DNA Methylation Patterns and Transcriptomic Data Were Integrated to Investigate Candidate Genes Influencing Reproductive Traits in Ovarian Tissue from Sichuan White Geese

Ovarian tissue is critical for goose reproduction. This study aimed to investigate gene regulation by DNA methylation in relation to the reproductive traits of geese. We performed whole-genome bisulfite sequencing (WGBS) on ovarian tissues from Sichuan white geese (high-laying-rate group: HLRG, ♀ = 3; low-laying-rate group: LLRG, ♀ = 3) during the laying period. The results showed a higher level of hypermethylated differentially methylated regions (DMRs) in the HLRG, indicating a higher overall methylation level compared to the LLRG. In total, we identified 2831 DMRs and 733 differentially methylated genes (DMGs), including 363 genes with upregulated methylation. These DMGs were significantly enriched in pathways related to microtubule function (GO:0005874; GO:0000226), GnRH secretion, thyroid hormone signaling, ECM-receptor interaction, and PI3K-Akt signaling. Integration with RNA-seq data identified eight overlapping genes between DMGs and differentially expressed genes (DEGs), with five genes (<i>CUL9</i>, <i>MEGF6</i>, <i>EML6</i>, <i>SYNE2</i>, <i>AK1BA</i>) exhibiting a correlation between hypomethylation and high expression. <i>EML6</i>, in particular, emerged as a promising candidate, potentially regulating follicle growth and development in Sichuan white geese. Future studies should focus on further verifying the role of the <i>EML6</i> gene. In conclusion, this study provides important insights into the regulatory mechanisms of DNA methylation influencing reproductive traits in geese, offering novel candidate markers for future goose breeding programs.