Genetics and breeding in seed supply for inland aquaculture

It is estimated that no more than 20 percent of global aquaculture production utilizes genetically improved stocks. Furthermore, the vast majority (>95 percent) of freshwater aquaculture production comes from the developed world where resources are limited and breeding technologies less advanced. Thus, the proportion of production derived from genetically improved fish in freshwater aquaculture is likely to be considerably lower than the global average. The past 15 years have seen a rapid increase in the number and scope of breeding programmes for genetic improvement of aquaculture species and a number of important national and regional programmes for improving, commercializing and disseminating important aquaculture species are now underway or planned. There have been a number of important advances in research, most notably in the verification of the potential gains to be had from well-managed selection programmes with genetic gains for growth related traits of 7-10 percent readily achievable in wellmanaged programs. However, it is also evident that there has been genetic deterioration of existing domesticated and cultured stocks through poor genetic management during and subsequent to the domestication process. These effects need to be reversed and whilst progress has been made there remains a need to support implementation of best practices in basic genetic management when domesticating, translocating and maintaining discrete aquaculture stocks. Whilst the success with selective breeding in recent times has placed this technology at the core of efforts to improve aquaculture stocks, there has been some successes with other technologies such as sex control, hybridisation and polyploidy induction and these do have a role as components of integrated approaches to genetic improvement. Some extreme improvements in culture performance have been demonstrated using transgenesis but societal and regulatory concerns continue to preclude commercial application. Major research advances have been made in recent times with the application of genetic markers and the costs of widely applied and, to some degree standardized, techniques such as the application of microsatellite markers which have come down considerably. Genetic markers are thus now becoming valuable tools and will be increasingly applied to enhance traditional selection programmes and in more specific programmes of marker-assisted selection. 1 This paper was peer-reviewed by Dr Devin Bartley of the Aquaculture Management and Conservation Service, Fisheries and Aquaculture Department, FAO, Rome, Italy. 520 Assessment of freshwater fish seed resources for sustainable aquaculture Of the major freshwater aquaculture species, there have been very significant genetic gains through the application of genetics in tilapia and carps in particular. Efforts are now expanding to include shellfish species such as Macrobrachium. This paper reviews core issues and progress in genetic management and improvement of species for inland aquaculture and highlights some of the technical, environmental and socio-economic issues still constraining the full implementation of genetic improvement programmes and the equitable dissemination of their outputs and benefits. A number of recommendations are made concerning the appropriate role of applied genetics in seed supply systems for the future development of inland aquaculture. INTRODUCTION With a few exceptions, aquaculture is a relatively recent development and contributor to global food security, having expanded at an average rate of 8.9 percent since 1970. During this time, aquaculture has increased from representing just 3.9 percent of global fisheries production volume up to almost 50 percent in 2004 (FAO, 2006). It is inevitable that aquaculture production will overtake capture fisheries production within the next 10-20 years. All future predictions call for further significant increases in aquaculture production to meet expanding demand from a growing population and increases in per capita consumption of seafood. In this context, the supply of quality seed has increased, and must continue to increase dramatically to sustain growth in aquaculture. Gjedrem (2002) estimated then that genetically improved stock accounted for no more than 10 percent of aquaculture production. Whilst this figure is undoubtedly rising, as the benefits of genetic improvement become apparent, it is unlikely to be more than 20 percent at present. It is almost certainly much lower in most developing countries. Relatively high adoption rates of genetically improved stocks exists in some developed countries such as Norway where Gjedrem (2000) estimates 65 percent of aquaculture production takes place using stocks resulting from modern and efficient breeding programs. Likewise, for species such as Atlantic salmon, over 97 percent of global production is from genetically improved lines. The major factor in the relatively low impact of genetic improvement in aquaculture is the embryonic status of aquaculture production sectors. During the early stage of aquaculture development, rapid advances can be made in production volumes and efficiency with relatively simple and cost effective improvements or innovations in general husbandry, nutrition and health management. In contrast, genetic changes whilst capable of dramatic improvements inevitably require long-term strategic planning and investment in order to secure medium to long-term gains. A further reason for the ‘slow start’ in implementing genetically based technologies, was an early misconception that, despite positive evidence from livestock and crop sectors, selective breeding might prove ineffective in aquatic organisms. This view was perpetuated by the failure to bring about significant improvements during early attempts to consciously select for commercially important traits in carps and tilapia (e.g. Moav and Wohlfarth, 1976; Moav, 1979; Wohlfarth, 1983). An era of substantial genetic improvement, contributing to a “blue revolution” in aquaculture, is undoubtedly upon us with some form of genetic improvement evident in the majority of important aquaculture species. This paper focuses on the role that genetics is playing, and will play, in developing the supply of quality seed for inland aquaculture. Given that FAO statistics (FAO, 2006) record that 97 percent of freshwater aquaculture production (27.8 million tonnes in 2005) comes from the developing world (95 percent from Asia) this paper will, by default, focus on seed supply for aquaculture in developing countries. The paper will review the current status of genetic improvement technologies focusing on finfish, molluscs and crustacea and will describe their applications to some important species in inland production 8.2 Genetics and breeding in seed supply for inland aquaculture 521 systems. One of the key objectives, in the context of current developments and status of genetic improvement, will be to identify and discuss the key issues facing the future application and uptake of genetics based technologies and genetically improved stocks in inland aquaculture. This will include a review of technological and environmental constraints to genetic advancement, identification of research priorities to address these along with issues related to human and physical resource capacity and mechanisms for disseminating improved seed focused on equitable uptake of benefits. GENETIC TECHNOLOGIES IN AQUACULTURE This section of the review focuses on the technology options for genetic improvement. Over recent decades there has been a very significant body of research on applying genetic technologies to aquacultured species and distinct trends are visible. An analysis of the main subject areas of papers published in the proceedings of triennial symposia on genetics in aquaculture from the first in 1982, up to 2003, shows the trends in the main focal areas of aquaculture genetics research (Figure 8.2.1). This indicates a decline in selective breeding research up to 1991 followed by a steady increase. This decline was mirrored by an increase in research on alternative or ‘competing’ technologies such as chromosome set manipulation and transgenesis. The basis of this was the prevailing belief, at this time, that these technologies were likely to bring about more rapid genetic and culture performance gains than selective breeding. Research in both these areas has now declined and some of the reasons behind this will be discussed later in this paper. Another evident trend, since the early 1990s, is the rapid increase in the volume of research focused on the applications of genetic markers. DOMESTICATION AND MANAGEMENT OF GENETIC VARIATION Domestication and subsequent broodstock management practices have very important implications for the long-term quality of cultured stocks. A domesticated species is defined broadly by the Convention on Biological Diversity to be one in which the evolutionary process has been influenced by humans to meet their needs. In the context of aquaculture, domestication is the process whereby a population becomes adapted to man and the captive environment by some combination of genetic change over several generations and environmentally induced developmental events recurring during each generation. The consequence of domestication for the subsequent development of aquaculture based on these domesticated stocks can be profound. Due to the relative infancy of aquaculture as a major form of primary production, many cultured stocks