Gene function & annotation

Swine leukocyte antigen (SLA) gene typing of four commercial pig breeds using long-read whole genome sequencing

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Abstract

The Major Histocompatibility Complex (MHC) is a genomic region present in all vertebrates. It encodes the MHC molecules which are responsible for processing and presenting antigens to the immune system. Genetic variation in the MHC genes can alter the repertoire of antigens that can be bound and presented to the immune system, making these genes highly relevant to study at the genomic level. In pigs, the MHC is known as the Swine Leukocyte Antigen (SLA) complex. Traditional SLA typing methods rely on targeted amplification of SLA genes using specific primers. While such methods provide high accuracy, they require laboratory-based assays and produce data restricted to the SLA genes. In this study, we aimed to perform high-resolution SLA typing using long-read whole genome sequencing (WGS) data, to create a versatile approach that can be applied to existing long-read WGS datasets. We analyzed 56 pigs from four breeds (Large White, Duroc, Landrace and a Large White-derived synthetic line), using Oxford Nanopore long-read WGS data. We generated de novo assemblies for each animal using NextDenovo and proceeded to resolve the haplotypes through phasing and haplotagging. The SLA gene sequences from the IPD-MHC database were aligned to the haplotype-resolved assemblies using minimap2, finally resulting in perfect matches for over 95% of genes (SLA-1, SLA-2, SLA-3, SLA-DRB1 & SLA-DQB1). Our results matched well with previously-reported SLA haplotypes, and additionally included two potential novel SLA-2 alleles and six potential novel class I haplotypes. We observed that several SLA haplotypes show evidence of gene duplication, highlighting the complex genomic architecture of this locus. Furthermore, we observed a strong linkage between the SLA haplotypes and the medium-density genotype results for a set of 23 SNPs distributed across the class I region and 9 SNPs across the class II region, enabling efficient identification and monitoring of SLA diversity within populations.In conclusion, we present a novel approach for typing SLA genes and haplotypes using long-read WGS data. We successfully applied this method in several breeds, providing valuable knowledge on SLA diversity. This method can support and advance research into fields where MHC diversity plays an important role, such as disease resistance, host-pathogen interaction and potential peptide-based vaccine development.

Keywords: 2026

How to Cite:

Boshove, A., Dunkelberger, J., Sevillano, C., Callison, S., Lewiner, T., Jansen, C. & Derks, M., (2026) “Swine leukocyte antigen (SLA) gene typing of four commercial pig breeds using long-read whole genome sequencing”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285440. doi: https://doi.org/10.31274/wcgalp.23709

Rights: 1