Copy Number Variation and SNP Affect Egg Production in Chickens by Regulating AP2M1 Expression to Inhibit GnRH Synthesis

Deciphering egg laying-related genetic basis and aggregating its key genes or genetic markers will be helpful for genetic improvement of chicken laying-oriented breeding. Our previous research found adaptor related protein complex 2 mu 1 subunit (<i>AP2M1</i>) gene is a key candidate gene related to egg production. However, its functions and genetic regulatory mechanisms remain unclear. This study aims to clarify <i>AP2M1</i> functions and identify its functional variants. Expression characteristic analysis of <i>AP2M1</i> within and between breeds confirmed the negative regulatory relationship of hypothalamic <i>AP2M1</i> expression on egg production. Overexpression and interference tests indicated that <i>AP2M1</i> inhibited GnRH synthesis and secretion in chicken hypothalamic neuron cells. To explore molecular markers influencing <i>AP2M1</i> expression, a copy number variation (CNV) region containing <i>AP2M1</i> were verified in different chicken breeds by qRT-PCR; a copy number loss of <i>AP2M1</i> were observed in layers compared to native breeds, commercial broilers, and wild breed. Correlation analysis between CNV and egg number, as well as differential expression analysis of different copy numbers, indicated that the CNV contributed to the differences in egg production by influencing <i>AP2M1</i> expression. Meanwhile, through association analysis of whole-genome SNPs in <i>AP2M1</i> with 13 egg production traits, 15 egg-laying related SNPs were identified. Further difference expression analysis among the different genotypes of SNPs and dual-luciferase reporter assay confirmed that chr9:15994879T>C was a functional SNP regulating <i>AP2M1</i> expression. These findings unveil egg laying-related functional molecular markers will help accelerate molecular design breeding process of chicken egg production.