# GWAS on early sexual maturation across freshwater and seawater environments in domesticated Lochy strain of Atlantic salmon

## TL;DR

This study identifies genetic markers linked to early sexual maturation in Atlantic salmon, which could help improve breeding strategies in farming.

## Contribution

The study reports GWAS results for early maturation in the Lochy strain of Atlantic salmon across freshwater and seawater environments.

## Key findings

- Genomic heritability of early maturation was high in both seawater and freshwater environments.
- Significant SNPs associated with early maturation were identified on specific chromosomes in both environments.
- Candidate genes chmp2b and vgll3 were linked to early maturation and show convergence with other domesticated populations.

## Abstract

Early sexual maturation is a challenging obstacle to overcome in Atlantic salmon farming. This trait primarily affects males and occurs in both freshwater fish farms and sea culture cages during the fattening phase. Current strategies for preventing early maturation include a combination of genetic selection and management practices. However, the genetic architecture of early maturation appears to vary across populations, strains and environments. Our study aimed to elucidate the genetic architecture of early maturation in the Lochy strain of Atlantic salmon using genome-wide SNP panels. This European-origin strain grows rapidly but is prone to high rates of precocious male maturation if not properly managed.

We report two genome-wide association (GWAS) results focusing on males of the Lochy strain of Atlantic salmon. The first included seawater-cultured fish (Group-SA: 714 males, 80 precocious and 634 immature) with an artificial continuous light photoperiod, while the second included freshwater-cultured fish (Group-FN: 707 males, 333 precocious and 374 immature) with a natural photoperiod. Group-SA was genotyped using a custom 46,115-SNP Illumina microarray, whereas Group-FN employed a custom 62,044-SNP Thermo microarray. Genomic heritability of early maturation in males was consistently high across models—ranging from 0.62–0.79 in seawater and from 0.54–0.62 in freshwater. In Group-SA, one significant SNP associated with early sexual maturation were identified on chromosome Ssa25. In Group-FN, sixty significant SNPs associated with early sexual maturation were identified on chromosomes Ssa5, Ssa7, and Ssa25. The genetic variance explained by these SNPs ranged from 16.1–53.7%, while the proportion of phenotypic variance explained varied from 8.7% to 29.1%. The identified candidate genes included chmp2b and vgll3, both previously reported in other domesticated European-origin populations, suggesting some degree of convergence.

The SNPs associated with early maturation are promising candidates for application in breeding programs in the Lochy strain aimed at implementing improved control strategies against early maturation in both freshwater and sea environments.

The online version contains supplementary material available at 10.1186/s12711-025-01026-5.