Selective Breeding in Aquaculture: An Introduction Reviews: Methods and Technologies in Fish Biology and Fisheries VOLUME 10 Series editor: Jennifer L. Nielsen U.S. Geological Survey, Alaska Science Center Anchorage, Alaska For further volumes: http://www.springer.com/series/6481 Trygve Gjedrem · Matthew Baranski Selective Breeding in Aquaculture: An Introduction 123 Trygve Gjedrem Matthew Baranski Nofima Marin Nofima Marin 1432 Aas 1432 Aas Norway Norway trygve.gjedrem@nofima.no ISSN 1571-3075 ISBN 978-90-481-2772-6 e-ISBN 978-90-481-2773-3 DOI 10.1007/978-90-481-2773-3 Springer Dordrecht Heidelberg London New York Library of Congress Control Number: 2009928426 c Springer Science+Business Media B.V. 2009 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. Cover illustration: Larvae of Atlantic Cod by Saskia Mennen, Nofima Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com) Preface The foundation of quantitative genetics theory was developed during the last century and facilitated many successful breeding programs for cultivated plants and ter- restrial livestock. The results have been almost universally impressive, and today nearly all agricultural production utilises genetically improved seed and animals. The aquaculture industry can learn a great deal from these experiences, because the basic theory behind selective breeding is the same for all species. The first published selection experiments in aquaculture started in 1920 s to improve disease resistance in fish, but it was not before the 1970 s that the first family based breeding program was initiated for Atlantic salmon in Norway by AKVAFORSK. Unfortunately, the subsequent implementation of selective breeding on a wider scale in aquaculture has been slow, and despite the dramatic gains that have been demonstrated in a number of species, less than 10% of world aquaculture production is currently based on improved stocks. For the long-term sustainability of aquaculture production, there is an urgent need to develop and implement effi- cient breeding programs for all species under commercial production. The ability for aquaculture to successfully meet the demands of an ever increasing human pop- ulation, will rely on genetically improved stocks that utilise feed, water and land resources in an efficient way. Technological advances like genome sequences of aquaculture species, and advanced molecular methods means that there are new and exciting prospects for building on these well-established methods into the future. The main purpose of this book is to demonstrate the success that selective breed- ing programs have achieved so far in aquaculture, and to highlight the tremendous potential this technology offers for efficient and productive aquaculture production in the future. The main sections of the book are: • Why improve production traits in fish and shellfish? • What has been accomplished in selective breeding programs in aquaculture? • A brief outline of the theory of quantitative genetics • Establishing and running breeding programs • Integration of molecular genetic tools v vi Preface The book is primarily written for aquaculture students with selective breeding as a subject, farmers, advisory consultants and farm managers. Students specialis- ing in selective breeding may also find it useful to consult the book ‘Selection and breeding programs in aquaculture’ (Springer, 2005), which provides a more in-depth coverage of the topics discussed here. We hope that this book will stimulate aquaculture industries to consider the use of improved stocks in their production of fish and shellfish. The development and implementation of breeding programs must be driven by industry, with the support of scientists, farmers organisations and governments. The benefits will be far reaching. Ås, Norway Trygve Gjedrem February 2009 Matthew Baranski Acknowledgements We express our sincere appreciation to our employer, Nofima Marin, Ås, for their continuous support and financial contribution to the publication of this book. It has been inspiring to work together with the skilled scientists at the institute. We are particularly grateful to Dr. Solveig van Nes, Reidun Lilleholt and Grethe Tuven for technical help. Furthermore, we thank the director of AKVAFORSK Genetics Center AS (AFGC), Dr. Morten Rye, for his valuable contribution to the manuscript. Finally, we would like to thank Dr. Hans B. Bentsen, Dr. Bjarne Gjerde and Dr. Nicholas Robinson for their valuable support. Ås, Norway Trygve Gjedrem February 2009 Matthew Baranski vii Contents 1 Introduction ............................... 