Detection of QTL affecting flesh quality traits (body lipid percentage and flesh colour) using molecular markers (microsatellites and AFLP markers) in Atlantic salmon (Salmo salar L.)

Abstract

Flesh colour and fillet fat percentage are the two most important attributes to salmon fillet quality. A medium genetic component to body lipid percentage within commercial lines has previously been shown (h2 = 0.17-0.24). A low level of heritability (h2 = 0.16) has also been reported for flesh colour in Atlantic salmon. To investigate whether this genetic component includes loci of major effect, a genome-wide QTL scan was performed with commercially bred Atlantic salmon (Landcatch Natural Selection). Five large full-sib families (10 parents with 153 offspring) were genotyped using microsatellite markers. To utilize the large difference between sire and dam recombination rate, a two-stage genotyping was employed. Initially, the parents and offspring were genotyped for two microsatellite markers per linkage group, and sire based QTL analysis was used to detect linkage groups with significant effects on those flesh quality traits. A linear-regression based interval as analytical method was applied for QTL detection. The results revealed evidence of QTLs affecting percentage fat percentage and flesh colour on linkage groups LNS16 and LNS1 respectively. To confirm the QTL and to provide an improved estimate of position, a dam-based analysis was then employed. One major QTL was located on the genome-wide significance level for percentage fat percentage. Microsatellite marker Ssa0016NVH (at position of 1.3 cM) was found to be tightly linked to QTL affecting percentage fat percentage. In addition, a QTL affecting flesh colour was found to be flanked by microsatellite markers Ssa9.44NUIG at position of 68.7 cM and Ssa0021NVH at position of 50.6 on linkage group LNS16. The evidence for suggestive QTL affecting flesh colour on linkage group LNS1 was also revealed. In order to increase marker density within these and other linkage groups, AFLP markers were employed, 24 primer combinations resulted in a total of 489 polymorphic fragments. Among 11 fragments that were found to be linked to the microsatellite markers on linkage group LNS16, four fragments (AAG-CAC328, AGG-CAG447, AGG-CTA237 and AGG-CTC237) were tightly linked to microsatellite marker Ssa9.44NUIG, but none were found to be linked to microsatellite Ssa0021NVH. Moreover, none of the AFLP markers were found to be linked to microsatellites residing on linkage group LNS1. Using a constructed map of microsatellite and AFLP markers for linkage group LNS16, the dam based analysis revealed a significant QTL for flesh colour at the location of 189 cM, while the sire based analysis detected a significant QTL for fat percentage at the location of 80 cM. Considering the dominant nature and clustering character of AFLP markers, it was concluded that a certain primer combination in AFLP markers could be of limited use for fine mapping and QTL detection in Atlantic salmon.