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Chacko Kaitholil SR, Mooney MH, Aubry A, Rezwan F, Shirali M. Insights into the influence of diet and genetics on feed efficiency and meat production in sheep. Anim Genet 2024; 55:20-46. [PMID: 38112204 PMCID: PMC10952161 DOI: 10.1111/age.13383] [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: 07/03/2023] [Revised: 10/06/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023]
Abstract
Feed costs and carcass yields affect the profitability and sustainability of sheep production. Therefore, it is crucial to select animals with a higher feed efficiency and high-quality meat production. This study focuses on the impact of dietary and genetic factors on production traits such as feed efficiency, carcass quality, and meat quality. Diets promote optimal sheep growth and development and provide sufficient protein can lead to higher-quality meat. However, establishing an optimized production system requires careful consideration and balance of dietary parameters. This includes ensuring adequate protein intake and feeding diets with higher intestinal absorption rates to enhance nutrient absorption in the gut. The study identifies specific genes, such as Callipyge, Calpastatin, and Myostatin, and the presence of causal mutations in these genes, as factors influencing animal growth rates, feed efficiency, and meat fatty acid profiles. Additionally, variants of other reported genes, including PIGY, UCP1, MEF2B, TNNC2, FABP4, SCD, FASN, ADCY8, ME1, CA1, GLIS1, IL1RAPL1, SOX5, SOX6, and IGF1, show potential as markers for sheep selection. A meta-analysis of reported heritability estimates reveals that residual feed intake (0.27 ± 0.07), hot carcass weight (0.26 ± 0.05), dressing percentage (0.23 ± 0.05), and intramuscular fat content (0.45 ± 0.04) are moderately to highly heritable traits. This suggests that these traits are less influenced by environmental factors and could be improved through genetic selection. Additionally, positive genetic correlations exist between body weight and hot carcass weight (0.91 ± 0.06), dressing percentage (0.35 ± 0.15), and shear force (0.27 ± 0.24), indicating that selecting for higher body weight could lead to favorable changes in carcass quality, and meat quality.
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Affiliation(s)
- Steffimol Rose Chacko Kaitholil
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
- Agri‐Food and Biosciences InstituteHillsboroughUK
| | - Mark H. Mooney
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
| | | | - Faisal Rezwan
- Department of Computer ScienceAberystwyth UniversityAberystwythUK
| | - Masoud Shirali
- Institute for Global Food Security, School of Biological SciencesQueen's University BelfastBelfastUK
- Agri‐Food and Biosciences InstituteHillsboroughUK
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Hosseini SF, Bakhtiarizadeh MR, Salehi A. Meta-analysis of RNA-Seq datasets highlights novel genes/pathways involved in fat deposition in fat-tail of sheep. Front Vet Sci 2023; 10:1159921. [PMID: 37252399 PMCID: PMC10213422 DOI: 10.3389/fvets.2023.1159921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/11/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Fat-tail in sheep is considered as an important energy reservoir to provide energy as a survival buffer during harsh challenges. However, fat-tail is losing its importance in modern sheep industry systems and thin-tailed breeds are more desirable. Using comparative transcriptome analysis to compare fat-tail tissue between fat- and thin-tailed sheep breeds provides a valuable approach to study the complex genetic factors associated with fat-tail development. However, transcriptomic studies often suffer from issues with reproducibility, which can be improved by integrating multiple studies based on a meta-analysis. Methods Hence, for the first time, an RNA-Seq meta-analysis on sheep fat-tail transcriptomes was performed using six publicly available datasets. Results and discussion A total of 500 genes (221 up-regulated, 279 down-regulated) were identified as differentially expressed genes (DEGs). A jackknife sensitivity analysis confirmed the robustness of the DEGs. Moreover, QTL and functional enrichment analysis reinforced the importance of the DEGs in the underlying molecular mechanisms of fat deposition. Protein-protein interactions (PPIs) network analysis revealed the functional interactions among the DEGs and the subsequent sub-network analysis led to identify six functional sub-networks. According to the results of the network analysis, down-regulated DEGs in green and pink sub-networks (like collagen subunits IV, V, and VI, integrins 1 and 2, SCD, SCD5, ELOVL6, ACLY, SLC27A2, and LPIN1) may impair lipolysis or fatty acid oxidation and cause fat accumulation in tail. On the other hand, up-regulated DEGs, especially those are presented in green and pink sub-networks (like IL6, RBP4, LEPR, PAI-1, EPHX1, HSD11B1, and FMO2), might contribute to a network controlling fat accumulation in the tail of sheep breed through mediating adipogenesis and fatty acid biosynthesis. Our results highlighted a set of known and novel genes/pathways associated with fat-tail development, which could improve the understanding of molecular mechanisms behind fat deposition in sheep fat-tail.
