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Li W, Xu M, Zhang Z, Liang J, Fu R, Lin W, Luo W, Zhang X, Ren T. Regulatory Effects of 198-bp Structural Variants in the GSTA2 Promoter Region on Adipogenesis in Chickens. Int J Mol Sci 2024; 25:7155. [PMID: 39000259 PMCID: PMC11241197 DOI: 10.3390/ijms25137155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024] Open
Abstract
Molecular breeding accelerates animal breeding and improves efficiency by utilizing genetic mutations. Structural variations (SVs), a significant source of genetic mutations, have a greater impact on phenotypic variation than SNPs. Understanding SV functional mechanisms and obtaining precise information are crucial for molecular breeding. In this study, association analysis revealed significant correlations between 198-bp SVs in the GSTA2 promoter region and abdominal fat weight, intramuscular fat content, and subcutaneous fat thickness in chickens. High expression of GSTA2 in adipose tissue was positively correlated with the abdominal fat percentage, and different genotypes of GSTA2 exhibited varied expression patterns in the liver. The 198-bp SVs regulate GSTA2 expression by binding to different transcription factors. Overexpression of GSTA2 promoted preadipocyte proliferation and differentiation, while interference had the opposite effect. Mechanistically, the 198-bp fragment contains binding sites for transcription factors such as C/EBPα that regulate GSTA2 expression and fat synthesis. These SVs are significantly associated with chicken fat traits, positively influencing preadipocyte development by regulating cell proliferation and differentiation. Our work provides compelling evidence for the use of 198-bp SVs in the GSTA2 promoter region as molecular markers for poultry breeding and offers new insights into the pivotal role of the GSTA2 gene in fat generation.
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Affiliation(s)
- Wangyu Li
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
| | - Meng Xu
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zihao Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China;
| | - Jiaying Liang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
| | - Rong Fu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
| | - Wujian Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
| | - Tuanhui Ren
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China (R.F.); (W.L.); (W.L.)
- Guangdong Key Laboratory of Genome and Molecular Breeding of Agricultural Animals and Key Laboratory of Chicken Genetic Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China
- State Key Laboratory of Swine and Poultry Breeding Industry, Guangzhou 510642, China
- College of Veterinary Medicine, Jilin University, Changchun 130062, China
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Liu X, Wang Y, Wang Y, Cui H, Zhao G, Guo Y, Wen J. Effect of myristic acid supplementation on triglyceride synthesis and related genes in the pectoral muscles of broiler chickens. Poult Sci 2024; 103:104038. [PMID: 39079330 PMCID: PMC11340564 DOI: 10.1016/j.psj.2024.104038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 06/20/2024] [Accepted: 06/23/2024] [Indexed: 08/25/2024] Open
Abstract
Fatty acids (FAs) can serve as energy for poultry, maintain normal cell structure and function, and support a healthy immune system. Although the addition of polyunsaturated fatty acids (PUFAs) to the diet has been extensively studied and reported, the mechanism of action of saturated fatty acids (SFAs) remains to be elucidated. We investigated the effect of 0.04% dietary myristic acid (MA) on slaughter performance, lipid components, tissue FAs, and the transcriptome profile in chickens. The results showed that dietary MA had no effect on slaughter performance (body weight, carcass weight, eviscerated weight, and pectoral muscle weight) (P > 0.05). Dietary MA enrichment increased MA (P < 0.001) and triglycerides (TGs) (P < 0.01) levels in the pectoral muscle. The levels of palmitic acid, linoleic acid (LA), arachidonic acid (AA), SFAs, monounsaturated fatty acids (MUFAs), and PUFAs were significantly higher (P < 0.01) in the MA supplementation group compared to the control group. However, there were no significant differences in the ratios of PUFA/SFA and n6/omega-3 (n3) between the two groups. The MA content was positively correlated with the contents of palmitic acid, LA, linolenic acid (ALA), n3, n6, SFAs, and unsaturated fatty acids (UFA). DHCR24, which is known to be involved in steroid metabolism and cholesterol biosynthesis pathways, was found to be a significantly lower in the MA supplementation group compared to the control group (P < 0.05, log2(fold change) = -0.85). Five overlapping co-expressed genes were identified at the intersection between the differential expressed genes and Weighted Gene Co‑expression Network Analysis-derived hub genes associated with MA phenotype, namely BHLHE40, MSL1, PLAGL1, SRSF4, and ENSGALG00000026875. For the TG phenotype, a total of 28 genes were identified, including CHKA, KLF5, TGIF1, etc. Both sets included the gene PLAGL1, which has a negative correlation with the levels of MA and TG. This study provides valuable information to further understand the regulation of gene expression patterns by dietary supplementation with MA and examines at the molecular level the phenotypic changes induced by supplementation with MA.
