What role for genomics in fisheries management and aquaculture?

15 Pages·2007·0.62 MB·English

Aquat.LivingResour.20,241–255(2007) Aquatic
(cid:2)c EDPSciences,IFREMER,IRD2007
Living
DOI:10.1051/alr:2007037
Resources
www.alr-journal.org
What role for genomics in fisheries management
and aquaculture?
Roman Wenne1,a,Pierre Boudry2, Jakob Hemmer-Hansen3,KrzysztofP. Lubieniecki4, AnnaWas5
and AnttiKause6
1 DepartmentofGeneticsandMarineBiotechnology,InstituteofOceanology,PolishAcademyofSciences,PowstañcówWarszawy55,
81-712Sopot,Poland
2 IFREMERLaboratoiredeGénétiqueetPathologie,17390LaTremblade,France
3 DanishInstituteforFisheriesResearch,DepartmentofInlandFisheries,Vejlsøvej39,8600Silkeborg,Denmark
4 DepartmentofMolecularBiologyandBiochemistry,SimonFraserUniversity,8888UniversityDr.,Burnaby,BC,V5A1S6,Canada
5 MolecularEcologyResearchGroup,Galway-MayoInstituteofTechnology,Galway,Ireland
6 MTTAgrifoodResearchFinland,BiotechnologyandFoodResearch,BiometricalGenetics,31600Jokioinen,Finland
Received16May2007;Accepted28August2007
Abstract– Thedevelopmentandapplicationofgenomicshasbeenfacilitatedinanumberoffieldsbytheavailability
ofnewmethodologiesandtools,suchashighthroughputDNAsequencingandcomplementaryDNA(cDNA)microar-
rays.Genomictoolsarealreadyusedinresearchoncommerciallyimportantfishandshellfishspecies.Thousandsof
expressedsequencetags(EST)arenowavailableforsomeofthesespecies,andthesequencingofcompletegenomes
of tilapia, cod, salmonids, flatfishes, sea bass and Pacificoyster has been proposed. Microarray technology through
simultaneousanalysisoftheexpressionofthousandsofgenesallowstheidentificationofcandidategenesinvolvedin
thefunctionofmultiplephysiological,morphologicalandbehaviouraltraitsofinterestsinorganismsandpopulations
fromdifferentenvironments.Thispaperreviewsthecurrentdevelopmentofgenomictechnologies,andpinpointstheir
potentialbeneficialapplicationsaswellasimplicationsforfisheriesmanagementandaquaculture.
Keywords: Genomics/Genetics/Fisheries/Mariculture/Quantitativetraitloci/Fish/Oyster
Résumé– Quelrôlepourlagénomiquedanslagestiondespêcheset del’aquaculture? Ledéveloppement et
l’applicationdelagénomique ontétéfacilitésdansuncertainnombrededomaines parladisponibilitédenouveaux
outilsetdenouvellesméthodes,telsqueleséquençaged’ADNàhautdébitetlespucesàADN(«microarrays»).Les
outilsdelagénomique sont déjàdéveloppés surlesespècesdepoissons etd’invertébrésd’importance commerciale.
Desmilliersd’étiquettes,marqueurs deséquence exprimée(EST)sontdésormaisdisponiblespour quelquesunesde
cesespècesetleséquençagedugénomecompletdetilapia,delamorue,desalmonidés,depoissonsplats,dubar,et
del’huîtrecreusesont demandés. Latechnologie despucesàADN,autraversd’analyse simultanéedel’expression
demilliersdegènes,permetl’identificationdegènescandidatsimpliquésdanslesmultiplesfonctionsphysiologiques,
morphologiquesetcomportementaleschezlesorganismesetlespopulationsd’environnementsvariés.Cetarticlepré-
sente la synthèse de récents développements de ces technologies du génome, et met en évidence leurs applications
potentiellesainsiquelesimplicationsdanslagestiondespêchesetdel’aquaculture.
1 Introduction in addition to morphological, biological and physiological
traits. The aquaculture industry has expanded especially in
It is well recognisedthatfisheries catcheshavereacheda South America and Asia, from where aquaculture products
plateau in recent years. Due to the high demand for fish and are also exportedworld-wide.Simultaneously,industryprac-
shellfish on the global market, aquaculture production con- tices should be sustainable and marine biodiversity should
tributesanincreasingamounttothefoodsupply.Management be maintained. Genomics tools combined with the already
of exploited wild stocks is undergoing systematic improve- well-established aquaculture and fisheries management prac-
ment. Results of population genetic investigations have re- tices can serve as a novelframeworkfor such developments.
centlybeenincorporatedasausefultoolinstockidentification Genomics is a field of science that deals with the structure,
function and evolution of genomes. Many current DNA and
a Correspondingauthor: [email protected]
242 R.Wenneetal.:Aquat.LivingResour.20,241–255(2007)
RNA-based studies fall into this field, even if they are often fish and shellfish species such as salmon and rainbow trout
not strictly part of it. Genomics often simply implies the use (cGRASP,www.cgrasp.org),cod(www.codgene.ca),seabass
of high throughput DNA- or RNA-based methods. It com- Dicentrarchuslabrax(Chinietal.2006)andthePacificoyster
prises comparative, functional and environmental genomics. Crassostrea gigas (Hedgecock et al. 2005). Full genome
Comparative genomics examines whole genomes, their gene sequences can be based on the sequencing and assemblage
content,geneorder,structure,evolutionandtaxonomy.Func- of bacterial artificial chromosomes (BAC) containing DNA
tional genomicsinvestigatesthe biochemicaland physiologi- fragments of the whole target genome, or using shotgun
cal role of gene products and their interactions on a large or approaches. BAC libraries are available for Atlantic salmon
smallscale. Environmentalgenomicsencompassesstudiesof (Thorsen et al. 2005), rainbow trout Oncorhynchus mykiss
molecularvariationinnaturalorartificialpopulationsofdiffer- (Palti et al. 2004), sea bass (Whitaker et al. 2006), channel
ent taxa and their response to environmentalconditionssuch catfish Ictalurus punctatus (Quiniou et al. 2003) and oysters
as temperature or pollutants. One of the main efforts in ge- CrassostreavirginicaandC.gigas(Cunninghametal.2006),
nomics has been to obtain high numbers of large pieces of and they have been used to construct physical maps (e.g.
genomesequencesand to assemble them into fullchromoso- salmon, Ng et al. 2005; sea bass, Volckaert et al. 2006 and
malsequences.Anothergoalhasbeentostudytheexpression channelcatfish,Quiniouetal.2007).
