Selective Breeding in Fish and Conservation of Genetic Resources for Aquaculture CE Lind, RW Ponzoni, NH Nguyen and HL Khaw The WorldFish Center, Penang, Malaysia Content To satisfy increasing demands for fish as food, progress must occur towards greater aquaculture productivity whilst retain- ing the wild and farmed genetic resources that underpin global fish production. We review the main selection methods that have been developed for genetic improvement in aquaculture, and discuss their virtues and shortcomings. Examples of the application of mass, cohort, within family, and combined between-family and within-family selection are given. In addition, we review the manner in which fish genetic resources can be lost at the intra-specific, species and ecosystem levels and discuss options to best prevent this. We illustrate that fundamental principles of genetic management are common in the implementation of both selective breeding and conserva- tion programmes, and should be emphasized in capacity development efforts. We highlight the value of applied genetics approaches for increasing aquaculture productivity and the conservation of fish genetic resources. Introduction Aquaculture is predicted to play a major and ever increasing role in meeting human needs for animal- source food. In terrestrial animal and plant species genetic improvement programmes have made a sub- stantial contribution to agricultural productivity and viability. As a result of decades, if not centuries, of selective breeding and domestication in these terrestrial species, thousands of genetically distinct breeds, strains and varieties now exist worldwide and are collectively termed ‘genetic resources’. By contrast, with the excep- tion of a few fish species (see Gjedrem 2000, 2010; Ponzoni et al. 2011b), aquatic animals have undergone a limited amount of genetic improvement or domestica- tion, and most aquaculture stocks in current use in developing countries are genetically similar or inferior to wild, undomesticated stocks (Brummett et al. 2004). This contrast raises two important differences between fish and terrestrial species in the context of conservation and use of genetic resources. Firstly, an enormous potential exists to improve aquaculture productivity though the application of selective breeding pro- grammes and capitalize on the broad genetic diversity present in many wild fish populations. Secondly, because of the lack of well-defined domesticated breeds, the conservation of fish genetic resources is generally concerned with (i) the application of appropriate genetic management to ensure that cultured populations remain viable and productive, (ii) the possible impacts of cultured fish on of wild populations and (iii) the preservation of habitats where (unique) wild popula- tions reside. A range of methods of varying complexity is available for the selection purposes, but their suit- ability for different circumstances in aquaculture is not always clear. Similarly, there are several biological levels at which the loss of a genetic resource is important, yet are not always considered when developing aquatic conservation initiatives or policies. In this review, we briefly present the main selection methods that have been used or advocated for aquaculture, and discuss their virtues and shortcomings. In addition, we review the manner in which fish genetic resources can be lost and discuss options to best prevent this. When possible, we make reference to practical examples of the appli- cation of both selective breeding and conservation approaches in aquatic animals. We also present evidence about the economic worth of genetic improvement programmes and discuss some of the challenges faced when implementing such programmes in aquatic animals. Approaches to Genetic Improvement Aquatic animals allow the implementation of several approaches to genetic improvement. These include hybridization and cross-breeding, chromosome manip- ulation, sex control, transgenesis and selective breeding. These are almost always mentioned in aquaculture genetics reports, papers and meetings without making a judgement about their relative practical value (e.g. FAO 2008). For instance, it is seldom, if ever, stated that of all the genetic approaches only selective breeding offers the opportunity of continued genetic gain, that the gains made can be permanent, that it is the only approach in which the gain can be transmitted from generation to generation and that gains in a nucleus can be multiplied and expressed in thousands or millions of individuals in the production sector (Ponzoni et al. 2007, 2008). In the cases they are useful, the other approaches result in ‘once off’ expressions of the benefit. They may be applied at the multiplication (hatchery) level, but not at the nucleus level. Selection Approaches General We present the different selection approaches in increas- ing order of complexity, beginning with the simplest one. In each case, we refer to specific requirements that may constitute a limitation for their implementation in developing countries (a more detailed description of the methods is given by Ponzoni et al. (2006, 2009). Note that we assume that there is genetic variation for the trait(s) of interest in the population undergoing selection and that it does not suffer from problems (e.g. bottlenecks, inbreeding) created by earlier genetic mis- management. Such problems could undermine the effec- tiveness of any selection programme (e.g. Smitherman Reprod Dom Anim 47 (Suppl. 4), 255–263 (2012); doi: 10.1111/j.1439-0531.2012.02084.x ISSN 0936-6768 Ó 2012 Blackwell Verlag GmbH