Genetics explains seasonal dynamics in sperm quality of farmed Arctic charr

Short summary

In aquaculture, timing is critical, especially when it comes to fish reproduction. For Arctic charr, a cold-water salmonid farmed in northern latitudes, sperm quality is not constant within and throughout the reproductive period. Instead, it can fluctuate substantially. We worked on uncovering how genetics is involved in these changes, revealing that some fish are better than others at producing high-quality sperm at the right time. Understanding these genetic effects can help improve breeding success and support more sustainable aquaculture practices.

How do we define a fertile male?

To define a fertile male, we assess several key aspects of sperm quality. This includes measuring progressive motility (how many sperm cells are actively swimming forward) as well as the swimming speed of those cells and the sperm concentration in the sample. One of the most important indicators is the proportion of highly motile sperm cells directly related to a male’s reproductive potential. Progressive sperm motility is a key parameter commonly used to assess male fertility in livestock and aquaculture species. This is typically measured using an automated system called computer-assisted semen analysis (CASA). Generally, males with sperm motility above 80% are considered highly fertile.

Arctic charr typically spawn from early October to November (natural spawning), but on farms, spawning can be delayed until December through photoperiod manipulation (delayed spawning). To understand how fertility changes over time, we evaluated sperm quality from the same male at three points during the spawning season (early, mid-season, and late season) under both natural and delayed conditions. This approach allowed us to track changes in sperm performance within individual males, providing valuable insights into seasonal patterns of fertility.

How genomic tools uncover patterns in seasonal fertility changes

Powerful tools like next-generation sequencing (NGS) are used to uncover the genetic effects on fertility. This can include partial genome sequencing, such as double digest restriction site-associated DNA sequencing (ddRAD-seq), or full-scale methods like whole-genome sequencing (WGS). These technologies allow us to scan either targeted parts of the genome or the entire DNA sequence, in order to find genetic markers linked to a trait of interest. By examining differences in allele frequencies between test and control groups, we can identify the most genetically differentiated regions of the genome. These regions act like genomic "hotspots," highlighting candidate genes linked to sperm features and overall fertility.

In our study, we focused on two groups of Arctic charr males: one with variable sperm quality throughout the spawning season, and another with consistently high-quality sperm across the entire period. To explore the genetic differences between these groups, we used ddRAD sequencing for 92 males and whole-genome sequencing (WGS) for 16 males. 

Genomics explains patterns in sperm quality variability in Arctic charr

We found that males kept under similar environmental conditions (rearing tanks, water quality, feeding regime) performed differently in terms of fertility. In particular, 29% and 42% of males from the natural and delayed spawning groups, respectively, had a highly variable progressive motility.

By analyzing differences in allele frequencies across the genome, we used a method called an F_ST scan to measure genetic differentiation between males with consistently good vs. highly variable sperm motility. This approach allowed us to identify specific genomic regions across eight chromosomes that may be linked to variable fertility throughout the spawning season. Near these regions, we found 16 genes known to be involved in key sperm quality functions in mammalian species.

These results provide a detailed view of seasonal and genetic effects on sperm quality and can be used to guide decisions on broodstock selection and hatchery management.

Link to the publication

Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus) (2023)

Authors: Khrystyna Kurta, Henrik Jeuthe, Rakan Naboulsi, Dirk-Jan de Koning & Christos Palaiokostas