Table Of ContentSELECTION AND BREEDING PROGRAMS IN AQUACULTURE
Selection and Breeding Programs
in Aquaculture
edited by
TRYGVE GJEDREM
AKVAFORSK, Institute of Aquaculture Research AS, Norway
AC.I.P. Catalogue record for this book is available from the Library of Congress.
ISBN-10 1-4020-3341-9 (HB) Springer Dordrecht, Berlin, Heidelberg, New York
ISBN-10 1-4020-3342-7 (e-book) Springer Dordrecht, Berlin, Heidelberg, New York
ISBN-13 978-1-4020-3341-4 (HB) Springer Dordrecht, Berlin, Heidelberg, New York
ISBN-13 978-1-4020-3342-1 (e-book) Springer Dordrecht, Berlin, Heidelberg, New York
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PREFACE
Although aquaculture as a biological production system has a long history, systematic
and efficient breeding programs to improve economically important traits in the farmed
species have rarely been utilized until recently, except for salmonid species. This means
that the majority of aquaculture production (more than 90 %) is based on genetically
unimproved stocks. In farm animals the situation is vastly different: practically no
terrestrial farm production is based on genetically unimproved and undomesticated
populations. This difference between aquaculture and livestock production is in spite of
the fact that the basic elements of breeding theory are the same for fish and shellfish as
for farm animals. One possible reason for the difference is the complexity of
reproductive biology in aquatic species, and special consideration needs to be taken in
the design of breeding plans for these species. Since 1971 AKVAFORSK, has
continuously carried out large scale breeding research projects with salmonid species,
and during the latest 15 years also with a number of fresh water and marine species.
Results from this work and the results from other institutions around the world have
brought forward considerable knowledge, which make the development of efficient
breeding programs feasible. The genetic improvement obtained in selection programs
for fish and shellfish is remarkable and much higher than what has been achieved in
terrestrial farm animals.
The main purpose of this book is to summarise quantitative genetic theory, the basic
ingredient for selective breeding, and present methods for developing efficient breeding
programs for aquatic species based on the latest scientific findings. Many books have
been published about the development of breeding programs in farm animals, but so far
no similar book has been available for aquatic species.
We hope that university students, biologists and consultants who plan and implement
breeding programs in aquaculture will make use of the book. We also hope that the
book will encourage the industry to use selective breeding in order to increase
productivity and improve the utilisation of available feed, land and water resources for
the benefit of the growing human population.
Many people have assisted in the writing process of this book. In particular, my
colleagues at AKVAFORSK and in some other collaborating institutions have made
crucial contributions. Their efforts, support and advice have been decisive for the
completion of the work. I also owe a lot to Ms. Grethe Tuven (Department of Animal
Science and Aquaculture, Agricultural University of Norway) who has been in charge
of processing the figures, and to Dr. Ben Hayes and Dr. Nick Robinson
(AKVAFORSK) who read the manuscripts and made the language readable and
understandable. Finally I am grateful to the leaders of AKVAFORSK, who have
encouraged us to complete and publish the book.
Trygve Gjedrem
Ås June 2004
CONTRIBUTORS
Øivind Andersen, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010,
1432 Ås, Norway
Hans Bernhard Bentsen, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX
5010, 1432 Ås, Norway
Kjersti Turid Fjalestad, Norwegian Institute of Fisheries and Aquaculture Research,
P.O.BOX 6122, 9291 Tromsø, Norway
Trygve Gjedrem, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010,
1432 Ås, Norway
Bjarne Gjerde, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010,
1432 Ås, Norway
Ben Hayes, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010, 1432
Ås, Norway
Kari Kolstad,Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010, 1432
Ås, Norway
Theo H.E. Meuwissen, Department of Animal Science and Aquaculture, P.O.BOX
5003, 1432 Ås, Norway
Ingrid Olesen, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010,
1432 Ås, Norway
Terje Refstie,AKVAFORSK Genetics Center, 6600 Sunndalsøra, Norway
Morten Rye, AKVAFORSK Genetics Center, 6600 Sunndalsøra, Norway
Anna Sonesson, Institute of Aquaculture Research, AKVAFORSK, P.O.BOX 5010,
1432 Ås, Norway
Jørn Thodesen, AKVAFORSK Genetics Center, 6600 Sunndalsøra, Norway.
