1. Ammonia is a toxic gas and an air pollutant of great concern. The effects of ammonia-induced damage in ducks are rarely reported. 2. A total of 176 laying ducks were randomly allocated to one of two groups with four replicates and were exposed to ammonia at 5 ± 5 ppm (low ammonia, LA) or 75 ± 5 ppm (high ammonia, HA), respectively, for 30 days. 3. The results showed that atmospheric ammonia exposure significantly decreased body weight and laying performance (P < 0.05). It significantly changed serum biochemical indices by increasing alanine aminotransferase and aspartate aminotransferase (P < 0.05), and decreasing superoxide dismutase activity (P < 0.05). Haematoxylin and eosin staining of hepatocytes revealed severe fatty degeneration. Results of RNA-seq analyses revealed that eight genes were significantly up-regulated in the HA group, which were involved in catalytic activity, single-organism metabolic processes, oxidation-reduction processes, and carbohydrate metabolic processes. 4. These results indicated that atmospheric ammonia exposure reduced production performance, affected serum biochemical indices, and led to severe fatty degeneration in the liver of laying ducks. Differentially expressed genes in liver indicated that there were effects of ammonia exposure on the metabolism and detoxification capabilities in ducks.

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