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Li F, He Z, Lu Y, Zhou J, Cao H, Zhang X, Ji H, Lv K, Yu D, Yu M. Identification of relevant differential genes to the divergent development of pectoral muscle in ducks by transcriptomic analysis. Anim Biosci 2024; 37:1345-1354. [PMID: 38575126 PMCID: PMC11222850 DOI: 10.5713/ab.23.0505] [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: 12/01/2023] [Revised: 01/12/2024] [Accepted: 01/26/2024] [Indexed: 04/06/2024] Open
Abstract
OBJECTIVE The objective of this study was to identify candidate genes that play important roles in skeletal muscle development in ducks. METHODS In this study, we investigated the transcriptional sequencing of embryonic pectoral muscles from two specialized lines: Liancheng white ducks (female) and Cherry valley ducks (male) hybrid Line A (LCA) and Line C (LCC) ducks. In addition, prediction of target genes for the differentially expressed mRNAs was conducted and the enriched gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes signaling pathways were further analyzed. Finally, a protein-to-protein interaction network was analyzed by using the target genes to gain insights into their potential functional association. RESULTS A total of 1,428 differentially expressed genes (DEGs) with 762 being up-regulated genes and 666 being down-regulated genes in pectoral muscle of LCA and LCC ducks identified by RNA-seq (p<0.05). Meanwhile, 23 GO terms in the down-regulated genes and 75 GO terms in up-regulated genes were significantly enriched (p<0.05). Furthermore, the top 5 most enriched pathways were ECM-receptor interaction, fatty acid degradation, pyruvate degradation, PPAR signaling pathway, and glycolysis/gluconeogenesis. Finally, the candidate genes including integrin b3 (Itgb3), pyruvate kinase M1/2 (Pkm), insulinlike growth factor 1 (Igf1), glucose-6-phosphate isomerase (Gpi), GABA type A receptorassociated protein-like 1 (Gabarapl1), and thyroid hormone receptor beta (Thrb) showed the most expression difference, and then were selected to verification by quantitative realtime polymerase chain reaction (qRT-PCR). The result of qRT-PCR was consistent with that of transcriptome sequencing. CONCLUSION This study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.
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Affiliation(s)
- Fan Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Zongliang He
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing, Jiangsu 210036,
China
| | - Yinglin Lu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Jing Zhou
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Heng Cao
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Xingyu Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Hongjie Ji
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing, Jiangsu 210036,
China
| | - Kunpeng Lv
- Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing, Jiangsu 210036,
China
| | - Debing Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
| | - Minli Yu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095,
China
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Atallah E, Trehiou S, Alquier-Bacquie V, Lasserre F, Arroyo J, Molette C, Remignon H. Development of hepatic steatosis in male and female mule ducks after respective force-feeding programs. Front Physiol 2024; 15:1392968. [PMID: 38974520 PMCID: PMC11224645 DOI: 10.3389/fphys.2024.1392968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/24/2024] [Indexed: 07/09/2024] Open
Abstract
Male and female mule ducks were subjected to a force-feeding diet to induce liver steatosis as it is generally done only with male ducks for the production of foie gras. The different biochemical measurements indicated that the course of hepatic steatosis development was present in both sexes and associated with a huge increase in liver weight mainly due to the synthesis and accumulation of lipids in hepatocytes. In livers of male and female ducks, this lipid accumulation was associated with oxidative stress and hypoxia. However, certain specific modifications (kinetics of lipid droplet development and hepatic inflammation) indicate that female ducks may tolerate force-feeding less well, at least at the hepatic level. This is in contradiction with what is generally reported concerning hepatic steatosis induced by dietary disturbances in mammals but could be explained by the very specific conditions imposed by force-feeding. Despite this, force-feeding female ducks seems entirely feasible, provided that the final quality of the product is as good as that of the male ducks, which will remain to be demonstrated in future studies.
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Affiliation(s)
- Elham Atallah
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, UPS, Université de Toulouse, Toulouse, France
| | - Sabrina Trehiou
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, UPS, Université de Toulouse, Toulouse, France
| | - Valérie Alquier-Bacquie
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, UPS, Université de Toulouse, Toulouse, France
| | - Frédéric Lasserre
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, UPS, Université de Toulouse, Toulouse, France
| | | | | | - Hervé Remignon
- Toxalim (Research Centre in Food Toxicology), INRAE, ENVT, UPS, Université de Toulouse, Toulouse, France
- INP-ENSAT, Université de Toulouse, Castanet-Tolosan, France
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Jiang Z, Huang B, Cui Z, Lu Z, Ma H. Synergistic effect of genistein and adiponectin reduces fat deposition in chicken hepatocytes by activating the ERβ-mediated SIRT1-AMPK signaling pathway. Poult Sci 2024; 103:103734. [PMID: 38636201 PMCID: PMC11040169 DOI: 10.1016/j.psj.2024.103734] [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: 02/10/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
Dietary supplementation with bioactive substances that can regulate lipid metabolism is an effective approach for reducing excessive fat deposition in chickens. Genistein (GEN) has the potential to alleviate fat deposition; however, the underlying mechanism of GEN's fat-reduction action in chickens remains unclear. Therefore, the present study aimed to explore the underlying mechanism of GEN on the reduction of fat deposition from a novel perspective: intercellular transmission of adipokine between adipocytes and hepatocytes. The findings showed that GEN enhanced the secretion of adiponectin (APN) in chicken adipocytes, and the enhancement effect of GEN was completely blocked when the cells were pretreated with inhibitors targeting estrogen receptor β (ERβ) or proliferator-activated receptor γ (PPARγ) signals, respectively. Furthermore, the results demonstrated that both co-treatment with GEN and APN or treatment with the medium supernatant (Med SUP) derived from chicken adipocytes treated with GEN significantly decreased the content of triglyceride and increased the protein levels of ERβ, Sirtuin 1 (SIRT1) and phosphor-AMP-activated protein kinase (p-AMPK) in chicken hepatocytes compared to the cells treated with GEN or APN alone. Moreover, the increase in the protein levels of SIRT1 and p-AMPK induced by GEN and APN co-treatment or Med SUP treatment were blocked in chicken hepatocytes pretreated with the inhibitor of ERβ signals. Importantly, the up-regulatory effect of GEN and APN co-treatment or Med SUP treatment on the protein level of p-AMPK was also blocked in chicken hepatocytes pretreated with a SIRT1 inhibitor; however, the increase in the protein level of SIRT1 induced by GEN and APN co-treatment or Med SUP treatment was not reversed when the hepatocytes were pretreated with an AMPK inhibitor. In conclusion, the present study demonstrated that GEN enhanced APN secretion by activating the ERβ-Erk-PPARγ signaling pathway in chicken adipocytes. Subsequently, adipocyte-derived APN synergized with GEN to activate the ERβ-mediated SIRT1-AMPK signaling pathway in chicken hepatocytes, ultimately reducing fat deposition. These findings provide substantial evidence from a novel perspective, supporting the potential use of GEN as a dietary supplement to prevent excessive fat deposition in poultry.
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Affiliation(s)
- Zhihao Jiang
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Benzeng Huang
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziyi Cui
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Ze Lu
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
| | - Haitian Ma
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China.
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Zhao J, Ge X, Li T, Yang M, Zhao R, Yan S, Wu H, Liu Y, Wang K, Xu Z, Jia J, Liu L, Dou T. Integrating metabolomics and transcriptomics to analyze the differences of breast muscle quality and flavor formation between Daweishan mini chicken and broiler. Poult Sci 2024; 103:103920. [PMID: 38909504 PMCID: PMC11253666 DOI: 10.1016/j.psj.2024.103920] [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: 03/24/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/25/2024] Open
Abstract
The quality and flavor of chicken are affected by muscle metabolites and related regulatory genes, and the molecular regulation mechanism of meat quality is different among different breeds of chicken. In this study, 40 one-day-old Daweishan mini chicken (DM) and Cobb broiler (CB) were selected from each group, with 4 replicates and 10 chickens in each replicate. The chickens were reared until 90 d of age under the same management conditions. Then, metabolomics and transcriptomics data of 90-day-old DM (n = 4) and CB (n = 4) were integrated to analyze metabolites affecting breast muscle quality and flavor, and to explore the important genes regulating meat quality and flavor related metabolites. The results showed that a total of 38 significantly different metabolites (SDMs) and 420 differentially expressed genes (DEGs) were detected in the breast muscle of the 2 breeds. Amino acid and lipid metabolism may be the cause of meat quality and flavor difference between DM and CB chickens, involving metabolites such as L-methionine, betaine, N6, N6, N6-Trimethyl-L-lysine, L-anserine, glutathione, glutathione disulfide, L-threonine, N-Acetyl-L-aspartic acid, succinate, choline, DOPC, SOPC, alpha-linolenic acid, L-palmitoylcarnitine, etc. Important regulatory genes with high correlation with flavor amino acids (GATM, GSTO1) and lipids (PPARG, LPL, PLIN1, SCD, ANGPTL4, FABP7, GK, B4GALT6, UGT8, PLPP4) were identified by correlation analysis, and the gene-metabolite interaction network of breast muscle mass and flavor formation in DM chicken was constructed. This study showed that there were significant differences in breast metabolites between DM and CB chickens, mainly in amino acid and lipid metabolites. These 2 kinds of substances may be the main reasons for the difference in breast muscle quality and flavor between the 2 breeds. In general, this study could provide a theoretical basis for further research on the molecular regulatory mechanism of the formation of breast muscle quality and flavor differences between DM and CB chickens, and provide a reference for the development, utilization and genetic breeding of high-quality meat chicken breeds.
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Affiliation(s)
- Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuehai Ge
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tao Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Min Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ruohan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Institute of Science and Technology, Chuxiong Normal University, Chuxiong 675099, China
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China.
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Yu B, Cai Z, Liu J, Zhang T, Feng X, Wang C, Li J, Gu Y, Zhang J. Identification of key differentially methylated genes in regulating muscle development and intramuscular fat deposition in chickens. Int J Biol Macromol 2024; 264:130737. [PMID: 38460642 DOI: 10.1016/j.ijbiomac.2024.130737] [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: 12/20/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Muscle development and intramuscular fat (IMF) deposition are intricate physiological processes characterized by multiple gene expressions and interactions. In this research, the phenotypic variations in the breast muscle of Jingyuan chickens were examined at three different time points: 42, 126, and 180 days old. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were performed to identify differentially methylated genes (DMGs) responsible for regulating muscle development and IMF deposition. The findings indicate a significant increase in breast muscle weight (BMW), myofiber diameter, and cross-sectional area, as well as IMF content, in correlation with the progressive number of growing days in Jingyuan chickens. The findings also revealed that 380 hypo-methylated and 253 hyper-methylated DMGs were identified between the three groups of breast muscle. Module gene and DMG association analysis identified m6A methylation-mediated multiple DMGs associated with muscle development and fat metabolism. In vitro cell modeling analysis reveals stage-specific differences in the expression of CUBN, MEGF10, BOP1, and BMPR2 during the differentiation of myoblasts and intramuscular preadipocytes. Cycloleucine treatment significantly inhibited the expression levels of CUBN, BOP1, and BMPR2, and promoted the expression of MEGF10. These results suggest that m6A methylation-mediated CUBN, MEGF10, BOP1, and BMPR2 can serve as potential candidate genes for regulating muscle development and IMF deposition, and provide an important theoretical basis for further investigation of the functional mechanism of m6A modification involved in adipogenesis.
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Affiliation(s)
- Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiamin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xiaofang Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Chuanchuan Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiwei Li
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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Zhu J, Wang Y, Su Y, Zheng M, Cui H, Chen Z. RNA sequencing identifies key genes involved in intramuscular fat deposition in chickens at different developmental stages. BMC Genomics 2024; 25:219. [PMID: 38413888 PMCID: PMC10900564 DOI: 10.1186/s12864-023-09819-y] [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: 07/04/2023] [Accepted: 11/20/2023] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Intramuscular fat (IMF) is an important factor in meat quality, and triglyceride (TG) and Phospholipids (PLIP), as the main components of IMF, are of great significance to the improvement of meat quality. RESULTS In this study, we used 30 RNA sequences generated from the transcriptome of chicken breast muscle tissues at different developmental stages to construct a gene expression matrix to map RNA sequence reads to the chicken genome and identify the transcript of origin. We used weighted gene co-expression network analysis (WGCNA) and identified 27 co-expression modules, 10 of which were related to TG and PLIP. We identified 150 highly-connected hub genes related to TG and PLIP, respectively, which were found to be mainly enriched in the adipocytokine signaling pathway, MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, and TGF-beta signaling pathway. Additionally, using the BioMart database, we identified 134 and 145 candidate genes related to fat development in the TG-related module and PLIP-related module, respectively. Among them, RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 were identified as candidate genes related to fat development and highly-connected hub genes in the module, suggesting that these ten genes may be important candidate genes affecting IMF deposition. CONCLUSIONS RPS6KB1, BRCA1, CDK1, RPS3, PPARGC1A, ACSL1, NDUFAB1, NDUFA9, ATP5B and PRKAG2 may be important candidate genes affecting IMF deposition. The purpose of this study was to identify the co-expressed gene modules related to chicken IMF deposition using WGCNA and determine key genes related to IMF deposition, so as to lay a foundation for further research on the molecular regulation mechanism underlying chicken fat deposition.
