Prosjektnummer
900255
Mitigating the Effects of Escaped Farmed Salmon: Combining SNPs, Lipid Acid Profiling and Statistical Methods to Trace Escapees to Origin (MENTOR)
Prosjektet ble finansiert av Norges forskningsråd med delfinansiering fra FHF via Havbruksprogrammet i Forskningsrådet.
Samandrag av resultat frå sluttrapporten til Forskningsrådet
Målet med MENTOR-prosjektet er å auka presisjonen i metodar som blir brukt for identifisering av opphavet til rømt oppdettslaks, gjennom ein kombinasjon av SNP-markørar, lipidprofilar og statistiske metodar.
Samanlikning mellom 300 polymorfe SNP(1) og 14 STR(2)-markørar vart gjennomført på eit datasett med 10 populasjonar og 500 atlanterhavslaks. Global Fst varierte frå 0.033 til 0.115 og frå -0.002 til 0.316 for dei 14 STR- og dei 300 SNP-markørane respektivt. Dei 15 beste SNP (30 allel)-markørane gav ein presisjon som tilsvarte dei 4 beste STR (83 allel)-markørane. Tillegg av fleire STR-markørar gav kun liten auke i presisjon medan tillegg av opptil 100 SNP loci auka presisjonen i identifiseringa.
Eit common garden feltforsøk vart initiert i 2003 i Guddalselva for å samanlikna overleving, vekst mv. hos avkom av oppdettslaks, villaks og kryssingar frå rogn til smolt i naturen. Signifikante skilnadar vart registrert i vekst, kroppsfasong (kondisjonsfaktor) og overleving mellom dei 69 familiane og mellom dei tre hovudgruppene. I MENTOR-prosjektet har ein gått vidare for å gje ei meir inngåande forståing av det genetiske grunnlaget for desse observerte skilnadane i vekst, kroppsfasong og overleving mellom oppdrettslaks, villaks og kryssingar. Genom-scan for QTL(3) som påverkar lengde (L), vekt (W) og kondisjonsfaktor (CF) avdekka fleire genom-regionar med signifikant påverknad på desse tre fenotypane. Genom-posisjonane for desse QTL'ane og andel av variansen i karakteren er identifisert. Vekt er signifikant påverka av to QTL’ar: ein på kromosom 2, som forklarar 8,4 % av observert varians i vekt i populasjonen, og ein på kromosom 11 som forklarar 7,7 % av variansen i vekt. Kollektivt er desse to QTL’ane ansvarlege for 14,8 % av vekt-variansen. QTL-posisjonen på kromosom 2 er ein særleg interessant region som påverkar både vekst og overleving i naturen.
Interessant er det også at denne genom regionen viser signifikant redusert variasjon i oppdrettsmaterialet, medan variasjonen framleis er høg i villaksmaterialet. QTL på kromosom 2 framstår difor som ein genom region som potensielt viser fotavtrykk av pågåande domestiserings hos Atlantisk laks. Prosjektet omfattar den første undersøkinga av den genetiske arkitekturen som ligg til grunn for skilnadane som er observert mellom oppdrettslaks og villaks i naturen.
Det er også vist i prosjektet at fettsyreprofilen i fiskeskjell er avhengig av både miljømessige og genetiske faktorer, og kan være en mulig faktor å analysere for å identifisere opphav til rømt fisk.
Målet med MENTOR-prosjektet er å auka presisjonen i metodar som blir brukt for identifisering av opphavet til rømt oppdettslaks, gjennom ein kombinasjon av SNP-markørar, lipidprofilar og statistiske metodar.
Samanlikning mellom 300 polymorfe SNP(1) og 14 STR(2)-markørar vart gjennomført på eit datasett med 10 populasjonar og 500 atlanterhavslaks. Global Fst varierte frå 0.033 til 0.115 og frå -0.002 til 0.316 for dei 14 STR- og dei 300 SNP-markørane respektivt. Dei 15 beste SNP (30 allel)-markørane gav ein presisjon som tilsvarte dei 4 beste STR (83 allel)-markørane. Tillegg av fleire STR-markørar gav kun liten auke i presisjon medan tillegg av opptil 100 SNP loci auka presisjonen i identifiseringa.
