Haplotype-resolved swine leukocyte antigen (SLA) gene typing using long-read whole genome sequencing

The Major Histocompatibility Complex (MHC) is a genomic region present in all vertebrates encoding genes essential for the immune response. In pigs, the MHC is named the Swine Leukocyte Antigen (SLA) complex. Traditional methods for SLA gene typing rely on targeted amplification and sequencing of SLA genes. In this study, we evaluated whether SLA genes can be identified from non-targeted Oxford Nanopore long-read sequencing data, to create a versatile approach that can be applied to existing long-read sequencing datasets.

We analyzed 56 pigs from four breeds (Large White, Duroc, Landrace and a Large White-derived synthetic line) and generated de novo genome assemblies that were separated into haplotypes through phasing and haplotagging. SLA gene sequences from the IPD-MHC database were mapped to the haplotype-resolved assemblies, and candidate novel alleles and haplotypes were assessed using targeted NGS-based SLA typing.

This approach enabled confident allele assignment for over 95% of SLA-1, SLA-2, SLA-3, SLA-DRB1, and SLA-DQB1 genes. The majority of results consisted of haplotypes which have been previously reported and additionally included several potential novel alleles and haplotypes. Targeted NGS-based SLA typing confirmed seven novel class I haplotypes as well as the presence of three novel SLA-2 alleles, although additional sequencing is required to fully resolve the exon 2 sequence for two of them. We also observed strong linkage between assembly-derived SLA haplotypes and medium-density genotypes within the SLA region, supporting efficient identification and monitoring of SLA diversity in populations with similar linkage disequilibrium structures.

Existing long-read sequencing and genotype datasets can be leveraged to characterize SLA variation, identify candidate novel haplotypes and alleles, and provide insight into SLA diversity within the pig populations studied.