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Gao G, Liu R, Hu S, He M, Zhang J, Gao D, Li J, Hu J, Wang J, Wang Q, Li M, Jin L. Exploring the dynamic three-dimensional chromatin architecture and transcriptional landscape in goose liver tissues underlying metabolic adaptations induced by a high-fat diet. J Anim Sci Biotechnol 2024; 15:60. [PMID: 38693536 PMCID: PMC11064361 DOI: 10.1186/s40104-024-01016-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/29/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Goose, descendants of migratory ancestors, have undergone extensive selective breeding, resulting in their remarkable ability to accumulate fat in the liver and exhibit a high tolerance for significant energy intake. As a result, goose offers an excellent model for studying obesity, metabolic disorders, and liver diseases in mammals. Although the impact of the three-dimensional arrangement of chromatin within the cell nucleus on gene expression and transcriptional regulation is widely acknowledged, the precise functions of chromatin architecture reorganization during fat deposition in goose liver tissues still need to be fully comprehended. RESULTS In this study, geese exhibited more pronounced changes in the liver index and triglyceride (TG) content following the consumption of the high-fat diet (HFD) than mice without significant signs of inflammation. Additionally, we performed comprehensive analyses on 10 goose liver tissues (5 HFD, 5 normal), including generating high-resolution maps of chromatin architecture, conducting whole-genome gene expression profiling, and identifying H3K27ac peaks in the livers of geese and mice subjected to the HFD. Our results unveiled a multiscale restructuring of chromatin architecture, encompassing Compartment A/B, topologically associated domains, and interactions between promoters and enhancers. The dynamism of the three-dimensional genome architecture, prompted by the HFD, assumed a pivotal role in the transcriptional regulation of crucial genes. Furthermore, we identified genes that regulate chromatin conformation changes, contributing to the metabolic adaptation process of lipid deposition and hepatic fat changes in geese in response to excessive energy intake. Moreover, we conducted a cross-species analysis comparing geese and mice exposed to the HFD, revealing unique characteristics specific to the goose liver compared to a mouse. These chromatin conformation changes help elucidate the observed characteristics of fat deposition and hepatic fat regulation in geese under conditions of excessive energy intake. CONCLUSIONS We examined the dynamic modifications in three-dimensional chromatin architecture and gene expression induced by an HFD in goose liver tissues. We conducted a cross-species analysis comparing that of mice. Our results contribute significant insights into the chromatin architecture of goose liver tissues, offering a novel perspective for investigating mammal liver diseases.
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Affiliation(s)
- Guangliang Gao
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Sciences, Rongchang District, Chongqing, 402460, China
| | - Rui Liu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Silu Hu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengnan He
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaman Zhang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Dengfeng Gao
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiwei Hu
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiwen Wang
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qigui Wang
- Chongqing Engineering Research Center of Goose Genetic Improvement, Institute of Poultry Science, Chongqing Academy of Animal Sciences, Rongchang District, Chongqing, 402460, China
| | - Mingzhou Li
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Long Jin
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Wei R, Teng Y, Han C, Wei S, Li L, Liu H, Hu S, Kang B, Xu H. Multi-omics reveals goose fatty liver formation from metabolic reprogramming. Front Vet Sci 2024; 11:1122904. [PMID: 38348107 PMCID: PMC10859500 DOI: 10.3389/fvets.2024.1122904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/08/2024] [Indexed: 02/15/2024] Open
Abstract
To comprehensively provide insight into goose fatty liver formation, we performed an integrative analysis of the liver transcriptome, lipidome, and amino acid metabolome, as well as peripheral adipose tissue transcriptome analysis using samples collected from the overfed geese and normally fed geese. Transcriptome analysis showed that liver metabolism pathways were mainly enriched in glucolipid metabolism, amino acid metabolism, inflammation response, and cell cycle; peripheral adipose tissue and the liver cooperatively regulated liver lipid accumulation during overfeeding. Liver lipidome patterns obviously changed after overfeeding, and 157 different lipids were yielded. In the liver amino acid metabolome, the level of Lys increased after overfeeding. In summary, this is the first study describing goose fatty liver formation from an integrative analysis of transcriptome, lipidome, and amino acid metabolome, which will provide a whole new dimension to understanding the mechanism of goose fatty liver formation.
