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Keywords:

  • Arvicola terrestris;
  • MegaBACE;
  • population genetics;
  • quisca;
  • RT1.Ba

Abstract

Analysis of a single strand conformation polymorphism (SSCP) using capillary electrophoresis (CE) is a novel method to study polymorphism of DNA sequences in large scale population studies. We optimized CE-SSCP analysis to study the major histocompatibility complex (MHC) class II alpha gene (DQA) polymorphism. Short-chain linear polyacrylamide (6%) as sieving matrix, TrisCl (pH 8.5) as buffer for sample dilution, and 27 °C, 9 kV as electrophoresis parameters were suitable for sufficient resolution of all alleles. We found that almost 25% of clones contained a PCR (polymerase chain reaction) artefact and strict criteria have to be applied when using cloning and sequencing to analyse the allelic diversity of MHC genes.