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Affiliation(s)
- Jinmei Zhu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yongli Wang
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yongchun Su
- Guangxi Jingling Agriculture and animal Husbandry Group Co., LTD, Nanning, 530049, China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Huanxian Cui
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Zhiwu Chen
- Guangxi Jingling Agriculture and animal Husbandry Group Co., LTD, Nanning, 530049, China.
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Quaresma MAG, Dos Santos FA, Roseiro LC, Ribeiro AP, Ferreira JD, Alves SP, Bessa RJB. Nutritional value of meat lipid fraction obtained from mallard duck (Anas platyrhynchos) reared in semiextensive conditions for hunting purposes. Poult Sci 2024; 103:103290. [PMID: 38100942 PMCID: PMC10762460 DOI: 10.1016/j.psj.2023.103290] [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: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
The mallard duck or wild duck (Anas platyrhynchos) is the world's most widespread and numerous dabbling duck, being traditionally hunted across many countries in Europe and North America. This study aims to provide a detailed characterization of mallard duck's meat lipid fraction obtained from farmed specimens, reared for hunting purposes, under semiextensive conditions. The mallard's duck meat total lipid content averaged 2.0 and 4.26 g/100 g of fresh meat in breast and leg meat portions, and its meat comprised 23 individual fatty acids (FA) and 3 dimethylacetals (DMA), independently of the sex or meat portion. The oleic (C18:1 cis-9), palmitic (C16:0), stearic (C18:0), linoleic (C18:2n-6), arachidonic (C20:4n-6), palmitoleic (C16:1 cis-9), and cis-vaccenic (C18:1 cis-11) acids were the predominant FA (representing >1% of total fatty acids in both breast and leg meat portions and independently of the sex), and together, these 7 fatty acids were accountable for 92.4 to 96.5% of total FA plus DMA in mallard duck meat. The monounsaturated, saturated and polyunsaturated fatty acids were accountable for 40.4, 35.0, and 21.0% of total FA plus DMA in breast and 54.6, 38.7, and 5.7% of total fatty acids in leg, while total DMA were liable for 3.6 and 0.9% of total FA plus DMA in breast and leg, respectively. The mallard duck meat total cholesterol content averaged 49.8 and 57.1 mg/100 g of fresh meat for breast and leg meat portions. Five tocochromanols were quantified in mallard duck meat, affording it with a total vitamin E content of 5.48 and 3.63 µg/g of fresh meat in breast and leg portions. The sex had no influence (P > 0.05) on mallard's duck meat lipid composition, but meat portion had a strong influence on mallard's duck meat lipid composition, influencing total lipid, total cholesterol, total vitamin E contents, FA partial sums, FA ratios (exception made for the n-6/n-3 ratio), and all nutritional lipid indices. The breast meat presented lower total lipid and total cholesterol contents, better FA ratios and nutritional quality indices and higher vitamin E content, being regarded as a healthier meat than leg. The study presented herein shows that mallard duck production in semiextensive conditions, similar to those used herein, could be used for the production of mallard duck beyond hunting. A production of duck's meat under natural or organic production practices, oriented to a market niche within the gourmet/organic markets.
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Affiliation(s)
- M A G Quaresma
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal; AL4AnimalS - Associate Laboratory for Animal and Veterinary Sciences, Faculty of Veterinary Medicine, Lisboa, Portugal.
| | - F Abade Dos Santos
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal; AL4AnimalS - Associate Laboratory for Animal and Veterinary Sciences, Faculty of Veterinary Medicine, Lisboa, Portugal; Faculty of Veterinary Medicine, Universidade Lusófona de Humanidades e Tecnologias, 1749-024 Lisboa, Portugal
| | - L C Roseiro
- Food Technology and Safety Division, National Institute for Agricultural and Veterinary Research (INIAV, IP), 2780-159 Oeiras, Portugal; GeoBioTec - Geobiosciences, Geoengineering e Geobiotechnologies, NOVA School of Science and Technology, 2829-516 Caparica, Portugal
| | - A P Ribeiro
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal
| | - J D Ferreira
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal
| | - S P Alves
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal; AL4AnimalS - Associate Laboratory for Animal and Veterinary Sciences, Faculty of Veterinary Medicine, Lisboa, Portugal
| | - R J B Bessa
- CIISA - Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisboa, Portugal; AL4AnimalS - Associate Laboratory for Animal and Veterinary Sciences, Faculty of Veterinary Medicine, Lisboa, Portugal
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Cao Y, Jia Q, Xing Y, Ma C, Guan H, Tian W, Kang X, Tian Y, Liu X, Li H. STC2 Inhibits Hepatic Lipid Synthesis and Correlates with Intramuscular Fatty Acid Composition, Body Weight and Carcass Traits in Chickens. Animals (Basel) 2024; 14:383. [PMID: 38338026 PMCID: PMC10854843 DOI: 10.3390/ani14030383] [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: 10/26/2023] [Revised: 12/18/2023] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Stanniocalcin 2 (STC2) is a secreted glycoprotein involved in multiple biological processes. To systemically study the biological role of STC2 in chickens, phylogenetic tree analysis and conservation analysis were conducted. Association analysis between variations in the STC2 gene and the economic traits of Gushi-Anka F2 was conducted. The tissue expression patterns of STC2 expression in different chicken tissues and liver at different stages were detected. The biological role of STC2 in chicken liver was investigated through overexpression and interfering methods in the LMH cell line. Correlation analyses between STC2 expression and lipid components were conducted. (1) The phylogenetic tree displayed that chicken STC2 is most closely related with Japanese quail and most distantly related with Xenopus tropicalis. STC2 has the same identical conserved motifs as other species. (2) rs9949205 (T > C) found in STC2 intron was highly significantly correlated with chicken body weight at 0, 2, 4, 6, 8, 10 and 12 weeks (p < 0.01). Extremely significant correlations of rs9949205 with semi-evisceration weight (SEW), evisceration weight (EW), breast muscle weight (BMW), leg muscle weight (LMW), liver weight and abdominal fat weight (AFW) were revealed (p < 0.01). Significant associations between rs9949205 and abdominal fat percentage, liver weight rate, breast muscle weight rate and leg muscle weight rate were also found (p < 0.05). Individuals with TT or TC genotypes had significantly lower abdominal fat percentage and liver weight rate compared to those with the CC genotype, while their body weight and other carcass traits were higher. (3) STC2 showed a high expression level in chicken liver tissue, which significantly increased with the progression of age (p < 0.05). STC2 was observed to inhibit the content of lipid droplets, triglycerides (TG) and cholesterol (TC), as well the expression level of genes related to lipid metabolism in LMH cells. (4) Correlation analysis showed that the STC2 gene was significantly correlated with 176 lipids in the breast muscle (p < 0.05) and mainly enriched in omega-3 and omega-6 unsaturated fatty acids. In conclusion, the STC2 gene in chicken might potentially play a crucial role in chicken growth and development, as well as liver lipid metabolism and muscle lipid deposition. This study provides a scientific foundation for further investigation into the regulatory mechanism of the STC2 gene on lipid metabolism and deposition in chicken liver.
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Affiliation(s)
- Yuzhu Cao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Qihui Jia
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Yuxin Xing
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Chenglin Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Hongbo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (X.L.)
| | - Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (Y.C.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (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.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (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.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (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.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (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.); (Q.J.); (Y.X.); (C.M.); (H.G.); (W.T.); (X.K.); (Y.T.); (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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9
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Shen N, Li C, Yang S, Ma Y, Wang HL. Liver proteomics analysis reveals the differentiation of lipid mechanism and antioxidant enzyme activity during chicken embryonic development. Int J Biol Macromol 2023; 253:127417. [PMID: 37848110 DOI: 10.1016/j.ijbiomac.2023.127417] [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: 08/11/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/19/2023]
Abstract
Chicken embryo development is a dynamic process. However, no detailed information is available about the protein abundance changes associated with the lipid mechanism and antioxidant enzyme activity during the egg embryo development. Thus, in the present study, an TMT-based proteomic approach was used to quantify protein abundance changes at different stages of chicken embryonic development. A total of 289 significantly differentially abundant hepatic proteins were quantified, of which 180 were upregulated and 109 were downregulated in the comparison of Day 20 with Day 12 in chicken embryos. Pathway analysis showed that metabolic pathways were the most highly enriched pathways, followed by arachidonic acid metabolism and steroid biosynthesis. Integration of proteomic-based studies profiling of three incubation stages revealed that the two compare groups (Day 12 vs Day 20 and Day 16 vs Day 20) shared some key differentially abundant proteins (DAPs), including LBFABP, FABP5, CYP4V2, PDCD4, LAL, APOA1, APOA4, SAA, FABP2, ACBSG2, FABP2, CYP51A1, and FBXO9. The STRING database and GO analysis results showed that there was close connectivity between APOA4, LBFABP, SERPINC1, APOA1, FGB, FGA, ANGPTL3 and these proteins were involved in the oxidation-reduction process, lipid transport, iron ion, heme, and lipid binding. Importantly, APOA4, FABP2, and CYP51A1 might be key factors to control fat deposition and antioxidant enzyme activity during chicken embryonic development. These findings will facilitate a better understanding of antioxidant and lipid mechanisms in chicken embryo and these DAPs can be further investigated as candidate markers to predict lipid deposition and the activity of antioxidant enzymes.
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Affiliation(s)
- Nan Shen
- College of Food and Biological Engineering, Hefei University of Technology, 193 Tunxi Road, Hefei, Anhui 230009, PR China
| | - Changqing Li
- College of Food and Biological Engineering, Hefei University of Technology, 193 Tunxi Road, Hefei, Anhui 230009, PR China
| | - Shaohua Yang
- College of Food and Biological Engineering, Hefei University of Technology, 193 Tunxi Road, Hefei, Anhui 230009, PR China.
| | - Yilong Ma
- College of Food and Biological Engineering, Hefei University of Technology, 193 Tunxi Road, Hefei, Anhui 230009, PR China
| | - Hui-Li Wang
- College of Food and Biological Engineering, Hefei University of Technology, 193 Tunxi Road, Hefei, Anhui 230009, PR China.
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10
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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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11
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Gai K, Ge Y, Liu D, Zhang H, Cong B, Guo S, Liu Y, Xing K, Qi X, Wang X, Xiao L, Long C, Guo Y, Chen L, Sheng X. Identification of key genes related to intramuscular fat deposition in Beijing-You chicken by mRNA and miRNA transcriptome analysis. Poult Sci 2023; 102:103035. [PMID: 37672836 PMCID: PMC10494259 DOI: 10.1016/j.psj.2023.103035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 09/08/2023] Open
Abstract
Intramuscular fat (IMF) is an important factor affecting chicken quality. However, the age-related mechanism of IMF deposition has not yet been elucidated. In this study, the IMF, phospholipids (PL), triglycerides (TG), and fatty acid (FA) content in the breast muscle of Beijing-You chicken (BJY) at 1, 56, 98, and 120 d of age was measured, and mRNA and miRNA sequencing was integrated to explore the regulatory genes of IMF deposition. The results showed that the IMF content of BJY at 1 d of age was significantly higher than that at later stage of birth (P < 0.05). The transcriptome sequencing results showed that 7, 225 differentially expressed genes (DEGs) and 243 differentially expressed miRNAs (DE-miRNAs) were identified. The cluster analysis showed that the expression of DEGs and DE-miRNAs at 1 d of age was significantly different from that at later stages of birth. Furthermore, a potential mRNA-miRNA regulatory network related to IMF deposition was established by weighted gene co-expression network analysis (WGCNA); gga-miR-29c-3p-PIK3R1, gga-miR-6701-3p-PTEN, gga-miR-363-3p-PTEN, gga-miR-1563-WWP1, gga-miR-449c/d-5p-TRAF6, and gga-miR-6701-3p-BMPR1B were identified as key mRNA-miRNA pairs for the regulation of IMF deposition. These results will help elucidate the mechanism of IMF formation mediated by miRNAs in chickens, and provide a theoretical foundation for the genetic improvement of broiler meat quality.
