Rapid characterization of MHC class I diversity in desert bighorn sheep reveals population-specific allele expression

Abstract

Abstract Diversity of MHC class I alleles within animal populations is necessary to prevent pathogen escape from adaptive immune responses. However, demonstrating this phenomenon is difficult especially in wild animal species where the effect of pathogen escape is more profound than in laboratory animal models. Desert bighorn sheep (Ovis canadensis nelsoni) are a charismatic megafauna native to the southwest of North America which are threatened by a number of infectious diseases and, more recently, paranasal tumors. We sought to develop a relatively inexpensive and rapid way to identify the diversity of MHC class I genes and alleles within individual bighorn sheep. Both DNA and RNA were isolated from leukocytes collected from 154 adult bighorn sheep from across different mountain ranges in Southern California. Previously identified primers from domestic sheep were used to amplify exons 2 and 3 from OMHC I genes while appending adapters for PacBio circular consensus sequencing. PCR amplicons from individual animals were then subjected to a second round of PCR to append index sequences to allow assigning of individual sequences to unique animals. We successfully identified over 40 unique MHC class I sequences expressed by bighorn sheep. Between 2 and 5 loci were amplified in each individual animal. Analysis of gDNA revealed several pseudogenes and other DNA sequences which were not transcribed. Finally, we demonstrate that particular DNA sequences are found within particular populations, suggesting that as bighorn populations fragment, there is a loss of MHC class I diversity.