Comparative analysis of genetic diversity in rainbow trout (Oncorhynchus mykiss) populations from Denmark and Finland using SNP data

Summary

Rainbow trout (Oncorhynchus mykiss) is a key species in European aquaculture, and the most dominant species in aquaculture production in Denmark, where it accounts for over 70% of total aquaculture production. Despite its economic importance, the precise origins of many European strains remain poorly characterized. This study evaluated the genetic diversity of two Danish farmed subpopulations – 76 conventional (DK-CONV) individuals and 116 organic (DK-ORG) individuals – and compared them with 2952 individuals from the Finnish national breeding program (FI-BP). We analyzed population structure, heterozygosity, inbreeding coefficient, runs of homozygosity (ROH) and inbreeding rates using SNP data. Samples were genotyped on the 57 K Axiom™ Trout Genotyping Array, with 32,162 SNPs remaining after quality control. Principal component analysis (PCA) and Wright's F statistic (FST) revealed substantial genetic differentiation between the Danish and Finnish populations (FST ~ 0.25) and low differentiation between the Danish subpopulations (FST = 0.0254), indicating historical or more recent gene flow between the two Danish subpopulations. All groups exhibited a slight heterozygosity deficit and positive FIS values, with the DK-CONV subpopulation showing the highest FIS. The ROH analysis showed longer and more frequent homozygous segments in the Danish subpopulations, indicating more recent inbreeding compared to FI-BP. ROH based inbreeding rates (ΔFROH) were below 1% per generation in DK-ORG and FI-BP. The results of this study demonstrate that sufficient genetic diversity exists within Danish rainbow trout subpopulations to support a sustainable organic breeding program. Enhanced inbreeding management is recommended, such as incorporation of pedigree records or genomic information, to ensure long-term genetic diversity.