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RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue. Metabolites 2022; 12:metabo12100996. [PMID: 36295898 PMCID: PMC9607389 DOI: 10.3390/metabo12100996] [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: 09/06/2022] [Revised: 10/03/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
During the early postnatal period, lambs have the ability to thermoregulate body temperature via non-shivering thermogenesis through brown adipose tissue (BAT), which soon after birth begins to transform into white adipose tissue. An RNA seq approach was used to characterize the transcriptome of BAT and thyroid tissue in newborn lambs exposed to cold conditions. Fifteen newborn Romney lambs were selected and divided into three groups: group 1 (n = 3) was a control, and groups 2 and 3 (n = 6 each) were kept indoors for two days at an ambient temperature (20–22 °C) or at a cold temperature (4 °C), respectively. Sequencing was performed using a paired-end strategy through the BGISEQ-500 platform, followed by the identification of differentially expressed genes using DESeq2 and an enrichment analysis by g:Profiler. This study provides an in-depth expression network of the main characters involved in the thermogenesis and fat-whitening mechanisms that take place in the newborn lamb. Data revealed no significant differential expression of key thermogenic factors such as uncoupling protein 1, suggesting that the heat production peak under cold exposure might occur so rapidly and in such an immediate way that it may seem undetectable in BAT by day three of life. Moreover, these changes in expression might indicate the start of the whitening process of the adipose tissue, concluding the non-shivering thermogenesis period.
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Cavalieri R, Hazebroek MK, Cotrim CA, Lee Y, Kunji ERS, Jastroch M, Keipert S, Crichton PG. Activating ligands of Uncoupling protein 1 identified by rapid membrane protein thermostability shift analysis. Mol Metab 2022; 62:101526. [PMID: 35691529 PMCID: PMC9243162 DOI: 10.1016/j.molmet.2022.101526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 06/05/2022] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE Uncoupling protein 1 (UCP1) catalyses mitochondrial proton leak in brown adipose tissue to facilitate nutrient oxidation for heat production, and may combat metabolic disease if activated in humans. During the adrenergic stimulation of brown adipocytes, free fatty acids generated from lipolysis activate UCP1 via an unclear interaction. Here, we set out to characterise activator binding to purified UCP1 to clarify the activation process, discern novel activators and the potential to target UCP1. METHODS We assessed ligand binding to purified UCP1 by protein thermostability shift analysis, which unlike many conventional approaches can inform on the binding of hydrophobic ligands to membrane proteins. A detailed activator interaction analysis and screening approach was carried out, supported by investigations of UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1 expression-controlled cell lines. RESULTS We reveal that fatty acids and other activators influence UCP1 through a specific destabilising interaction, behaving as transport substrates that shift the protein to a less stable conformation of a transport cycle. Through the detection of specific stability shifts in screens, we identify novel activators, including the over-the-counter drug ibuprofen, where ligand analysis indicates that UCP1 has a relatively wide structural specificity for interacting molecules. Ibuprofen successfully induced UCP1 activity in liposomes, isolated brown fat mitochondria and UCP1-expressing HEK293 cells but not in cultured brown adipocytes, suggesting drug delivery differs in each cell type. CONCLUSIONS These findings clarify the nature of the activator-UCP1 interaction and demonstrate that the targeting of UCP1 in cells by approved drugs is in principle achievable as a therapeutic avenue, but requires variants with more effective delivery in brown adipocytes.
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Affiliation(s)
- Riccardo Cavalieri
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Marlou Klein Hazebroek
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Camila A Cotrim
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Yang Lee
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Keith Peters Building, CB2 0XY, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council, Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Keith Peters Building, CB2 0XY, United Kingdom
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Susanne Keipert
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Paul G Crichton
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom.
