Genotyping MHC classIIB in non-model species by reference strand-mediated conformational analysis (RSCA)

Abstract

Major histocompatibility complex (MHC)diversity is described in many species and, in particular, is germane to the conservation of endangered species. However, studies addressing the functional link between individual MHC-variation and, for example, disease susceptibility are underrepresented. This is most likely due to the complex nature of MHC in most species, which hampers reliable individual typing. To date MHC-genotyping by reference strand-mediated conformational analysis (RSCA) has been used in only a few model species where extensive prior information on MHC-gene sequences was available. In those cases, RSCA was found to be a highly accurate and reliable method. Here we adapt this method to two non-model species, Eurasian perch (Perca fluviatilis) and Alpine whitefish (Coregonus spp.). We show that RSCA can be quickly applied as a flexible genotyping method to any species, even with only limited prior information about its MHC-genes.