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Affiliation(s)
- Rongxue Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yongqiang Teng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chunchun Han
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shouhai Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bo Kang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hengyong Xu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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3
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Gao G, Zhang H, Ni J, Zhao X, Zhang K, Wang J, Kong X, Wang Q. Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis. J Anim Sci Biotechnol 2023; 14:150. [PMID: 38001525 PMCID: PMC10675864 DOI: 10.1186/s40104-023-00944-y] [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: 05/23/2023] [Accepted: 10/06/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Domestic goose breeds are descended from either the Swan goose (Anser cygnoides) or the Greylag goose (Anser anser), exhibiting variations in body size, reproductive performance, egg production, feather color, and other phenotypic traits. Constructing a pan-genome facilitates a thorough identification of genetic variations, thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability. RESULTS To comprehensively facilitate population genomic and pan-genomic analyses in geese, we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples. By constructing the pan-genome for geese, we generated non-reference contigs totaling 612 Mb, unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes, 1,324 softcore genes, 2,734 shell genes, and 878 cloud genes in goose genomes. Furthermore, we detected an 81.97 Mb genomic region showing signs of genome selection, encompassing the TGFBR2 gene correlated with variations in body weight among geese. Genome-wide association studies utilizing single nucleotide polymorphisms (SNPs) and presence-absence variation revealed significant genomic associations with various goose meat quality, reproductive, and body composition traits. For instance, a gene encoding the SVEP1 protein was linked to carcass oblique length, and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length. Notably, the pan-genome analysis revealed enrichment of variable genes in the "hair follicle maturation" Gene Ontology term, potentially linked to the selection of feather-related traits in geese. A gene presence-absence variation analysis suggested a reduced frequency of genes associated with "regulation of heart contraction" in domesticated geese compared to their wild counterparts. Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation. CONCLUSION This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits, thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese. Moreover, assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome, establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.
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Affiliation(s)
- Guangliang Gao
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Livestock and Poultry Multi-Omics Key Laboratory of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Hongmei Zhang
- Department of Cardiovascular Ultrasound and Non-Invasive Cardiology, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital,University of Electronic Science and Technology of China, Chengdu, 611731, China
- Ultrasound in Cardiac Electrophysiology and Biomechanics Key Laboratory of Sichuan Province, University of Electronic Science and Technology of China, Chengdu, 611731, China
| | - Jiangping Ni
- JiguangGene Biotechnology Co., Ltd., Nanjing, 210032, China
| | - Xianzhi Zhao
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Keshan Zhang
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China
| | - Jian Wang
- Jiangsu Agri-Animal Vocational College, Taizhou, 225300, China
| | - Xiangdong Kong
- JiguangGene Biotechnology Co., Ltd., Nanjing, 210032, China.
| | - Qigui Wang
- Chongqing Academy of Animal Science, Rongchang District, Chongqing, 402460, China.
- Chongqing Engineering Research Center of Goose Genetic Improvement, Rongchang District, Chongqing, 402460, China.
- Present Address: Poultry Science Institute, Chongqing Academy of Animal Science, No. 51 Changzhou Avenue, Rongchang District, Chongqing, 402460, P. R. China.
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4
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Dong H, Zhang J, Li Y, Ahmad HI, Li T, Liang Q, Li Y, Yang M, Han J. Liver Transcriptome Profiling Identifies Key Genes Related to Lipid Metabolism in Yili Geese. Animals (Basel) 2023; 13:3473. [PMID: 38003091 PMCID: PMC10668734 DOI: 10.3390/ani13223473] [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: 09/29/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The Yili goose is the only indigenous goose breed that originates from Anser anser in China, known for its adaptability, strong flying ability, and tender meat with a low body lipid content. The liver plays a crucial role in lipid and glucose metabolism, including the intake, secretion, transportation, and storage of fatty acids (FAs). In this study, RNA-sequencing (RNA-seq) technology was performed to analyze the liver differentially expressed genes of Yili geese and their hybrid geese to investigate differences in liver lipid and glucose metabolism. A total of 452 differentially expressed genes (Q-value < 0.05) were identified. Notably, in KEGG enrichment analysis, four pathways (Q-value < 0.05) were enriched to be associated with lipid and glucose metabolism, including the metabolic pathway, PI3K-Akt signaling pathway, glycolysis/gluconeogenesis, and steroid biosynthesis. This study provides insights into potential candidate genes and metabolic pathways that affect the liver lipid metabolism of Yili goose. These findings provide a better understanding of animal liver lipid deposition and metabolism.
