2.2 Genotyping
In total, n =2,582 brown trout were genotyped for the present study. Genomic DNA was extracted from c. 50 mg muscle tissue using DNeasy Blood & Tissue Kit (Qiagen) according to the manufacturer’s instructions and eluted in 100 μl elution buffer. DNA quality was assessed by electrophoresing an aliquot through a 1% agarose gel and subjectively assessing the proportion of high-molecular weight DNA relative to degraded DNA. Double-stranded DNA was quantified using a Qubit fluorometer (ThermoScientific) and normalised to 30–50 ng/μl.
Genotyping was carried out using an EP1TM 96.96 Dynamic array IFCs genotyping platform (Fluidigm) comprising 96 SNPs. Our present 96 SNPs were selected from 3,782 SNPs variable in Danish brown trout (Bekkevold et al., 2019). The 96 SNPs are distributed across the genome, with 1-3 SNPs on each of the 40 chromosomes (Saha et al., 2021).