of thousands of genes using techniques such as microarrays
or other high throughputexpressionRNA profiling(i.e. tran-
scriptomics).Theanalysisoftheimmenseamountofdatagen- 3 Fisheries
erated by such approaches often requires the use of specific
computerisedmethods,or“bioinformatics”.Theknowledgeof 3.1 Discriminationofwildpopulations
genomicsopensnewperspectivesforthebiotechnologyofma-
rineorganisms,withimplicationsforfisheriesandaquaculture. Population genetic research has contributed substantially
toourunderstandingofhowfishandshellfishspeciesarege-
netically structured into reproductively isolated populations
2 Sequencing and analysesof genomes throughouttheirdistributions.Suchknowledgeisofmajorim-
portance for fisheries managementbecause local populations
Sequencing of genomes facilitates the development of a areoftenconsideredworthconservingduetotheiruniquecon-
variety of DNA-based genetic markers that can be used for tribution to the genetic diversity of the species, which may
the managementofwild andculturedpopulations.Expressed allow them to sustain productivityin changing environments
SequenceTags(EST)areobtainedbysequencingcomplemen- (e.g. Hilborn et al. 2003). In addition, local populations are
tary DNA (cDNA) libraries. Such libraries can be obtained oftenadaptedtolocalenvironmentalconditionsandarethere-
from tissue specific libraries or generated by Suppressive forecharacterisedbyuniquemorphological,physiologicaland
Subtractive Hybridization (SSH). EST databases for various life history traits that have a genetic basis and are therefore
important marine species have been established (e.g. in At- ofconservationinterest.Moreover,suchpopulationsareoften
lantic salmon Salmo salar: http://web.uvic.ca/cbr/grasp/ and of great economic interest. However,the actual genetic basis
oyster Crassostrea gigas: http://www.ifremer.fr/GigasBase/) of quantitative traits remains largely unknown, because their
and most sequences are submitted to databases (http:// analysishas,untilrecently,beenlogisticallydifficultandtime
www.ncbi.nlm.nih.gov/Genbank/, http://www.ncbi.nlm.nih. consumingtoconductinmostspecies.Thus,theidentification
gov/sites/entrez, http://compbio.dfci.harvard.edu/tgi/). EST of local adaptations in natural populations has recently been
are the first step towards obtaining full-length cDNA and highlightedasworthyofspecialattentionintheyearstocome
gene sequences. Sequencing of whole fish and shellfish (e.g.Moritz2002;vanTienderenetal.2002;ICES2006).
genomes contributes not only to the understanding of ver- Many fish and shellfish populations have been over ex-
tebrate and invertebrate evolution but also to environmental ploited or reduced by changes in local environments. These
genomics and aquaculture (Crollius and Weissenbach 2005; populationsareendangeredandsomeindigenouspopulations
Cossins and Crawford 2005). Full genome sequences are are already extinct (e.g. Dulvy et al. 2003; Reynolds et al.
now available for a few model fish species such as zebrafish 2005), and hence there is an urgent need for knowledge on
Daniorerio (http://www.sanger.ac.uk/Projects/D_rerio/),fugu the basic population structure of many species. Various ge-
Takifigu rubripes (http://www.fugu-sg.org/),pufferfish Tetr- neticmarkershavebeenusedinordertoidentifyandcharac-
aodon nigroviridis (http://www. genome.gov/11008305), terise populations. Studies using markers such as allozymes,
medaka Oryzias latipes (http://dolphin.lab.nig.ac.jp/medaka/ mitochondrial (mt) DNA polymorphism, microsatellites, re-
index.php) and stickleback Gasterosteus aculeatus: strictionfragmentslengthpolymorphism(RFLP)andrecently,
(http://www.genome.gov/12512292). To date, only one amplifiedfragmentslengthpolymorphism/randomamplified
commerciallyimportantfish–Tilapia(CichlidGenomeCon- polymorphic DNA (AFLP/RAPD) have successfully demon-
sortium,http://hcgs.unh.edu/cichlid/)hasobtainedfundingfor strated significantgenetic differencesbetween populationsof
sequencing; however, knowledge of the genome sequences manyspecies.However,thesemarkersrepresentonlyasmall
of other commercially important species is critical for an fractionofthetotalgenomicpolymorphism.Furthermore,they
efficient identification of economically important genes are mostly believed to be selectively neutral, and have thus
and polymorphisms. Recently, international collaborative mainly been used to draw inferences about the interplay of
initiatives have been undertaken with the aim of obtaining gene flow,geneticdriftand historicalprocesses, therebylim-
full or partial genomic sequences of commercially important iting inferences about local adaptations in the species under
R.Wenneetal.:Aquat.LivingResour.20,241–255(2007) 243
study.Singlenucleotidepolymorphisms(SNP)isanewclass Outliers can be detected using model based (e.g. Beaumont
of genetic markers with powerful applications in population andNichols1996)ormodelfree(e.g.Schlötterer2002;Kauer
genetics(Morinetal.2004).Itwillbeveryhelpfulinmanag- et al. 2003)methods.Conclusionswith respectto outliersta-
ingnaturalandcaptivepopulationsinthe future.SNPcanbe tus ofparticularlociwill oftenbe considerablystrengthened,
identifiedininter-individualcomparisonofgenomicDNAse- ifsignalsofselectionaresupportedbyseveraldifferentanalyt-
quences (e.g. Smith et al. 2005a) or sequences derived from icalapproachesaswellasdifferentpairwisepopulationcom-
EST (e.g. Hayes et al. 2007). Thus, both coding and non- parisons (e.g. Vasemägi et al. 2005; Bonin et al. 2006). Al-
codingDNA sequencescanbeusedtoidentifySNPandsev- lozymes,microsatellitesandAFLPhavebeenusedingenome
eralrecentstudieshaveusedsomeoftheseapproachesforini- scans in non-model species (e.g. Storz and Dubach 2004;
tialSNPidentificationinspeciesofrelevancetofisheriesand Vasemägi et al. 2005; Bonin et al. 2006), but SNP will also
aquaculture(e.g.salmon,RyynänenandPrimmer2006;Hayes beveryusefulfortheseapproaches(seee.g.Akeyetal.2002).
etal.2007;rainbowtrout,Smithetal.2005aandArcticcharr A major advantage of genome scans is that they can be ap-
Salvelinusalpinus,TaoandBoulding2003).Currently,highly pliedtonaturalpopulations,therebyincreasingthenumberof
informative(i.e.highlydivergent)SNPcanbeusedtodiscrim- speciesforwhichsuchapproachesarepossible.
inate betweennaturalpopulationsofbothsalmon(e.g.Smith
etal.2005b)andAtlanticcod(Stenviketal.2006).
3.2 Futureapplicationsinmanagement
Newly developed techniques enable screening for poly-
andconservationofnaturalpopulations
morphismsthroughoutthegenome.Screeningformanymore
lociwillopennewpossibilitiesinpopulationgeneticresearch,
Genomics offers new and exciting possibilities for con-
moving to populationgenomics (Luikartet al. 2003).Global
servation genetics in several ways. First of all, the number
geneexpressioncanbeexaminedthroughtheuseofmicroar-
of neutral genetic markers available will increase for most
ray techniques, enabling the simultaneous analysis of thou-
species. This will likely improve estimates of the effects of
sands of genes. Different expression levels can be observed
demographicprocesses, such as populationdeclinesand bot-
in specimens originating from different localities and differ-
tlenecks,effectivepopulationsizes, identificationofwild and
ing in functional traits (Rise et al. 2004a). Microarrays have
farmedindividualsetc.(Morinetal.2004;Kohnetal.2006).It
beendevelopedforanumberoffishandshellfishspeciessuch
mayalsoresultinincreasedstatisticalpowertodetectminute
as salmonids(Rise et al. 2004a;von Schalburget al. 2005a),
levels of population structuring and to assign individuals of
killifish Fundulus (Oleksiak et al. 2002), carp Cyprinus car-
unknown origin to known baseline populations, for instance
pio(Graceyetal.2004),zebrafish(Tonetal.2002),catfish(Li
in mixedstockanalyses(seee.g.Maneletal. 2005).Inaddi-
andWaldbieser2006),medaka(Kimuraetal.2004),European
tion,theidentificationofoutlierlociingenomescansoffernew
flounder Platichthys flesus (Williams et al. 2003), Japanese
possibilities to identify informativemarkerswhich are suited
flounder Paralichthys olivaceus (Kurobe et al. 2005), mus-
for the specific question raised in each managementscenario
sel Mytilus galloprovincialis(Venieret al. 2006)and Pacific
(seee.g.Banksetal.2003;Beachametal.2004;Smithetal.
