Fascioloidosis is a parasitic disease caused by a trematode Fascioloides magna. Since major histocompatibility complex (MHC) genes play an important role in the immune response, the aim of this study was to compare the potential differences in MHC class II SLA-DRB1 exon 2 genes between wild boar populations from infected (cases) and non-infected areas (controls). During the winter of 2021, a total of 136 wild boar tissue samples were collected, 39 cases and 97 controls. DNA was extracted and sequenced using the Illumina platform. Differences in distributions of allele combinations were calculated using the Chi-Square test for homogeneity and between proportions using the large-sample test and Fisher–Irwin test. Analysis revealed 19 previously described swine leucocyte antigen (SLA) alleles. The number of polymorphic sites was 79 (29.6%), with 99 mutations in total. Nucleotide diversity π was estimated at 0.11. Proportions of the alleles SLA-DRB1*12:05 (p = 0.0008379) and SLA-DRB1*0101 (p = 0.0002825) were statistically significantly higher in controls, and proportions of the SLA-DRB1*0602 (p = 0.006059) and SLA-DRB1*0901 (p = 0.0006601) in cases. Alleles SLA-DRB1*04:09, SLA-DRB1*0501, SLA-DRB1*11:09, and SLA-DRB1*1301 were detected only in cases, while SLA-DRB1*0404, SLA-DRB1*0701, SLA-DRB1*02:10, and SLA-DRB1*04:08 were present only in controls. We did not confirm the existence of specific alleles that could be linked to F. magna infection. Detected high variability of the MHC class II SLA-DRB1 exon 2 genes indicate high resistance potential against various pathogens.

Major histocompatibility complex (MHC) genes are widely recognised as valuable markers for wildlife genetic studies given their extreme polymorphism and functional importance in fitness-related traits. Newly developed genotyping methods, which rely on the use of next-generation sequencing (NGS), are gradually replacing traditional cloning and Sanger sequencing methods in MHC genotyping studies. Allele calling in NGS methods remains challenging due to extreme polymorphism and locus multiplication in the MHC coupled with allele amplification bias and the generation of artificial sequences. In this study, we compared the performance of molecular cloning with Illumina and Ion Torrent NGS sequencing in MHC-DRB genotyping of single-locus species (roe deer) and species with multiple DRB loci (red deer) in an attempt to adopt a reliable and straightforward method that does not require complex bioinformatic analyses. Our results show that all methods work similarly well in roe deer, but we demonstrate non-consistency in results across methods in red deer. With Illumina sequencing, we detected a maximum number of alleles in 10 red deer individuals (42), while other methods were somewhat less accurate as they scored 69–81% of alleles detected with Illumina sequencing.