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

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


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.

MeSH terms

  • Animals
  • Base Sequence
  • Breeding
  • Databases, Genetic
  • Female
  • Fisheries*
  • Fresh Water
  • Gene Expression
  • Gene Frequency
  • Genetic Variation
  • Genome-Wide Association Study
  • Genotype
  • Guanylate Kinases / genetics
  • Male
  • Monomeric Clathrin Assembly Proteins / genetics
  • Multifactorial Inheritance*
  • Polymorphism, Single Nucleotide
  • Salmo salar / genetics*
  • Seawater
  • Sex Factors
  • Sexual Maturation / genetics*
  • Sexual Maturation / physiology*
  • Tasmania
  • Whole Genome Sequencing


  • Monomeric Clathrin Assembly Proteins
  • Guanylate Kinases