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Wang T, Ma X, Zheng Q, Ma C, Zhang Z, Pan H, Guo X, Wu X, Chu M, Liang C, Yan P. A comprehensive study on the longissius dorsi muscle of Ashdan yaks under different feeding regimes based on transcriptomic and metabolomic analyses. Anim Biotechnol 2024; 35:2294785. [PMID: 38193799 DOI: 10.1080/10495398.2023.2294785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Yak is an important dominant livestock species at high altitude, and the growth performance of yak has obvious differences under different feeding methods. This experiment was conducted to compare the effects of different feeding practices on growth performance and meat quality of yaks through combined transcriptomic and metabolomic analyses. In terms of yak growth performance, compared with traditional grazing, in-house feeding can significantly improve the average daily weight gain, carcass weight and net meat weight of yaks; in terms of yak meat quality, in-house feeding can effectively improve the quality of yak meat. A combined transcriptomic and metabolomic analysis revealed 31 co-enriched pathways, among which arginine metabolism, proline metabolism and glycerophospholipid metabolism may be involved in the development of the longissimus dorsi muscle of yak and the regulation of meat quality-related traits. The experimental results increased our understanding of yak meat quality and provided data materials for subsequent deep excavation of the mechanism of yak meat quality.
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Affiliation(s)
- Tong Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Xiaoming Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Qingbo Zheng
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Chaofan Ma
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Zhilong Zhang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Heping Pan
- Life science and Engineering College, Northwest Minzu University, Lanzhou, China
| | - Xian Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyun Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Chunnian Liang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
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Zhou Z, Ren F, Huang Q, Cheng H, Cun Y, Ni Y, Wu W, Xu B, Yang Q, Yang L. Characterization and interactions of spoilage of Pseudomonas fragi C6 and Brochothrix thermosphacta S5 in chilled pork based on LC-MS/MS and screening of potential spoilage biomarkers. Food Chem 2024; 444:138562. [PMID: 38330602 DOI: 10.1016/j.foodchem.2024.138562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/17/2024] [Accepted: 01/21/2024] [Indexed: 02/10/2024]
Abstract
Pseudomonas and Brochothrix are the main spoilage organisms in pork, and each of these plays an essential role in the spoilage process. However, the effect of co-contamination of these two organisms in pork has not been elucidated. The changing bacterial communities during spontaneous spoilage of pork at 4 °C were evaluated using high-throughput sequencing. The dominant spoilage bacteria were isolated and these were identified as Pseudomonas fragi C6 and Brochothrix thermosphacta S5. Chilled pork was then experimentally contaminated with these strains, individually and in combination, and the progression of spoilage was assessed by analyzing various physicochemical indicators. These included total viable counts (TVC), pH, color, total volatile basic nitrogen (TVB-N), and detection of microbial metabolites. After 7 days of chilled storage, co-contaminated pork produced higher TVC and TVB-N values than mono-contaminated samples. Metabolomic analysis identified a total of 8,084 metabolites in all three groups combined. Differential metabolites were identified, which were involved in 38 metabolic pathways. Among these pathways, the biosynthesis of alkaloids derived from purine and histidine was identified as an important pathway related to spoilage. Specifically, histidine, histamine, AMP, IMP, GMP, succinic acid, and oxoglutaric acid were identified as potential spoilage biomarkers. The study showed that the combined presence of P. fragi C6 and B. thermosphacta S5 bacteria makes chilled pork more prone to spoilage, compared to their individual presence. This study provides insights that can assist in applying appropriate techniques to maintain quality and safety changes in meat during storage and further the assessment of freshness.
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Affiliation(s)
- Zhonglian Zhou
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Fangqi Ren
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Qianli Huang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Haoran Cheng
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Yu Cun
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Yongsheng Ni
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Wenda Wu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Baocai Xu
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Qinghua Yang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Liu Yang
- China Light Industry Key Laboratory of Meat Microbial Control and Utilization, Hefei University of Technology, Hefei 230009, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China.
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Kuang L, Zeng J, Li Y, Zheng J, Ren Y, Guo Z, Zhang X, Zhang C, Yang C, Mei X, Yang R, Tang L, Ji Y, Xie X, Lei M, Li C. Delineating molecular regulatory network of meat quality of longissimus dorsi indicated by transcriptomic, proteomic, and metabolomics analysis in rabbit. J Proteomics 2024; 300:105179. [PMID: 38657733 DOI: 10.1016/j.jprot.2024.105179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 04/26/2024]
Abstract
This study aims to investigate the potential regulatory network responsible for the meat quality using multi-omics to help developing better varieties. Slaughter performance and meat quality of Shuxing No.1 rabbit outperformed IRA rabbit according to the tested rabbit parameters. Differentially expressed genes (DEGs) and differentially abundance proteins (DAPs) were involved in meat quality-related pathways, such as PI3K - Akt and MAPK signaling pathways. Only SMTNL1 and PM20D2 shared between DEGs and DAPs. Olfactory-sensitive undecanal, a differentially abundant metabolite (DAM) in volatilomics (vDAMs), correlated with all of the remaining 11 vDAMs, and most of 12 vDAMs were associated with amino acid metabolism. Integration revealed that 829 DEGs/DAPs were associated with 15 DAMs in four KEGG pathways, such as melatonin (a DAM in widely targeted metabolomics) was significantly positively correlated with ALDH and negatively correlated with RAB3D and CAT in the tryptophan metabolism pathway. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor. SIGNIFICANCE: Shuxing No.1 rabbit is a new breed of meat rabbit in the Chinese market. In meat marketing, meat quality usually determines the purchase intention of consumers. Determining the biological and molecular mechanisms of meat quality in meat rabbit is essential for developing strategies to improve meat quality. According to the tested rabbit parameters, this study ascertained that the slaughter performance and meat quality of Shuxing No.1 rabbit surpasses that of IRA rabbit. The present study profiled the transcriptome, proteome, widely targeted metabolome, and volatilome of longissimus dorsi from Shuxing No.1 rabbit and IRA rabbit. The study found that meat quality and flavor-related tryptophan metabolism pathway is enriched with many DEGs/DAPs (including ALDH, RAB3D, and CAT), as well as a DAM, melatonin. This study sheds light on the potential mechanisms that contribute to the improved meat quality and flavor.
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Affiliation(s)
- Liangde Kuang
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Jianhong Zeng
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Yuying Li
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Jie Zheng
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Yongjun Ren
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Zhiqiang Guo
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Xiangyu Zhang
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Cuixia Zhang
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Chao Yang
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Xiuli Mei
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Rui Yang
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Li Tang
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Yang Ji
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Xiaohong Xie
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China
| | - Min Lei
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China.
| | - Congyan Li
- Sichuan Animal Science Academy, Chengdu 610066, Sichuan, China; Animal Breeding and Genetics Key Laboratory of Sichuan Province, Chengdu 610066, Sichuan, China.
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Yu J, Li X, Qi X, Ding Z, Su S, Yu L, Zhou L, Li Y. Translatomics reveals the role of dietary calcium addition in regulating muscle fat deposition in pigs. Sci Rep 2024; 14:12295. [PMID: 38811812 PMCID: PMC11136974 DOI: 10.1038/s41598-024-62986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024] Open
Abstract
Intramuscular fat (IMF) in pork holds significant importance for economic performance within the pig industry and dietary calcium supplementation enhances the accumulation of intramuscular fat. Additionally, calcium ions inhibit translation and reduce protein synthesis. However, the mechanism by which calcium regulates IMF deposition in muscle through translation remains largely unknown. In this study, we compared the ribosome profiles of the longissimus dorsi muscles of Duroc × Landrace × Large white pigs from the normal calcium (NC) group or calcium supplement (HC) group by Ribo-seq, and RNA-seq. By integrating multiple-omics analysis, we further discovered 437 genes that were transcriptionally unchanged but translationally altered and these genes were significantly enriched in the oxidative phosphorylation signaling pathway. Furthermore, experimental data showed that inhibiting the expression of COX10 and mtND4L increased triglyceride accumulation in C2C12 cells, providing new targets for intramuscular fat deposition. Finally, this work links dietary calcium, translation regulation and IMF deposition, providing a new strategy for both meat quality and economic performance within the pig industry.
