Genome-wide selection and association analyses implicate retinal and reproductive genes in laying-period variation of domestic geese.

Geese are key domesticated waterfowl in Asia, where annual egg number and laying duration influence economic value. To investigate the genomic basis of laying seasonality, we generated whole-genome resequencing data for 314 geese from six Chinese breeds and focused on three with contrasting reproductive schedules: low-latitude Ding'an geese, which have a prolonged laying period with moderate annual egg yield, and high-latitude Huoyan and Zi geese, which show short, highly seasonal laying but high egg production. By integrating Fst, GWAS and haplotype-based statistics, we identified 16 candidate genes, including reproduction-related loci (AGTR2, IARS, PCGF6) and retinal genes (FRMD4B, PROS1, SH2D3C, ZEB2). Genomic regions surrounding PCGF6 and PROS1 showed clear signatures of selection, with reduced nucleotide diversity and strongly differentiated haplotypes between latitude-defined groups. Multiple downstream and 3' untranslated-region SNPs at these loci exhibited large allele-frequency shifts and are predicted to alter transcriptional regulation, suggesting a link between retinal photoreception, photoperiodic or circadian signaling and the timing and duration of egg laying. These findings highlight the role of retinal pathways in goose reproductive seasonality and provide targets for genomic selection to potentially extend the laying period.