Vu Dang Ha Quyen¹, Truong Thi Oanh¹, Doan Vu Thinh², Tran Linh Thuoc³, Kent Carpenter⁴, Dang Thuy Binh¹

¹ Institute for Biotechnology and Enviroment, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Viet Nam, (Email: quyenvdh.ntu@gmail.com)

²Faculty of Information Technology, Nha Trang University, 02 Nguyen Dinh Chieu, Nha Trang, Viet Nam

³Department of Molecular & Environmental Biotechnology, University of Science, 227 Nguyen Van Cu Str., Dist. 5, Ho Chi Minh City, VietNam

⁴Department of Biological Science, Old Dominion University, Norfolk, Virginia 23529, USA

⁵ Phd Student in Biotechnology, University of Science, 227 Nguyen Van Cu Str.,Dist. 5, Ho Chi Minh City, VietNam

Vietnamese Mekong River is one of the most vulnerable places to the impacts of environmental changes, which compounds existing and projected threats. Our understanding of genetic diversity of fish species in Vietnamese Mekong River in adaptation to environmental changes will become important for directing conservation and management of biodiversity. Here, we report the use of Enzyme Restriction site Associated DNA (EzRAD) from genomic DNA approach for assessing level of genetic diversity of ecologically and economically important fish species in Vietnamese Mekong, the blackhand paradise fish (Polynemus melanochir Bleeker, 1852). 164 DNA samples was collected from upstream to downstream of two branch of rivers in Vietnamese Mekong (include in 7 provinces: An Giang, Dong Thap, Can Tho, Vinh Long, Tien Giang, Tra Vinh, and Ben Tre). A pooled sample of regional EzRAD libraries was sequenced using the HiSeq 2500 Illumina platform. Reference genome generated 7446 reads. A total of 34,590 raw SNPs among geographic regions were detected. Using Vcftool software to filter criteria, 2657 high quality SNPs were used to analysis population structure with 145 individuals.

Our result showed population structure has also been detected (F_ST = 0.003 - 0.013). Highest genetic diversity of fish population in Tra Vinh Province is observed (Hs = 0.43 and Ht = 0.43 with 95% confidence intervals of F-statistics). This result is accepted hypothesis for fish population live in Hau River mouth that are big estuary affected strongly by the discharge flow of the upstream Mekong River and the semi-diurnal tides of the East Sea. It is an interference aquatic ecosystem area when the upstream freshwater river-flow and saltwater sea-tides flow are mixed up. Continue sampling and EzRAD libraries need to be implemented for resource management in the Mekong Delta.

Keywords: EzRAD, Polynemus melanochir , genetic diversity.