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Affiliation(s)
- Huajiao Dong
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Jie Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Yingying Li
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Hafiz Ishfaq Ahmad
- Department of Animal Breeding and Genetics, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Tiantian Li
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Qianqian Liang
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Yan Li
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Min Yang
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
| | - Jilong Han
- College of Animal Science and Technology, Shihezi University, Shihezi 832061, China; (H.D.); (J.Z.); (Y.L.); (T.L.); (Q.L.); (Y.L.)
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5
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Lewis NL, Ware C, Griffin MJ. Edwardsiella tarda Isolated from a Kidney Mass in a Common Loon (Gavia immer). J Wildl Dis 2023; 59:804-806. [PMID: 37486877 DOI: 10.7589/jwd-d-22-00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/15/2023] [Indexed: 07/26/2023]
Abstract
A Common Loon (Gavia immer) was found recumbent at Island Beach State Park, New Jersey, US, and euthanized. Necropsy revealed a caseous mass in the kidney, from which bacteria were isolated and phenotypically and molecularly identified as Edwardsiella tarda.
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Affiliation(s)
- Nicole L Lewis
- Division of Fish and Wildlife, Office of Fish and Wildlife Health and Forensics, Hampton, New Jersey 08827, USA
| | - Cynthia Ware
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi 38776, USA
- Thad Cochran National Warmwater Aquaculture Center, Delta Research and Extension Center, Mississippi State University, Stoneville, Mississippi 38776, USA
| | - Matt J Griffin
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Stoneville, Mississippi 38776, USA
- Thad Cochran National Warmwater Aquaculture Center, Delta Research and Extension Center, Mississippi State University, Stoneville, Mississippi 38776, USA
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6
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Zhang X, Tang B, Li J, Ouyang Q, Hu S, Hu J, Liu H, Li L, He H, Wang J. Comparative transcriptome analysis reveals mechanisms of restriction feeding on lipid metabolism in ducks. Poult Sci 2023; 102:102963. [PMID: 37586191 PMCID: PMC10450974 DOI: 10.1016/j.psj.2023.102963] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/03/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023] Open
Abstract
Presently, excessive fat deposition is the main reason to limit the development of duck industry. In the production, the methods of restricted feeding (RF) were widely used to reduce the lipid deposition of ducks. The liver (L), abdominal adipose (AA), and subcutaneous adipose (SA) were the main tissues of lipid metabolism and deposition of ducks. However, the mechanisms of lipid metabolism and deposition of ducks under RF have not been fully clarified. In this study, in order to better understand the mechanisms of lipid metabolism and deposition in ducks under RF, a total of 120 male Nonghua ducks were randomly divided into a free feeding group (FF, n = 60) and RF group (RF, n = 60), then comparative transcriptomic analysis of L, AA, and SA between FF (n = 3) and RF (n = 3) ducks was performed at 56 d of age. Phenotypically, L, AA, and SA index of FF group was higher than that in RF group. There were 279, 390, and 557 differentially expressed genes (DEGs) in L, AA, and SA. Functional enrichment analysis revealed that ECM-receptor interaction and metabolic pathways were significantly enriched in L, AA, and SA. Lipid metabolism-related pathways including fatty acid metabolism, unsaturated fatty acid synthesis, and steroidogenesis were significantly enriched in AA and SA. Moreover, through integrated analysis weighted gene coexpression network (WGCNA) and protein-protein interaction network, 10 potential candidate genes involved in the ECM-receptor interaction and lipid metabolism pathways were identified, including 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), aldolase B (ALDOB), formimidoyltransferase cyclodeaminase(FTCD), phosphoenolpyruvate carboxykinase 1 (PCK1), tyrosine aminotransferase (TAT), stearoyl-CoA desaturase (SCD), squalene epoxidase (SQLE), phosphodiesterase 4B (PDE4B), choline kinase A (CHKA), and elongation of very-long-chain fatty acids-like 2 (ELOVL2), which could play a key role in lipid metabolism and deposition of ducks under RF. Our study reveals that the liver might regulate the lipid metabolism of abdominal adipose and subcutaneous adipose through ECM-receptor interaction and metabolic pathways (fatty acid metabolism, unsaturated fatty acid synthesis, and steroid synthesis), thus to reduce the lipid deposition of ducks under RF. These results provide novel insights into the avian lipid metabolism and will help better understand the underlying molecular mechanisms.
