Selective breeding programmes of rainbow trout and European whitefish (Coregonus lavaretus L.)

Luke maintains and develops breeding programmes for farmed rainbow trout and European whitefish (Coregonus lavaretus). The goal of the breeding programmes is more environmentally friendly, ethical and profitable aquaculture that can produce high quality products for consumers. Over 15 production, quality and fish health traits are recorded from individually tagged fish. Co-operation between breeding programme developer and fish farmers has made the programmes internationally competitive.

1) Breeding value estimation

The programmes deploy the latest computational breeding and genomics methods. The genetic superiority of broodstock fish is estimated using trait records, pedigree and DNA variation from hundreds of thousands of individually tagged fish (Kudinov et al. 2024; https://doi.org/10.1016/j.aquaculture.2024.740677). Breeding values are estimated using MiX99 software that is capable of analysing large data sets from breeding programmes (https://www.luke.fi/mix99). The software is developed by Luke, and it is used globally in over 15 countries in livestock and plant breeding programmes. Luke's fish breeding programmes use genomic selection in which the genetic potential of broodstock fish is estimated based on natural variation among individuals in thousands of DNA markers. Genomic selection is more accurate than traditional pedigree-based breeding, and is especially suitable for the improvement of product quality, processing traits and disease resistance (Calboli et al. 2023; https://doi.org/10.1093/jas/skad333).

Genetic improvement of traits is effective in aquaculture breeding programmes. It has been estimated that growth at sea has been improved by 5-6.7% per generation, and feed conversion ratio by 1.7% per generation (Kause et al. 2022; https://doi.org/10.1093/jas/skac214). Selection is carried out every year and improved by R&D activity, leading to compound interest-type of impact in a long term. Continuous research and development work on trait phenotyping, selection tools and genomics is used to upgrade the breeding programmes fulfilling customer needs.

2) Selection lines

The base population of the rainbow trout programme was established in 1989-90 by combining four superior strains, and the first individually tagged family-based generation was established in 1992. Over ten generations of selection have been practiced so far. Rainbow trout has two selection lines. Growth-line is more suitable for simultaneous production of fillet and caviar. Late maturity-line is more suitable for production of immature fish with high quality fillet.

For European whitefish, the base population was established in 1999 from the best performing strain, and the first family-based generation was established in 2004.

In both species, families are initially incubated separately and reared in family tanks, and once the fingerlings are large enough to be individually tagged, all families are pooled into a single large stock.

3) Selection indices

Breeding programmes of both rainbow trout and European whitefish are based on individually tagged fish with decades long pedigrees. The fish are recorded and selected for traits that improve resource efficiency and animal welfare and reduce environmental footprint in a balanced way. Using a selection index, multiple traits are combined into a single index based on which the best fish can be selected and used to make the next generation. In rainbow trout growth-line, rapid growth is emphasised more, whereas in Delayed maturity-line, late maturity is emphasized more.

Selection index weightings in rainbow trout and Eur whitefish:

Trait group Rainbow trout Eur whitefish

Production (growth, maturity age) 73.3 % 32.5 %

Quality (carcass%, lipid%, body shape, appearance) 16.5 % 45.5 %

Fish health (survival, deformations, cataract) 10.3 % 22.0 %

4) Protection of genetically improved fish material

The breeding programmes aim at increasing the productivity of its clients, but simultaneously at protecting its genetically unique fish material from being misused by other broodstock owners.

To provide fish for farmers and multipliers, the breeding programme utilises a method to produce large numbers of eggs and fingerlings with a very narrow genetic background which prevents the establishment of new broodstock populations. Simultaneously, the method results in more homogeneous stock of production fish, and enables the customisation of fish batches.

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Selective breeding programmes are a part of the EU-funded Research Infrastructure project 'AquaServ - Research services for sustainable aquaculture, fisheries and blue economy', through which Luke's infrastructure is available for international researchers and developers (https://www.luke.fi/en/projects/aquaserv; aquaserv.eu).