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Affiliation(s)
- Jingsu Yu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Xiangling Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Xinyu Qi
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Zhaoxuan Ding
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Songtao Su
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Lin Yu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China
| | - Lei Zhou
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China.
| | - Yixing Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Zhuang Autonomous Region, China.
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Xu G, Pan H, Fan L, Zhang L, Li J, Cheng S, Meng L, Shen N, Liu Y, Li Y, Huang T, Zhou L. Dietary Betaine Improves Glucose Metabolism in Obese Mice. J Nutr 2024; 154:1309-1320. [PMID: 38417550 DOI: 10.1016/j.tjnut.2024.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/17/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND Obesity caused by the overconsumption of energy-dense foods high in fat and sugar has contributed to the growing prevalence of type 2 diabetes. Betaine, found in food or supplements, has been found to lower blood glucose concentrations, but its exact mechanism of action is not well understood. OBJECTIVES A comprehensive evaluation of the potential mechanisms by which betaine supplementation improves glucose metabolism. METHODS Hyperglycemic mice were fed betaine to measure the indexes of glucose metabolism in the liver and muscle. To explore the mechanism behind the regulation of betaine on glucose metabolism, Ribonucleic Acid-Seq was used to analyze the livers of the mice. In vitro, HepG2 and C2C12 cells were treated with betaine to more comprehensively evaluate the effect of betaine on glucose metabolism. RESULTS Betaine was added to the drinking water of high-fat diet-induced mice, and it was found to reduce blood glucose concentrations and liver triglyceride concentrations without affecting body weight, confirming its hypoglycemic effect. To investigate the specific mechanism underlying its hypoglycemic effect, protein-protein interaction enrichment analysis of the liver revealed key nodes associated with glucose metabolism, including cytochrome P450 family activity, insulin sensitivity, glucose homeostasis, and triglyceride concentrations. The Kyoto Encyclopedia of Genes and Genomes and gene ontogeny enrichment analyses showed significant enrichment of the Notch signaling pathway. These results provided bioinformatic evidence for specific pathways through which betaine regulates glucose metabolism. Key enzyme activities involved in glucose uptake, glycogen synthesis, and glycogenolysis pathways of the liver and muscle were measured, and improvements were observed in these pathways. CONCLUSIONS This study provides new insight into the mechanisms by which betaine improves glucose metabolism in the liver and muscle and supports its potential as a drug for the treatment of metabolic disorders related to glucose.
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Affiliation(s)
- Gaoxiao Xu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Hongyuan Pan
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liping Fan
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Lifang Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jian Li
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Shimei Cheng
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Libing Meng
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Nana Shen
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Yong Liu
- Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, and Environmental Hormone and Reproduction, School of Biological and Food Engineering, Fuyang Normal University, Fuyang, China
| | - Yixing Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tengda Huang
- College of Animal Science and Technology, Guangxi University, Nanning, China.
| | - Lei Zhou
- Guangxi Academy of Medical Sciences, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
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Yang S, Zhang X, Li X, Zheng J, Zhao L, Fan C, Zhao Y. Integrated Metabolomics and Transcriptomics Analyses Reveal the Candidate Genes Regulating the Meat Quality Change by Castration in Yudong Black Goats ( Capra hircus). Genes (Basel) 2023; 15:43. [PMID: 38254933 PMCID: PMC10815812 DOI: 10.3390/genes15010043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Yudong black goats (YDGs) are a local breed in southwest China that possess unique meat qualities and produce a high meat yield, making them ideal models for studying goat meat quality. Castration may decrease off-odors, significantly change metabolites and improve meat quality. Using multi-omics techniques, this study focused on Yudong black goat wethers (YDW, n = 4) and Yudong black bucks (YDB, n = 4). The findings revealed that 33 differentially expressed genes (DEGs) and 279 significantly changed metabolites (SCMs) influenced goat meat quality by affecting fat accumulation and lipolysis regulatory processes. Herein, several candidate genes (IGF1, TNNT2, PPP2R2C, MAPK10 and VNN1, etc.) were identified that play a role in regulating meat quality, non-castrated and castrated, alongside a series of metabolites that may serve as potential meat quality biomarkers. Lipids (triglycerides, oxidized lipids_5-iso PGF2VI, ceramide (t18:1/36:2(2OH)) and Carnitine C20:5, etc.) were significantly higher in the castrated goats. These results revealed that lipids and hydrophilic metabolites were affected by castration, which might be beneficial in terms of goat meat quality. This study aimed to investigate the differences in meat quality between uncastrated and castrated male goats and the possible molecular regulatory mechanisms.
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Affiliation(s)
- Songjian Yang
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Xinyue Zhang
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Xingchun Li
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Jikang Zheng
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Le Zhao
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Chengli Fan
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
| | - Yongju Zhao
- Chongqing Key Laboratory of Forage & Herbivore, Chongqing 400715, China; (S.Y.); (X.Z.); (X.L.); (J.Z.); (L.Z.); (C.F.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China
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7
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Cao Y, Xing Y, Guan H, Ma C, Jia Q, Tian W, Li G, Tian Y, Kang X, Liu X, Li H. Genomic Insights into Molecular Regulation Mechanisms of Intramuscular Fat Deposition in Chicken. Genes (Basel) 2023; 14:2197. [PMID: 38137019 PMCID: PMC10742768 DOI: 10.3390/genes14122197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Intramuscular fat (IMF) plays an important role in the tenderness, water-holding capacity, and flavor of chicken meat, which directly affect meat quality. In recent years, regulatory mechanisms underlying IMF deposition and the development of effective molecular markers have been hot topics in poultry genetic breeding. Therefore, this review focuses on the current understanding of regulatory mechanisms underlying IMF deposition in chickens, which were identified by multiple genomic approaches, including genome-wide association studies, whole transcriptome sequencing, proteome sequencing, single-cell RNA sequencing (scRNA-seq), high-throughput chromosome conformation capture (HiC), DNA methylation sequencing, and m6A methylation sequencing. This review comprehensively and systematically describes genetic and epigenetic factors associated with IMF deposition, which provides a fundamental resource for biomarkers of IMF deposition and provides promising applications for genetic improvement of meat quality in chicken.
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Affiliation(s)
- Yuzhu Cao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
| | - Yuxin Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
| | - Hongbo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
| | - Chenglin Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Y.X.); (H.G.); (C.M.); (Q.J.); (W.T.); (G.L.); (Y.T.); (X.K.); (X.L.)
