Phylogenetic analysis of the swine leukocyte antigen — 2 gene for Korean native pigs

The objective of this study was to investigate genetic relationships of the SLA-2 gene, to characterize SLA-2 alleles, and to provide basic genetic information of Korean pigs. The swine leukocyte antigen - 2 (SLA-2) gene in the MHC classical region was cloned with spleen tissues from Korean native pigs selected from the main land (KNP) and Jeju Island (KJP). Primer sequences based on swine cDNA (GenBank accession numbers AF464049 and AF464005) were used to amplify the entire SLA-2 gene, and the amplification product including both 3′ and 5′ UTRs was sized 1,520 bp. A BAC clone was selected from miniature pigs and sequenced for the genomic region of the SLA-2 gene showing that 4,585 bp in total length consisted of exons (1,087 bp) and introns (3,498 bp). A sequence analysis confirmed 58 SNPs in coding regions, which revealed higher numbers of SNPs in KNP than other pig breeds, implicating more genetic variability in Korean pigs. Approximately 82% of the SLA-2 SNPs were located in the highly polymorphic exons 2 and 3. Newly identified sequences of the SLA-2 gene for KNP and KJP were submitted into the IPD-MHC database with new nomenclatures (SLA-2*1501, SLA-2*1601, and SLA-2*w08hy01 allele), while the representative sequences of KNP and KJP were submitted into GenBank with accession numbers (DQ992495, DQ992496, and DQ992501), respectively. The identified KNP allele (SLA-2*1501) clustered with previously defined alleles for Korean pigs (SLA-2*kn02 and SLA-2*jh01), but SLA-2*1601 (KNP) and SLA-2*w08hy01 (KJP) alleles showed no significant genetic relationships with any other allele. A sequence comparison revealed that KNP has departed from KJP both genetically and phenotypically. The results of SLA-2 SNP in KNP and KJP reported here will serve as the SLA-2 reference for Korean pigs.