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The low egg production of goose greatly limits the development of the industry. China possesses the most abundant goose breeds resources. In this study, genome resequencing data of swan goose (Anser cygnoides) and domesticated high and low laying goose breeds (Anser cygnoides domestiation) were used to identify key genes related to egg laying ability in geese and verify their functions. Selective sweep analyses revealed 416 genes that were specifically selected during the domestication process from swan geese to high laying geese. Furthermore, SNPs and Indels markers were used in GWAS analyses between high and low laying breed geese. The results showed that RTCB, BPIFC, SYN3, SYNE1, VIP,and ESR1may be related to the differences in laying ability of geese. Notably, only ESR1was identified simultaneously by GWAS and selective sweep analysis. The genotype of Indelchr3:54429172,located downstream of ESR1, was confirmed to affect the expression of ESR1in the ovarian stroma and showed significant correlation with body weight at first egg and laying frequency of geese. CCK-8, EdU, and flow cytometry confirmed that ESR1can promote the apoptosis of goose pre-hierarchical follicles ganulosa cells (phGCs) and inhibit their proliferation. Combined with transcriptome data, it was found ESR1involved in the function of goose phGCs may be related to MAPK and TGF-beta signaling pathways. Overall, our study used genomic information from different goose breeds to identify an indel located in the downstream of ESR1associated with goose laying ability. The main pathways and biological processes of ESR1involved in the regulation of goose laying ability were identified by cell biology and transcriptomics methods. These results are helpful to further understand the laying ability characteristics of goose and improve the egg production of geese.