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Background  Genes in the major histocompatibility complex (MHC) have a critical role in both the innate and adaptive immune responses because of their involvement in presenting foreign peptides to T cells. However, the nature has remained largely unknown.    Results  We examined the genetic variation in MHC class IIB in half-smooth tongue sole ( Cynoglossus semilaevis ) after challenge with  vibrio anguillarum . Two thousand and four hundred fry from 12 half-smooth tongue sole families were challenged with  Vibrio anguillarum . To determine any association between alleles and resistance or susceptibility to  V. anguillarum , 160 individuals from four high-resistance (HR, < 40.55% mortality) families and four low-resistance (LR, > 73.27% mortality) families were selected for MHC IIB exon2 gene sequence analysis. The MHC IIB exon2 genes of tongue sole displayed a high level of polymorphism and were discovered at least four loci. Meanwhile, the d N /d S  [the ratio of non-synonymous (d N ) substitutions to synonymous (d S ) substitutions] in the peptide-binding region (PBR) was higher than that in the non-peptide-binding region (non-PBR). Eighty-eight alleles were discovered among 160 individuals, and 13 out of 88 alleles were used to analyze the distribution pattern between the resistant and susceptible families. Certain alleles presented in HR and LR with a different frequency, while other alleles were discovered in only the HR or LR families, not both. Five alleles,  Cyse-DBB*6501 ,  Cyse-DBB*4002 ,  Cyse-DBB*6102 ,  Cyse-DBB*5601  and  Cyse-DBB*2801 , were found to be associated with susceptibility to  V. anguillarum  with a frequency of 1.25%, 1.25%, 1.25%, 1.25% and 2.5% in the HR families, and 35%, 33.75%, 27.5%, 16.25%, 15% in the LR families ( p  < 0.01, 0.01, 0.01, 0.01, 0.01), respectively. Four alleles,  Cyse-DBB*3301 ,  Cyse-DBB*4701 ,  Cyse-DBB*6801  and  Cyse-DBB*5901 , were found to be associated with resistance to  V. anguillarum , with a frequency of 13.75%, 11.25%, 11.25%, 8.75% in the HR families and 1.25%, 1.25%, 1.25%, 1.25% and 1.25% in the LR families ( p  < 0.01, 0.05, 0.05 and p = 0.064), respectively.    Conclusions  Elucidation of the role of MHC II B genes in half-smooth tongue sole should prove to be helpful to the in-depth development of marker-assisted selective breeding in half-smooth tongue sole.

MHC polymorphism and disease resistance to vibrio anguillarum in 8 families of half-smooth tongue sole (Cynoglossus semilaevis)