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Affiliation(s)
- Xiaojing Liu
- State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yanke Wang
- State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yidong Wang
- State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Huanxian Cui
- State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Yuming Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jie Wen
- State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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Lu T, Abdalla Gibril BA, Xu J, Xiong X. Unraveling the Genetic Foundations of Broiler Meat Quality: Advancements in Research and Their Impact. Genes (Basel) 2024; 15:746. [PMID: 38927682 PMCID: PMC11202585 DOI: 10.3390/genes15060746] [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: 04/25/2024] [Revised: 06/01/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
As societal progress elevates living standards, the focus on meat consumption has shifted from quantity to quality. In broiler production, optimizing meat quality has become paramount, prompting efforts to refine various meat attributes. Recent advancements in sequencing technologies have revealed the genome's complexity, surpassing previous conceptions. Through experimentation, numerous genetic elements have been linked to crucial meat quality traits in broiler chickens. This review synthesizes the current understanding of genetic determinants associated with meat quality attributes in broilers. Researchers have unveiled the pivotal insights detailed herein by employing diverse genomic methodologies such as QTL-based investigations, candidate gene studies, single-nucleotide polymorphism screening, genome-wide association studies, and RNA sequencing. These studies have identified numerous genes involved in broiler meat quality traits, including meat lightness (COL1A2 and ACAA2), meat yellowness (BCMO1 and GDPD5), fiber diameter (myostatin and LncIRS1), meat pH (PRDX4), tenderness (CAPN1), and intramuscular fat content (miR-24-3p and ANXA6). Consequently, a comprehensive exploration of these genetic elements is imperative to devise novel molecular markers and potential targets, promising to revolutionize strategies for enhancing broiler meat quality.
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Affiliation(s)
| | | | | | - Xinwei Xiong
- Jiangxi Provincial Key Laboratory of Poultry Genetic Improvement, Nanchang Normal University, Nanchang 330032, 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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Wang Y, Liu L, Liu X, Wang Y, Yang W, Zhao W, Zhao G, Cui H, Wen J. Identification of characteristic aroma compounds in chicken meat and their metabolic mechanisms using gas chromatography-olfactometry, odor activity values, and metabolomics. Food Res Int 2024; 175:113782. [PMID: 38129007 DOI: 10.1016/j.foodres.2023.113782] [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: 08/12/2023] [Revised: 10/08/2023] [Accepted: 11/29/2023] [Indexed: 12/23/2023]
Abstract
Aroma has an important influence on the aroma quality of chicken meat. This study aimed to identify the characteristic aroma substances in chicken meat and elucidate their metabolic mechanisms. Using gas chromatography-olfactometry and odor activity values, we identified nonanal, octanal, and dimethyl tetrasulfide as the basic characteristic aroma compounds in chicken meat, present in several breeds. Hexanal, 1-octen-3-ol, (E)-2-nonenal, heptanal, and (E,E)-2,4-decadienal were breed-specific aroma compounds found in native Chinese chickens but not in the meat of white-feathered broilers. Metabolomics analysis showed that L-glutamine was an important metabolic marker of nonanal, hexanal, heptanal, octanal, and 1-octen-3-ol. Exogenous supplementation experiments found that L-glutamine increased the content of D-glucosamine-6-P and induced the degradation of L-proline, L-arginine, and L-lysine to enhance the Maillard reaction and promote the formation of nonanal, hexanal, heptanal, octanal, and 1-octen-3-ol, thus improving the aroma profile of chicken meat.
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Affiliation(s)
- Yanke Wang
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Li Liu
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Xiaojing Liu
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Yidong Wang
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Weifang Yang
- Beijing General Station of Animal Husbandry, Beijing 100107, China.
| | - Wenjuan Zhao
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Guiping Zhao
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Huanxian Cui
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
| | - Jie Wen
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China.
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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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Praetorius JP, Walluks K, Svensson CM, Arnold D, Figge MT. IMFSegNet: Cost-effective and objective quantification of intramuscular fat in histological sections by deep learning. Comput Struct Biotechnol J 2023; 21:3696-3704. [PMID: 37560127 PMCID: PMC10407270 DOI: 10.1016/j.csbj.2023.07.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/21/2023] [Accepted: 07/22/2023] [Indexed: 08/11/2023] Open
Abstract
The assessment of muscle condition is of great importance in various research areas. In particular, evaluating the degree of intramuscular fat (IMF) in tissue sections is a challenging task, which today is still mostly performed qualitatively or quantitatively by a highly subjective and error-prone manual analysis. We here realize the mission to make automated IMF analysis possible that (i) minimizes subjectivity, (ii) provides accurate and quantitative results quickly, and (iii) is cost-effective using standard hematoxylin and eosin (H&E) stained tissue sections. To address all these needs in a deep learning approach, we utilized the convolutional encoder-decoder network SegNet to train the specialized network IMFSegNet allowing to accurately quantify the spatial distribution of IMF in histological sections. Our fully automated analysis was validated on 17 H&E-stained muscle sections from individual sheep and compared to various state-of-the-art approaches. Not only does IMFSegNet outperform all other approaches, but this neural network also provides fully automated and highly accurate results utilizing the most cost-effective procedures of sample preparation and imaging. Furthermore, we shed light on the opacity of black-box approaches such as neural networks by applying an explainable artificial intelligence technique to clarify that the success of IMFSegNet actually lies in identifying the hard-to-detect IMF structures. Embedded in our open-source visual programming language JIPipe that does not require programming skills, it can be expected that IMFSegNet advances muscle condition assessment in basic research across multiple areas as well as in research fields focusing on translational clinical applications.
