Validation of a QTL for Flavobacterium psychrophilum resistance in rainbow trout Oncorhynchus mykiss

Rainbow trout (1000 fish) was exposed to the bacterial pathogen F. psychrophilum by simple bath challenge without any pre-treatment with hydrogen peroxide. Samples (fin clip for Affymetrix QTL analysis) were taken from 167 moribund fish during the course of infection. When mortality/morbidity ended (day 40) we euthanized a total of 197 specimens of the remaining fish and took samples for DNA (QTL analysis) and assigned the status: Survivor. For gene expression analysis we took samples from gill, spleen and liver between day 11 and 15 from fish with clinical signs (CS) and no clinical signs (NCS), whereas samples from survivors were taken at day 40. Rainbow trout (1000 fish) from an outbred batch were used for infection and additionally 1,000 fish were kept as non-infected controls (3.3 ± 0.75 g; 6.9 ± 0.5 cm). Samples for gene expression (gills, liver and spleen) were taken at three different time-points, at day 0 (before exposure), at day 11-14 (when the mortality rate peaked) and at day 40 (termination of experiment). At day 0, samples were taken from 15 uninfected control fish. At day 11 to 14 we sampled from 15 uninfected control fish, 15 infected fish showing clinical signs (CS) and 15 fish infected fish showing no clinical signs (NCS). The samples at day 40 was from 15 uninfected control and from 15 surviving rainbow trout. All samples were fixed in RNAlater (cat. no. R90901. Sigma-Aldrich, Denmark) and stored at 4°C for 24 h before being placed at -20°C until further analysis.