- International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou 450046, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
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Zhao X, Jia W, Wang J, Wang S, Zheng Q, Shan T. Identification of a Candidate Gene Regulating Intramuscular Fat Content in Pigs through the Integrative Analysis of Transcriptomics and Proteomics Data. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19154-19164. [PMID: 37987700 DOI: 10.1021/acs.jafc.3c05806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Pork is a widely consumed source of animal protein worldwide, and the intramuscular fat (IMF) content in pork plays a crucial role in determining its quality. In this study, we sought to identify candidate genes that regulate IMF deposition in pigs. We performed tandem mass tags (TMT)-based quantitative proteomics analysis using Longissimus dorsi (LD) muscle samples obtained from eight pigs with extremely high and low IMF content among a group of 28 Duroc pigs and identified 50 differentially abundant proteins (DAPs). Additionally, we compared the proteomics data with RNA-sequencing data obtained in our previous study and identified TUSC5 as a differentially expressed gene corresponding to the relevant DAP. To investigate the potential role of TUSC5 in adipogenesis, we suppressed TUSC5 expression in mouse 3T3-L1 preadipocytes using short hairpin RNA (shRNA) and observed a significant reduction in the differentiation of 3T3-L1 cells into adipocytes, as indicated by Oil Red O staining and triglyceride content. Moreover, we observed a reduction in the expression of genes associated with adipogenesis (PPARG, CEBPA, FABP4, and FASN) following TUSC5 suppression. Through an integrative analysis of transcriptomics and proteomics data, our study identified TUSC5 as a crucial candidate gene associated with the regulation of IMF content in pigs.
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Affiliation(s)
- Xueyan Zhao
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Wanli Jia
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Jiying Wang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, Shandong 250100, China
| | - Shouwei Wang
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
| | - Qiankun Zheng
- DELISI GROUP Co. Ltd., Weifang, Shandong 262200, China
| | - Tizhong Shan
- Zhejiang University, No. 866 Yuhangtang Road, Hangzhou, Zhejiang 310058, China
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Wu G, Qiu X, Jiao Z, Yang W, Pan H, Li H, Bian Z, Geng Q, Wu H, Jiang J, Chen Y, Cheng Y, Chen Q, Chen S, Man C, Du L, Li L, Wang F. Integrated Analysis of Transcriptome and Metabolome Profiles in the Longissimus Dorsi Muscle of Buffalo and Cattle. Curr Issues Mol Biol 2023; 45:9723-9736. [PMID: 38132453 PMCID: PMC10741837 DOI: 10.3390/cimb45120607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023] Open
Abstract
Buffalo meat is gaining popularity for its nutritional properties, such as its low fat and cholesterol content. However, it is often unsatisfactory to consumers due to its dark color and low tenderness. There is currently limited research on the regulatory mechanisms of buffalo meat quality. Xinglong buffalo are raised in the tropical Hainan region and are undergoing genetic improvement from draught to meat production. For the first time, we evaluated the meat quality traits of Xinglong buffalo using the longissimus dorsi muscle and compared them to Hainan cattle. Furthermore, we utilized a multi-omics approach combining transcriptomics and metabolomics to explore the underlying molecular mechanism regulating meat quality traits. We found that the Xinglong buffalo had significantly higher meat color redness but lower amino acid content and higher shear force compared to Hainan cattle. Differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were identified, with them being significantly enriched in nicotinic acid and nicotinamide metabolic and glycine, serine, and threonine metabolic pathways. The correlation analysis revealed that those genes and metabolites (such as: GAMT, GCSH, PNP, L-aspartic acid, NADP+, and glutathione) are significantly associated with meat color, tenderness, and amino acid content, indicating their potential as candidate genes and biological indicators associated with meat quality. This study contributes to the breed genetic improvement and enhancement of buffalo meat quality.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Lianbin Li
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (G.W.); (X.Q.); (Z.J.); (W.Y.); (H.P.); (Q.G.); (H.W.); (Y.C.); (S.C.); (L.D.)
| | - Fengyang Wang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (G.W.); (X.Q.); (Z.J.); (W.Y.); (H.P.); (Q.G.); (H.W.); (Y.C.); (S.C.); (L.D.)
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10
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Tang X, Huang Z, Wang F, Chen J, Qin D, Peng D, Yu B. Macrophage-specific deletion of MIC26 (APOO) mitigates advanced atherosclerosis by increasing efferocytosis. Atherosclerosis 2023; 386:117374. [PMID: 37995600 DOI: 10.1016/j.atherosclerosis.2023.117374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 10/01/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND AND AIMS Recent studies have suggested that MIC26 (apolipoprotein O, APOO), a novel mitochondrial inner membrane protein, is involved in inflammation. Thus, the role of macrophage MIC26 in acute inflammation and chronic inflammatory disease atherosclerosis was investigated. METHODS Macrophage-specific MIC26 knockout mice (MIC26LysM) were generated by crossing Apooflox/flox and LysMcre+/- mice. An endotoxemia mouse model was generated to explore the effects of macrophage MIC26 deficiency on acute inflammation, while an atherosclerosis mouse model was constructed by crossing MIC26LysM mice with Apoe-/- mice and challenged with a Western diet. Atherosclerotic plaques, primary macrophage function, and mitochondrial structure and function were analyzed. RESULTS MIC26 knockout did not affect the median survival time and post-injection serum interleukin 1β concentrations in mice with endotoxemia. Mice with MIC26 deficiency in an Apoe-/- background had smaller atherosclerotic lesions and necrotic core than the control group. In vitro studies found that the loss of MIC26 did not affect macrophage polarization, apoptosis, or lipid handling capacity, but increased efferocytosis (the ability to clear apoptotic cells). An in situ efferocytosis assay of plaques also showed that the ratio of macrophage-associated apoptotic cells to free apoptotic cells was higher in the MIC26-deficient group than in the control group, indicating increased efferocytosis. In addition, an in vivo thymus efferocytosis assay indicated that MIC26 deletion promoted efferocytosis. Mechanistically, the loss of MIC26 resulted in an abnormal mitochondrial inner membrane structure, increased mitochondrial fission, and decreased mitochondrial membrane potential. Loss of MIC26 reduced mitochondria optic atrophy type 1 (OPA1) protein, and OPA1 silencing in macrophages promoted efferocytosis. Overexpression of OPA1 abolished the increase in efferocytosis produced by MIC26 deficiency. CONCLUSIONS Macrophage MIC26 deletion alleviated advanced atherosclerosis and necrotic core expansion by promoting efferocytosis. This mechanism may be related to the increased mitochondrial fission caused by reduced mitochondrial OPA1.
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Affiliation(s)
- Xiaoyu Tang
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Department of Rheumatology and Immunology, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Clinical Medical Research Center for Systemic Autoimmune Diseases in Hunan Province, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Zhijie Huang
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Research Institute of Blood Lipid and Atherosclerosis, Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Hunan Key Laboratory of Cardiometabolic Medicine, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Fengjiao Wang
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Research Institute of Blood Lipid and Atherosclerosis, Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Hunan Key Laboratory of Cardiometabolic Medicine, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Jin Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Research Institute of Blood Lipid and Atherosclerosis, Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Hunan Key Laboratory of Cardiometabolic Medicine, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Donglu Qin
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Research Institute of Blood Lipid and Atherosclerosis, Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Hunan Key Laboratory of Cardiometabolic Medicine, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China
| | - Daoquan Peng
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Research Institute of Blood Lipid and Atherosclerosis, Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Hunan Key Laboratory of Cardiometabolic Medicine, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China.
| | - Bilian Yu
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Research Institute of Blood Lipid and Atherosclerosis, Central South University, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; Hunan Key Laboratory of Cardiometabolic Medicine, No. 139 Middle Renmin Road, Changsha, 410011, Hunan, China; FuRong Laboratory, Changsha, 410078, Hunan, China.
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Deng X, Zhang Y, Song G, Fu Y, Chen Y, Gao H, Wang Q, Jin Z, Yin Y, Xu K. Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring. Animals (Basel) 2023; 13:3321. [PMID: 37958077 PMCID: PMC10647668 DOI: 10.3390/ani13213321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/28/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F1 offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F1 offspring, and Ningxiang pigs vs. F1 offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F1 offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F1 offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F1 pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies.
