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. 2019 Feb 15;20(1):139.
doi: 10.1186/s12864-019-5525-4.

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon

Amin R Mohamed  1   2 , Klara L Verbyla  3 , Hawlader A Al-Mamun  3 , Sean McWilliam  1 , Bradley Evans  4 , Harry King  5 , Peter Kube  5 , James W Kijas  6
Affiliations

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon

Amin R Mohamed et al. BMC Genomics. .

Abstract

Background: A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts.

Results: We report genome wide association studies (GWAS) using fish measured for sexual maturation in freshwater or the marine environment. Genotypic data from a custom 50 K single nucleotide polymorphism (SNP) array was used to identify 13 significantly associated SNP for freshwater maturation with the most strongly associated on chromosomes 10 and 11. A higher number of associations (48) were detected for marine maturation, and the two peak loci were found to be the same for both traits. The number and broad distribution of GWAS hits confirmed a highly polygenetic nature, and GWAS performed separately within males and females revealed sex specific genetic behaviour for loci co-located with positional candidate genes phosphatidylinositol-binding clathrin assembly protein-like (picalm) and membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (magi2).

Conclusions: The results extend earlier work and have implications for future applied breeding strategies to delay maturation in this important aquaculture species.

Keywords: Atlantic salmon (Salmo salar); GWAS; Genetic architecture; Picalm; SNP; Sexual maturation.

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Conflict of interest statement

Ethics approval and consent to participate

All animals used in this study were part of the commercial operations of Tassal Operations and Salmon Enterprises of Tasmania. Their use was in accordance with authorised management practises of both companies and compliant with the Tasmanian Animal Welfare Act (1993) which is under the jurisdiction of Biosecurity Tasmania, Department of Primary Industries, Parks, Water and Environment. Under this Act, those animals that are expressly killed for purposes other than research, such as abattoir specimens, do not need specific approval of an Animal Ethics Committee and that was the case for this study.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Relationship of sex and weight for two maturation traits. The observed proportions of mature and immature fish are shown for each sex and trait (a). The distribution of weight is shown separately as a function of both sex and maturation status for freshwater (b) and marine maturation (c)
Fig. 2
Fig. 2
GWAS for two maturation traits in Atlantic salmon. SNP associations with freshwater (FMAT, a) and marine maturation (MMAT, b) are shown in genomic order for a karyotype consisting of 29 autosomes. The strength of association is given as the –Log10(p-value) and the horizontal lines represents the genome wide (red) or chromosome wide (blue line) significance thresholds. Expression levels from 45,531 genes was used to cluster a set of eight Atlantic salmon tissues. This was compared with heat maps of tissue-specific expression observed using positional candidate genes obtained from GWAS for FMAT (d) and MMAT (e). The values used are the log2 transformed fragment per kilobase million estimates (refer to the materials and methods)
Fig. 3
Fig. 3
GWAS for freshwater maturation traits conducted separately within females (a) and males (b). As for Fig. 2, SNP associations are represented as–Log10(p-values) and positional genes obtained from GWAS were used to examine the relationship between eight tissues based on gene expression (c)
Fig. 4
Fig. 4
GWAS for marine maturation traits conducted separately within females (a) and males (b). SNP associations are represented as –Log10(p-values) and positional genes obtained from GWAS were used to examine the relationship between eight tissues based on gene expression (c)
See this image and copyright information in PMC

References

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