Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese (Anser cygnoides orientalis)

BACKGROUND: Wulong geese (Anser cygnoides orientalis) are known for their excellent egg-laying performance. However, they show considerable population differences in egg-laying behavior. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to identify the genes related to high egg production in Wulong geese. RESULTS: A total of 132 selected genomic regions were screened using genome-wide selection signal analysis, and 130 genes related to high egg production were annotated in these regions. These selected genes were enriched in pathways related to egg production, including oocyte meiosis, the estrogen signaling pathway, the oxytocin signaling pathway, and progesterone-mediated oocyte maturation. Furthermore, a total of 890 differentially expressed genes (DEGs), including 340 up-regulated and 550 down-regulated genes, were identified by RNA-seq. Two genes — GCG and FAP — were common to the list of selected genes and DEGs. A non-synonymous single nucleotide polymorphism was identified in an exon of FAP. CONCLUSIONS: Based on genome-wide selection signal analysis and transcriptome data, GCG and FAP were identified as candidate genes associated with high egg production in Wulong geese. These findings could promote the breeding of Wulong geese with high egg production abilities and provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-023-09603-y.