Genomic selection for selective breeding of tiger pufferfish (Takifugu rubripes) for integration with surrogate broodstock technology

Abstract

Aquacultural breeding and production of many commercially valuable fish species have been advanced by recent biotechnological breakthroughs and their integration. Here, we report our selective breeding program with the objectives of producing an elite all male population of the tiger pufferfish (Takifugu rubripes) that uses a combination of a genomic selection program and surrogate broodstock technology, a state-of-the-art form of reproductive engineering. In this species, the testis (shirako; marketable size >100 g) is regarded as a favored delicacy and has the highest price of the edible parts; by contrast, the ovary is poisonous. In 2016, we initiated a genomic selection program with the aim of generating the tiger pufferfish populations in which more than 80 % of the males have testes larger than marketable size in December, when the fish are approximately 20 months old and the price is at its highest. The selection program started with commercially farmed individuals (F₀ generation) with mean testes weight (TW) of 67.6 g. Two cycles of selective breeding were carried out using TW and standard length; selected individuals were crossed in a partial factorial manner without increasing genetic relatedness between parents. An increase in mean TW to 94.2 g was found in the F₁ generation and to 117.5 g in the F₂ generation. The proportion of individuals with a TW larger than 100 g increased from 34.0 % in the F₀ generation to 42.9 % in the F₁ generation and 61.7 % in the F₂ generation. The narrow sense heritability estimated from single nucleotide polymorphism (SNP) markers was still high for each trait (h² = 0.6–0.7) in the F2 generation. Large variations were observed in the values of both phenotypes and genomic estimated breeding values of the selected individuals of this generation. In addition, pedigree information reconstructed from the SNPs showed that F₂ individuals had similar genetic diversity to the F₀ generation. These results indicate that the selection scheme has been effective to date and that the selected population still has the potential for further genetic improvements in these traits. The revenue from the sale of testes could be doubled by production of all-male populations. The generation of such all-male populations can be facilitated through surrogate broodstock technology even for a species such as the tiger pufferfish in which conventional sex control techniques such as hormone administration do not work well.