Research note: Genome-wide association study reveals candidate genes for egg production in Muscovy duck

The Muscovy duck is a high-quality lean-meat duck breed, yet it exhibits relatively poor reproductive performance. In this study, GWAS was used to screen candidate genes controlling egg production of Muscovy duck. Transcriptomics were further used to explore their regulatory mechanisms. Results showed PPP3CA, ZFYVE28, DENND2B, UBAP1, MAP1B were associated with total egg production. LD analysis identified 4_7070908_G>A as tagSNP of PPP3CA, in which GG genotype had significantly higher egg production than AA genotype (P < 0.05) in both the sequenced group and their next two generation. Transcriptomic analysis of large white follicles from the two genotypes revealed that differentially expressed genes, mainly those involved in steroid biosynthesis, extracellular matrix-receptor interaction, and the MAPK signaling pathway, were upregulated in GG; meanwhile, in small yellow follicles, steroid biosynthesis, PPAR, calcium, and TGF-β signaling pathways were upregulated in GG. Among these, PPP3CA is a potential key candidate gene influencing egg production, and it may exert a negative regulatory effect on the proliferation of granulosa cells in Muscovy duck follicles.