Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides
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Codominant marker systems are better suited to analyze population structure and assess the source of an individual in admixture analyses. Currently, there is no codominant marker system using microsatellites developed for the sea sandwort, Honckenya peploides (L.) Ehrh., an early colonizer in island systems. We developed and characterized novel microsatellite loci from H. peploides, using reads collected from whole genome shotgun sequencing on a 454 platform. The combined output from two shotgun runs yielded a total of 62,669 reads, from which 58 loci were screened. We identified 12 polymorphic loci that amplified reliably and exhibited disomic inheritance. Microsatellite data were collected and characterized for the 12 polymorphic loci in two Alaskan populations of H. peploides: Fossil Beach, Kodiak Island (n = 32) and Egg Bay, Atka Island (n = 29). The Atka population exhibited a slightly higher average number of alleles (3.9) and observed heterozygosity (0.483) than the Kodiak population (3.3 and 0.347, respectively). The overall probability of identity values for both populations was PID = 2.892e−6 and PIDsib = 3.361e−3. We also screened the 12 polymorphic loci in Wilhelmsia physodes (Fisch. ex Ser.) McNeill, the most closely related species to H. peploides, and only one locus was polymorphic. These microsatellite markers will allow future investigations into population genetic and colonization patterns of the beach dune ruderal H. peploides on new and recently disturbed islands.
KeywordsHonckenya peploides Sea sandwort Microsatellites Disomic inheritance Next-generation sequencing
Stephen Talbot and Hunter Gravley (USFWS) assisted in sample collection of Honckenya peploides. Special thanks to Janet Jorgensen and her team (USFWS) for collecting cross-species screen specimens (Wilhelmsia physodes) and William Leacock (USFWS) for field support on Kodiak Island. Funding was provided by the USGS Regional Director’s Office and a North Pacific Research Board Grant to USGS. Travel to Kodiak was made possible through a LGL Alaska Graduate Ecology Research Award to MCG provided through the University of Alaska Anchorage (UAA). This manuscript was improved by comments from Brandon Briggs (UAA), John Pearce (USGS) and two anonymous reviewers. Special thanks to Barbara Pierson (USGS) for data curation. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
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