Novel genotyping technology helps to breed farmed fish more resistant to Saprolegnia fungus
Technology created by the Natural Resources Institute Finland (Luke) enables the use of genomic selection for the first time in European whitefish. The genotyping procedure facilitates the development of healthier and more productive stocks and genomic analyses in many species.
Saprolegnia fungus occurs in natural waters and infects wild and farmed fishes alike. It causes serious economic losses at fish farms and reduces fish health, especially in freshwater growing conditions. Modern breeding programmes of farmed fish are based on genomic selection in which the genetic superiority of broodstock fish is estimated based on natural variation among individuals in thousands of DNA markers and phenotypic data on traits of interest.
"This has proven to be a powerful method for improving traits, including disease resistance," says Antti Kause, principal scientist at Luke.
For some farmed fishes such as rainbow trout and Atlantic salmon, ready-made DNA marker panels exist and can be used in genomic selection, but this is not the case for more novel farmed fish species such as European whitefish, Coregonus lavaretus L. This salmonid species is the second most important farmed fish species in Finland, and it suffers from Saprolegnia infections. Currently, there is no effective treatment to Saprolegnia, and genetic improvement of resistance is an appealing option.
Luke's solution to increase resistance
A genotyping method that is applicable across species and enables the use of genomic selection in European whitefish has been developed at Luke.
Researchers applied the method in European whitefish to identify naturally occurring DNA variation that is also linked to disease resistance. Altogether 65.000 DNA variants were found of which several thousands were used in the subsequent analysis to identify genetic variation that is available to improve whitefish's resistance to Saprolegnia.
Around 20-43% of the variation in disease resistance was determined by genetics, and in addition, a genome region was identified that has a major impact on resistance to Saprolegnia. The expected mortality of offspring from the resistant and susceptible broodstock fish can differ up to 47 %-point, a major difference that can be exploited by genomic selection to produce generations that are more resistance to Saprolegnia.
The developed DNA markers can be used to improve other production, quality, and fish health traits by selection. The work can be also used to develop a standardized analysis panel with thousands of DNA markers for routine use.
Luke runs a national selective breeding programme for European whitefish for the benefit of the sea food sector. Genetic improvement of disease resistance is in line with a goal to improve fish health, and to reduce the use of antibiotics.
Genotyping-by-sequencing methodology
- The genotyping and bioinformatics strategy used (genotyping-by-sequencing; GBS) is a general low-cost high-throughput tool that can be applied to most species.
- It is based on reliable resequencing of genome locations across individuals using modern genome sequencing.
- Its' strength is that no previous knowledge about the genome of the target species is needed. Hence it can be applied to a wide range of species that have not been studied before and for which no genomic analysis tools are available.
- GBS can also be used for DNA marker discovery, validation and screening, parentage and traceability analysis, gene-mapping, and population analyses.
- In addition to European whitefish, Luke has applied the developed methodology to study Arctic charr, brown trout, oat, tall fescue, timothy, raccoon dog, and black soldier fly.
- A general bioinformatics pipeline has been developed that is publicly available on-line.
- The analysis still requires expertise in modern genome sequencing methods, but the method makes genome analyses much more accessible for many species.
Funding
This work was conducted at Luke's Enonkoski farm and Jokioinen campus. The initial genome method design was done in 'GENOTYPE – General genotyping-by-sequencing pipeline, validated with European whitefish' -project funded by Luke. The method was refined and implemented in the project funded by EU's Cross-Border-Cooperation Programme 2014-2020, with a grant contract number 4/2018/095/KO4058 'ArctAqua - Cross-Border Innovations in Arctic Aquaculture’ project', and the Statutory Services of Natural Resources Institute Finland.
