Cost-efficient analysis helps breed disease-resistant fish

Genetic technique makes breeding healthy animals more accessible to small and medium-scale fish farming producers.

Source: Roslin Institute
October 5, 2023

A cost-effective method for breeding rainbow trout to be resistant to a common bacterial infection has been developed by scientists from the Roslin Institute, in collaboration with the Natural Resources Institute of Finland. Researchers applied a novel analysis strategy, based on a relatively small number of variations within DNA, to rainbow trout. This enabled the team to identify fish that are naturally resistant to the disease and guide breeding for healthier animals.

The team found that their approach using a relatively low number of variations, or genome markers, was as reliable as outcomes based on large sets of markers. Sidestepping the financial burden of obtaining large sets of markers allows breeders to adopt a cost-effective, yet equally feasible, route to leverage genomic selection for breeding, making it more accessible to small fish producers.

This approach could be extended to target other desirable traits, such as growth rate, resistance to other diseases or tolerance to environmental changes, presenting an avenue for comprehensive, accelerated trait improvement in farmed fish species, the team suggests.

Accessible genomics

Researchers focused their study on resistance to a bacteria that causes columnaris, a disease affecting farmed rainbow trout. Their findings could help alleviate growing concern over the infection, as rising environmental temperatures linked to global warming provide a favorable environment for its proliferation.

Findings from the study suggest that analyzing 300 genetic variants combined with computer modeling was as effective as using up to 28,000 genetic variants, with significantly lower costs.

“Analysing smaller sets of markers could be cheaper than applying more complex genomic selection methods, and more effective than traditional selective breeding without the use of technology. The cost-effective method we tested presents an avenue for comprehensive, accelerated trait improvement in aquaculture,” said Clemence Fraslin, Postdoctoral Research Fellow, Roslin Institute.

The research was carried out in collaboration with commercial partner Benchmark Genetics and funded by the European Union’s Horizon 2020 research and innovation program.


Fraslin, C., Robledo, D., Kause, A. et al. Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss). Genet Sel Evol 55, 59 (2023).