Genome mapping and genomics in fishes and aquatic animals

195 Pages·2008·7.24 MB·English

by  Cristian Araneda

Genome Mapping and Genomics in Animals
Volume2
SeriesEditor:ChittaranjanKole
Thomas D. Kocher, Chittaranjan Kole
(Editors)
Genome Mapping
and Genomics
in Fishes and
Aquatic Animals
With29Illustrations,12inColor
123
ThomasD.Kocher ChittaranjanKole
Professor DepartmentofGenetics&Biochemistry
DepartmentofBiology ClemsonUniversity
1210Biology/PsychologyBuilding 111JordanHall
UniversityofMaryland Clemson,SC29634
CollegePark USA
MD20742
USA e-mail:[email protected]
e-mail:[email protected]
ISBN 978-3-540-73836-7 e-ISBN978-3-540-73837-4
DOI10.1007/978-3-540-73837-4
LibraryofCongressControlNumber:2008922501
©Springer-VerlagBerlinHeidelberg2008
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Preface to the Series
Thedecipheringofthesequenceofageneforthefirsttime,thegeneforbacterio-
phageMS2coatproteintobespecific,byWalterFiersandhiscoworkersin1972
markedthebeginningofaneweraingenetics,popularlyknownasthegenomics
era. This was followed by the complete nucleotide sequence of the same bacte-
riophagein1976bythesamegroup;DNAsequencing of anotherbacteriophage
Φ
( -X174)in1977byFredSanger,WalterGilbert,andAllanMaxam,workingin-
dependently; and first use of any DNA marker in gene mapping in 1980 for the
humansystembyDavidBotstein.Theselandmarkdiscoverieswereimmediately
embraced by the life science community and were followed by an array of ele-
gantexperimentsleadingtothedevelopmentofseveralnovelconcepts,tools,and
strategiesforelucidationofgenesandgenomesoflivingorganismsofacademic
andeconomicintereststomankind.
Thelasttwodecadesofthetwentiethcenturywitnessedtheinventionofthe
polymerase chain reaction; several types of molecular markers; techniques of
cloninglargeDNAsegmentsinartificialchromosomes;approachestoisolateand
characterizegenes;andtoolsforhigh-throughputsequencing,tonamejustafew.
Anothernoteworthydevelopmenthadbeentheformulationofdifferentcomputer
softwaretoanalyzethehugeamountofdatageneratedbygenomemappingexper-
iments,andabovealldeploymentofinformationtechnologytostore,search,and
utilizeenormousamountsofdataparticularlyofclonedgenes,transcripts,ESTs,
proteins,andmetabolites.Thissweetandswiftmarriageofbiologyandinforma-
tiontechnologygavebirthtobioinformaticsandthenew“omics”disciplinessuch
asgenomics,transcriptomics,proteomics,andmetabolomics.
The tide of genome mapping and genomics flooded all phyla of the animal
kingdomandalltaxaoftheplantkingdomandmostobviouslytheprokaryotes.
Intheanimalsystems,wealreadyhadthegenesequencefortheCFTRproteinin
humansin1989;genomesequenceofthemodelorganismCaenorhabditiselegans
in 1998; genetic maps of many higher animals with map positions of genes and
gene-clusters during the nineties. We also happily witnessed the beginning of
genome sequencing projects of three domestic animals (cow, dog, and horse)
and poultry in 1993. All these achievements and endeavors culminated in the
whole-genomesequenceofthefruit-flyDrosophila,thegardenpeaoftheanimal
system,in2000declaringasuccessfulandpleasantendingofthegenomescience
efforts of the twentieth century. The new millennium in 2001 started with the
publicationofthedraftsequenceofthehumangenomeonFebruary15thbyThe
InternationalHumanGenomeMappingConsortiumandonFebruary16thbyThe
CeleraGenomicsSequencingTeam.
A flurry of new concepts and tools in the first few years of the first decade
of the twenty-first century has enriched the subject of genomics and the field
has broadened to include the young and fast-growing disciplines of structural
genomics, functional genomics, comparative genomics, evolutionary genomics,
andneutraceuticalgenomics,tonamejustafew.Wenowhavemore,faster,cheaper,
and cleverer mapping and sequencing strategies, association mapping and the
VI PrefacetotheSeries
454 for example; several tools, such as microarrays and cDNA-AFLP to isolate
hundredsofknownandunknowngeneswithinashortperiod,elegantlyassisted
by transcript-profiling and metabolic-profiling; identifying new genes from the
knowledge-baseofhomologousgenomes;andprecisedepictionoftheroadmap
of evolution of human and other members of the animal kingdom and their
phylogeneticrelationshipswithmembersofotherspeciesorgenera.Withinless
than a decade of the deciphering of the first complete genome sequence for an
animalspeciesin1998,wehavecompletesequencesofsomeseventeenspeciesof
theanimalkingdomincludingnematodes(2),arthropods(4),domesticanimals
andpoultry(2),marsupial(1),wildanimals(2),aquaticanimals(4),human(1),
andnon-humanprimate(1).Manymoregenomemappingprojectsareprogressing
rapidlyandtheirresultsareexpectedtobepublishedsoon.
