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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