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Sex-Associated SNP Confirmation of Sex-Reversed Male Farmed Japanese Flounder Paralichthys olivaceus

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Abstract

Female Japanese flounder Paralichthys olivaceus grow more rapidly than the male. The goal of all-female commercial production requires an efficient method of genetic sex identification. We conducted genome-wide association analysis of female and male farmed Japanese flounder (n = 24 per phenotypic sex) and found all regions of chromosome 24 to be significantly associated with phenotypic sex, suggesting it as the sex chromosome. Genetic sex was identified based on single nucleotide polymorphisms (SNP) on chromosome 24 (n = 3568) using multidimensional scaling analysis, and individuals were clearly separated according to sex by the first dimension. The 61 SNPs most highly associated with sex were selected, and an amplicon-based SNP panel was developed. This was used to determine genetic sex of 39 females and 40 males. Eleven phenotypic males were assigned as female with XX genotype, suggesting sex reversal. Genetic sex was also assessed based on the indel of the amh gene promoter, which is the major candidate sex gene of Japanese flounder. We found four SNPs perfectly associated with genotypic sex in the sex-associated SNP panel, one of which was located in exon 2 of the amh gene. Along with the indel of the amh gene promoter, the sex-associated SNP panel will be of value in identifying genetic sex of farmed Japanese flounder. Molecular sexing will facilitate all-female production by breeding sex-reversed males.

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Data Availability

All the read data were available at the DDBJ database (BioProject accession: PRJDB15261).

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Acknowledgements

We thank the staff of Marua Suisan Co., Ltd., for collecting the fish samples.

Funding

This work was partially supported by a research grant from the Toyo Suisan Foundation.

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Authors and Affiliations

  1. Department of Marine Science, College of Bioresource Sciences, Nihon University, Kanagawa, Japan

    Mari Maekawa, Emiri Yoshii & Eitaro Sawayama

  2. R&D Division, Marua Suisan Co., Ltd., Ehime, Japan

    Yuri Akase

  3. Bioengineering Lab. Co., Ltd., Kanagawa, Japan

    He Huang

  4. Nagasaki Prefectural Institute of Fisheries, Nagasaki, Japan

    Sota Yoshikawa, Masahiko Matsuda & Yosuke Kuruma

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  1. Mari Maekawa
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  2. Emiri Yoshii
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Contributions

Mari Maekawa and Eitaro Sawayama conceived and designed the study. Mari Maekawa, Emili Yoshii, and Eitaro Sawayama conducted genetic analysis and analyzed the data. Yuri Akase, Sota Yoshikawa, Masahiko Matsuda, and Yosuke Kuruma provided fish sample with phenotype data. He Huang provided PacBio sequencing data. Mari Maekawa and Eitaro Sawayama drafted and revised the manuscript. All authors have read and validated the manuscript.

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Correspondence to Eitaro Sawayama.

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Maekawa, M., Yoshii, E., Akase, Y. et al. Sex-Associated SNP Confirmation of Sex-Reversed Male Farmed Japanese Flounder Paralichthys olivaceus. Mar Biotechnol 25, 718–728 (2023). https://doi.org/10.1007/s10126-023-10235-2

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