The SNPs of three immunity genes in striped catfish, Pangasianodon hypophthalmus are associated with resistance against infection of Aeromonas hydrophila

Abstract

Three important immunity-related genes, NLRC3 (nucleotide-oligomerization domain (NOD)-like receptor subfamily C), IL4R (interleukin 4 receptor), and C4 (complement component 4), can respond to infection by Aeromonas hydrophila in the spleen of striped catfish, Pangasianodon hypophthalmus. However, their association with resistance against infection by A. hydrophila are unknown. In this study, the expression of NLRC3, IL4R, and C4 in heart, liver, spleen, head kidney, trunk kidney, and gill of striped catfish after A. hydrophila infection was determined using quantitative real-time PCR. Single nucleotide polymorphism (SNP) identification and genotyping were performed by Sanger sequencing. We then analyzed the correlation between these polymorphisms and resistance to A. hydrophila infection. NLRC3, IL4R, and C4 were strongly induced by A. hydrophila infection in the liver, spleen, trunk kidney, and gill that peaked in the liver at 12 h post-infection. Three SNPs from NLRC3, two SNPs from IL4R, and two SNPs from C4 were identified by direct sequencing, in which NLRC3-CM018541.1-359661A/T, NLRC3-CM018541.1-359672G/T, NLRC3-CM018541.1-359815G/C, IL4R-CM018563.1-17094599G > A, and C4-CM018554.1-20401796A > T were associated with the incidence of resistant and susceptible phenotypes in striped catfish. Additionally, three SNP loci (NLRC3-CM018541.1-359661A/T, NLRC3-CM018541.1-359672G/T, and NLRC3-CM018541.1-359815G/C) showed strong pairwise linkage disequilibrium, and the haplotype AGC generated with these three SNPs was associated with resistance to A. hydrophila in striped catfish. These findings suggest strongly a relationship between the NLRC3, IL4R, C4 polymorphisms and A. hydrophila resistance in striped catfish, and that the NLRC3 gene could be used as a candidate marker for genetic selection of A. hydrophila-resistant striped catfish.