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Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar).

Gutierrez AP, Yáñez JM, Fukui S, Swift B, Davidson WS - PLoS ONE (2015)

Bottom Line: Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation.The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21.However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

ABSTRACT
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼ 480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.

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Results from GWAS for days to 5 kg.Horizontal dotted line represents the genome-wide significant threshold.
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pone.0119730.g001: Results from GWAS for days to 5 kg.Horizontal dotted line represents the genome-wide significant threshold.

Mentions: Only one marker (GCR_cBin15343_Ctg1_36) located on chromosome 13 (Ssa13) was found to be significantly associated (according to the empirical method) with growth (see Fig. 1), but only at the chromosome-wide level of significance (p < 2.55e-4 for Ssa13) according to the Bonferroni threshold. Marker GCR_cBin15343_Ctg1_36, localized in Ssa13 was assigned to the Atlantic salmon genome contig AGKD01005773 and annotation of this contig showed that the marker is located in a hypothetical protein in the vicinity of a membrane-associated guanylate kinase protein as shown in Table 1.


Genome-wide association study (GWAS) for growth rate and age at sexual maturation in Atlantic salmon (Salmo salar).

Gutierrez AP, Yáñez JM, Fukui S, Swift B, Davidson WS - PLoS ONE (2015)

Results from GWAS for days to 5 kg.Horizontal dotted line represents the genome-wide significant threshold.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4355585&req=5

pone.0119730.g001: Results from GWAS for days to 5 kg.Horizontal dotted line represents the genome-wide significant threshold.
Mentions: Only one marker (GCR_cBin15343_Ctg1_36) located on chromosome 13 (Ssa13) was found to be significantly associated (according to the empirical method) with growth (see Fig. 1), but only at the chromosome-wide level of significance (p < 2.55e-4 for Ssa13) according to the Bonferroni threshold. Marker GCR_cBin15343_Ctg1_36, localized in Ssa13 was assigned to the Atlantic salmon genome contig AGKD01005773 and annotation of this contig showed that the marker is located in a hypothetical protein in the vicinity of a membrane-associated guanylate kinase protein as shown in Table 1.

Bottom Line: Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation.The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21.However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.

ABSTRACT
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼ 480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.

Show MeSH