Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle
Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mecha...
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2025-04-01
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| author | Siwei Wang Tingting Liu Peng Peng Yurong Fu Shaoqing Shi Shuang Liang Xi Chen Kun Wang Rongyan Zhou |
| author_facet | Siwei Wang Tingting Liu Peng Peng Yurong Fu Shaoqing Shi Shuang Liang Xi Chen Kun Wang Rongyan Zhou |
| author_sort | Siwei Wang |
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| description | Intramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mechanisms governing IMF regulation in these crossbreeds remain poorly understood. To elucidate the mechanism of IMF deposition in these crossbred cattle, we conducted a comparative transcriptomic analysis of <i>longissimus dorsi</i> muscles and livers from cattle with divergent IMF content. RNA-seq revealed 940 and 429 differentially expressed genes (DEGs) in the liver and muscle, respectively, with 60 genes co-differentially expressed (co-DEGs) in both tissues. Functional enrichment highlighted lipid metabolism pathways including fatty acid β-oxidation, PPAR signaling, and glycerolipid metabolism. A total of eleven genes including <i>ACAA2</i>, <i>ACADL</i>, <i>ACOX2</i>, <i>CPT1B</i>, <i>CPT2</i>, <i>LPL</i>, <i>SLC27A1</i>, <i>ACAT1</i>, <i>GK</i>, <i>ACOX3</i>, and <i>ACSM5</i>, were screened as key candidate genes for IMF deposition. A “liver–muscle” regulatory network of IMF deposition was built to illustrate the tissues’ interaction. The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). Our findings provide novel molecular markers for increasing the IMF content and accelerating the genetic improvement of beef quality traits in crossbred cattle. |
| format | Article |
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| language | English |
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| spelling | doaj-art-ae36d1b457bf4915bca3bda44a9a90df2025-08-20T03:52:57ZengMDPI AGAnimals2076-26152025-04-01159130610.3390/ani15091306Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef CattleSiwei Wang0Tingting Liu1Peng Peng2Yurong Fu3Shaoqing Shi4Shuang Liang5Xi Chen6Kun Wang7Rongyan Zhou8College of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaKey Laboratory of Crop Cultivation Physiology and Green Production of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, ChinaCollege of Animal Science and Technology, Hebei Agricultural University, Baoding 071000, ChinaIntramuscular fat (IMF) content in beef cattle is a critical determinant of beef meat quality, as it positively influences juiciness, tenderness, and palatability. In China, the crossbreeding of Wagyu and Angus is a prevalent method for achieving a better marbling level. However, the molecular mechanisms governing IMF regulation in these crossbreeds remain poorly understood. To elucidate the mechanism of IMF deposition in these crossbred cattle, we conducted a comparative transcriptomic analysis of <i>longissimus dorsi</i> muscles and livers from cattle with divergent IMF content. RNA-seq revealed 940 and 429 differentially expressed genes (DEGs) in the liver and muscle, respectively, with 60 genes co-differentially expressed (co-DEGs) in both tissues. Functional enrichment highlighted lipid metabolism pathways including fatty acid β-oxidation, PPAR signaling, and glycerolipid metabolism. A total of eleven genes including <i>ACAA2</i>, <i>ACADL</i>, <i>ACOX2</i>, <i>CPT1B</i>, <i>CPT2</i>, <i>LPL</i>, <i>SLC27A1</i>, <i>ACAT1</i>, <i>GK</i>, <i>ACOX3</i>, and <i>ACSM5</i>, were screened as key candidate genes for IMF deposition. A “liver–muscle” regulatory network of IMF deposition was built to illustrate the tissues’ interaction. The reliability of the transcriptomic data was verified by quantitative reverse real-time PCR (qRT-PCR). Our findings provide novel molecular markers for increasing the IMF content and accelerating the genetic improvement of beef quality traits in crossbred cattle.https://www.mdpi.com/2076-2615/15/9/1306intramuscular fatbeef cattletranscriptomic<i>longissimus dorsi</i> muscleliver |
| spellingShingle | Siwei Wang Tingting Liu Peng Peng Yurong Fu Shaoqing Shi Shuang Liang Xi Chen Kun Wang Rongyan Zhou Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle Animals intramuscular fat beef cattle transcriptomic <i>longissimus dorsi</i> muscle liver |
| title | Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle |
| title_full | Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle |
| title_fullStr | Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle |
| title_full_unstemmed | Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle |
| title_short | Integrated Transcriptomic Analysis of Liver and Muscle Tissues Reveals Candidate Genes and Pathways Regulating Intramuscular Fat Deposition in Beef Cattle |
| title_sort | integrated transcriptomic analysis of liver and muscle tissues reveals candidate genes and pathways regulating intramuscular fat deposition in beef cattle |
| topic | intramuscular fat beef cattle transcriptomic <i>longissimus dorsi</i> muscle liver |
| url | https://www.mdpi.com/2076-2615/15/9/1306 |
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