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Xu B, Luo X, Yang X, Zhang Y, Sebranek JG, Liang R. Comparative proteomic analyses to investigate premature browning in high‑oxygen modified atmosphere packaged beef patties. Food Chem 2024; 456:140022. [PMID: 38876067 DOI: 10.1016/j.foodchem.2024.140022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/23/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024]
Abstract
This study compared the proteomics of beef patties under high‑oxygen modified atmosphere packaging (HiOx-MAP) and vacuum packaging (VP) during heating. The color and oxidation stability of fresh patties, and myoglobin denaturation of cooked patties were also measured. The results suggested that HiOx-MAP patties contained more oxymyoglobin in fresh meat and had higher myoglobin denaturation during heating than VP patties, resulting in premature browning (PMB) during cooking. Proteomic analysis found that the overabundance of proteasome subunit beta type-2 (PSMB2) and peroxiredoxin-2 (PRDX2) in HiOx-55 °C, which can remove the damaged proteins and inhibit oxidation respectively, are of benefit to meat color stability during storage, however, this was still insufficient to inhibit the occurrence of PMB during cooking. The high abundance of lamin B1 (LMNB1) in VP-55 °C can maintain the stability of meat color. This research provides greater understanding, based on proteomic perspectives, of the molecular mechanism of PMB.
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Affiliation(s)
- Baochen Xu
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China
| | - Xin Luo
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Xiaoyin Yang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Yimin Zhang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
| | - Joseph G Sebranek
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA; Department of Food Science and Human Nutrition, Iowa State University, Ames, IA 50011-3150, USA.
| | - Rongrong Liang
- Lab of Beef Processing and Quality Control, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; National R&D Center for Beef Processing Technology, Tai'an, Shandong 271018, PR China.
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2
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Shi M, Huang L, Meng S, Wang H, Zhang J, Miao Z, Li Z. Identification of several lncRNA-mRNA pairs associated with marbling trait between Nanyang and Angus cattle. BMC Genomics 2024; 25:696. [PMID: 39014336 PMCID: PMC11250971 DOI: 10.1186/s12864-024-10590-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/03/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND The marbling trait of cattle muscles, being a key indicator, played an important role in evaluating beef quality. Two breeds of cattle, namely a high-marbling (Angus) and a low-marbling (Nanyang) one, with their cattle muscles selected as our samples for transcriptome sequencing, were aimed to identify differentially expressed long non-coding RNAs (lncRNAs) and their targets associated with the marbling trait. RESULTS Transcriptome sequencing identified 487 and 283 differentially expressed mRNAs and lncRNAs respectively between the high-marbling (Angus) and low-marbling (Nanyang) cattle muscles. Twenty-seven pairs of differentially expressed lncRNAs-mRNAs, including eighteen lncRNAs and eleven target genes, were found to be involved in fat deposition and lipid metabolism. We established a positive correlation between fourteen up-regulated (NONBTAT000849.2, MSTRG.9591.1, NONBTAT031089.1, MSTRG.3720.1, NONBTAT029718.1, NONBTAT004228.2, NONBTAT007494.2, NONBTAT011094.2, NONBTAT015080.2, NONBTAT030943.1, NONBTAT021005.2, NONBTAT021004.2, NONBTAT025985.2, and NONBTAT023845.2) and four down-regulated (NONBTAT000850.2, MSTRG.22188.3, MSTRG.22188.4, and MSTRG.22188.5) lncRNAs and eleven genes related to adiponectin family protein (ADIPOQ), cytochrome P450 family (CYP4V2), 3-hydroxyacyl-CoA dehydratase family (HACD4), kinesin family (KIF5C), lipin family (LPIN2), perilipin family (PLIN1), prostaglandin family (PTGIS), solute carrier family (SLC16A7, SLC2213, and SLCO4C1), and containing a transmembrane domain protein family (VSTM1). CONCLUSIONS These candidate genes and lncRNAs can be regarded as being responsible for regulating the marbling trait of cattle. lncRNAs along with the variations in intramuscular fat marbling established a foundation for elucidating the genetic basis of high marbling in cattle.
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Affiliation(s)
- Mingyan Shi
- Life Science College, Luoyang Normal University, Luoyang, Henan, 471934, China
| | - Luyao Huang
- College of Animal Science and Veterinary Medicine, Henan institute of Science and Technology, Xinxiang, 453003, China
| | - Shuaitao Meng
- College of Animal Science and Veterinary Medicine, Henan institute of Science and Technology, Xinxiang, 453003, China
| | - Heming Wang
- College of Animal Science and Veterinary Medicine, Henan institute of Science and Technology, Xinxiang, 453003, China
| | - Jinzhou Zhang
- College of Animal Science and Veterinary Medicine, Henan institute of Science and Technology, Xinxiang, 453003, China
| | - Zhiguo Miao
- College of Animal Science and Veterinary Medicine, Henan institute of Science and Technology, Xinxiang, 453003, China.
| | - Zhichao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.
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EL Nagar AG, Heddi I, Sosa-Madrid BS, Blasco A, Hernández P, Ibáñez-Escriche N. Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits. Animals (Basel) 2023; 13:3071. [PMID: 37835677 PMCID: PMC10571580 DOI: 10.3390/ani13193071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from -0.53 to -0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits.
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Affiliation(s)
- Ayman G. EL Nagar
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha 13736, Egypt
| | - Imen Heddi
- Centro Regional de Selección y Reproducción Animal (CERSYRA), Av. del Vino, 10, 13300 Valdepeñas, Spain
| | - Bolívar Samuel Sosa-Madrid
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Agustín Blasco
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Pilar Hernández
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
| | - Noelia Ibáñez-Escriche
- Institute for Animal Science and Technology, Universitat Politècnica de València, 46022 Valencia, Spain; (A.G.E.N.)
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Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs. Biomolecules 2022; 12:biom12091294. [PMID: 36139132 PMCID: PMC9496231 DOI: 10.3390/biom12091294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/05/2022] [Accepted: 09/09/2022] [Indexed: 11/24/2022] Open
Abstract
In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs.
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5
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Zhou Z, Li K, Liu J, Zhang H, Fan Y, Chen Y, Han H, Yang J, Liu Y. Expression Profile Analysis to Identify Circular RNA Expression Signatures in Muscle Development of Wu'an Goat Longissimus Dorsi Tissues. Front Vet Sci 2022; 9:833946. [PMID: 35518637 PMCID: PMC9062782 DOI: 10.3389/fvets.2022.833946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
The growth and development of skeletal muscle is a physiological process regulated by a variety of genes and signaling pathways. As a posttranscriptional regulatory factor, circRNA plays a certain regulatory role in the development of animal skeletal muscle in the form of a miRNA sponge. However, the role of circRNAs in muscle development and growth in goats is still unclear. In our study, apparent differences in muscle fibers in Wu'an goats of different ages was firstly detected by hematoxylin-eosin (HE) staining, the circRNA expression profiles of longissimus dorsi muscles from 1-month-old (mon1) and 9-month-old (mon9) goats were screened by RNA-seq and verified by RT-qPCR. The host genes of differentially expressed (DE) circRNAs were predicted, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses (KEGG) of host genes with DE circRNAs were performed to explore the functions of circRNAs. The circRNA-miRNA-mRNA networks were then constructed using Cytoscape software. Ten significantly differentially expressed circRNAs were also verified in the mon1 and mon9 groups by RT-qPCR. Luciferase Reporter Assay was used to verify the binding site between circRNA and its targeted miRNA. The results showed that a total of 686 DE circRNAs were identified between the mon9 and mon1 groups, of which 357 were upregulated and 329 were downregulated. Subsequently, the 467 host genes of DE circRNAs were predicted using Find_circ and CIRI software. The circRNA-miRNA-mRNA network contained 201 circRNAs, 85 miRNAs, and 581 mRNAs; the host mRNAs were associated with "muscle fiber development" and "AMPK signaling pathway" and were enriched in the FoxO signaling pathway. Competing endogenous RNA (ceRNA) network analysis showed that novel_circ_0005314, novel_circ_0005319, novel_circ_0009256, novel_circ_0009845, novel_circ_0005934 and novel_circ_0000134 may play important roles in skeletal muscle growth and development between the mon9 and mon1 groups. Luciferase Reporter Assay confirmed the combination between novel_circ_0005319 and chi-miR-199a-5p, novel_circ_0005934 and chi-miR-450-3p and novel_circ_0000134 and chi-miR-655. Our results provide specific information related to goat muscle development and a reference for the goat circRNA profile.
