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Characterization of newly developed expressed sequence tag-derived microsatellite markers revealed low genetic diversity within and low connectivity between European Saccharina latissima populations

Abstract

The kelp Saccharina latissima is a species of high ecological and economic importance. We developed a novel set of S. latissima-specific genetic markers that will find applications in conservation biology, biodiversity assessment, and commercial exploitation of this macroalga. Thirty-two expressed sequence tag (EST)-derived microsatellite markers (SSRs) were developed and characterized in this study using publically available EST sequences. Twenty-seven percent of the 7064 analyzed ESTs contained repeat motifs, and polymerase chain reaction (PCR) amplification primers were designed for 96 selected loci. Fifty-one (53 %) of the primer pairs amplified their target loci, of which 32 (33 %) were polymorphic within a sample of 96 S. latissima sporophytes collected from six localities distributed along the European Atlantic coast from Southern Brittany (France) to Spitzbergen (Norway). The 32 loci harbored moderate levels of polymorphism with 2–13 alleles per locus (mean 5.4). The 25 loci that were retained for population genetic analyses revealed substantial genetic differentiation among the European populations (pairwise F ST values ranging from 0.077 to 0.562) that did not follow any pattern of isolation by distance. In addition, within-population genetic diversity was generally low (Hs < 0.323). Two non-mutually exclusive hypotheses were proposed to explain this low diversity pattern: (1) lower variability of the EST-derived microsatellites compared to the random distribution of SSRs developed from genomic DNA since the former are frequently located in coding regions, which are generally less variable, or (2) reduced effective population size of S. latissima. The particularly high genetic differentiation between the French and Scandinavian S. latissima populations is in agreement with the reported ecotypic differentiation, which may reflect an important resource for genetic improvement. The pattern of genetic diversity revealed in this study thus suggests that care should be taken to avoid the transfer of strains between different geographic regions.

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Acknowledgments

This work benefited from the support of the French Government through the National Research Agency with regards to an investment expenditure program IDEALG, which reference is stated as ANR-10-BTBR-04, and was carried out within the context of the international research network “Diversity, Evolution and Biotechnology of Marine Algae” (GDRI No. 0803). The authors are deeply indebted to the Service Mer & Observation (SMO) of Roscoff, G. Cervin, and J. Coyer for sampling. The authors would also like to thank Gildas Le Corguille of the ABiMS Platform, Roscoff for his help with bioinformatics analyses. We are most grateful to the Biogenouest Genomics core facility for its technical support. We also would like to thank the two anonymous reviewers for their suggestions and comments.

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Correspondence to Jaromir Guzinski.

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Guzinski, J., Mauger, S., Cock, J.M. et al. Characterization of newly developed expressed sequence tag-derived microsatellite markers revealed low genetic diversity within and low connectivity between European Saccharina latissima populations. J Appl Phycol 28, 3057–3070 (2016). https://doi.org/10.1007/s10811-016-0806-7

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Keywords

  • Saccharina latissima
  • Phaeophyceae
  • NE Atlantic
  • EST
  • Population genetic structure
  • Simple sequence repeat