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Affiliation(s)
- Kai Gai
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yu Ge
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Dapeng Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - He Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bailin Cong
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Shihao Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yizheng Liu
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiaolong Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiangguo Wang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Longfei Xiao
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Cheng Long
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Li Chen
- College of Food Science and Engineering, Beijing University of Agriculture, Beijing, 102206, China
| | - Xihui Sheng
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
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12
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Cherian G, Fraz A, Bionaz M. Evaluating the impact of organic chromium on hepatic phospholipid fatty acid molecular species, transcription of genes associated with lipid metabolism and oxidative status in broiler chickens fed flaxseed. Poult Sci 2023; 102:102976. [PMID: 37562127 PMCID: PMC10432843 DOI: 10.1016/j.psj.2023.102976] [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: 03/21/2023] [Revised: 06/22/2023] [Accepted: 07/24/2023] [Indexed: 08/12/2023] Open
Abstract
Flaxseed is a rich source of α-linolenic acid (ALA, 18:3 n-3) and can be used to enrich chicken tissues with n-3 fatty acids (FA). However, antinutritional factors in flaxseed compromise the live performance of birds coupled with increased oxidative stress. Chromium (Cr) is a trace element with antioxidant properties. It is hypothesized that Cr supplementation will affect the hepatic total lipid profile, phospholipid n-3 and n-6 FA molecular species, lipid oxidation products, and transcription of genes associated with lipid metabolism in broiler chickens fed flaxseed. Ninety (n = 90), day-old Cornish cross chicks were fed a corn-soybean meal-based diet containing 0% flaxseed (CTR), 10% flaxseed (FLAX), and FLAX + 0.05% organic Cr (FLAXCr) for 42 d. The chicks were kept in 18 pens with 5 chicks per pen. For all response variables, the effect of dietary treatments were compared separately using SAS 9.4. P values were considered significant at ≤0.05. Total lipids, saturated FA, long-chain (≥20C) n-6 FA were reduced while total n-3 FA and long-chain n-3 FA were higher in the liver of FLAX and FLAXCr than CTR (P < 0.05). Hepatic phosphatidylcholine (PC) and phosphatidylethnolamine (PE) n-3 species (36:5, 38:6) were higher in FLAX and FLAXCr compared to CTR (P < 0.05). On the contrary, n-6 species in PC (36:4, 38:4) and PE (38:4) were lower in FLAX and FLAXCr compared to CTR (P < 0.05). Addition of Cr to a flaxseed-containing diet led to an increase in PE 36:4 (P < 0.05). A decrease in the transcription of ELOVL6 gene involved in de novo lipid synthesis was observed in FLAXCr (P = 0.01). An increase in the transcription of genes involved in FA oxidation (ACAA2, ACOX1) was observed in FLAX compared to FLAXCr (P = 0. 05; P = 0.02). A trend for a decrease in the transcription of FADS2 and HMGCS1 was observed in FLAXCr than CTR and FLAX (P = 0.06; 0.08). Transcription of other genes involved in de novo lipid synthesis (FASN, PPARA), FA oxidation (CPT1A, CPT2, ACAA1), and oxidative stress response (GPX1, NQO11, GSTA2, SLC40A1, NFE2L2) were not affected by the diets (P > 0.05). Lipid peroxidation products measured as thiobarbituric acid reactive substances (TBARS) in liver was reduced in FLAXCr than CTR (P < 0.05) and was not different from FLAX (P > 0.05). Serum cholesterol and aspartic aminotransferase were reduced in FLAX and FLAXCr compared to CTR (P < 0.05). The serum glucose level was decreased in FLAX compared to CTR (P < 0.05) and a trend in decrease was noticed in FLAXCr vs. CTR (P = 0.10). Serum TBARS were higher in CTR and FLAXCr compared to FLAX (P < 0.05). In conclusion, flaxseed supplementation enhances total and long-chain n-3 FA while reducing total lipids, saturated, and n-6 FA in the liver. Supplementing Cr along with flaxseed increased n-6 FA species in the hepatic PE and decreased the transcription of genes involved in FA oxidation and lipid synthesis.
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Affiliation(s)
- Gita Cherian
- Department of Animal and Rangeland Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331, USA.
| | - Ahmad Fraz
- Department of Animal and Rangeland Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331, USA
| | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331, USA
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13
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Zhang T, Yu B, Cai Z, Jiang Q, Fu X, Zhao W, Wang H, Gu Y, Zhang J. Regulatory role of N 6-methyladenosine in intramuscular fat deposition in chicken. Poult Sci 2023; 102:102972. [PMID: 37573849 PMCID: PMC10448335 DOI: 10.1016/j.psj.2023.102972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/15/2023] Open
Abstract
Intramuscular fat (IMF) has a pivotal influence on meat quality, with its deposition being a multifaceted physiological interaction of several regulatory factors. N6-methyladenosine (m6A), the preeminent epigenetic alteration among eukaryotic RNA modifications, holds a crucial role in moderating post-transcriptional gene expression. However, there is a dearth of comprehensive understanding regarding the functional machinery of m6A modification in the context of IMF deposition in poultry. Our current study entails an analysis of the disparities in IMF within the breast and leg of 180-day-old Jingyuan chickens. We implemented methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) to delve into the distribution of m6A and its putative regulatory frameworks on IMF deposition in chickens. The findings demonstrated a markedly higher IMF content in leg relative to breast (P < 0.01). Furthermore, the expression of METTL14, WTAP, FTO, and ALKBH5 was significantly diminished in comparison to that of breast (P < 0.01). The m6A peaks in the breast and leg primarily populated 3'untranslated regions (3'UTR) and coding sequence (CDS) regions. The leg, when juxtaposed with the breast, manifested 176 differentially methylated genes (DMGs), including 151 hyper-methylated DMGs and 25 hypo-methylated DMGs. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed a pronounced enrichment of DMGs in the biosynthesis of amino acids, peroxisome, Fatty acid biosynthesis, fatty acid elongation, and cell adhesion molecules (CAMs) pathways. Key DMGs, namely ECH1, BCAT1, and CYP1B1 were implicated in the regulation of muscle lipid anabolism. Our study offers substantial insight and forms a robust foundation for further exploration of the functional mechanisms of m6A modification in modulating IMF deposition. This holds profound theoretical importance for improving and leveraging meat quality in indigenous chicken breeds.
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Affiliation(s)
- Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Qiufei Jiang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xi Fu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Wei Zhao
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Haorui Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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14
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Zhang J, Chen X, Cao J, Chang C, Geng A, Wang H, Chu Q, Yan Z, Zhang Y, Liu H. Proteomic Profiling of Thigh Meat at Different Ages of Chicken for Meat Quality and Development. Foods 2023; 12:2901. [PMID: 37569170 PMCID: PMC10418907 DOI: 10.3390/foods12152901] [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: 07/03/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Chicken age contributes to the meat characteristics; however, knowledge regarding the pathways and proteins associated with meat quality and muscle development are still scarce, especially in chicken thigh meat. Hence, the objective of this study was to elucidate the intricate relationship between these traits by liquid chromatography mass spectrometry at three different ages. A total of 341 differential expressed proteins (DEPs) were screened out (fold change ≥ 1.50 or ≤0.67 and p < 0.05) among 45 thigh meat samples (15 samples per age) of Beijing-You chicken (BYC), collected at the age of 150, 300, or 450 days (D150, D300, and D450), respectively. Subsequently, based on the protein interaction network and Markov cluster algorithm (MCL) analyses, 91 DEPs were divided into 26 MCL clusters, which were associated with pathways of lipid transporter activity, nutrient reservoir activity, signaling pathways of PPAR and MAPK, focal adhesion, ECM-receptor interaction, the cell cycle, oocyte meiosis, ribosomes, taurine and hypotaurine metabolism, glutathione metabolism, muscle contraction, calcium signaling, nucleic acid binding, and spliceosomes. Overall, our data suggest that the thigh meat of BYC at D450 presents the most desirable nutritional value in the term of free amino acids (FAAs) and intramuscular fat (IMF), and a series of proteins and pathways associated with meat quality and development were identified. These findings also provide comprehensive insight regarding these traits across a wide age spectrum.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China; (J.Z.); (X.C.); (J.C.); (C.C.); (A.G.); (H.W.); (Q.C.); (Z.Y.); (Y.Z.)
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15
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Yu B, Liu J, Cai Z, Wang H, Feng X, Zhang T, Ma R, Gu Y, Zhang J. RNA N 6-methyladenosine profiling reveals differentially methylated genes associated with intramuscular fat metabolism during breast muscle development in chicken. Poult Sci 2023; 102:102793. [PMID: 37276703 PMCID: PMC10258505 DOI: 10.1016/j.psj.2023.102793] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/14/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023] Open
Abstract
Intramuscular fat (IMF) is an important indicator for determining meat quality, and IMF deposition during muscle development is regulated by a complex molecular network involving multiple genes. The N6-methyladenosine (m6A) modification of mRNA plays an important regulatory role in muscle adipogenesis. However, the distribution of m6A and its role in IMF metabolism in poultry has not been reported. In the present study, a transcriptome-wide m6A profile was constructed using methylated RNA immunoprecipitation sequence (MeRIP-seq) and RNA sequence (RNA-seq) to explore the potential mechanism of regulating IMF deposition in the breast muscle based on the comparative analysis of IMF differences in the breast muscles of 42 (group G), 126 (group S), and 180-days old (group M) Jingyuan chickens. The findings revealed that the IMF content in the breast muscle increased significantly with the increase in the growth days of the Jingyuan chickens (P < 0.05). The m6A peak in the breast muscles of the 3 groups was highly enriched in the coding sequence (CDS) and 3' untranslated regions (3' UTR), which corresponded to the consensus motif RRACH. Moreover, we identified 129, 103, and 162 differentially methylated genes (DMGs) in the breast muscle samples of the G, S, and M groups, respectively. Functional enrichment analyses revealed that DMGs are involved in many physiological activities of muscle fat anabolism. The m6A-induced ferroptosis pathway was identified in breast muscle tissue as a new target for regulating IMF metabolism. In addition, association analysis demonstrated that LMOD2 and its multiple m6A negatively regulated DMGs are potential regulators of IMF differential deposition in muscle. The findings of the present study provide a solid foundation for further investigation into the potential role of m6A modification in regulating chicken fat metabolism.
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Affiliation(s)
- Baojun Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Jiamin Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Zhengyun Cai
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Haorui Wang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Xiaofang Feng
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Tong Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Ruoshuang Ma
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Yaling Gu
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
| | - Juan Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China.
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16
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Chen C, Chen W, Ding H, Zhang G, Xie K, Zhang T. Integrated Metabolomic and Transcriptomic Analysis Reveals Potential Gut-Liver Crosstalks in the Lipogenesis of Chicken. Animals (Basel) 2023; 13:ani13101659. [PMID: 37238090 DOI: 10.3390/ani13101659] [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: 04/22/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Growing evidence has shown the involvement of the gut-liver axis in lipogenesis and fat deposition. However, how the gut crosstalk with the liver and the potential role of gut-liver crosstalk in the lipogenesis of chicken remains largely unknown. In this study, to identify gut-liver crosstalks involved in regulating the lipogenesis of chicken, we first established an HFD-induced obese chicken model. Using this model, we detected the changes in the metabolic profiles of the cecum and liver in response to the HFD-induced excessive lipogenesis using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis. The changes in the gene expression profiles of the liver were examined by RNA sequencing. The potential gut-liver crosstalks were identified by the correlation analysis of key metabolites and genes. The results showed that a total of 113 and 73 differentially abundant metabolites (DAMs) between NFD and HFD groups were identified in the chicken cecum and liver, respectively. Eleven DAMs overlayed between the two comparisons, in which ten DAMs showed consistent abundance trends in the cecum and liver after HFD feeding, suggesting their potential as signaling molecules between the gut and liver. RNA sequencing identified 271 differentially expressed genes (DEGs) in the liver of chickens fed with NFD vs. HFD. Thirty-five DEGs were involved in the lipid metabolic process, which might be candidate genes regulating the lipogenesis of chicken. Correlation analysis indicated that 5-hydroxyisourate, alpha-linolenic acid, bovinic acid, linoleic acid, and trans-2-octenoic acid might be transported from gut to liver, and thereby up-regulate the expression of ACSS2, PCSK9, and CYP2C18 and down-regulate one or more genes of CDS1, ST8SIA6, LOC415787, MOGAT1, PLIN1, LOC423719, and EDN2 in the liver to enhance the lipogenesis of chicken. Moreover, taurocholic acid might be transported from the gut to the liver and contribute to HFD-induced lipogenesis by regulating the expression of ACACA, FASN, AACS, and LPL in the liver. Our findings contribute to a better understanding of gut-liver crosstalks and their potential roles in regulating chicken lipogenesis.
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Affiliation(s)
- Can Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Weilin Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Hao Ding
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Yangzhou University, Yangzhou 225009, China
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17
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Romanov MN, Abdelmanova AS, Fisinin VI, Gladyr EA, Volkova NA, Koshkina OA, Rodionov AN, Vetokh AN, Gusev IV, Anshakov DV, Stanishevskaya OI, Dotsev AV, Griffin DK, Zinovieva NA. Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds. J Anim Sci Biotechnol 2023; 14:35. [PMID: 36829208 PMCID: PMC9951459 DOI: 10.1186/s40104-022-00813-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/27/2022] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes. RESULTS Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) FST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF). CONCLUSION Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.
