Abstract：Nucleotide binding and oligomerization domain 1 gene (NOD1) plays important role in fish innate immunity. In order to obtain the SNPs associated with the disease resistance in Nile tilapia (Oreochromis niloticus), genome sequence NOD1 (GenBank No. MF479261) was cloned. Through cloning sequencing or direct sequencing of PCR products, 44 SNPs were obtained from 39 individuals of 20 Nile tilapia parents family. By directly sequencing or SNaPshot method, 83 individuals from susceptible group (SG) and 83 individuals from resistance group (RG) of offspring were used to analyze polymorphisms and genetic parameter. Popgen 32 was used to calculate the genetic parameter and polymorphisms of the NOD1 SNPs in susceptible group and resistance group. The results showed that 24 SNPs were genotyped successfully. The polymorphism information content (PIC) value of the 24 SNPs of NOD1 gene ranged from 0.09 to 0.37, which suggested that all 24 SNPs were low or moderate polymorphism. The correlation between the NOD1 SNPs and the trait of S.agalactiae resistance was analyzed. The results showed that SNP5 (G-2284C) was significantly associated with S. agalactiae susceptible trait (P＜0.05), SNP13 (G-8956C) were significantly associated with S. agalactiae resistant trait (P＜0.05). SNP12 (G-8955C) was significantly associated with S. agalactiae resistant/susceptible trait (P＜0.05). The linkage disequilibrium analysis and prediction of haplotypes showed that all the 24 NOD1 SNPs formed 5 haplotype blocks and 16 haplotypes. The haplotypes H4-2 (AC) was significantly associated with S. agalactiae resistant trait. These results indicate that the SNP site SNP5, SNP12, SNP13 and the haplotypes H4-2 of NOD1 gene can be candidate molecular markers for molecular marker assisted selection. This study provides data base for breeding resistant strains of Nile tilapia.
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