Multi-Omics Analysis of the Effects of INHA and FNDC1 on Clutch Length in Zi Geese.

Clutch length is a key determinant of egg production in geese and has a direct impact on breeding efficiency. However, the genetic and molecular mechanisms underlying variation in clutch length remain largely unclear in Zi geese. In this study, we integrated whole-genome resequencing with ovarian transcriptomic and proteomic analyses to identify candidate genes and functional single nucleotide polymorphisms (SNPs) associated with clutch length. A total of 200 female Zi geese were monitored throughout a 230-day laying period, from which 20 individuals with the longest clutch length and 20 with the shortest clutch length were selected for multi-omics analyses. Comparative analyses identified 424 differentially expressed genes and 856 differentially expressed proteins between the two groups. Integration of population-differentiated SNPs, genome-wide association study signals, transcriptomic, and proteomic datasets converged on two key candidate genes, INHA (inhibin subunit alpha) and FNDC1 (fibronectin type III domain containing 1). INHA expression was negatively associated with clutch length, whereas FNDC1 expression showed a positive association. Eight missense SNPs were detected across these two genes. Notably, structural modelling and molecular docking analyses demonstrated that the Gly10Cys substitution in INHA markedly increased the binding affinity of INHA homodimerisation (binding energy: -10.4 kcal/mol versus -8.6 kcal/mol for the wild-type protein), promoting the formation of more stable but functionally inactive INHA-INHA homodimers. This finding provides a plausible molecular explanation for the reduced INHA mRNA and INHA protein expression observed in geese with longer clutch lengths. These structural analyses suggest that the biological effects of these identified missense SNPs are primarily mediated through protein conformational changes. Collectively, our findings identify INHA and FNDC1 as key regulators of clutch length in Zi geese and reveal a previously unrecognised structural mechanism by which an INHA missense variant may influence reproductive performance. These results provide valuable molecular markers and mechanistic insights for the genetic improvement of egg production in geese.