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Affiliation(s)
- Xin Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Bincheng Tang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jiangming Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Qingyuan Ouyang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu 611130, PR China.
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7
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Hu L, Long J, Lin Y, Gu Z, Su H, Dong X, Lin Z, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan S, Zhan X. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun 2022; 13:6413. [PMID: 36302769 PMCID: PMC9613686 DOI: 10.1038/s41467-022-34138-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 10/14/2022] [Indexed: 12/25/2022] Open
Abstract
The Qinghai-Tibet Plateau (QTP), possesses a climate as cold as that of the Arctic, and also presents uniquely low oxygen concentrations and intense ultraviolet (UV) radiation. QTP animals have adapted to these extreme conditions, but whether they obtained genetic variations from the Arctic during cold adaptation, and how genomic mutations in non-coding regions regulate gene expression under hypoxia and intense UV environment, remain largely unknown. Here, we assemble a high-quality saker falcon genome and resequence populations across Eurasia. We identify female-biased hybridization with Arctic gyrfalcons in the last glacial maximum, that endowed eastern sakers with alleles conveying larger body size and changes in fat metabolism, predisposing their QTP cold adaptation. We discover that QTP hypoxia and UV adaptations mainly involve independent changes in non-coding genomic variants. Our study highlights key roles of gene flow from Arctic relatives during QTP hypothermia adaptation, and cis-regulatory elements during hypoxic response and UV protection.
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Affiliation(s)
- Li Hu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Juan Long
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Yi Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhongru Gu
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Han Su
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuemin Dong
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhenzhen Lin
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Qian Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.20513.350000 0004 1789 9964Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Nyambayar Batbayar
- Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Batbayar Bold
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,Wildlife Science and Conservation Center, Union Building B-802, Ulaanbaatar, 14210 Mongolia
| | - Lucia Deutschová
- grid.455051.0Raptor Protection of Slovakia, Trhová 54, SK-841 01, Bratislava, Slovakia
| | - Sergey Ganusevich
- Wild Animal Rescue Centre, Krasnostudencheskiy pr., 21-45, Moscow, 125422 Russia
| | - Vasiliy Sokolov
- grid.426536.00000 0004 1760 306XInstitute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 202-8 Marta Street, Ekaterinburg, 620144 Russia
| | - Aleksandr Sokolov
- Arctic Research Station of the Institute of Plant and Animal Ecology, Ural Division Russian Academy of Sciences, 21 Zelenaya Gorka, Labytnangi, Yamalo-Nenetski District 629400 Russia
| | - Hardip R. Patel
- grid.1001.00000 0001 2180 7477The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601 Australia
| | - Paul D. Waters
- grid.1005.40000 0004 4902 0432School of Biotechnology and Biomolecular Science, Faculty of Science, UNSW Sydney, Sydney, NSW 2052 Australia
| | | | - Andrew Dixon
- Emirates Falconers’ Club, Al Mamoura Building (A), P.O. Box 47716, Muroor Road, Abu Dhabi, UAE ,grid.511767.30000 0004 5895 0922International Wildlife Consultants, P.O. Box 19, Carmarthen, SA33 5YL UK
| | - Shengkai Pan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiangjiang Zhan
- grid.9227.e0000000119573309Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China ,grid.9227.e0000000119573309Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, 100101 Beijing, China ,grid.410726.60000 0004 1797 8419University of the Chinese Academy of Sciences, 100049 Beijing, China ,grid.9227.e0000000119573309Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223 China
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8
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Xu P, Hong Y, Chen P, Wang X, Li S, Wang J, Meng F, Zhou Z, Shi D, Li Z, Cao S, Xiao Y. Regulation of the cecal microbiota community and the fatty liver deposition by the addition of brewers’ spent grain to feed of Landes geese. Front Microbiol 2022; 13:970563. [PMID: 36204629 PMCID: PMC9530188 DOI: 10.3389/fmicb.2022.970563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
