Swine leukocyte antigens play indispensable roles in immune responses by recognizing a large numberof 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. open Scientific RepoRtS | (2020) 10:743 | https://doi.org/10.1038/s41598-020-57712-5www.nature.com/scientificreports www.nature.com/scientificreports/ SLA-1, SLA-2, and SLA-3 are constitutively expressed classical MHC class I genes, but their expression may vary depending on the genetic differences. For example, SLA-1 is duplicated in the haplotypes Hp-2.0, Hp-8.0, Hp-11.0, Hp-12.0, Hp-19.0, Hp-20.0, and Hp-27.0 14,24-26 . In addition, SLA-1, 3, and 6 were not expressed in the haplotypes Hp-3.0, Hp-2.0, and Hp-5.0, respectively 24 . Recently, a method was reported to estimate the copy number of SLA-1 and to facilitate our understanding on the functional aspect of SLA-1 duplication 27 . The frequency of SLA-1 duplication could be abundant, but the detailed functional analysis is not been available.Therefore, we developed a genomic DNA based high resolution SLA-1 typing method with high accuracy regardless of CNVs and present the extensive analysis results of SLA-1 diversity including new alleles and haplotypes, and allelic distribution among different breeds. We also analyzed the level of SLA-1 expression in pig cells according to their copy numbers which could affect MHC class I-specific immune responses. The information presented in this study should contribute to improving our understanding on the genetic polymorphisms of SLA-1 in diverse pig breeds. ResultsDetermination of the SLA-1 specific region. To develop a genomic DNA-based typing method of SLA-1, the determination of conserved locus specific region to design SLA-1 specific primers is required. We previously reported the locus specific nucleotide sequence variations at the downstream promoter region from six classical SLA class I-related genes including . Here, we extended the results by incorporating genomic sequences from additional cloning and sequence analysis. As a result, we identified a SLA-1 specific motif between the TATA box and the CAP site in the 5ʹ UTR and designe...

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