{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T02:03:38Z","timestamp":1784167418042,"version":"3.55.0"},"reference-count":71,"publisher":"MDPI AG","issue":"14","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"STI2030-Major Projects","award":["2023ZD0405502"],"award-info":[{"award-number":["2023ZD0405502"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund, South China Sea Fisheries Research Institute, CAFS","award":["2023TS02"],"award-info":[{"award-number":["2023TS02"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Grass carp (Ctenopharyngodon idella) is an important freshwater aquaculture species in China. However, high-density farming often leads to significant growth differentiation among individuals, seriously affecting yield and product quality. Here, we conducted an integrated transcriptomic and data-independent acquisition (DIA) proteomic analysis across the brain, liver, and muscle tissues of fast-growing (FG) and slow-growing (SG) grass carp after 9 months of high-density culture. Our analysis revealed that the core mechanism driving growth differentiation is a deep decoupling of transcription and translation, where enhanced muscle translational efficiency dictates the fast-growth phenotype, while slow growth is constrained by central stress and hepatic energy depletion. In the slow growth group, the brain exhibited translational arrest and neuroinflammation, and the liver entered a state of hypermetabolism mediated by AMPK, evidenced by the post-transcriptional up-regulation of key sensors such as CAB39 (PRM ratio = 1.634) and CAMKK2 (PRM ratio = 1.295). Conversely, in the fast-growing group, the mTOR\u2013ribosome signaling axis was strongly activated at the post-transcriptional level in the muscle (GSEA NES = \u22121.852), triggering myofibrillar protein deposition despite transcriptional silence in classical growth pathways. These findings elucidate the systemic molecular mechanisms of growth divergence and provide high-confidence molecular targets for developing fast-growing, stress-resilient grass carp strains for precision aquaculture breeding.<\/jats:p>","DOI":"10.3390\/ani16142205","type":"journal-article","created":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T01:05:07Z","timestamp":1784163907000},"page":"2205","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated Transcriptomic and Proteomic Analysis Unveils the Multi-Organ Regulatory Mechanisms of Growth Divergence in Grass Carp (Ctenopharyngodon idella)"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-5379-6503","authenticated-orcid":false,"given":"Tengfei","family":"Zhu","sequence":"first","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hao","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhipeng","family":"Zheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0883-9065","authenticated-orcid":false,"given":"Huayang","family":"Guo","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"},{"name":"Guangdong Engineering Research Center of Key Technologies and Equipment R&D on Modern Marine Ranching, Guangzhou 510300, China"},{"name":"Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6244-5510","authenticated-orcid":false,"given":"Baosuo","family":"Liu","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"},{"name":"Guangdong Engineering Research Center of Key Technologies and Equipment R&D on Modern Marine Ranching, Guangzhou 510300, China"},{"name":"Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0712-5514","authenticated-orcid":false,"given":"Kecheng","family":"Zhu","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"},{"name":"Guangdong Engineering Research Center of Key Technologies and Equipment R&D on Modern Marine Ranching, Guangzhou 510300, China"},{"name":"Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"},{"name":"Guangdong Engineering Research Center of Key Technologies and Equipment R&D on Modern Marine Ranching, Guangzhou 510300, China"},{"name":"Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lin","family":"Xian","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingying","family":"Yu","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Animal Science and Technology, Foshan University, Foshan 528225, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-8416-0400","authenticated-orcid":false,"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Songlin","family":"Chen","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8711-2595","authenticated-orcid":false,"given":"Dianchang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China"},{"name":"Sanya Tropical Fisheries Research Institute, Sanya 572018, China"},{"name":"Guangdong Engineering Research Center of Key Technologies and Equipment R&D on Modern Marine Ranching, Guangzhou 510300, China"},{"name":"Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou 510300, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"ref_1","unstructured":"FAO (2022). 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