Genomic and transcriptomic analyses revealed potential candidate genes for egg production traits in domesticated ducks

The process of domestication in ducks has led to distinct morphological, behavioral, and physiological traits that differentiate from their wild ancestors. Among these traits, reproductive performance, particularly egg production, has been specifically enhanced. In this study, in order to understand the molecular mechanisms underlying the great differences of egg production between domesticated ducks and their wild ancestors, we integrated genomic and transcriptomic analyses to identify candidate genes and pathways associated with egg production. Selective sweep analyses based on Di revealed genomic regions under selection in multiple egg-type duck breeds. A total of 987 candidate genes were identified, with 11 genes shared across breeds, suggesting common selection pressures. Transcriptomic analyses between egg-type ducks and mallard revealed differentially expressed genes involved in hormone regulation, lipid transport, and follicular development in the liver and gonads. Multiple candidate genes (such as FN1, PDE10A, SEMA5B, UBE2E3) and enriched pathways (such as ECM-receptor interaction, Wnt signaling, steroid hormone biosynthesis) were found to be potentially linked to egg production traits. Notably, only FN1 and SEMA5B were identified by both genomic and transcriptomic analyses. Our study provide additional insights into the genetic basis of egg production in ducks.