Association between MHC II beta chain gene polymorphisms and resistance to infectious haematopoietic necrosis virus in rainbow trout (Oncorhynchus mykiss, Walbaum, 1792)

Infectious haematopoietic necrosis virus (IHNV) is a serious pathogenic threat to rainbow trout (Oncorhynchus mykiss) and other salmonids. Major histocompatibility complex (MHC) polymorphisms have been closely linked to disease susceptibility. In this study, polymerase chain reaction-single-strand conformation polymorphism, cloning and sequencing were used to examine MHC class II chain gene (DAB) polymorphisms and analyse their association with IHNV in rainbow trout. The DAB exon 2 was amplified from 104 resistant and 91 susceptible fish. Forty-five different alleles were identified, 30 of which were novel. Individuals possessed between one and four alleles, indicating that the genome harbours at least two closely related DAB exon 2 loci. The percentages of amino acid mutations in the peptide binding region (PBR) and non-PBR were 66.67% and 45.28% respectively. The rate of non-synonymous substitutions occurred at a significantly higher frequency than synonymous substitutions, suggesting the existence of balancing selection for maintenance of polymorphisms at the DAB exon 2 locus. The alleles Onmy-DAB*0201 (P<0.001), Onmy-DAB*0904 (P<0.001) and Onmy-DAB*1102 (P<0.01) were associated with susceptibility to IHNV, while Onmy-DAB*0103, Onmy-DAB*0601 and Onmy-DAB*1402 were associated with resistance (P<0.001). These alleles could be used as molecular markers for IHNV resistance breeding in rainbow trout.