Limits...
Characterisation of a novel paralog of scavenger receptor class B member I (SCARB1) in Atlantic salmon (Salmo salar).

Sundvold H, Helgeland H, Baranski M, Omholt SW, Våge DI - BMC Genet. (2011)

Bottom Line: Red flesh colour is a unique trait found in some salmonid genera.A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon.A total of seven different SCARB1-2 alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Integrative Genetics, Dept. of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1432 Aas, Norway. Hilde.Sundvold@oslo-universitetssykehus.no

ABSTRACT

Background: Red flesh colour is a unique trait found in some salmonid genera. Carotenoid pigments are not synthesized de novo in the fish, but are provided by dietary uptake. A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon. In addition, from an evolutionary point of view, the establishment and maintenance of this trait is still poorly understood. It has been demonstrated in several species that scavenger receptor class B, member 1 (SCARB1) is involved in intestinal absorption of carotenoids, which makes this gene a possible source of genetic variation in salmonid flesh pigmentation.

Results: In this study, a novel paralog of SCARB1 (SCARB1-2) was detected through screening for genetic variation in Atlantic salmon SCARB1. Full length SCARB1-2 encodes a protein with 89% identity to Atlantic salmon SCARB1, except for the C-terminal cytoplasmic tail that shows only 12% identity. The most prominent site of SCARB1 mRNA expression was in the mid gut, while a five-fold lower level was detected in Atlantic salmon skeletal muscle and liver. The SCARB1-2 mRNA was equally expressed in liver, muscle and mid gut, and at a lower level than SCARB1 mRNA. A total of seven different SCARB1-2 alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population. We mapped the SCARB1-2 paralog to a region on Atlantic salmon chromosome 1, containing a putative QTL for flesh colour. Addition of the SCARB1-2 marker increased the significance of this QTL, however the large confidence interval surrounding the QTL precludes confirmation of SCARB1-2 as a causative gene underlying variation in this trait.

Conclusion: We have characterised a novel paralog of SCARB1 (SCARB1-2), have mapped it to Atlantic salmon chromosome 1 and have described its expression in various tissues. Mapping with SCARB1-2 alleles added further evidence for a QTL affecting flesh colour on this chromosome, however further studies are needed to confirm a functional role for this gene in flesh colour pigmentation.

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QTL analysis of Atlantic salmon chromosome 1. F-statistic profiles (blue lines) and QTL position bootstrap frequencies (red bars) for the male (A) and female (B) chromosome 1 linkage maps. Chromosome-wide significance thresholds are indicated by the horizontal broken lines. The position of SCARB1-2 is indicated by a black diamond on the upper x axis.
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Figure 3: QTL analysis of Atlantic salmon chromosome 1. F-statistic profiles (blue lines) and QTL position bootstrap frequencies (red bars) for the male (A) and female (B) chromosome 1 linkage maps. Chromosome-wide significance thresholds are indicated by the horizontal broken lines. The position of SCARB1-2 is indicated by a black diamond on the upper x axis.

Mentions: In the sire-based, across-family analysis, the QTL peak exceeded the chromosome-wide significance threshold (Figure 3), and the two parents M1 and M4 were found to be segregating for the QTL (table 3). In the dam-based across-family analysis, the overall F-value of 2.26 was not significant (Figure 3). However, parent F4 demonstrated strong evidence for QTL segregation, with an absolute t-value of 3.0, and significant QTL linkage was found when this parent was analysed individually (data not shown). In both sire and dam based analyses, the 95% confidence interval for the QTL position covered the entire linkage group, however the actual QTL peaks were 9 cM from SCARB1-2 in the male analysis and 2 cM from SCARB1-2 in the female analysis. After correction for an approximate selective genotyping fraction of 0.5 (averaged over families), the QTL explained 4.4% of the phenotypic variation for flesh colour. In family four, both parents appeared to be segregating for the QTL (table 4). The flesh colour averages for the different progeny genotypes (representing QQ, Qq and qq QTL allele combinations), indicated that the QTL alleles conferring redder flesh were inherited from both the Bleke and commercial founding parents in the two F1 parents.


Characterisation of a novel paralog of scavenger receptor class B member I (SCARB1) in Atlantic salmon (Salmo salar).

