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Characterization of microsatellite loci for a threatened species, the King Rail, Rallus elegans, using a next-generation sequencing protocol

  • Microsatellite Letters
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Abstract

The King Rail Rallus elegans (Audubon) has experienced population declines of 4.6 % per year on average since the 1960s. Wetland loss, most severely affecting inland marshes, has significantly reduced this species’ distribution to the coastal margins of its historic range. Polymorphic microsatellite markers were generated by 454 pyrosequencing of genomic DNA from King Rails, and Clapper Rails R. longirostris from Louisiana after AFLP enrichment and barcoding of restriction fragment cut sites across individuals. Of 1,419 microsatellite-containing sequences, 20 hypervariable microsatellite loci with up to 20 different alleles were identified at the alignment stage. We characterized nine loci, tested variability in 45 Atlantic coast King Rail samples, and detected 4–19 alleles per locus. Cross-species amplification revealed variability in the Virginia Rail, R. limicola, and Sora, Porzana carolina. These loci will be useful for studying secretive marsh rails, many of which are threatened or endangered.

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References

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Acknowledgments

We thank Mike Hoff and Jordan Black at Mackay Island NWR, J. Huner, L. Richard Jr., and P. Smith Jr., for access to private land, and Denise Mayer at ECU’s Genomics Core Facility. Permits were provided by the USFWS (JMM, SBM), the Louisiana Department of Wildlife and Fisheries (JMM), the North Carolina Wildlife Resources Commission (SBM), Mackay Island NWR (SBM), and the USGS Bird Banding Lab (SBM). This research was supported by the Wilson’s Society Paul A. Stewart Award (CLB), an ECU Graduate Scholarship (CLB), a Southeastern Region CESU Cooperative and Joint Venture Agreement (SBM), a USFWS Webless Migratory Game Bird Program Grant (SBM), and grants DEB-0841729 (RTB), DEB-0956909 (RTB), and DEB-1110624 (RTB, JMM) from the NSF.

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Authors and Affiliations

  1. Department of Biology and Center for Biodiversity, East Carolina University, Greenville, NC, 27858-4353, USA

    Carol L. Brackett & Susan B. McRae

  2. Museum of Natural Science, Department of Biological Sciences, Louisiana State University, 119 Foster Hall, Baton Rouge, LA, 70803, USA

    James M. Maley & Robb T. Brumfield

Authors
  1. Carol L. Brackett
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  2. James M. Maley
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  3. Robb T. Brumfield
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  4. Susan B. McRae
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Corresponding author

Correspondence to Susan B. McRae.

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Brackett, C.L., Maley, J.M., Brumfield, R.T. et al. Characterization of microsatellite loci for a threatened species, the King Rail, Rallus elegans, using a next-generation sequencing protocol. Conservation Genet Resour 5, 1189–1191 (2013). https://doi.org/10.1007/s12686-013-9999-0

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  • DOI: https://doi.org/10.1007/s12686-013-9999-0

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