The effects of brewers’ spent grain (BSG) diets on the fatty liver deposition and the cecal microbial community were investigated in a total of 320 healthy 5-day-old Landes geese. These geese were randomly and evenly divided into 4 groups each containing 8 replicates and 10 geese per replicate. These four groups of geese were fed from the rearing stage (days 5–60) to the overfeeding stage (days 61–90). The Landes geese in group C (control) were fed with basal diet (days 5–90); group B fed first with basal diet in the rearing stage and then basal diet + 4% BSG in the overfeeding stage; group F first with basal diet + 4% BSG during the rearing stage and then basal diet in the overfeeding stage; and group W with basal diet + 4% BSG (days 5–90). The results showed that during the rearing stage, the body weight (BW) and the average daily gain (ADG) of Landes geese were significantly increased in groups F and W, while during the overfeeding stage, the liver weights of groups W and B were significantly higher than that of group C. The taxonomic structure of the intestinal microbiota revealed that during the overfeeding period, the relative abundance of Bacteroides in group W was increased compared to group C, while the relative abundances of Escherichia–Shigella and prevotellaceae_Ga6A1_group were decreased. Results of the transcriptomics analysis showed that addition of BSG to Landes geese diets altered the expression of genes involved in PI3K-Akt signaling pathway and sphingolipid metabolism in the liver. Our study provided novel experimental evidence based on the cecal microbiota to support the application of BSG in the regulation of fatty liver deposition by modulating the gut microbiota in Landes geese.
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Affiliation(s)
- Ping Xu
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yuxuan Hong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Pinpin Chen
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Xu Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shijie Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Jie Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Fancong Meng
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zutao Zhou
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Deshi Shi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Zili Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Shengbo Cao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
| | - Yuncai Xiao
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Yuncai Xiao,
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Ouyang Q, Hu S, Tang B, Hu B, Hu J, He H, Li L, Wang J. Comparative Transcriptome Analysis Provides Novel Insights into the Effect of Lipid Metabolism on Laying of Geese. Animals (Basel) 2022; 12:ani12141775. [PMID: 35883321 PMCID: PMC9311715 DOI: 10.3390/ani12141775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The importance of lipid metabolism in the egg production of poultry has been widely reported. Meanwhile, geese have lower egg production and unique lipid metabolism patterns compared with chicken and duck. It is of great significance to further improve egg laying performance to explore the differences of fat metabolism and the molecular mechanisms in geese with different egg laying performance. This study compared the phenotypic differences of liver and abdominal fat, as well as the transcriptome level differences of liver, abdominal fat, and ovarian stroma among high-, low-, and no-egg production groups. The results reveal that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat. Abstract The lower egg production of geese (20~60 eggs per year) compared with chicken and duck limits the development of the industry, while the yolk weight and fatty liver susceptibility of geese was higher than that of other poultry. Therefore, the relationship between lipid metabolism and the laying performance of geese remains to be explored. Phenotypically, we observed that the liver fat content of the high-, low-, and no-egg production groups decreased in turn, while the abdominal fat weight increased in turn. For transcriptional regulation, the KEGG pathways related to lipid metabolism were enriched in all pairwise comparisons of abdominal fat and liver through functional analysis. However, some KEGG pathways related to inflammation and the circadian rhythm pathway were enriched by DEGs only in abdominal fat and the liver, respectively. The DEGs in ovarian stroma among different groups enriched some KEGG pathways related to ovarian steroidogenesis and cell adhesion. Our research reveals that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat. These results offer new insights into the regulation mechanisms of goose reproductive traits.
