Molecular insights into how maternal investment shapes embryonic development for improving conservation breeding of the Chinese alligator (Alligator sinensis).

The Chinese alligator (Alligator sinensis) remains critically endangered in the wild due to severe habitat loss and historical hunting. Although ex situ breeding has achieved demographic success, the low recruitment of reintroduced populations highlights the importance of improving offspring quality. Egg weight, a direct measure of maternal investment, is known to affect hatchling phenotype, but its molecular effects on embryogenesis remain poorly understood. Here, large-sample analyses confirmed that heavy eggs had higher hatching success and produced heavier hatchlings than light eggs. We further performed transcriptome sequencing of the brain, heart, liver, lung, and skin at four embryonic stages (days 29, 35, 41, and 46) in heavy- and light-egg groups. Weighted Gene Co-Expression Network Analysis (WGCNA) identified tissue-specific co-expression modules enriched in neural signaling, cardiac muscle contraction, metabolism, immunity, and epidermal development. Across all tissues, CEP55 and SNRPA, two genes associated with cell proliferation, were consistently downregulated during development and positively correlated with proliferation markers. Meanwhile, retinol metabolism showed progressively increased activity, negative correlations with CEP55 and SNRPA, and positive correlations with tissue-specific functional genes, suggesting its involvement in the shift from proliferation to differentiation. Heavy-egg embryos exhibited upregulation of genes related to brain energy homeostasis (QRFP, NPVF), cardiac lipid transport (FABP1, HNF1A), and skin epithelial differentiation (FOSL1, FOXI2), alongside downregulation of hepatic PRKAA2 and lung immune-related genes (C3, GC). These findings indicate that increased maternal investment may enhance embryonic developmental quality by promoting energy allocation and tissue maturation, providing molecular insights to support conservation-oriented breeding strategies in the Chinese alligator.