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Mulberry leaf flavonoids (MLFs) are the primary bioactive constituents of a traditional medicinal plant and are potent antioxidants. The aim of this study was to investigate the protective effects of MLFs against exercise-induced muscle damage. In this study, twelve Mongolian horses were used in a 3 \u00d7 3 Latin square design to investigate the protective effects of MLFs. Our results showed that high-intensity exercise negatively impacted the immune status, metabolic state, myofibrillar structure, and antioxidant capacity of the horses. Conversely, MLFs significantly reduced blood levels of white blood cells (WBC), monocytes (MON), aspartate aminotransferase (AST), creatine kinase (CK), and malondialdehyde (MDA) across various exercise distances and during recovery. Simultaneously, MLFs increased serum glutathione peroxidase (GPx), superoxide dismutase (SOD), and total antioxidant capacity (T-AOC). Mechanistically, transcriptomic analysis revealed that dietary MLFs upregulated genes associated with myofibrillar structural proteins (MYOZ2, MYOM3), the antioxidant defense system (GPX3, SOD3), and skeletal muscle satellite cell proliferation and differentiation (MYOD1, MRF6). Furthermore, quantitative proteomics indicated the enrichment of the PI3K-Akt and TGF-\u03b2 signaling pathways, as well as ECM\u2013receptor interactions, suggesting their potential involvement in regulating protein metabolism and facilitating myofibrillar restoration. Overall, MLFs effectively alleviated inflammation, metabolic disorder, and exercise-induced muscle damage. Under the tested conditions, a daily dosage of 10 g MLFs provided superior protective effects.<\/jats:p>","DOI":"10.3390\/ani16101548","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T07:35:43Z","timestamp":1779176143000},"page":"1548","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Transcriptomic and Proteomic Analysis of the Skeletal Muscle Revealed the Effects and Mechanism of Mulberry Leaf Flavonoids on Alleviating Exercise-Induced Muscle Damage in Mongolian Horses"],"prefix":"10.3390","volume":"16","author":[{"given":"Aopan","family":"Geng","sequence":"first","affiliation":[{"name":"Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, College of Animal Science and Technology, Inner Mongolia Agricultural University, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuejiao","family":"Wang","sequence":"additional","affiliation":[{"name":"Rural Revitalization Research Institute, Inner Mongolia Agricultural University, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lianhao","family":"Li","sequence":"additional","affiliation":[{"name":"Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, College of Animal Science and Technology, Inner Mongolia Agricultural University, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah","family":"Cowie","sequence":"additional","affiliation":[{"name":"School of Psychology, The University of Auckland City Campus, Private Bag 92019, Auckland 1142, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongyi","family":"Bai","sequence":"additional","affiliation":[{"name":"Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, College of Animal Science and Technology, Inner Mongolia Agricultural University, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manglai","family":"Dugarjaviin","sequence":"additional","affiliation":[{"name":"Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, College of Animal Science and Technology, Inner Mongolia Agricultural University, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinzhuang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, College of Animal Science and Technology, Inner Mongolia Agricultural University, Hohhot 010018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Legg, K.A., Gee, E.K., Breheny, M., Gibson, M.J., and Rogers, C.W. 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