oyster (Lang et al. 2006). However, even if arrays have not
2005b).
been developed for a species, reliable estimates of gene ex-
Another, and very promising, application of genomics in
pression may still be achieved through alternative measures
relationtoconservationisthedetectionofthegeneticbasisof
such as cross species hybridization(Renn et al. 2004) or the
local adaptation.Giventhat we knowvery little aboutthis in
useofnon-arraybasedquantificationofgeneexpression,such
mostspeciesoffishandshellfish,suchknowledgewillgreatly
as cDNA-AFLP or differential display (Breyne et al. 2003;
improveourabilitytomanagegeneticdiversityinnaturalpop-
Venkatesh et al. 2005). It should be noted that gene expres-
ulations. The fact that genomic resources can sometimes be
sionanalysesessentiallymeasureexpressionphenotypes.The
transferred between closely related species means that many
degreeofheritabilityofgeneexpressiontraitshasrarelybeen
speciesof fish andshellfish willeffectivelybecome“genome
assessed, but is often assumed (Gibson and Weir 2005). For
enabled”inthecomingyears(StorzandHoekstra2007),facil-
thesemeasurestobeusedtoillustratepopulationgeneticdif-
itatingstudiesofthegeneticbasisoflocaladaptation.
ferences, the environment needs to be controlled to rule out
environmentaleffectsongeneexpression.Therefore,analyses
ofglobalgeneexpressionrequirecommongardenapproaches.
3.2.1 CasestudyusingAtlanticsalmon
Still,ifproperlydesignedsuchstudieshavegreatpotentialto
disclosethegeneticbasisofadaptationsinlocalpopulationsof
Atlanticsalmonisoneofthe speciesofrelevancetoboth
fishandshellfish(e.g.WhiteheadandCrawford2006;Larsen
fisheries management and aquaculture, where genomic re-
etal.2007)
sourcesarebuildinguprapidly.Hencethisspeciescouldserve
Genome scans are another important group of genomic as an important case study to demonstrate the resources that
tools applying the screening of a high number of markers to may become available in other species in the near future, as
covertheentiregenomeofaspeciesunderstudy(e.g.Luikart wellasthepotentialapplicationsoftheseresources.Genomic
et al. 2003; Storz 2005). Genome scans allow for the identi- approaches in Atlantic salmon have targeted both RNA and
fication of outlier loci that are potentially under selection or DNA levelsofvariation.Forinstance,asalmonidmicroarray
linked to a locus under selection (i.e. hitch-hiking selection, containing cDNA representing 16 006 genes has been devel-
MaynardSmithandHaigh1974),therebyfacilitatingdetection oped. The genesspotted on the arrayhave been carefullyse-
ofthegeneticbasisoflocaladaptationinnaturalpopulations. lectedfromAtlanticsalmonandrainbowtroutESTdatabases.
244 R.Wenneetal.:Aquat.LivingResour.20,241–255(2007)
This array will serve as an important resource for genetic, Theexamplesoutlinedaboveillustratetheimmensepoten-
physiological and ecological studies as well as many other tial that genomicshas to improveboth fisheries management
fieldsofsalmonidresearch(vonSchalburgetal.2005a).Gene andaquaculture.Particularlythelastcaseshowshowthetwo
expressionpatternsdeterminedeitherfortargetgenesorusing fieldscouldbe integratedthroughthe availabilityof genomic
microarrayshavealreadybeenusedtoinvestigatethesalmonid resources,withconsiderablepotentialtoadvanceconservation
immuneresponse,severaldiseaseprocessesanddiseaseresis- effortsinthespecies.
tance(Lindenstrometal.2003,2006;Rise etal.2004b;Sigh
etal.2004;Bridleetal.2006a,b;Fastetal.2006;Martinetal.
2006;Purcell et al. 2006).Moreover,they have been used to 4 Aquaculture
surveythegenesinvolvedinthematurationanddevelopment
oftherainbowtroutovarianandtesticulartissues(vonSchal- 4.1 Usinggenomicinformation
burgetal.2005b,2006;Bonnetetal.2007),toexaminebrain inaquaculturebreeding
geneexpressionprofilesinmalesalmonwithdifferentlifehis-
torystrategies(Aubin-Horthetal.2005a,b),tocarryouttoxi- 4.1.1 ConstructingDNApedigrees
cogenomicprofiling of hepatic tumour promotersin rainbow
trout (Tilton et al. 2006), to investigate the response of the In breeding programmes,informationon family relations
rainbow trout transcriptome to model chemical contaminants ofindividualsisusedwhenestimatinggeneticparameters(her-
(Koskinenetal.2004)andtostudygeneexpressioninatrophy- itabilities and genetic correlations) and breeding values for
ingmuscle(Salemetal.2006).Microarrayshavealsobeenap- traits, and when optimising selection and mating in order to
pliedtodiscriminatebetweenfarmedandwildAtlanticsalmon avoid inbreeding.Similarly, pedigrees are useful in the man-
using genome wide transcription profiles. Thus, similar tran- agement of conservation programmes and wild populations
scription profiles characterised farmed strains from Norway (e.g.whencontrollinginbreeding,WilsonandFerguson2002).
and Canada and suggested adaptation via gene expression to Inadditiontophysicalindividualtagging,pedigreescanbede-
commoncaptiveenvironments(Robergeetal.2006). terminedusingDNAmarkers.Thisprocedureisquitestraight-
forward using microsatellites. Typically 10–20 variable ge-
TheDNAlevelhasbeentargetedthroughmarkerssuchas
netic markers are needed to assign >95% of individuals to
microsatellitesandSNP.Forexample,Vasemägietal.(2005)
single pairs of parents (e.g. Vandeputte et al. 2006). To do
used EST linked microsatellites in a genome scan of nat-
this, one needs tissues samples from both potential parents
ural populations of Atlantic salmon and identified a num-
and their offspring,and severalfreelyavailable softwaresex-
ber of outlier loci potentially under selection and it has been
ists for parental assignment (reviewed by Jones and Ardren
shownthatthesemarkerscanbeusedinothersalmonids(Ng
2003). Physical individualmarkers are useful when large fa-
et al. 2005). SNP have been identified through different ap-
cilitiesexistwherefamilygroupscanbeheldseparatelyuntil
proaches. For example, five populations of chinook salmon
fisharelargeenoughtobeindividuallytagged.Forinstance,in
OncorhynchustshawytschafromPacificNorthAmericawere
salmonidbreedingprogramsfisharetypicallyheldinhundreds
surveyed for SNP at 19 loci by sequencing (Campbell and
of family tanksuntilthey are individuallytagged at a weight
Narum 2007). Of these 13 were chosen for Taqman assays
of approximately 50g (Kause et al. 2005). Using DNA pedi-
(5’ exonuclease assays) out of 58 SNP. Similarly, 1195 SNP
greesisusefulinmanyaquaculturebreedingandconservation
have been identified from EST and 121 of these have been
programmes when individual tagging is difficult or when fa-
characterisedbypedigreeanalysis.Asaresultofthegenome
cilitiesforfamilytanksdonotexist.Threeexamplesofusing
duplication that took place in common ancestor of extant
DNApedigreesarepresentedbelow:walk-backselection,es-
salmonids25–120millions years ago (MYA), it has been es-
timationofgeneticparameters,andconservationprogrammes.
