Heritability and predictive ability for the heterobothriosis resistance and growth performance in the tiger pufferfish Takifugu rubripes fed standard or low fishmeal diets

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Heterobothriosis resistance and high growth performance are major concerns in the tiger pufferfish (Takifugu rubripes) farming. Our previous small-scale study suggested the feasibility of genomic selection (GS) for these traits but also identified an undesired genetic correlation between them, which could hamper simultaneous genetic improvement. Here, we sought to validate these initial findings through larger samples and crosses and also explore the potential of GS for the individuals fed a normal fishmeal diet and a low fishmeal (LFM) diet. We produced three populations: one was fed a normal diet (PopFM: 1100 individuals) and two were fed an LFM diet (PopLFM1: 993 individuals; PopLFM2: 1017 individuals); all three populations were artificially infected with Heterobothrium okamotoi, a monogenean parasite causing heterobothriosis. We recorded standard lengths of the fish after artificial infection (SLEAI) and the number of parasites on the gill cavity wall (HC) and genotyped genome-wide single nucleotide polymorphisms (SNPs) using genotyping by random amplicon sequencing, direct (GRAS-Di) technology for each sample: PopFM, 12 K SNPs; PopLFM1, 19 K SNPs; PopLFM2, 21 K SNPs. Heritability and prediction ability for each trait were estimated for each population using genomic best linear unbiased prediction (GBLUP), Bayes C, and Bayesian ridge regression methods. SNP effects on each trait were estimated by Bayes C, Bayesian ridge regression, and genome-wide association analyses (GWAS) using the same data sets. We observed moderate to high levels of heritability for HC (0.16–0.57) and SLEAI (0.50–0.77), with predictive ability of 0.25–0.55 for HC and of 0.51–0.73 for SLEAI. These values were slightly larger in LFM diet groups. As reported previously, a weak undesired genetic correlation was observed between the traits, and the correlation was more pronounced in the LFM groups. In conclusion, our results indicate that genetic gain in growth and parasite resistance traits can be expected for the tiger pufferfish through GS, especially for individuals reared on an LFM diet. However, close attention should be paid to the extent of the undesirable genetic correlation between the two traits that may be amplified in the populations fed an LFM diet.