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Affiliation(s)
- Zuyang Zhou
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Kunyu Li
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Jiannan Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan, China
| | - Hui Zhang
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Yekai Fan
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Yulin Chen
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Haiyin Han
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Junqi Yang
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Yufang Liu
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
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6
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Garrett L, Da Silva-Buttkus P, Rathkolb B, Gerlini R, Becker L, Sanz-Moreno A, Seisenberger C, Zimprich A, Aguilar-Pimentel A, Amarie OV, Cho YL, Kraiger M, Spielmann N, Calzada-Wack J, Marschall S, Busch D, Schmitt-Weber C, Wolf E, Wurst W, Fuchs H, Gailus-Durner V, Hölter SM, de Angelis MH. Post-synaptic scaffold protein TANC2 in psychiatric and somatic disease risk. Dis Model Mech 2021; 15:273891. [PMID: 34964047 PMCID: PMC8906171 DOI: 10.1242/dmm.049205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 12/17/2021] [Indexed: 11/20/2022] Open
Abstract
Understanding the shared genetic aetiology of psychiatric and medical comorbidity in neurodevelopmental disorders (NDDs) could improve patient diagnosis, stratification and treatment options. Rare tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (TANC2)-disrupting variants were disease causing in NDD patients. The post-synaptic scaffold protein TANC2 is essential for dendrite formation in synaptic plasticity and plays an unclarified but critical role in development. We here report a novel homozygous-viable Tanc2-disrupted function model in which mutant mice were hyperactive and had impaired sensorimotor gating consistent with NDD patient psychiatric endophenotypes. Yet, a multi-systemic analysis revealed the pleiotropic effects of Tanc2 outside the brain, such as growth failure and hepatocellular damage. This was associated with aberrant liver function including altered hepatocellular metabolism. Integrative analysis indicates that these disrupted Tanc2 systemic effects relate to interaction with Hippo developmental signalling pathway proteins and will increase the risk for comorbid somatic disease. This highlights how NDD gene pleiotropy can augment medical comorbidity susceptibility, underscoring the benefit of holistic NDD patient diagnosis and treatment for which large-scale preclinical functional genomics can provide complementary pleiotropic gene function information. Summary: Disruption of mouse Tanc2 causes brain and liver abnormality, increasing psychiatric and somatic disease risk long term, highlighting the benefit of holistic diagnosis and treatment approaches for human neurodevelopmental disorder.
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Affiliation(s)
- Lillian Garrett
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Patricia Da Silva-Buttkus
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Lore Becker
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Adrian Sanz-Moreno
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Seisenberger
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annemarie Zimprich
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Technische Universität München, Freising-Weihenstephan, Germany
| | - Antonio Aguilar-Pimentel
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Oana V Amarie
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Yi-Li Cho
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Markus Kraiger
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Nadine Spielmann
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Julia Calzada-Wack
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Dirk Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstrasse 30, 81675 Munich, Germany
| | - Carsten Schmitt-Weber
- Center of Allergy & Environment (ZAUM), Technische Universität München, and Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising-Weihenstephan, Germany.,Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Feodor-Lynen-Str. 17, 81377 Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 17, 81377 Munich, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sabine M Hölter
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Technische Universität München, Freising-Weihenstephan, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
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7
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Liu Y, Long H, Feng S, Ma T, Wang M, Niu L, Zhang X, Wang L, Lei Y, Chen Y, Wang Q, Xu X. Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat. BMC Genomics 2021; 22:805. [PMID: 34749647 PMCID: PMC8577010 DOI: 10.1186/s12864-021-08141-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat quality, and the reason remains unknown. RESULTS In the present study, we identified 212 IMF-correlated genes (FDR ≤ 0.01) using correlation analysis between gene expression level and the value of IMF content. The IMF-correlated genes were significantly enriched in the processes of lipid metabolism and mitochondrial energy metabolism, as well as the AMPK/PPAR signaling pathway. From the IMF-correlated genes, we identified 99 genes associated with expression quantitative trait locus (eQTL) or allele-specific expression (ASE) signals, including 21 genes identified by both cis-eQTL and ASE analyses and 12 genes identified by trans-eQTL analysis. Genome-wide association study (GWAS) of IMF identified a significant QTL on SSC14 (p-value = 2.51E-7), and the nearest IMF-correlated gene SFXN4 (r = 0.28, FDR = 4.00E-4) was proposed as the candidate gene. Furthermore, we highlighted another three novel IMF candidate genes, namely AGT, EMG1, and PCTP, by integrated analysis of GWAS, eQTL, and IMF-gene correlation analysis. CONCLUSIONS The AMPK/PPAR signaling pathway together with the processes of lipid and mitochondrial energy metabolism plays a vital role in regulating porcine IMF content. Trait correlated expression combined with eQTL and ASE analysis highlighted a priority list of genes, which compensated for the shortcoming of GWAS, thereby accelerating the mining of causal genes of IMF.
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Affiliation(s)
- Yan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
| | - Huan Long
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Simin Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Tingting Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Mufeng Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Lizhu Niu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Xinyi Zhang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Lianni Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yu Lei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Yilong Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Qiankun Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China. .,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070, China. .,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China.
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8
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Albuquerque A, Óvilo C, Núñez Y, Benítez R, López-Garcia A, García F, Félix MDR, Laranjo M, Charneca R, Martins JM. Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds. Animals (Basel) 2021; 11:ani11051423. [PMID: 34065673 PMCID: PMC8156922 DOI: 10.3390/ani11051423] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Screening and interpretation of differentially expressed genes and associated biological pathways was conducted among experimental groups with divergent phenotypes providing valuable information about the metabolic events occurring and identification of candidate genes with major regulation roles. This comparative transcriptomic analysis includes the first RNA-seq analysis of the Longissimus lumborum muscle tissue from two Portuguese autochthonous pig breeds with different genetic backgrounds, Alentejano and Bísaro. Moreover, a complementary candidate gene approach was employed to analyse, by real time qPCR, the expression profile of relevant genes involved in lipid metabolism, and therefore with potential impacts on meat composition. This study contributes to explaining the biological basis of phenotypical differences occurring between breeds, particularly the ones related to meat quality traits that affect consumer interest. Abstract Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.
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Affiliation(s)
- André Albuquerque
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
- Correspondence: (A.A.); (J.M.M.)
| | - Cristina Óvilo
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Yolanda Núñez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Rita Benítez
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Adrián López-Garcia
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Fabián García
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain; (C.Ó.); (Y.N.); (R.B.); (A.L.-G.); (F.G.)
| | - Maria do Rosário Félix
- MED & Departamento de Fitotecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Marta Laranjo
- MED-Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada & Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - Rui Charneca
- MED & Departamento de Medicina Veterinária, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal;
| | - José Manuel Martins
- MED & Departamento de Zootecnia, Escola de Ciências e Tecnologia, Universidade de Évora, Pólo da Mitra, Ap. 94, 7006-554 Évora, Portugal
- Correspondence: (A.A.); (J.M.M.)
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9
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Liu YX, Ma XM, Xiong L, Wu XY, Liang CN, Bao PJ, Yu QL, Yan P. Effects of Intensive Fattening With Total Mixed Rations on Carcass Characteristics, Meat Quality, and Meat Chemical Composition of Yak and Mechanism Based on Serum and Transcriptomic Profiles. Front Vet Sci 2021; 7:599418. [PMID: 33553278 PMCID: PMC7859351 DOI: 10.3389/fvets.2020.599418] [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: 08/27/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
The objective of this study was to investigate the effects of intensive fattening with total mixed rations (TMR) on carcass characteristics, meat quality, and chemical composition of the yak meat. Theoretical data has been provided for evaluating the quality of yak meat during natural grazing and short-term fattening. Based on the analysis, we found that in fattening yak, the carcass weight (CWT) was increased by 106.43%, whereas the cooking loss, tenderness, and drop loss were significantly improved due to higher intramuscular fat content and lower moisture (P < 0.05). Protein, fat, calcium, and amino acids were also much higher (P < 0.01) in fattening yak compared with the grazing yak. The levels of albumin (ALB), lactate dehydrogenase (LDH), triglyceride (TRIG), and amylase (AMYL) in serum indicated better nutritional status for fattening yaks. The transcriptomics analysis showed that the high expression of ACSL1 and ACACB genes improved the synthesis and deposition of fat in fattening yak, whereas the regulation of SLC7A8, ATP1A4, ATP1A1, SLC3A2, and CPA3 gene expression weakened the proteolysis. These results indicated that fattening with TMR improves the yield and quality of the yak meat.