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Affiliation(s)
- Jan-Philipp Praetorius
- Applied Systems Biology, Leibniz institute for natural Product Research and infection Biology – Hans Knöll institute (HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Kassandra Walluks
- Applied Systems Biology, Leibniz institute for natural Product Research and infection Biology – Hans Knöll institute (HKI), Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
- Institute of Zoology and Evolutionary Research, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Carl-Magnus Svensson
- Applied Systems Biology, Leibniz institute for natural Product Research and infection Biology – Hans Knöll institute (HKI), Jena, Germany
| | - Dirk Arnold
- Department of Otorhinolaryngology, Jena University Hospital, Jena, Germany
- Facial-Nerve-Center Jena, Jena University Hospital, Jena, Germany
| | - Marc Thilo Figge
- Applied Systems Biology, Leibniz institute for natural Product Research and infection Biology – Hans Knöll institute (HKI), Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
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8
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Yin L, Liu L, Tang Y, Chen Q, Zhang D, Lin Z, Wang Y, Liu Y. The Implications in Meat Quality and Nutrition by Comparing the Metabolites of Pectoral Muscle between Adult Indigenous Chickens and Commercial Laying Hens. Metabolites 2023; 13:840. [PMID: 37512547 PMCID: PMC10384229 DOI: 10.3390/metabo13070840] [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: 06/15/2023] [Revised: 06/30/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Aged chickens are often a secondary dietary choice, owing to the poor organoleptic qualities of their meat. With regard to the meat quality of chickens, the metabolic profiles of pectoral muscle in Guangyuan grey chickens (group G) and Hy-Line grey hens (group H) aged 55 weeks were compared via ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). A total of 74 metabolites were identified with differential changes in the ion model. Lipids and lipid-like molecules comprised the largest proportion among the different metabolites. The content of myristic acid and palmitic acid were found to be higher in the pectoral muscle of group G, while group H showed significantly higher levels of glycerophospholipid molecules, such as LPC(18:2/0:0), Pi(38:5), Pc(16:0/16:0), and Pe(16:1e/14-hdohe). KEGG pathway analysis indicated that the abundant metabolites in group G were mainly involved in energy metabolism and fatty acid biosynthesis and metabolism, whereas those of group H were mainly attributed to the metabolism of unsaturated fatty acids and amino acids. Overall, the differences in lipid and amino acid metabolism in pectoral muscle appear to be responsible for the difference in meat quality between indigenous chickens and commercial laying hens.
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Affiliation(s)
- Lingqian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuan Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Qian Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Donghao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongzhen Lin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Yiping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Wen C, Gou Q, Gu S, Huang Q, Sun C, Zheng J, Yang N. The cecal ecosystem is a great contributor to intramuscular fat deposition in broilers. Poult Sci 2023; 102:102568. [PMID: 36889043 PMCID: PMC10011826 DOI: 10.1016/j.psj.2023.102568] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/11/2023] Open
Abstract
Intramuscular fat (IMF) content is a meat quality trait of major economic importance in animal production. Emerging evidence has demonstrated that meat quality can be improved by regulating the gut microbiota. However, the organization and ecological properties of the gut microbiota and its relationship with the IMF content remain unclear in chickens. Here, we investigated the microbial communities of 206 cecal samples from broilers with excellent meat quality. We noted that the cecal microbial ecosystem obtained from hosts reared under the same management and dietary conditions showed clear compositional stratification. Two enterotypes, in which the ecological properties, including diversity and interaction strengths, were significantly different, described the microbial composition pattern. Compared with enterotype 2, enterotype 1, distinguished by the Clostridia_vadinBB60_group, had a higher fat deposition, although no discrepancy was found in growth performance and meat yield. A moderate correlation was observed in the IMF content between 2 muscle tissues, despite the IMF content of thigh muscle was 42.76% greater than that of breast muscle. Additionally, the lower abundance of cecal vadinBE97 was related to higher IMF levels in both muscle tissues. Although vadinBE97 accounted for 0.40% of the total abundance of genera in the cecum, it exhibited significant and positive correlations with other genera (accounting for 25.3% of the tested genera). Our results highlight important insights into the cecal microbial ecosystem and its association with meat quality. Microbial interactions should be carefully considered when developing approaches to improve the IMF content by regulating the gut microbiota in broilers.
