Abstract：The selection of disease resistance related SNP markers is the basis and prerequisite for disease resistance breeding. Interferon-b promoter stimulator 1 (IPS-1) plays a pivotal role in the production of type I interferon (IFN) and pro-inflammatory cytokines. In order to obtain the SNPs associated with the disease resistance in nile tilapia (Oreochromis niloticus), in this paper we designed four pairs primers to amplify the IPS-1 gene (ENSONIG00000012278). Through sequencing by cloning or directly sequencing of PCR products, 36 SNPs were obtained from 39 individuals of 20 nile tilapia parents family. Seventeen sites (S1 and S21-S36) located in exon region, and 9 SNPs were nonsynonymous mutation, 4 SNPs were synonymous mutation. Nineteen sites located in intron region. By directly sequencing or SNaPshot method, 82 individuals from susceptible group and 84 individuals from resistance group of offspring were used to analyze polymorphisms and Genetic parameter. Popgen32 was used to calculated the polymorphisms and genetic parameter of the IPS-1 SNPs in susceptible group and resistance group. The results showed that the polymorphism information content (PIC) value of the IPS-1 SNPs ranged from 0.02 to 0.37, suggesting that all SNPs locus had low or moderate polymorphism. Significant departure from Hardy-Weinberg equilibrium was observed at 16 SNPs in resistance group and 5 SNPs in susceptible group (P＜0.001). The genotype frequency and allele frequency of the 36 SNPs in IPS-1 gene were analyzed by SPSS 20 and tested by χ2 test. And the correlation between the IPS-1 SNPs and the phenotype of Streptococcus agalactiae resistance was analyzed. The results showed that One SNP (S8(T-3756C)) was significantly associated with S. agalactiae susceptible trait (P＜0.05). In resistance group, the frequency of CC, CT, and TT genotype was 97.5%, 2.5% and 0%, respectively, and in susceptible group, the frequency was 75.7%, 12.2% and 12.2%, respectively. The linkage disequilibrium analysis and prediction of haplotypes showed that all the 36 IPS-1 SNPs formed 6 haplotype blocks and 22 haplotypes. Three of the haplotypes H2-3 (GTTG), H3-2 (CCDGTTGAGCGCCA) and H3-4 (TTDGTTGAGCGCCA) were significantly associated with S. agalactiae susceptible trait. And 3 of the haplotypes H3-5 (TCDGTTGAGCGCCA) were significantly associated with S. agalactiae resistance trait (P＜0.05). These results indicate that the SNP site S8 and the four haplotypes H2-3, H3-2, H3-4, H3-5 of IPS-1 gene can be candidate molecular marker for disease resistance breeding of nile tilapia. This study provided a data base for breeding resistant strains of Nile tilapia.