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Affiliation(s)
- Yi-Xuan Liu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Xiao-Ming Ma
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Lin Xiong
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Xiao-Yun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Chun-Nian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Peng-Jia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
| | - Qun-Li Yu
- College of Food Science and Engineering, Gansu Agricultural University, Lanzhou, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China.,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, China
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10
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Mullins Y, Keogh K, Kenny DA, Kelly A, O' Boyle P, Waters SM. Label-free quantitative proteomic analysis of M. longissimus dorsi from cattle during dietary restriction and subsequent compensatory growth. Sci Rep 2020; 10:2613. [PMID: 32054912 PMCID: PMC7018817 DOI: 10.1038/s41598-020-59412-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 01/18/2020] [Indexed: 12/12/2022] Open
Abstract
Compensatory growth (CG) is a naturally occurring physiological process whereby an animal has the ability to undergo enhanced growth following a period of restricted feeding. This studies objective was to identify key proteins involved in the expression of CG. Forty Holstein Friesian bulls were equally assigned to one of four groups. R1 and R2 groups were subjected to restricted feed allowance for 125 days (Period 1). A1 and A2 animals had ad libitum access to feed in Period 1. Following Period 1, all animals from R1 and A1 were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum access to feed for successive 55 days (Period 2). M. longissimus dorsi samples were collected at slaughter from all animals. Proteins were isolated from samples and subjected to label-free mass spectrometry proteomic quantification. Proteins which were differentially abundant during CG (n = 39) were involved in cellular binding processes, oxidative phosphorylation and mitochondrial function. There was also evidence for up regulation of three pathways involved in nucleotide biosynthesis. Genetic variants in or regulating genes pertaining to proteins identified in this study may hold potential for use as DNA based biomarkers for genomic selection of animals with a greater ability to undergo CG.
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Affiliation(s)
- Yvonne Mullins
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland.,School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Kate Keogh
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland
| | - Alan Kelly
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Padraig O' Boyle
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Athenry, Co., Galway, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co., Meath, Ireland.
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11
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Berri C, Picard B, Lebret B, Andueza D, Lefèvre F, Le Bihan-Duval E, Beauclercq S, Chartrin P, Vautier A, Legrand I, Hocquette JF. Predicting the Quality of Meat: Myth or Reality? Foods 2019; 8:E436. [PMID: 31554284 PMCID: PMC6836130 DOI: 10.3390/foods8100436] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/16/2019] [Accepted: 09/20/2019] [Indexed: 01/19/2023] Open
Abstract
This review is aimed at providing an overview of recent advances made in the field of meat quality prediction, particularly in Europe. The different methods used in research labs or by the production sectors for the development of equations and tools based on different types of biological (genomic or phenotypic) or physical (spectroscopy) markers are discussed. Through the various examples, it appears that although biological markers have been identified, quality parameters go through a complex determinism process. This makes the development of generic molecular tests even more difficult. However, in recent years, progress in the development of predictive tools has benefited from technological breakthroughs in genomics, proteomics, and metabolomics. Concerning spectroscopy, the most significant progress was achieved using near-infrared spectroscopy (NIRS) to predict the composition and nutritional value of meats. However, predicting the functional properties of meats using this method-mainly, the sensorial quality-is more difficult. Finally, the example of the MSA (Meat Standards Australia) phenotypic model, which predicts the eating quality of beef based on a combination of upstream and downstream data, is described. Its benefit for the beef industry has been extensively demonstrated in Australia, and its generic performance has already been proven in several countries.
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Affiliation(s)
- Cécile Berri
- UMR Biologie des Oiseaux et Aviculture, INRA, Université de Tours, 37380 Nouzilly, France.
| | - Brigitte Picard
- UMR Herbivores, INRA, VetAgro Sup, Theix, 63122 Saint-Genès Champanelle, France.
| | - Bénédicte Lebret
- UMR Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Élevage, INRA, AgroCampus Ouest, 35590 Saint-Gilles, France.
| | - Donato Andueza
- UMR Herbivores, INRA, VetAgro Sup, Theix, 63122 Saint-Genès Champanelle, France.
| | - Florence Lefèvre
- Laboratoire de Physiologie et Génomique des poissons, INRA, 35000 Rennes, France.
| | | | - Stéphane Beauclercq
- UMR Biologie des Oiseaux et Aviculture, INRA, Université de Tours, 37380 Nouzilly, France.
| | - Pascal Chartrin
- UMR Biologie des Oiseaux et Aviculture, INRA, Université de Tours, 37380 Nouzilly, France.
| | - Antoine Vautier
- Institut du porc, La motte au Vicomte, 35651 Le Rheu, CEDEX, France.
| | - Isabelle Legrand
- Institut de l'Elevage, Maison Régionale de l'Agriculture-Nouvelle Aquitaine, 87000 Limoges, France.
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12
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Skugor A, Kjos NP, Sundaram AYM, Mydland LT, Ånestad R, Tauson AH, Øverland M. Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome, production efficiency and meat quality traits in Norwegian Landrace growing-finishing pigs. PLoS One 2019; 14:e0220441. [PMID: 31390356 PMCID: PMC6685631 DOI: 10.1371/journal.pone.0220441] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/16/2019] [Indexed: 12/30/2022] Open
Abstract
This study was performed to investigate the effects of dietary inclusion of 20% rapeseed meal (RSM) as an alternative to soybean meal (SBM) in a three-month feeding experiment with growing finishing pigs. Dietary alteration affected growth performance, several carcass traits and transcriptional responses in the skeletal muscle, but did not affect measured meat quality traits. In general, pigs fed the RSM test diet exhibited reduced growth performance compared to pigs on SBM control diet. Significant transcriptional changes in the skeletal muscle of growing pigs fed RSM diet were likely the consequence of an increased amount of fiber and higher polyunsaturated fatty acids, and presence of bioactive phytochemicals, such as glucosinolates. RNAseq pipeline using Tophat2-Cuffdiff identified 57 upregulated and 63 downregulated genes in RSM compared to SBM pigs. Significantly enriched among downregulated pathways was p53-mediated signalling involved in cellular proliferation, while activation of negative growth regulators (IER5, KLF10, BTG2, KLF11, RETREG1, PRUNE2) in RSM fed pigs provided further evidence for reduced proliferation and increased cellular death, in accordance with the observed reduction in performance traits. Upregulation of well-known metabolic controllers (PDK4, UCP3, ESRRG and ESRRB), involved in energy homeostasis (glucose and lipid metabolism, and mitochondrial function), suggested less available energy and nutrients in RSM pigs. Furthermore, several genes supported more pronounced proteolysis (ABTB1, OTUD1, PADI2, SPP1) and reduced protein synthesis (THBS1, HSF4, AP1S2) in RSM muscle tissue. In parallel, higher levels of NR4A3, PDK4 and FGF21, and a drop in adropin, ELOVL6 and CIDEC/FSP27 indicated increased lipolysis and fatty acid oxidation, reflective of lower dressing percentage. Finally, pigs exposed to RSM showed greater expression level of genes responsive to oxidative stress, indicated by upregulation of GPX1, GPX2, and TXNIP.