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Affiliation(s)
- Chaoliang Wen
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Qinli Gou
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Shuang Gu
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Qiang Huang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Congjiao Sun
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Jiangxia Zheng
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China.
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10
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Wang Y, Liu L, Liu X, Tan X, Zhu Y, Luo N, Zhao G, Cui H, Wen J. SLC16A7 Promotes Triglyceride Deposition by De Novo Lipogenesis in Chicken Muscle Tissue. BIOLOGY 2022; 11:1547. [PMID: 36358250 PMCID: PMC9687483 DOI: 10.3390/biology11111547] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 10/08/2022] [Indexed: 07/30/2023]
Abstract
Triglyceride (TG) content in chicken muscle tissue signifies intramuscular fat (IMF) content, which is important for improving meat quality. However, the genetic basis of TG deposition in chicken is still unclear. Using 520 chickens from an artificially selected line with significantly increased IMF content and a control line, a genome-wide association study (GWAS) with TG content reports a region of 802 Kb located in chromosome 1. The XP-EHH and gene expression analysis together reveal that the solute carrier family 16 member A7 (SLC16A7) gene is the key candidate gene associated with TG content in chicken muscle tissue. Furthermore, the weighted gene co-expression network analysis (WGCNA) confirmed the regulatory effects of SLC16A7 on promoting TG deposition by de novo lipogenesis (DNL). Functional verification of SLC16A7 in vitro also supports this view, and reveals that this effect mainly occurs in myocytes. Our data highlight a potential IMF deposition pathway by DNL, induced by SLC16A7 in chicken myocytes. These findings will improve the understanding of IMF regulation in chicken and guide the formulation of breeding strategies for high-quality chicken.
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Affiliation(s)
- 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
| | - Lu Liu
- College of Animal Science and Technology, College of Veterinary Medicine of Zhejiang A&F University, Hangzhou 311300, China
| | - Xiaojing Liu
- 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
| | - Xiaodong Tan
- 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
| | - Yuting Zhu
- 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
| | - Na Luo
- 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
| | - Guiping Zhao
- 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
| | - Jie Wen
- 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
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Yuan X, Cui H, Jin Y, Zhao W, Liu X, Wang Y, Ding J, Liu L, Wen J, Zhao G. Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken. Front Genet 2022; 13:902180. [PMID: 36035160 PMCID: PMC9412053 DOI: 10.3389/fgene.2022.902180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Aldehydes are primary volatile organic compounds (VOCs) in local Chinese chicken meat and contribute green grass, fatty, citrus, and bitter almond aromas to chicken meat. To understand the genetic basis of these aldehyde VOC aromas, we used approximately 500 Chinese Jingxing Yellow (JXY) chickens to conduct genome-wide association studies (GWAS) on the flavor traits with the data of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs). In total, 501 association variants (253 SNPs and 248 INDELs) were found to be suggestively (SNPs: p-value < 2.77e-06 and INDELs: p-value < 3.78e-05) associated with total aldehydes (the sum of nine aldehydes), hexanal, heptanal, benzaldehyde, (E,E)-2,4-nonadienal, octanal, (E)-2-decenal, nonanal, decanal, and octadecanal. Of them, six SNPs and 23 INDELs reached a genome-wide significance level (SNPs: p-value < 1.38e-07 and INDELs: p-value < 1.89e-06). Potential candidate aldehyde genes were functionally annotated for lipid metabolism, especially fatty acid-related pathways and phospholipid-related gene ontology (GO) terms. Moreover, the GWAS analysis of total aldehydes, hexanal, and nonanal generated the most significant signals, and phenotypic content differed between different genotypes at candidate gene-related loci. For total aldehydes and hexanal traits, candidate genes were annotated based on the significant and suggestive variants on chromosomes 3 and 8 with highly polymorphic linkage blocks. The following candidate genes were also identified: GALM, MAP4K3, GPCPD1, RPS6KA2, CRLS1, ASAP1, TRMT6, SDC1, PUM2, ALDH9A1, MGST3, GMEB1, MECR, LDLRAP1, GPAM and ACSL5. We also found that polyunsaturated fatty acids (PUFAs) (C18:2n6c linoleic acid and C18:3n3 linolenic acid) were significantly correlated with total aldehydes and hexanal contents. PUFAs are important aldehyde precursors, and consistently, our results suggested that candidate genes involved in fatty acid pathways and phospholipid GO terms were identified in association loci. This work provides an understanding of the genetic basis of aldehyde formation, which is a key flavor-forming compound.
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