Genetic Admixture Analysis of Fecundity-associated Genes in Captive Deer Populations and Its Implications for Reproductive Management

The decline in the fertility of captive deer populations presents significant challenges for wildlife farming and conservation breeding programs. This study investigated whether genetic admixture in fecundity-associated genes contributes to reduced reproductive performance in a captive population comprising three deer breeds (Axis axis, Rusa timorensis, and Rusa unicolor). We analyzed sequence variation in five key fertility genes (BMP15, FOXL2, GDF9, MTNR1A, and MHCDQA1) across 26 individuals via ADMIXTURE analysis. Cross-validation identified K=4 as the optimal number of ancestral populations, exceeding the three recognized breeds and revealing complex admixture patterns, particularly between R. timorensis and R. unicolor. Gene-specific analyses revealed differential evolutionary dynamics, with MTNR1A exhibiting the greatest breed differentiation (Fst=0.31) and MHCDQA1 the lowest (Fst=0.09). Notably, we found a significant negative correlation between admixture complexity (Shannon entropy) and conception rate (r=-0.58, p=0.012) in females with reproductive records (n=18), which remained significant after controlling for age and parity. Specific ancestral components showed contrasting associations with fertility: Ancestry 2 correlated positively with the conception rate (r=0.61, p=0.007), whereas Ancestry 1 correlated negatively (r=-0.47, p=0.049). These findings provide strong evidence that hybridization disrupts coadapted gene complexes governing reproduction, which may result in outbreeding depression. Our results highlight the importance of genetic management in multibreed captive settings and offer a foundation for developing targeted breeding strategies to mitigate fertility decline in managed cervid populations, with broader implications for wildlife conservation and animal breeding programs worldwide.