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Development of EST-SSRs from the ark shell (Scapharca broughtonii) transcriptome and their application in genetic analysis of four populations

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Abstract

Background

The ark shell (Scapharca broughtonii) is one of the most economically important mollusks in the Bohai Sea and Yellow Sea of China. In recent years, ark shells from the Korean population were introduced to China for seed propagation and culture.

Objective

To explore the impact of the introduction of Korean ark shell on the genetic diversity of native population in China.

Methods

Simple sequence repeat (SSR) is effective and widely used tool for genetic analysis. In this study, 180 EST-SSRs were selected and verified by polymerase chain reaction and polyacrylamide gel electrophoresis. Subsequently, five polymorphic EST-SSRs were screened and their primers were modified by fluorescein for use in the genetic analysis of four populations.

Results

Genetic analysis showed that 361 alleles amplified by five SSR loci were detected in the four populations. The number of alleles for the five SSRs ranged from 8 to 30, with a mean of 18.05 (standard deviation, SD = 6.492). The effective number of alleles varied from 2.253 to 22.222, with a mean of 10.596 (SD = 4.713). Observed heterozygosity and expected heterozygosity were 0.167–0.833 and 0.566–0.971, with average values of 0.520 (SD = 0.177) and 0.891 (SD = 0.062), respectively. Polymorphic information content ranged from 0.521 to 0.953, with a mean of 0.865 (SD = 0.070). The pairwise genetic differentiation coefficient (FST) of the four populations ranged from 0.0267 to 0.0477, showing low genetic differentiation. The phylogenetic tree constructed by neighbor-joining method showed that the genetic distance between the Chinese Dalian native population and three Korean populations was relatively more far than that among those Korean populations.

Conclusion

The results indicated that the genetic structure of the Dalian wild population was less affected by the introduced Korean wild populations.

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Acknowledgements

We would like to thank the financial grants from Key R & D project of Shandong Province (2018GHY115030, 2019JZZY020706), National Key R&D Pro-gram of China (2018YFD0900304) and Central Public-interest Scientific Institution Basal Research Fund (HY2019-JC02, 20603022019003).

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Authors and Affiliations

  1. Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, People’s Republic of China

    Wenjing Wang, Biao Wu, Zhihong Liu, Liqing Zhou, Xiujun Sun, Jiteng Tian & Aiguo Yang

  2. Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266273, People’s Republic of China

    Biao Wu, Zhihong Liu, Liqing Zhou, Xiujun Sun, Jiteng Tian & Aiguo Yang

  3. National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, People’s Republic of China

    Wenjing Wang

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  1. Wenjing Wang
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  3. Zhihong Liu
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Correspondence to Biao Wu.

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Wang, W., Wu, B., Liu, Z. et al. Development of EST-SSRs from the ark shell (Scapharca broughtonii) transcriptome and their application in genetic analysis of four populations. Genes Genom 43, 669–677 (2021). https://doi.org/10.1007/s13258-021-01090-3

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