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Affiliation(s)
- Adrijana Skugor
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Nils Petter Kjos
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | | | - Liv Torunn Mydland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Ragnhild Ånestad
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
| | - Anne-Helene Tauson
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Margareth Øverland
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Aas, Norway
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13
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Gagaoua M, Monteils V, Picard B. Data from the Farmgate-to-Meat Continuum Including Omics-Based Biomarkers to Better Understand the Variability of Beef Tenderness: An Integromics Approach. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13552-13563. [PMID: 30512949 DOI: 10.1021/acs.jafc.8b05744] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study is based on an integromic approach of 71 young bulls' data from the farmgate-to-meat continuum including omics-based biomarkers, to understand beef tenderness variability in two muscle cuts that differ by their contractile and metabolic properties. By the means of chemometrics using partial least-squares (PLS) and principal component regressions (PCR), important variables from a list of 49 that characterize four levels of the continuum (rearing factors-carcass-muscle-meat) were identified to explain tenderness of Longissimus thoracis (LT) and Semitendinosus (ST) muscles evaluated by a sensory panel and instrumental Warner-Bratzler shear force (WBSF). The PLS and PCR analyses validated 16 and 15 variables for LT and 12 and 14 for ST from the whole continuum to explain sensory tenderness and WBSF, respectively. Among the explanatory variables in the four models and in line with the role of apoptosis in tenderness determinism, HSP70-1A/B (a heat shock protein) was retained to explain beef tenderness irrespective of muscle and evaluation method. Similarly, dressing percentage from the carcass level was another robust predictor but in a muscle-dependent direction manner. HSP20, ENO3, and MyHC-I as three muscle protein biomarkers and dry matter intake (DMI) as a rearing factor were involved in three models to explain beef tenderness. This study highlighted also that several variables were muscle-specific irrespective of the evaluation method of tenderness. For LT muscle, six variables including three carcass traits (fatness score, fat carcass %, and muscle carcass %), two muscle biomarkers (HSP70-8 and MyHC-IIx/b), and one meat quality trait (pH3h) were found. For ST muscle, five variables were validated from two rearing factors (average daily gain and feed efficiency) and three structural protein biomarkers (α-actin, MyBP-H, and CapZ-β). Finally, for WBSF only, lactate dehydrogenase chain B (LDH-B) was retained positively for LT and negatively for ST muscles. Overall, this trial showed that tenderness of LT and ST muscle cuts is influenced by variables belonging to the whole continuum with relationships that depend on both the muscle type and the evaluation method. It further highlighted the potential of integromic/chemometric approaches on the farmgate-to-meat continuum data to better understand the sophisticated biological processes that orchestrate the conversion of muscle into meat and tenderness determinism.
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Affiliation(s)
- Mohammed Gagaoua
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Valérie Monteils
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
| | - Brigitte Picard
- Université Clermont Auvergne , INRA, VetAgro Sup, UMR Herbivores , F-63122 Saint-Genès-Champanelle , France
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14
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The study of protein biomarkers to understand the biochemical processes underlying beef color development in young bulls. Meat Sci 2017; 134:18-27. [DOI: 10.1016/j.meatsci.2017.07.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/06/2017] [Accepted: 07/17/2017] [Indexed: 01/05/2023]
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15
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Li C, Li X, Yao Y, Ma Q, Ni W, Zhang X, Cao Y, Hazi W, Wang D, Quan R, Hou X, Liu Z, Zhan Q, Liu L, Zhang M, Yu S, Hu S. Genome-wide analysis of circular RNAs in prenatal and postnatal muscle of sheep. Oncotarget 2017; 8:97165-97177. [PMID: 29228601 PMCID: PMC5722553 DOI: 10.18632/oncotarget.21835] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/23/2017] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs), a type of non-coding RNA with circular structure, were generated by back splicing and widely expressed in animals and plants. Recent studies have shown that circRNAs extensively participate in cell proliferation, cell differentiation, cell autophagy and other biological processes. However, the role and expression of circRNAs in the development and growth of muscle have not been studied in sheep. In our study, we first used RNA-seq to study the circRNAs in prenatal and postnatal longissimus dorsi muscle of sheep. A total of 6113 circRNAs were detected from the RNA-seq data. Several circRNAs were identified using reverse transcription PCR, DNA sequencing and RNase R digestion experiments. The expression levels of several circRNAs in prenatal and postnatal muscle were confirmed by Real-Time RT-PCR. The gene ontology (GO) and KEGG enrichment analysis of the host gene of the circRNAs showed that these circRNAs were mainly involved in the growth and development of muscle related signaling pathways. These circRNAs might sponge microRNAs (miRNAs) in predicted circRNA-miRNA-mRNA networks. The circRNAs expression profiles in muscle provided an important reference for the study of circRNAs in sheep.
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Affiliation(s)
- Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qiman Ma
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiangyu Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Yang Cao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Wureli Hazi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Dawei Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Zhijin Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Qianqian Zhan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, China
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16
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Lim D, Choi BH, Cho YM, Chai HH, Jang GW, Gondro C, Jeoung YH, Lee SH. Analysis of extended haplotype in Korean cattle (Hanwoo) population. BMB Rep 2017; 49:514-9. [PMID: 27470211 PMCID: PMC5227145 DOI: 10.5483/bmbrep.2016.49.9.074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Indexed: 12/22/2022] Open
Abstract
Korean cattle (Hanwoo) are categorized into three breeds based on color: brown, brindle, and black. Among these breeds, brown Hanwoo has been subjected to intensive selection to improve meat traits. To identify genetic traces driven by recent selection in brown Hanwoo, we scanned the genomes of brown and brindle Hanwoo using a bovine SNP chip. We identified 17 candidate selection signatures in brown Hanwoo and sequenced four candidate regions from 10 individuals each of brown and brindle Hanwoo. In particular, non-synonymous SNPs in the ADSL gene (K88M, L189H, and R302Q) might have had mutational effects on protein structure as a result of altering the purine pathway during nucleotide breakdown. The ADSL gene was previously reported to affect meat quality and yield in livestock. Meat quality and yield are main breeding goals for brown Hanwoo, and our results support a potential causal influence of non-synonymous SNPs in the ADSL gene. [BMB Reports 2016; 49(9): 514-519]
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Affiliation(s)
- Dajeong Lim
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Bong Hwan Choi
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Yong Min Cho
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Han Ha Chai
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Gul Won Jang
- Division of Animal Genomics & Bioinformatics, National Institute of Animal Science, RDA, Jeonju 55365, Korea
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
| | - Yeoung Ho Jeoung
- Hanwoo Department, Korea Animal Improvement Association, Seoul 06668, Korea
| | - Seung Hwan Lee
- Division of Animal and Dairy Science, Chung Nam National University, Daejeon 34134, Korea
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Zheng X, Kuang Y, Lv W, Cao D, Sun Z, Sun X. Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio). PLoS One 2016; 11:e0169127. [PMID: 28030623 PMCID: PMC5193488 DOI: 10.1371/journal.pone.0169127] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/12/2016] [Indexed: 12/24/2022] Open
Abstract
Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.
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Affiliation(s)
- Xianhu Zheng
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Youyi Kuang
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Weihua Lv
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
- College of Life Science, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Dingchen Cao
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Zhipeng Sun
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
| | - Xiaowen Sun
- National & Local United Engineering Laboratory of Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, Heilongjiang, China
- * E-mail:
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Welzenbach J, Neuhoff C, Heidt H, Cinar MU, Looft C, Schellander K, Tholen E, Große-Brinkhaus C. Integrative Analysis of Metabolomic, Proteomic and Genomic Data to Reveal Functional Pathways and Candidate Genes for Drip Loss in Pigs. Int J Mol Sci 2016; 17:E1426. [PMID: 27589727 PMCID: PMC5037705 DOI: 10.3390/ijms17091426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/12/2016] [Accepted: 08/22/2016] [Indexed: 01/21/2023] Open
Abstract
The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes.
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Affiliation(s)
- Julia Welzenbach
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Christiane Neuhoff
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Hanna Heidt
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
- Institute for Organic Agriculture Luxembourg, Association sans but lucratif (A.S.B.L.), 13 Rue Gabriel Lippmann, L-5365 Munsbach, Luxembourg.
| | - Mehmet Ulas Cinar
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
- Department of Animal Science, Faculty of Agriculture, Erciyes University, Talas Bulvari No. 99, 38039 Kayseri, Turkey.
| | - Christian Looft
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany.