Eit common garden feltforsøk vart initiert i 2003 i Guddalselva for å samanlikna overleving, vekst mv. hos avkom av oppdettslaks, villaks og kryssingar frå rogn til smolt i naturen. Signifikante skilnadar vart registrert i vekst, kroppsfasong (kondisjonsfaktor) og overleving mellom dei 69 familiane og mellom dei tre hovudgruppene. I MENTOR-prosjektet har ein gått vidare for å gje ei meir inngåande forståing av det genetiske grunnlaget for desse observerte skilnadane i vekst, kroppsfasong og overleving mellom oppdrettslaks, villaks og kryssingar. Genom-scan for QTL(3) som påverkar lengde (L), vekt (W) og kondisjonsfaktor (CF) avdekka fleire genom-regionar med signifikant påverknad på desse tre fenotypane. Genom-posisjonane for desse QTL'ane og andel av variansen i karakteren er identifisert. Vekt er signifikant påverka av to QTL’ar: ein på kromosom 2, som forklarar 8,4 % av observert varians i vekt i populasjonen, og ein på kromosom 11 som forklarar 7,7 % av variansen i vekt. Kollektivt er desse to QTL’ane ansvarlege for 14,8 % av vekt-variansen. QTL-posisjonen på kromosom 2 er ein særleg interessant region som påverkar både vekst og overleving i naturen.
Interessant er det også at denne genom regionen viser signifikant redusert variasjon i oppdrettsmaterialet, medan variasjonen framleis er høg i villaksmaterialet. QTL på kromosom 2 framstår difor som ein genom region som potensielt viser fotavtrykk av pågåande domestiserings hos Atlantisk laks. Prosjektet omfattar den første undersøkinga av den genetiske arkitekturen som ligg til grunn for skilnadane som er observert mellom oppdrettslaks og villaks i naturen.
Det er også vist i prosjektet at fettsyreprofilen i fiskeskjell er avhengig av både miljømessige og genetiske faktorer, og kan være en mulig faktor å analysere for å identifisere opphav til rømt fisk.
Noen forklaringer av forkortelser
(1) SNP - (genetics) genetic variation in a DNA sequence that occurs when a single nucleotide in a genome is altered;
(2) A short tandem repeat (STR) in DNA occurs in non-coding region when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other.
(3) Quantitative trait loci (QTLs) are stretches of DNA containing or linked to the genes that underlie a quantitative trait. Mapping regions of the genome that contain genes involved in specifying a quantitative trait is done using molecular tags such as AFLP or, more commonly SNPs. This is an early step in identifying and sequencing the actual genes underlying trait variation.
Relaterte artikler i vitenskapelige tidsskrift
Glover K. A., Quintela M., Wennevik V., Besnier F., Sørvik A. G. E., Skaala Ø. (2012). Three Decades of Farmed Escapees in the Wild: A Spatio-Temporal Analysis of Atlantic Salmon Population Genetic Structure throughout Norway (PLoS ONE 7(8):
Besnier F., Glover K. A., Skaala Ø. (2011). Investigating genetic change in wild populations: Modelling gene flow from farm escapees (Aquacult Environ Interact vol 2: 75–86:
Grahl-Nielsen O., Glover K. A. (2010). Fatty acids in fish scales. Marine Biology 157(7):
Glover K. A., Hansen M. M., Lien S., Als T. D., Høyheim B., Skaala Ø. (2010). BMC Genetics 11:2. A comparison of SNP and STR loci for delineating population structure and performing individual genetic assignment
Glover K. A., Skaala Ø., Sørvik A. G. E., Helle T.A. (2010). Aquaculture Research 42(9): Genetic differentiation among Atlantic salmon reared in sea-cages reveals a non-random distribution of genetic material from a breeding programme to commercial production
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Final report: Mitigating the effects of escaped farmed Atlantic salmon: Combining single nucleotide polymorphisms, lipid acid profiling, and statistical methods to trace escaped salmon back to origin
Havforskningsinstituttet. Report 18-2013. June 2013. By Øystein Skaala (project manager), Francois Besnier and Kevin A. Glover.
