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 β 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.