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Affiliation(s)
- Xiaoxiao Deng
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yuebo Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Gang Song
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yawei Fu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Yue Chen
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Hu Gao
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Qian Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Zhao Jin
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, College of Animal Science and Technology, Hunan Agricultural University, Changsha 410125, China
| | - Yulong Yin
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
| | - Kang Xu
- Laboratory of Animal Nutrition Physiology and Metabolism, The Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha 410125, China; (X.D.); (Y.F.); (Y.C.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; (Y.Z.); (G.S.); (H.G.); (Q.W.); (Z.J.)
- CAS Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Changsha 410125, China
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Hou X, Zhang R, Yang M, Niu N, Zong W, Yang L, Li H, Hou R, Wang X, Wang L, Liu X, Shi L, Zhao F, Wang L, Zhang L. Characteristics of Transcriptome and Metabolome Concerning Intramuscular Fat Content in Beijing Black Pigs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15874-15883. [PMID: 37847170 DOI: 10.1021/acs.jafc.3c02669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
To study the characteristics of genes and metabolites related to intramuscular fat (IMF) content with less influence by breed background and individual differences, the skeletal muscle samples from 40 Beijing black pigs with either high or low IMF content were used to perform transcriptome and metabolome analyses. About 99 genes (twofold-change) were differentially expressed. Up-regulated genes in the high IMF pigs were mainly related to fat metabolism. The key genes in charge of IMF deposition are ADIPOQ, CIDEC, CYP4B1, DGAT2, LEP, OPRL1, PLIN1, SCD, and THRSP. KLHL40, TRAFD1, and HSPA6 were novel candidate genes for the IMF trait due to their high abundances. In the low IMF pigs, the differentially expressed genes involved in virus resistance were up-regulated. About 16 and 18 differential metabolites (1.5 fold-change) were obtained in the positive and negative modes, respectively. Pigs with low IMF had weaker fatty acid oxidation due to the down-regulation of various carnitines. Differentially expressed genes were more important in determining IMF deposition than differential metabolites because relatively few differential metabolites were obtained, and they were merely the products under the physiological status of diverged IMF content. This study provided valuable information for further studies on IMF deposition.
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Affiliation(s)
- Xinhua Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Run Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Man Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Naiqi Niu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Wencheng Zong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Liyu Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Huihui Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Renda Hou
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiaoqing Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lijun Shi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Fuping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
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Chen B, Yue Y, Li J, Yuan C, Guo T, Zhang D, Liu J, Yang B, Lu Z. Global DNA Methylation, miRNA, and mRNA Profiles in Sheep Skeletal Muscle Promoted by Hybridization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15398-15406. [PMID: 37815113 DOI: 10.1021/acs.jafc.3c02173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
With the development of high-throughput sequencing technology, several nongenetic variations, including noncoding RNAs such as miRNAs, and DNA methylation, have been found to play an important role in animal muscle development and fat metabolism. In this study, Southdown and Suffolk were selected as male parents for hybridization with Hu sheep (Southdown × Hu (NH), Suffolk × Hu (SH), and Hu × Hu (HH)). RNA sequencing, bisulfite sequencing, and small-RNA sequencing were used to study the methylation patterns and differences in miRNA and mRNA expression in the F1 sheep longissimus dorsi muscle tissue. We identified 765 differentially expressed genes (DEGs), 10,161 differentially methylated regions (DMRs), and 164 differentially expressed miRNAs, which were significantly enriched in AMPK signaling, fatty acid degradation, metabolism, and other related pathways (P < 0.05). In addition, we constructed a DNA methylation-mRNA and miRNA-mRNA coexpression network. A total of 42 common genes were identified from DMRs and DEGs. Importantly, we predicted that 33 differentially expressed miRNAs directly or indirectly targeted the SLC27A6. The data obtained in this study provide useful information and evidence to support further understanding of the miRNA and DNA methylation of key genes regulating muscle growth and fat metabolism in hybrid sheep populations.
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Affiliation(s)
- Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Chao Yuan
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Tingting Guo
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Dan Zhang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Bohui Yang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
- Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, People's Republic of China
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Zhang D, Wang L, Wang W, Liu D. The Role of lncRNAs in Pig Muscle in Response to Cold Exposure. Genes (Basel) 2023; 14:1901. [PMID: 37895249 PMCID: PMC10606478 DOI: 10.3390/genes14101901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Cold exposure is an essential factor affecting breeding efforts in cold regions. Muscle, as an important tissue for homeothermic animals, can produce heat through shivering thermogenesis (ST) and non-shivering thermogenesis (NST) under cold exposure. Long non-coding RNAs (lncRNAs) play important roles in regulating gene expression. However, the regulatory mechanisms of lncRNAs and their role in the thermogenesis of pigs are unclear. We examined lncRNAs in the skeletal muscle of an indigenous pig breed, the Enshi black pig, when the pigs were exposed to acute or chronic cold. Three pigs were maintained inside a pig house (control group), three pigs were maintained outside the pig house for 55 d (chronic cold group), and three pigs were suddenly exposed to the conditions outside the pig house for 3 days (acute cold group). After the experiment, the longissimus dorsi of each pig were collected, and their lncRNA profiles were sequenced and analyzed. Each sample obtained nearly 12.56 Gb of clean data. A total of 11,605 non-coding RNAs were obtained, including 10,802 novel lncRNAs. The number of differentially expressed lncRNAs (DElncRNAs) was identified under acute cold (427) and cold acclimation (376), with 215 and 192 upregulated lncRNAs, respectively. However, only 113 lncRNAs were commonly upregulated by acute cold and cold acclimation. In addition, 65% of the target genes were trans-regulated by DElncRNAs. The target genes were enriched in signal transduction, immune system, cell growth and death pathways, and amino acid and carbohydrate metabolism. Compared to cold acclimation, acute cold stress-induced more DElncRNAs and response pathways. In conclusion, low temperatures altered the expression levels of lncRNAs and their target genes in muscle tissue. Some potential mechanisms were revealed, including ion migration and the metabolism of amino acids and carbohydrates.
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Affiliation(s)
| | | | | | - Di Liu
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (D.Z.); (L.W.); (W.W.)
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15
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Chen Q, Zhang W, Xiao L, Sun Q, Wu F, Liu G, Wang Y, Pan Y, Wang Q, Zhang J. Multi-Omics Reveals the Effect of Crossbreeding on Some Precursors of Flavor and Nutritional Quality of Pork. Foods 2023; 12:3237. [PMID: 37685169 PMCID: PMC10486348 DOI: 10.3390/foods12173237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Over the last several decades, China has continuously introduced Duroc boars and used them as breeding boars. Although this crossbreeding method has increased pork production, it has affected pork quality. Nowadays, one of the primary goals of industrial breeding and production systems is to enhance the quality of meat. This research analyzed the molecular mechanisms that control the quality of pork and may be used as a guide for future efforts to enhance meat quality. The genetic mechanisms of cross-breeding for meat quality improvement were investigated by combining transcriptome and metabolome analysis, using Chinese native Jiaxing black (JXB) pigs and crossbred Duroc × Duroc × Berkshire × JXB (DDBJ) pigs. In the longissimus Dorsi muscle, the content of inosine monophosphate, polyunsaturated fatty acid, and amino acids were considerably higher in JXB pigs in contrast with that of DDBJ pigs, whereas DDBJ pigs have remarkably greater levels of polyunsaturated fatty acids than JXB pigs. Differentially expressed genes (DEGs) and differential metabolites were identified using transcriptomic and metabolomic KEGG enrichment analyses. Differential metabolites mainly include amino acids, fatty acids, and phospholipids. In addition, several DEGs that may explain differences in meat quality between the two pig types were found, including genes associated with the metabolism of lipids (e.g., DGKA, LIPG, and LPINI), fatty acid (e.g., ELOVL5, ELOVL4, and ACAT2), and amino acid (e.g., SLC7A2, SLC7A4). Combined with the DEGS-enriched signaling pathways, the regulatory mechanisms related to amino acids, fatty acids, and phospholipids were mapped. The abundant metabolic pathways and DEGs may provide insight into the specific molecular mechanism that regulates meat quality. Optimizing the composition of fatty acids, phospholipids, amino acids, and other compounds in pork is conducive to improving meat quality. Overall, these findings will provide useful information and further groundwork for enhancing the meat quality that may be achieved via hybrid breeding.
