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United States Department of Agriculture

Agricultural Research Service

Research Project: ENHANCING GENETIC MERIT OF DAIRY CATTLE THROUGH GENOME SELECTION AND ANALYSIS Title: Phylogenetic analysis of the swine leukocyte antigen - 2 gene for Korean native pigs

Authors
item Chung, Hoyoung -
item McClure, Matthew
item Kim, Jaeyoung -

Submitted to: Genes and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 4, 2011
Publication Date: August 31, 2011
Citation: Chung, H., Mcclure, M.C., Kim, J. 2011. Phylogenetic analysis of the swine leukocyte antigen - 2 gene for Korean native pigs. Genes and Genomics. 33:345-351.

Interpretive Summary: For the native Korean pig to be a potential alternative to the NIH miniature pigs for medical research and swine leukocyte antigen (SLA) class I studies, genetic characterization of the SLA-2 gene is needed. This study’s objectives is to investigate phylogenetic distances of the SLA-2 gene, characterize SLA-2 alleles, and provide basic genetic information for selection for Korean pigs that were domesticated on the Korean peninsula (KNP) and Jeju Island (KJP). Phylogenetic analysis of SLA-2 sequences indicates that both KNP and KJP are significantly different from most European and Western pig breeds. Additionally, the genetic variation in the SLA-2 coding regions was greater in both KNP (58 SNP identified) and KJP (60 SNP) than the NIH miniature pigs (38 SNP). Therefore KNP and KJP should be considered in future research studies.

Technical Abstract: The objective of this study was to investigate genetic distances 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 the swine cDNA (GenBank accession numbers AF464049 and AF464005) were used to amplify the SLA-2 gene, and the amplification product being 1,520 bp in length includes both the 3’ and 5’ UTRs. A BAC clone was selected from miniature pig (MIP) 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 total of 58 SNPs in coding regions were identified, with higher numbers of SNPs being found 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 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 in this study showed close genetic distances with SLA-2*w10 (Hanford) and SLA-2*w08 (Yucatan) alleles, respectively. According to the results, we conclude that KNP departed from KJP genetically and phenotypically, and possible uses of Korean pigs in medical research areas should be considered with reducing genetic variability in the SLA-2 gene.

Last Modified: 10/20/2014
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