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Yang H, Xu XL, Ma HM, Jiang J. Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed. BMC Genet 2016; 17:80. [PMID: 27296698 PMCID: PMC4906580 DOI: 10.1186/s12863-016-0389-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/02/2016] [Indexed: 11/08/2022] Open
Abstract
Background The Shaziling pig (Sus scrofa) is a well-known indigenous breed in China. One of its main advantages over European breeds is its high meat quality. However, little genetic information is available for the Shaziling pig. To screen for differentially expressed genes and proteins that might be responsible for the meat quality, the longissimus dorsi muscles from Shaziling and Yorkshire pig breeds were investigated using an integrative analysis of transcriptomics and proteomics, involving high-throughput sequencing, the two-dimensional gel electrophoresis, and mass spectrometry. Results Sequencing produced 79,320 unigenes by de novo assembly, and 488 differentially expressed genes in the longissimus dorsi muscle of Shaziling pig compared with the Yorkshire breed were identified. Gene Ontology term enrichment of biological functions and Kyoto Encyclopedia of Genes and Genomes analysis showed that the gene products were mainly involved in metabolism, protein binding, and regulation of skeletal muscle development. At the protein level, 23 differentially expressed proteins were identified, which were potentially associated with fatty acid metabolism, the glycolytic pathway, and skeletal muscle growth. Eight differentially expressed genes were confirmed by real-time PCR. These results give an insight into the mechanisms underlying the formation of skeletal muscle in the Shaziling pig. Conclusions Certain differentially expressed genes and proteins are involved in fatty acid metabolism, intramuscular fat deposition, and skeletal muscle growth in the Shaziling pig. These results provide candidate genes for improving meat quality and will promote further transcriptomic research in Shaziling pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0389-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hu Yang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.,College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Xing-Li Xu
- College of Life Science and Resource Environment, Yichun University, Yichun, 336000, People's Republic of China
| | - Hai-Ming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China.
| | - Jun Jiang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, People's Republic of China
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Mao Y, Hopkins DL, Zhang Y, Li P, Zhu L, Dong P, Liang R, Dai J, Wang X, Luo X. Beef quality with different intramuscular fat content and proteomic analysis using isobaric tag for relative and absolute quantitation of differentially expressed proteins. Meat Sci 2016; 118:96-102. [PMID: 27064846 DOI: 10.1016/j.meatsci.2016.03.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 03/29/2016] [Accepted: 03/30/2016] [Indexed: 12/23/2022]
Abstract
Intramuscular fat (IMF) is an important trait for beef eating quality. The mechanism of how IMF is deposited in beef cattle muscle is not clear at the molecular level. The muscle (M. longissimus lumborum: LL) of a group of Xiangxi yellow×Angus cattle with high fat levels (HF), was compared to the muscle of a low fat group (LF). The meat quality and the expressed protein patterns were compared. It was shown that LL from the HF animals had a greater fat content (P<0.05) and lower moisture content (P<0.05) than LL from LF animals. Forty seven sarcoplasmic proteins were differentially expressed and identified between the two groups. These proteins are involved in 6 molecular functions and 16 biological processes, and affect the Mitogen-activated protein kinases pathway, insulin pathway and c-Jun N-terminal kinases leading to greater IMF deposition. Cattle in the HF group had greater oxidative capacity and lower glycolytic levels suggesting a greater energetic efficiency.
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Affiliation(s)
- Yanwei Mao
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - David L Hopkins
- Centre for Red Meat and Sheep Development, NSW Department of Primary Industries, Cowra, NSW 2794, Australia
| | - Yimin Zhang
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - Peng Li
- Department of Food Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong, PR China
| | - Lixian Zhu
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - Pengcheng Dong
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - Rongrong Liang
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - Jin Dai
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China
| | - Xiaoyun Wang
- College of Life Science, Shandong Agricultural University, Tai'an, Shandong, PR China.
| | - Xin Luo
- College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, PR China; Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, PR China.
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Welzenbach J, Neuhoff C, Looft C, Schellander K, Tholen E, Große-Brinkhaus C. Different Statistical Approaches to Investigate Porcine Muscle Metabolome Profiles to Highlight New Biomarkers for Pork Quality Assessment. PLoS One 2016; 11:e0149758. [PMID: 26919205 PMCID: PMC4769069 DOI: 10.1371/journal.pone.0149758] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/04/2016] [Indexed: 12/04/2022] Open
Abstract
The aim of this study was to elucidate the underlying biochemical processes to identify potential key molecules of meat quality traits drip loss, pH of meat 1 h post-mortem (pH1), pH in meat 24 h post-mortem (pH24) and meat color. An untargeted metabolomics approach detected the profiles of 393 annotated and 1,600 unknown metabolites in 97 Duroc × Pietrain pigs. Despite obvious differences regarding the statistical approaches, the four applied methods, namely correlation analysis, principal component analysis, weighted network analysis (WNA) and random forest regression (RFR), revealed mainly concordant results. Our findings lead to the conclusion that meat quality traits pH1, pH24 and color are strongly influenced by processes of post-mortem energy metabolism like glycolysis and pentose phosphate pathway, whereas drip loss is significantly associated with metabolites of lipid metabolism. In case of drip loss, RFR was the most suitable method to identify reliable biomarkers and to predict the phenotype based on metabolites. On the other hand, WNA provides the best parameters to investigate the metabolite interactions and to clarify the complex molecular background of meat quality traits. In summary, it was possible to attain findings on the interaction of meat quality traits and their underlying biochemical processes. The detected key metabolites might be better indicators of meat quality especially of drip loss than the measured phenotype itself and potentially might be used as bio indicators.
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Affiliation(s)
- Julia Welzenbach
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Christiane Neuhoff
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Christian Looft
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Karl Schellander
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Ernst Tholen
- Institute of Animal Science, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
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22
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Recent advances in omic technologies for meat quality management. Meat Sci 2015; 109:18-26. [PMID: 26002117 DOI: 10.1016/j.meatsci.2015.05.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/10/2015] [Accepted: 05/11/2015] [Indexed: 12/24/2022]
Abstract
The knowledge of the molecular organization of living organisms evolved considerably during the last years. The methodologies associated also progressed with the development of the high-throughput sequencing (SNP array, RNAseq, etc.) and of genomic tools allowing the simultaneous analysis of hundreds or thousands of genes, proteins or metabolites. In farm animals, some proteins, mRNAs or metabolites whose abundance has been associated with meat quality traits have been detected in pig, cattle, chicken. They constitute biomarkers for the assessment and prediction of qualities of interest in each species, with potential biomarkers across species. The ongoing development of rapid methods will allow their use for decision-making and management tools in slaughterhouses, to better allocate carcasses or cuts to the appropriate markets. Besides, their application on living animals will help to improve genetic selection and to adapt a breeding system to fulfill expected quality level. The ultimate goal is to propose effective molecular tools for the management of product quality in meat production chains.
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23
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Hao R, Adoligbe C, Jiang B, Zhao X, Gui L, Qu K, Wu S, Zan L. An Optimized Trichloroacetic Acid/Acetone Precipitation Method for Two-Dimensional Gel Electrophoresis Analysis of Qinchuan Cattle Longissimus Dorsi Muscle Containing High Proportion of Marbling. PLoS One 2015; 10:e0124723. [PMID: 25893432 PMCID: PMC4404140 DOI: 10.1371/journal.pone.0124723] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 03/04/2015] [Indexed: 11/24/2022] Open
Abstract
Longissimus dorsi muscle (LD) proteomics provides a novel opportunity to reveal the molecular mechanism behind intramuscular fat deposition. Unfortunately, the vast amounts of lipids and nucleic acids in this tissue hampered LD proteomics analysis. Trichloroacetic acid (TCA)/acetone precipitation is a widely used method to remove contaminants from protein samples. However, the high speed centrifugation employed in this method produces hard precipitates, which restrict contaminant elimination and protein re-dissolution. To address the problem, the centrifugation precipitates were first grinded with a glass tissue grinder and then washed with 90% acetone (TCA/acetone-G-W) in the present study. According to our result, the treatment for solid precipitate facilitated non-protein contaminant removal and protein re-dissolution, ultimately improving two-dimensional gel electrophoresis (2-DE) analysis. Additionally, we also evaluated the effect of sample drying on 2-DE profile as well as protein yield. It was found that 30 min air-drying did not result in significant protein loss, but reduced horizontal streaking and smearing on 2-DE gel compared to 10 min. In summary, we developed an optimized TCA/acetone precipitation method for protein extraction of LD, in which the modifications improved the effectiveness of TCA/acetone method.
