Association between PPAR-δ gene SNPs, haplotypes and resistances to SGIV and RGNNV in the orange-spotted grouper, Epinephelus coioides

Objective  To obtain the disease-resistant molecular markers in grouper (Epinephelus spp.), and serve for the selective breeding program of disease-resistant grouper strains, so as to solve the problem of frequent occurrence of grouper disease.

Method  Single nucleotide polymorphisms (SNPs) were screened based on PPAR-δ genomic DNA sequence, and association analysis of resistance to Singapore grouper iridovirus (SGIV) and red-spotted grouper nervous necrosis virus (RGNNV) was performed on these SNPs.

Result  A total of nine SNPs were detected in the susceptible and resistant groups against SGIV infection, all of which were located in the introns, with the polymorphism information contents (PICs) ranging from 0.177−0.375. Among the SNPs, SNP-S1(g.940T>A) showed low degree polymorphism (PIC<0.25), while the rest SNPs showed moderate degree polymorphism(0.25≤PIC<0.50). The association analysis showed that the genotype frequencies of SNP-S7 (g.4595T>A) were significantly different between SGIV susceptible and resistant groups (P<0.05), the TT and AA homozygous genotypes of SNP-S7 were correlated with SGIV resistance traits, while the AT heterozygous genotypes were correlated with SGIV susceptibility traits. In addition, a total of eight SNPs were detected in the susceptible and resistant groups agasinst RGNNV infection, among which SNP-N1 was located in the exon, with a synonymous mutation, and the rest SNPs were located in the introns, with the PICs ranging from 0.106−0.317. Among the SNPs, SNP-N1 (g.324G>A) and SNP-N2 (g.883A>G) showed low degree polymorphism (PIC<0.25), while the rest SNPs showed moderate degree polymorphism (0.25≤PIC<0.50). The association analysis showed that SNP-N5 (g.2510C>T) genotype frequencies were significantly different between RGNNV susceptible and resistant groups (P<0.05), the CT genotype of SNP-N5 was correlated with RGNNV resistance traits and the CC genotype was correlated with RGNNV susceptibility traits.

Conclusion  In this study, we successfully screened one SNP marker related to SGIV resistance and one SNP marker related to RGNNV resistance from PPAR-δ genomic DNA sequence. This finding can offer a technical support and a theoretical basis for resistance breeding of grouper.