MHC polymorphism and disease resistance to Singapore grouper iridovirus (SGIV) in the orange-spotted grouper, Epinephelus coioides

Major histocompatibility complex (MHC) genes are critical members in both innate and adaptive immunity, and the association between their polymorphism and disease resistance has been reported in many teleosts. In the present study, we first investigated the genetic variation at the MHC II β gene in orange-spotted grouper (Epinephelus coioides) after a challenge with Singapore grouper iridovirus (SGIV). The results reveal that a high polymorphism level of the MHC II β gene (H = 1.000; K = 20.206; π = 0.081) and at least three loci exist in grouper. The rate of dN/dS in the peptide-binding region (PBR) and non-PBR were both >1, suggesting the loci were evolving under positive selection. A high ratio of heterozygous individuals (37.26 %) and high rate of dN/dS were discovered, suggesting that both heterozygote advantage and frequency-dependent selection might result in the high polymorphism levels in MHC II β genes in grouper. A total of 33 MHC II β alleles were identified from 40 high-susceptibility (HS) and 40 high-resistance group (HR) individuals, and 15 alleles were used in the association analysis. Three alleles, EPCO-DBB*0302, EPCO-DBB*0307, EPCO-DBB*0603, and EPCO-DBB*1001 were significantly associated with resistance ability to SGIV, and the EPCO-DBB*0607 and EPCO-DBB*1303 alleles were associated with susceptibility (P < 0.05). To further confirm the association, another independent challenge experiment was performed. The result of association analysis in the verification test found that only EPCO-DBB*1001 alleles were significantly associated with resistance to SGIV (P < 0.05), while the other alleles showed no significance (P > 0.05) in the frequency distribution between HR and HS groups. Therefore, the EPCO-DBB*1001 alleles could be used as a disease resistance-related MHC marker in the molecular marker-assisted selective breeding program of grouper.