‰ Chile
‰ Ireland
‰ Norway
‰ Scotland
Salmon disease & management
„ Diseases are major problems with domesticating salmon
„ Major concerns:
IPN (Infectious Pancreatic Necrosis) virus
„ PD (Pancreatic disease) virus
„ ISA (Infectious salmon anaemia) virus
„ Sea louse
„
„ Breeding for disease resistance is a priority
Resources in disease management
„ LNS has its own geneticists, molecular biologists & veterinarians
„ Also collaborates with other organisations:
„
„
„
„
„
The Roslin Institute
The University of Stirling-Institute of Aquaculture
Scottish Agriculture College
The University of Glasgow Veterinary School
The University of Edinburgh Genepool Laboratories
GENESIS FARADY (KTN) HAS BEEN CRUCIAL TO ALL OF THESE
COLLABORATIONS
Infectious Pancreatic Necrosis (IPN)
„ A serious disease of wild/farmed
salmon fry
„ Up to 80% of the fry die
„ Also a severe problem when the fish
first go to sea
„ Up to 30-40% of post-smolt may die
Infectious Pancreatic Necrosis (IPN) Virus
„ Caused by an aquatic birnavirus
„ Birnaviruses cause immuno-
suppression and grow in immune
tissues (e.g. spleen, kidney)
„ Very resistant virus- survive for
weeks or even months
The IPN Sentinel study
„ Landcatch Breeding Programme consists of 4 year
classes x 200 selected families
„ 200 fish from each family were sent to
Three commercial farm sites in Shetland, North West
Highlands, and South West Highlands
„ All dead fish from IPN were collected, and identified to
family of origin
„ Results from each site were compared
„
Genetic background of IPN
Low mortality rate
(resistant)
Intermediate
mortality rate
High mortality rate
(susceptible)
Clear evidence of family variation of IPN resistance
– indicates possibility of improvement through
selective breeding
But what sort of programme?
Types of Breeding Programmes
„ Mass Selection – Breeding from the biggest
„ Family Selection – Based on knowledge of the commercial
performance of fish from the same family
„ Molecular Marker-Assisted Selection – Breeding from
genetically ideal individuals, based on the performance of the
best commercial siblings with the same gene pattern
Mass Selection
Easy- Choose the best looking eggs, smolts or broodstock
Family Selection – More Difficult
„ Requires correct identification of
families for each fish
„
Family separation during early life
„
Microchip identification of individuals
at later stage
Molecular Marker-Assisted Selection
Selective breeding for disease resistance
Conventional Selection
Allows selection of only
resistant families
Marker-Assisted-Selection
Allows selection of resistant
individuals within each family
Marker-assisted selection for
improvement of IPN resistance
Marker-assisted-selection (MAS) principle
Very difficult to identify
Gene for disease resistance
Molecular markers
Molecular markers are widespread
across the genome and are much
easier to identify
Closely located markers and
their variants are used in MAS
Marker-assisted selection
Resistant (R) gene
FATHER
MOTHER
Resistant (R) gene
X
Susceptible (S) gene
Susceptible (S) gene
OFFSPRING 1 (RR)
OFFSPRING 2 (RS)
OFFSPRING 3 (SS)
Background genetics for IPN MAS
Most Likely position of LG21 QTL
„ Three regions on chromosomes
were identified to have effect on
IPN resistance
„ One region (LG21-QTL) has
major effect on IPN resistance
Source: Houston et al. 2008; Genetics
Effect of LG21-QTL on survival
Survival of Landcatch salmon with differing variants of the
IPN resistance gene
Survival rate
Mother’s
variants
Resistant (+)
Susceptible (-)
Father’s variant
Resistant (+) Susceptible (–)
(+ +)
91-100%
(– +)
67-78%
(+ –)
38-60%
(– –)
0-29%
Marker system in use by LNS
Markers
BHMS217
Rsa476
SSA0139
SSA374BSFU
SSA0019
Alu333
SSA680BSFU
SSA0039
New markers are being continually generated and evaluated
Commercial Application
„ LNS deliver the first commercial application of MAS in
aquaculture
„
MAS for IPN resistance was piloted in 2007 and applied to
LNS breeding programme from 2008 onwards
„ MAS for IPN resistance in Chile
„
In 2010 MAS was applied in the Landcatch Breeding
Programme in Chile
„ MAS for IPN resistance in Norway
„
LNS are carrying out MAS as a commercial service to
Salmon breeders in Norway
Further studies
„ Roslin Institute is undertaking further research in
collaboration with LNS
„ Transcriptomic analysis
„ Studying the expressed genes in IPN resistant and
susceptible individuals
„ Trying to determine the underlying pathways of disease
expression
„ Possibility of detecting causal gene
„ Fine mapping the LG21- QTL
Acknowledgements
‰
‰
‰
‰
John Woolliams
Chris Haley
Ross Houston
Ricardo Pong-Wong
‰
‰
‰
‰
Alan Tinch
Derrick Guy
Jose Mota-Velasco
Alastair Hamilton