Atlantic salmon - determining run timing proportions: report

Executive summary

While Atlantic salmon (Salmo salar L.) spawn in late autumn/early winter, their return migration to freshwater from the sea can occur at any time during the year. The diversity in the run timing of Atlantic salmon (defined as the time of return of adults to rivers from the sea) is of great significance to fisheries, as it results in fresh-run fish being spread out through the year, increasing the temporal extent of the catching period. In order to maintain the wide diversity observed in salmon fisheries, it is important to maintain the diversity of the populations that underpin them.

Recently, a number of genetic markers associated with run timing were identified which raised the possibility of developing these into a panel that could be used to screen juvenile salmon and characterise stocks according to their run timing composition. Here, we describe the development and calibration of a panel of genetic markers that could be used as a cost-effective tool to determine run timing proportions in juvenile Atlantic salmon.

The rationale for the Single Nucleotide Polymorphism (SNP) choice was based around the three peaks previously identified as being associated with run timing. For each of these peaks, the two top ranked SNPs were selected, to provide back-up in case of failing of one of these SNPs. To this, the six highest ranked SNPs outwith the peaks were included, resulting in a panel of twelve markers.

In order to determine the effectiveness of the new twelve SNP panel, its ability to identify the different run components was calculated and compared to a panel consisting of the top nine ranked SNPs previously described. Adult fish of known return timing were used as reference individuals and combined across rivers to create two run timing groups (early v late). Individual assignment of each test fish to the run timing groups was then carried out and the probability of running early was plotted against Julian return day.

Although the shape of the relationships between Julian day and the probability of being an early running fish were similar in the two SNP panels, the strength of the relationship was seen to be higher in the twelve SNP panel, as the probabilities were higher across all return times compared to the nine SNP panel. The 12 SNP panel has shown it is capable of quantifying the heritable variation in run timing and, as such, provides a tool for screening of juvenile salmon within rivers in order to determine return time distributions.