{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T21:28:37Z","timestamp":1789680517154,"version":"4.0.1"},"reference-count":52,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2024,6,30]],"date-time":"2024-06-30T00:00:00Z","timestamp":1719705600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Postdoctoral Innovation Project of Hubei Province","award":["2022"],"award-info":[{"award-number":["2022"]}]},{"name":"Postdoctoral Innovation Project of Hubei Province","award":["CARS-45"],"award-info":[{"award-number":["CARS-45"]}]},{"name":"Postdoctoral Innovation Project of Hubei Province","award":["2023TD36"],"award-info":[{"award-number":["2023TD36"]}]},{"name":"Earmarked Fund for China Agriculture Research System","award":["2022"],"award-info":[{"award-number":["2022"]}]},{"name":"Earmarked Fund for China Agriculture Research System","award":["CARS-45"],"award-info":[{"award-number":["CARS-45"]}]},{"name":"Earmarked Fund for China Agriculture Research System","award":["2023TD36"],"award-info":[{"award-number":["2023TD36"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["2022"],"award-info":[{"award-number":["2022"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["CARS-45"],"award-info":[{"award-number":["CARS-45"]}]},{"name":"Central Public-interest Scientific Institution Basal Research Fund","award":["2023TD36"],"award-info":[{"award-number":["2023TD36"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>The common carp (Cyprinus carpio) is one of the most important aquaculture species in China, known for its remarkable adaptability and nutritional profile. However, the specific molecular response mechanisms regulating the nutritional deposition of carp remain inadequately elucidated. This study conducted a comprehensive analysis of muscle nutritional content and transcriptome data from liver and muscle tissues of three distinct carp varieties. The aim was to elucidate the key genes and signaling pathways that regulate muscle nutritional composition in carp. The findings revealed that FFRC carp (FFRC) exhibited significantly higher levels of crude fat, total n-3 polyunsaturated fatty acids, and total n-6 polyunsaturated fatty acids in muscle tissue compared to Ying carp (YC) and Huanghe carp (HC) (p &lt; 0.05). Transcriptomic analyses correlated these elevated levels with a marked upregulation of genes involved in the activation and transportation of fatty acid (fabp7, acsl5, acsbg2) as well as biosynthesis and elongation of long-chain unsaturated fatty acids (elovl2, fads2) within the liver. Furthermore, the flavor amino acid, essential amino acids, and crude protein content in the muscle of HC were significantly higher than in FFRC and YC (p &lt; 0.05). Transcriptomic analyses indicated that this was associated with significant changes in the expression of genes related to amino acid metabolism (asns, alt, ldha, glul, setd, prodh, l3hypdh, hoga1) within their muscle tissue. This research provides a theoretical foundation for the precise modulation of the muscle nutritional composition in carp.<\/jats:p>","DOI":"10.3390\/ani14131939","type":"journal-article","created":{"date-parts":[[2024,7,1]],"date-time":"2024-07-01T04:53:27Z","timestamp":1719809607000},"page":"1939","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Transcriptome Analysis Reveals the Potential Key Genes in Nutritional Deposition in the Common Carp (Cyprinus carpio)"],"prefix":"10.3390","volume":"14","author":[{"given":"Yunya","family":"Wu","sequence":"first","affiliation":[{"name":"Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Xiao","sequence":"additional","affiliation":[{"name":"Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China"},{"name":"College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Sha","sequence":"additional","affiliation":[{"name":"Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangzhong","family":"Luo","sequence":"additional","affiliation":[{"name":"Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guiwei","family":"Zou","sequence":"additional","affiliation":[{"name":"Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongwei","family":"Liang","sequence":"additional","affiliation":[{"name":"Yangtze River Fisheries Research Institute, Chinese Academy of Fisheries Science, Wuhan 430223, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2024,6,30]]},"reference":[{"key":"ref_1","unstructured":"FAO (2009). Agriculture Organization of the United Nation Fish Stat: Universal Software for Fishery Statistical Time Series V. 23, Data and statistics Unit, FAO."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1111\/j.1753-5131.2009.01012.x","article-title":"Use and exchange of aquatic resources relevant for food and aquaculture: Common carp (Cyprinus carpio L.)","volume":"1","author":"Jeney","year":"2009","journal-title":"Rev. Aquac."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1077","DOI":"10.1111\/raq.12513","article-title":"Microbiome diversity and dysbiosis in aquaculture","volume":"13","author":"Huerlimann","year":"2021","journal-title":"Rev. Aquac."