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Affiliation(s)
- Qiangqiang Chen
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Wei Zhang
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Lixia Xiao
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Qian Sun
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Fen Wu
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Guoliang Liu
- Zhejiang Qinglian Food Co., Ltd., Jiaxing 314317, China;
| | - Yuan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100107, China;
| | - Yuchun Pan
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Qishan Wang
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
| | - Jinzhi Zhang
- College of Animal Science, Zhejiang University, Hangzhou 310058, China; (Q.C.); (W.Z.); (L.X.); (Q.S.); (F.W.); (Y.P.); (Q.W.)
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16
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Zhang N, Xu F, Wang L, Emu Q, Wei Y, Zhang L, Xu Y, Fan J, Sun Y, Shama S, Zhou H, Li C, Zhou L, Li B, Min J. Integrated metabolomics and transcriptomics analyses reveal the key genes regulating differential metabolites of longissimus dorsi muscle in castrated South Sichuan black goats (Capra hircus). Funct Integr Genomics 2023; 23:274. [PMID: 37574510 DOI: 10.1007/s10142-023-01199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/15/2023]
Abstract
The main aim of the current work was to explore the differential metabolites and differentially expressed genes of longissimus dorsi muscle (LDM) between castrated and uncastrated fattening male South Sichuan black goats (Capra hircus). Then, the key genes regulating important differential metabolites (DMs) in castrated male goats were observed by integrated metabolomics and transcriptomics analyses. In addition, we evaluated the effects of castration on blood constituents, dressing percentage, and water holding capacity of LDM in male black goats. The results showed that the concentrations of alkaline phosphatase (ALP), total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) were significantly increased and testosterone was significantly decreased in castrated male goats compared with the uncastrated male goats, while dressing percentage of black goats and water holding capacity of longissimus dorsi muscle were not significant differences. Through metabolomics and transcriptomics analyses, 23 important KEGG pathways, 13 important DMs, 32 important differentially expressed genes (DEGs), and 13 key genes related to the "Metabolism" and "Organismal systems" pathways were screened. Lipid accumulation may be elevated in the blood of fattening South Sichuan black goats after castration. Castration might play a positive role in energy provision, intercellular signaling, muscle function, softening of meat, disease reduction, and anti-oxidation of LDM. P4HA2, AKR1B1, GPT2, L2HGDH, ENSCHIG00000021660, ENSCHIG00000023861, DGAT2, ULK1, SLC38A3, PLA2G4A, SLC6A1, ENSCHIG00000026624, and ND2 might be the key genes regulating important DMs in the KEGG pathways related to "Metabolism" and "Organismal systems" of castrated male goats compared with the uncastrated male goats.
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Affiliation(s)
- Nanchi Zhang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China
| | - Feng Xu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu, 610066, China
| | - Li Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization of Ministry of Education, Southwest Minzu University, Chengdu, 610041, China.
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu, 610066, China.
| | - Yong Wei
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu, 610066, China
| | - Lin Zhang
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu, 610066, China
| | - Yuan Xu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu, 610066, China
| | - Jingsheng Fan
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Sciences Academy, Chengdu, 610066, China
| | - Yan Sun
- Liangshan Academy of Agricultural Sciences, Xichang, 615000, China
| | - Shuobu Shama
- Meigu Bureau of Agriculture and Rural Affairs, Liangshan, 616450, China
| | - Hongyan Zhou
- Ningnan Bureau of Agriculture and Rural Affairs, Liangshan, 615400, China
| | - Chunmei Li
- Fushun Bureau of Agriculture and Rural Affairs, Zigong, 643200, China
| | - Li Zhou
- Fushun Bureau of Agriculture and Rural Affairs, Zigong, 643200, China
| | - Bo Li
- Rongxian Bureau of Agriculture and Rural Affairs, Zigong, 643100, China
| | - Jie Min
- Weiyuan Bureau of Agriculture and Rural Affairs, Zigong, 642450, China
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17
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Huang J, Rao L, Zhang W, Chen X, Li H, Zhang F, Xie J, Wei Q. Effect of crossbreeding and sex on slaughter performance and meat quality in Xingguo gray goose based on multiomics data analysis. Poult Sci 2023; 102:102753. [PMID: 37267641 PMCID: PMC10244692 DOI: 10.1016/j.psj.2023.102753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/17/2023] [Accepted: 04/23/2023] [Indexed: 06/04/2023] Open
Abstract
Here, we examined the effects of crossbreeding and sex on growth performance, slaughter performance, and meat quality in Xingguo gray (XG) goose, using transcriptomic and metabolomic techniques. The experiment was conducted using 400 goslings (1-day old) of 2 genotypes: the XG breed and its ternary hybrids [F2 geese; (XG Goose♂ × Yangzhou Goose♀)♀ × Shitou Goose♂]. The goslings were divided into 4 groups: female XG, male XG, female F2 geese, and male F2 geese, and growth parameters were examined at 70 d of age, using 30 birds from each group. Following slaughter, samples of breast and thigh muscles were collected from each group for chemical, metabolome, and transcriptome analyses. Growth rate, live body and slaughter weights, meat chemical composition, and muscle fiber diameter were affected by crossbreeding and sex. Crossbreeding significantly improved the dressing percentage, semieviscerated rate, eviscerated yield, and abdominal fat yield of XG geese. To clarify the potential regulatory network affected by crossbreeding and sex, we used RNA-seq and nontargeted metabolomics to detect changes in male and female goose breast muscle. The transcriptome results showed that there were 534, 323, 297, and 492 differently expressed genes (DEGs) among the 4 comparison groups (XG-Female vs. F2-Female, XG-Male vs. F2-Male, F2-Male vs. F2-Female, and XG-Male vs. XG-Female, respectively) that were mainly related to muscle growth and development and fatty acid metabolism pathways. A total of 141 significantly differentially accumulated metabolites (DAMs) were enriched in serine and threonine, propionate, and pyruvate metabolism. Finally, we comprehensively analyzed the metabolome and transcriptome data and found that many DEGs and DAMs played crucial roles in lipid metabolism and muscle growth and development. In summary, crossbreeding can improve XG goose production performance and affect breast muscle gene expression and metabolites in both female and male geese.
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Affiliation(s)
- Jiangnan Huang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Linjie Rao
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Weihong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Xiaolian Chen
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Haiqin Li
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Fanfan Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jinfang Xie
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Qipeng Wei
- Institute of Animal Husbandry and Veterinary Medicine, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.
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18
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He X, Qin Z, Teng R, Tian M, Wang W, Feng Y, Chen H, He H, Zhang H, Liu D, Jiang X. Characterization of Growth Secondary Hair in Min Pig Activated by Follicle Stem Cell Stimulated by Wnt and BMP Signaling Pathway. Animals (Basel) 2023; 13:ani13071239. [PMID: 37048495 PMCID: PMC10093081 DOI: 10.3390/ani13071239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
In China, the national-level protected pig, the Min pig, is characterized by the development of secondary hairs and hair follicles in winter. Factors that dominate the genotype in the growth of secondary hairs are not clear through the concrete cell signaling pathways. This study compared hair phenotypes based on morphological structure, transcriptomics, and potential targeting molecules in the breeds of Min, Berkshire, and Yorkshire pigs. The results indicated that Min pigs have specific characteristics for the growth of secondary hairs compared with the Berkshire and Yorkshire pigs. The transcriptome analyses and quantitative reverse transcription-polymerase chain reaction results revealed that secondary hair growth was activated by follicle stem cells. The specific inhibitors of Wnt and BMP were studied using respective signals. The density of follicles, activity of follicle stem cells, and relative gene expression results have shown that Wnt and BMP stimulate the activity of follicle stem cells, and the Wnt signaling molecule has a significantly better effect than the BMP signaling molecule on stem cells. Wnt and BMP can promote the growth of local secondary hair and gene expression. Therefore, this study was conducted to verify the development mechanisms of secondary hairs, which have potential applications in laboratory animals and comparative medicine.
