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The scented gland, a musk-secreting organ of male muskrats, shows clear seasonal changes. When entering the secreting season in March, scented glands gradually increase in size and active secretion starts. In September, scented glands become gradually smaller and secretion decreases. By November, scented glands are gradually replaced by adipose tissue. In this study, six healthy adult male muskrats were analysed: three from the secreting season (March) and three from the non-secreting season (November). Using RNA-Seq analysis, gene expression profiles of scented glands from both seasons were determined. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found that genes involved in calcium and TGF-beta signalling pathways were significantly more expressed in the non-secreting than in the secreting season. These changes in gene expression correlated with alterations in scented gland size. Both calcium and TGF-beta signalling pathways are important regulators of cell apoptosis, which may thus be involved in muskrat scented gland degeneration.