Genomics & Informatics

Korea Genome Organization (한국유전체학회)
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Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus)

  • Visarut Chailertrit (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Thitipong Panthum (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Lalida Kongkaew (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Piangjai Chalermwong (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Worapong Singchat (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Syed Farhan Ahmad (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Ekaphan Kraichak (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Narongrit Muangmai (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Prateep Duengkae (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Surin Peyachoknagul (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Kyudong Han (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University) ;
  • Kornsorn Srikulnath (Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University)
  • Received : 2023.09.18
  • Accepted : 2023.12.09
  • Published : 2023.12.31
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Abstract

Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.

Keywords

Acknowledgement

This research was financially supported in part by a Ph.D. Scholarship for Chalermprakiat 70 years of reign under the Agricultural Research Development Agency (Public Organization) (ARDA) and the Royal Golden Jubilee PhD program under the Thailand Research Fund (TRF) and Agricultural Research Development Agency (Public Organization): The Seventieth Anniversary Celebrations of His Majesty's Accession to the Throne Ph.D. Scholarship Programme (HRD6401028) awarded to V.C. (6317400245) and K.S. The High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA) was awarded to T.P. (6417400247) and K.S. The Center of Excellence on Agricultural Biotechnology, Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation (AG-BIO/MHESI no. 60-003-005) was awarded to K.S. The National Research Council of Thailand (NRCT) (N42A650233); National Research Council of Thailand: High-Potential Research Team Grant Program (N42A660605) awarded to V.C., W.S., S.F.A., E.K., N.M., P.D., and K.S. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank the Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division (Department of Fisheries, Thailand) for supplying the silver barb specimens.

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