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Affiliation(s)
- Michael N. Romanov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia ,grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Alexandra S. Abdelmanova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Vladimir I. Fisinin
- grid.4886.20000 0001 2192 9124Federal State Budget Scientific Institution Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Elena A. Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Olga A. Koshkina
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Andrey N. Rodionov
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Anastasia N. Vetokh
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Igor V. Gusev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Dmitry V. Anshakov
- grid.4886.20000 0001 2192 9124Breeding and Genetic Centre “Zagorsk Experimental Breeding Farm” – Branch of the Federal Research Centre “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad, Moscow Region Russia
| | - Olga I. Stanishevskaya
- grid.473314.6Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, St. Petersburg, Russia
| | - Arsen V. Dotsev
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
| | - Darren K. Griffin
- grid.9759.20000 0001 2232 2818School of Biosciences, University of Kent, Canterbury, UK
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region Russia
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Effects of Dietary Vitamin E on Intramuscular Fat Deposition and Transcriptome Profile of the Pectoral Muscle of Broilers. J Poult Sci 2023; 60:2023006. [PMID: 36756043 PMCID: PMC9884639 DOI: 10.2141/jpsa.2023006] [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: 07/08/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023] Open
Abstract
Vitamin E is an essential micronutrient for animals. The aim of this study was to determine the effect of vitamin E on intramuscular fat (IMF) deposition and the transcriptome profile of the pectoral muscle in broiler chickens. Arbor Acres chickens were divided into five treatment groups fed a basal diet supplemented with 0, 20, 50, 75, and 100 IU/kg dietary DL-α-tocopheryl acetate (vitamin E), respectively. Body weight, carcass performance, and IMF content were recorded. Transcriptome profiles of the pectoral muscles of 35-day-old chickens in the control and treatment groups (100 IU/kg of vitamin E) were obtained by RNA sequencing. The results showed that diets supplemented with 100 IU/kg of vitamin E significantly increased IMF deposition in chickens on day 35. In total, 159 differentially expressed genes (DEGs), including 57 up-regulated and 102 down-regulated genes, were identified in the treatment (100 IU/kg vitamin E) group compared to the control group. These DEGs were significantly enriched in 13 Gene Ontology terms involved in muscle development and lipid metabolism; three signaling pathways, including the mitogen-activated protein kinase and FoxO signaling pathways, which play key roles in muscular and lipid metabolism; 28 biofunctional categories associated with skeletal and muscular system development; 17 lipid metabolism functional categories; and three lipid metabolism and muscle development-related networks. The DEGs, pathways, functional categories, and networks identified in this study provide new insights into the regulatory roles of vitamin E on IMF deposition in broilers. Therefore, diets supplemented with 100 IU/kg of vitamin E will be more beneficial to broiler production.
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Cui X, El-Senousey HK, Gou Z, Li L, Lin X, Fan Q, Wang Y, Jiang Z, Jiang S. Evaluation of dietary metabolizable energy concentrations on meat quality and lipid metabolism-related gene expression in yellow-feathered chickens. J Anim Physiol Anim Nutr (Berl) 2023; 107:275-285. [PMID: 36262057 DOI: 10.1111/jpn.13776] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 01/10/2023]
Abstract
This study evaluated the effects of different dietary metabolizable energy (ME) concentrations on the meat quality, carcass traits, volatile flavour and lipid metabolism-related gene expression levels in yellow-feathered chickens. In total, 600 Huxu female chickens aged 90 days were randomly assigned to six dietary treatments, each with 10 replicates of 10 birds. During the finisher phase, the birds were fed diets containing 2880 (low), 2940, 3000, 3060, 3120 and 3180 (high) kcal ME/kg. The results showed that the average daily gain of chickens increased as the dietary ME concentration increased, while the feed to gain improved (p < 0.05), and the intramuscular fat content of breast muscle increased (p < 0.05). The energy concentration had no effect on the breast muscle pH (45 min and 24 h), colour parameter (L*) or percentage of drip loss (p > 0.05), but the shear force values decreased significantly (p < 0.05). The diameter and area of the breast muscle fiber decreased and the muscle fibre density increased as the dietary ME concentration increased (p < 0.05). The highest ME concentration (3180 kcal) increased the percentages of aldehydes (hexanal, heptanal, 2,4-nonadienal, octanal, nonanal and 2-decenal), alcohols (2-nonen-1-ol, trans-2-undecen-1-ol, 7-hexadecenal, 2-hexyl-1-decanoal and n-nonadecanol-1,3,7,11-trimethyl-1-dodecanol), alkanes (2,6-dimethyl-heptadecane) and carboxylic acids (9-hexadecenoic acid), but reduced the percentages of octadecanal, octadecane, heneicosane and tetradecanal (p < 0.05). In addition, the mRNA gene expression levels of fatty acid-binding protein 3 and apolipoprotein B were significantly upregulated in the liver, whereas that of cholesteryl ester transfer protein was significantly downregulated. In conclusion, increasing the ME diet to 3180 kcal/kg significantly improved the quality and flavour of the meat from yellow-feathered broilers. our finding may help poultry producers to improve the taste of meat by regulating genes related to lipid metabolism, thereby achieving the flavour and taste characteristics preferred by consumers.
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Affiliation(s)
- Xiaoyan Cui
- College of Animal Science and Technology, Yangzhou University, P.R. China.,Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | | | - Zhongyong Gou
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | - Long Li
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | - Xiajing Lin
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | - Qiuli Fan
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | - Yibing Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | - Zongyong Jiang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
| | - Shouqun Jiang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, State Key Laboratory of Livestock and Poultry Breeding, Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Guangzhou, P.R. China
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20
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Alsoufi MA, Liu Y, Cao C, Zhao J, Kang J, Li M, Wang K, He Y, Ge C. Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits. Genes (Basel) 2022; 14:95. [PMID: 36672833 PMCID: PMC9859260 DOI: 10.3390/genes14010095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.
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Affiliation(s)
- Mohammed Abdulwahid Alsoufi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Department of Animal Production, Faculty of Agriculture, Sana’a University, Alwehdah Street, Sana’a P.O. Box 19509, Yemen
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changwei Cao
- Department of Food Science and Engineering, College of Biological Sciences, Southwest Forestry University, Kunming 650224, China
| | - Jinbo Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajia Kang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengyuan Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yang He
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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21
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Chen J, You R, Lv Y, Liu H, Yang G. Conjugated linoleic acid regulates adipocyte fatty acid binding protein expression via peroxisome proliferator-activated receptor α signaling pathway and increases intramuscular fat content. Front Nutr 2022; 9:1029864. [PMID: 36523338 PMCID: PMC9745092 DOI: 10.3389/fnut.2022.1029864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/19/2022] [Indexed: 06/22/2024] Open
Abstract
Intramuscular fat (IMF) is correlated positively with meat tenderness, juiciness and taste that affected sensory meat quality. Conjugated linoleic acid (CLA) has been extensively researched to increase IMF content in animals, however, the regulatory mechanism remains unclear. Adipocyte fatty acid binding protein (A-FABP) gene has been proposed as candidates for IMF accretion. The purpose of this study is to explore the molecular regulatory pathways of CLA on intramuscular fat deposition. Here, our results by cell lines indicated that CLA treatment promoted the expression of A-FABP through activated the transcription factor of peroxisome proliferator-activated receptor α (PPARα). Moreover, in an animal model, we discovered that dietary supplemental with CLA significantly enhanced IMF deposition by up-regulating the mRNA and protein expression of PPARα and A-FABP in the muscle tissues of mice. In addition, our current study also demonstrated that dietary CLA increased mRNA expression of genes and enzymes involved in fatty acid synthesis and lipid metabolism the muscle tissues of mice. These findings suggest that CLA mainly increases the expression of A-FABP through PPARα signaling pathway and regulates the expression of genes and enzymes related to IMF deposition, thus increasing IMF content. These results contribute to better understanding the molecular mechanism of IMF accretion in animals for the improvement of meat quality.
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Affiliation(s)
| | | | | | | | - Guoqing Yang
- Laboratory of Animal Gene Engineering, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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22
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Sarrami Z, Sedghi M, Mohammadi I, Kim WK, Mahdavi AH. Effects of bacteriophage supplement on the growth performance, microbial population, and PGC-1α and TLR4 gene expressions of broiler chickens. Sci Rep 2022; 12:14391. [PMID: 35999253 PMCID: PMC9399175 DOI: 10.1038/s41598-022-18663-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022] Open
Abstract
Bacteriophages (BP) are viruses that invade bacteria and propagate inside them, leading to the lysis of the bacterial cells. The aim of this study was to investigate the effect of adding BP to the broiler's diet and its effect on the performance, morphology and bacterial population of the gut, some immune responses and expression of some intestinal genes. Accordingly, dietary treatments were as follows: basal diet (control), and control + 0.3 g/kg colistin or 0.5, 1 and 1.5 g BP/kg of diet. BP increased the body weight gain and reduced the feed conversion ratio (FCR), as compared to the colistin treatment, in the finisher and overall period (P < 0.05). European efficiency factor was significantly higher in 1.5 g BP-fed birds, as compared to the control and colistin treatments. meanwhile, bacteriophage and colistin-fed birds had higher Lactobacillus and lowered coliform bacteria counts, as compared to the control treatment (P < 0.05). Cecal concentrations of propionate in the 1.5 g BP-fed birds were higher than those in the control treatment (P < 0.05). BP-fed birds had a significantly increased villus height to crypt depth ratio, as compared to the control treatment. BP increased the serum concentrations of the total antibody, immunoglobulin (Ig) M, and IgG, as compared to the control treatment (P < 0.05). In the ileum, the expression of the Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) gene was decreased by dietary BP supplementation (P < 0.05). Furthermore, Toll-like receptor 4 (TLR4) gene expression was down-regulated in the BP-fed birds, whereas Interleukin 10 (IL-10) gene expression was up-regulated (P < 0.05). Overall, the use of BP may be a promising alternative to growth-promoting antibiotics in broilers by altering the gastrointestinal tract microbiota, enhancing immunological responses and improving the gut's morphology.
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Affiliation(s)
- Zahra Sarrami
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Mohammad Sedghi
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
| | - Ishmael Mohammadi
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
| | - Woo Kyun Kim
- Department of Poultry Science, University of Georgia, Athens, GA, USA
| | - Amir Hossein Mahdavi
- Department of Animal Sciences, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Iran
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3’UTR-Seq analysis of chicken abdominal adipose tissue reveals widespread intron retention in 3’UTR and provides insight into molecular basis of feed efficiency. PLoS One 2022; 17:e0269534. [PMID: 35776773 PMCID: PMC9249230 DOI: 10.1371/journal.pone.0269534] [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: 07/21/2021] [Accepted: 05/24/2022] [Indexed: 11/19/2022] Open
Abstract
Feed efficiency (FE) is an important trait in the broiler industry due to its direct correlation to efficient muscle growth instead of fat deposition. The present study characterized and compared gene expression profiles in abdominal fat from broiler chickens of different FE levels to enhance the understanding of FE biology. Specifically, traditional whole-transcript RNA-sequencing (RNA-seq) and 3’ UTR-sequencing (3’ UTR-seq) were applied to 22 and 61 samples, respectively. Overall, these two sequencing techniques shared a high correlation (0.76) between normalized counts, although 3’ UTR-seq showed a higher variance in sequencing and mapping performance statistics across samples and a lower rate of uniquely mapped reads. A higher percentage of 3’ UTR-seq reads mapped to introns suggested the frequent presence of cleavage sites in introns, thus warranting future research to study its regulatory function. Differential expression analysis identified 1198 differentially expressed genes (DEGs) between high FE (HFE) and intermediate FE (IFE) chickens with False Discovery Rate < 0.05 and fold change > 1.2. The processes that were significantly enriched by the DEGs included extracellular matrix remodeling and mechanisms impacting gene expression at the transcriptional and translational levels. Gene ontology enrichment analysis suggested that the divergence in fat deposition and FE in broiler chickens could be associated with peroxisome and lipid metabolism possibly regulated by G0/G1 switch gene 2 (G0S2).
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Zhang J, Zhuang H, Cao J, Geng A, Wang H, Chu Q, Yan Z, Zhang X, Zhang Y, Liu H. Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period. Front Vet Sci 2022; 9:908862. [PMID: 35782537 PMCID: PMC9240433 DOI: 10.3389/fvets.2022.908862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 01/05/2023] Open
Abstract
The disparity in fatty acids (FA) composition exhibits a significant impact on meat quality, however, the molecular regulatory mechanisms underlying this trait in chicken are far from clear. In this study, a total of 45 female Beijing-You chicken (BYC) hens, fed on the same diet, were collected at the slaughter age of 150, 300, or 450 days (D150, D300, and D450) from sexual maturation stage to culling stage (15 birds per age). Gas chromatography-mass spectrometry (GC-MS) and tandem mass tag labeling technology based on liquid chromatography mass spectrometry (TMT-LC-MS/MS) analysis strategies were applied to profile FA compositions and to compare differential expressed proteins (DEPs) between these different slaughter ages, respectively. The FA profiling showed that increasing hen ages resulted in increased contents of both saturated and unsaturated fatty acids. Proteomic analyses showed a total of 4,935 proteins in chicken breast muscle with the false discovery rate (FDR) < 1% and 664 of them were differentially expressed (fold change > 1.50 or < 0.67 and P < 0.01). There were 410 up- and 116 down-regulated proteins in D150 vs. D300 group, 32 up- and 20 down-regulated in D150 vs. D450 group, and 72 up- and 241 down-regulated in D300 vs. D450 group. A total of 57 DEPs related to FA/lipid-related metabolisms were obtained according to the enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). These DEPs were involved in 21 significantly enriched (P < 0.05) pathways, including well-known pathways for FA synthesis (metabolism, desaturation, and elongation) and the signaling pathways for lipid metabolism (PPAR, adipocytokine, calcium, VEGF, MAPK, and Wnt). In addition, there existed several representative DEPs (FABP, FABP3, apoA-I, apoA-IV, apoC-III, apoB, VTG1, and VTG2) involved in the regulation of FA/lipid transportation. The construction of the interaction networks indicated that HADH, ACAA2, HADHA, ACSL1, CD36, CPT1A, PPP3R1, and SPHK1 were the key core nodes. Finally, eight DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. These results expanded our understanding of how the laying age affects the FA compositions and metabolism in hen breast meat.
