Development of microsatellite markers for the seagrass Zostera japonica using next-generation sequencing

Abstract

The seagrass Zostera japonica Asch. & Graebn. is among the few seagrass species that thrive both in temperate and tropical intertidal zones. The degradation of Z. japonica in its native range and continued expansion in some localities have raised concerns with regard to its conservation and management. Population genetic studies of Z. japonica across its biogeographic range and within meadows are scarce. Previously developed microsatellites via traditional methods are not sufficient in quantity and perform inconsistently between the temperate and tropical populations. Thus, this study aimed to develop more reliable polymorphic markers for Z. japonica using next generation sequencing. In total, 6479 sequences containing loci were identified and 1619 pairs of primers were successfully designed. Of these, 63 loci were selected for primary validation in 16 individuals from four populations, with 48 (76.2%) polymorphic loci detected. Seventeen polymorphic loci were selected for further evaluation in 62 individuals from one temperate and one tropical population. The overall probability of identity (PID) for both populations was 2.375e−22 (PIDsib = 3.557e−08). The number of alleles, and expected and observed heterozygosity in the two populations were both relatively high and not significantly different from each other. The pairwise FST = 0.232 (p < 0.0001) and Principal Coordinates Analysis both suggested a large and significant genetic divergence between the two populations. This study makes abundant molecular markers available for genetic studies in Z. japonica, and facilitates its conservation and management strategies.

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Acknowledgements

The authors thank all the individuals who assisted in the collection of samples. This research was supported by the National Science & Technology Basic Work Program (2015FY110600), the NSFC-Shandong Joint Fund for Marine Science Research Centers (U1606404), the CPSF-CAS Joint Foundation for Excellent Postdoctoral Fellows (2016LH0032), the China Postdoctoral Science Foundation (2016M600562), the key Research and Development Project of Shandong Province (2017GHY15111), the Key Research Project of Frontier Sciences of CAS (QYZDB-SSW-DQC041-1), the Science and Technology Service Network Initiative of CAS (KFJ-STS-ZDTP-023), the Creative Team Project of the Laboratory for Marine Ecology and Environmental Science from the Qingdao National Laboratory for Marine Science and Technology (LMEES-CTSP-2018-1), and the Taishan Scholars Program (Distinguished Taishan Scholars).

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Correspondence to Yi Zhou or Jin-Xian Liu.

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Zhang, X., Zhou, Y., Li, YL. et al. Development of microsatellite markers for the seagrass Zostera japonica using next-generation sequencing. Mol Biol Rep 46, 1335–1341 (2019). https://doi.org/10.1007/s11033-018-4491-2

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Keywords

  • Zostera japonica
  • NGS
  • Microsatellites
  • Population genetics