Simple SummaryThe follicular selection stage during the development of goose follicles is a decisive step in egg production, but current research is still incomplete. With the help of high-throughput sequencing technology, we analyzed the mRNAs, miRNAs, and lncRNAs that play a critical role only in the follicular selection stage and ultimately constructed a ceRNA regulatory network. We confirmed the significant changes in the extracellular matrix, cell junction, and glucose and lipid metabolism during follicular selection. More importantly, using a new analytical approach, we identified miRNAs that play an important role in follicle selection, including miR-222-3p, miR-2954-3p, miR-126-5p, miR-2478, and miR-425-5p. This study provides potential regulatory targets for precise regulation of goose production performance.AbstractThe selection of follicles determines the reproductive performance of birds, but the process of follicle selection in geese is still elusive. This study focuses on Yangzhou geese during the egg-laying period and divides the follicular development process into three stages: small follicle development, follicle selection, and follicle maturation. Transcriptome sequencing was performed on granulosa cells from large white follicles, small yellow follicles, and F5 and F4 follicles. In addition, we selected the transcripts that remained unchanged during the development and maturation of small follicles but significantly changed during the follicular selection stage as the transcript collection that plays an important role in the follicular selection process. Then, we performed functional analysis on these transcripts and constructed a ceRNA network. The results showed that during the follicular selection stage, the number of differentially expressed mRNAs, miRNAs, and lncRNAs was the highest. In addition, miR-222-3p, miR-2954-3p, miR-126-5p, miR-2478, and miR-425-5p are potential key core regulatory molecules in the selection stage of goose follicles. These results can provide a reference for a better understanding of the basic mechanisms of the goose follicle selection process and potential targets for the precise regulation of goose egg production performance.