A Novel Method for Comprehensive Equine MHC Class I Immunotyping from RNAseq-Derived White Blood Cell Transcriptome

Investigation of MHC variability is essential for monitoring genetic diversity within/between breeds or populations as well as for association studies on immune response phenotypes. In addition, knowledge about MHC compatibility is essential for tissue transplantation. While there are more than 2000 classical MHC class I alleles described in humans, respective data bases for non-model organisms are only poorly populated. MHC class I immunotyping in horse or cattle is complicated due to the fact that in both species individuals can vary in the number of MHC class I genes present and expressed in their genomes. Recently, we developed a novel method for RNAseq derived holistic, non-targeted MHC class I typing. We now extended this method also to the equine transcriptome taking advantage of publicly available whole blood transcriptome data. We successfully describe a number of novel MHC class I alleles in addition to alleles already deposited in the MHC data base. The new alleles were tested for open reading frames and homology to sequences in public data bases. A total of 13 classical and 5 non-classical novel alleles were identified and confirmed by analyzing repetitive samples of four individuals. RNAseq-based PCR-template free MHC class I immunotyping provides the opportunity to comprehensively describe equine MHC diversity.