Abstract
BackgroundFlesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective. The aim of this study was to identify quantitative trait loci (QTL) affecting flesh colour and growth related traits in an F2 population derived from an isolated, landlocked wild population in Norway (Byglands Bleke) and a commercial production population.MethodsOne hundred and twenty-eight informative microsatellite loci distributed across all 29 linkage groups in Atlantic salmon were genotyped in individuals from four F2 families that were selected from the ends of the flesh colour distribution. Genotyping of 23 additional loci and two additional families was performed on a number of linkage groups harbouring putative QTL. QTL analysis was performed using a line-cross model assuming fixation of alternate QTL alleles and a half-sib model with no assumptions about the number and frequency of QTL alleles in the founder populations.ResultsA moderate to strong phenotypic correlation was found between colour, length and weight traits. In total, 13 genome-wide significant QTL were detected for all traits using the line-cross model, including three genome-wide significant QTL for flesh colour (Chr 6, Chr 26 and Chr 4). In addition, 32 suggestive QTL were detected (chromosome-wide P < 0.05). Using the half-sib model, six genome-wide significant QTL were detected for all traits, including two for flesh colour (Chr 26 and Chr 4) and 41 suggestive QTL were detected (chromosome-wide P < 0.05). Based on the half-sib analysis, these two genome-wide significant QTL for flesh colour explained 24% of the phenotypic variance for this trait.ConclusionsA large number of significant and suggestive QTL for flesh colour and growth traits were found in an F2 population of Atlantic salmon. Chr 26 and Chr 4 presented the strongest evidence for significant QTL affecting flesh colour, while Chr 10, Chr 5, and Chr 4 presented the strongest evidence for significant QTL affecting growth traits (length and weight). These QTL could be strong candidates for use in marker-assisted selection and provide a starting point for further characterisation of the genetic components underlying flesh colour and growth.
Highlights
Flesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective
Phenotypic data analysis Analysis of raw phenotypic data in the F2 population revealed that all traits exhibited substantial levels of phenotypic variation (Table 2), and strong phenotypic correlations were observed between numerous traits (Table 3)
Under the across family half-sib model, genome-wide significant quantitative trait loci (QTL) were identified for flesh colour on Chr 4, for body weight on Chr 4 and for length on Chr 10 and Chr 4 (Table 4)
Summary
Flesh colour and growth related traits in salmonids are both commercially important and of great interest from a physiological and evolutionary perspective. A dynamic model of carotenoid metabolism in salmonids, based on ordinary differential equations, has identified the uptake process of carotenoid over the muscle membrane as a potential important source of genetic variation [10]. Given that this model mimics the real situation, the existence of key regulatory sites could possibly suggest the presence of loci with relatively large effects. This does not necessarily mean that the trait will be regulated via polymorphisms with major effects within the genes encoding these sites
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