SELECTION AND BREEDING PROGRAMS IN AQUACULTURE

Transcription

1 SELECTION AND BREEDING PROGRAMS IN AQUACULTURE

2 Selection and Breeding Programs in Aquaculture edited by TRYGVE GJEDREM AKVAFORSK, Institute of Aquaculture Research AS, Norway

3 A C.I.P. Catalogue record for this book is available from the Library of Congress. ISBN (e-book) Springer Dordrecht, Berlin, Heidelberg, New York ISBN (HB) Springer Dordrecht, Berlin, Heidelberg, New York ISBN (HB) Springer Dordrecht, Berlin, Heidelberg, New York ISBN (e-book) Springer Dordrecht, Berlin, Heidelberg, New York Published by Springer, P.O. Box 17, 3300 AA Dordrecht, The Netherlands. Cover photo by Vidar Vassvik Printed on acid-free paper All Rights Reserved 2005 Springer No part of this work may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording or otherwise, without written permission from the Publisher, with the exception of any material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Printed in the Netherlands.

4 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

5 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

6 TABLE OF CONTENTS Preface Contributors v vii 1. Status and scope of aquaculture 1 Trygve Gjedrem 1.1 Introduction Domestication History of animal breeding Aim of breeding - Why change a population? Effect of breeding programs in farm animals What has been accomplished? Breeding in aquaculture Present status of breeding in aquaculture 7 2. Basic genetics 9 Trygve Gjedrem and Øivind Andersen 2.1 Molecular genetics DNA-molecule Replication of DNA Protein synthesis Cell division Mitosis Meiosis Location of genes Mendelian inheritance Example of mendelian traits in fish Gene action Population genetics 23 Øivind Andersen and Ben Hayes 3.1 Introduction Hardy-Weinberg equilibrium Inbreeding Crossbreeding Selection Mutation Genetic drift Migration Genetic distance and population divergence Summary 32

7 x 4. Polygenic inheritance 35 Hans Bernhard Bentsen 4.1 Introduction Limitations of the single gene model A simplified polygenic model How many genes? Implications for the response to selection Limitations of the simplified polygenic model Summary Basic statistical parameters 45 Trygve Gjedrem and Ingrid Olesen 5.1 Variation in traits Mean, standard deviation and variance Coefficient of variation Distribution of observations Normal distributions Non-normal distributions Variance Analysis of variance Variance of a sum Genetic variance Environmental variance Maternal variance Genotype environment interaction Relationship between traits Correlation and regression Analysis of covariance Genetic and phenotypic correlation Heritability Path coefficients Kinship, relationship and inbreeding 73 Anna K. Sonesson, John A. Woolliams and Theo H.E. Meuwissen 6.1 Introduction Concepts Calculating coefficients of kinship and relationship Paths and loops The tabular method :3 Properties of the relationship matrix (A matrix) Consequences of inbreeding Change of mean and variances Reduced heterozygosity Inbreeding depression Management of genetic variation in fish breeding schemes 84

8 xi 7. Selection 89 Trygve Gjedrem and Jørn Thodesen 7.1 Introduction Natural selection Artificial selection Prediction of response to selection Predicting genetic gain, an example Multiple trait selection Selection for a trait as a ratio Indirect selection Selection for disease resistance Selection for feed conversion efficiency Selection for increased absorption of nutrient Selection for reduced fat deposition Effect of selection on genetic variance and covariance Selection response obtained Disease resistance Growth rate Feed conversion efficiency Date of spawning Sexual maturation Selection limits Effect of selection on domestication Socio-economic effects of improved stocks Reproductive traits in aquatic animals 113 Terje Refstie and Trygve Gjedrem 8.1 Reproductive cycle Sex determination Unisexual fishes Hermaphrodites Bisexual fishes Sex ratio Sexual characteristics Age of maturation Egg and sperm production Production of egg Production of sperm Fertilization Genetic determination of sex Hormone induced sex reversal Hormone induced ovulation Preservation of gametes Influence of reproduction on strategies for genetic improvement 119

9 xii 9. Methods for estimating phenotypic and genetic parameters 121 Kari Kolstad 9.1 Estimating genetic variance components from resemblance between relatives Phenotypic covariances between relatives Genetic covariance between relatives Utilising phenotypic covariances between individuals for estimating genetic parameters Estimating additive genetic variance by utilising phenotypic covariance between parent and offspring Estimating additive genetic variance by regression of phenotypic value of offspring on phenotypic value on parents Estimating additive genetic variance by utilising phenotypic covariance between sibs Mixed model types of analysis Estimation of heritability Estimating heritability from regression and correlations between relatives Combinating information by REML Heritability of family means and within-family deviations Estimation of repeatability Phenotypic and genetic correlations between traits Estimating correlation from covariances between relatives Correlations estimated from multi-trait models based on mixed linear model techniques and pedigree information Threshold characters Liability and threshold Concluding remarks Breeding strategies 145 Kjersti Turid Fjalestad 10.1 Introduction Inbreeding Application of inbreeding Inbreeding depression Results from inbreeding experiments Crossbreeding Heterosis Combining ability Reciprocal recurrent selection Overdominance Diallel cross Three-way and four-way crosses, backcrosses Synthetic populations Application of crossbreeding in fish and shellfish Examples and results from crossbreeding experiments 155

