Abstract
The Guizhou pony (GZP) is an indigenous species of equid found in the mountains of the Guizhou province in southwest China. We selected four regions of the equine leukocyte antigen (ELA), including DQA, DRA, DQB, and DRB, and used them to assess the diversity of the major histocompatibility complex (MHC) class II gene using direct sequencing technology. DRA had the lowest dN/dS ratio (0.560) compared with the other three loci, indicating that DRA was conserved and could be conserved after undergoing selective processes. Nine DQA, five DQB, nine DRA, and seven DRB codons were under significant positive selection at the antigen binding sites (ABS), suggesting that the selected residues in ABS may play a significant role in the innate immune system of the GZP. Two GZP alleles were shared with Przewalski’s horse, and six older GZP haplotypes had a better relationship with other horse species by one or two mutational steps, indicating that the GZP may be a natural ancient variety of equid. The specific diversity of ABS and the numbers of unique haplotypes in the evolutionary process affords this species a better genetic fitness and ability to adapt to the native environment.
Highlights
The major histocompatibility complex (MHC) genes play a major role in vertebrate immune systems and have a high degree of genetic diversity associated with the adaptive immune response and evolution (Lian et al, 2017; Kamath & Getz, 2011)
The nucleotide diversity in DRA was much lower than in DQA/B and DRB in Guizhou pony (GZP), which is comparable with the level of nucleotide diversity in DRA from other species in the Equus genus (Kamath & Getz, 2011)
Within the GZP, the genetic diversity was much higher in DQA, DQB, and DRB than in DRA and the ratio was the lowest at the DRA locus (15.04%) and highest at the DQB locus (46.08%)
Summary
The major histocompatibility complex (MHC) genes play a major role in vertebrate immune systems and have a high degree of genetic diversity associated with the adaptive immune response and evolution (Lian et al, 2017; Kamath & Getz, 2011). The MHC class II genes are highly polymorphic parts of the immune response that act by presenting extracellular antigens to T lymphocytes. These molecules are heterodimers with α and β chains encoded by A and B genes. The polymorphic sites of the class II genes are typically located at exon 2, which codes for the first extracellular domain or the antigen binding sites (ABS). The ABS mainly encoded the second exon of the MHC class II gene and have more variation than the neighboring regions in this sequence (Li et al, 2014), indicating that ABS variation may help to determine the rates of evolution across the MHC (Hughes & Hughes, 1995). Previous studies have shown that exon 2 of MHC class II genes
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