Cloning and characterization of a new swine MHC (SLA) class II DQB allele

Simple and comprehensive SLA-DQB1 genotyping using genomic PCR and direct sequencing

To enable the efficient analysis of a highly polymorphic swine major histocompatibility complex (MHC) class II gene, swine leukocyte antigen (SLA)-DQB1, we developed a simple and comprehensive high-resolution genotyping protocol. To obtain sufficient sequence information to design a set of common genotyping primers for SLA-DQB1, we cloned SLA-DQB1 introns 1 and 2 from 11 alleles with official four-digit allelic designations and sequenced the regions directly surrounding the SLA-DQB1 exon 2. Significant intronic nucleotide variations, including several deletions, were identified. Based on 733-bp assembled genomic sequences including introns 1 and 2 and exon 2 from 11 different alleles, a primer set was identified that allowed the ubiquitous amplification and analysis of the complete SLA-DQB1 exon 2 sequence. We then developed a method to directly sequence the amplified polymerase chain reaction (PCR) products without further experimental steps. We especially focused on avoiding superimposed peaks, which arose from the presence of allelic deletions, in the sequencing electropherogram of SLA-DQB1 heterozygous animals. The genotyping accuracy was evaluated by comparing the results of genomic sequence-based typing (GSBT) with those of other available methods, including cDNA sequence-based typing (SBT), low-resolution PCR typing with sequence-specific primers, allelic segregation analysis, and heterozygote simulation typing. In all cases, the results were consistent between SLA-DQB1 GSBT and previously reported methods or expected results. We applied it to genotype 350 animals from seven pig breeds. The observed level of heterozygosity from our genotyping was ∼51%, reflecting that a large portion of the animals were inbred miniature pigs. Among the seven pig breeds tested, the allelic diversity of SLA-DQB1 was highest in Berkshire pigs. In conclusion, we have developed a simple and effective SLA-DQB1 GSBT method by combining simple genomic DNA PCR and direct sequencing. Our new method may aid in the study of SLA diversity and disease resistance and susceptibility.

Nomenclature for factors of the swine leukocyte antigen class II system, 2005

A systematic nomenclature for the genes and alleles of the swine major histocompatibility complex (MHC) is essential to the development and communication of research in swine immunology. The Swine Leukocyte Antigen (SLA) Nomenclature Committee of the International Society for Animal Genetics (ISAG) has reviewed all of the DNA-sequence information for MHC class II genes, available in GenBank/EMBL/DDBJ databases, and the associated published reports to develop such a systematic nomenclature. This article summarizes the proposed nomenclature, which parallels the World Health Organization's nomenclature for factors of the human MHC. The SLA class II genes expressed on the cell membrane will be noted as SLA-DRA, SLA-DRB1, SLA-DQA, and SLA-DQB1. Nomenclature assignments for all SLA class II GenBank sequences are now noted. The committee will add new SLA class II allele designations, as they are discovered, and will maintain a publicly available list of all recognized genes and alleles using the Immuno Polymorphism Database (IPD). The sequences will be available from the IPD-MHC section of the database which contains non-human MHC sequences (http://www.ebi.ac.uk/ipd/mhc/sla/).

Differential alloreactivity at SLA-DR and -DQ matching in two-way mixed lymphocyte culture

The major histocompatibility complex (MHC) class II molecules are heterodimeric cell surface glycoproteins important for antigen presentation to CD4+ T lymphocytes. Class II molecules of the pig MHC, termed SLA, identified so far include DR and DQ. Thus far, functional differences between products of different loci in SLalpha class II have not been well characterized. For detailed research on this issue, SLalpha-DRbeta1 and -DQbeta typings were newly developed by restriction fragment length polymorphism (RFLP) of the reverse transcriptase-polymerase chain reaction (RT-PCR) products. Using this method, several RFLP types were chosen from 13 CSK miniature pigs, and alloreactivities in two-way mixed lymphocyte culture (MLC) derived from these pigs were examined by cell proliferation assay using flow cytometry. The responses in MLC varied according to the degree of phenotype difference. In MLC from individuals of the same RFLP type in both SLA-DRbeta1 and -DQbeta, the proliferative responses showed slight reaction indicating that they were not so stimulated by each other. On the other hand, for the RFLP type-mismatching combination, the responses were strong indicating that they recognized each others alloantigens. The reactivity of only the DQbeta mismatching combination was as strong as those of only the DRbeta1 mismatching combination. These data indicate the important role of the DQ as well as DR molecule on alloreactivity in MLC.