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Affiliation(s)
- Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hong Zhuang
- United States Department of Agriculture, Agricultural Research Service, U.S. National Poultry Research Center, Athens, GA, United States
| | - Jing Cao
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ailian Geng
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haihong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoyue Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yao Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- *Correspondence: Huagui Liu
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Shao M, Shi K, Zhao Q, Duan Y, Shen Y, Tian J, He K, Li D, Yu M, Lu Y, Tang Y, Feng C. Transcriptome Analysis Reveals the Differentially Expressed Genes Associated with Growth in Guangxi Partridge Chickens. Genes (Basel) 2022; 13:genes13050798. [PMID: 35627183 PMCID: PMC9140345 DOI: 10.3390/genes13050798] [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: 03/21/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
The Guangxi Partridge chicken is a well-known chicken breed in southern China with good meat quality, which has been bred as a meat breed to satisfy the increased demand of consumers. Compared with line D whose body weight is maintained at the average of the unselected group, the growth rate and weight of the selected chicken group (line S) increased significantly after breeding for four generations. Herein, transcriptome analysis was performed to identify pivotal genes and signal pathways of selective breeding that contributed to potential mechanisms of growth and development under artificial selection pressure. The average body weight of line S chickens was 1.724 kg at 90 d of age, which showed a significant increase at 90 d of age than line D chickens (1.509 kg), although only the internal organ ratios of lung and kidney changed after standardizing by body weight. The myofiber area and myofiber density of thigh muscles were affected by selection to a greater extent than that of breast muscle. We identified 51, 210, 31, 388, and 100 differentially expressed genes (DEGs) in the hypothalamus, pituitary, breast muscle, thigh muscle, and liver between the two lines, respectively. Several key genes were identified in the hypothalamus-pituitary-muscle axis, such as FST, THSB, PTPRJ, CD36, PITX1, PITX2, AMPD1, PRKAB1, PRKAB2, and related genes for muscle development, which were attached to the cytokine–cytokine receptor interaction signaling pathway, the PPAR signaling pathway, and lipid metabolism. However, signaling molecular pathways and the cell community showed that elevated activity in the liver of line S fowl was mainly involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules, and signal transduction. Collectively, muscle development, lipid metabolism, and several signaling pathways played crucial roles in the improving growth performance of Guangxi Partridge chickens under artificial selection for growth rate. These results support further study of the adaptation of birds under selective pressure.
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Affiliation(s)
- Minghui Shao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kai Shi
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Qian Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Ying Duan
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangyang Shen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Jinjie Tian
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Kun He
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Dongfeng Li
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Minli Yu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
| | - Yangqing Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China;
| | - Yanfei Tang
- Guangxi Fufeng Agricultural and Animal Husbandry Group Co., Ltd., Nanning 530024, China;
| | - Chungang Feng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.S.); (K.S.); (Q.Z.); (Y.D.); (Y.S.); (J.T.); (K.H.); (D.L.); (M.Y.)
- Correspondence:
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Zhang J, Cao J, Geng A, Wang H, Chu Q, Yan Z, Zhang X, Zhang Y, Liu H. UHPLC-QTOF/MS-based comparative metabolomics in pectoralis major of fast- and slow-growing chickens at market ages. Food Sci Nutr 2022; 10:487-498. [PMID: 35154685 PMCID: PMC8825714 DOI: 10.1002/fsn3.2673] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 11/03/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022] Open
Abstract
The molecular regulatory mechanism underlying meat quality between different chicken genotypes remains elusive. This study aimed to identify the differences in metabolites and pathways in pectoralis major (breast muscle) between a commercial fast-growing chicken genotype (Cobb500) and a slow-growing Chinese native chicken genotype (Beijing-You chickens, BYC) at market ages respectively based on ultra-high-performance liquid chromatography-quadrupole/time of flight mass spectrometry (UHPLC-QTOF/MS). Eighteen metabolites were identified as potential biomarkers between BYC and Cobb500 at market ages. Among them, L-cysteine exhibited a higher relative intensity in BYC compared with Cobb500 and was enriched into 10 potential flavor-associated KEGG pathways. In addition, the glycerophospholipid metabolism pathway was found to be associated with chicken meat flavor and the accumulation of sn-glycerol 3-phosphate and acetylcholine was more predominant in BYC than that in Cobb500, which were catalyzed by glycerophosphocholine phosphodiesterase (GPCPD1, EC:3.1.4.2), choline O-acetyltransferase (CHAT, EC:2.3.1.6), and acetylcholinesterase (ACHE, EC:3.1.1.7). Overall, the present study provided some metabolites and pathways for further investigating the roles of the differences in meat flavor quality in breast muscle between Cobb500 and BYC at market ages.
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Affiliation(s)
- Jian Zhang
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Jing Cao
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Ailian Geng
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Haihong Wang
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Xiaoyue Zhang
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Yao Zhang
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary medicineBeijing Academy of Agriculture and Forestry SciencesBeijingChina
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Evaluation of Commercial Meat Products of Red Chicken Reared under LED Lights. Foods 2022; 11:foods11030370. [PMID: 35159519 PMCID: PMC8834572 DOI: 10.3390/foods11030370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary The aim of the study was to investigate the role of three different light-color temperatures of Light-Emitting Diodes (LEDs) (Neutral, Cool and Warm) on some attributes of breast meat. Various changes were observed in the physical and chemical characteristics of breast meat samples and the results obtained in fatty and volatile profiles indicate that the LEDs change the characteristics of meat. Abstract The objective of our study was to investigate the role of three different light-color temperatures of Light-Emitting Diodes (LEDs) [Neutral (K=3300−3700); Warm (K=3000−2500) and Cool (K=5500−6000)] on the qualitative attributes of breast meat obtained from male AZ Extra Heavy Red chickens. The comparison was made with meat deriving from chickens reared in the presence of classic neon lighting (Control). The meat was analyzed for the determination of both physical and chemical properties (cooking loss, moisture, total lipids and fatty acid composition). Furthermore, meat samples subjected to cooking were also analyzed for the identification of volatile compounds produced during the process; such evaluation was performed both immediately after cooking (T0) and after 7 days (T7) of cooked-meat storage at 4 °C. Cooking-loss values were higher for samples from chickens raised with Neutral LED (p < 0.05) compared to the other groups. For the fatty acid profiles of the meat, higher values were found for monounsaturated fatty acids (MUFAs) such as C18:1, C9 and C16:1 in Cool LED compared to the Control. Regarding the volatile profile of cooked meat, compounds belonging to the families of aldehydes, alcohols, ketones, and aromatic compounds were identified. Compounds belonging to the aldehyde family, such as hexanal, increased in Cool LED samples at T0 in comparison to the Control. On the other hand, the amounts of 1-Pentanol, 1-Octanol and 2-Octen-1-ol, which belong to the alcohol family, increased at T7 in Cool LED samples compared to the Warm LED. In conclusion, LED lighting showed to be effective in inducing significant variations on chicken breast meat ready to be introduced to the market, in particular regarding fatty acid profiles and the accumulation of volatile compounds. However more in-depth evaluation is needed for the identification of modifications regarding the sensorial sphere, which could have an impact on the consumer acceptability of the product.
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Cheng J, Wang L, Wang S, Chen R, Zhang T, Ma H, Lu H, Yuan G. Transcriptomic analysis of thigh muscle of Lueyang black-bone chicken in free-range and caged feeding. Anim Biotechnol 2021:1-11. [PMID: 34965837 DOI: 10.1080/10495398.2021.1993235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Lueyang black-bone chicken is free-range in hilly areas and has unique genetic characteristics and excellent muscle quality. However, the molecular mechanisms of breeding mode influence growth and meat quality in Lueyang black-bone chicken are still unclear. Here we analyzed the meat quality and transcriptome data of thigh muscle by comparing free-range and caged modes at the age of 60 and 120 days in Lueyang black-boned chicken. The results demonstrated that the free-range mode could improve the pH value, tenderness, and reducing the hardness of the thigh muscle. Intramuscular fat (IMF) content of the thigh muscle was markedly higher in the caged chickens compared with free-range animals at the age of 60 days. Functional pathway analysis illustrated that tight junction signaling was associated with the formation of slow-twitch fibers in free-range chickens at age of 120 days. All research data proved that the free-range mode could improve muscle quality by promoting the formation of slow-twitch fibers and IMF in thigh muscle in Lueyang black-bone chicken. Based on the animal benefit and healthy, the free-range feeding should be considered during the breeding process of broiler chicken. The results provide good knowledge of the functional molecular mechanisms associated with muscle quality in Lueyang black-bone chicken.
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Affiliation(s)
- Jia Cheng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Rui Chen
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Haidong Ma
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Guoqiang Yuan
- Shaanxi Baiweiyuan Network Technology Co., Ltd, Hanzhong, China
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Zhao L, Zhou L, Hao X, Wang L, Han F, Liu L, Duan X, Guo F, He J, Liu N. Identification and Characterization of Circular RNAs in Association With the Deposition of Intramuscular Fat in Aohan Fine-Wool Sheep. Front Genet 2021; 12:759747. [PMID: 34938314 PMCID: PMC8685527 DOI: 10.3389/fgene.2021.759747] [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: 08/17/2021] [Accepted: 11/02/2021] [Indexed: 01/20/2023] Open
Abstract
Aohan fine-wool sheep (AFWS) is a high-quality fine-wool sheep breed that supplies wool and meat. Research is needed on the molecular mechanism behind intramuscular fat (IMF) deposition that greatly improves mutton quality. The widely expressed non-coding RNA is physiologically used in roles such as competitive endogenous RNA (ceRNA) that includes circular RNAs (circRNAs). Although circRNAs were studied in many fields, little research was devoted to IMF in sheep. We used the longissimus dorsi muscle of 2 and 12-month-old AWFS as research material to identify circRNAs related to IMF deposition in these sheep by RNA-seq screening for differentially expressed circRNAs in the two age groups. A total of 11,565 candidate circRNAs were identified, of which the 104 differentially expressed circRNAs in the two age groups were analyzed. Enrichment analysis was performed using Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes. The enriched pathways included lipid transport (GO:0006869), negative regulation of canonical Wnt signaling pathway (GO:0090090), fat digestion and absorption (ko04975), and sphingolipid metabolism (ko00600). The differentially expressed circRNAs included ciRNA455, circRNA9086, circRNA7445, circRNA4557, and others. The source genes involved in these pathways might regulate IMF deposition. We used the TargetScan and miRanda software for interaction analysis, and a network diagram of circRNA-miRNA interactions was created. CircRNA455-miR-127, circRNA455-miR-29a, circRNA455-miR-103, circRNA4557-mir149-5p, and circRNA2440-mir-23a might be involved in the IMF deposition process. The targeting relationship of circRNA4557-miR-149-5p was verified by a dual-luciferase reporter assay. The RT-qPCR results of seven randomly selected circRNAs were consistent with the sequencing results. This study provides additional information on circRNA regulation of IMF deposition in AFWS and is a useful resource for future research on this sheep breed.