John A. Woolliams, Roslin Institute, Roslin, Midlothian EH25 9PS, United Kingdom
TABLE OF CONTENTS
Preface v
Contributors vii
1. Status and scope of aquaculture 1
Trygve Gjedrem
1.1 Introduction 1
1.2 Domestication 2
1.3 History of animal breeding 3
1.4 Aim of breeding - Why change a population? 5
1.5 Effect of breeding programs in farm animals 5
1.5.1 What has been accomplished? 5
1.6 Breeding in aquaculture 6
1.7 Present status of breeding in aquaculture 7
2. Basic genetics 9
Trygve Gjedrem and Øivind Andersen
2.1 Molecular genetics 9
2.1.1 DNA-molecule 9
2.1.2 Replication of DNA 14
2.1.3 Protein synthesis 14
2.2 Cell division 14
2.2.1 Mitosis 15
2.2.2 Meiosis 15
2.2.3 Location of genes 17
2.3 Mendelian inheritance 17
2.3.1 Example of mendelian traits in fish 18
2.4 Gene action 19
3. Population genetics 23
Øivind Andersen and Ben Hayes
3.1 Introduction 23
3.2 Hardy-Weinberg equilibrium 23
3.3 Inbreeding 25
3.4 Crossbreeding 26
3.5 Selection 27
3.6 Mutation 28
3.7 Genetic drift 29
3.8 Migration 30
3.9 Genetic distance and population divergence 31
3.10 Summary 32
x
4. Polygenicinheritance 35
Hans Bernhard Bentsen
4.1 Introduction 35
4.2 Limitations of the single gene model 35
4.3 A simplified polygenic model 37
4.4 How many genes? 40
4.5 Implications for the response to selection 40
4.6 Limitations of the simplified polygenic model 42
4.7 Summary 43
5. Basic statistical parameters 45
Trygve Gjedrem and Ingrid Olesen
5.1 Variation in traits 45
5.1.1 Mean, standard deviation and variance 45
5.1.2 Coefficient of variation 47
5.2 Distribution of observations 47
5.2.1 Normal distributions 47
5.2.2 Non-normal distributions 49
5.3 Variance 51
5.3.1 Analysis of variance 51
5.3.2 Variance of a sum 53
5.3.3 Genetic variance 54
5.3.4 Environmental variance 54
5.3.5 Maternal variance 57
5.3.6 Genotype – environment interaction 58
5.4 Relationship between traits 59
5.4.1 Correlation and regression 59
5.4.2 Analysis of covariance 60
5.4.3 Genetic and phenotypic correlation 61
5.5 Heritability 64
5.6 Path coefficients 65
6. Kinship, relationship and inbreeding 73
Anna K. Sonesson, John A. Woolliams and Theo H.E. Meuwissen
6.1 Introduction 73
6.2 Concepts 73
6.3 Calculating coefficients of kinship and relationship 76
6.3.1 Paths and loops 76
6.3.2 The tabular method 78
6.3:3 Properties of the relationship matrix (A matrix) 79
6.4 Consequences of inbreeding 81
6.4.1 Change of mean and variances 81
6.4.2 Reduced heterozygosity 83
6.4.3 Inbreeding depression 83
6.5 Management of genetic variation in fish breeding schemes 84
xi
7. Selection 89
Trygve Gjedrem and Jørn Thodesen
7.1 Introduction 89
7.2 Natural selection 89
7.3 Artificial selection 90
7.4 Prediction of response to selection 91
7.4.1 Predicting genetic gain, an example 93
7.5 Multiple trait selection 94
7.5.1 Selection for a trait as a ratio 95
7.6 Indirect selection 96
7.6.1 Selection for disease resistance 96
7.6.2 Selection for feed conversion efficiency 97
7.6.3 Selection for increased absorption of nutrient 100
7.6.4 Selection for reduced fat deposition 100
7.7 Effect of selection on genetic variance and covariance 101
7.8 Selection response obtained 102
7.8.1 Disease resistance 102
7.8.2 Growth rate 103
7.8.3 Feed conversion efficiency 104
7.8.4 Date of spawning 105
7.8.5 Sexual maturation 105
7.9 Selection limits 106
7.10 Effect of selection on domestication 108
7.11 Socio-economic effects of improved stocks 110
8. Reproductive traits in aquatic animals 113
Terje Refstie and Trygve Gjedrem
8.1 Reproductive cycle 113
8.2 Sex determination 113
8.2.1 Unisexual fishes 113
8.2.2 Hermaphrodites 114
8.2.3 Bisexual fishes 114
