Domestication and genetic improvement: balancing improved production against increased disease risks from inbreeding.

Successful selective breeding programmes have been under way in aquacultural species for many decades. Gains in growth rate as high as 900% have been reported. Programmes selecting for resistance and/or tolerance of specific pathogens have had similar success. However, no more than 10-20% of global aquaculture production is sourced from well-documented breeding programmes. Direct selection for resistance and/or tolerance in biosecure breeding programmes is difficult when classical breeding methods are used. Genomic selection is widely expected to become the most effective mode of selection against pathogens in fish and shellfish. In this paper, the authors explore the possible negative effects of genetic improvement programmes, especially those that stem from interactions between genetics and other components of the aquaculture production system, particularly disease. The main focus is the interaction between selective breeding and biosecurity. They suggest that a self-amplifying feedback loop can be created when biosecurity regulation causes a progressive reduction in genetic diversity and an increase in inbreeding, especially in smallholder hatcheries and farms in developing countries. The resulting inbreeding depression causes increased susceptibility to disease, which in turn increases the frequency and severity of epizootics. Greater losses due to disease again increase regulatory pressures and the cycle begins once more. This 'biosecurity-agro-economic-genetic' feedback loop is analogous to an 'extinction vortex' in wild populations. The authors believe that the loop can be broken by biosecure, aquacultural, genetic exchange networks, modelled on existing breed associations for terrestrial domestic animals. Such networks would constitute a global aquacultural gene pool, with enhanced environmental resilience, long-term capacity for adaptation and minimal inbreeding depression. However, such networks will also require innovative new pathogen management procedures, documentation and regulations to facilitate the exchange of broodstock and seed while still maintaining effective biosecurity.