Unlocking pig immune-system diversity with long-read genomics

Researchers from Animal Breeding and Genomics and the Topigs Norsvin Research Centre explored whether the Swine Leukocyte Antigen (SLA) complex – a genomic region which plays an important role in the immune system of pigs – can be identified from non-targeted Oxford Nanopore long-read sequencing data. By analysing 56 pigs from different breeds, the researchers successfully identified most SLA alleles and discovered previously unreported genetic variants and haplotypes.

The SLA complex is the pig equivalent of the Major Histocompatibility Complex (MHC), a highly polymorphic genomic region which plays an essential role in the immune response. Genetic variation in SLA genes influences which pathogen-derived peptides can be recognised by the immune system, making knowledge of SLA diversity relevant for studies of disease response, vaccination and population diversity.

Identifying SLA genes in existing genomic data

Traditional methods for SLA gene typing rely on targeted amplification and sequencing of SLA genes, which is very time consuming and requires dedicated lab work. In the study that was recently published in Frontiers in Immunology, researchers 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.

The researchers analysed 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.

Uncovering hidden diversity and expanding monitoring opportunities

“More than 95 percent of the investigated SLA genes could be confidently assigned,” says Anne Boshove, researcher at Animal Breeding and Genomics and first author of the study. “This demonstrates that non-targeted long-read whole genome sequencing can provide detailed SLA information without SLA-specific sequencing.” Beyond identifying known diversity, the researchers’ approach enabled discovery of previously undescribed SLA variation. Seven novel SLA class I haplotypes were identified and subsequently confirmed using independent targeted sequencing, including three novel SLA-2 gene variants.

The researchers also found strong linkage between the assembly-derived SLA haplotypes and SNP haplotypes constructed from routine medium-density genotype data and used an independent SLA-typed dataset to support these associations. These results suggest that once SLA haplotypes have been characterised using long-read or targeted sequencing, routine SNP-chip data may provide a more accessible and cost-effective way to monitor SLA diversity on population-wide scales.