Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies—sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter‐ and intra‐species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Aquaculture creates ‘aquatic foods’ such as fish, shellfish, and seaweeds that are critical for food security. Gene editing using CRISPR‐Cas9 has the potential to transform aquaculture by improving animal welfare, nutritional attributes, and farming efficiency, with benefits for environmental sustainability. However, gene editing also poses risks of harm via side effects on other important traits or genetic introgression into wild populations. Public acceptance of gene edited aquatic species will rapidly erode if risk mitigation is ineffective or not applied. Here, we review the benefits and risks for gene editing in aquaculture. A general framework for risk–benefit analysis of gene editing in aquaculture is proposed, incorporating nine key considerations: genetic impacts, ecological impacts, disease risk mitigation, nature of edit, supply chain environmental footprint, animal welfare, human nutrition, ethical business implications and impacts on local communities. When applied on a case‐by‐case basis, the framework will help identify how gene editing of a farmed species can most enhance production and nutritional benefits while minimising harms to animal welfare, the environment, and society.

Atlantic cod is a historically abundant species in the North Atlantic region and has contributed to the prosperity of many nations. But a decline in stocks in the last century has prompted to initiate commercial farming of cod in captive conditions. Several approaches have been employed ranging from stock enhancement, capture‐based aquaculture and intensive cod farming. However, except for the enhancement efforts which were carried out for almost a century, efforts on other methods were intermittent coinciding with lower quotas. Intensive farming was attempted in Norway, Scotland, Ireland, Canada, Iceland and Faroe Islands in the 2000s. But it was carried out hastily to cash in the demand for cod in the market even though there were many biological knowledge gaps that are required for a successful aquaculture venture. The reasons for the failure of commercial farming in Norway during the 2000s were not only because of limited knowledge of the biology of cod but also the economic meltdown in Europe in 2008. Cod farming came to a halt; however, the Norwegian National Cod Breeding Program (NCBP) initiated in 2003 continued to operate and produced a fifth generation of a domesticated cod in 2019. Efforts to fill the gaps and the selective breeding for better growth and disease resistance within NCBP have improved the quality of the juveniles produced. We will discuss the past efforts and reasons for failure in farming of cod, how the current situation looks and the future direction in terms of cod biology, political atmosphere and market.

The Norwegian Lundehund is a highly endangered native dog breed. Low fertility and high frequency predisposition to intestinal disorder imply inbreeding depression. We assessed the genetic diversity of the Lundehund population from pedigree data and evaluated the potential of optimal contribution selection and cross-breeding in the long-term management of the Lundehund population. The current Norwegian Lundehund population is highly inbred and has lost 38.8% of the genetic diversity in the base population. Effective population size estimates varied between 13 and 82 depending on the method used. Optimal contribution selection alone facilitates no improvement in the current situation in the Lundehund due to the extremely high relatedness of the whole population. Addition of (replacement with) 10 breeding candidates of foreign breed to 30 Lundehund breeders reduced the parental additive genetic relationship by 40–42% (48–53%). Immediate actions are needed to increase the genetic diversity in the current Lundehund population. The only option to secure the conservation of this rare breed is to introduce individuals from foreign breeds as breeding candidates.

The Faroese horse, an endangered indigenous horse breed, is a part of the cultural and societal heritage of the Faroe Islands. Population history describes a severe bottleneck, prompting for quantification of the genetic diversity (level of inbreeding, probability of gene origin, effective population size) and assessment of sustainable conservation potential (Optimum Contribution Selection, OCS) of the Faroese horse population. The pedigree completeness (PCI) of the Faroese horse is adequate for a realistic estimation of the level of inbreeding (PCI5 = 0.96). In concordance with the known population history, the average inbreeding is exceptionally high; in the last cohort, it was equal to 26.8%. An estimate of the effective population size, based on individual increase in inbreeding and coancestry, accounting for the whole population history, was eight. OCS offers a tool to understand and control the increase in the average relationships in the population. Within a fixed number of matings, the repetitive use of stallions resulted in the lowest level of average relationships. Successful follow-up of mating schemes planned together with a holistic assessment of the suitability of an individual as a breeding candidate, will minimize the increase in inbreeding in future generations and maximize the possibility to increase the census size of the Faroese horse population.