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Affiliation(s)
- Xinmiao He
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Ziliang Qin
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Ran Teng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Ming Tian
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Wentao Wang
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Yanzhong Feng
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Heshu Chen
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Haijuan He
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Haifeng Zhang
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
| | - Di Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture and Rural Affairs, Animal Husbandry Research Institute, Heilongjiang Academy of Agricultural Sciences, No. 368 Xuefu Road, Harbin 150086, China
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
| | - Xinpeng Jiang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China
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19
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Yu H, Raza SHA, Pan Y, Cheng G, Mei C, Zan L. Integrative Analysis of Blood Transcriptomics and Metabolomics Reveals Molecular Regulation of Backfat Thickness in Qinchuan Cattle. Animals (Basel) 2023; 13:ani13061060. [PMID: 36978600 PMCID: PMC10044415 DOI: 10.3390/ani13061060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
A crucial goal of reducing backfat thickness (BFT) is to indirectly improve feed conversion efficiency. This phenotype has been reported in certain papers; however, the molecular mechanism has yet to be fully revealed. Two extreme BFT groups, consisting of four Qinchuan cattle, were chosen for this study. We performed metabolite and transcriptome analyses of blood from cattle with a high BFT (H-BFT with average = 1.19) and from those with a low BFT (L-BFT with average = 0.39). In total, 1106 differentially expressed genes (DEGs) and 86 differentially expressed metabolites (DEMs) were identified in the extreme trait. In addition, serum ceramide was strongly correlated with BFT and could be used as a potential biomarker. Moreover, the most notable finding was that the functional genes (SMPD3 and CERS1) and metabolite (sphingosine 1-phosphate (S1P)) were filtered out and significantly enriched in the processes related to the sphingolipid metabolism. This investigation contributed to a better understanding of the subcutaneous fat depots in cattle. In general, our results indicated that the sphingolipid metabolism, involving major metabolites (serum ceramide and S1P) and key genes (SMPD3 and CERS1), could regulate BFT through blood circulation.
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Affiliation(s)
- Hengwei Yu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Yueting Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
- National Beef Cattle Improvement Center, Xianyang 712100, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
- National Beef Cattle Improvement Center, Xianyang 712100, China
- Correspondence:
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20
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Identification of Key Genes Affecting Flavor Formation in Beijing-You Chicken Meat by Transcriptome and Metabolome Analyses. Foods 2023; 12:foods12051025. [PMID: 36900542 PMCID: PMC10000371 DOI: 10.3390/foods12051025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/01/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
The flavor of chicken meat is influenced by muscle metabolites and regulatory genes and varies with age. In this study, the metabolomic and transcriptomic data of breast muscle at four developmental stages (days 1, 56, 98, and 120) of Beijing-You chickens (BJYs) were integrated and 310 significantly changed metabolites (SCMs) and 7,225 differentially expressed genes (DEGs) were identified. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that SCMs and DEGs were enriched in amino acid, lipid, and inosine monophosphate (IMP) metabolism pathways. Furthermore, genes highly associated with flavor amino acids, lipids, and IMP were identified by a weighted gene co-expression network analysis (WGCNA), including cystathionine β-synthase (CBS), glycine amidinotransferase (GATM), glutamate decarboxylase 2 (GAD2), patatin-like phospholipasedomain containing 6 (PNPLA6), low-specificity L-threonine aldolase (ItaE), and adenylate monophosphate deaminase 1 (AMPD1) genes. A regulatory network related to the accumulation of key flavor components was constructed. In conclusion, this study provides new perspectives regarding the regulatory mechanisms of flavor metabolites in chicken meat during development.
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21
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Feeding Aquilaria sinensis Leaves Modulates Lipid Metabolism and Improves the Meat Quality of Goats. Foods 2023; 12:foods12030560. [PMID: 36766087 PMCID: PMC9914005 DOI: 10.3390/foods12030560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 02/03/2023] Open
Abstract
Aquilaria (A.) sinensis is a medicinal plant widely grown in tropical South China. Given the abundant pruning waste of its leaves, the use of A. sinensis leaves is valuable. In this study, goats were fed a diet containing 20% A. sinensis leaves. Compared with the basal diet, feeding A. sinensis leaves to goats did not affect growth performance but considerably reduced the feeding cost. Strikingly, feeding A. sinensis leaves resulted in a significant decrease in the blood cholesterol levels (2.11 vs. 1.49 mmol/L, p = 0.01) along with a significant increase in the high-density lipoprotein levels (1.42 vs. 1.82 mmol/L, p = 0.01). There was also a tendency to lower the content of low-density lipoprotein levels in goats (0.78 vs. 0.45 mmol/L, p = 0.09). Furthermore, metabolomics analysis demonstrated that the reduction in cholesterol levels occurred in both the serum (0.387-fold change) and muscle (0.382-fold change) of goats during A. sinensis leaf feeding. The metabolic responses to feeding A. sinensis leaves suggest that the activation of lipolysis metabolism might happen in goats. These observed changes would be conducive to improving animal health and meat quality, ultimately benefiting human health.
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22
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Profiles of muscular amino acids, fatty acids, and metabolites in Shaziling pigs of different ages and relation to meat quality. SCIENCE CHINA. LIFE SCIENCES 2022:10.1007/s11427-022-2227-6. [PMID: 36564558 DOI: 10.1007/s11427-022-2227-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/21/2022] [Indexed: 12/25/2022]
Abstract
Pork meat is closely related to physicochemical alterations during growth and development, resulting in differences in nutritional value and meat flavor. This study aimed to evaluate the composition of amino acids, fatty acids, and metabolic profiles in the longissimus thoracis muscle (LM) of Shaziling pigs aged 30, 90, 150, 210, and 300 days. The results showed that the predominant fatty acids identified in the LM of Shaziling pigs were C16:0, C16:1, C18:0, C18:1n9c, and C18:2n6c. An opposite correlation was observed for C18:2n6c and n6/n3 polyunsaturated fatty acids (P<0.05). Alanine, aspartate, glutamate, D-glutamine, and D-glutamate metabolism were the main metabolic pathways for the Shaziling pig meat flavor (P<0.05). Moreover, the correlation coefficients revealed that the contents of anserine, C16:0, C16:1, and C18:1n9c were positively correlated with intramuscular fat and/or pH24h and were negatively correlated with the values of L* (lightness) and b* (yellowness) (P<0.05). In conclusion, age greatly affected the meat quality of Shaziling pigs, and the contents of muscular anserine, C16:0, C16:1, and C18:1n9c might be promising indicators for better meat quality.
