Gene organization and polymorphism of the swine major histocompatibility complex

The recent availability of the full-length sequence of one haplotype of the swine leukocyte antigen (SLA) complex, the swine major histocompatibility complex (MHC), and significant progress in the studies on gene expression and polymorphisms led to major advances in deciphering its role in resistance to diseases in animals. The present status of the genomic organization and polymorphism of the SLA complex is presented in this Review. Additionally, a comparative analysis with mammalian MHC has also been provided. The sequenced SLA-H01 haplotype harbors 152 loci including genuine SLA genes, non-MHC genes and pseudogenes. Although the numbers of expressed SLA genes could vary across haplotypes, three SLA class la, three SLA class Ib, four SLA class IIa and four SLA class IIb genes are currently expressed. Except for the class I genes, which have no clear orthologs, the gene organization of the loci was highly conserved between humans and pigs. Moreover, the human leukocyte antigen (HLA) complex lies on a single chromosomal segment, whereas a centromere at the class II and III junction splits the SLA complex into two segments, without disturbing gene organization or impeding functionality. Over 400 SLA class I and II allele sequences available in databases have been recently clustered and assigned to a specific SLA locus according to a newly defined nomenclature system.