A large group of catfish gathered in a net.

Researcher Story

Aquaculture Genomics and the Biology of Sex Determination

Genomic and bioinformatics research is revealing how economically important traits, reproductive isolation, and sex determination are regulated in aquaculture species.

Our laboratory studies aquaculture genomics and bioinformatics to understand the genetic and molecular mechanisms underlying economically important traits in aquaculture species. This research has expanded into reproductive biology, with particular emphasis on sex determination and the genetic and epigenetic regulation of sexual differentiation.

Channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus) serve as the laboratory’s primary research models. Researchers use these species to investigate genome similarities and divergence, reproductive isolation, and the genetic basis of heterosis in interspecific hybrids.

How RCD Supports the Research

Research Computing & Data provides the computational infrastructure and technical support required for bioinformatics analyses, including RNA sequencing (RNA-seq), whole-genome bisulfite sequencing (WGBS), genome-wide association studies (GWAS), and whole-genome sequencing (WGS).

Research Team

Dr. John Liu, Dr. Dongya Gao, Tong Chen
Department of Biology

Illustrations comparing a channel catfish above and a blue catfish.

Comparing a channel catfish above and a blue catfish.

Explore the Research

Publications

  1. Chen, T., Su, B., Gao, D., Shang, M., Dunham, R., & Liu, Z. (2026). Y-chromosome insertions and their applications as sex markers of blue catfish (Ictalurus furcatus). Aquaculture, 744108.

  2. Chen, T., Gao, D., Su, B., Dunham, R., & Liu, Z. (2025). Transcriptome analyses suggest distinct master sex determination genes in closely related blue catfish and channel catfish. Aquaculture, 603, 742364.

  3. Liu, Z., & Gao, D. (2025). Hydin as the candidate master sex determination gene in channel catfish (Ictalurus punctatus) and its epigenetic regulation. Marine Biotechnology, 27(1), 6.

  4. Liu, Z., & Gao, D. (2025). The Cause–Effect model of master sex determination gene acquisition and the evolution of sex chromosomes. International Journal of Molecular Sciences, 26(7), 3282.

  5. Liu, Z., & Gao, D. (2025). Current state of fish reference genome and pangenome: Methodologies, sampling strategies, quality assessment and future perspectives to aquaculture breeding. Marine Biotechnology, 27(6), 158.

  6. Waldbieser, G., Liu, S., Yuan, Z., Older, C., Gao, D., Shi, C., Bosworth, B., Li, N., Bao, L., Kirby, M., Jin, Y., Wood, M., Scheffler, B., Simpson, S., Youngblood, R., Duke, M., Phillippy, A., Koren, S., & Liu, Z. J. (2023). Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biology, 21, 67.

  7. Khalil, K., Elaswad, A., Page-McCaw, P., Abdelrahman, H., Michel, M., Chen, W., Liu, S., Odin, R., Ye, Z., Drescher, D., Vo, K., Bugg, W., Qin, G., Yang, Y., Backenstose, N., Liu, Z. J., Cone, R., & Dunham, R. (2023). Editing melanocortin-4 receptor gene in channel catfish using the CRISPR-Cas9 system. Fishes, 8, 116.

  8. Wang, W., Yang, Y., Tan, S., Zhou, T., Liu, Y., Tian, C., Bao, L., Xing, D., Su, B., Wang, J., Zhang, Y., Liu, S., Shi, H., Gao, D., Dunham, R., & Liu, Z. J. (2022). Genomic imprinting-like monoallelic paternal expression determines sex of channel catfish. Science Advances, 8, eadc8786.

  9. Liu, Z. J., Zhou, T., & Gao, D. (2022). Genetic and epigenetic regulation of growth, reproduction, disease resistance and stress responses in aquaculture. Frontiers in Genetics, 13, 994471.

  10. Wang, W., Tan, S., Yang, Y., Zhou, T., Xing, D., Su, B., Wang, J., Li, S., Shang, M., Gao, D., Dunham, R., & Liu, Z. J. (2022). Feminization of channel catfish with 17β-estradiol involves methylation and expression of a specific set of genes independent of the sex determination region. Epigenetics, 17, 1820–1837.

  11. Yang, Y., Zhou, T., Liu, Y., Tian, C., Bao, L., Zhang, Y., Liu, S., Shi, H., Wang, W., Tan, S., Gao, D., Dunham, R., & Liu, Z. J. (2022). Identification of an epigenetically marked locus within the sex determination region of channel catfish. International Journal of Molecular Sciences, 23, 5471.

  12. Jin, Y., Zhou, T., Jiang, W., Li, N., Xu, X., Tan, S., Shi, H., Yang, Y., Yuan, Z., Wang, W., Qin, G., Liu, S., Gao, D., Dunham, R., & Liu, Z. J. (2022). Allelically and differentially expressed genes after infection of Edwardsiella ictalurid in channel catfish as determined by bulk segregant RNA-Seq. Marine Biotechnology, 24, 174–189. This paper was highlighted on the cover.

  13. Wong, L. L., Razali, S. A., Deris, Z. M., Muhd, D.-D., Tan, M. P., Nor, S. A. M., Ma, H., Min, W., Liang, Y., Asaduzzaman, M., Sung, Y. Y., Liu, Z. J., Sorgeloos, P., Van de Peer, Y., & Nor, A.-A. (2022). Application of second-generation sequencing (SGS) and third generation sequencing (TGS) in aquaculture breeding program. Aquaculture, 548, 737633.

  14. Li, Y., Ren, L., Fu, H., Yang, B., Tian, J., Li, Q., Liu, Z. J., & Liu, S. (2021). Crosstalk between dopamine and insulin signaling in growth control of the oyster. General and Comparative Endocrinology, 313, 113895.