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23
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Ding Y, Hou Y, Ling Z, Chen Q, Xu T, Liu L, Yu N, Ni W, Ding X, Zhang X, Zheng X, Bao W, Yin Z. Identification of Candidate Genes and Regulatory Competitive Endogenous RNA (ceRNA) Networks Underlying Intramuscular Fat Content in Yorkshire Pigs with Extreme Fat Deposition Phenotypes. Int J Mol Sci 2022; 23:ijms232012596. [PMID: 36293455 PMCID: PMC9603960 DOI: 10.3390/ijms232012596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/13/2022] [Accepted: 10/15/2022] [Indexed: 11/27/2022] Open
Abstract
Intramuscular fat (IMF) content is vital for pork quality, serving an important role in economic performance in pig industry. Non-coding RNAs, with mRNAs, are involved in IMF deposition; however, their functions and regulatory mechanisms in porcine IMF remain elusive. This study assessed the whole transcriptome expression profiles of the Longissimus dorsi muscle of pigs with high (H) and low (L) IMF content to identify genes implicated in porcine IMF adipogenesis and their regulatory functions. Hundreds of differentially expressed RNAs were found to be involved in fatty acid metabolic processes, lipid metabolism, and fat cell differentiation. Furthermore, combing co-differential expression analyses, we constructed competing endogenous RNAs (ceRNA) regulatory networks, showing crosstalk among 30 lncRNAs and 61 mRNAs through 20 miRNAs, five circRNAs and 11 mRNAs through four miRNAs, and potential IMF deposition-related ceRNA subnetworks. Functional lncRNAs and circRNAs (such as MSTRG.12440.1, ENSSSCT00000066779, novel_circ_011355, novel_circ_011355) were found to act as ceRNAs of important lipid metabolism-related mRNAs (LEP, IP6K1, FFAR4, CEBPA, etc.) by sponging functional miRNAs (such as ssc-miR-196a, ssc-miR-200b, ssc-miR10391, miR486-y). These findings provide potential regulators and molecular regulatory networks that can be utilized for research on IMF traits in pigs, which would aid in marker-assisted selection to improve pork quality.
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Affiliation(s)
- Yueyun Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Yinhui Hou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Zijing Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Qiong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Tao Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Lifei Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Na Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Wenliang Ni
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoling Ding
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Xiaodong Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Xianrui Zheng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: (W.B.); (Z.Y.)
| | - Zongjun Yin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (W.B.); (Z.Y.)
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Liu H, Chai Y, Chen H, Chen W, Li Y, Liu W, Guo S, Sun L, Zhou X, Huang C, Tang X, Luo C, Chen D, Cheng X. Analysis of terpenoids and their gene regulatory networks on the basis of the transcriptome and metabolome of Opisthopappus longilobus. FRONTIERS IN PLANT SCIENCE 2022; 13:1015942. [PMID: 36212386 PMCID: PMC9533026 DOI: 10.3389/fpls.2022.1015942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Opisthopappus longilobus, which is a unique wild plant resource in China, produces leaves and flowers with distinct aromas. However, there have been relatively few molecular studies on its floral aroma, which has hindered the research on this plant species at the molecular level and the breeding of novel varieties. In this study, transcriptome and metabolome analyses were performed using O. longilobus leaves, buds, and inflorescences at the exposure, initial opening, and blooming stages. Using high-quality reads and assembly software, a total of 45,674 unigenes were annotated according to the Nr, Swiss-Prot, KOG, and KEGG databases. Additionally, a GC-MS system and a self-built database were used to detect 1,371 metabolites in the leaves, buds, and inflorescences. Terpene metabolites were the most common compounds (308 in total). We analyzed the gene network regulating terpenoid accumulation in O. longilobus and identified 56 candidate genes related to terpenoid synthesis. The expression of OlPMK2, OlMVK1, OlTPS1, and OlTPS3 may lead to the accumulation of 11 different terpenoids specifically in the inflorescences at the exposure, initial opening, and blooming stages. The generated data may be useful for future research on O. longilobus genetic resources and the molecular mechanism regulating aroma formation in this plant species. The findings of this study may be used to accelerate the breeding of new O. longilobus varieties with enhanced aromatic traits.
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Affiliation(s)
- Hua Liu
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yuhong Chai
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Haixia Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wendan Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yushu Li
- Beijing Vocational College of Agriculture, Beijing, China
| | - Wenchao Liu
- Beijing Liu Wenchao Institute of Summer Chrysanthemum Breeding Science and Technology, Beijing, China
| | - Shuang Guo
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Lei Sun
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiumei Zhou
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
| | - Conglin Huang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaowei Tang
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chang Luo
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Dongliang Chen
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xi Cheng
- Institute of Grassland, Flowers and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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25
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Zhang X, Liu C, Kong Y, Li F, Yue X. Effects of intramuscular fat on meat quality and its regulation mechanism in Tan sheep. Front Nutr 2022; 9:908355. [PMID: 35967801 PMCID: PMC9366309 DOI: 10.3389/fnut.2022.908355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/08/2022] [Indexed: 11/23/2022] Open
Abstract
Intramuscular fat (IMF) contributes importantly to various aspects of meat quality, and genetic regulation is an effective pathway to improve IMF deposition in sheep. In this study, we systematically explored the effect of IMF content on meat quality in Tan sheep and investigated the regulatory mechanism of flavor precursors metabolism and IMF deposition. The results revealed that IMF significantly affected meat color, total muscle fiber numbers, and muscle fiber types in Tan sheep. Widely-targeted metabolomic analysis showed that amino acids were the main differential flavor precursors between lambs with different IMF content. Importantly, the comparison of fatty acid profiles revealed that saturated fatty acids and monounsaturated fatty acids are beneficial for IMF deposition. Furthermore, integrated analysis between metabolome and transcriptome indicated that MME is a key gene resulting in the reduction of amino acids in lambs with high IMF content; and the joint analysis between fatty acid profiles and transcript profiles showed that ADIPOQ, FABP4, PLIN1, PPARGC1A, SLC2A1 accelerated IMF deposition through positive regulation of saturated fatty acids and monounsaturated fatty acids metabolism. These results revealed key changes in meat quality affected by IMF content and the corresponding genetic mechanism, which may provide a new insight for understanding the IMF differential deposition and for improving meat quality in Tan sheep.
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Affiliation(s)
- Xueying Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chongyang Liu
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuanyuan Kong
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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26
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Zhou H, Yang Y, Wang L, Ye S, Liu J, Gong P, Qian Y, Zeng H, Chen X. Integrated multi-omic data reveal the potential molecular mechanisms of the nutrition and flavor in Liancheng white duck meat. Front Genet 2022; 13:939585. [PMID: 36046229 PMCID: PMC9421069 DOI: 10.3389/fgene.2022.939585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
The Liancheng white (LW) duck is one of the most valued Chinese indigenous poultry breeds. Its meat is rich in nutrients and has distinct flavors, but the molecular mechanisms behind them are unknown. To address this issue, we measured and compared multi-omic data (genome, transcriptome, and metabolome) of breast meat from LW ducks and the Mianyang Shelduck (MS) ducks. We found that the LW duck has distinct breed-specific genetic features, including numerous mutant genes with differential expressions associated with amino acid metabolism and transport activities. The metabolome driven by genetic materials was also seen to differ between the two breeds. For example, several amino acids that are beneficial for human health, such as L-Arginine, L-Ornithine, and L-lysine, were found in considerably higher concentrations in LW muscle than in MS duck muscle (p < 0.05). SLC7A6, a mutant gene, was substantially upregulated in the LW group (p < 0.05), which may lead to excessive L-arginine and L-ornithine accumulation in LW duck meat through transport regulation. Further, guanosine monophosphate (GMP), an umami-tasting molecule, was considerably higher in LW muscle (p < 0.05), while L-Aspartic acid was significantly abundant in MS duck meat (p < 0.05), showing that the LW duck has a different umami formation. Overall, this study contributed to our understanding of the molecular mechanisms driving the enriched nutrients and distinct umami of LW duck meat, which will provide a useful reference for duck breeding.