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Affiliation(s)
- Le Zhao
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lisheng Zhou
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Xiaojing Hao
- Qingdao Animal Husbandry and Veterinary Research Institute, Qingdao, China
| | - Lei Wang
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Fuhui Han
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Lirong Liu
- China Animal Health and Epidemiology Center, Qingdao, China
| | - Xinming Duan
- Nongfayuan Zhejiang Agricultural Development Co. Ltd., Huzhou, China
| | - Feng Guo
- Tongliao Animal Agriculture Development Service Center, Tongliao, China
| | - Jianning He
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Nan Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
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Kang H, Zhao D, Xiang H, Li J, Zhao G, Li H. Large-scale transcriptome sequencing in broiler chickens to identify candidate genes for breast muscle weight and intramuscular fat content. Genet Sel Evol 2021; 53:66. [PMID: 34399688 PMCID: PMC8369645 DOI: 10.1186/s12711-021-00656-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/15/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In broiler production, breast muscle weight and intramuscular fat (IMF) content are important economic traits. Understanding the genetic mechanisms that underlie these traits is essential to implement effective genetic improvement programs. To date, genome-wide association studies (GWAS) and gene expression analyses have been performed to identify candidate genes for these traits. However, GWAS mainly detect associations at the DNA level, while differential expression analyses usually have low power because they are typically based on small sample sizes. To detect candidate genes for breast muscle weight and IMF contents (intramuscular fat percentage and relative content of triglycerides, cholesterol, and phospholipids), we performed association analyses based on breast muscle transcriptomic data on approximately 400 Tiannong partridge chickens at slaughter age. RESULTS First, by performing an extensive simulation study, we evaluated the statistical properties of association analyses of gene expression levels and traits based on the linear mixed model (LMM) and three regularized linear regression models, i.e., least absolute shrinkage and selection operator (LASSO), ridge regression (RR), and elastic net (EN). The results show that LMM, LASSO and EN with tuning parameters that are determined based on the one standard error rule exhibited the lowest type I error rates. Using results from all three models, we detected 43 candidate genes with expression levels that were associated with breast muscle weight. In addition, candidate genes were detected for intramuscular fat percentage (1), triglyceride content (2), cholesterol content (1), and phospholipid content (1). Many of the identified genes have been demonstrated to play roles in the development and metabolism of skeletal muscle or adipocyte. Moreover, weighted gene co-expression network analyses revealed that many candidate genes were harbored by gene co-expression modules, which were also significantly correlated with the traits of interest. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that these modules are involved in muscle development and contraction, and in lipid metabolism. CONCLUSIONS Our study provides valuable insight into the transcriptomic bases of breast muscle weight and IMF contents in Chinese indigenous yellow broilers. Our findings could be useful for the genetic improvement of these traits in broiler chickens.
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Affiliation(s)
- Huimin Kang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Di Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Jing Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China
| | - Guiping Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China. .,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China.
| | - Hua Li
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding; Key Laboratory of Animal Molecular Design and Precise Breeding of Guangdong Higher Education Institutes; School of Life Science and Engineering, Foshan University, #33 Guang-yun-lu, Shishan, Nanhai, Foshan, 528231, Guangdong, People's Republic of China. .,Guangdong Tinoo's Foods Group Co., Ltd, Jiangkou, Feilaixia, Qingcheng, Qingyuan, 511827, Guangdong, People's Republic of China.
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Wang J, Clark DL, Jacobi SK, Velleman SG. Alpha-tocopherol acetate and alpha lipoic acid may mitigate the development of wooden breast myopathy in broilers at an early age. Br Poult Sci 2021; 62:749-758. [PMID: 33988058 DOI: 10.1080/00071668.2021.1927985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
1. The objective of this study was to identify the effects of the antioxidant alpha-tocopherol acetate (ATA) and alpha lipoic acid (ALA) which have anti-inflammatory effects on developmental onset, severity and the progression of wooden breast (WB) based on Pectoralis major (P. major) muscle morphology and expression of genes associated with WB during the first three weeks post-hatch.2. A total of 160 newly hatched Ross 708 broiler chicks were randomly assigned in a replicated trial to either a control group or three dietary treatments (ATA 160 mg/kg feed, ALA 500 mg/kg feed or in combination).3. Microscopic changes associated with WB began at one week of age in all groups. The ATA acetate and ALA fed in combination decreased WB severity at two weeks of age (P = 0.05) and ATA alone or in combination reduced severity at three weeks of age compared to the control group (P = 0.05). Expression of myogenic determination factor 1 and peroxisome proliferator-activated receptor gamma was reduced in all dietary treatments compared to the control at three weeks of age (P ≤ 0.05), which suggested reduced muscle degeneration and lipid deposition.4. ATA and ALA fed both independently and in combination had a positive effect on mitigating WB severity microscopically as early as two weeks of age.
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Affiliation(s)
- J Wang
- Department of Animal Sciences, The Ohio State University, Wooster, OH, USA
| | - D L Clark
- Department of Animal Sciences, The Ohio State University, Wooster, OH, USA
| | - S K Jacobi
- Department of Animal Sciences, The Ohio State University, Wooster, OH, USA
| | - S G Velleman
- Department of Animal Sciences, The Ohio State University, Wooster, OH, USA
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Abstract
One of the main problems in the analysis of real data is often related to the presence of anomalies. Namely, anomalous cases can both spoil the resulting analysis and contain valuable information at the same time. In both cases, the ability to detect these occurrences is very important. In the biomedical field, a correct identification of outliers could allow the development of new biological hypotheses that are not considered when looking at experimental biological data. In this work, we address the problem of detecting outliers in gene expression data, focusing on microarray analysis. We propose an ensemble approach for detecting anomalies in gene expression matrices based on the use of Hierarchical Clustering and Robust Principal Component Analysis, which allows us to derive a novel pseudo-mathematical classification of anomalies.
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Angiopoietin-like protein 4 regulates breast muscle lipid metabolism in broilers. Poult Sci 2021; 100:101159. [PMID: 34077847 PMCID: PMC8181176 DOI: 10.1016/j.psj.2021.101159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 12/20/2020] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
The objective of this study was to determine the effects of angiopoietin-like protein 4 (ANGPTL4) on breast muscle lipid metabolism in broilers. In experiment 1, 36 thirty-five-day-old male Arbor Acres broilers were randomly allocated into 6 treatment groups with 6 birds in a completely randomized design. The broilers were subjected to intravenous injection of His-SUMO-ANGPTL4 at the dose of 0 (injection of normal saline [NS]), 20, 100, 500, 2,500, or 12,500 ng/kg BW, respectively. The results showed that broilers at 30 min after His-SUMO-ANGPTL4 at the level of 12,500 ng/kg BW intravenous injection had higher (P < 0.05) concentrations of triglyceride and non-esterified fatty acid in the serum, higher (P < 0.05) adipose triglyceride lipase and carnitine palmitoyltransferase 1 mRNA expression in the breast muscle, but lower (P < 0.05) lipoprotein lipase (LPL) mRNA expression in the breast muscle. In experiment 2, 18 thirty-five-day-old male Arbor Acres broilers were randomly allocated into 3 treatment groups with 6 birds in a completely randomized design. The broilers were subjected to intravenous injection of NS, His-SUMO, or His-SUMO-ANGPTL4 (12,500 ng/kg BW) in order to rule out the effect of His-SUMO tag. It's confirmed that ANGPTL4 could increase (P < 0.05) concentrations of triglyceride and non-esterified fatty acid in the serum, enhance (P < 0.05) adipose triglyceride lipase mRNA expression in the breast muscle, and decrease (P < 0.05) LPL mRNA expression in the breast muscle. In experiment 3 and 4, co-culture experiments of chicken primary myoblasts and NS, His-SUMO, or His-SUMO-ANGPTL4 (250 pg/mL, physiological dose) were set up to monitor the cytotoxicity of ANGPTL4 and the changes of lipid metabolism-related genes expression. It was found that cell viability was not affected but LPL mRNA expression in chicken primary myoblasts was highly reduced (P < 0.05) by ANGPTL4. In conclusion, ANGPTL4 could promote lipodieresis and inhibit LPL in the breast muscle of broilers.
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Zhang J, Cao J, Geng A, Wang H, Chu Q, Yang L, Yan Z, Zhang X, Zhang Y, Dai J, Liu H. Comprehensive Proteomic Characterization of the Pectoralis Major at Three Chronological Ages in Beijing-You Chicken. Front Physiol 2021; 12:658711. [PMID: 33815156 PMCID: PMC8012914 DOI: 10.3389/fphys.2021.658711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Chronological age is one of the important factors influencing muscle development and meat quality in chickens. To evaluate the protein expression profiles during skeletal muscle development, we performed a tandem mass tag (TMT)-based quantitative proteomic strategy in pectoralis major (breast muscle) of Beijing-You chicken (BYC) at the chronological age of 90, 120, and 150 days. Each chronological age contained 3 pooling samples or 15 birds (five birds per pooling sample). A total of 1,413 proteins were identified in chicken breast muscle with FDR < 1% and 197 of them were differentially expressed (fold change ≥1.2 or ≤0.83 and p < 0.05). There were 110 up- and 71 down-regulated proteins in 120 d vs 90 d group, 13 up- and 10 down-regulated proteins in 150 d vs 120 d group. The proteomic profiles of BYC at 120 d were very similar to those at 150 d and highly different from those at 90 d, suggesting that 120 d might be an important chronological age for BYC. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that these differentially expressed proteins were mainly involved in the pathway of glycolysis/gluconeogenesis, adrenergic signaling in cardiomyocytes, focal adhesion, oocyte meiosis and phagosome. Furthermore, some DEPs were quantified using parallel reaction monitoring (PRM) to validate the results from TMT analysis. In summary, these results provided some candidate protein-coding genes for further functional validation and contribute to a comprehensive understanding of muscle development and age-dependent meat quality regulation by proteins in chickens.
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Affiliation(s)
- Jian Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jing Cao
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ailian Geng
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Haihong Wang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Qin Chu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Linbing Yang
- Shanghai Bioprofile Technology Co., Ltd., Shanghai, China
| | - Zhixun Yan
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoyue Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yao Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jie Dai
- Shanghai Bioprofile Technology Co., Ltd., Shanghai, China
| | - Huagui Liu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Nematbakhsh S, Pei Pei C, Selamat J, Nordin N, Idris LH, Abdull Razis AF. Molecular Regulation of Lipogenesis, Adipogenesis and Fat Deposition in Chicken. Genes (Basel) 2021; 12:genes12030414. [PMID: 33805667 PMCID: PMC8002044 DOI: 10.3390/genes12030414] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 12/13/2022] Open
Abstract
In the poultry industry, excessive fat deposition is considered an undesirable factor, affecting feed efficiency, meat production cost, meat quality, and consumer’s health. Efforts to reduce fat deposition in economically important animals, such as chicken, can be made through different strategies; including genetic selection, feeding strategies, housing, and environmental strategies, as well as hormone supplementation. Recent investigations at the molecular level have revealed the significant role of the transcriptional and post-transcriptional regulatory networks and their interaction on modulating fat metabolism in chickens. At the transcriptional level, different transcription factors are known to regulate the expression of lipogenic and adipogenic genes through various signaling pathways, affecting chicken fat metabolism. Alternatively, at the post-transcriptional level, the regulatory mechanism of microRNAs (miRNAs) on lipid metabolism and deposition has added a promising dimension to understand the structural and functional regulatory mechanism of lipid metabolism in chicken. Therefore, this review focuses on the progress made in unraveling the molecular function of genes, transcription factors, and more notably significant miRNAs responsible for regulating adipogenesis, lipogenesis, and fat deposition in chicken. Moreover, a better understanding of the molecular regulation of lipid metabolism will give researchers novel insights to use functional molecular markers, such as miRNAs, for selection against excessive fat deposition to improve chicken production efficiency and meat quality.
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Affiliation(s)
- Sara Nematbakhsh
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia; (S.N.); (J.S.); (N.N.)
| | - Chong Pei Pei
- Faculty of Health and Medical Sciences, School of Biosciences, Taylor’s University, Subang Jaya 47500, Selangor, Malaysia;
| | - Jinap Selamat
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia; (S.N.); (J.S.); (N.N.)
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Noordiana Nordin
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia; (S.N.); (J.S.); (N.N.)
| | - Lokman Hakim Idris
- Department of Veterinary Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia;
| | - Ahmad Faizal Abdull Razis
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia; (S.N.); (J.S.); (N.N.)
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Correspondence:
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Increasing Fat Deposition Via Upregulates the Transcription of Peroxisome Proliferator-Activated Receptor Gamma in Native Crossbred Chickens. Animals (Basel) 2021; 11:ani11010090. [PMID: 33466503 PMCID: PMC7824829 DOI: 10.3390/ani11010090] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Crossbreeding using exotic breeds is usually employed to improve the growth characteristics of indigenous chickens. This mating not only provides growth but adversely affects excess fat deposition as well. This deposition was regulated by a complicated cellular mechanism including peroxisome proliferator-activated receptors (PPARs) function. Thus, we hypothesized that native chickens breed percentage might be related to PPARs gene expression. This study aimed to study the role of PPARs on fat deposition in chickens which was the different native genetic background. Our results indicated that increasing commercial breed percentage in the chicken leads to increased fat deposition via the increasing of PPARG gene expression. Therefore, the PPARG gene notable as a major gene of cellular fat deposition and might be applied in further study. Abstract This study aimed to study the role of PPARs on fat deposition in native crossbred chicken. We studied the growth, abdominal, subcutaneous, and intramuscular fat, and mRNA expression of PPARA and PPARG in adipose and muscle tissues of four chicken breeds (CH breed (100% Thai native chicken), KM1 (50% CH background), KM2 (25% CH background), and broiler (BR)). The result shows that the BR chickens had higher abdominal fat than other breeds (p < 0.05) and the KM2 had an abdominal fat percentage higher than KM1 and CH respectively (p < 0.05). The intramuscular fat of BR was greater than KM1 and CH (p < 0.05). In adipose tissue, PPARA expression was different among the chicken breeds. However, there were breed differences in PPARG expression. Study of abdominal fat PPARG expression showed the BR breed, KM1, and KM2 breed significantly greater (p < 0.05) than CH. In 8 to 12 weeks of age, the PPARG expression of the CH breed is less than (p < 0.05) KM2. Crossbreeding improved the growth of the Thai native breed, there was also a corresponding increase in carcass fatness. However, there appears to be a relationship between PPARG expression and fat deposition traits. therefore, PPARG activity hypothesized to plays a key role in lipid accumulation by up-regulation.
