Polymorphism analysis of major histocompatibility complex (MHC) DQB gene in the Asiatic black bear (Ursus thibetanus)

High polymorphism in major histocompatibility complex (MHC) genes plays an essential role in adaptive immune response among vertebrates through antigen recognition and presentation. For vulnerable Asiatic black bear, a lack of DQB gene sequences from continental populations hindered further genetic diversity analysis in a large geographical region. Here, we used PCR cloning and sequencing to characterize genetic diversity of DQB gene among different populations of the species. Trans-species polymorphism (TSP) and selective strength of DQB gene were assessed by sequence analysis in Ursidae. Forty-seven novel Urth-MHC haplotypes, including 32 putative functional alleles (PFA, Urth-DQB*33-Urth-DQB *64) and one presumed pseudogene (Urth-DQB*65), were identified in the population. Allelic frequency varied greatly (Urth-DQB*4601 had the highest value) and number of rare alleles was high (34.04%). This might suggest a risk of allele loss by inbreeding and genetic drift if the effective populations continue to be subdivided and decline without appropriate conservation strategies. In the southern continental population (captive animals), the total number of alleles and population-specific alleles were higher than those in the northern. This suggested the southern continental population was exposed to various pathogens and close conservation attention is required to keep the population safe. Based on values of Hd, pi, and K, genetic diversity of the island population was lower when compared to continental populations. This could be explained by fewer pathogen communities in island populations, and confirmed the prediction that large majority of island populations would be less genetically diverse than their continental counterparts. No any allele including those ancestral alleles being similar among Ursidae species was shared between the continental and island populations. In phylogenetic analysis, DQB alleles did not show monophyletic for any single species and four alleles were shared among Ursidae. This pattern was TSP. The ratio (omega = d(N) / d(S)) was significantly higher than unity on PBR codons (4.029). These features supported the influence of balancing selection of the DQB locus among continental populations and contributing to the genetic diversity of Urth-DQB. All codons under positive selection matched the PBR sites inferred by HLA-DQB using four testing methods. Pathogen-driven positive selection could be the other important mechanism to maintain the advantageous mutation for DQB alleles. This information will not only promote the understanding of MHC diversity and polymorphism in the Asiatic black bear but will also increase the implication of protecting vulnerable species in the wild and captive for the appropriate management and conservation initiatives.