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Hu, X., Ge, Y., Li, C., Jia, Z., Shang, M., Wang, S., and Shi, L. (2018). Developments in Common Carp Culture and Selective Breeding of New Varieties. Aquaculture in China, John Wiley & Sons Ltd.","DOI":"10.1002\/9781119120759.ch2_3"},{"key":"ref_5","first-page":"20","article-title":"The creation and applications of fish distant hybridization","volume":"48","author":"Wang","year":"2018","journal-title":"Sci. China Life Sci."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1016\/j.foodres.2016.09.020","article-title":"Nutritive values, flavor amino acids, healthcare fatty acids and flesh quality improved by manganese referring to up-regulating the antioxidant capacity and signaling molecules TOR and Nrf2 in the muscle of fish","volume":"89","author":"Jiang","year":"2016","journal-title":"Food Res. Int."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Wu, G. (2021). Nutrition and Functions of Amino Acids in Fish. Amino Acids in Nutrition and Health: Amino Acids in the Nutrition of Companion, Zoo and Farm Animals, Springer International Publishing.","DOI":"10.1007\/978-3-030-54462-1"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"740392","DOI":"10.1016\/j.aquaculture.2023.740392","article-title":"Comparison of muscle nutritional composition, texture quality, carotenoid metabolites and transcriptome to underling muscle quality difference between wild-caught and pond-cultured Yellow River carp (Cyprinus carpio haematopterus)","volume":"581","author":"Wang","year":"2024","journal-title":"Aquaculture"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1080\/10408398.2018.1425978","article-title":"How does high DHA fish oil affect health? A systematic review of evidence","volume":"59","author":"Wang","year":"2019","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"101328","DOI":"10.1016\/j.aqrep.2022.101328","article-title":"Effects of replacing soybean meal and rapeseed meal with faba bean meal on growth performance and muscle quality of tilapia (Oreochromis niloticus)","volume":"26","author":"Peng","year":"2022","journal-title":"Aquac. Rep."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1016\/j.aquaculture.2011.02.016","article-title":"Fish oil replacement with different vegetable oils in Murray cod: Evidence of an \u201comega-3 sparing effect\u201d by other dietary fatty acids","volume":"315","author":"Turchini","year":"2011","journal-title":"Aquaculture"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2174","DOI":"10.1111\/are.12373","article-title":"Fish oil\u2013based finishing diets strongly increase long-chain polyunsaturated fatty acid concentrations in farm-raised common carp (Cyprinus carpio L.)","volume":"46","author":"Schultz","year":"2015","journal-title":"Aquac. Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"133799","DOI":"10.1016\/j.foodchem.2022.133799","article-title":"Dietary cinnamaldehyde improves muscle protein content by promoting muscle fiber growth via PTP1B\/IGF1\/PI3K\/AKTs-TOR\/FOXO3a signaling pathway in grass carp (Ctenopharyngodon idella)","volume":"399","author":"Zhou","year":"2023","journal-title":"Food Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"740005","DOI":"10.1016\/j.aquaculture.2023.740005","article-title":"Improvement of flesh quality, muscle growth and protein deposition in adult grass carp (Ctenopharyngodon idella): The role of tryptophan","volume":"577","author":"Xiao","year":"2023","journal-title":"Aquaculture"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"7965735","DOI":"10.1155\/2023\/7965735","article-title":"Determining the Potential Roles of Branched-Chain Amino Acids in the Regulation of Muscle Growth in Common Carp (Cyprinus carpio) Based on Transcriptome and MicroRNA Sequencing","volume":"2023","author":"Cao","year":"2023","journal-title":"Aquac. Nutr."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"319","DOI":"10.1016\/j.fsi.2018.03.046","article-title":"Applications of transcriptomics and proteomics in understanding fish immunity","volume":"77","author":"Ye","year":"2018","journal-title":"Fish Shellfish. Immunol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Rise, M.L., Martyniuk, C.J., and Chen, M. (2019). Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production. Comp. Biochem. Physiol. Part D Genom. Proteom., 31.","DOI":"10.1016\/j.cbd.2019.100603"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Wu, Y., Li, R., Wu, X., Guo, W., Zhong, W., Li, Y., Song, Y., Tao, B., Chen, J., and Han, D. (2022). Overexpression of growth hormone improved hepatic glucose catabolism and relieved liver lipid deposition in common carp (Cyprinus carpio L.) fed a high-starch diet. Front. Endocrinol., 13.","DOI":"10.3389\/fendo.2022.1038479"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/s41586-019-1592-6","article-title":"Harnessing global fisheries to tackle micronutrient deficiencies","volume":"574","author":"Hicks","year":"2019","journal-title":"Nature"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.jjcc.2015.08.002","article-title":"Cardioprotective mechanism of omega-3 polyunsaturated fatty acids","volume":"67","author":"Endo","year":"2016","journal-title":"J. Cardiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1007\/s13105-013-0265-4","article-title":"Role of omega-3 fatty acids in obesity, metabolic syndrome, and cardiovascular diseases: A review of the evidence","volume":"69","author":"Costa","year":"2013","journal-title":"J. Physiol. Biochem."