timated that up to 15–20% of salmonid loci have functional
Walk-backselectionreferstoaselectionprogrammewhere
duplicates. Therefore, when identifying putative SNP in the
agroupofsuperiorindividualsarefirstselected,andthenonly
Atlantic salmon EST database, it is important to be able to
the selected animals are genotyped for family relations. Us-
distinguishbetweentrueSNP(i.e.,thosecorrespondingtoal-
ingthe establishedpedigree,onlythosesuperioranimalsthat
lelesatasinglelocus)andparalogoussequencevariants(PSV;
are not too closely related are used in matings (Doyle and
i.e.,sequencedifferencesbetweenduplicateloci),(WrightJ.J.,
Herbinger 1994; Sonesson 2005). This is an improved mass
SimonFraserUniversity,Burnaby,BC,Canada,pers.comm.;
selectionschemetoobtaingeneticimprovementwhilesimul-
Hayesetal.2007).
taneouslycontrollingforinbreeding.Thisiscost-effectivebe-
SNPwithknownlocationsonalinkagemapcanbeusedto causeonlysomehundredsofindividualsamongthepotentially
identifyQTL,whichcansubsequentlybegenotypedinnatural (tensof)thousandsofindividualsrearedneedtobegenotyped.
populations.An exampleof such research is Atlantic salmon This is especially useful for species for which no extensive
inwhich4fullsibfamilies(backcrossedF1malestoafemale resources are available, or for new species whose reproduc-
fromEuropeanandAmericanparentalpopulations)wereused tioncannotbefullycontrolled.Furthermore,therearestudies
to identifySNP for knownQTL. The identifiedSNP in traits showingthatmicrosatellitemarkersareusefulfordetermining
underselectionwillbegenotypedinendangeredwildAtlantic theeffectivenumberofparentsandtheirindividualreproduc-
salmonto demonstrategenetic differencesin functionaltraits tive success (e.g. Boudry et al. 2002), and level of inbreed-
among these endangered salmon populations and may help ing in mass selection scheme in the Nile tilapia Oreochromis
in their conservation (Boulding E.G., University of Guelph, niloticus (Komen H., Animal Breeding and Genetics Group,
Canada,pers.comm.). Wageningen University, The Netherlands, pers. comm.) and
R.Wenneetal.:Aquat.LivingResour.20,241–255(2007) 245
theflatoyster,Ostreaedulis(Launeyetal.2001).Afullpop- usefulhere,ageneticmarkerneedstobelocatedverycloseto
ulation can be genotypedfor parental analysis, which allows the actualgene,i.e.,withinless than1centiMorgan(cM).If
oneto estimate heritabilitiesandgeneticcorrelationsto traits thisisnotthecase,thenitisunlikelythattheQTLwillbeap-
ofinterest.Suchanapproachhasbeenusedoncommoncarp plicableacrossthewholepopulation,andthelinkagebetween
(Vandeputteetal.2005). the marker and the gene will be brokendown by recombina-
Likewise, DNA pedigreesare useful in conservationpro- tionduringthenextfewgenerations.Thus,QTLfinemapping
grammes of wild fish and shellfish, especially when aiming isneededfortheQTLtobepracticallyuseful.Markerbreed-
atcontrollinginbreeding.Microsatellitegenotypinginthein- ingvaluesareusedindairycowselection,e.g.,inFranceand
duced mass spawns of lion-paw scallop Nodipecten subn- Germany(Hayesetal.2006a).
odosus demonstrated that some parents contribute a much Genomic selection refers to selection directed on allelic
higher percent to the progeny than expected (Petersen J.L., variationidentifiedacrossthewholegenome.Allelicvariation
GenomicVariationLaboratory,UniversityofCaliforniaDavis, atthousandsoflociaswellastheireffectsoneconomictraits
Davis,CAUSA,pers.comm.).Similarly,theimpactofhatch- canbeestimated,andgenomicbreedingvaluescanbethuses-
ery practices on the genetic variability of progenies can timated(Meuvissenetal.2001).Aftertheeffectsofthealleles
be monitored (Taris et al. 2006). That is, when the effec- havebeenestablished,nophenotypicinformationonanimals
tive population size is reduced and inbreeding can decrease is needed in selection. The use of SNP analysis is the most
hatchery stocks. Microsatellite genotyping can be also use- promisingmethodforsuchwhole-genomeanalysis.Usingcur-
ful in assessment of introgression to/from a natural popula- renttechnology,variationintensofthousandsofSNPcanbe
tion. Mutli-plexing (i.e. simultaneous PCR amplification) of simultaneouslyestimated.Forthismethodtobeeffectivehow-
microsatellites(e.g.Taris et al. 2005)andSNP-based parent- ever,Hayesetal. (2006a)suggestedthat10–20QTL needto
age assignment (Rengmark et al. 2006; Anderson and Garza befoundforeachtraitandupto30000SNPmaybeneededto
2006)arenowgreatlyfacilitatingthesetypesofstudies. obtainadenseenoughmarkermap.Methodstoperformsuch
analyses,togetherwith genomicselectiontools,arecurrently
underdevelopment.ThousandsofputativeSNPhavebeende-
4.1.2 Markerassistedselection tected in Atlantic salmon (Hayes et al. 2007). Sauvage et al.
(2007) reported a very high level of DNA polymorphism in
Markerassistedselection(MAS)referstoaselectionpro- thePacificoyster(i.e.oneSNPevery60bpincodingregions
cedure which is improved using information from genetic andoneevery40bpinnon-codingregions).
markers. Allelic variation in genetic markers can be linked
to the variation in traits of economic interest, and thus the
markerprovidesDNAlevelinformationontheinheritanceof 4.1.3 LinkagemapsandQTLinaquaticspecies
the traits. MAS is especiallyusefulfortraits thatare difficult
to breed using traditionalmeans. Such traits can be costly or Linkagemapsareneededformappingmajorchromosome
difficulttorecord(e.g.feedefficiency,diseaseresistance,con- regionsinfluencingphenotypictraits(i.e.QTL).Examplesof
centrationofomega-3-acids),theymayrequireslaughteringof publishedlinkagemapsforseveralmajoraquaculturespecies
individuals(e.g.filletquality,bodycomposition),maybefrom are givenin Table 1. The list is illustrative rather than an ex-
onlyonesex(e.g.caviarproduction),ortheycannotbedirectly haustive list of linkage maps. For most of the marker maps,
recordedfrombreedingcandidates(e.g.seaperformancewhen theaveragedistancebetweenmarkersis2–15cM.Anaverage
breedingcandidatesareheldatafreshwaterbreedingstation). markerdistanceof20cMwouldbesuitableforthelocationof
Moreover, MAS can be used early in life to breed for traits a QTL to a correctchromosomearm.A usefulfeatureis that
that are expressed later in life (e.g. caviar production, matu- the male maps are often shorter than the female maps. Thus,
rityage),allowingonetocullthepopulationtosavefeedand the initial QTL mapping revealing chromosomes harbouring
managementcosts(e.g.Martinezetal.2005). QTL can be more easily performedusing male parents. Fine
The practical use of markers in selection can be roughly mapping of QTL positions, in turn, is more effectively per-
divided into three classes: 1) removing genetic disorders, 2) formed using female parents (Hayes et al. 2006b). For fine
marker breeding value-selection, and 3) genomic selection. mapping,amarkerdistanceof1cMorlessisneeded.
