Genetic Parameters and Sex‐Specific Architecture of Observed and Latent Fertility Phenotypes in a Closed Breeding Nucleus of an Arctic Salmonid

Successful reproduction is a key factor for efficient breeding schemes and sustainable animal farming. Aquaculture breeding programs rely heavily on small fractions of selected breeders to yield large production stocks, given the high fecundity typically observed in these species. In Sweden, Arctic charr (Salvelinus alpinus) is a salmonid with notable commercial potential, with a selective breeding program operating for 10 generations under a growth-rate focused breeding goal. Despite significant gains, the nucleus faces challenges with low and fluctuating fertility impeding expansion efforts. In this study, we estimate genetic parameters for charr milt quality phenotypes measured with specialised cytometry and Computer-Assisted Sperm Analysis (CASA). At the same time, we assess the sex-specific architecture governing egg count and sperm concentration along body size. Finally, we propose a novel analytical framework for the analysis of realised fertilisation success rates by considering a multiplicative system of latent maternal and paternal contributions. Low to moderate heritability estimates and genetic correlations were obtained from multi-trait modelling for traits reflecting sperm quality along with high estimates for fork length. Genetic correlations among sperm kinematic parameters appeared strong, while the same traits showed weak positive and weak negative correlations with sperm concentration and fork length, respectively. Furthermore, a negative genetic correlation between sperm concentration and both male body size and egg count suggests a complex interplay of a possible trade-off and sexual antagonism. Our latent fertility analytical approach returned low to moderate heritability estimates depending on the modelling configuration. Overall, our study demonstrated the complexity characterising the heritable portions of reproductive traits in Arctic charr and tested alternative tools that have the potential for integration into selective breeding programs.