Biotechnology and Genetics in Fisheries and Aquaculture, Second Edition

212 Pages·2010·1.54 MB·English

by  Andy Beaumont

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BIOTECHNOLOGY AND
GENETICS IN FISHERIES AND
AQUACULTURE
Second Edition
Biotechnology and Genetics in Fisheries and Aquaculture, Second Edition A. Beaumont, P. Boudry and K. Hoare
© 2010 Andy R. Beaumont, Pierre Boudry and Kathrin Hoare. ISBN: 978-1-405-18857-9
i
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BIOTECHNOLOGY AND
GENETICS IN FISHERIES AND
AQUACULTURE
Second Edition
Andy Beaumont
SchoolofOceanSciences
BangorUniversity
Wales,UK
Pierre Boudry
Ifremer
UMRM100PhysiologieetEcophysiologiedesMollusquesMarins
TechnopoledeBrest-Iroise
Plouzane´,France
Kathrin Hoare
SchoolofOceanSciences
BangorUniversity
Wales,UK
A John Wiley & Sons, Ltd., Publication
iii
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Thiseditionfirstpublished2010
(cid:2)C 2010byAndyR.Beaumont,PierreBoudryandKathrinHoare
Firsteditionpublished2003
BlackwellPublishingwasacquiredbyJohnWiley&SonsinFebruary2007.Blackwell’spublishing
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LibraryofCongressCataloging-in-PublicationData
Beaumont,A.R.(AndyR.)
Biotechnologyandgeneticsinfisheriesandaquaculture/AndyR.
Beaumont,PierreBoudry,KathrinHoare.–2nded.
p.cm.
Includesbibliographicalreferencesandindex.
ISBN978-1-4051-8857-9(hardback:alk.paper)
1.Fishes–Moleculargenetics. 2.Fishes–Breeding. I.Boudry,Pierre. II.Hoare,K.. III.Title.
SH155.5.B432010
639.3–dc22
2009031829
AcataloguerecordforthisbookisavailablefromtheBritishLibrary.
(cid:2)
Setin10/12ptTimesbyAptaraR Inc.,NewDelhi,India
PrintedinSingapore
1 2010
iv
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Contents
Prefacetothesecondedition ix
Acknowledgements xi
Chapter1 Whatisgeneticvariation? 1
Deoxyribosenucleicacid 1
Ribosenucleicacid 5
Whatisthegeneticcode? 7
Proteinstructure 7
Sowhataboutchromosomes? 9
Howdoessexualreproductionproducevariation? 11
MitochondrialandchloroplastDNA 16
Chapter2 Howcangeneticvariationbemeasured? 19
DNAsequencevariation 19
DNAfragmentsizevariation 36
Proteinvariation 44
Phenotypicvariation 47
Chapter3 Geneticstructureinnaturalpopulations 49
Whatisapopulation? 49
Howareallelefrequenciesestimated? 51
Whatistherelationshipbetweenallelesandgenotypes? 51
Howdoallelefrequencieschangeovertime? 53
Howdoespopulationstructurearise? 54
Howaregeneticmarkersusedtostudypopulationstructure? 55
Levelsofgeneticdifferentiationinaquaticorganisms 60
Potentialproblemswithallozymesandcodingmarkers 61
mtDNAvariation 63
Microsatellitevariation 66
Populationstructureintheflatoyster 68
Mixedstockanalysis(MSA) 73
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vi Contents
Chapter4 Geneticsofpopulationsizeinconservation
andaquaculture 77
Geneticsofsmallpopulationsizeinthewild 78
Geneticmarkersinconservation 82
Geneticsofsmallpopulationsizeinthehatchery 85
Isthereevidenceoflossofgeneticvariationinthehatchery? 87
Howdoeshatcherypropagationaffectheterozygosity? 89
Geneticmarkersforidentificationofhatcheryproduct 93
Geneticmarkersforpathogenidentification 94
Chapter5 Geneticvariationoftraits 99
Qualitativetraits 99
Quantitativetraits 105
Whatkindsoftraitsareimportant? 106
Variationofaquantitativetrait 106
Howcanweestimatenarrow-senseheritability? 109
Realisedheritability 115
Correlatedtraits 118
Whattypesofartificialselectionsarethere? 118
Settingupabreedingprogramme 122
Inbreeding,cross-breedingandhybridisation 123
Currentstatusofselectivebreedingprogrammesinaquaculture 126
Chapter6 Fromgeneticstogenomics 129
Whatisthegenome? 129
Genomemapping 130
Wholegenomesequencing:the‘bigpicture’ 137
QTLmapping 137
ApplicationofQTLsinaquacultureandfisheriesmanagement 138
Marker-assistedselection(MAS):fromQTLstogenomicselection 139
Transcriptomics 139
Chapter7 Triploidsandbeyond:whymanipulateploidy? 145
Howisitdone? 146
Productionofgynogensandandrogens 148
Identificationofploidychange 149
ValueofTriploids 151
Tetraploids 155
Gynogensandandrogens 157