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Zhang W, Xu M, Wang J, Wang S, Wang X, Yang J, Gao L, Gan S. Comparative Transcriptome Analysis of Key Genes and Pathways Activated in Response to Fat Deposition in Two Sheep Breeds With Distinct Tail Phenotype. Front Genet 2021; 12:639030. [PMID: 33897762 PMCID: PMC8060577 DOI: 10.3389/fgene.2021.639030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 03/08/2021] [Indexed: 01/21/2023] Open
Abstract
Fat tail in sheep presents a valuable energy reserve that has historically facilitated adaptation to harsh environments. However, in modern intensive and semi-intensive sheep industry systems, breeds with leaner tails are more desirable. In the present study, RNA sequencing (RNA-Seq) was applied to determine the transcriptome profiles of tail fat tissues in two Chinese sheep breeds, fat-rumped Altay sheep and thin-tailed Xinjiang fine wool (XFW) sheep, with extreme fat tail phenotype difference. Then the differentially expressed genes (DEGs) and their sequence variations were further analyzed. In total, 21,527 genes were detected, among which 3,965 displayed significant expression variations in tail fat tissues of the two sheep breeds (P < 0.05), including 707 upregulated and 3,258 downregulated genes. Gene Ontology (GO) analysis disclosed that 198 DEGs were related to fat metabolism. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, the majority of DEGs were significantly enriched in "adipocytokine signaling," "PPAR signaling," and "metabolic pathways" (P < 0.05); moreover, some genes were involved in multiple pathways. Among the 198 DEGs, 22 genes were markedly up- or downregulated in tail fat tissue of Altay sheep, indicating that these genes might be closely related to the fat tail trait of this breed. A total of 41,724 and 42,193 SNPs were detected in the transcriptomic data of tail fat tissues obtained from Altay and XFW sheep, respectively. The distribution of seven SNPs in the coding regions of the 22 candidate genes was further investigated in populations of three sheep breeds with distinct tail phenotypes. In particular, the g.18167532T/C (Oar_v3.1) mutation of the ATP-binding cassette transporter A1 (ABCA1) gene and g.57036072G/T (Oar_v3.1) mutation of the solute carrier family 27 member 2 (SLC27A2) gene showed significantly different distributions and were closely associated with tail phenotype (P < 0.05). The present study provides transcriptomic evidence explaining the differences in fat- and thin-tailed sheep breeds and reveals numerous DEGs and SNPs associated with tail phenotype. Our data provide a valuable theoretical basis for selection of lean-tailed sheep breeds.
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Affiliation(s)
- Wei Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
- Xinjiang Agricultural Vocational Technical College, Changji, China
| | - Mengsi Xu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Juanjuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Shiyin Wang
- Xinjiang Agricultural Vocational Technical College, Changji, China
| | - Xinhua Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Jingquan Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Lei Gao
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, China
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Regulatory Roles of SREBF1 and SREBF2 in Lipid Metabolism and Deposition in Two Chinese Representative Fat-Tailed Sheep Breeds. Animals (Basel) 2020; 10:ani10081317. [PMID: 32751718 PMCID: PMC7460493 DOI: 10.3390/ani10081317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 11/22/2022] Open
Abstract
Simple Summary Sterol regulatory element binding proteins (SREBPs) play the crucial role in regulating the cholesterol and fatty acid metabolism. However, it is unclear whether SREBPs are involved in the regulation of lipid metabolism in fat-tailed sheep. This study reveals the expression profiles of SREBF1 and SREBF2 in liver and adipose tissues of two Chinese representative fat-tailed sheep breeds, and provides a new insight for the regulatory role of SREBP1 and SREBP2 in fat metabolism and deposition in fat-tailed sheep. Abstract Sterol regulatory element binding proteins (SREBPs) can regulate the lipid homeostasis by regulating its target genes, which are crucial for the cholesterol and fatty acid metabolism. However, the transcriptional regulation role of SREBPs in fat-tailed sheep is unclear. In this study, two Chinese representative breeds of total 80 fat-tailed sheep were employed, serum triglyceride, total cholesterol (TC), non-esterified fatty acid (NEFA), high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and mRNA expressions of SREBF1 and SREBF2 in seven different adipose tissues and liver were examined in sheep at the ages of 4, 6, 8, 10, and 12 months, respectively. The subcellular localization and function of SREBP1/2 were predicted through bioinformatics approaches. The results demonstrated that serum TC and NEFA levels among breeds were significantly different, and most serum indices were dynamically altered in an age-dependent manner. The mRNA expression profiling of SREBF1 and SREBF2 are breed-specific with temporal and spatial expressions differences. Further analysis shows that SREBF1/2 transcriptional levels and tail traits are closely related. All investigations simplify that SREBF1/2 play a crucial role in lipid metabolism and deposition during growth and development of the fat-tailed sheep, which also provides a novel insight for revealing the genetic mechanism of different tail type and meat quality.
