SLA-1 Genetic Diversity in Pigs: Extensive Analysis of Copy Number Variation, Heterozygosity, Expression, and Breed Specificity

Sci Rep. 2020 Jan 20;10(1):743. doi: 10.1038/s41598-020-57712-5.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • Breeding*
  • Cell Line
  • DNA Copy Number Variations*
  • Gene Expression
  • Genetic Variation*
  • Haplotypes
  • Heterozygote*
  • High-Throughput Nucleotide Sequencing / methods*
  • Histocompatibility Antigens Class I / genetics*
  • Histocompatibility Testing / methods*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Swine / genetics*
  • Swine / immunology*

Substances

  • Histocompatibility Antigens Class I
  • RNA, Messenger
  • swine leukocyte antigen