Atlantic salmon - determining run timing proportions: report

SNP marker choice

The study of Cauwelier et al. (2018) identified SNP markers linked to run timing using a Genome Wide Association Study (GWAS), which used mixed modelling to identify significant marker trait associations. Association probabilities, together with SNP chromosome positions, were plotted and chromosome regions associated with the trait identified in this way. A single position on chromosome Ssa09 was identified as significantly associated with run timing and, within this chromosome, two sub-peaks were observed. Together with these associations, a further SNP marker was significantly linked to the trait but its chromosome position remains unknown. There was also some evidence of a second region of interest on chromosome Ssa14; however, after correction for multiple tests, the association of this region to run timing was no longer significant.

Development of the SNP screening tool was based around the Flex Six^TM integrated fluidic circuit (IFC) array, run on the Standard Biotools EP1 SNP genotyping platform (Standard Biotools, San Francisco, CA, USA). This flexible IFC includes provision for the simultaneous running of twelve SNP markers against 72 fish samples, giving a total of 864 genotypes in a single run. Twelve SNP markers were therefore chosen to form a run timing panel to be run using this system.

The rationale for the SNP choice was based around the peaks previously identified as being associated with run timing, whilst trying to avoid duplication of data due to the inclusion of tightly linked SNPs, which would give no extra information (i.e. there would be no point including all the SNPs of interest on chromosome Ssa09, as they are tightly linked and so will act as a single entity giving redundant information).

The first SNP, AX-87609372, was the top ranked in both the GWAS and selection analysis carried out by Cauwelier et al. (2018). Three more SNPs were also chosen, comprising the top ranked SNPs within both peaks on Ssa09 and the suggestive peak on Ssa014. To provide back-up in case of non-amplification of one or more of these SNPs, the second ranked SNP from each of these three peaks were also included. Finally, the remaining five SNPs were the highest ranked SNP from the GWAS analysis from chromosomes other than Ssa09 or Ssa14. The list and rationale of the SNPs in the panel is outlined in Table 1.