The list of achievements in the fields of genome mapping and genomics in
human and other members of the animal kingdom is enormous. It is also true
thatintoday’sworld,intheglobalvillageofthenewmillennium,wehaveaccess
to almost all information regarding the initiation, progress, and completion of
all endeavors of animal genome sciences and can enrich our knowledge of the
concepts, strategies, tools, and outcomes of the efforts being made in animal
genomemappingandgenomics.However,allthisinformationisdispersedover
thepages ofperiodicals, reviewsonparticulartypesofanimalsortheirspecific
groupsinhardcopyversions,andalsoinelectronicsourcesatinnumerablelinks
of web pages for research articles, reports, and databases. But we believe that
thereshouldbeasinglecompilation,inbothhardcopyandelectronicversions,
embodyingtheinformationontheworkalreadydoneandtobedoneinthefields
ofgenomemappingandgenomicsofallmembersoftheanimalkingdomthatare
ofdiverseintereststomankind:academic,health,company,orenvironment.
We,therefore,plannedforthisseriesonGenomeMappingandGenomicsin
Animals with five book volumes dedicated to Arthropods; Fishes and Aquatic
Animals;Domestic Animals;Laboratory Animals;andHumanandNon-Human
Primates.Wehaveincludedchaptersonthespeciesforwhichsubstantialresults
havebeenobtainedsofar.Genomesofmanyofthesespecieshavebeensequenced
orareawaitingcompletionofsequencingsoon.Overviewonthecontentsofthese
volumeswillbepresentedintheprefacesoftheindividualvolumes.
Itisanamazinglyinterestingandperplexingtruththatonlyfournucleotides
producingonlytwentyaminoacidsintheirtripletcombinationcouldcreateany-
wherebetweenfivetothirtymillionspeciesoflivingorganismsontheearth.An
estimatednumberofaboutahalfmillionvertebrateanimalspecieshavebeende-
scribedsofar!Genomesofthefewanimalspeciesfromthisenormouslistthatwe
knowtodayarealsotoodiversetoelucidate.Itisthereforedaringtoeditaseries
on depiction of thediverse genomes we are presenting in over sixty chapters in
thefivevolumes.Sevengloballycelebratedscientistswithknowledgeandexper-
tiseondifferentgroupsofanimalsystems,andhumanandnon-humanprimates
provided me with the inspiration and encouragement to undertake the job of
the series editor. Noelle (Noelle E. Cockett), Paul (Paul Denny), Wayne (Wayne
B.Hunter),Tom(ThomasD.Kocher),Ravi(RavindranathDuggirala),Tony(An-
thonyG.Comuzzie),andSarah(SarahWilliams-Blangero)werealwaysavailable
for consultations and clarifications on any aspect while editing the manuscripts
ofthisseries.Whileworkingonthisseries,Ihavebeenastudentfirst,ascientist
second,andaneditorthirdandlast,withthemissiontopresentacomprehensive
PrefacetotheSeries VII
compilationofanimalgenomemappingandgenomicstothestudents,scientists,
and industries currently involved and to be involved in the study and practice
of animal genome sciences. I express my thanks and gratitude as a humble sci-
enceworkertothesesevenvolumeeditorsforgivingmeanopportunitytohave
an enriching and pleasant view of the wide canvas of animal genome mapping
and genomics. I also extend my thanks and gratitude to all the scientists who
havegenerouslycollaboratedwiththeirelegantandlucidreviewsontherationale,
concepts, methodologies, achievements, and future prospects of the particular
systemstheyareworkingon,andforthesubtletouchesoftheirownexperiences
andphilosophies.