Background
There is a strong focus on reducing the number of escaped farmed salmon in Norway through improvement of technological standards in fish farms and by inspections. Also, work has been initiated to develop technology to identify farm of origin of escapees as a preventive measure to reduce the numbers of unreported escapes. See FHF-project 542022 “Tracing escaped farmed salmon by means of naturally occurring DNA markers, fatty acid profiles, trace elements and stable isotopes (TRACES), Norwegian Research Council, project 172628”.
Some of the negative environmental consequences of farmed escapees have been documented, and it is clear that escapees are capable of having negative genetic and ecological effects. For this reason, it is an explicit goal of both the national management authorities and the aquaculture industry that the number of escapes should be reduced. As a follow-up of White Paper no. 12 (2001–2002), “A Clean and Rich Sea”, and Recommendation no. 134 of the Parliamentary Committee on Energy and the Environment (2002–2003) regarding the setting up of national salmon rivers and salmon fjords, the Ministry of Fisheries and Coastal Affairs took the initiative in 2003 to set up a national committee to study questions related to marking farmed salmon. According to the Marking Committee (Norwegian Directorate of Fisheries, 2004), there is a great deal of uncertainty as to just how many salmon actually escape from Norwegian fish farms. Where do these escapees come from, and what are the relative proportions of reported and unreported escapes? How many escape from smolt farms?
Recently DNA microsatellites have been successfully used to identify individual farmed escaped salmon back to cage of origin. In some cases, however, the information drawn from DNA based markers must be followed with supplementary information from other markers, such as lipid acid profiles.
There is a strong focus on reducing the number of escaped farmed salmon in Norway through improvement of technological standards in fish farms and by inspections. Also, work has been initiated to develop technology to identify farm of origin of escapees as a preventive measure to reduce the numbers of unreported escapes. See FHF-project 542022 “Tracing escaped farmed salmon by means of naturally occurring DNA markers, fatty acid profiles, trace elements and stable isotopes (TRACES), Norwegian Research Council, project 172628”.
Some of the negative environmental consequences of farmed escapees have been documented, and it is clear that escapees are capable of having negative genetic and ecological effects. For this reason, it is an explicit goal of both the national management authorities and the aquaculture industry that the number of escapes should be reduced. As a follow-up of White Paper no. 12 (2001–2002), “A Clean and Rich Sea”, and Recommendation no. 134 of the Parliamentary Committee on Energy and the Environment (2002–2003) regarding the setting up of national salmon rivers and salmon fjords, the Ministry of Fisheries and Coastal Affairs took the initiative in 2003 to set up a national committee to study questions related to marking farmed salmon. According to the Marking Committee (Norwegian Directorate of Fisheries, 2004), there is a great deal of uncertainty as to just how many salmon actually escape from Norwegian fish farms. Where do these escapees come from, and what are the relative proportions of reported and unreported escapes? How many escape from smolt farms?
Recently DNA microsatellites have been successfully used to identify individual farmed escaped salmon back to cage of origin. In some cases, however, the information drawn from DNA based markers must be followed with supplementary information from other markers, such as lipid acid profiles.
Microsatellites are subject to inter-laboratory calibration problems and are technically demanding. The statistical power of a microsatellite locus is typically 4–10 times higher than for a SNP (single nucleotide polymorphism) locus, but the ability to screen a large number of SNP loci simultaneously, in combination with the opportunity to analyse a large number of loci to find those that are diagnostic, far outweighs the advantage of microsatellites. Recently, the Centre for Integrated Genetics (CIGENE) in Norway started production of a genome wide genotyping chip interrogating a large number of SNPs for the Atlantic salmon.
