Gene organization and polymorphism of the swine major histocompatibility complex

Abstract

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 Ia, 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.

Giant Panda Genomic Data Provide Insight into the Birth-and-Death Process of Mammalian Major Histocompatibility Complex Class II Genes

“…The giant panda MHC class II region presented a linked gene cluster containing DOB, TAP2, PSMB8, TAP1, PSMB9, DMB, DMA, BRD2, and DOA. This gene group is present in this identical order in other sequenced mammals, including humans [5] , cats [12] , dogs [8] , cattle [13] , pigs [14] , and mice [4] . We designated this DOB∼TAP2∼PSMB8∼TAP1∼PSMB9∼DMB∼DMA∼BRD2∼DOA gene cluster as the DO_box.…”

“…A phylogenetic tree was constructed from predicted functional giant panda alpha and beta genes and the expressed loci identified from the completely sequenced MHC class II regions of the mammals under study. These loci included human HLA (NT_007592: DRA, DRB1, DRB5, DQA1, DQA2, DQB1, DPA1, DPB1, DOA, DOB, DMA, and DMB), cat FLA ( [12] : DRA1, DRA2, DRA3, DRB1, DRB3, DRB4, DOA, DOB, DMA, and DMB), dog DLA (AJ63062–66: DRA, DRB1, DQA1, DQB1, DOA, DOB, DMA, and DMB), bovine BoLA (Btau 3.1 and AY957499: DRA, DRB, DRB3, DSB, DQA1, DQA2, DQA3, DYA, DYB, DOA, DOB, DMA, and DMB), pig SLA ( [14] : DRA, DRB1, DQA1, DQB1, DOA, DOB, DMA, and DMB), and mouse H2 ( [4] : Ea, Eb1, Aa, Ab, Oa, Ob, Ma, Mb1, and Mb2). All pseudogenes were excluded from the phylogenetic analysis because of the distorting effect of their atypical evolutionary rates and because many of their coding sequences were incomplete.…”

“…In contrast, the greater longevity of class II genes has made it relatively easy to identify orthologous class II loci in different orders of mammals [10] – [11] . As a result, and in view of the pivotal role of MHC genes in the immune system and the birth-and-death characteristics of class II genes, the MHC class II genomic regions for several mammals, including cat [12] , dog [8] , cattle [13] , and pig [14] , were sequenced to identify a complete and ordered set of MHC class II genes and resolve MHC evolutionary history from a comparative genomics perspective.…”

Isolation of a 97-kb Minimal Essential MHC B Locus from a New Reverse-4D BAC Library of the Golden Pheasant

“…Due to its important role in immunity and its exceptionally high level of genetic variation, the MHC has attracted considerable attention from many different fields of biological researches, especially for mammals [6] . The mammalian MHC region always occupies more than half a million kilobases in length, as revealed in human [7] , cow [8] , pig [9] , dog [10] and giant panda [11] , which were determined by constructing BAC genomic library and physical map. The intact avian MHC genomic data were available from chicken [12] , quail [13] and turkey [3] and all of them showed that the Galliform possessed a minimal essential MHC genomic structure spanning about one hundred kiolobases, which is so small that one BAC is enough to hold.…”

Analysis of gene expression patterns by microarray hybridization in blood mononuclear cells of SLA-DRB1 defined Canadian Yorkshire pigs

“…The two main classes, I and II, are involved in antigen presentation to T-cells. However, a large number of the genes in the MHC, like class III genes, are not directly related to this function [ 1 , 2 ]. A total of 152 loci have been annotated within this region.…”