Weighted Gene Co-Expression Network Analysis and Alternative Splicing Analysis Reveal Key Genes Regulating Overfeeding-Induced Fatty Liver in Lion-Head Goose

Lion-head goose is a large-sized breed native to Guangdong Province, China, exhibits remarkable capacity for fatty liver production under overfeeding conditions and is highly valued by local farmers and consumers. However, the molecular mechanisms driving fatty liver development in this breed are still unknown. In this study, we evaluated liver weight differences between normally fed and overfed Lion-head geese and further examined sex-specific differences following overfeeding. Overfeeding significantly increased liver weight more than 340%, and males possess a stronger capacity for lipid deposition under the same feeding regimen compared with females. RNA-Seq analysis identified 1476 differentially expressed genes (DEGs) shared by both sexes, which were mainly enriched in lipid and energy metabolism, oxidative stress, and mitochondrial pathways. In addition, 627 male-specific and 420 female-specific DEGs revealed sex-dependent differences, with males showing stronger transcriptional regulation and females exhibiting enhanced antioxidant and detoxification responses. Weighted gene co-expression network analysis (WGCNA) revealed 320 co-hub genes enriched in lipid and energy metabolism in overfeeding-induced fatty liver, along with 9 co-hub genes related to sex differences. Alternative splicing (AS) analysis detected 131 differentially spliced genes (DSGs). Integration of both approaches identified 7 overlapping genes, <i>HYCC2</i> (Hyccin PI4KA lipid kinase complex subunit 2), <i>AGL</i> (Amylo-Alpha-1,6-Glucosidase and 4-Alpha-Glucanotransferase), <i>CCDC62</i> (Coiled-coil domain containing 62), <i>IGSF5</i> (Immunoglobulin superfamily member 5), <i>MGARP</i> (Mitochondria-localized glutamic acid-rich protein), <i>CD80</i> (Cluster of Differentiation 80), and <i>FPGS</i> (Folylpolyglutamate synthase), as potential key regulators. These findings provide new insights into transcriptional and post-transcriptional regulation of overfeeding-induced fatty liver in geese.