  15. Guo, E., Yang, Y., Kong, L., Yu, H., Liu, S., Liu, Z. J., & Li, Q. (2021). Mitogenomic phylogeny of Trochoidea (Gastropoda: Vetigastropoda): New insights from increased complete genomes. Zoologica Scripta, 50, 43–57.

  16. Zhang, Y., Liu, Z. J., & Li, H. (2020). Genomic prediction of columnaris disease resistance in catfish. Marine Biotechnology, 22, 145–151.

  17. Wang, E., Yuan, Z., Wang, K., Gao, D., Liu, Z. J., & Liles, M. R. (2019). Consumption of florfenicol-medicated feed alters the composition of the channel catfish intestinal microbiota including enriching the relative abundance of opportunistic pathogens. Aquaculture, 501, 111–118.

  18. Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Yang, Y., Gao, D., & Liu, Z. J. (2019). Post-transcriptional regulation through alternative splicing after infection with Flavobacterium columnare in channel catfish (Ictalurus punctatus). Fish and Shellfish Immunology, 91, 188–193.

  19. Rexroad, C., Vallet, J., Matukumalli, L. K., Reecy, J., Bickhart, D., Blackburn, H., Boggess, M., Cheng, H., Clutter, A., Cockett, N., Ernst, C., Fulton, J., Liu, Z. J., Lunney, J., Neibergs, H., Purcell, C., Smith, T., Sonstegard, T., Taylor, J., Telugu, B., Van Eenennaam, A., Van Tassell, C., & Wells, K. (2019). Genome to phenome: Improving animal health, production and well-being: A new USDA blueprint for animal genome research 2018–2027. Frontiers in Genetics, 10, 327.

  20. Tan, S., Wang, W., Zhou, T., Yang, Y., Gao, D., & Liu, Z. J. (2019). Polyadenylation sites and their characteristics in the genome of channel catfish (Ictalurus punctatus) as revealed by using RNA-Seq data. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 30, 248–255.

  21. Gao, L., Yuan, Z., Zhou, T., Yang, Y., Gao, D., Dunham, R., & Liu, Z. J. (2019). Foxo genes in channel catfish and their response after bacterial infection. Developmental and Comparative Immunology, 97, 38–44.

  22. Wang, W., Tan, S., Luo, J., Shi, H., Jin, Y., Zhou, T., Wang, X., Yang, Y., Niu, D., Yuan, Z., Gao, D., Dunham, R., & Liu, Z. J. (2019). GWAS analysis indicated importance of NF-κB signaling pathway in host resistance against motile Aeromonas septicemia disease in catfish. Marine Biotechnology, 21, 335–347.

  23. Bao, L., Tian, C., Liu, S., Zhang, Y., Elaswad, A., Yuan, Z., Khalil, K., Sun, F., Yang, Y., Zhou, T., Li, N., Tan, S., Zeng, Q., Liu, Y., Li, Y., Li, Y., Gao, D., Dunham, R., Davis, K., Waldbieser, G., & Liu, Z. J. (2019). The Y chromosome sequence of the channel catfish suggests novel sex determination mechanisms in teleost fish. BMC Biology, 17, 6.

  24. Tan, S., Wang, W., Tian, C., Niu, D., Zhou, T., Jin, Y., Yang, Y., Gao, D., Dunham, R., & Liu, Z. J. (2019). Heat stress induced alternative splicing in catfish as determined by transcriptome analysis. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 29, 166–172.

  25. Zhang, X., Yuan, J., Sun, Y., Li, S., Gao, Y., Yu, Y., Liu, C., Wang, Q., Lv, X., Zhang, X., Ma, K. Y., Wang, X.,., Lin, W., Wang, L., Zhu, X., Zhang, C., Zhang, J., Jin, S., Yu, K., Kong, J., Xu, P., Chen, N., Zhang, H.-B., Sorgeloos, P., Sagi, A., Warren, A., Liu, Z. J., Wang, L., Ruan, J., Chu, K., Liu, B., Li, F., & Xiang, J. (2019). Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Nature Communications, 10, 356.

  26. Li, N., Bao, L., Zhou, T., Yuan, Z., Liu, S., Dunham, R., Li, Y., Wang, K., Xu, X., Jin, Y., Zeng, Q., Gao, S., Fu, Q., Liu, Y., Yang, Y., Li, Q., Meyer, A., Gao, D., & Liu, Z. J. (2019). Genome sequence of walking catfish (Clarias batrachus) provides insight into terrestrial adaptation. BMC Genomics, 19, 952.

  27. Zhou, T., Yuan, Z., Tan, S., Jin, Y., Yang, Y., Shi, H., Wang, W., Niu, D., Gao, L., Jiang, W., Gao, D., & Liu, Z. J. (2018). A review of molecular responses of catfish to bacterial diseases and abiotic stresses. Frontiers in Physiology, 9, 1113.

  28. Yang, Y., Wang, X., Liu, Y., Fu, Q., Tian, C., Wu, C., Liu, S., Gao, D., Dunham, R., & Liu, Z. J. (2018). Transcriptome analysis reveals enrichment of genes associated with auditory system in swimbladder of channel catfish. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 27, 30–39.

  29. Liu, Z., Liu, S., Yao, J., Bao, L., Zhang, J., Li, Y., et al. (2016). The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nature Communications, 7(1), 11757.

  30. Tan, S., Zhou, T., Wang, W., Jin, Y., Wang, X., Geng, X., Gao, D., Dunham, R., & Liu, Z. J. (2018). GWAS analysis using F2 interspecific hybrids reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish. Molecular Genetics and Genomics, 293, 1107–1120.