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10
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Lin X, Xing Y, Zhang Y, Dong B, Zhao M, Wang J, Geng T, Gong D, Zheng Y, Liu L. Glucose participates in the formation of goose fatty liver by regulating the expression of miRNA-33/CROT. Anim Sci J 2021; 92:e13674. [PMID: 34935255 DOI: 10.1111/asj.13674] [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: 09/02/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/27/2022]
Abstract
Glucose oversupply promotes formation of fatty liver, and fatty liver is usually accompanied with hyperglycemia. However, the mechanism by which glucose promotes formation of fatty liver is not very clear. In this study, fatty liver was successfully induced in Landes goose by 19 days of overfeeding with corn-based feed, the overfed geese had a significantly higher level of blood glucose than the normally fed geese (control group). In goose primary liver cells, high level of glucose promoted fat deposition and induced the expression of SREBF2(or SREBP2), a key regulator of lipid metabolism, and its intronic gene, miR-33. Moreover, overexpression of miRNA-33(miR-33) promotes lipid accumulation in goose primary liver cells. Consistently, miR-33 inhibitor suppressed glucose induced lipid accumulation in liver cells. Interestingly, the relative abundance of miR-33 in goose fatty liver was significantly higher than that in normal liver, while the relative mRNA and protein abundances of CROT, the target gene of miR-33, in goose fatty liver were significantly lower than those in goose normal liver. Taken together, these findings suggest that miR-33 mediates glucose promotion of lipid accumulation in goose primary liver cells, and that glucose participates in formation of goose fatty liver by regulating the expression of miR-33/CROT.
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Affiliation(s)
- Xiao Lin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ya Xing
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yihui Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Biao Dong
- Department of Animal Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, China
| | - Minmeng Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jian Wang
- Department of Animal Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, China
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Yun Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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11
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A Prognostic Model for Brain Glioma Patients Based on 9 Signature Glycolytic Genes. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6680066. [PMID: 34222480 PMCID: PMC8225435 DOI: 10.1155/2021/6680066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/16/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022]
Abstract
Objective To screen glycolytic genes linked to the glioma prognosis and construct the prognostic model. Methods The relevant data of glioma were downloaded from TCGA and GTEx databases. GSEA of glycolysis-related pathways was carried out, and enriched differential genes were extracted. Screening out prognostic-related genes with conspicuous significance and construction of the prognostic model were conducted by multivariate Cox regression analysis and Lasso regression analysis. The model was evaluated, and cBioPortal was used to analyze the mutation of the model gene. The expression of the model gene in tumor and normal colon tissue was analyzed. The model was used to evaluate the prognosis of patients in different groups to verify the applicability of the model. Results 339 differentially glycolytic-related genes were enriched in REACTOME_GLYCOLYSIS, GLYCOLYTIC_PROCESS, HALLMARK_GLYCOLYSIS, and other pathways. We obtained 9 key prognostic genes and constructed the prognostic evaluation model. The 3-year AUC values of the ROC curve display model are greater than 0.75, which indicates that the accuracy of the model is good. The relation of age and risk score to prognosis is shown by univariate and multivariate Cox analysis. The expression of SRD5A3, MDH2, and B3GAT3 genes was significantly upregulated in the tumor tissues, while the HDAC4 and G6PC2 genes were downregulated. The mutation rate of MDH2 and HDAC4 genes was the highest. This model could effectively distinguish the risk of poor prognosis of patients in any age stage. Conclusion The prognostic assessment models based on glycolysis-related nine-gene signature could accurately predict the prognosis of patients with GBM.