These three methods differ in the complexity of computa- A variety of markers have been used for identification of
tional selection tools needed and requirements of the ge- populationsandstrainsinthewildandinaquaculturewiththe
nomicdata.Recessivegeneticdisorders,determinedbyasim- aim of improving management. These markers can be used
ple Mendelian one-locus method can be effectively removed for construction of high-resolution genetic linkage maps and
from a population using a gene test done on a small tissues search for QTL, and finally to MAS (Liu and Cordes 2004;
sample. Individuals carrying a deleterious allele are culled, Sarropoulouetal.2005a;Sengeretal.2006;Silversteinetal.
andnocomputationallydemandingselectiontoolsareneeded. 2006; Montano-Perez et al. 2006). Table 2 presents an illus-
Suchtestsareinpracticaluseinterrestrialfarmanimals(e.g. trative list of QTL studies performed on several aquaculture
Sironenetal.2006).Markerbreedingvaluesofindividualscan species. Two observations can be made from these studies.
be estimated by combining informationon phenotypesand a First,mostofthestudiesareongrowth-relatedtraits,followed
singleorseveralQTLsegregatingwithinapedigreedpopula- bydiseaseresistancetraits.Onlyafewstudiesexistforquality
tion(FernandoandGrossman1989).Whenestimatingbreed- orfeedutilisationtraits.MASwillbeespeciallyusefulfordis-
ingvalues,geneticvariationcanbeexplainedbytheQTLef- easeandqualitytraits.Second,mostofthestudiesonaquatic
fect(s) and the remainingpolygeneticparts. For a QTL to be specieshavenotprogressedtofine-mapping.Consequently,a
246 R.Wenneetal.:Aquat.LivingResour.20,241–255(2007)
arm;
econdtothefemalemap. ReferenceM) Franchetal.(2006)Chistiakovetal.(2005)Moenetal.(2004a)Gilbeyetal.(2004)Youngetal.(1998)Nicholsetal.(2003b)Guyomardetal.(2006)Sakamotoetal.(2000)Gharbietal.(2006)Matsuokaetal.(2004)Worametal.(2004)Kocheretal.(1998)Leeetal.(2005)Agrestietal.(2000)SunandLiang(2004)Liuetal.(2003)Waldbieseretal.(2001)PoompuangandNa-Nakorn(2004)Coimbraetal.(2003)Watanabeetal.(2004) LiandGuo(2004)HubertandHedgecock(2004)YuandGuo(2003)Baranskietal.(2006)Liuetal.(2006)SekinoandHara(2007)Lalliasetal.(2007b)Lalliasetal.(2007a)Lietal.(2005) Zhouetal.(2006)Zhouetal.(2006)Mooreetal.(1999)Lietal.(2003)Wilsonetal.(2002)Pérezetal.(2004)Lietal.(2006b) 4peats;-SINESmallinterspersednucleestrictionfragmentlengthpolymorphis
hemaleandthes Averagedistanceweenmarkers(c 9.7/a3.55.6/a0.413.9n.a.a5.67.4a3.0a4.8/a1.23.8n.a.n.a.a4.3a2.4/a7.68.3a15.3a3.88.717.1/8.06.611.7 /8.89.5/8.010.4/6.312.6/7.39.8/18.218.3/4.76.3/8.18.0/4.94.2/9.210.2 17.115.415.0/9.710.922/15.617.1/11.013.5 beroftandemre9hism;-RFLPR
tot bet nummorp
ftwovaluesaregivenforaparameter,thefirstrefers umberandtypeofMaplength(cM)Numberofmarkersinamaplinkagegroups 1198124226/116256790625,///122512301039013133150n.a.15−16476262831−11013144359301275031903,−∼168209100029,///172792423469123543722n.a.8,,/12830139099246,1216270430,18131124545,///122146216325142414,16268411150241815934412621958322134203731,///127416702527231304,12178166036 ///29611975810311011///188866167711112,,///1210114846479041212///1102986217661720,,///12694119136617741922///17028881819167160///21161218258631414///2137149471450910///2197166163115042019 219429882422615231992129127644///2227125178110264331263141219///2182212211627714751///2194197173821913635 3fragmentlengthpolymorphism;-VNTRVariable78DNA;-Allozymes;-SNPSinglenucleotidepoly
I N dc
pecies. bicus mplifiemorphi
s m Ay
Table1.Asampleofpublishedlinkagemapsonaquaculture SpeciesLatinname Vertebrate SeabreamSparusaurataSeabassDicentrarchuslabraxAtlanticsalmonSalmosalar RainbowtroutOncorhynchusmykiss BrowntroutSalmotruttaPinksalmonOncorhynchusgorbuschaArcticcharrSalvelinusalpinusTilapiaOreochromisniloticus×TilapiaO.niloticusOreochromisaureus××TilapiaO.niloticusO.aureusO.mossaCommoncarpCyprinuscarpioChannelcatfishIctaluruspunctatus WalkingcatfishClariasmacrocephalusJapaneseflounderParalichthysolivaceusAyuPlecoglossusaltivelisInvertebratePacificoysterCrassostreagigas EasternoysterCrassostreavirginicaBlacklipabaloneHaliotisrubraPacificabaloneHaliotisdiscushannai BluemusselMytilusedulisEuropeanflatoysterOstreaedulisZhikongscallopChlamysfarreri SeaurchinStrongylocentrotusnudusSeaurchinStrongylocentrotusintermediusKurumaprawnPenaeusjaponicus BlacktigershrimpPenaeusmonodonWhiteshrimpPenaeusvannameiChineseshrimpPenaeuschinensisn.a.-Notavailable.12Typesofgeneticmarkersused:-Microsatellites;-AFLP56element;-Minisatellites;-RAPDRandomlyamplifiedpol10-SSCPSinglestrandconformationpolymorphism./a-Calculatedas:maplengthnumberofmarkers.
R.Wenneetal.:Aquat.LivingResour.20,241–255(2007) 247
9)
9
9
1
(
al.
et
n
n
a
m
z
n
Reference Moenetal.(2004b)Kjoglumetal.(2005) Grimholtetal.(2003)Reidetal.(2005) Aranedaetal.(2005)Martinezetal.(2005)Robisonetal.(2001)Sundinetal.(2005)Perryetal.(2005)Martyniuketal.(2003)Sakamotoetal.(1999)Nicholsetal.(2004)Zimmermanetal.(2005)Jacksonetal.(1998);DaOzakietal.(2001)Rodriquezetal.(2004)Nicholsetal.(2003a)Zimmermanetal.(2004)Nakamuraetal.(2001)TaoandBoulding(2003)Cnaanietal.(2004)Moenetal.(2004c) SunandLiang(2004)Fujietal.(2006)Wangetal.(2006) YuandGuo(2006)Lalliasetal.(2007a)Liuetal.(2007)Lietal.(2006a)Hizeretal.(2002)
s
u
o
cti us
e r
nf ht vi
culosis,i h gillweig necrosis
especies. Traitsstudied InfectioussalmonanaemiaInfectiouspancreaticnecrosisvirus,furunsalmonanaemiaFurunculosis,infectioussalmonanaemiaBodyweight,conditionfactor FilletcolourHatchingtime,embryoniclength,weightEmbryonicdevelopmentrateDevelopmentrateBodylength,thermotoleranceGrowth,conditionfactor,maturityageSpawningtimeLength,pyloriccaeca,noofscalesPyloriccaecaThermotoleranceInfectiouspancreaticnecrosisvirusInfectioushematopoieticnecrosisCeratomyxashastaresistanceKiller-cellactivityAlbinismGrowthrateInnateimmunity,responsetostress,growtThermotolerance ColdtoleranceLymphocystisdiseaseresistanceBodyweight,length,conditionfactor PerkinsusmarinusresistanceBonamiaostreaearesistanceShell,muscle,gonad,digestiveglandandBodyweight,lengthInfectioushypodermalandhematopoieticresistance
ur
ult us
c e
a r
u u
q a
udiesina O.aureusherodon×cusO.