Sundvold H, Helgeland H, Baranski M, Omholt SW, Våge DI - BMC Genet. (2011)

QTL analysis of Atlantic salmon chromosome 1. F-statistic profiles (blue lines) and QTL position bootstrap frequencies (red bars) for the male (A) and female (B) chromosome 1 linkage maps. Chromosome-wide significance thresholds are indicated by the horizontal broken lines. The position of SCARB1-2 is indicated by a black diamond on the upper x axis.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3118963&req=5

Figure 3: QTL analysis of Atlantic salmon chromosome 1. F-statistic profiles (blue lines) and QTL position bootstrap frequencies (red bars) for the male (A) and female (B) chromosome 1 linkage maps. Chromosome-wide significance thresholds are indicated by the horizontal broken lines. The position of SCARB1-2 is indicated by a black diamond on the upper x axis.
Mentions: In the sire-based, across-family analysis, the QTL peak exceeded the chromosome-wide significance threshold (Figure 3), and the two parents M1 and M4 were found to be segregating for the QTL (table 3). In the dam-based across-family analysis, the overall F-value of 2.26 was not significant (Figure 3). However, parent F4 demonstrated strong evidence for QTL segregation, with an absolute t-value of 3.0, and significant QTL linkage was found when this parent was analysed individually (data not shown). In both sire and dam based analyses, the 95% confidence interval for the QTL position covered the entire linkage group, however the actual QTL peaks were 9 cM from SCARB1-2 in the male analysis and 2 cM from SCARB1-2 in the female analysis. After correction for an approximate selective genotyping fraction of 0.5 (averaged over families), the QTL explained 4.4% of the phenotypic variation for flesh colour. In family four, both parents appeared to be segregating for the QTL (table 4). The flesh colour averages for the different progeny genotypes (representing QQ, Qq and qq QTL allele combinations), indicated that the QTL alleles conferring redder flesh were inherited from both the Bleke and commercial founding parents in the two F1 parents.

Bottom Line: Red flesh colour is a unique trait found in some salmonid genera.A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon.A total of seven different SCARB1-2 alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centre for Integrative Genetics, Dept. of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1432 Aas, Norway. Hilde.Sundvold@oslo-universitetssykehus.no

ABSTRACT

Background: Red flesh colour is a unique trait found in some salmonid genera. Carotenoid pigments are not synthesized de novo in the fish, but are provided by dietary uptake. A better understanding of the molecular mechanisms underlying the cellular uptake and deposition of carotenoids could potentially be used to improve the low muscle deposition rate that is typically found in farmed Atlantic salmon. In addition, from an evolutionary point of view, the establishment and maintenance of this trait is still poorly understood. It has been demonstrated in several species that scavenger receptor class B, member 1 (SCARB1) is involved in intestinal absorption of carotenoids, which makes this gene a possible source of genetic variation in salmonid flesh pigmentation.

Results: In this study, a novel paralog of SCARB1 (SCARB1-2) was detected through screening for genetic variation in Atlantic salmon SCARB1. Full length SCARB1-2 encodes a protein with 89% identity to Atlantic salmon SCARB1, except for the C-terminal cytoplasmic tail that shows only 12% identity. The most prominent site of SCARB1 mRNA expression was in the mid gut, while a five-fold lower level was detected in Atlantic salmon skeletal muscle and liver. The SCARB1-2 mRNA was equally expressed in liver, muscle and mid gut, and at a lower level than SCARB1 mRNA. A total of seven different SCARB1-2 alleles comprising repetitive enhancer of zeste motifs (EZH2) were identified in the founding parents of a resource Atlantic salmon population. We mapped the SCARB1-2 paralog to a region on Atlantic salmon chromosome 1, containing a putative QTL for flesh colour. Addition of the SCARB1-2 marker increased the significance of this QTL, however the large confidence interval surrounding the QTL precludes confirmation of SCARB1-2 as a causative gene underlying variation in this trait.

Conclusion: We have characterised a novel paralog of SCARB1 (SCARB1-2), have mapped it to Atlantic salmon chromosome 1 and have described its expression in various tissues. Mapping with SCARB1-2 alleles added further evidence for a QTL affecting flesh colour on this chromosome, however further studies are needed to confirm a functional role for this gene in flesh colour pigmentation.

Show MeSH