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12
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Huo W, Weng K, Gu T, Zhang Y, Zhang Y, Xu Q, Chen G. Identification and characterization of the adipogenesis in intramuscular and subcutaneous adipocytes of the goose ( Anser cygnoides). Anim Biotechnol 2021; 33:1181-1189. [PMID: 33749492 DOI: 10.1080/10495398.2021.1880420] [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
Chinese geese are domesticated from wild swan (Anser cygnoides), which have maintained a strong capacity of fat deposit. Fat mainly distributes subcutaneous, abdominal, intermuscular or intramuscular in poultry, and they display some special physiological and biochemical characteristics in different parts. This study aimed to characterize the adipogenesis in intramuscular (IM) and subcutaneous (SC) adipocytes of the goose. Here, IM and SC preadipocytes were isolated from the 26-day-old Yangzhou goose embryos, and subsequently induced them to differentiate into mature adipocytes. The results showed that SC preadipocytes grew a little faster than IM preadipocytes during the logarithmic multiplication phase (p < 0.05). Meanwhile, SC adipocytes accumulated more lipid than IM adipocytes during the differentiation process in vitro (p < 0.01). In addition, the expression level of key genes involved in adipogenesis, including peroxisome proliferator activated receptor γ/α (PPARγ/α), CCAAT/enhancer binding protein-α/β (C/EBPα/β), adipocyte fatty acid binding protein 4 (FABP4), and lipoprotein lipase (LPL) were detected. PPARγ, C/EBPα, FABP4, and LPL, were predominantly expressed in SC adipocytes, whereas C/EBPβ was highly expressed in IM adipocytes. Taken together, these results demonstrated that SC preadipocytes tended to grow faster and accumulate more lipid than IM adipocytes, and show greater potential for adipogenesis.
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Affiliation(s)
- Weiran Huo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kaiqi Weng
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tiantian Gu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yang Zhang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qi Xu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, China
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13
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Liu T, Xing Y, Fan X, Chen Z, Zhao C, Liu L, Zhao M, Hu X, Dong B, Wang J, Cui H, Gong D, Geng T. Fasting and overfeeding affect the expression of the immunity- or inflammation-related genes in the liver of poultry via endogenous retrovirus. Poult Sci 2021; 100:973-981. [PMID: 33518151 PMCID: PMC7858184 DOI: 10.1016/j.psj.2020.11.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 11/06/2020] [Accepted: 11/22/2020] [Indexed: 12/19/2022] Open
Abstract
It is known that nutrition and immunity are connected, but the mechanism is not very clear. Endogenous retroviruses (ERV) account for 8 to 10% of the human and mouse genomes and play an important role in some biological processes of animals. Recent studies indicate that the activation of ERV can affect the expression of the immunity- or inflammation-related genes, and the activities of ERV are subjected to regulation of many factors including nutritional factors. Therefore, we hypothesize that nutritional status can affect the expression of the immunity- or inflammation-related genes via ERV. To verify this hypothesis, the nutritional status of animals was altered by fasting or overfeeding, and the expression of intact ERV (ERVK18P, ERVK25P) and immunity- or inflammation-related genes (DDX41, IFIH1, IFNG, IRF7, STAT3) in the liver was determined by quantitative PCR, followed by overexpressing ERVK25P in goose primary hepatocytes and determining the expression of the immunity- or inflammation-related genes. The data showed that compared with the control group (no fasting), the expression of ERV and the immunity- or inflammation-related genes was increased in the liver of the fasted chickens but decreased in the liver of the fasted geese. Moreover, compared with the control group (routinely fed), the expression of ERV and the immunity- or inflammation-related genes was increased in the liver of the overfed geese. In addition, overexpression of ERVK25P in goose primary hepatocytes can induce the expression of the immunity- or inflammation-related genes. In conclusion, these findings suggest that ERV mediate the effects of fasting and overfeeding on the expression of the immunity- or inflammation-related genes, the mediation varied with poultry species, and ERV and the immunity- or inflammation-related genes may be involved in the development of goose fatty liver. This study provides a potential mechanism for the connection between nutrition and immunity.