1 1.1 Historic Development of Aquaculture . ............. 1 1.2 Definition of a Breeding Program . ............. 3 2 Domestication and the Application of Genetic Improvement in Aquaculture ............................. 5 2.1 DomesticationofAnimals.................... 5 2.2 Selective Breeding . ....................... 6 2.3 Quality Traits ........................... 7 2.4 Better Utilization of Resources .................. 7 2.5 Genetic Improvement is Accumulative . ............. 7 2.6 Genetic Improvement Produces Permanent Gains ........ 8 2.7 Initiating a Selective Breeding Program ............. 9 2.8 Selective Breeding Programs in Aquaculture . ........ 10 2.9 Prerequisites for a Breeding Program . ............. 11 3 The Success of Selective Breeding in Aquaculture .......... 13 3.1 Introduction ............................ 13 3.2 AtlanticSalmon......................... 13 3.3 RainbowTrout.......................... 15 3.4 CohoSalmon........................... 16 3.5 Tilapia.............................. 17 3.6 Carp................................ 18 3.7 Channel Catfish . ....................... 19 3.8 SeaBream............................ 20 3.9 Shrimp.............................. 20 3.10Oysters.............................. 21 3.11Scallops.............................. 21 3.12 Genetic Improvement in Aquatic Species Compared to Terrestrial Livestock Species . .................. 22 3.13 Summary and Conclusion . .................. 22 4 The Theoretical Basis for Breeding and Selection .......... 25 4.1 Introduction ............................ 25 4.2 TheCell.............................. 25 ix x Contents 4.3 BasicGenetics.......................... 26 4.3.1 Introduction ....................... 26 4.3.2 Genes . ....................... 26 4.3.3 Effect of Genes . .................. 29 4.4 Variation............................. 29 4.4.1 Introduction ....................... 29 4.4.2 SingleGeneTraits.................... 30 4.4.3 Quantitative Traits . .................. 30 4.4.4 Variation in Quantitative Traits ............. 31 4.4.5 Variation Between Species . ............. 32 4.4.6 Variation Within Species . ............. 33 4.5 EstimationofVariationandCovariation............. 33 4.5.1 Mean and Standard Deviation . ............. 33 4.5.2 Variance of a Sum . .................. 35 4.5.3 Genetic Variance . .................. 36 4.5.4 Heritability ....................... 36 4.5.5 Environmental Variance ................. 38 4.5.6 CorrelationsBetweenTraits............... 40 4.5.7 Regression........................ 42 4.6 Inbreeding and Relatedness . .................. 43 4.6.1 GeneticRelationship.................. 43 4.6.2 Inbreeding . ....................... 44 4.6.3 Effective Population Size . ............. 47 4.6.4 Effect of Inbreeding on Genetic Variance ........ 48 4.6.5 Inbreeding Depression ................. 48 4.7 Crossbreeding . ....................... 50 4.7.1 Introduction ....................... 50 4.7.2 Heterosis........................ 50 4.8 Purebreeding ........................... 52 4.9 Selection............................. 52 4.9.1 Introduction ....................... 52 4.9.2 NaturalSelection.................... 53 4.9.3 ArtificialSelection................... 53 4.9.4 Predicting Selection Change . ............. 54 4.9.5 Multiple Trait Selection ................. 56 4.9.6 Correlated Response to Selection ............ 57 4.9.7 Effect of Selection on Genetic Variance ........ 58 4.9.8 Methods of Selection .................. 58 4.9.9 SelectionLimits..................... 59 5 Initiating Breeding Programs ..................... 63 5.1 Introduction ............................ 63 5.2 The Fundamental Basis of a Breeding Program . ........ 64 5.3 Establishment of a Base Population . ............. 65 Contents xi 5.4 Breeding Goal . ....................... 67 5.4.1 Introduction ....................... 67 5.4.2 GrowthRate....................... 68 5.4.3 Feed Conversion Ratio (FCR) and Efficiency (FCE) . 69 5.4.4 Disease Resistance . .................. 70 5.4.5 Age at Sexual Maturation . ............. 74 5.4.6 Product Quality . .................. 75 5.4.7 Cold Tolerance . .................. 78 5.4.8 Fecundity . ....................... 78 5.4.9 Behaviour........................ 78 5.4.10 Recapture Frequency .................. 79 5.4.11 Central Breeding Goals ................. 79 5.5 Registration of Records ...................... 80 5.5.1 Introduction ....................... 80 5.5.2 BodyWeight...................... 81 5.5.3 Survival......................... 81 5.5.4 Feed Conversion Efficiency . ............. 82 5.5.5 Product Quality .