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Suárez-Vega A, Arranz JJ, Pérez V, de la Fuente LF, Mateo J, Gutiérrez-Gil B. Early adipose deposits in sheep: comparative analysis of the perirenal fat transcriptome of Assaf and Churra suckling lambs. Anim Genet 2018; 49:605-617. [PMID: 30311245 DOI: 10.1111/age.12725] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2018] [Indexed: 11/28/2022]
Abstract
Adipose deposits influence the quality of ruminant carcasses, and in suckling lambs, internal types of adipose deposits represent a notable proportion of total fat. The aim of this study was to perform a comparative analysis of the perirenal fat transcriptomes of suckling lambs from two breeds with different growth and carcass characteristics. The perirenal fat tissue from 14 suckling lambs (Assaf, n = 8; Churra, n = 6) was used for the RNA-seq analysis. The functional enrichment analysis of the 670 highly expressed genes (>150 fragments per kilobase of exon per million fragments mapped) in the perirenal fat transcriptome of both breeds revealed that the majority of these genes were involved in energy processes. The expression of the UCP1 gene, a classical biomarker of brown fat, and the presence of multilocular adipocytes in the two breeds supported the presence of brown fat at the transition stage towards white fat tissue. The differential expression analysis performed identified 373 differentially expressed genes (DEGs) between the two compared breeds. Brown/white fat gene biomarkers were not included in the list of DEGs. In Assaf lambs, DEGs were enriched in Gene Ontology (GO) biological processes related to fatty-acid oxidation, whereas in Churra lambs, the majority of the significantly enriched GO terms were related to cholesterol synthesis, which suggests that upregulated DEGs in Assaf lambs are implicated in fat burning, whereas the Churra upregulated DEGs are linked to fat accumulation. These results can help to increase knowledge of the genes controlling early fat deposition in ruminants and shed light on fundamental aspects of adipose tissue growth.
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Affiliation(s)
- A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - V Pérez
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - L F de la Fuente
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - J Mateo
- Departamento de Higiene y Tecnología de los Alimentos, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
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Li B, Qiao L, An L, Wang W, Liu J, Ren Y, Pan Y, Jing J, Liu W. Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition. BMC Genomics 2018; 19:338. [PMID: 29739312 PMCID: PMC5941690 DOI: 10.1186/s12864-018-4747-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/30/2018] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. RESULTS Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5, and CD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene, and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that PPAR signaling pathway and ECM-receptor interaction were specifically enriched. Four genes, namely LOC101102230, PLTP, C1QTNF7, and OLR1 were up-regulated and two genes, SCD and UCP-1, were down-regulated in all the tested tissues of STH. Among the genes involved in ECM-receptor interaction, the genes encoding collagens, laminins, and integrins were quite different depending on the depots or the breeds. In STH, genes such as LAMB3, RELN, TNXB, and ITGA8, were identified to be up regulated and LAMB4 was observed to be down regulated. CONCLUSIONS This study unravels the complex transcriptome profiles in sheep fat tissues, highlighting the candidate genes involved in fat deposition. Further studies are needed to investigate the roles of the candidate genes in fat deposition and in determining the meat quality of sheep.
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Affiliation(s)
- Baojun Li
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Liying Qiao
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Lixia An
- Shanxi Agricultural University, College of Information, Taigu, 030800, China
| | - Weiwei Wang
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Jianhua Liu
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Youshe Ren
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Yangyang Pan
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Jiongjie Jing
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China
| | - Wenzhong Liu
- Shanxi Agricultural University, College of Veterinary and Animal Science, Taigu, 030801, China.