10 xiii 10.4 Pure breeding Selection methods 159 Kjersti Turid Fjalestad 11.1 Introduction Individual selection Pedigree selection Family selection Within family selection Progeny testing Combined selection Prediction/Expected response Correlated response Indirect selection Relative merit of the methods Design of breeding programs 173 Bjarne Gjerde 12.1 Introduction Base population Maintenance of additive genetic variance Inbreeding and risk Mating design Mass spawning Single pairs Nested Full factorial Partly factorial Future mating design Mating design and inbreeding Selection Individual selection Within family selection Individual versus BLUP selection Sib selection Progeny testing Selection and mating Connectedness Physical tags versus DNA-markers for parental assignment Small scale breeding program Large scale breeding program Breeding nucleus Test animals Selection Multiplier units Concluding remarks 194

11 xiv 13. Prediction of breeding values 197 Bjarne Gjerde 13.1 Introduction Derivation of predictors Best predictor (BP) Best Linear Predictor (BLP) Best Linear Unbiased Predictor (BLUP) Selection Index Procedure (SIP) Selection for several traits Selection for one trait Individual selection Within full-sib family selection Sib selection Family selection Own, full and half-sib selection Progeny testing Accuracy of predicted breeding value Individual selection Within family selection Sib selection Family selection Combined own, full- and half-sib selection Accuracy for different selection methods Prediction error variance Best Linear Unbiased Predictor (BLUP) Differences between SIP and BLUP Prediction of breeding values with BLUP BLUP with A 1,h 2 = BLUP with A 1,h 2 = BLUP without A 1,h 2 = Least squares estimates Breeding values for the progeny The effect of A Scaling the predicted values Effects common to full-sibs other than additive genetics Genotype - environment interaction 233 Trygve Gjedrem 14.1 Introduction Causes of interaction Estimation of interaction Solving the problem of interaction Estimates of genotype-environment interaction in aquaculture species Carp Salmonides Tilapia 239

12 xv Catfish Shrimp Molluscs Conclusion Measuring genetic change 243 Morten Rye and Trygve Gjedrem 15.1 Introduction Control population Divergent selection Repeated mating Use of average breeders Genetic trend analyses Prediction of response based on selection paths Breeding plans 251 Trygve Gjedrem 16.1 Introduction Fish and shellfish as targets for breeding programs as compared with farm animals Consequences of level of fecundity Breeding goal Growth rate Feed conversion efficiency Disease resistance Age at sexual maturation Quality traits Fecundity Recapture frequency Behaviour Summary Forming a base population Breeding strategies Selection methods Genotype - environment interaction Identification of animals Closed life cycle and controlled mating Mating design Testing strategies Registration of records Systems for selection procedures Individual selection Family selection Progeny testing Estimation of breeding value Selection of broodstock 273

13 xvi Controlling the amount of genetic gain Constraints to breeding programs Negative correlated effects Change of breeding goal Spread of diseases Genotype-environment interaction Inbreeding accumulation Reduction in genetic variation Dissemination of genetic improvement Combining selective breeding and marker assisted selection Summary of main elements in a breeding plan Organising breeding program 279 Trygve Gjedrem and Terje Refstie 17.1 Practise in farm animals Organisation of breeding programs in aquaculture species Atlantic salmon in Norway Structure of breeding programs Fecundity of the species Different breeding goals The chase of sex limited traits Economic value of each animal Wether fertilization takes place internally or externally the female Cost of broodstock production Farmers cooperatives breeding companies Initiatives to start breeding programs National or local breeding programs? Chromosome engineering 287 Terje Refstie and Trygve Gjedrem 18.1 Introduction Gynogenesis Inactivation of sperm Shock to produce gynogenetic diploids Production of inbred lines Androgenesis Triploidy Production of triploids Methods to determine ploidy Sexual maturation of triploids Triploids for fish farming Production of YY stocks Tetraploid Conclusion 298

14 xvii 19. Modern biotechnology and aquaculture 301 Ben Hayes and Øivind Andersen 19.1 Introduction DNA markers Linkage maps Linkage mapping and QTL analysis Detection of quantitative traits loci Strategies to minimise the number of genotypings Results of QTL detection Implementing marker assisted selection in breeding programs for aquaculture species Other applications of DNA markers Transgenic fish Future prospects Genetic interactions between farmed and wild fish, with examples from the Atlantic salmon case in Norway 319 Hans Bernard Bentsen and Jørn Thodesen 20.1 Introduction Conservation of biological diversity Diversity of species Genetic diversity Biological diversity Long-term conservation Introduction of exotic species of fish Effects on the genetic diversity Introduction of micro organisms and parasites Genetic interactions between genetically improved and wild fish of the same species Genetic differences between farmed and wild populations Gene flow from genetically improved breeds to wild populations Case study: Interactions between farmed and wild Atlantic salmon in Norway Genetic composition of Norwegian farmed salmon Genetic composition of the wild river populations Gene flow from farmed to wild populations Effects of genetic interactions between farmed and wild Atlantic salmon Summary 334 Appendix A 335 References 337 Index 361