dquantitativetraitlociQTLst Latinname Salmosalar /SalmosalarOncorhynchu/mykissSalvelinusalpinusOncorhynchuskisutchOncorhynchusmykiss Salvelinusalpinus×Oreochromismossambicus×OreochromisniloticusSarot×galilaeusmaleO.mossambifemaleCyprinuscarpioParalichthysolivaceusLatescalcarifer CrassostreavirginicaOstreaedulisHaliotisdiscushannaiPenaeusjaponicusLitopenaeusstylirostris
e
h
blis ow
u b
Table2.Asampleofp SpeciesVertebrateAtlanticsalmon /AtlanticsalmonRain/troutArcticcharrCohosalmonRainbowtrout ArcticcharrTilapiaTilapia CommoncarpJapaneseflounderAsianseabassInvertebrateEasternoysterEuropeanFlatoysterPacificabaloneKurumaprawnBlueshrimp
248 R.Wenneetal.:Aquat.LivingResour.20,241–255(2007)
lotofeffortmustbefocusedonthisarea,inorderforgenomic andwhataretheeconomicalbenefitsandpracticalconstraints
studiestobeusefulinpracticalbreedingprogrammes. ofthealternativeselectionstrategies.Todate,nosuchstudies
Studies of large scale gene expression using microarrays havebeenperformedinaquaticspecies.
containingclonesfromcDNA librariesarehelpfulin thedis-
covery of candidate genes for particular/multifactorial traits
(Sarropoulouet al. 2005b).However,the challenge is to find 4.2 Culturedfishandshellfishhealth
between-individualvariationingeneexpressionthatcouldbe
exploitedinselectivebreeding.Bysimplyknowingthatacer- Genomics can help to overcome problems related to in-
taingeneisexpressedornotisnotenough,thegenemustalso fectious diseases by better understanding host defence sys-
display alternative gene variants that can be selected. More- tems and identifying QTL or candidate genes. Aquaculture
over, gene expression is tissue and time specific, inducing productivityisreducedbyvariouspathogens.Examplesofge-
methodologicalchallengesforthedevelopmentofgeneralse- nomicsbasedstudiesincludeoomyceteSaprolegniaparasitica
lection tools. Hedgecock et al. (2007) recently reported tran- (Torto-Alaliboetal.2005),abacterialagentofcold-waterdis-
scriptomicanalysisofgrowthheterosisinlarvaeusingmega- ease Flavobacterium psychrophilum (Soule et al. 2005) and
cloning and massively parallel signature sequencing (MPSS) a parasitic protozoan ciliate Ichthyophthirius multifiliis, the
inthePacificoysterCrassostreagigas.Microarrayshavebeen agentofthewhitespotdiseasethroughvirulentfactors(Aber-
produced(Langetal.2006;Jennyetal.2007)andarecurrently nathyetal.2007).Theacutephaseresponsefollowinginfec-
underdevelopmenttostudysummermortalityfollowingSSH tion of catfish with Edwarsiella ictaluri, causing enteric sep-
approaches(Huvetetal.2004;SaavedraandBachère2006). ticaemia, was studied by high density in situ oligonucleotide
microarray(Peatmanetal.2007).Numerousacutephasepro-
teinswereupregulatedandmanypathogenrecognitionrecep-
4.1.4 Identificationofsexdeterminingfactors torsandchemokinesweredifferentiallyexpressedintheliver.
Theseresultswereconfirmedwithreal-timePCR.Acandidate
The understanding of sex determination systems is one geneapproachwasemployedtofindmarkersassociatedwith
of the most sought after aspects of genomics in finfish aqua- diseaseresistanceinwhich28microsatelliteslocatednearand
culture. Aquaculture farmers often prefer to farm only one within the immune genes were developed (Karsi A., Missis-
of the sexes, because of its superior characteristics (Kause sippiStateUniversityUSA,pers.comm.).Severalmicrosatel-
etal.2003).Moreover,productionof sterileanimals(e.g.us- lites were associated with resistance and susceptible pheno-
ing triploidy)will enable furtherreductionof risks related to types. These markers have been incorporated in the catfish
escape effects of farmed animals on natural marine popula- linkagemap,whichwillfacilitatefindingresistanceQTLand
tions.MalesaretheheterogameticsexinAtlanticsalmonand willhelpindevelopmentofMASprogrammes.Cytokinesare
Arctic charr Salvelinus alpinus. Several microsatellite mark- importantimmunesystemregulatorsinfish,andgenomicsand
ersarelinkedtothesex-determiningfactor(SEX)inthelink- proteomics can help to develop vaccines and immunostimu-
ageanalysis(Worametal.2003;Artierietal.2006;FujikiK. lantsforaquaculture(SavanandSakai2006).Baoetal.(2007)
andKwitkowskiC.N.,SimonFraserUniversityBurnaby,B.C. identified26chemotacticcytokinegenes,sequencedthemand
Canadapers.comm.).BACorfosmidclonespositiveforthese studiedtheirexpressionincatfish.
microsatellites were isolated from libraries. Fluorescence in Whirling disease, caused by Myxobolus cerebralis,
situ hybridisation(FISH) was used to identify their positions stronglyaffects Americanhatcheriesand certainnaturalpop-
on chromosomes. Fosmids, BACs and BAC-ends sequences ulations of rainbow trout. A European hatchery Hofer strain
were used for the identification of the SEX candidate genes. exhibitsalmostcompleteresistancetothispathogen.Microar-
Despite the great recent progress in this area, the SEX fac- ray technology was used to study differences in global gene
tor(s)continuestobeelusiveinsalmonidsaswellasinmany expression between resistant and susceptible rainbow trout
otherfishandshellfishspecies. strains(BaerwaldM.R.,UniversityofCalifornia,DavisUSA,
pers. comm.). Several candidate genes were discovered that
indicate genetic mechanisms of resistance to whirling dis-
4.1.5 Cost-benefitanalyses ease in fish. To pinpoint these genetic mechanisms of resis-
tance,rainbowtroutfullsibfamiliesunderhatcheryconditions
Thedevelopmentandextensiveuseofgenomictoolsinse- wereexposedtothebacterialpathogenYersiniaruckeri,which
lection are resource demanding. Consequently,a cost-benefit causes enteric redmouthdisease and to Flavobacteriumpsy-
analysiswouldbeusefulfordeterminingtheadvantageofus- chrophilum (Palti Y., NCCCWA-ARS-USDAKearneysville,
inggenomictools.Break-evencostofgenotypingdependson USA, pers. comm.). Linkage disecquilibrium and the resis-
the efficiency of marker assisted selection (MAS, relative to tancetothepathogenswasassessed bygenotypingusingmi-
traditional selection), the duration until the selected loci are crosatelliteslinkedtothefourmajorhistocompatibility(MH)
fixed,thesizeoftheproducerlevelandcostsofgenotyping,as genomic regions, to toll-like receptor genes and to the two
shownbytheanalysisofpigenterprisebyHayesandGoddard copiesoftumournecrosisfactorsuperfamily13b.Knowledge
(2004).Likewise, breedersshould determine in advancehow ofthebase-lineMHsequencevariationinthebroodstockand
MAScanbemosteffectivelyused.Forinstance,shouldallin- its association/linkage disequilibrium with resistance to spe-
dividualsbegenotyped,shouldindividualsbegenotypedearly cificpathogensisusefulinmonitoringlossofMHvariability
inlifeoratmaturity,shouldonlypre-selectedbreedingcandi- andthepotentialincreaseinsusceptibilityto otherpathogens
datesbegenotyped,couldwithin-familyselectionbeeffective, that are not part of the selective breeding. Atlantic salmon
R.Wenneetal.:Aquat.LivingResour.20,241–255(2007) 249
T-cellreceptoralpha/deltagenesexhibitvastdiversityforanti- BAClibraries,finescalelinkagemaps,ESTdatabasesand
genrecognition(Yazawaetal.2007).Differencesinsuscepti- expressionprofiling.