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Sequence and Haplotypes Variation of the Ovine Uncoupling Protein-1 Gene (UCP1) and Their Association with Growth and Carcass Traits in New Zealand Romney Lambs. Genes (Basel) 2018; 9:genes9040189. [PMID: 29601527 PMCID: PMC5924531 DOI: 10.3390/genes9040189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/12/2018] [Accepted: 03/28/2018] [Indexed: 11/21/2022] Open
Abstract
Uncoupling protein-1 gene (UCP1) plays an important role in the regulation of thermogenesis, energy expenditure, and protection against oxidative stress. In this study, six separate UCP1 regions: region-1 and region-2 (two parts of the promoter), region-3 and region-4 (two parts of intron 1), region-5 (spanning part of intron 5 and part of exon 6), and region-6 (spanning part of exon 6 and part of the 3′-UTR) from a variety of sheep breeds, were analysed using polymerase chain reaction-single-stranded conformational polymorphism (PCR-SSCP) analyses. In total, 30 single nucleotide polymorphisms (SNPs) were detected. Of these, 14 were located in the promoter, eight were found in intron 1, six were found in intron 5, and one was found in the 3′-UTR. One substitution in exon 6 (c.910A/G) would putatively result in an amino acid change (p.Thr304Ala). Twenty-eight novel SNPs and nine new haplotypes spanning region-2 to region-5 were identified. Of these nine haplotypes, five were common (B2-A5, C2-A5, C2-C5, A2-A5, and A2-B5) and four were rare (C2-B5, A2-C5, B2-C5, and B2-B5) in the sheep investigated. Of the five common haplotypes found in 314 New Zealand Romney sheep for which growth and carcass trait data were available, the presence of A2-B5 was associated with decreased hot carcass weight (HCW) and loin lean-meat yield (p = 0.006, p = 0.032, respectively), and the presence of C2-C5 was associated with a decreased proportion of leg lean-meat yield (p = 0.047) in the carcasses. No associations were found with growth traits. These results confirm that ovine UCP1 is a variable gene and may have value as a genetic marker for sheep breeding.
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Abstract
Uncoupling protein-1 (UCP1) plays a role in the regulation of body temperature, metabolic rate and energy expenditure in animals. While variation in UCP1 and its phenotypic effect has been investigated in humans and sheep, little is known about this gene in cattle. In this study, four regions of bovine UCP1 were investigated in 612 Holstein-Friesian × Jersey (HF × J) dairy cows using polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) analyses. In the four regions of the gene analysed, a total of 13 SNPs were detected. Three sequences (a, b and c) were found in Region-2 and three sequences (A, B and C) were found in Region-4, and these were assembled into three (a-B, b-B and c-A) common and three (b-C, c-B and c-C) rare haplotypes. Of the three common haplotypes, b-B and c-A were associated (P < 0·007 and P < 0·043, respectively) with increased milk yield and tended to be associated (P < 0·085 and P < 0·070, respectively) with decreased fat percentage. Cows with genotype b-B/a-B produced more milk (P < 0·004), but with a lower percentage of fat (P < 0·035) and protein (P < 0·038) than cows with genotype a-B/a-B. Cows of genotype a-B/c-A had milk of low fat percentage (P < 0·017), but tended to produce more milk (P < 0·059) than cows of genotype a-B/a-B. This suggests that UCP1 affects milk yield, milk fat percentage and milk protein percentage.
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13
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Arfuso F, Rizzo M, Giannetto C, Giudice E, Fazio F, Piccione G. Age-related changes of serum mitochondrial uncoupling 1, rumen and rectal temperature in goats. J Therm Biol 2016; 59:47-51. [PMID: 27264887 DOI: 10.1016/j.jtherbio.2016.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/07/2016] [Indexed: 10/21/2022]
Abstract
Thermoregulatory processes are induced not only by exposure to cold or heat but also by a variety of physiological situations including age, fasting and food intake that result in changes in body temperature. The aim of the present study was to evaluate the differences in serum mitochondrial uncoupling protein 1 (UCP1), rumen temperature (TRUMEN) and rectal temperature (TRECTAL) values between adult and kids goats. Ten adult male Maltese goats aged 3-5 years old (Group A) and 30 male kids, raised for meat, were enrolled in this study. The kids were equally divided into 3 groups according to their age: Group B included kids aged 3 months, Group C included kids aged 4 months and Group D included kids aged 5 months. Blood samples and measurements of TRUMEN and TRECTAL were obtained from each animal. One-way repeated measures analysis of variance (ANOVA) was applied to evaluate the effect of age on the studied parameters. Statistically significant higher serum UCP1 levels (P<0.001) were found in Group A as compared to Groups B, C and D. Higher TRUMEN values (P<0.001) were found in Group A than in Groups B, C and D, and in Group B than in Groups C and D. Group A showed lower TRECTAL values (P<0.001) than Groups B, C and D. The Pearson's Correlation test was applied to assess significant relationship among studied parameters showing a statistically significant negative correlation between the values of TRECTAL and serum UCP1 in all studied Groups (P<0.001). These results indicate that goats have good control of body temperature suggesting that further details about the thermogenic capacity and the function of UCP1 in kids and adult goats are worth exploring.
