First genome-wide association and genomic prediction of ammonia‑nitrogen tolerance in tiger pufferfish (Takifugu rubripes)

Abstract

Ammonia‑nitrogen stress is a significant threat to the growth and survival of tiger pufferfish (Takifugu rubripes), especially in high-density stocking integrated aquaculture systems. This study aimed to decipher the genetic background of ammonia‑nitrogen stress tolerance via heritability estimation and identification of variants associated with this stress via genome-wide association studies (GWAS). We also assessed the potential of applying genomic selection (GS) to improve this trait in T. rubripes. A customized a low-density 20 K SNP array was used to genotype 780 fish, and low-density genotypes were imputed to a high-density genotype dataset comprising over 1.3 million SNPs. The heritability of ammonia‑nitrogen tolerance was estimated as 0.20 and 0.15 and 0.21 for pedigree, low-density and high-density SNP markers panels, respectively. A suggestively significant quantitative trait locus (QTL) was detected on chromosome 8, containing 16 significant SNPs within a 70.0 kb region. Notably, two candidate genes, fgf11A and serinc5, were associated with ammonia‑nitrogen stress tolerance. Use of different genomic prediction models to estimate genetic merit of selection candidates showed improvement in accuracy of breeding value estimation by at least 57 % compared to traditional pedigree-based methods. Interestingly, the prediction remained significantly high even with the lowest number of panel markers (500 markers). These findings highlight the potential of GS to enhance ammonia‑nitrogen stress tolerance in T. rubripes breeding programs, thus contributing to the sustainability and productivity of the species.