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Affiliation(s)
- Ruijie Hao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Camus Adoligbe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Bijie Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Xianlin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Linsheng Gui
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Kaixing Qu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Sen Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
- National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi, P.R. China, 712100
- * E-mail:
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24
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Bassols A, Costa C, Eckersall PD, Osada J, Sabrià J, Tibau J. The pig as an animal model for human pathologies: A proteomics perspective. Proteomics Clin Appl 2014; 8:715-31. [DOI: 10.1002/prca.201300099] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 04/28/2014] [Accepted: 07/30/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Anna Bassols
- Departament de Bioquímica i Biologia Molecular; Facultat de Veterinària; Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - Cristina Costa
- New Therapies of Genes and Transplants Group; Institut d'Investigació Biomèdica de Bellvitge (IDIBELL); L'Hospitalet de Llobregat; Barcelona Spain
| | - P. David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Glasgow UK
| | - Jesús Osada
- Departamento de Bioquímica y Biología Molecular; Facultad de Ciencias; Universidad de Zaragoza; CIBEROBN; Zaragoza Spain
| | - Josefa Sabrià
- Departament de Bioquímica i Biologia Molecular; Facultat de Medicina; Institut de Neurociències (INc); Universitat Autònoma de Barcelona; Cerdanyola del Vallès Spain
| | - Joan Tibau
- IRTA - Food Technology; Animal Genetics Program; Finca Camps i Armet; Monells Spain
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25
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Herault F, Vincent A, Dameron O, Le Roy P, Cherel P, Damon M. The Longissimus and Semimembranosus muscles display marked differences in their gene expression profiles in pig. PLoS One 2014; 9:e96491. [PMID: 24809746 PMCID: PMC4014511 DOI: 10.1371/journal.pone.0096491] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 04/09/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Meat quality depends on skeletal muscle structure and metabolic properties. While most studies carried on pigs focus on the Longissimus muscle (LM) for fresh meat consumption, Semimembranosus (SM) is also of interest because of its importance for cooked ham production. Even if both muscles are classified as glycolytic muscles, they exhibit dissimilar myofiber composition and metabolic characteristics. The comparison of LM and SM transcriptome profiles undertaken in this study may thus clarify the biological events underlying their phenotypic differences which might influence several meat quality traits. METHODOLOGY/PRINCIPAL FINDINGS Muscular transcriptome analyses were performed using a custom pig muscle microarray: the 15 K Genmascqchip. A total of 3823 genes were differentially expressed between the two muscles (Benjamini-Hochberg adjusted P value ≤0.05), out of which 1690 and 2133 were overrepresented in LM and SM respectively. The microarray data were validated using the expression level of seven differentially expressed genes quantified by real-time RT-PCR. A set of 1047 differentially expressed genes with a muscle fold change ratio above 1.5 was used for functional characterization. Functional annotation emphasized five main clusters associated to transcriptome muscle differences. These five clusters were related to energy metabolism, cell cycle, gene expression, anatomical structure development and signal transduction/immune response. CONCLUSIONS/SIGNIFICANCE This study revealed strong transcriptome differences between LM and SM. These results suggest that skeletal muscle discrepancies might arise essentially from different post-natal myogenic activities.
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Affiliation(s)
- Frederic Herault
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
| | - Annie Vincent
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
| | - Olivier Dameron
- Université de Rennes1, F-35000 Rennes, France
- IRISA team Dyliss, F-35000 Rennes, France
| | - Pascale Le Roy
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
| | - Pierre Cherel
- iBV-institut de Biologie Valrose, Université Nice-Sophia Antipolis UMR CNRS 7277 Inserm U1091, Parc Valrose, F-06108 Nice, France
| | - Marie Damon
- INRA, UMR1348, PEGASE, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348, PEGASE, F-35000 Rennes, France
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26
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Pena RN, Quintanilla R, Manunza A, Gallardo D, Casellas J, Amills M. Application of the microarray technology to the transcriptional analysis of muscle phenotypes in pigs. Anim Genet 2014; 45:311-21. [DOI: 10.1111/age.12146] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/05/2014] [Indexed: 01/09/2023]
Affiliation(s)
- R. N. Pena
- Department of Animal Production; University of Lleida-Agrotecnio Center; 25198 Lleida Spain
| | | | - A. Manunza
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - D. Gallardo
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - J. Casellas
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
| | - M. Amills
- Department of Animal Genetics; Center for Research in Agricultural Genomics (CSIC-IRTA-UAB-UB); Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
- Departament de Ciència Animal i dels Aliments; Facultat de Veterinària; Universitat Autònoma de Barcelona; 08193 Bellaterra Spain
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Hamill RM, Aslan O, Mullen AM, O'Doherty JV, McBryan J, Morris DG, Sweeney T. Transcriptome analysis of porcine M. semimembranosus divergent in intramuscular fat as a consequence of dietary protein restriction. BMC Genomics 2013; 14:453. [PMID: 23829541 PMCID: PMC3710489 DOI: 10.1186/1471-2164-14-453] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/26/2013] [Indexed: 12/23/2022] Open
Abstract
Background Intramuscular fat (IMF) content is positively correlated with aspects of pork palatability, including flavour, juiciness and overall acceptability. The ratio of energy to protein in the finishing diet of growing pigs can impact on IMF content with consequences for pork quality. The objective of this study was to compare gene expression profiles of Musculus semimembranosus (SM) of animals divergent for IMF as a consequence of protein dietary restriction in an isocaloric diet. The animal model was derived through the imposition of low or high protein diets during the finisher stage in Duroc gilts. RNA was extracted from post mortem SM tissue, processed and hybridised to Affymetrix porcine GeneChip® arrays. Results IMF content of SM muscle was increased on the low protein diet (3.60 ± 0.38% versus 1.92 ± 0.35%). Backfat depth was also greater in animals on the low protein diet, and average daily gain and feed conversion ratio were lower, but muscle depth, protein content and moisture content were not affected. A total of 542 annotated genes were differentially expressed (DE) between animals on low and high protein diets, with 351 down-regulated and 191 up-regulated on the low protein diet. Transcript differences were validated for a subset of DE genes by qPCR. Alterations in functions related to cell cycle, muscle growth, extracellular matrix organisation, collagen development, lipogenesis and lipolysis, were observed. Expression of adipokines including LEP, TNFα and HIF1α were increased and the hypoxic stress response was induced. Many of the identified transcriptomic responses have also been observed in genetic and fetal programming models of differential IMF accumulation, indicating they may be robust biological indicators of IMF content. Conclusion An extensive perturbation of overall energy metabolism in muscle occurs in response to protein restriction. A low protein diet can modulate IMF content of the SM by altering gene pathways involved in lipid biosynthesis and degradation; however this nutritional challenge negatively impacts protein synthesis pathways, with potential consequences for growth.
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Affiliation(s)
- Ruth M Hamill
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.
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29
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Pena RN, Noguera JL, Casellas J, Díaz I, Fernández AI, Folch JM, Ibáñez-Escriche N. Transcriptional analysis of intramuscular fatty acid composition in the longissimus thoracis muscle of Iberian × Landrace back-crossed pigs. Anim Genet 2013; 44:648-60. [PMID: 23826865 DOI: 10.1111/age.12066] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/29/2013] [Indexed: 11/29/2022]
Abstract
This study aimed at identifying differential gene expression conditional on the fatty acid profile of the longissimus thoracis (Lt) muscle, a prime cut of economic relevance for fresh and cured pork production. A population of 110 Iberian (25%) × Landrace (75%) back-crossed pigs was used, because these two breeds exhibit extreme profiles of intramuscular saturated fatty acid, monounsaturated fatty acid (MUFA) and polyunsaturated fatty acid (PUFA) contents. Total RNA from Lt muscle was individually hybridized to GeneChip Porcine Genome arrays (Affymetrix). A principal component analysis was performed with data from the 110 animals to select 40 extreme animals based on the total fatty acid profile and the MUFA composition (MAP). Comparison of global transcription levels between extreme fatty acid profile pigs (n = 40) resulted in 219 differentially expressed probes (false discovery rate <0.10). Gene ontology, pathway and network analysis indicated that animals with higher percentages of PUFA exhibit a shift toward a more oxidative muscular metabolism state, with a raise in mitochondria function (PPARGC1A, ATF2), fatty acid uptake and oxidation (FABP5, MGLL). On the other hand, 87 probes were differentially expressed between MUFA composition groups (n = 40; false discovery rate <0.10). In particular, muscles rich in n-7 MUFA expressed higher levels of genes involved in lipid metabolism (GLUL, CRAT, PLA2G15) and lower levels of fatty acid elongation genes (ELOVL5). Moreover, the chromosomal position of FABP5, PAQR3, MGLL, PPARGC1A, GLUL and ELOVL5 co-localized with very relevant QTL for fat deposition and composition described in the same resource population. This study represents a complementary approach to identifying genes underlying these QTL effects.
