Genetic Mapping of Quantitative Trait Loci (QTL) for Body Weight in Atlantic Salmon (Salmo salar)

We examined five families from the Mainstream Canada Atlantic salmon broodstock program, to identify QTL associated with body weight at four time points during the production cycle. The parents and 45-65 progeny from each family were genotyped using a relatively dense 6.5K SNP chip array developed by the Centre for Integrative Genetics (CIGENE). Uninformative markers were removed from each family dataset and approximately 2500 informative markers were found per family. Male and female linkage maps were adjusted according to a recently developed map described by Lien et al, (BMC Genomics 2011) that is based on the same SNP chip. QTL analysis was carried out using GridQTL software utilizing the Sib-Pair model to take advantage of the full-sib nature of the families and half-sib analyses to identify alleles from dams or sires segregating at a QTL. Significance thresholds to assess QTL effect were obtained from a 10000 permutation test. We identified genome wide significant QTL (p<0.05) on Ssa02, Ssa07, Ssa09, Ssa13, Ssa17 and Ssa26, but also several chromosomes which contain significant (p<0.01) and suggestive QTL (p<0.05) associated with body weight, and some of them have previously been identified as being associated with body weight QTL in Atlantic salmon. Our findings provide useful evidence of QTL associated with body weight traits. These QTL should be valuable candidates for use in the Mainstream Canada marker-assisted selection breeding program. Moreover, it is an important step towards the identification of genes and the understanding of the genetic components underlying growth and body weight in Atlantic salmon.