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Identification of Differentially Expressed Genes and Lipid Metabolism Signaling Pathways between Muscle and Fat Tissues in Broiler Chickens. J Poult Sci 2021; 58:131-137. [PMID: 33927567 PMCID: PMC8076620 DOI: 10.2141/jpsa.0200040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In this study, signaling pathways and key differentially expressed genes (DEGs) involved in lipid metabolism in muscle and fat tissues were investigated. Muscle and abdominal fat tissues were obtained from 35-day-old female broilers for RNA sequencing. DEGs between muscle and fat tissues were identified. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of DEGs were performed. A total of 6130 DEGs were identified to be significantly enriched in 365 GO terms, most of which were involved in biological processes, cellular components, and molecular functions in muscle and fat tissues. Three important lipid signaling pathways (pyruvate metabolism, the insulin signaling pathway, and the adipocytokine signaling pathway) were identified among the fat and muscle tissues of broilers. The key common DEGs in these pathways included phosphoenolpyruvate carboxykinase 2 (PCK2), acetyl-CoA carboxylase 1 alpha and beta (ACACA and ACACB), and the mitogen-activated protein kinase (AMPK) gene family. Hence, our findings revealed the pathways and key genes and gene families involved in the regulation of fat deposition in the muscle and fat tissues of broilers.
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Li J, Xing S, Zhao G, Zheng M, Yang X, Sun J, Wen J, Liu R. Identification of diverse cell populations in skeletal muscles and biomarkers for intramuscular fat of chicken by single-cell RNA sequencing. BMC Genomics 2020; 21:752. [PMID: 33129271 PMCID: PMC7603756 DOI: 10.1186/s12864-020-07136-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/11/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The development of skeletal muscle is closely related to the efficiency of meat production and meat quality. Chicken skeletal muscle development depends on myogenesis and adipogenesis and occurs in two phases-hyperplasia and hypertrophy. However, cell profiles corresponding to the two-phase muscle development have yet to be determined. Single-cell RNA-sequencing (scRNA-seq) can elucidate the cell subpopulations in tissue and capture the gene expression of individual cells, which can provide new insights into the myogenesis and intramuscular adipogenesis. RESULTS Ten cell clusters at the post-hatching developmental stage at Day 5 and seven cell clusters at the late developmental stage at Day 100 were identified in chicken breast muscles by scRNA-seq. Five myocyte-related clusters and two adipocyte clusters were identified at Day 5, and one myocyte cluster and one adipocyte cluster were identified at Day 100. The pattern of cell clustering varied between the two stages. The cell clusters showed clear boundaries at the terminal differentiation stage at Day 100; by contrast, cell differentiation was not complete at Day 5. APOA1 and COL1A1 were selected from up-regulated genes in the adipocyte cluster and found to be co-expressed with the ADIPOQ adipocyte marker gene in breast muscles by RNA in situ hybridization. CONCLUSIONS This study is the first to describe the heterogeneity of chicken skeletal muscle at two developmental stages. The genes APOA1 and COL1A1 were identified as biomarkers for chicken intramuscular fat cells.
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Affiliation(s)
- Jinghui Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
| | - Siyuan Xing
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
| | - Xinting Yang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
| | - Jiahong Sun
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences; State Key Laboratory of Animal Nutrition, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Beijing, 100193 P. R. China
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Szalai K, Tempfli K, Zsédely E, Lakatos E, Gáspárdy A, Bali Papp Á. Linseed oil supplementation affects fatty acid desaturase 2, peroxisome proliferator activated receptor gamma, and insulin-like growth factor 1 gene expression in turkeys (Meleagris gallopavo). Anim Biosci 2020; 34:662-669. [PMID: 32810939 PMCID: PMC7961277 DOI: 10.5713/ajas.20.0030] [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: 01/15/2020] [Accepted: 05/17/2020] [Indexed: 12/01/2022] Open
Abstract
Objective Effects of linseed oil (LO) supplementation on the fat content and fatty acid profile of breast meat, and the expression of three genes in the liver, breast muscle and fat tissues of commercial 154-day-old hybrid male turkeys were investigated. Methods The animals in the control group were fed a commercially available feed and received no LO supplementation (n = 70), whereas animals in the LO group (n = 70) were fed the same basic diet supplemented with LO (day 15 to 21, 0.5%; day 22 to 112, 1%). The effect of dietary LO supplementation on fatty acid composition of breast muscle was examined by gas chromatography, and the expression of fatty acid desaturase 2 (FADS2), peroxisome proliferator activated receptor gamma (PPARγ), and insulin-like growth factor 1 (IGF1) genes was analysed by means of quantitative reverse transcription polymerase chain reaction. Results The LO supplementation affected the fatty acid composition of breast muscle. Hepatic FADS2 levels were considerably lower (p<0.001), while adipose tissue expression was higher (p<0.05) in the control compared to the LO group. The PPARγ expression was lower (p<0.05), whereas IGF1 was higher (p<0.05) in the fat of control animals. There were no significant (p>0.05) differences in FADS2, PPARγ, and IGF1 gene expressions of breast muscle; however, omega-6/omega-3 ratio of breast muscle substantially decreased (p<0.001) in the LO group compared to control. Conclusion Fatty acid composition of breast meat was positively influenced by LO supplementation without deterioration of fattening parameters. Remarkably, increased FADS2 expression in the liver of LO supplemented animals was associated with a significantly decreased omega-6/omega-3 ratio, providing a potentially healthier meat product for human consumption. Increased PPARγ expression in fat tissue of the LO group was not associated with fat content of muscle, whereas a decreased IGF1 expression in fat tissue was associated with a trend of decreasing fat content in muscle of the experimental LO group.
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Affiliation(s)
- Klaudia Szalai
- Department of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, 9200 Mosonmagyaróvár, Hungary
| | - Károly Tempfli
- Department of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, 9200 Mosonmagyaróvár, Hungary
| | - Eszter Zsédely
- Department of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, 9200 Mosonmagyaróvár, Hungary
| | - Erika Lakatos
- Department of Food Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, 9200 Mosonmagyaróvár, Hungary
| | - András Gáspárdy
- Department of Animal Breeding and Genetics, University of Veterinary Medicine, 1078 Budapest, Hungary
| | - Ágnes Bali Papp
- Department of Animal Science, Faculty of Agricultural and Food Sciences, Széchenyi István University, 9200 Mosonmagyaróvár, Hungary
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Fan W, Liu W, Liu H, Meng Q, Xu Y, Guo Y, Wang B, Zhou Z, Hou S. Dynamic accumulation of fatty acids in duck (Anas platyrhynchos) breast muscle and its correlations with gene expression. BMC Genomics 2020; 21:58. [PMID: 31952469 PMCID: PMC6969424 DOI: 10.1186/s12864-020-6482-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 01/10/2020] [Indexed: 12/13/2022] Open
Abstract
Background Fatty acid composition contributes greatly to the quality and nutritional value of meat. However, the molecular regulatory mechanisms underlying fatty acid accumulation in poultry have not yet been cleared. The aims of this study were to characterize the dynamics of fatty acid accumulation in duck breast muscle and investigate its correlations with gene expression. Results Here, we analyzed the fatty acid profile and transcriptome of breast muscle derived from Pekin ducks and mallards at the ages of 2 weeks, 4 weeks, 6 weeks and 8 weeks. Twenty fatty acids were detected in duck breast muscle, with palmitic acid (C16:0, 16.6%~ 21.1%), stearic acid (C18:0, 9.8%~ 17.7%), oleic acid (C18:1n-9, 15.7%~ 33.8%), linoleic acid (C18:2n-6, 10.8%~ 18.9%) and arachidonic acid (C20:4n-6, 11.7%~ 28.9%) as the major fatty acids. Our results showed that fatty acid composition was similar between the two breeds before 6 weeks, but the compositions diverged greatly after this point, mainly due to the stronger capacity for C16:0 and C18:1n-9 deposition in Pekin ducks. By comparing the multistage transcriptomes of Pekin ducks and mallards, we identified 2025 differentially expressed genes (DEGs). Cluster analysis of these DEGs revealed that the genes involved in oxidative phosphorylation, fatty acid degradation and the PPAR signaling pathway were upregulated in mallard at 8 weeks. Moreover, correlation analysis of the DEGs and fatty acid composition traits suggested that the DEGs involved in lipogenesis, lipolysis and fatty acid β-oxidation may interact to influence the deposition of fatty acids in duck breast muscle. Conclusions We reported the temporal progression of fatty acid accumulation and the dynamics of the transcriptome in breast muscle of Pekin ducks and mallards. Our results provide insights into the transcriptome regulation of fatty acid accumulation in duck breast muscle, and will facilitate improvements of fatty acid composition in duck breeding.
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Affiliation(s)
- Wenlei Fan
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan W Rd, Beijing, 100193, China.,College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.,College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Wenjing Liu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Hehe Liu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan W Rd, Beijing, 100193, China
| | - Qingshi Meng
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan W Rd, Beijing, 100193, China
| | - Yaxi Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan W Rd, Beijing, 100193, China
| | - Yuming Guo
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China
| | - Baowei Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China
| | - Zhengkui Zhou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan W Rd, Beijing, 100193, China.
| | - Shuisheng Hou
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, No. 2 Yuanmingyuan W Rd, Beijing, 100193, China.
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Cerolini S, Vasconi M, Abdel Sayed A, Iaffaldano N, Mangiagalli MG, Pastorelli G, Moretti VM, Zaniboni L, Mosca F. Free-range rearing density for male and female Milanino chickens: carcass yield and qualitative meat traits. J APPL POULTRY RES 2019. [DOI: 10.3382/japr/pfz058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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42
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Zhang M, Li F, Ma XF, Li WT, Jiang RR, Han RL, Li GX, Wang YB, Li ZY, Tian YD, Kang XT, Sun GR. Identification of differentially expressed genes and pathways between intramuscular and abdominal fat-derived preadipocyte differentiation of chickens in vitro. BMC Genomics 2019; 20:743. [PMID: 31615399 PMCID: PMC6794883 DOI: 10.1186/s12864-019-6116-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 09/20/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The distribution and deposition of fat tissue in different parts of the body are the key factors affecting the carcass quality and meat flavour of chickens. Intramuscular fat (IMF) content is an important factor associated with meat quality, while abdominal fat (AbF) is regarded as one of the main factors affecting poultry slaughter efficiency. To investigate the differentially expressed genes (DEGs) and molecular regulatory mechanisms related to adipogenic differentiation between IMF- and AbF-derived preadipocytes, we analysed the mRNA expression profiles in preadipocytes (0d, Pre-) and adipocytes (10d, Ad-) from IMF and AbF of Gushi chickens. RESULTS AbF-derived preadipocytes exhibited a higher adipogenic differentiation ability (96.4% + 0.6) than IMF-derived preadipocytes (86.0% + 0.4) (p < 0.01). By Ribo-Zero RNA sequencing, we obtained 4403 (2055 upregulated and 2348 downregulated) and 4693 (2797 upregulated and 1896 downregulated) DEGs between preadipocytes and adipocytes in the IMF and Ad groups, respectively. For IMF-derived preadipocyte differentiation, pathways related to the PPAR signalling pathway, ECM-receptor interaction and focal adhesion pathway were significantly enriched. For AbF-derived preadipocyte differentiation, the steroid biosynthesis pathways, calcium signaling pathway and ECM-receptor interaction pathway were significantly enriched. A large number of DEGs related to lipid metabolism, fatty acid metabolism and preadipocyte differentiation, such as PPARG, ACSBG2, FABP4, FASN, APOA1 and INSIG1, were identified in our study. CONCLUSION This study revealed large transcriptomic differences between IMF- and AbF-derived preadipocyte differentiation. A large number of DEGs and transcription factors that were closely related to fatty acid metabolism, lipid metabolism and preadipocyte differentiation were identified in the present study. Additionally, the microenvironment of IMF- and AbF-derived preadipocyte may play a significant role in adipogenic differentiation. This study provides valuable evidence to understand the molecular mechanisms underlying adipogenesis and fat deposition in chickens.
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Affiliation(s)
- Meng Zhang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.,The First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Fang Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Xiang-Fei Ma
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Wen-Ting Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Rui-Rui Jiang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Rui-Li Han
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Guo-Xi Li
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Yan-Bin Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Zi-Yi Li
- The First Hospital, Jilin University, Changchun, 130021, Jilin, China
| | - Ya-Dong Tian
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Xiang-Tao Kang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China
| | - Gui-Rong Sun
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, China. .,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, 450002, China.