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Affiliation(s)
- R N Pena
- Genètica i Millora Animal, IRTA, 191 Av. Rovira Roure, 25198, Lleida, Spain; Departament de Producció Animal, ETSEA, Universitat de Lleida, 191 Av. Rovira Roure, 25198, Lleida, Spain
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30
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Damon M, Denieul K, Vincent A, Bonhomme N, Wyszynska-Koko J, Lebret B. Associations between muscle gene expression pattern and technological and sensory meat traits highlight new biomarkers for pork quality assessment. Meat Sci 2013; 95:744-54. [PMID: 23481319 DOI: 10.1016/j.meatsci.2013.01.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 01/15/2013] [Accepted: 01/23/2013] [Indexed: 01/03/2023]
Abstract
Meat quality (MQ) results from complex phenomenon and despite improved knowledge on MQ development, its variability remains high. The identification of biomarkers and the further development of rapid tests would thus be helpful to evaluate MQ in pork industries. Using transcriptomics, the present study aimed at identifying biomarkers of eight pork quality traits: ultimate pH, drip loss, lightness, redness, hue angle, intramuscular fat, shear force and tenderness, based on an experimental design inducing a high variability in MQ. Associations between microarray gene expression and pork traits (n=50 pigs) highlighted numerous potential biomarkers of MQ. Using quantitative RT-PCR, 113 transcript-trait correlations including 40 of these genes were confirmed (P<0.05, |r|≤0.73), out of which 60 were validated (P<0.05, |r|≤0.68) on complementary experimental data (n=50). Multiple regression models including 3 to 5 genes explained up to 59% of MQ trait variability. Moreover, functional analysis of correlated-trait genes provided information on the biological phenomena underlying MQ.
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Affiliation(s)
- Marie Damon
- INRA, UMR1348 PEGASE, F-35590 Saint-Gilles, France; Agrocampus Ouest, UMR1348 PEGASE, F-35000 Rennes, France
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31
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Differential effects of reduced protein diets on fatty acid composition and gene expression in muscle and subcutaneous adipose tissue of Alentejana purebred and Large White × Landrace × Pietrain crossbred pigs. Br J Nutr 2013; 110:216-29. [DOI: 10.1017/s0007114512004916] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The present study assessed the effect of pig genotype (fatty v. lean) and dietary protein and lysine (Lys) levels (normal v. reduced) on intramuscular fat (IMF) content, subcutaneous adipose tissue (SAT) deposition, fatty acid composition and mRNA levels of genes controlling lipid metabolism. The experiment was conducted on sixty intact male pigs (thirty Alentejana purebred and thirty Large White × Landrace × Pietrain crossbred), from 60 to 93 kg of live weight. Animals were divided into three groups fed with the following diets: control diet equilibrated for Lys (17·5 % crude protein (CP) and 0·7 % Lys), reduced protein diet (RPD) equilibrated for Lys (13·2 % CP and 0·6 % Lys) and RPD not equilibrated for Lys (13·1 % CP and 0·4 % Lys). It was shown that the RPD increased fat deposition in the longissimus lumborum muscle in the lean but not in the fatty pig genotype. It is strongly suggested that the effect of RPD on the longissimus lumborum muscle of crossbred pigs is mediated via Lys restriction. The increase in IMF content under the RPD was accompanied by increased stearoyl-CoA desaturase (SCD) and PPARG mRNA levels. RPD did not alter backfat thickness, but increased the total fatty acid content in both lean and fatty pig genotype. The higher amount of SAT in fatty pigs, when compared with the lean ones, was associated with the higher expression levels of ACACA, CEBPA, FASN and SCD genes. Taken together, the data indicate that the mechanisms regulating fat deposition in pigs are genotype and tissue specific, and are associated with the expression regulation of the key lipogenic genes.
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32
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D'Alessandro A, Zolla L. Meat science: From proteomics to integrated omics towards system biology. J Proteomics 2013; 78:558-77. [DOI: 10.1016/j.jprot.2012.10.023] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 10/25/2012] [Accepted: 10/26/2012] [Indexed: 12/16/2022]
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33
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Zhao SM, Li WZ, Pan HB, Huang Y, Yang MH, Wei HJ, Gao SZ. Expression levels of candidate genes for intramuscular fat deposition in two Banna mini-pig inbred lines divergently selected for fatness traits. Genet Mol Biol 2012; 35:783-9. [PMID: 23271939 PMCID: PMC3526086 DOI: 10.1590/s1415-47572012005000079] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 06/28/2012] [Indexed: 01/01/2023] Open
Abstract
Intramuscular fat (IMF) content plays an important role in meat quality. Many genes involved in lipid and energy metabolism were identified as candidate genes for IMF deposition, since genetic polymorphisms within these genes were associated with IMF content. However, there is less information on the expression levels of these genes in the muscle tissue. This study aimed at investigating the expression levels of sterol regulating element binding protein-1c (SREBP-1c), diacylglycerol acyltransferase (DGAT-1), heart-fatty acids binding protein (H-FABP), leptin receptor (LEPR) and melanocortin 4 receptor (MC4R) genes and proteins in two divergent Banna mini-pig inbred lines (BMIL). A similar growth performance was found in both the fat and the lean BMIL. The fat meat and IMF content in the fat BMIL were significantly higher than in the lean BMIL, but the lean meat content was lower. The serum triacylglycerol (TAG) and free fatty acid (FFA) contents were significantly higher in the fat than in the lean BMIL. The expression levels of SREBP-1c, DGAT-1 and H-FABP genes and proteins in fat BMIL were increased compared to the lean BMIL. However, the expression levels of LEPR and MC4R genes and proteins were lower.
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Affiliation(s)
- Su-Mei Zhao
- Yunnan Key Laboratory of Animal Nutrition and Feed Science, Yunnan Agricultural University, Kunming, China
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34
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Picard B, Lefèvre F, Lebret B. Meat and fish flesh quality improvement with proteomic applications. Anim Front 2012. [DOI: 10.2527/af.2012-0058] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- B. Picard
- INRA, UMR1213 Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - F. Lefèvre
- INRA, UR1037 Fish Physiology and Genomics, F-35042 Rennes, France
| | - B. Lebret
- INRA, UMR1348 Pegase, F-35590 Saint-Gilles, France
- Agrocampus Ouest, UMR1348 Pegase, F-35000 Rennes, France
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35
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de Almeida AM, Bendixen E. Pig proteomics: A review of a species in the crossroad between biomedical and food sciences. J Proteomics 2012; 75:4296-314. [DOI: 10.1016/j.jprot.2012.04.010] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/04/2012] [Accepted: 04/08/2012] [Indexed: 11/29/2022]
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36
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Molette C, Théron L, Marty-Gasset N, Fernandez X, Rémignon H. Current advances in proteomic analysis of (fatty) liver. J Proteomics 2012; 75:4290-5. [DOI: 10.1016/j.jprot.2012.04.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 04/24/2012] [Accepted: 04/27/2012] [Indexed: 01/29/2023]
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37
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Hamill RM, McBryan J, McGee C, Mullen AM, Sweeney T, Talbot A, Cairns MT, Davey GC. Functional analysis of muscle gene expression profiles associated with tenderness and intramuscular fat content in pork. Meat Sci 2012; 92:440-50. [PMID: 22688437 DOI: 10.1016/j.meatsci.2012.05.007] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 02/21/2012] [Accepted: 05/09/2012] [Indexed: 01/17/2023]
Abstract
Warner-Bratzler shear force (WBSF) and % intramuscular fat content (IMF) are objective meat quality measurements that are significantly correlated with aspects of palatability such as tenderness, flavour and juiciness. Using cDNA microarrays, Musculus longissimus transcriptomic profiles at slaughter were compared in samples displaying lower or higher IMF (n=8) and WBSF values on day 1 post mortem (n=8). 101 identified genes were differentially expressed in relation to WBSF, while 160 genes were associated with differences in IMF. Reduced expression of protein synthesis genes and enhanced expression of genes involved in protein degradation were associated with lower WBSF values on day 1. Pathways including oxidative phosphorylation and the citrate cycle were significantly associated with higher IMF. Many lipid oxidation and fatty acid metabolism pathway genes were down-regulated in high IMF tissue, suggesting a suppression of fatty acid turnover in muscle with higher fat content. Identified genes provide targets for the discovery of novel genetic variation influential on pork palatability.