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Affiliation(s)
- Tongjun Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Ya Xing
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xue Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhenzhen Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Minmeng Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xuming Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Biao Dong
- Department of Animal Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Jian Wang
- Department of Animal Science and Technology, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China
| | - Hengmi Cui
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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14
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Li Y, Gao G, Lin Y, Hu S, Luo Y, Wang G, Jin L, Wang Q, Wang J, Tang Q, Li M. Pacific Biosciences assembly with Hi-C mapping generates an improved, chromosome-level goose genome. Gigascience 2020; 9:giaa114. [PMID: 33099628 PMCID: PMC7585555 DOI: 10.1093/gigascience/giaa114] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 08/12/2020] [Accepted: 09/23/2020] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The domestic goose is an economically important and scientifically valuable waterfowl; however, a lack of high-quality genomic data has hindered research concerning its genome, genetics, and breeding. As domestic geese breeds derive from both the swan goose (Anser cygnoides) and the graylag goose (Anser anser), we selected a female Tianfu goose for genome sequencing. We generated a chromosome-level goose genome assembly by adopting a hybrid de novo assembly approach that combined Pacific Biosciences single-molecule real-time sequencing, high-throughput chromatin conformation capture mapping, and Illumina short-read sequencing. FINDINGS We generated a 1.11-Gb goose genome with contig and scaffold N50 values of 1.85 and 33.12 Mb, respectively. The assembly contains 39 pseudo-chromosomes (2n = 78) accounting for ∼88.36% of the goose genome. Compared with previous goose assemblies, our assembly has more continuity, completeness, and accuracy; the annotation of core eukaryotic genes and universal single-copy orthologs has also been improved. We have identified 17,568 protein-coding genes and a repeat content of 8.67% (96.57 Mb) in this genome assembly. We also explored the spatial organization of chromatin and gene expression in the goose liver tissues, in terms of inter-pseudo-chromosomal interaction patterns, compartments, topologically associating domains, and promoter-enhancer interactions. CONCLUSIONS We present the first chromosome-level assembly of the goose genome. This will be a valuable resource for future genetic and genomic studies on geese.
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Affiliation(s)
- Yan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Guangliang Gao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
- Institute of Poultry Science, Chongqing Academy of Animal Science, No. 51 Changlong Avenue, Rongchang District, Chongqing 402460, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Yi Luo
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Guosong Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, Texas 77843, USA
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Qigui Wang
- Institute of Poultry Science, Chongqing Academy of Animal Science, No. 51 Changlong Avenue, Rongchang District, Chongqing 402460, China
| | - Jiwen Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, No.211 Huimin Road, Wenjiang District, Chengdu 611130, China
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15
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Yang Y, Wang H, Li G, Liu Y, Wang C, He D. Exploring the genetic basis of fatty liver development in geese. Sci Rep 2020; 10:14279. [PMID: 32868783 PMCID: PMC7459336 DOI: 10.1038/s41598-020-71210-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/13/2020] [Indexed: 12/22/2022] Open
Abstract
Although geese possess an adaptive physiological capacity for lipid storage, few candidate genes contributing to this ability are characterised. By comparing the genomes of individuals with extremely high and low fatty liver weights (FLW), candidate genes were identified, including ARAP2, GABRE, and IL6. Single-nucleotide polymorphisms in or near these genes were significantly (p < 0.05) associated with carcass traits (FLW) and biochemical indexes (very-low-density lipoprotein and N-terminal procollagen III), suggesting contribution to trait variation. A common variant at the 5'-end of LCORL explained ~ 18% and ~ 26% of the phenotypic variance in body weight with/without overfeeding and had significant effects on FLW (p < 0.01). ZFF36L1, ARHGEF1 and IQCJ, involved in bile acid metabolism, blood pressure, and lipid concentration modulation, were also identified. The presence of highly divergent haplotypes within these genes suggested involvement in protection against negative effects from excessive lipids in the liver or circulatory system. Based on this and transcriptomic data, we concluded that geese hepatosteatosis results from severe imbalance between lipid accumulation and secretion, comparable to human non-alcohol fatty liver disease but involving other genes. Our results provided valuable insights into the genesis of geese fatty liver and detected potential target genes for treatment of lipid-related diseases.
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Affiliation(s)
- Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, People's Republic of China.
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden.
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, People's Republic of China
| | - Guangquan Li
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, People's Republic of China
| | - Yi Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, People's Republic of China
| | - Cui Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, People's Republic of China
| | - Daqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, People's Republic of China.
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