Abstract
Swine leukocyte antigens play indispensable roles in immune responses by recognizing a large number of foreign antigens and thus, their genetic diversity plays a critical role in their functions. In this study, we developed a new high-resolution typing method for pig SLA-1 and successfully typed 307 individuals from diverse genetic backgrounds including 11 pure breeds, 1 cross bred, and 12 cell lines. We identified a total of 52 alleles including 18 novel alleles and 9 SLA-1 duplication haplotypes, including 4 new haplotypes. We observed significant differences in the distribution of SLA-1 alleles among the different pig breeds, including the breed specific alleles. SLA-1 duplication was observed in 33% of the chromosomes and was especially high in the biomedical model breeds such as SNU (100%) and NIH (76%) miniature pigs. Our analysis showed that SLA-1 duplication is associated with the increased level of SLA-1 mRNA expression in porcine cells compared to that of the single copy haplotype. Therefore, we provide here the results of the most extensive genetic analysis on pig SLA-1.
Highlights
Swine leukocyte antigens play indispensable roles in immune responses by recognizing a large number of foreign antigens and their genetic diversity plays a critical role in their functions
We previously developed the genomic sequence-based high-resolution typing (GSBT) methods for swine leukocyte antigen (SLA)-2, -DQA, -DQB1, and -DRB1, and presented the results of new allele identification using a large number of field samples and population genetic analysis on diverse breeds[18,19,20,21,22]
We developed a comprehensive high-resolution typing of SLA-1 using single-genomic PCR and subsequent direct sequencing, and reported the identification of new alleles and duplication haplotypes from the typing of over 300 animals from diverse breeds and cell lines
Summary
Swine leukocyte antigens play indispensable roles in immune responses by recognizing a large number of foreign antigens and their genetic diversity plays a critical role in their functions. Several methods have been used to investigate the genetic diversity of SLA genes, including the polymerase chain reaction sequence-specific primer methods (PCR-SSP)[13,14,15], PCR-restriction fragment length polymorphism (PCR-RFLP)[13,16], and cDNA based typing[17] These DNA based typing methods still require further improvement in the resolution of the typing results, comprehensiveness in allele coverage, and usability for large-scale typing. We previously developed the genomic sequence-based high-resolution typing (GSBT) methods for SLA-2, -DQA, -DQB1, and -DRB1, and presented the results of new allele identification using a large number of field samples and population genetic analysis on diverse breeds[18,19,20,21,22]. 89 alleles for SLA-1 have been reported in the IPD database including the results from this study[23]
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