Selective analysis of resistance and susceptibility to duck hepatitis A virus genotype 3 in Pekin duck

Duck viral hepatitis (DVH), mainly caused by duck hepatitis A virus genotype 3 (DHAV-3) in China, is an important disease affecting Pekin ducks. Using artificial selection breeding based on genealogical and phenotypic observations, a susceptible line (Z7) and a resistant line (Z8) of Pekin ducks to DHAV-3 were identified. Here, we performed a genome-wide analysis to identify selected genes in the genomes of Pekin ducks underlying resistance/susceptible breeding. Following selection, the mortality rate of the Z8 line reduced from 59.2% to 7.8% in the fourth generation (Z8G4), whereas the death rate of the Z7 line increased from 67.5% to 81% in the third generation (Z7G3). Moreover, directed breeding caused the allele frequencies of Z8 and Z7 changing in opposite direction, accompanied by declines in genomic genetic diversity. With the G0 generation as the reference group, a total of 49 selected genes were identified in the Z7-susceptible population and 109 selected genes in the Z8-resistant population based on the top 5% F_ST and PI ratio, and two candidate key genes were further fine-mapped. Susceptibility selection led to 17 mutations in the LRIG3 gene in the Z7 population (chr1: 169,757,982–169,772,687), and resistance selection led to 134 mutations in the CRHR2 gene in the Z8 population (chr2: 4,190,154–4,273,970). Our results provide new insights into the resistance and susceptibility to DHAV-3 and lay a theoretical foundation for further research on the mechanism of resistance/susceptibility of Pekin ducks to DHAV-3.