Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese

Abstract Background: Wulong geese are known for their excellent egg-laying performance. However, there are considerable population differences in egg-laying performance among Wulong geese. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to screen candidate 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 for egg production-related pathways such as oocyte meiosis, estrogen signaling pathway, 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. Importantly, two genes — GCG and FAP — were identified both as 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 FAPwere identified as candidate genes associated with high egg production in Wulong geese. These findings could serve as a reference for breeding Wulong geese varieties with high egg production abilities. They also provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry.