Genomics Inform.
2023 Dec;21(4):e47. 10.5808/gi.23075.
Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus)
- Chailertrit V
1,2,3,4 - Panthum T1,3,4
- Kongkaew L1,3,4
- Chalermwong P1,5
- Singchat W1,3,4
- Ahmad SF1,3
- Kraichak E1,6
- Muangmai N1,7
- Duengkae P1,4
- Peyachoknagul S1
- Han K1,8,9
- Srikulnath K1,3,4,5,10
- Affiliations
-
- 1Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- 2Pathum Thani Aquatic Animal Genetics Research and Development Center, Aquatic Animal Genetics Research and Development Division, Department of Fisheries, Pathum Thani 12120, Thailand
- 3Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- 4Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- 5Sciences for Industry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- 6Department of Botany, Kasetsart University, Bangkok 10900, Thailand
- 7Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok 10900, Thailand
- 8Department of Microbiology, Dankook University, Cheonan 31116, Korea
- 9Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan 31116, Korea
- 10Center for Advanced Studies in Tropical Natural Resources (CASTNAR), National Research University-Kasetsart University (NRU-KU), Kasetsart University, Bangkok 10900, Thailand
- KMID: 2550888
- DOI: http://doi.org/10.5808/gi.23075
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.
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