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Djuricic, I., and Calder, P.C. (2021). Beneficial Outcomes of Omega-6 and Omega-3 Polyunsaturated Fatty Acids on Human Health: An Update for 2021. Nutrients, 13.","DOI":"10.3390\/nu13072421"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1016\/j.bbadis.2011.02.014","article-title":"PPARs are a unique set of fatty acid regulated transcription factors controlling both lipid metabolism and inflammation","volume":"1812","author":"Varga","year":"2011","journal-title":"Biochim. Et Biophys. Acta (BBA) Mol. Basis Dis."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"101095","DOI":"10.1016\/j.plipres.2021.101095","article-title":"Regulation of long-chain polyunsaturated fatty acid biosynthesis in teleost fish","volume":"82","author":"Xie","year":"2021","journal-title":"Prog. Lipid Res."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Burdge, G.C. (2018). Chapter 3\u2014Polyunsaturated Fatty Acid Biosynthesis and Metabolism in Fish. Polyunsaturated Fatty Acid Metabolism, AOCS Press.","DOI":"10.1016\/B978-0-12-811230-4.00011-9"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.cbpb.2014.06.005","article-title":"Characterization of the fatty acyl elongase (elovl) gene family, and hepatic elovl and delta-6 fatty acyl desaturase transcript expression and fatty acid responses to diets containing camelina oil in Atlantic cod (Gadus morhua)","volume":"175","author":"Xue","year":"2014","journal-title":"Comp. Biochem. Physiol. Part B Biochem. Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Jin, Y., Datsomor, A.K., Olsen, R.E., Vik, J.O., Torgersen, J.S., Edvardsen, R.B., Wargelius, A., Winge, P., and Grammes, F. (2020). Targeted mutagenesis of \u22065 and \u22066 fatty acyl desaturases induce dysregulation of lipid metabolism in Atlantic salmon (Salmo salar). BMC Genom., 21.","DOI":"10.1186\/s12864-020-07218-1"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11745-007-3111-z","article-title":"Role of Fatty Acid Binding Proteins and Long Chain Fatty Acids in Modulating Nuclear Receptors and Gene Transcription","volume":"43","author":"Schroeder","year":"2008","journal-title":"Lipids"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"3492","DOI":"10.3748\/wjg.v21.i12.3492","article-title":"Long-chain acyl-CoA synthetase in fatty acid metabolism involved in liver and other diseases: An update","volume":"21","author":"Yan","year":"2015","journal-title":"World J. Gastroenterol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1146\/annurev-nutr-071813-105541","article-title":"Acyl-CoA Metabolism and Partitioning","volume":"34","author":"Grevengoed","year":"2014","journal-title":"Annu. Rev. Nutr."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"R281","DOI":"10.1152\/ajpregu.00222.2022","article-title":"Atorvastatin remodels lipid distribution between liver and adipose tissues through blocking lipoprotein efflux in fish","volume":"324","author":"Li","year":"2022","journal-title":"Am. J. Physiol.-Regul. Integr. Comp. Physiol."},{"key":"ref_32","first-page":"9953927","article-title":"Dietary Bile Acid Supplementation Could Regulate the Glucose, Lipid Metabolism, and Microbiota of Common Carp (Cyprinus carpio L.) Fed with a High-Lipid Diet","volume":"2023","author":"Yang","year":"2023","journal-title":"Aquac. Nutr."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Tahri-Joutey, M., Andreoletti, P., Surapureddi, S., Nasser, B., Cherkaoui-Malki, M., and Latruffe, N. (2021). Mechanisms Mediating the Regulation of Peroxisomal Fatty Acid Beta-Oxidation by PPAR\u03b1. Int. J. Mol. Sci., 22.","DOI":"10.3390\/ijms22168969"},{"key":"ref_34","first-page":"919","article-title":"Physiological regulation of lipoprotein lipase","volume":"1841","author":"Kersten","year":"2014","journal-title":"Biochim. Et Biophys. Acta (BBA) Mol. Cell Biol. Lipids"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"735158","DOI":"10.1016\/j.aquaculture.2020.735158","article-title":"Lipid metabolism and plasma metabolomics of juvenile largemouth bass Micropterus salmoides were affected by dietary oxidized fish oil","volume":"522","author":"Xie","year":"2020","journal-title":"Aquaculture"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"561","DOI":"10.1016\/j.foodchem.2017.11.039","article-title":"Nutritional composition of food fishes and their importance in providing food and nutritional security","volume":"293","author":"Mohanty","year":"2019","journal-title":"Food Chem."