bility to infectioushematopoieticnecrosis viruswere studied - Open access web-based resources, joining available ge-
with microarray technology between four salmonid species nomic data (EST, mapping data, BAC fingerprinting and
(Salmo salar, Oncorhynchus nerka, O. keta and O. kisutch). annotation) should be developed in order to favour inte-
Theobserveddifferenceswererelatedto species-specificdif- gratedcollaborations.
ferences in viral ability to enter cells, and possibly to ef- - Studiesoflocaladaptationsinthewildandhatcherypop-
fectiveness in taking controlover cellular mechanisms rather ulationsshouldincorporategenomicapproachestofurther
thanfromstrengthofthehostimmunologicalresponse(Miller understand the footprints of selection at a genome wide
K. and Traxler G., Pacific Biological Station Fisheries and level.
Oceans,Nanaimo,Canada,pers.comm.). - The potential of molecular marker assisted selection and
Examples of related studies in cultured invertebrates in- thedomesticationprocessinaquaculturespeciesshouldbe
volve activated protein kinase (AMP) and other elements of furtherexplored,benefitingfromthedevelopmentofnew
theimmunesysteminpeneidshrimpsandPacificoyster(Cras- genomicresourcesandcomputationalandanalyticaltools.
sostrea gigas, Bachère et al. 2004). In oysters, the availabil- - CurrentQTLstudieshaveusedsparselinkagemaps.Thus,
ityofanimalsselectedtoimprovetheirresistanceagainstdis- wedonothaveDNAmarkersthatarelocatedcloseenough
eases can greatly contribute to the identification of genes or to the actual gene that would allow their use in practical
proteins involved in defence mechanisms (e.g. summer mor- breeding programmes. Consequently, there is a need for
talityinC. gigas:Huvetetal.2004;MarteliasydneyiinSac- densergeneticmapsforaquaculturespecies.
costreaglomerata:Newtonetal.2004).Anotherpathogenof - MostoftheQTLstudiesareongrowthrelatedtraits,andto
shrimp is the white spot syndrome virus, which can be con- alesserextentondiseaseresistancetraits.MoreQTLstud-
trolledbytheanti-viralimmunityofinjecteddoublestranded iesareneededonbodycomposition,fillet/productquality,
(ds)RNAmoleculesandsinglestranded(si)RNA(Westenberg andfeedefficiency.
etal.2005). - SNPdataprovideattractivepossibilitiesforgenomicselec-
tion.GenomicmethodsforSNPdataanalysisneedfurther
development.
4.3 Alternativefeed - Alternative strategies of using genomic information in
broodstock selection need to be assessed, and their cost-
Functional genomics can contribute to the production of effectivenessneedstobeevaluated.
newkindsoffeedforculturedfishes.Twosuchexamplesare
the possibility of production of novel feed sources (such as
Acknowledgements. Thispaper isbased ontheTermsof Reference
plantbased proteinfor carnivorousfish) and terrestrialtrans-
“b”oftheICESWorkingGrouponApplicationofGeneticstoFish-
genicplant(e.g.soybeanorrapeseed)asfeed.Theuseoftra-
eriesandMariculture,whichmetinIspra,Italyin2007.
ditionallymarinefeedcomponentsforaquaculturefaceslower
Theauthors thankDr.ElisabethGoslingandananonymous referee
availabilityofmarineresources.Thesemarinecomponentscan
forthetexteditingandconstructivecomments.
bereplacedbyterrestrialvegetableingredients,asoils.How-
ever,thequalityofvegetableoilsneedstobeimprovedinor-
dertomeetnutritionaldemandsoffarmedfish(Opsahl-Ferstad
References
etal.2003).Transgenicplantswithincreasedamountsofsome
fattyacidsinseeds,andwithpossibilityoftheirextensioninto
longer, marine – similar fatty acids can improve quality of Abernathy J., Xu P., Li P., Xu D., Kucuktas H., Klesiun P., Arias
vegetableoils for use as fish feed.Presentevidenceindicates C.,LiuZ.,2007,Generationandanalysisofexpressedsequence
thatinsalmonids,novelplant-basedfeedsourcesmayinduce tagsfromtheciliateprotozoanparasiteIchthyophthiriusmultifil-
onlyweakgenotype-by-dietinteractionsthatwouldneedspe- iis.BMCGenomics8,176.
cial attention from fish breeders(Quinton et al. 2007).How- Agresti J.J., Seki S., Cnaani A., Poompuang S., Hallerman E.M.,
ever, novel feed ingredients may have deleterious effects on UmielN.,HulataG.,GallG.A.E.,MayB.,2000,Breedingnew
quality or biological efficiency of aquatic species, and it is a strainsoftilapia:developmentofanartificialcenteroforiginand
linkagemapbasedonAFLPandmicrosatelliteloci.Aquaculture
challenge to develop the feed and the hatchery animals fur-
185,43-56.
ther. Moreover,genomic approaches could also contribute to
Akey J.M., Zhang G., Zhang K., Jin L., Shriver M.D., 2002,
abetterunderstandingoflipidpathwaysandsynthesisoflong
Interrogating a high-density SNP map for signatures of natural
chain polyunsaturatedfatty acids, facilitating the selection of
selection.GenomeRes.12,1805-1814.
genotypesthatproducea goodperformancewhenfeeda low
Anderson E.C., Garza J.C., 2006, Power of single-nucleotide poly-
fishoilorproteindiet.
morphisms for large-scale parentage inference. Genetics 172,
2567-2582.
Araneda C., Neira R., Iturra P., 2005, Identification of a domi-
5 Conclusion nantSCARmarkerassociatedwithcolourtraitsinCohosalmon
(Oncorhynchuskisutch).Aquaculture247,67-73.
- Theimplementationofgenomicapproachesshouldbeen- Artieri C.G., Mitchell L.A., Ng S.H.S., Parisotto S.E., Danzmann
couragedinthefieldsoffisheriesandaquaculturebysup- R.G., Hoyheim B., Phillips R.B., Morasch M., Koop B.F.,
porting the development of genomic resources, such as DavidsonW.S.,2006,Identificationofthesex-determininglocus
250 R.Wenneetal.:Aquat.LivingResour.20,241–255(2007)
ofAtlanticsalmon(Salmosalar)onchromosome2.Cytogenet. ChistiakovD.A.,HellemansB.,HaleyC.S.,LawA.S.,Tsigenopoulos
GenomeRes.112,152-159. C.S., Kotoulas G., Bertotto D., Libertini A., Volckaert F.A.M.,
Aubin-HorthN.,LetcherB.H.,HofmannH.A.,2005a,Interactionof 2005, A microsatellite linkage map of the European sea bass
rearingenvironment andreproductive tacticongene expression DicentrarchuslabraxL.Genetics170,1821-1826.
profilesinAtlanticsalmon.J.Hered.96,261-278. CoimbraM.R.M.,KobayashiK.,KoretsuguS.,HasegawaO.,Ohara
Aubin-HorthN.,LandryC.R.,LetcherB.H.,HofmannH.A.,2005b, E., Ozaki A., Sakamoto T., Naruse K., Okamoto N., 2003, A
Alternativelifehistoriesshapebraingeneexpressionprofilesin genetic linkage map of the Japanese flounder Paralichthys oli-
malesofthesamepopulation.Proc.Biol.Sci.272,1655-1662. vaceus.Aquaculture220,203-218.