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Affiliation(s)
- Francesca Arfuso
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Maria Rizzo
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Claudia Giannetto
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Elisabetta Giudice
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, 98166 S. Agata-Messina, Italy
| | - Francesco Fazio
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy
| | - Giuseppe Piccione
- Department of Veterinary Sciences, University of Messina, Polo Universitario dell'Annunziata, 98168 Messina, Italy.
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Jiao XL, Jing JJ, Qiao LY, Liu JH, Li LA, Zhang J, Jia XL, Liu WZ. Ontogenetic Expression of Lpin2 and Lpin3 Genes and Their Associations with Traits in Two Breeds of Chinese Fat-tailed Sheep. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2016; 29:333-42. [PMID: 26950863 PMCID: PMC4811783 DOI: 10.5713/ajas.15.0467] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/17/2015] [Accepted: 09/10/2015] [Indexed: 12/14/2022]
Abstract
Lipins play dual function in lipid metabolism by serving as phosphatidate phosphatase and transcriptional co-regulators of gene expression. Mammalian lipin proteins consist of lipin1, lipin2, and lipin3 and are encoded by their respective genes Lpin1, Lpin2, and Lpin3. To date, most studies are concerned with Lpin1, only a few have addressed Lpin2 and Lpin3. Ontogenetic expression of Lpin2 and Lpin3 and their associations with traits would help to explore their molecular and physiological functions in sheep. In this study, 48 animals with an equal number of males and females each for both breeds of fat-tailed sheep such as Guangling Large Tailed (GLT) and Small Tailed Han (STH) were chosen to evaluate the ontogenetic expression of Lpin2 and Lpin3 from eight different tissues and months of age by quantitative real-time polymerase chain reaction (PCR). Associations between gene expression and slaughter and tail traits were also analyzed. The results showed that Lpin2 mRNA was highly expressed in perirenal and tail fats, and was also substantially expressed in liver, kidney, reproductive organs (testis and ovary), with the lowest levels in small intestine and femoral biceps. Lpin3 mRNA was prominently expressed in liver and small intestine, and was also expressed at high levels in kidney, perirenal and tail fats as well as reproductive organs (testis and ovary), with the lowest level in femoral biceps. Global expression of Lpin2 and Lpin3 in GLT both were significantly higher than those in STH. Spatiotemporal expression showed that the highest levels of Lpin2 expression occurred at 10 months of age in two breeds of sheep, with the lowest expression at 2 months of age in STH and at 8 months of age in GLT. The greatest levels of Lpin3 expression occurred at 4 months of age in STH and at 10 months of age in GLT, with the lowest expression at 12 months of age in STH and at 8 months of age in GLT. Breed and age significantly influenced the tissue expression patterns of Lpin2 and Lpin3, respectively, and sex significantly influenced the spatiotemporal expression patterns of Lpin3. Meanwhile, Lpin2 and Lpin3 mRNA expression both showed significant correlations with slaughter and tail traits, and the associations appear to be related with the ontogenetic expression as well as the potential functions of lipin2 and lipin3 in sheep.
