Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus

Marion Sinclair-Waters, Nikolai Piavchenko, Annukka Ruokolainen, Tutku Aykanat, Jaakko Erkinaro, Craig Primmer

Research output: Contribution to journalArticleScientificpeer-review


Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.

Original languageEnglish
JournalMolecular Ecology
Issue number2
Pages (from-to)562-570
Number of pages9
Publication statusPublished - Jan 2022
MoE publication typeA1 Journal article-refereed

Fields of Science

  • 1181 Ecology, evolutionary biology
  • Atlantic salmon
  • candidate gene
  • genotype-phenotype association
  • maturation
  • vgll3
  • AGE

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