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Lake JA, Papah MB, Abasht B. Increased Expression of Lipid Metabolism Genes in Early Stages of Wooden Breast Links Myopathy of Broilers to Metabolic Syndrome in Humans. Genes (Basel) 2019; 10:E746. [PMID: 31557856 PMCID: PMC6826700 DOI: 10.3390/genes10100746] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 09/20/2019] [Indexed: 12/20/2022] Open
Abstract
Wooden breast is a muscle disorder affecting modern commercial broiler chickens that causes a palpably firm pectoralis major muscle and severe reduction in meat quality. Most studies have focused on advanced stages of wooden breast apparent at market age, resulting in limited insights into the etiology and early pathogenesis of the myopathy. Therefore, the objective of this study was to identify early molecular signals in the wooden breast transcriptional cascade by performing gene expression analysis on the pectoralis major muscle of two-week-old birds that may later exhibit the wooden breast phenotype by market age at 7 weeks. Biopsy samples of the left pectoralis major muscle were collected from 101 birds at 14 days of age. Birds were subsequently raised to 7 weeks of age to allow sample selection based on the wooden breast phenotype at market age. RNA-sequencing was performed on 5 unaffected and 8 affected female chicken samples, selected based on wooden breast scores (0 to 4) assigned at necropsy where affected birds had scores of 2 or 3 (mildly or moderately affected) while unaffected birds had scores of 0 (no apparent gross lesions). Differential expression analysis identified 60 genes found to be significant at an FDR-adjusted p-value of 0.05. Of these, 26 were previously demonstrated to exhibit altered expression or genetic polymorphisms related to glucose tolerance or diabetes mellitus in mammals. Additionally, 9 genes have functions directly related to lipid metabolism and 11 genes are associated with adiposity traits such as intramuscular fat and body mass index. This study suggests that wooden breast disease is first and foremost a metabolic disorder characterized primarily by ectopic lipid accumulation in the pectoralis major.
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Affiliation(s)
- Juniper A Lake
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711, USA.
| | - Michael B Papah
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA.
| | - Behnam Abasht
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716, USA.
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Wang L, Zhao L, Zhang L, Liu X, Hou X, Gao H, Yan H, Zhao F, Wang L. NTN1 Affects Porcine Intramuscular Fat Content by Affecting the Expression of Myogenic Regulatory Factors. Animals (Basel) 2019; 9:ani9090609. [PMID: 31461826 PMCID: PMC6770873 DOI: 10.3390/ani9090609] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/12/2019] [Accepted: 08/17/2019] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Intramuscular fat (IMF) is a key meat quality trait in the pork industry. In this study, we validated the effect of the copy number of Netrin-1 (NTN1-CNV) on Netrin-1 (NTN1) protein expression and explored the possible affective mechanism of NTN1 on IMF. The results indicated that NTN1-CNV may affect the expression of NTN1 protein by its gene dose, and the expression of NTN1 may affect the proliferation and differentiation of muscle cells by the AMP-activated protein kinase (AMPK) pathway and finally influence the IMF content. Abstract Intramuscular fat (IMF) content is an important economic trait for pork quality. Our previous results regarding the genome-wide association between IMF content and copy number variations (CNVs) indicated that the CNV within Netrin-1(NTN1-CNV) was significantly associated with IMF. In order to validate the effect of NTN1-CNV, we detected the Netrin-1 (NTN1) gene dose and protein expression content in the longissimus dorsi of different IMF content pigs using Western blotting and investigated the expression of NTN1 RNA in different tissues using real-time quantitative polymerase chain reaction (qPCR). The knock-down of the NTN1 gene in C2C12 and 3T3-L1 cells and over-expression in C2C12 cells during the proliferation and differentiation stage were also investigated to explore the possible pathway of action of NTN1. The results showed that in individuals with IMF content differences, the gene dose of NTN1 and the expression of NTN1 protein were also significantly different, which indicated that NTN1-CNV may directly affect IMF by its coding protein. NTN1 had the highest expression in pig longissimus dorsi and backfat tissues, which indicates that NTN1 may play an important role in muscle and fat tissues. The in vitro validation assay indicated that NTN1 silencing could promote the proliferation and inhibit the differentiation of C2C12 cells, with no effect on 3T3-L1 cells. Additionally, NTN1 over-expression could inhibit the proliferation and promote the differentiation of C2C12 cells. Combined with previous research, we conclude that NTN1-CNV may affect IMF by its gene dose, and the expression of NTN1 may affect the proliferation and differentiation of muscle cells by the AMP-activated protein kinase (AMPK) pathway and finally influence the IMF.
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Affiliation(s)
- Ligang Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lingling Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
| | - Longchao Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinhua Hou
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hongmei Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hua Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fuping Zhao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lixian Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zhou Q, Yang Y, Yang Z. Molecular dissection of cadmium-responsive transcriptome profile in a low-cadmium-accumulating cultivar of Brassica parachinensis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 176:85-94. [PMID: 30921700 DOI: 10.1016/j.ecoenv.2019.03.077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/17/2019] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Brassica parachinensis L., a daily consumed leaf vegetable, is a high-Cd accumulator that substantially threatens human health. Screening and breeding Cd pollution-safe cultivars (Cd-PSCs) of crops is a low-cost strategy to restrict human Cd intake from contaminated soils via the food chain. However, little is known about the molecular mechanisms underlying the low-Cd-accumulating traits of B. parachinensis Cd-PSCs. In the current study, we analyzed the transcriptomes of the Cd-treated (5 μM) roots and shoots of a low-Cd-accumulating cultivar (SJ19) and a high-Cd-accumulating cultivar (CX4) of B. parachinensis to reveal the molecular mechanisms in response to Cd stress. Compared to CX4, many pathways involved in carbohydrate and amino acid metabolisms were exclusively up-regulated in SJ19 roots upon exposure to low Cd concentrations, which may produce more energy and metabolites for Cd detoxification. Antioxidant enzymes in the peroxisome were up-regulated in both SJ19 and CX4 roots in response to Cd, while glutathione biosynthesis was only activated in SJ19 roots. In SJ19 shoots, pathways of photosynthesis and cell growth were activated to mitigate Cd-induced damages. Furthermore, Cd transport genes, such as MTP1, HMA3 and CAX family genes, were highly induced by Cd stress in SJ19 roots in accordance with the high Cd concentration in roots, while genes involved in root-to-shoot Cd translocation such as FRD3 and CESA3 were suppressed, which may contribute to the low Cd concertation in edible part of SJ19. Our study provides a genetic basis for further Cd-PSCs screening and breeding.
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Affiliation(s)
- Qian Zhou
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Yuchen Yang
- Department of Genetics, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC, 27599, USA.
| | - Zhongyi Yang
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China.
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Comparison of liver transcriptome from high- and low-intramuscular fat Chaohu ducks provided additional candidate genes for lipid selection. 3 Biotech 2019; 9:251. [PMID: 31218175 DOI: 10.1007/s13205-019-1780-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/26/2019] [Indexed: 10/26/2022] Open
Abstract
The meat quality of ducks is closely related to the intramuscular fat (IMF) content. This study explored the candidate regulatory genes of IMF formation and lipid deposition in Chaohu ducks. The IMF of breast muscle in 100 ducks was determined and statistically analysed by normal distribution test. Duck liver samples with high IMF (CH, n = 3) and low IMF (CL, n = 3) were selected for transcriptome analysis by RNA sequencing (RNA-Seq). The IMF was in accordance with normal distribution (T = 0.001, P = 0.999). The IMF from two tails of the normal distribution was significantly different with 2.9983% ± 0.3296% in the CH group and 1.1960% ± 0.1481% in the CL group (P < 0.0001). RNA-Seq revealed 147 differentially expressed genes, including 78 up-regulated and 69 down-regulated genes in both groups. Validation by qRT-PCR was in agreement with RNA-Seq (R 2 = 0.838). Gene ontology analysis revealed that organophosphate catabolism, oxidation-reduction process, cellular lipid catabolism, lipid transport, lipid localisation, lipid biosynthesis and cellular lipid catabolism were involved in lipid metabolism. Meanwhile, Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that steroid hormone biosynthesis, ovarian steroidogenesis, alpha-linolenic acid metabolism, glycosylphosphatidylinositol anchor biosynthesis and linoleic acid metabolism were involved in lipid deposition, wherein the genes COMT, NT5E, PDE4D, PLA2G4F, A-FABP, ADRA2A, HSD17B2, PPP1R3C, PPP1R3B and NR0B2 were involved in lipid deposition. This study provided insights into the molecular mechanism for regulating lipid metabolism and identified candidate genes for selecting markers to control IMF formation in Chaohu ducks.
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Li G, Zhao Y, Li Y, Chen Y, Jin W, Sun G, Han R, Tian Y, Li H, Kang X. Weighted gene coexpression network analysis identifies specific transcriptional modules and hub genes related to intramuscular fat traits in chicken breast muscle. J Cell Biochem 2019; 120:13625-13639. [PMID: 30937957 DOI: 10.1002/jcb.28636] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/15/2019] [Accepted: 02/28/2019] [Indexed: 12/31/2022]
Abstract
Intramuscular fat (IMF) traits are important factors that influence meat quality. However, the molecular regulatory mechanisms that underlie this trait in chickens are still poorly understood at the gene coexpression level. Here, we performed a weighted gene coexpression network analysis between IMF traits and transcriptome profile in breast muscle in the Chinese domestic Gushi chicken breed at 6, 14, 22, and 30 weeks. A total of 26 coexpressed gene modules were identified. Six modules, which included the dark gray, purple, cyan, pink, light cyan, and blue modules, showed a significant positive correlation (P < 0.05) with IMF traits. The strongest correlation was observed between the dark gray module and IMF content (r = 0.85; P = 4e-04) and between the blue module and different fatty acid content (r = 0.87~0.91; P = 5e-05~2e-04). Enrichment analysis showed that the enrichment of biological processes, such as fatty acid metabolic process, fat cell differentiation, acylglycerol metabolic process, and glycerolipid metabolism were significantly different in the six modules. In addition, the 32, 24, 4, 7, 6, and 25 hub genes were identified from the blue, pink, light cyan, cyan, dark gray, and purple modules, respectively. These hub genes are involved in multiple links to fatty acid metabolism, phospholipid metabolism, cholesterol metabolism, diverse cellular behaviors, and cell events. These results provide novel insights into the molecular regulatory mechanisms for IMF-related traits in chicken and may also help to uncover the formation mechanism for excellent meat quality traits in local breeds of Chinese chicken.
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Affiliation(s)
- Guoxi Li
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Yinli Zhao
- Department of Animal Science, College of Biological Engineering, Henan University of Technology, Zheng Zhou, Henan, P. R. China
| | - Yuanfang Li
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Yi Chen
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Wenjiao Jin
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Guirong Sun
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Ruili Han
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Yadong Tian
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Hong Li
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
| | - Xiangtao Kang
- Department of Animal Production Systems and Engineering, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zheng Zhou, Henan, P. R. China
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Wu Y, Zhang Y, Hou Z, Fan G, Pi J, Sun S, Chen J, Liu H, Du X, Shen J, Hu G, Chen W, Pan A, Yin P, Chen X, Pu Y, Zhang H, Liang Z, Jian J, Zhang H, Wu B, Sun J, Chen J, Tao H, Yang T, Xiao H, Yang H, Zheng C, Bai M, Fang X, Burt DW, Wang W, Li Q, Xu X, Li C, Yang H, Wang J, Yang N, Liu X, Du J. Population genomic data reveal genes related to important traits of quail. Gigascience 2018; 7:4995262. [PMID: 29762663 PMCID: PMC5961004 DOI: 10.1093/gigascience/giy049] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 04/27/2018] [Indexed: 12/18/2022] Open
Abstract
Background Japanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies. Results Here, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs. Conclusions This study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.
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Affiliation(s)
- Yan Wu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China.,Key Laboratory of Animal Embryo Engineering and Molecular Breeding of Hubei Province,Wuhan 430064, China.,Hubei Innovation Center of Agricultural Science and Technology, Wuhan, Hubei, 430064, China
| | - Yaolei Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China
| | - Guangyi Fan
- BGI-Shenzhen, Shenzhen 518083, China.,BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.,State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinsong Pi
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jiang Chen
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Huaqiao Liu
- Hubei Shendan Healthy Food Co., Ltd., Wuhan 430206, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Jie Shen
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Gang Hu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Ailuan Pan
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Pingping Yin
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | | | - Yuejin Pu
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - He Zhang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Zhenhua Liang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | - Hao Zhang
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Jing Sun
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | - Hu Tao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Ting Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Hongwei Xiao
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | - Huan Yang
- BGI-Shenzhen, Shenzhen 518083, China
| | - Chuanwei Zheng
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
| | | | | | - David W Burt
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Wen Wang
- Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, China
| | - Qingyi Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Chengfeng Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, China; Agricultural University, Beijing 100193, China
| | - Xin Liu
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Jinping Du
- Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Science, Wuhan 430064, China
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