Background: Feed efficiency (FE) is a major determinant of productivity, economic sustainability, and environmental impact in livestock production. Although Pekin ducks constitute a substantial proportion of global poultry meat production, improvement of FE has progressed slowly, largely due to an incomplete understanding of its complex biological basis. In particular, how host genomic variation and gut microbial communities—especially across different intestinal segments—jointly contribute to FE remains poorly characterized in ducks. Results: We integrated whole-genome sequencing (WGS) with segment-resolved microbiota profiles from 313 Pekin ducks to delineate host–microbiota architecture underlying feed conversion ratio (FCR), which exhibited moderate heritability ( h ² =0.23, P _LRT = 2.53 × 10 ^–2 ). Genome-wide association study (GWAS) identified two major genomic regions involving two genes ALG13 and TRPC5 , which implicated in appetite regulation and energy balance to impact FE. Meanwhile, gut microbial communities exhibited spatial heterogeneity along the intestinal tract, with host genetics-associated taxa such as Solobacterium (cecum) and Eubacterium_eligens_group (jejunum) negatively correlating with FCR, likely via enhanced short-chain fatty acid production and improved energy harvest. Variation partitioning revealed that host genetics explained the largest FCR variance (36.96%), followed by cecal microbiota. Conclusions: Our results highlight coordinated host–microbiota interactions influencing FE, offering targets for breeding and microbiota-based interventions.

RNA editing is increasingly recognized as a post-transcriptional modification that directly affects viral infection by regulating RNA stability and recoding proteins. the duck hepatitis A virus genotype 3 (DHAV-3) infection is seriously detrimental to the Asian duck industry. However, the landscape and roles of RNA editing in the susceptibility and resistance of Pekin ducks to DHAV-3 remain unclear. Here, we profiled dynamic RNA editing events in liver tissue and investigated their potential functions during DHAV-3 infection in Pekin ducks. We identified 11,067 informative RNA editing sites in liver tissue from DHAV-3-susceptible and -resistant ducklings at three time points during virus infection. Differential RNA editing sites (DRESs) between S and R ducks were dynamically changed during infection, which were enriched in genes associated with vesicle-mediated transport and immune-related pathways. Moreover, we predicted and experimentally verified that RNA editing events in 3′-UTR could result in loss or gain of miRNA–mRNA interactions, thereby changing the expression of target genes. We also found a few DRESs in coding sequences (CDSs) that altered the amino acid sequences of several proteins that were vital for viral infection. Taken together, these data suggest that dynamic RNA editing has significant potential to tune physiological processes in response to virus infection in Pekin ducks, thus contributing to host differential susceptibility to DHAV-3.