8.3 Sex ratio 114
8.4 Sexual characteristics 116
8.5 Age of maturation 116
8.6 Egg and sperm production 117
8.6.1 Production of egg 117
8.6.2 Production of sperm 117
8.7 Fertilization 117
8.8 Genetic determination of sex 118
8.9 Hormone induced sex reversal 118
8.10 Hormone induced ovulation 118
8.11 Preservation of gametes 119
8.12 Influence of reproduction on strategies for genetic improvement 119
xii
9. Methods for estimating phenotypic and genetic parameters 121
Kari Kolstad
9.1 Estimating genetic variance components from resemblance
between relatives 121
9.1.1 Phenotypic covariances between relatives 121
9.1.2. Genetic covariance between relatives 122
9.2 Utilising phenotypic covariances between individuals for
estimating genetic parameters 123
9.2.1 Estimating additive genetic variance by utilising
phenotypic covariance between parent and offspring 124
9.2.2 Estimating additive genetic variance by regression of
phenotypic value of offspring on phenotypic value on parents 125
9.2.3 Estimating additive genetic variance by utilising
phenotypic covariance between sibs 126
9.3 Mixed model types of analysis 130
9.4 Estimation of heritability 131
9.4.1 Estimating heritability from regression and correlations
between relatives 131
9.4.2 Combinating information by REML 133
9.4.3 Heritability of family means and within-family deviations 133
9.5 Estimation of repeatability 134
9.6 Phenotypic and genetic correlations between traits 135
9.6.1 Estimating correlation from covariances between relatives 135
9.7 Correlations estimated from multi-trait models based on
mixed linear model techniques and pedigree information 138
9.8 Threshold characters 140
9.8.1 Liability and threshold 140
9.9 Concluding remarks 143
10. Breeding strategies 145
Kjersti Turid Fjalestad
10.1 Introduction 145
10.2 Inbreeding 146
10.2.1 Application of inbreeding 147
10.2.2 Inbreeding depression 147
10.2.3 Results from inbreeding experiments 148
10.3 Crossbreeding 150
10.3.1 Heterosis 150
10.3.2 Combining ability 150
10.3.3 Reciprocal recurrent selection 151
10.3.4 Overdominance 152
10.3.5 Diallel cross 153
10.3.6 Three-way and four-way crosses, backcrosses 154
10.3.7 Synthetic populations 154
10.3.8 Application of crossbreeding in fish and shellfish 154
10.3.9 Examples and results from crossbreeding experiments 155
xiii
10.4 Pure breeding 157
11. Selection methods 159
Kjersti Turid Fjalestad
11.1 Introduction 159
11.2 Individual selection 159
11.3 Pedigree selection 161
11.4 Family selection 161
11.5 Within family selection 164
11.6 Progeny testing 165
11.7 Combined selection 165
11.8 Prediction/Expected response 166
11.9 Correlated response 167
11.10 Indirect selection 168
11.11 Relative merit of the methods 170
12. Design of breeding programs 173
Bjarne Gjerde
12.1 Introduction 173
12.2 Base population 174
12.3 Maintenance of additive genetic variance 175
12.4 Inbreeding and risk 176
12.5 Mating design 178
12.5.1 Mass spawning 179
12.5.2 Single pairs 179
12.5.3 Nested 180
12.5.4 Full factorial 181
12.5.5 Partly factorial 181
12.5.6 Future mating design 182
12.5.7 Mating design and inbreeding 182
12.6 Selection 182
12.6.1 Individual selection 182
12.6.2 Within family selection 185
12.6.3 Individual versus BLUP selection 185
12.6.4 Sib selection 187
12.6.5 Progeny testing 188
12.7 Selection and mating 188
12.8 Connectedness 189
12.9 Physical tags versus DNA-markers for parental assignment 190
12.10 Small scale breeding program 191
12.11 Large scale breeding program 192
12.11.1 Breeding nucleus 192
12.11.2 Test animals 193
12.11.3 Selection 193
12.11.4 Multiplier units 193
12.12 Concluding remarks 194