Objectives
To improve the precision in methods for identification of origin of farmed salmon escaping from sea cages and smolt farms, by a combination of SNP markers and lipid acid profiles and an evaluation of new assignment methods with the purpose of optimizing the information provided by large SNP data sets for tracing escaped salmon back to cage of origin.
To improve the precision in methods for identification of origin of farmed salmon escaping from sea cages and smolt farms, by a combination of SNP markers and lipid acid profiles and an evaluation of new assignment methods with the purpose of optimizing the information provided by large SNP data sets for tracing escaped salmon back to cage of origin.
Expected project impact
There is a strong focus on reducing the number of escaped farmed salmon in Norway. Methods that can identify the origin of escaped farmed salmon is expected to have a preventive effect on escapement. The project will be run in close cooperation with the ongoing activity on genetic research on farmed and wild Atlantic salmon within the collaborating institutions, including:
• Running activities on tracing escaped farmed salmon in collaboration with the Norwegian Fisheries Directorate.
• Monitoring genetic stability in salmon populations linked to the national assessment of the National salmon fjords and rivers, funded by the Ministry of Fisheries and Coastal affairs.
There is a strong focus on reducing the number of escaped farmed salmon in Norway. Methods that can identify the origin of escaped farmed salmon is expected to have a preventive effect on escapement. The project will be run in close cooperation with the ongoing activity on genetic research on farmed and wild Atlantic salmon within the collaborating institutions, including:
• Running activities on tracing escaped farmed salmon in collaboration with the Norwegian Fisheries Directorate.
• Monitoring genetic stability in salmon populations linked to the national assessment of the National salmon fjords and rivers, funded by the Ministry of Fisheries and Coastal affairs.
Project design and implementation
Four different work packages have been designed in order to gain the information required to meet the objectives of the project:
Work package 1: SNPs for tracing escaped salmon back to farm of origin
Main aims
• To identify an optimal panel of diagnostic SNPs discriminating both among and between the major farmed salmon strains used in Norway.
• To compare diagnostic power of SNPs with microsatellites for tracing farmed escapees back to farm of origin.
• To implement the new panel of SNPs into a “real-life” escapement episode.
Work package 2: Quantification of natural selection on SNPs
Main aims
• To quantify the degree to which the SNP markers are influenced by natural selection.
• To compare the strength and direction of natural selection on SNP variation in salmon of farmed, wild and hybrid parentage i n the wild (will molecular selection be greater in farmed salmon displaying higher mortality than planted wild salmon?)
• To gain a better understanding of the molecular basis of natural selection in the wild.
Work package 3: Investigation of new statistical methods for identifying the origin for farmed escaped salmon and detecting offspring of farmed salmon in wild populations
Main aims
• To evaluate new assignment methods with the purpose of optimizing the information provided by large SNP data sets for tracing farmed escaped salmon back to cage of origin.
• To evaluate the use of statistical programs (STRUCTURE and related methods) for identifying populations without making prior assumptions about the population of origin for groups of salmon originating from different farms.
• To establish a standard statistical protocol for tracing farmed escaped fish with microsatellite and or SNP data.
Work package 4: Use of lipid acid profiling as a supplementary identification tool for farmed escaped salmon
Main aims
• To identify the tissue(s) providing the best diagnostic identification of farmed salmon that have been reared on different diets, and that have similar genetic background.
• To quantify the stability of fatty acid profiles in a range of tissues in periods of fasting and feeding.
• To test the efficiency of fatty acid profiling in a “real-life” escapement episode as a supplement to DNA analyses.
• To establish a standard protocol for sampling and analysis of fatty acid profiling for tracing farmed escaped salmon in combination with DNA analyses.
