Analysis of MHC class I genes across horse MHC haplotypes
- 325 Downloads
The genomic sequences of 15 horse major histocompatibility complex (MHC) class I genes and a collection of MHC class I homozygous horses of five different haplotypes were used to investigate the genomic structure and polymorphism of the equine MHC. A combination of conserved and locus-specific primers was used to amplify horse MHC class I genes with classical and nonclassical characteristics. Multiple clones from each haplotype identified three to five classical sequences per homozygous animal and two to three nonclassical sequences. Phylogenetic analysis was applied to these sequences, and groups were identified which appear to be allelic series, but some sequences were left ungrouped. Sequences determined from MHC class I heterozygous horses and previously described MHC class I sequences were then added, representing a total of ten horse MHC haplotypes. These results were consistent with those obtained from the MHC homozygous horses alone, and 30 classical sequences were assigned to four previously confirmed loci and three new provisional loci. The nonclassical genes had few alleles and the classical genes had higher levels of allelic polymorphism. Alleles for two classical loci with the expected pattern of polymorphism were found in the majority of haplotypes tested, but alleles at two other commonly detected loci had more variation outside of the hypervariable region than within. Our data indicate that the equine major histocompatibility complex is characterized by variation in the complement of class I genes expressed in different haplotypes in addition to the expected allelic polymorphism within loci.
KeywordsHorse MHC class I gene Polymorphism Haplotype structure
Antigen recognition site
Bacterial artificial chromosome
Cytotoxic T lymphocyte
Equine leukocyte antigen
Human leukocyte antigen
Major histocompatibility complex
This research was funded by NIH grants HD-34086, HD-15799, and HD-049545, the Harry M. Zweig Memorial Fund for Equine Research, the Dorothy Russell Havemeyer Foundation, Inc., and the USDA Regional Grants Program. We thank Dr. Shirley Ellis, Dr. Ashley Moffett, Dr. John Trowsdale, and Dr. Stephan Beck for helpful discussions and Dr. Robert H. Mealey of Washington State University for generously providing samples from horses of known ELA serotypes.
- Ando A, Kawata H, Shigenari A, Anzai T, Ota M, Katsuyama Y, Sada M, Goto R, Takeshima SN, Aida Y, Iwanaga T, Fujimura N, Suzuki Y, Gojobori T, Inoko H (2003) Genetic polymorphism of the swine major histocompatibility complex (SLA) class I genes, SLA-1, -2 and -3. Immunogenetics 55:583–593CrossRefPubMedGoogle Scholar
- Korber B (2000) HIV signature and sequence variation analysis. In: Rodrigo AG, Learn GH (eds) Computational analysis of HIV molecular sequences. The Netherlands, Kluwer Academic, pp 55–72Google Scholar
- Mealey RH, Lee JH, Leib SR, Littke MH, McGuire TC (2006) A single amino acid difference within the alpha-2 domain of two naturally occurring equine MHC class I molecules alters the recognition of Gag and Rev epitopes by equine infectious anemia virus-specific CTL. J Immunol 177:7377–7390PubMedGoogle Scholar
- Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK et al (2003) The DNA sequence and analysis of human chromosome 6. Nature 425:805–811CrossRefPubMedGoogle Scholar
- Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blocker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MC, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guerin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Roed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvanen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K (2009) Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 326:865–867CrossRefPubMedGoogle Scholar