Asexpected,theeditingjobsofthisseriescomprisedcommunicationwiththe
volumeeditors,authors,andpublishers;maintenanceofthefilesinhardandsoft
copies;regularinternetsearchesforverificationoffactsanddatabases;andabove
allmaintenanceofanenvironmenttopracticeandenjoyscience.MywifePhullara,
our son Sourav, and our daughter Devleena were always with me on my travels
asasmallscienceworkeronalongroadof“milestogobeforeIsleep,”notonly
forthesuccessfulcompletionofthisseriesbutalsoinallmyeffortsforteaching,
research,andextensionwhereverIworkedandstayedinmylife.
We have already completed a seven-volume series on Genome Mapping and
Molecular Breeding in Plants with Springer that has been very popular among
students,scientists, andindustries. Weare alsoworking on aseries on Genome
MappingandGenomicsinMicrobeswithSpringer.Itwas,is,andwillbeenriching
and entertaining to work with the experienced and wonderful people involved
in the production of this series, including Sabine (Dr. S. Schwarz), Jutta (Dr. J.
Lindenborn), and Cornelia (Mrs. C. Gründer), among many from the Springer
family. I record my thanks and gratitude to them, here (and also submit in the
databanksforfutureretrieval)foralltheirtimelyco-operationandadvicewhen
publishingthesevolumes.
Itrustandbelievethatwemusthavemisseddeliberationsonmanysignificant
animal species and left many mistakes on the pages of these volumes. All these
lapses are surely mine, and all the credits must go to the volume editors, the
authors,andthepublisher.Inthefuturetheseerrorswillberectifiedonreceiptof
suggestionsfromthereaders,andalsotherewillbefurtherimprovement ofthe
contentsandgeneralset-upofthevolumesofthisseries.
Clemson ChittaranjanKole
January10,2008
Preface to the Volume
Efforts to bring modern genetic tools tothe study of aquaculture species began
inearnestwithaninternationalworkshopinDartmouth,Massachusetts,in1997.
Intheyearsthatfollowed,researchers,manynewlyrecruitedtothefieldofaqua-
culture,developedgeneticmapsofDNApolymorphisms,contributedthousands
ofexpressedsequencetagstothepublicdatabases,andbegantoconstructphysi-
calmapsbyfingerprintinglargeinsertclonelibraries.Thisworklargelyfollowed
similarworkinlivestockspecieslikecows,pigs,andchickensandhasprovided
asolidfoundationforfutureresearch.
Ten years ago, the idea that the genomes of these aquaculture species might
be completely sequenced seemed hopelessly optimistic. The cost of sequencing
was high, and funding priorities favored traditional biomedical models. Since
then, costs have continued to drop, and several aquaculture species have been
recognizedasusefulbiomedicalmodels.Itisencouragingthatthetilapiagenome
isscheduledforsequencingattheBroadInstitutein2008.Weexpectthatmany
moreaquaculturespecieswillbesequencedoverthenextfewyears.
Thisvolumesummarizesthefirsteraofgenomicstudiesofaquaculturespecies,
inwhichthetoolsandresourcesnecessarytosupportwhole-genomesequencing
were developed. We nowlookforward totheapplicationofanewgeneration of
sequencingandgenotypingtechnologiesthatwilltransformtheselectivebreeding
ofthesespecies.Wehopethatimprovedstrainsoftheseaquaculturespecies,with
highergrowthratesandimprovedresistancetodisease,willcontributetoa“blue
revolution”thatwillhelpfeedanovercrowdedplanet.
Theeightchaptersincludedin thisvolumehavebeen contributed by 30sci-
entistsfrom13countries.Weexpressourthanksandgratitudetothemfortheir
cooperationandpatienceinbringingthisprojecttoasuccessfulconclusion.