Bachère E., Guéguen Y., Gonzalez M., de Lorgeril J., Garnier J., Cossins A.R., Crawford D.L., 2005, Opinion - Fish as models for
Romestand B., 2004, Insights into the anti-microbial defence environmentalgenomicsNat.Rev.Genet.6,324-333.
of marine invertebrates: the penaeid shrimps and the oyster Crollius H.R., Weissenbach J., 2005, Fish genomics and biology.
Crassostreagigas.Immunol.Rev.198,149-168. GenomeRes.15,1675-1682.
BanksM.A.,EichertW.,OlsenJ.B.,2003, Whichgeneticlocihave CunninghamC.,HikimaJ.I.,JennyM.J.,ChapmanR.W.,FangG.C.,
greaterpopulationassignmentpower?Bioinformatics19,1436- Saski C., Lundqvist M.L., Wing R.A., Cupit P.M., Gross P.S.,
1438. Warr G.W., Tomkins J.P., 2006, New resources for marine ge-
BaoB.,PeatmanE.,XuP.,BaoprasertkulP.,WangG.,LiuZ.,2006,
nomics:Bacterialartificialchromosomelibrariesfortheeastern
Characterizationof23CCchemokinegenesandanalysisoftheir
and pacific oysters (Crassostrea virginica and C. gigas). Mar.
expression inchannel catfish(Ictaluruspunctatus). Dev.Comp.
Biotech.8,521-533.
Immunol.30,783-796.
Danzmann R.G., Jackson T.R., Ferguson M.M., 1999, Epistasis in
BaranskiM.,Loughnan S.,AustinC.M.,RobinsonN.,2006,Ami-
allelicexpressionatuppertemperaturetoleranceQTLinrainbow
crosatellitelinkagemapoftheblacklipabalone, Haliotisrubra.
trout.Aquaculture173,45-58.
AnimGenet.37,563-570.
Doyle R.W., Herbinger C.M., 1994, The use of DNA fingerprint-
BeachamT.D.,LapointeM.,CandyJ.R.,MillerK.M.,WithlerR.E.,
ing for high-intensity within-family selection in fish breed-
2004, DNA in action: Rapid application of DNA variation to
ing,Proc.5th WorldCongressonGeneticsAppliedtoLivestock
sockeye salmon fisheries management. Conserv. Genet. 5, 411-
Production,7-12August1994,Vol.19,Dep.AnimalandPoultry
416.
Science,UniversityofGuelph,Guelph,pp.364-371.
Beaumont M.A.,NicholsR.A.,1996, Evaluating locifor useinthe
DulvyN.K.,SadovyY.,ReynoldsJ.D.2003.Extinctionvulnerability
genetic analysis of population structure. Proc. R. Soc. London
inmarinepopulations.FishFish.4,25-64.
Ser.B-Biol.Sci.263,1619-1626.
FastM.D.,MuiseD.M.,EasyR.E.,RossN.W.,JohnsonS.C.,2006,
Bonin A., Taberlet P., Miaud C., Pompanon F., 2006, Explorative
The effects of Lepeophthirius salmonis infection on the stress
genomescantodetectcandidatelociforadaptationalongagradi-
response and immunological status of Atlantic salmon (Salmo
entofaltitudeinthecommonfrog(Ranatemporaria)Mol.Biol.
salar).FishShellfishImmunol.21,228-241.
Evol.23,773-783.
FernandoR.L.,GrossmanM.,1989,Marker-assistedselectionusing
Bonnet E., Fostier A., Bobe J., 2007, Microarray-based analysis
bestlinearunbiasedprediction.Genet.Sel.Evol.33,209-229.
of fish egg quality after natural or controlled ovulation. BMC
Franch R., Louro B., Tsalavouta M., Chatziplis D., Tsigenopoulos
Genomics8,55.
C.S.,SarropoulouE.,AntonelloJ.,MagoulasA.,MylonasC.C.,
BoudryP.,ColletB.,CornetteF.,HervouetV.,BonhommeF.,2002,
BabbucciM.,PatarnelloT.,PowerD.M.,KotoulasG.,Bargelloni
High variance in reproductive success of the Pacific oyster
L.,2006,Ageneticlinkagemapofthehermaphroditeteleostfish
(Crassostrea gigas Thunberg) revealed by microsatellite-based
SparusaurataL.Genetics174,851-861.
parentage analysis of multifactorial crosses. Aquaculture 204,
Fuji K., Kobayashi K., Hasegawa O., Coimbra M.R.M., Sakamoto
283-296.
T.,OkamotoN.,2006,Identificationofasinglemajorgeneticlo-
Breyne P., Dreesen R., Cannoot B., Rombaut D., Vandepoele K.,
cuscontrollingtheresistancetolymphocystisdiseaseinJapanese
Rombauts S., Vanderhaeghen R., Inze D., Zabeau M., 2003,
flounder(Paralichthysolivaceus).Aquaculture254,203-210.
QuantitativecDNA-AFLPanalysisforgenome-wideexpression
Gharbi K., Gautier A., Danzmann R.G., Gharbi S., Sakamoto T.,
studiesMol.Genet.Genom.269,173-179.
Bridle A., Morrison R., Cupit P.M., Cunningham B.M., Nowak Hoyheim B., Taggart J.B., Cairney M., Powell R., Krieg F.,
B., 2006a, Quantitation of immune response gene expression Okamoto N., Ferguson M.M., Holm L.E., Guyomard R., 2006,
and cellular localisation of interleukin-1β mRNA in Atlantic A linkage map for brown trout (Salmo trutta): Chromosome
salmon, Salmo salar, affected by amoebic gill disease (AGD). homeologies and comparative genome organization with other
Vet.Immunol.Immunopathol.114,121-134. Salmonidfish.Genetics172,2405-2419.
Bridle A.R., Morrison R.N., Nowak B.F., 2006b, The expression GilbeyJ.,VerspoorE.,McLayA.,HoulihanD.,2004,Amicrosatel-
of immune-regulatory genes in rainbow trout, Oncorhynchus litelinkagemapforAtlanticsalmon(Salmosalar).AnimGenet.
mykiss, during an amoebic gill disease (AGD) infection. Fish 35,98-105.
ShellfishImmunol.20,346-364. GibsonG.,WeirB.,2005,Thequantitativegeneticsoftranscription.
Campbell N.R., Narum S.R., 2007, Identification of novel SNPsin TrendsGenet.21,616-623.
Chinook salmon and variation among life history types. Trans. GraceyA.Y.,FraserE.J.,LiW.,FangY.,TaylorR.R.,RogersJ.,Brass
Am.Fish.Soc.,inpress. A.,CossinsA.R.,2004, Copingwithcold:Anintegrative, mul-
Cnaani A., Zilberman N., Tinman S., Hulata G., Ron M., 2004, titissue analysis of the transcriptome of a poikilothermic verte-
Genome-scananalysisforquantitativetraitlociinanF-2tilapia brate.Proc.Natl.Acad.Sci.USA101,16970–16975.
hybrid.Mol.Genet.Genom.272,162-172. GrimholtU.,LarsenS.,NordmoR.,MidtlyngP.,KjoeglumS.,Storset
ChiniV.,RimoldiS.,TerovaG.,SarogliaM.,RossiF.,BernardiniG., A.,SaeboS.,StetR.J.M.,2003,MHCpolymorphismanddisease
GornatiR.,2006,EST-basedidentificationofgenesexpressedin resistance in Atlantic salmon (Salmo salar); facing pathogens
the liver of adult seabass (Dicentrarchus labrax L.). Gene 376, withsingleexpressedmajorhistocompatibilityclassIandclass
102-106. IIloci.Immunogenetics55,210-219.