Allelic diversity at class II DRB1 and DQB loci of the pig MHC (SLA)

The loci encoding the beta chain of the pig major histocompatibility comple x (MHC) class II antigens, SLA-DR and -DQ, have been known to exhibit a rem arkable degree of allelic polymorphism. Here, to understand the generation of SLA class II polymorphism, 25 SLA-DRB1 and 24 SLA-DQB genes including ne wly identified 12 SLA-DRB1 and 7 SLA-DQB genes obtained from miniature pigs were analyzed based on the nucleotide and deduced amino acid sequences. Mo st of the allelic diversity was attributed to the variable sequences which encode a beta(1) domain consisting of a beta-pleated sheet followed by an a lpha helix. In the beta(1) domain coding region, there were four GC-rich se quences, which have been considered to involve the intra-exon sequence exch ange also in other gene evolutions. The first and second GC-rich sequences were X-like sequences, which have been shown to be a putative recombination signal, and were stably conserved among SLA-DRB1 and DQB genes. These X-li ke sequences identified in SLA-DRB1 and SLA-DQB were found to encode the fi rst turning point of the beta-pleated sheet and the boundary between the be ta-pleated sheet and the alpha helix. Analysis of clustered sequence variat ion also suggested intra-exon gene conversions in which the chi-like sequen ces act as putative breakpoints. In addition to point mutations and selecti on mechanism, intra-exon gene conversions must be an important mechanism in the generation of allelic polymorphism at the SLA-DRB1 and SLA-DQB.