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Contents vii
Chapter8 Geneticengineeringinaquaculture 161
TheDNAconstruct 162
Transgenedelivery 164
Transgeneintegration 168
Detectingintegrationandexpressionofthetransgene 169
Resultsoftransgenesiseffortsinfish 171
Somuchfortransgenics–whataboutcloning? 176
Genethics 176
Glossary 181
Index 193
Colourplatesappearbetweenpages52and53
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Preface to the second edition
Therateofchangeinthefieldofmoleculargeneticshasbeenextremelyfastsincethe
development of DNA sequencing methodologies and the polymerase chain reaction.
The new millennium has seen increasing miniaturisation and sophistication of these
techniques,andthishasledtosecond-generationsequencingmethodsthatcanproduce
hundreds of thousands of DNA sequences from an organism in a very short space of
time.Becauseofthepaceofthesetechnologicalchanges,somepartsofthefirstedition
ofthisbookquicklybecameoutdated.
This second edition benefits from the addition of a new author (Dr Pierre Boudry)
and in updating the book to take account of new technologies, we have taken the
opportunitytocorrecterrors,improveandreorganisethematerialfromthefirstedition.
Several chapters retain the same headings but with new material added to bring them
rightuptodate.Usingmaterialfromthefirsteditionandaddingfreshtextandfigures,
we have introduced a new chapter based around the genetics of population size that
links directly to problems in aquaculture and in conservation. In addition, we have
providedanewchaptercalled‘Geneticstogenomics’thatcoversrecentdevelopments
in genetic mapping, the search for quantitative trait loci and introduces the subject of
transcriptomics–thetranscriptionofDNAsequencetoRNA.
We have retained the introductory-level nature of the book but have increased the
numberofreferencesattheendofeachchapterformoreadvancedreaders.
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Acknowledgements
The following have kindly given us permission to use some of their material in the
illustrations for the book: Dr Ann Wood, Dr Karen Abey, Dr Shelagh Malham, Dr
CraigWilding,ChrisBeveridge,AlixTaylorandNatalieHorton.Wethankthescientific
publishingcompaniesthathaveallowedustousefiguresfrompublishedsourcesandall
suchcompaniesareacknowledgedinfigurelegends.
WethankDavidRobertsfromtheSchoolofOceanSciences,BangorUniversity,for
photographyandassistingwithpreparationoffigures.
Dr Pierre Boudry thanks the members of the Working Group on the Application of
GeneticsinFisheriesandMariculture(InternationalCouncilfortheExplorationofthe
Sea)forsharingideasandknowledge.
This second edition of the book would not have appeared without the support and
encouragementofNigelBalmforthandthekeeneditorialassistanceofKateNuttalland
CatrionaDixonofWiley-Blackwell.
xi
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PlateB2.1 Athermalcyclerinwhichpolymerasechainreactioniscarriedout.During
polymerasechainreactiontheheatedlidisclosedoverthemicro-titreplatewhichispositionedin
theheatingblock.
PlateB2.2 Agarosemini-gelshowingpipettingofDNAsampleintoseparatewellspositioned
acrossthegel.Thegelispreparedbypouringitintoamouldandallowingittoset.Thewellsare
castintothegelduringthisprocess.Samplesarecolouredtomonitortheprogressof
electrophoresis.
Biotechnology and Genetics in Fisheries and Aquaculture, Second Edition A. Beaumont, P. Boudry and K. Hoare
© 2010 Andy R. Beaumont, Pierre Boudry and Kathrin Hoare. ISBN: 978-1-405-18857-9
1
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PlateB2.3 SlabgelDNAsequencershowingtheupperandlowerbuffertrays.Theverythingel
issandwichedbetweentwoglassplatesconnectedtotheupperandlowerbuffertrays.Inset
showsdetailofthesharks-toothcombrestingonthetopofthegel.Upto98samplescanbe
appliedindividuallyintoeachofthesmallchambersbetweentheteeth.
PlateB2.4 ReadoutfromacapillarygelDNAsequencerusingtheSangermethod.Each
colouredpeakrepresentsasinglebase(blue,cytosine;red,thymine;black,guanine;green,
adenine)andthesequenceofbasesisgivenabovethegraphic.
2