Duck viral hepatitis severely threatens the development of the duck industry, leading to economic losses every year. Using selected Pekin duck populations exhibiting varying resistance towards Duck Hepatitis A Virus type 3 (DHAV-3), screening for genetic variations, such as single nucleotide polymorphisms (SNP), associated with disease susceptibility will facilitate the breeding of Pekin ducks with enhanced disease resistance. The biological role of fucosyltransferases, which are a type of glycosyltransferase enzymes, is to catalyze the transfer of fucose to molecules such as oligosaccharides, glycoproteins and glycolipids, which is crucial for maintaining immune function by promoting effective pathogen recognition and modulating immune responses through specific fucosylation patterns. Previous studies found that the expression level of the Fucosyltransferase 9 (FUT9) gene in the liver of resistant Pekin ducks was significantly higher than that in susceptible ducks, suggesting its potential association with disease resistance. However, the association between genetic variations in FUT9 and susceptibility to DHAV-3 in ducks remains unclear. This study aims to detect SNPs in the FUT9 gene and explore their relationships with disease mortality and susceptibility, the result will provide a scientific basis for developing effective control strategies in duck breeding. 242 Pekin ducks with varying resistance to DHAV-3 were used in this experiment. 12 SNPs were identified in the coding region of FUT9. And g.76953686 T >
C and g.76954451C >
T were significantly associated with susceptibility to DHAV-3 in Pekin ducks. The results indicate that variations in the FUT9 gene significantly influence the susceptibility of ducks towards DHAV-3, providing potential genetic markers for enhancing disease resistance breeding in Pekin ducks.