CollegePark ThomasD.Kocher
Clemson ChittaranjanKole
January10,2008
Contents
Contributors ....................................................... XVII
Abbreviations...................................................... XXI
1 Salmonids
C.Araneda,R.Neira,N.Lam,P.Iturra ................................. 1
1.1 Introduction................................................... 1
1.2 HistoryofSalmonCulture....................................... 1
1.2.1 EarlyHistoryofSalmonCulture .......................... 1
1.2.2 From1890to1975....................................... 2
1.2.3 From1975tothePresentTime............................ 2
1.3 TaxonomicStatusandDistribution ............................... 2
1.3.1 GenusSalmo ........................................... 4
1.3.2 GenusOncorhynchus .................................... 4
1.3.3 GenusSalvelinus ........................................ 6
1.3.4 GenusCoregonus........................................ 6
1.3.5 GenusHucho ........................................... 6
1.4 GeneticImprovement........................................... 6
1.4.1 GeneticImprovementProgramsinSalmonAquaculture ..... 7
1.5 GeneticMappinginSalmonids................................... 7
1.5.1 FirstGenerationMap.................................... 9
1.5.2 SecondGenerationMap.................................. 18
1.5.3 MappingConsequencesofAncestralTetraploidy
ofSalmonids ........................................... 19
1.6 DetectionofQuantitativeTraitLoci............................... 20
1.6.1 UpperTemperatureTolerance ............................ 20
1.6.2 SpawningDate.......................................... 22
1.6.3 EmbryonicDevelopmentRate ............................ 23
1.6.4 MorphologicalandMeristicTraits......................... 24
1.6.5 ResistancetoDiseaseandImmunologicTraits .............. 26
1.7 AssociationofTraitswithSpecificMolecularMarkers............... 29
1.7.1 BulkedSegregantAnalysis ............................... 29
1.7.2 SelectiveGenotyping .................................... 31
1.7.3 OtherSingleLocusMarkers .............................. 31
1.8 PhysicalMapping .............................................. 32
1.8.1 Karyotypes............................................. 32
1.8.2 PhysicalMappingofCentromericRepeats.................. 33
1.8.3 PhysicalMappingofTelomericRepeatedSequences ......... 34
1.8.4 PhysicalMappingofMulticopyGenes:RibosomalGenes ..... 34
1.8.5 PhysicalMappingofCodingGenes ........................ 35
1.8.6 PhysicalMappingofSexMarkers ......................... 36
1.9 IntegrationofGeneticandCytogeneticMaps ...................... 37
References .......................................................... 37
XII Contents
2 Cyprinids
L.Orban,Q.Wu ..................................................... 45
2.1 Introduction................................................... 45
2.2 TheBiologyandHistoryofFarmedCyprinids ..................... 45
2.2.1 TheTaxonomyandPhysiologyofFarmedCyprinids......... 45
2.2.2 ClassicalStudiesontheTaxonomyandOrigin
ofFarmedCyprinids .................................... 46
2.2.3 TheHistoryofCyprinidAquaculture ...................... 47
2.3 ClassicalGenetics .............................................. 49
2.3.1 PhenotypicMarkers..................................... 49
2.3.2 BiochemicalMarkers .................................... 49
2.4 CyprinidChromosomeSetsandTheirManipulation................ 50
2.4.1 ChromosomeSets....................................... 50
2.4.2 Gynogenesis............................................ 51
2.4.3 Androgenesis........................................... 52
2.4.4 InducedTriploidy ....................................... 53
2.4.5 InducedTetraploidy ..................................... 54
2.4.6 NuclearTransfer ........................................ 56
2.5 GeneticandGenomicResourcesforCyprinidResearch ............. 56
2.5.1 DNAMarkersandTheirApplications...................... 56
2.5.2 GeneticMaps,Map-BasedCloning,andQTLs .............. 61
2.5.3 Libraries,cDNAsandProteins ............................ 63
2.5.4 TheZebrafishGenomeProject............................ 64
2.5.5 cDNAArraysandOligonucleotideChips................... 64
2.5.6 InducedMutantsandTransgenicLines..................... 66
2.6 SpeculationonSequencingtheGenome
ofaFarmedCyprinidSpecies .................................... 66
2.7 TheUrgentNeedforComparativeCyprinidGenomics .............. 68
2.7.1 GenomeMapsNeedtoBeEstablishedinFarmedCyprinids .. 68
2.7.2 MoreGenomicandcDNALibrariesAreNeeded............. 69
2.7.3 ComparativeTranscriptomicsofCyprinids–ATreasure
TroveWaitingtoBeOpened .............................. 69
2.7.4 ACallforCross-compatibleCyprinidandTeleostDatabases.. 70
2.8 Synopsis ...................................................... 70
References .......................................................... 71
3 Catfish
Z.Liu .............................................................. 85
3.1 Introduction................................................... 85
3.2 ConstructionofGeneticMaps ................................... 87
3.2.1 DevelopmentandEvaluationofMolecularMarkers.......... 88
3.2.2 DevelopmentofTypeIMarkers........................... 88
3.2.3 ResourceFamiliesandLinkageMaps ...................... 89
3.2.4 ASummaryoftheLinkageMap........................... 90
3.3 QTLMappingandIdentificationofCandidateGenes................ 90
3.4 LandscapeoftheCatfishGenome ................................ 90
3.5 BACLibrariesandPhysicalMapping.............................. 92
3.6 ESTAnalysisandTranscriptomeAnalysis ......................... 93
3.7 SystematicCharacterizationofGenesand/orFull-LengthcDNAs..... 95