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Affiliation(s)
- Hao Zhou
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Lixia Wang
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Shengqiang Ye
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Jiajia Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Gong
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Yunguo Qian
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Huijun Zeng
- Wuhan Institute for Food and Cosmetic Control, Wuhan, China
- Key Laboratory of Edible Oil Quality and Safety for State Market Regulation, Wuhan, China
- *Correspondence: Huijun Zeng, ; Xing Chen,
| | - Xing Chen
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
- *Correspondence: Huijun Zeng, ; Xing Chen,
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Transcriptomics and Metabolomics Analysis of the Ovaries of High and Low Egg Production Chickens. Animals (Basel) 2022; 12:ani12162010. [PMID: 36009602 PMCID: PMC9404446 DOI: 10.3390/ani12162010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The ovarian tissues of different breeds of hens during egg production were investigated through transcriptomics and metabolomics to provide a more comprehensive understanding of the molecular mechanisms of the ovary during egg production. Four genes involved in egg production were predicted by the transcriptome, including P2RX1, INHBB, VIPR2, and FABP3, and several close metabolites associated with reproduction were identified in the metabolome, including 17α-hydroxyprogesterone, iloprost, spermidine and adenosine. Correlation analysis of specific differential genes and differential metabolites identified important gene-metabolite pairs VIPR2–Spermidine and P2RX1–Spermidine in the reproductive process. Abstract Egg production is a pivotal indicator for evaluating the fertility of poultry, and the ovary is an essential organ for egg production and plays an indispensable role in poultry production and reproduction. In order to investigate different aspects of egg production mechanisms in different poultry, in this study we performed a metabolomic analysis of the transcriptomic combination of the ovaries of two chicken breeds, the high-production Ninghai indigenous chickens and the low-production Wuliangshan black-boned chickens, to analyze the biosynthesis and potential key genes and metabolic pathways in the ovaries during egg production. We predicted four genes in the transcriptomic that are associated with egg production, namely P2RX1, INHBB, VIPR2, and FABP3, and identified three important pathways during egg production, “Calcium signaling pathway”, “Neuroactive ligand–receptor interaction” and “Cytokine–cytokine receptor interaction”, respectively. In the metabolomic 149 significantly differential metabolites were identified, 99 in the negative model and 50 in the positive model, of which 17α-hydroxyprogesterone, iloprost, spermidine, and adenosine are important metabolites involved in reproduction. By integrating transcriptomics and metabolomics, the correlation between specific differential genes and differential metabolites identified important gene-metabolite pairs “VIPR2-Spermidine” and “P2RX1-Spermidine” in egg production. In conclusion, these data provide a better understanding of the molecular differences between the ovaries of low- and high-production hens and provide a theoretical basis for further studies on the mechanics of poultry egg production.
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Mo J, Lu Y, Xing T, Xu D, Zhang K, Zhang S, Wang Y, Yan G, Lan G, Liang J. Blood metabolic and physiological profiles of Bama miniature pigs at different growth stages. Porcine Health Manag 2022; 8:35. [PMID: 35941611 PMCID: PMC9358802 DOI: 10.1186/s40813-022-00278-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/30/2022] [Indexed: 11/15/2022] Open
Abstract
Background Bama miniature pigs aged between six (6 M) and twelve months (12 M) are usually used in human medical research as laboratory pigs. However, the difference in serum metabolic profiles from 6 to 12 M-old pigs remains unclear. This study aimed to identify the metabolic and physiological profiles present in the blood to further explain changes in Bama miniature pig growth. We collected blood samples from 6 M-, eight-month- (8 M-), ten-month- (10 M-), and 12 M-old healthy Guangxi Bama miniature pigs. A total of 20 blood physiological indices (BPIs) were measured: seven for white blood cells, eight for red blood cells, and five for platelet indices. Liquid chromatography and mass spectrometry-based non-targeted metabolomic approaches were used to analyze the difference in metabolites. The associations between the differences were calculated using Spearman correlations with Benjamini–Hochberg adjustment. The 100 most abundant differential metabolites were selected for analysis of their metabolic profiles. Results There were no significant differences in BPIs at different ages, but the mid cell ratio and red blood cell number increased with age. Seven BPIs in Bama miniature pigs were closer to human BPIs than to mouse BPIs. A total of 14 and 25 significant differential metabolites were identified in 6 M vs. 12 M and 8 M vs. 12 M, respectively. In total, 9 and 18 amino acids and their derivatives showed significantly lower concentrations in 6 M- and 8 M-old pigs than in 12 M-old pigs. They were identified as the core significantly different metabolites between the age groups 6 M vs. 12 M and 8 M vs. 12 M. Half of the enriched pathways were the amino acids metabolism pathways. The concentration of six amino acids (dl-tryptophan, phenylacetylglycine, muramic acid, N-acetylornithine, l(−)-pipecolinic acid, and creatine) and their derivatives increased with age. A total of 61 of the top 100 most abundant metabolites were annotated. The metabolic profiles contained 14 amino acids and derivatives, six bile acids and derivatives, 19 fatty acids and derivatives, and 22 others. The concentrations of fatty acids and derivatives were found to be inversely proportional to those of amino acids and derivatives. Conclusion These findings suggest high levels of MID cell ratio, red blood count, and amino acids in 12 M-old pigs as indicators for improved body function over time in Bama miniature pigs, similar to those in human development. This makes the pig a more suitable medical model organism than the mouse. The results of this study are limited to the characteristics of blood metabolism in the inbred Bama miniature pigs, and the effects of impacting factors such as breed, age, sex, health status and nutritional level should be considered when studying other pig populations. Supplementary Information The online version contains supplementary material available at 10.1186/s40813-022-00278-7.
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Affiliation(s)
- Jiayuan Mo
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Yujie Lu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Tianqi Xing
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Di Xu
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Kun Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Shuai Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Yubin Wang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Gang Yan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning, 530004, People's Republic of China.
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Loor JJ. Nutrigenomics in livestock: potential role in physiological regulation and practical applications. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Shen Y, Wang H, Xie J, Wang Z, Ma Y. Trait-specific Selection Signature Detection Reveals Novel Loci of Meat Quality in Large White Pigs. Front Genet 2021; 12:761252. [PMID: 34868241 PMCID: PMC8635012 DOI: 10.3389/fgene.2021.761252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/18/2021] [Indexed: 11/24/2022] Open
Abstract
In past decades, meat quality traits have been shaped by human-driven selection in the process of genetic improvement programs. Exploring the potential genetic basis of artificial selection and mapping functional candidate genes for economic traits are of great significance in genetic improvement of pigs. In this study, we focus on investigating the genetic basis of five meat quality traits, including intramuscular fat content (IMF), drip loss, water binding capacity, pH at 45 min (pH45min), and ultimate pH (pH24h). Through making phenotypic gradient differential population pairs, Wright’s fixation index (FST) and the cross-population extended haplotype homozogysity (XPEHH) were applied to detect selection signatures for these five traits. Finally, a total of 427 and 307 trait-specific selection signatures were revealed by FST and XPEHH, respectively. Further bioinformatics analysis indicates that some genes, such as USF1, NDUFS2, PIGM, IGSF8, CASQ1, and ACBD6, overlapping with the trait-specific selection signatures are responsible for the phenotypes including fat metabolism and muscle development. Among them, a series of promising trait-specific selection signatures that were detected in the high IMF subpopulation are located in the region of 93544042-95179724bp on SSC4, and the genes harboring in this region are all related to lipids and muscle development. Overall, these candidate genes of meat quality traits identified in this analysis may provide some fundamental information for further exploring the genetic basis of this complex trait.
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Affiliation(s)
- Yu Shen
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Haiyan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jiahao Xie
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Zixuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Yunlong Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
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