Microsatellite marker development from next-generation sequencing in the New England cottontail (Sylvilagus transitionalis) and cross-amplification in the eastern cottontail (S. floridanus).

Academic Article


  • OBJECTIVE: The New England cottontail (Sylvilagus transitionalis) is a species of high conservation priority in the Northeastern United States, and was a candidate for federal listing under the Endangered Species Act until a recent decision determined that conservation actions were sufficient to preclude listing. The aim of this study was to develop a suite of microsatellite loci to guide future research efforts such as the analysis of population genetic structure, genetic variation, dispersal, and genetic mark-recapture population estimation. RESULTS: Thirty-five microsatellite markers containing tri- and tetranucleotide sequences were developed from shotgun genomic sequencing of tissue from S. transitionalis, S. obscurus, and S. floridanus. These loci were screened in n = 33 wild S. transitionalis sampled from a population in eastern Massachusetts, USA. Thirty-two of the 35 loci were polymorphic with 2-6 alleles, and observed heterozygosities of 0.06-0.82. All loci conformed to Hardy-Weinberg Equilibrium proportions and there was no evidence of linkage disequilibrium or null alleles. Primers for 33 of the 35 loci amplified DNA extracted from n = 6 eastern cottontail (S. floridanus) samples, of which nine revealed putative species-diagnostic alleles. These loci will provide a useful tool for conservation genetics investigations of S. transitionalis and a potential diagnostic species assay for differentiating sympatric eastern and New England cottontails.
  • Authors

  • King, Timothy L
  • Eackles, Michael
  • Aunins, Aaron
  • McGreevy, Thomas J
  • Husband, Thomas P
  • Tur, Anthony
  • Kovach, Adrienne
  • Publication Date

  • December 16, 2017
  • Published In

  • BMC Research Notes  Journal
  • Keywords

  • Animals
  • Base Sequence
  • Cross-amplification
  • Genetic Loci
  • High-Throughput Nucleotide Sequencing
  • Microsatellite Repeats
  • Microsatellites
  • Next-generation sequencing
  • Rabbits
  • Sylvilagus floridanus
  • Sylvilagus obscurus
  • Sylvilagus transitionalis
  • Digital Object Identifier (doi)

    Start Page

  • 741
  • Volume

  • 10
  • Issue

  • 1