Abstract
Swine leukocyte antigen (SLA) plays a central role in controlling the immune response by discriminating self and foreign antigens and initiating an immune response. Studies on SLA polymorphism have demonstrated associations between SLA allelic variants, immune response, and disease resistance. The SLA polymorphism is due to host-pathogen co-evolution resulting in improved adaptation to diverse environments making SLA a crucial genomic region for comparative diversity studies. Although locally-adapted African pigs have small body sizes, they possess increased resilience under harsh environmental conditions and robust immune systems with reported tolerance to some diseases, including African swine fever. However, data on the SLA diversity in these pigs are not available. We characterized the SLA of unrelated locally-adapted domestic pigs from Homa Bay, Kenya, alongside exotic pigs and warthogs. We undertook SLA comparative diversity of the functionally expressed SLA class I (SLA-1, SLA-2) and II (DQB1) repertoires in these three suids using the reverse transcription polymerase chain reaction (RT-PCR) sequence-based typing (SBT) method. Our data revealed higher genetic diversity in the locally-adapted pigs and warthogs compared to the exotic pigs. The nucleotide substitution rates were higher in the peptide-binding regions of the SLA-1, SLA-2, and DQB1 loci, indicative of adaptive evolution. We obtained high allele frequencies in the three SLA loci, including some breed-specific private alleles, which could guide breeders to increase their frequency through selection if confirmed to be associated with enhanced resilience. Our study contributes to the growing body of knowledge on genetic diversity in free-ranging animal populations in their natural environment, availing the first DQB1 gene data from locally-adapted Kenyan pigs.
Highlights
The major histocompatibility complex (MHC) proteins play a vital role in binding and presenting endogenous and exogenous epitopes derived from the host or pathogen to the circulating T-cells, initiating a T-cell-mediated immune response [1,2,3,4,5]
reverse transcription polymerase chain reaction (RT-PCR) amplification was performed on blood samples from 59 animals (43 domestic pigs and 16 warthogs) using the locus-specific MHC Swine leukocyte antigen (SLA) primers (Table S1)
We reported a high proportion of SLA-1, SLA-2, and DQB1 breed-specific alleles among the locally-adapted pigs and warthogs compared to the exotic pigs [6,8]
Summary
The major histocompatibility complex (MHC) proteins play a vital role in binding and presenting endogenous and exogenous epitopes derived from the host or pathogen to the circulating T-cells, initiating a T-cell-mediated immune response [1,2,3,4,5]. Classical MHC I molecules are highly polymorphic and present antigenic peptide ligands on infected cells to CD8+ T cells, whereas the non-classical MHC I molecules facilitate repressively or activate stimuli in natural killer cells [12]. Seven classical SLA class, I loci are known: SLA-1, SLA-2, SLA-3, SLA-4, SLA-5, SLA-9, and SLA-11, of which only SLA-1, SLA-2, and SLA-3 are highly polymorphic and functional, with a classical MHC class I molecular structure consisting of a leader sequence, three exons encoding the extracellular α1, α2, and α3 domains, a transmembrane region, and three cytoplasmic exons [13,14]. The α1 and α2 domains form an 8- to 10-mer peptide-binding region (PBR). The PBRs are highly polymorphic and diverse regions of the SLA, thereby ensuring greater diversity for binding and presenting peptides [13,16,17,18]
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