Four different work packages have been designed in order to gain the information required to meet the objectives of the project:
Work package 1: SNPs for tracing escaped salmon back to farm of origin
Main aims
• To identify an optimal panel of diagnostic SNPs discriminating both among and between the major farmed salmon strains used in Norway.
• To compare diagnostic power of SNPs with microsatellites for tracing farmed escapees back to farm of origin.
• To implement the new panel of SNPs into a “real-life” escapement episode.
Work package 2: Quantification of natural selection on SNPs
Main aims
• To quantify the degree to which the SNP markers are influenced by natural selection.
• To compare the strength and direction of natural selection on SNP variation in salmon of farmed, wild and hybrid parentage i n the wild (will molecular selection be greater in farmed salmon displaying higher mortality than planted wild salmon?)
• To gain a better understanding of the molecular basis of natural selection in the wild.
Work package 3: Investigation of new statistical methods for identifying the origin for farmed escaped salmon and detecting offspring of farmed salmon in wild populations
Main aims
• To evaluate new assignment methods with the purpose of optimizing the information provided by large SNP data sets for tracing farmed escaped salmon back to cage of origin.
• To evaluate the use of statistical programs (STRUCTURE and related methods) for identifying populations without making prior assumptions about the population of origin for groups of salmon originating from different farms.
• To establish a standard statistical protocol for tracing farmed escaped fish with microsatellite and or SNP data.
Work package 4: Use of lipid acid profiling as a supplementary identification tool for farmed escaped salmon
Main aims
• To identify the tissue(s) providing the best diagnostic identification of farmed salmon that have been reared on different diets, and that have similar genetic background.
• To quantify the stability of fatty acid profiles in a range of tissues in periods of fasting and feeding.
• To test the efficiency of fatty acid profiling in a “real-life” escapement episode as a supplement to DNA analyses.
• To establish a standard protocol for sampling and analysis of fatty acid profiling for tracing farmed escaped salmon in combination with DNA analyses.
Dissemination of results
The previous project TRACES was strongly profiled and very actively communicated to the general public through interviews in the newspapers and via the web page of the Institute of Marine Research. The present project is also aiming at a very active communication, not only of results, but also the questions of concern and the research design. Schools in the Hardangerfjord region are actively invited and often visit the field station in River Guddal to introduce the students to science and active research. Results from the project are also used actively in teaching courses at the University of Bergen and the University for Environment and Biological Sciences at Ås. During the project, an active dialogue with the Norwegian directorate of Fisheries, fish farmers, and other interested parties will be maintained.
Deliverables
• Minimum 4 articles in peer reviewed scientific journals
• Minimum 2 popular scientific articles
• Protocol for statistical treatment of genetic data for tracing farmed escapees
• Protocol for use of fatty acid profiling as a supplement to D NA based identification methods
• An optimised set of SNP markers for tracing escaped salmon back to marine farm site or smolt farm
• Minimum 4 presentations at international meetings
The previous project TRACES was strongly profiled and very actively communicated to the general public through interviews in the newspapers and via the web page of the Institute of Marine Research. The present project is also aiming at a very active communication, not only of results, but also the questions of concern and the research design. Schools in the Hardangerfjord region are actively invited and often visit the field station in River Guddal to introduce the students to science and active research. Results from the project are also used actively in teaching courses at the University of Bergen and the University for Environment and Biological Sciences at Ås. During the project, an active dialogue with the Norwegian directorate of Fisheries, fish farmers, and other interested parties will be maintained.
Deliverables
• Minimum 4 articles in peer reviewed scientific journals
• Minimum 2 popular scientific articles
• Protocol for statistical treatment of genetic data for tracing farmed escapees
• Protocol for use of fatty acid profiling as a supplement to D NA based identification methods
• An optimised set of SNP markers for tracing escaped salmon back to marine farm site or smolt farm
• Minimum 4 presentations at international meetings