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Sex-Specific Genomic Region Identification and Molecular Sex Marker Development of Rock Bream (Oplegnathus fasciatus)

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Abstract

Rock bream (Oplegnathus fasciatus) is a valuable commercial marine teleost species, which exhibits sexual dimorphism in growth performance. However, the absence of a rapid and cost-effective sex identification method based on sex-specific genetic marker has impeded study on sex determination mechanisms and breeding applications. In the present study, we firstly developed the PCR method for identifying potential sex-specific sequences in Oplegnathus fasciatus with the next-generation sequencing. Sex-specific genomic regions/loci for sex determination were discovered on Chr2 and Chr6 by genome-wide association analysis, sequencing depth, and heterozygosity comparison between females and males. Candidate sex-determining genes (CCDC63, ITR, WNT4) were furtherly detected in transcriptome data of testes and ovaries. Taken together, a male-specific 34-bp deletion on the Chr2 was identified and developed into molecular marker of sex for O. fasciatus. After validation in individuals with known phenotypic sexes, the accuracy was 100%. This study gives an insight into the mechanism of sex determination in O. fasciatus, and the gender marker is crucial both for future genomic research and for development of efficient and sustainable aquaculture practice.

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Funding

This study was supported by National Key R&D Program of China (2019YFE0119000), Special Foundation for Major Research Program of Fujian Province (2020NZ08003), Ningbo Science and Technology Innovation 2025 Major Project (2021Z002), the special project of local science and technology development guided by the central government (2019L3032), China Agriculture Research System (CARS-47), and Zhejiang Provincial Natural Science Foundation of China (LQ20C190008).

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  1. Jie Gong and Bijun Li contributed equally to this work.

Authors and Affiliations

  1. Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China

    Jie Gong, Bijun Li, Ji Zhao, Zhixiong Zhou, Qiaozhen Ke, Tao Zhou & Peng Xu

  2. State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China

    Qiaozhen Ke & Peng Xu

  3. Zhejiang Marine Fisheries Research Institute, Zhoushan, China

    Qihui Zhu & Dongdong Xu

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  1. Jie Gong
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  2. Bijun Li
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  3. Ji Zhao
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  4. Zhixiong Zhou
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  5. Qiaozhen Ke
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  6. Qihui Zhu
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  7. Dongdong Xu
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  8. Tao Zhou
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  9. Peng Xu
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Contributions

PX conceived the project. JG, JZ, QZK, QHZ, DDX, and TZ collected the samples and extracted DNA. JG, BJL, and ZXZ performed the experiments and conducted the data analysis. JG wrote the manuscript. PX and BJL provided review and modification of the manuscript. All authors read and validated the manuscript.

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Correspondence to Peng Xu.

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Gong, J., Li, B., Zhao, J. et al. Sex-Specific Genomic Region Identification and Molecular Sex Marker Development of Rock Bream (Oplegnathus fasciatus). Mar Biotechnol 24, 163–173 (2022). https://doi.org/10.1007/s10126-022-10095-2

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