REPRODUCTIVE BIOTECHNOLOGY IN FINFISH AQUACULTURE

By SOPHIA SMITH

CONTENTS INTRODUCTION HISTORIC DEVELOPMENT OF AQUACULTURE DE?NITION OF A BREEDING PROGRAM DOMESTICATION AND THE APPLICATION OF GENETIC IMPROVEMENT IN AQUACULTURE DOMESTICATION OF ANIMALS SELECTIVE BREEDING QUALITY TRAITS BETTER UTILIZATION OF RESOURCES GENETIC IMPROVEMENT IS ACCUMULATIVE GENETIC IMPROVEMENT PRODUCES PERMANENT GAINS INITIATING A SELECTIVE BREEDING PROGRAM SELECTIVE BREEDING PROGRAMS IN AQUACULTURE PREREQUISITES FOR A BREEDING PROGRAM THE SUCCESS OF SELECTIVE BREEDING IN AQUACULTURE ATLANTIC SALMON RAINBOW TROUT COHO SALMON TILAPIA CARP CHANNEL CAT?SH SEA BREAM SHRIMP OYSTERS SCALLOPS GENETIC IMPROVEMENT IN AQUATIC SPECIES COMPARED TO TERRESTRIAL LIVESTOCK SPECIES SUMMARY AND CONCLUSION THE THEORETICAL BASIS FOR BREEDING AND SELECTION THE CELL BASIC GENETICS GENES EFFECT OF GENES VARIATION SINGLE GENE TRAITS QUANTITATIVE TRAITS VARIATION IN QUANTITATIVE TRAITS VARIATION BETWEEN SPECIES VARIATION WITHIN SPECIES ESTIMATION OF VARIATION AND COVARIATION MEAN AND STANDARD DEVIATION VARIANCE OF A SUM GENETIC VARIANCE HERITABILITY ENVIRONMENTAL VARIANCE CORRELATIONS BETWEEN TRAITS REGRESSION INBREEDING AND RELATEDNESS GENETIC RELATIONSHIP INBREEDING EFFECTIVE POPULATION SIZE EFFECT OF INBREEDING ON GENETIC VARIANCE INBREEDING DEPRESSION CROSSBREEDING HETEROSIS PUREBREEDING SELECTION NATURAL SELECTION ARTI?CIAL SELECTION PREDICTING SELECTION CHANGE MULTIPLE TRAIT SELECTION CORRELATED RESPONSE TO SELECTION EFFECT OF SELECTION ON GENETIC VARIANCE METHODS OF SELECTION SELECTION LIMITS INITIATING BREEDING PROGRAMS THE FUNDAMENTAL BASIS OF A BREEDING PROGRAM ESTABLISHMENT OF A BASE POPULATION BREEDING GOAL GROWTH RATE FEED CONVERSION RATIO (FCR) AND EF?CIENCY (FCE) DISEASE RESISTANCE AGE AT SEXUAL MATURATION PRODUCT QUALITY COLD TOLERANCE FECUNDITY BEHAVIOUR RECAPTURE FREQUENCY CENTRAL BREEDING GOALS REGISTRATION OF RECORDS BODY WEIGHT SURVIVAL FEED CONVERSION EF?CIENCY ADJUSTMENT OF DATA BREEDING STRATEGIES SELECTION METHODS FACTORS AFFECTING ALLELE FREQUENCIES MIGRATION MUTATION GENETIC DRIFT CHOICE OF SELECTION METHOD PEDIGREE SELECTION INDIVIDUAL SELECTION FAMILY SELECTION WITHIN-FAMILY SELECTION PROGENY TESTING CORRELATED RESPONSE AND INDIRECT SELECTION COMBINED SELECTION MULTIPLE TRAIT SELECTION AND INDEX SELECTION COMPARING DIFFERENT SELECTION METHODS MATING DESIGN MASS SPAWNING SINGLE PAIR MATING NESTED MATING DESIGN FACTORIAL MATING CONNECTEDNESS CONCLUSION ESTIMATION OF BREEDING VALUES BREEDING VALUE OF INDIVIDUAL ANIMALS BREEDING VALUE OF FULL-SIB FAMILIES BREEDING VALUE OF HALF-SIB FAMILIES BREEDING VALUES FOR MULTIPLE TRAITS USING A SELECTION INDEX SCALING OF SELECTION INDEXES BEST LINEAR UNBIASED PREDICTION (BLUP) GENOTYPE–ENVIRONMENT INTERACTION ESTIMATES OF GENOTYPE–ENVIRONMENT INTERACTIONS MEASURING RESPONSE TO SELECTION CONTROL POPULATION AVERAGE BREEDERS REPEATED MATINGS GENETIC TREND ANALYSIS STRUCTURE OF BREEDING PROGRAMS BREEDING PROGRAMS APPLYING INDIVIDUAL SELECTION ADVANCED BREEDING PROGRAMS MATING AND HATCHING TAGGING RECORDING DURING GROW-OUT HARVEST AND PRE-SELECTION OF BROODSTOCK AT BREEDING STATIONS FINAL SELECTION OF BROODSTOCK GENETIC MARKERS FOR PARENTAGE ASSIGNMENT TEST STATIONS PRODUCTION OF SPECIAL LINES DISSEMINATION OF GENETIC GAINS DIRECT DISSEMINATION FROM NUCLEUS DISSEMINATION FROM MULTIPLIERS BREEDING PROGRAMS FOR NEW SPECIES UNDESIRABLE SIDE EFFECTS IN BREEDING PROGRAMS CORRELATED EFFECTS BREEDING GOAL MAY CHANGE DISEASE PREVENTION INCREASE OF INBREEDING BIOTECHNOLOGY IN BREEDING PROGRAMS DNA MARKERS MICROSATELLITES SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) LINKAGE MAPS QUANTITATIVE TRAIT LOCI (QTL) CANDIDATE GENE APPROACH QTL MAPPING APPROACH LINKAGE ANALYSIS FINE MAPPING OF QTL LDLA MAPPING AN EXAMPLE OF QTL MAPPING TO GENE DISCOVERY STRATEGIES TO REDUCE GENOTYPING REQUIREMENTS MARKER ASSISTED SELECTION TYPES OF MARKER ASSISTED SELECTION GENE ASSISTED SELECTION (GAS) LINKAGE DISEQUILIBRIUM MAS (LD-MAS) LINKAGE EQUILIBRIUM MAS (LE-MAS) GENOMIC SELECTION OTHER APPLICATIONS OF GENETIC MARKERS PARENTAGE ASSIGNMENT AND TRACEABILITY GENETIC INTERACTIONS GENETIC VARIATION GENE EXPRESSION DATA TRANSGENICS GENOME SEQUENCING AND FUTURE TECHNOLOGIES REPRODUCTION TECHNIQUES GYNOGENESIS ANDROGENESIS TRIPLOIDY TETRAPLOIDY PRODUCTION OF SINGLE SEX, YY AND XX STOCKS ECONOMIC BENE?TS OF BREEDING PROGRAMS COST OF BROODSTOCK PRODUCTION COST OF RUNNING A BREEDING PROGRAM ECONOMIC BENE?T OF BREEDING PROGRAMS RELATIVE CONTRIBUTION OF SELECTION AND FEED REGIMES TO PERFORMANCE WHO BENE?TS FROM GENETIC IMPROVEMENTS? THE ANIMAL THE FARMER OWNERSHIP OF GENETICALLY IMPROVED MATERIAL