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Identification of Sex-Linked SNPs and Sex-Determining Regions in the Yellowtail Genome

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Abstract

Unlike the conservation of sex-determining (SD) modes seen in most mammals and birds, teleost fishes exhibit a wide variety of SD systems and genes. Hence, the study of SD genes and sex chromosome turnover in fish is one of the most interesting topics in evolutionary biology. To increase resolution of the SD gene evolutionary trajectory in fish, identification of the SD gene in more fish species is necessary. In this study, we focused on the yellowtail, a species widely cultivated in Japan. It is a member of family Carangidae in which no heteromorphic sex chromosome has been observed, and no SD gene has been identified to date. By performing linkage analysis and BAC walking, we identified a genomic region and SNPs with complete linkage to yellowtail sex. Comparative genome analysis revealed the yellowtail SD region ancestral chromosome structure as medaka-fugu. Two inversions occurred in the yellowtail linage after it diverged from the yellowtail-medaka ancestor. An association study using wild yellowtails and the SNPs developed from BAC ends identified two SNPs that can reasonably distinguish the sexes. Therefore, these will be useful genetic markers for yellowtail breeding. Based on a comparative study, it was suggested that a PDZ domain containing the GIPC protein might be involved in yellowtail sex determination. The homomorphic sex chromosomes widely observed in the Carangidae suggest that this family could be a suitable marine fish model to investigate the early stages of sex chromosome evolution, for which our results provide a good starting point.

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Acknowledgments

This work was supported by the Program for Promotion of Basic and Applied Researches for Innovations in Bio-oriented Industry (BRAIN).

Conflict of Interest

A patent regarding sex-linked SNP markers is pending (Japanese Unexamined Patent Application Publication No. 2014-180233).

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Authors and Affiliations

  1. Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7, Konan, Minato-ku, Tokyo, 108-8477, Japan

    Takashi Koyama, Junpei Suzuki, Kanako Fuji & Takashi Sakamoto

  2. National Research Institute of Aquaculture, Fisheries Research Agency, 422-1, Nakatsuhamaura, Minamiise-cho, Watarai-gun, Mie, 516-0193, Japan

    Akiyuki Ozaki, Jun-ya Aoki, Wataru Kai, Yumi Kawabata & Kazuo Araki

  3. Seikai National Fisheries Research Institute, Fisheries Research Agency, 122-7, Nunoura, Tamanoura-machi, Goto-shi, Nagasaki, 853-0508, Japan

    Kazunori Yoshida & Tatsuo Tsuzaki

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  1. Takashi Koyama
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  2. Akiyuki Ozaki
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  3. Kazunori Yoshida
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  4. Junpei Suzuki
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  11. Takashi Sakamoto
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Correspondence to Takashi Sakamoto.

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Koyama, T., Ozaki, A., Yoshida, K. et al. Identification of Sex-Linked SNPs and Sex-Determining Regions in the Yellowtail Genome. Mar Biotechnol 17, 502–510 (2015). https://doi.org/10.1007/s10126-015-9636-x

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  • DOI: https://doi.org/10.1007/s10126-015-9636-x

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