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Specific PCR-based Marker for Identification of Common Carp ‘Hainan’ in China

Specific PCR-based Marker for Identification of Common Carp ‘Hainan’ in China

Muhammad Younis Laghari1,2, Zixia Zhao1, Yiwen Gong3, Punhal Lashari1,2, Shangqi Li1, Jian Xu1 , Ateeque Rahman Khooharo4, Jiongtang Li1,* and Yan Zhang1*

1Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, 100141, China
2Department of Freshwater Biology and Fisheries, University of Sindh, Jamshoro, 76080, Pakistan
3National Demonstrain Center for Experimental Fisheries Science Education (Shanghai Ocean University)
4Centre of Excellence in Marine Biology, Karachi University, Sindh-Pakistan

*     Corresponding author:;



The common carp (Cyprinus carpio L.) is one of the most important aquaculture species in the world. In China, due to the geographical isolation of Hainan island from the mainland, the genetic diversity in Hainan island is different to that in the mainland. One of fifty sequences isolated from SINE element was polymorphic, including six haplotypes with an average sequence divergence of 11.03% (SE = 0.78%). Four haplotypes (MF177501-MF177504) were shared in these four population. However, two specific haplotypes (MF177499-MF177500) were only observed in Hainan population. To simplify procedure and improve effectiveness of identifying the Hainan population, one specific PCR-based marker acted as INDEL marker was developed and then 120 samples were used as templates for PCR validation. The specific marker will facilitate the assessment of genetic diversity and selective breeding programs for Hainan common carp.

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Pakistan Journal of Zoology


Vol. 52, Iss. 3, Pages 825-1224


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