Mapping of quantitative trait loci for flesh colour and growth traits in Atlantic salmon (Salmo salar)

Abstract

Background: Flesh 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.

Methods: One 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.

Results: A 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.

Conclusions: A 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.

Figure 1

Pedigree of the mapping population. Founding generation (P) consisting of Bleke males (Bleke) and Aqua Gen females (AGen).

Figure 2

Colour frequency distribution. Frequency distribution of colour scores over the six F2 families.

Figure 3

Line-cross and half-sib interval mapping analysis for flesh colour on Chr 26. F-statistic profiles for Chr 26 for both line-cross and half-sib models for flesh colour; diamonds on the top axis represent marker positions; horizontal dashed lines represent genome-wide significance thresholds (P < 0.05) for both line-cross (blue) and half-sib (red) analyses.

Figure 4

Line-cross and half-sib interval mapping analysis for flesh colour on Chr 4. F-statistic profiles for Chr 4 for both line-cross and half-sib models for flesh colour; diamonds on the top axis represent marker positions; horizontal dashed lines represent genome-wide significance thresholds (P < 0.05) for both line-cross (blue) and half-sib (red) analyses.

Figure 5

Line-cross and half-sib interval mapping analysis for length and body weight on Chr 4. F-statistic profiles for Chr 4 for both line-cross and half-sib models for length and body weight; diamonds on the top axis represent marker positions; horizontal solid and dashed black lines represent the genome-wide significance thresholds (P < 0.05) for both line-cross and half-sib analyses, respectively.

Figure 6

Line-cross and half-sib interval mapping analysis for length and body weight on Chr 10. F-statistic profiles for Chr 10 for both line-cross and half-sib models for length and body weight; diamonds on the top axis represent marker positions; horizontal solid and dashed black lines represent the genome-wide significance thresholds (P < 0.05) for both line-cross and half-sib analyses, respectively.

Figure 7

Line-cross and half-sib interval mapping analysis for length, body weight and slaughter weight on Chr 5. F-statistic profiles for Chr 5 for both line-cross and half-sib models for length and body weight; diamonds on the top axis represent marker positions; horizontal solid and dashed black lines represent the line-cross genome-wide significance threshold (P < 0.05) and half-sib chromosome-wide significance threshold (P < 0.05), respectively.