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Affiliation(s)
- Xiao-Li Jiao
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China ; College of Animal Science and Veterinary medicine, Tianjin Agricultural University, Tianjin 300-384, China
| | - Jiong-Jie Jing
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China
| | - Li-Ying Qiao
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China
| | - Jian-Hua Liu
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China
| | - Liu-An Li
- College of Animal Science and Veterinary medicine, Tianjin Agricultural University, Tianjin 300-384, China
| | - Jing Zhang
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China
| | - Xia-Li Jia
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China
| | - Wen-Zhong Liu
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030-801, China
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15
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Zhang J, Jing JJ, Jia XL, Qiao LY, Liu JH, Liang C, Liu WZ. mRNA Expression of Ovine Angiopoietin-like Protein 4 Gene in Adipose Tissues. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 29:615-23. [PMID: 26954186 PMCID: PMC4852221 DOI: 10.5713/ajas.15.0090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 04/06/2015] [Accepted: 08/02/2015] [Indexed: 11/30/2022]
Abstract
Angiopoietin-like protein 4 (ANGPTL4) is involved in a variety of functions, including lipoprotein metabolism and angiogenesis. To reveal the role of ANGPTL4 in fat metabolism of sheep, ovine ANGPTL4 mRNA expression was analyzed in seven adipose tissues from two breeds with distinct tail types. Forty-eight animals with the gender ratio of 1:1 for both Guangling Large Tailed (GLT) and Small Tailed Han (STH) sheep were slaughtered at 2, 4, 6, 8, 10, and 12 months of age, respectively. Adipose tissues were collected from greater and lesser omental, subcutaneous, retroperitoneal, perirenal, mesenteric, and tail fats. Ontogenetic mRNA expression of ANGPTL4 in these adipose tissues from GTL and STH was studied by quantitative real time polymerase chain reaction. The results showed that ANGPTL4 mRNA expressed in all adipose tissues studied with the highest in subcutaneous and the lowest in mesenteric fat depots. Months of age, tissue and breed are the main factors that significantly influence the mRNA expression. These results provide new insights into ovine ANGPTL4 gene expression and clues for its function mechanism.
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Affiliation(s)
- Jing Zhang
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
| | - Jiong-Jie Jing
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
| | - Xia-Li Jia
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
| | - Li-Ying Qiao
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
| | - Jian-Hua Liu
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
| | - Chen Liang
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
| | - Wen-Zhong Liu
- College of Animal Science and Technology, Shanxi Agricultural University, Taigu 030801, China
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16
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Restelli L, Lecchi C, Invernizzi G, Avallone G, Savoini G, Ceciliani F. UCP1 and UCP2 expression in different subcutaneous and visceral adipose tissue deposits in 30 days old goat kids and effect of fatty acid enriched diets. Res Vet Sci 2015; 100:131-7. [DOI: 10.1016/j.rvsc.2015.03.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Revised: 01/30/2015] [Accepted: 03/06/2015] [Indexed: 11/25/2022]
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17
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Yang G, Forrest R, Zhou H, Hodge S, Hickford J. Genetic variation in the ovine uncoupling protein 1 gene: association with carcass traits in New Zealand (NZ) Romney sheep, but no association with growth traits in either NZ Romney or NZ Suffolk sheep. J Anim Breed Genet 2014; 131:437-44. [PMID: 24909360 DOI: 10.1111/jbg.12097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 04/30/2014] [Indexed: 01/10/2023]
Abstract
The uncoupling protein 1 (UCP1) plays an important role in the regulation of lipolysis and thermogenesis in adipose tissues. Genetic variation within three regions (the promoter, intron 2 and exon 5) of the ovine UCP1 gene (UCP1) was investigated using polymerase chain reaction-single-strand conformational polymorphism (PCR-SSCP) analyses. These revealed three promoter variants (designated A, B and C) and two intron 2 variants (a and b). The association of this genetic variation with variation in lamb carcass traits and postweaning growth was investigated in New Zealand (NZ) Romney and Suffolk sheep. The presence of B in a lamb's genotype was associated with decreased subcutaneous carcass fat depth (V-GR) (p = 0.004) and proportion of total lean meat yield of loin meat (p = 0.005), and an increased proportion of total lean meat yield of hind-leg meat (p = 0.018). In contrast, having two copies of C was associated with increased V-GR (p < 0.001) and proportion of total lean meat yield of shoulder meat (p = 0.009), and a decreased hind-leg yield (p = 0.032). No associations were found with postweaning growth. These results suggest that ovine UCP1 is a potential gene marker for carcass traits.
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Affiliation(s)
- G Yang
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Science, Lanzhou, China
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