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1111\/jpn.13711","article-title":"Muscle proximate composition of various food fish species and their nutritional significance: A review","volume":"106","author":"Ahmed","year":"2022","journal-title":"J. Anim. Physiol. Anim. Nutr."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"736780","DOI":"10.1016\/j.aquaculture.2021.736780","article-title":"Comparative evaluation of nutritional value and flavor quality of muscle in triploid and diploid common carp: Application of genetic improvement in fish quality","volume":"541","author":"Cai","year":"2021","journal-title":"Aquaculture"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"101236","DOI":"10.1016\/j.aqrep.2022.101236","article-title":"Broken Xinyang Maojian tea supplementation in a high-fat diet improves the growth performance, flesh quality and lipid metabolism of Yellow River carp (Cyprinus carpio)","volume":"25","author":"Zhang","year":"2022","journal-title":"Aquac. Rep."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1080\/87559129809541156","article-title":"Basic properties of umami and its effects on food flavor","volume":"14","author":"Yamaguchi","year":"1998","journal-title":"Food Rev. Int."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1146\/annurev.biochem.75.103004.142520","article-title":"Asparagine Synthetase Chemotherapy","volume":"75","author":"Richards","year":"2006","journal-title":"Annu. Rev. Biochem."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1128\/ecosalplus.3.6.1.3","article-title":"Biosynthesis of Glutamate, Aspartate, Asparagine, L-Alanine, and D-Alanine","volume":"1","author":"Reitzer","year":"2004","journal-title":"EcoSal Plus"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"S968","DOI":"10.1111\/1750-3841.13229","article-title":"Effects of 3 Feeding Modes on the Volatile and Nonvolatile Compounds in the Edible Tissues of Female Chinese Mitten Crab (Eriocheir sinensis)","volume":"81","author":"Zhuang","year":"2016","journal-title":"J. Food Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"3775","DOI":"10.3748\/wjg.v18.i29.3775","article-title":"Alanine and aspartate aminotransferase and glutamine-cycling pathway: Their roles in pathogenesis of metabolic syndrome","volume":"18","author":"Sookoian","year":"2012","journal-title":"World J. Gastroenterol."},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Rogatzki, M.J., Ferguson, B.S., Goodwin, M.L., and Gladden, L.B. (2015). Lactate is always the end product of glycolysis. Front. Neurosci., 9.","DOI":"10.3389\/fnins.2015.00022"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1016\/j.molcel.2014.09.024","article-title":"Regulation of Substrate Utilization by the Mitochondrial Pyruvate Carrier","volume":"56","author":"Vacanti","year":"2014","journal-title":"Mol. Cell"},{"key":"ref_47","unstructured":"Miflin, B.J. (1980). 7\u2014Enzymes of Glutamate Formation: Glutamate Dehydrogenase, Glutamine Synthetase, and Glutamate Synthase. Amino Acids and Derivatives, Academic Press."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4257","DOI":"10.1007\/s00018-015-2001-4","article-title":"Emerging roles of lysine methylation on non-histone proteins","volume":"72","author":"Zhang","year":"2015","journal-title":"Cell. Mol. Life Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"2792","DOI":"10.1007\/s00018-006-6249-6","article-title":"Betaine homocysteine S-methyltransferase: Just a regulator of homocysteine metabolism?","volume":"63","author":"Pajares","year":"2006","journal-title":"Cell. Mol. Life Sci. CMLS"},{"key":"ref_50","first-page":"607","article-title":"Proline dehydrogenase: A key enzyme in controlling cellular homeostasis","volume":"17","author":"Servet","year":"2012","journal-title":"FBL"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"21654","DOI":"10.1074\/jbc.M112.363218","article-title":"Identification of a Human trans-3-Hydroxy-l-proline Dehydratase, the First Characterized Member of a Novel Family of Proline Racemase-like Enzymes","volume":"287","author":"Visser","year":"2012","journal-title":"J. Biol. Chem."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Belostotsky, R., and Frishberg, Y. (2022). Catabolism of Hydroxyproline in Vertebrates: Physiology, Evolution, Genetic Diseases and New siRNA Approach for Treatment. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms23021005"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/14\/13\/1939\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T15:08:06Z","timestamp":1760108886000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/14\/13\/1939"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6,30]]},"references-count":52,"journal-issue":{"issue":"13","published-online":{"date-parts":[[2024,7]]}},"alternative-id":["ani14131939"],"URL":"https:\/\/doi.org\/10.3390\/ani14131939","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,6,30]]}}}