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Affiliation(s)
- Ruth M Hamill
- Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.
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38
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Lamy E, Mau M. Saliva proteomics as an emerging, non-invasive tool to study livestock physiology, nutrition and diseases. J Proteomics 2012; 75:4251-8. [PMID: 22583933 DOI: 10.1016/j.jprot.2012.05.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 12/13/2022]
Abstract
Saliva is an extraordinary fluid in terms of research and diagnostic possibilities. Its composition in electrolytes, hormones and especially its proteome contains information about feeding status, nutritional requirements and adaptations to diet and environment, and also about health status of animals. It is easy to collect on a non-invasive and routine basis without any need for special training. Therefore, the analysis of salivary proteomes is going to emerge into a field of high interest with the future goal to maintain and improve livestock productivity and welfare. Moreover, the comprehensive analysis and identification of salivary proteins and peptides in whole and glandular saliva is a necessary pre-requisite to identify animal disease biomarkers and a powerful tool to better understand animal physiology. This review focuses on the different approaches used to study the salivary proteomes of farm animals, in respect to the physiology of nutrition and food perception in relation to food choices. The potential of animal saliva as a source of disease biomarkers will also be pointed out. Special emphasis is laid on the 'ruminating triad' - cattle, goat and sheep - as well as swine as major species of animal production in Western and Southern Europe.
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Affiliation(s)
- Elsa Lamy
- ICAAM - Institute of Mediterranean Agricultural and Environmental Sciences, University of Evora, Portugal
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39
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Bax M, Chambon C, Marty-Gasset N, Remignon H, Fernandez X, Molette C. Proteomic profile evolution during steatosis development in ducks. Poult Sci 2012; 91:112-20. [DOI: 10.3382/ps.2011-01663] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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40
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Tyra M, Ropka-Molik K. Effect of the FABP3 and LEPR gene polymorphisms and expression levels on intramuscular fat (IMF) content and fat cover degree in pigs. Livest Sci 2011. [DOI: 10.1016/j.livsci.2011.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Meat quality of the longissimus lumborum muscle of Casertana and Large White pigs: Metabolomics and proteomics intertwined. J Proteomics 2011; 75:610-27. [DOI: 10.1016/j.jprot.2011.08.024] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2011] [Revised: 08/04/2011] [Accepted: 08/28/2011] [Indexed: 01/06/2023]
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42
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Hazard D, Fernandez X, Pinguet J, Chambon C, Letisse F, Portais JC, Wadih-Moussa Z, Rémignon H, Molette C. Functional genomics of the muscle response to restraint and transport in chickens. J Anim Sci 2011; 89:2717-30. [PMID: 21512117 DOI: 10.2527/jas.2010-3288] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
In the present study, we used global approaches (proteomics, transcriptomics, and metabolomics) to assess the molecular basis of the muscle response to stress in chickens. A restraint test, combined with transport for 2 h (RT test) was chosen as the potentially stressful situation. Chickens (6 wk old) were either nontreated (control chickens) or submitted to the RT test (treated chickens). The RT test induced a 6-fold increase in corticosterone concentrations, suggesting hypothalamic-pituitary-adrenal axis activation. The RT test decreased the relative abundance of several hexose phosphates [glucose-1-P (G1P), glucose-6-P (G6P), fructose-6-P (F6P), and mannose-6-P (M6P)] in thigh muscle. In addition, 55 transcripts, among which 39 corresponded to unique annotated genes, were significantly up- (12 genes) or downregulated (27 genes) by treatment. Similarly, 45 proteic spots, among which 29 corresponded to unique annotated proteins, were overexpressed (11 proteins), underexpressed (14 proteins), or only expressed in treated chickens. Integrative analysis of differentially expressed genes and proteins showed that most transcripts and proteins belong to 2 networks whose genes were mainly related with cytoskeleton structure or carbohydrate metabolism. Whereas the decrease in energetic metabolites suggested an activation of glycogenolysis and glycolysis in response to the RT test, the reduced expression of genes and proteins involved in these pathways suggested the opposite. We hypothesized that the prolonged RT test resulted in a repression of glycogenolysis and glycolysis in thigh muscle of chickens. The down-expression of genes and proteins involved in the formation of fiber stress after the RT test suggests a reinforcement of myofibrils in response to stress.
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Affiliation(s)
- D Hazard
- Université de Toulouse, INPT ENSAT, UMR1289 Tissus Animaux Nutrition Digestion Ecosystème et Métabolisme, F-31326 Castanet-Tolosan, France
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Bendixen E, Danielsen M, Hollung K, Gianazza E, Miller I. Farm animal proteomics — A review. J Proteomics 2011; 74:282-93. [DOI: 10.1016/j.jprot.2010.11.005] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/04/2010] [Accepted: 11/05/2010] [Indexed: 11/28/2022]
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44
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Advances in research on the prenatal development of skeletal muscle in animals in relation to the quality of muscle-based food. II – Genetic factors related to animal performance and advances in methodology. Animal 2011; 5:718-30. [DOI: 10.1017/s1751731110002454] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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45
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Murgiano L, D’Alessandro A, Egidi MG, Crisà A, Prosperini G, Timperio AM, Valentini A, Zolla L. Proteomics and Transcriptomics Investigation on longissimus Muscles in Large White and Casertana Pig Breeds. J Proteome Res 2010; 9:6450-66. [DOI: 10.1021/pr100693h] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Leonardo Murgiano
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Angelo D’Alessandro
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Maria Giulia Egidi
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Alessandra Crisà
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Gianluca Prosperini
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Anna Maria Timperio
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Alessio Valentini
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
| | - Lello Zolla
- Dipartimento di Produzioni Animali, Università della Tuscia, Via de Lellis, 01100 Viterbo, Italy, and Dipartimento di Scienze Ambientali, Università della Tuscia, L.go dell’Università snc, 01100, Viterbo, Italy
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Lee SH, Gondro C, van der Werf J, Kim NK, Lim DJ, Park EW, Oh SJ, Gibson JP, Thompson JM. Use of a bovine genome array to identify new biological pathways for beef marbling in Hanwoo (Korean Cattle). BMC Genomics 2010; 11:623. [PMID: 21062493 PMCID: PMC3018137 DOI: 10.1186/1471-2164-11-623] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2010] [Accepted: 11/09/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marbling (intramuscular fat) is a valuable trait that impacts on meat quality and an important factor determining price of beef in the Korean beef market. Animals that are destined for this high marbling market are fed a high concentrate ration for approximately 30 months in the Korean finishing farms. However, this feeding strategy leads to inefficiencies and excessive fat production. This study aimed to identify candidate genes and pathways associated with intramuscular fat deposition on highly divergent marbling phenotypes in adult Hanwoo cattle. RESULTS Bovine genome array analysis was conducted to detect differentially expressed genes (DEGs) in m. longissimus with divergent marbling phenotype (marbling score 2 to 7). Three data-processing methods (MAS5.0, GCRMA and RMA) were used to test for differential expression (DE). Statistical analysis identified 21 significant transcripts from at least two data-processing methods (P < 0.01). All 21 differentially expressed genes were validated by real-time PCR. Results showed a high concordance in the gene expression fold change between the microarrays and the real time PCR data. Gene Ontology (GO) and pathway analysis demonstrated that some genes (ADAMTS4, CYP51A and SQLE) over expressed in high marbled animals are involved in a protein catabolic process and a cholesterol biosynthesis process. In addition, pathway analysis also revealed that ADAMTS4 is activated by three regulators (IL-17A, TNFα and TGFβ1). QRT-PCR was used to investigate gene expression of these regulators in muscle with divergent intramuscular fat contents. The results demonstrate that ADAMTS4 and TGFβ1 are associated with increasing marbling fat. An ADAMTS4/TGFβ1 pathway seems to be associated with the phenotypic differences between high and low marbled groups. CONCLUSIONS Marbling differences are possibly a function of complex signaling pathway interactions between muscle and fat. These results suggest that ADAMTS4, which is involved in connective tissue degradation, could play a role in an important biological pathway for building up marbling in cattle. Moreover, ADAMTS4 and TGFβ1could potentially be used as an early biological marker for marbling fat content in the early stages of growth.
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Affiliation(s)
- Seung-Hwan Lee
- Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, Suwon 441-706, Korea.
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Switonski M, Stachowiak M, Cieslak J, Bartz M, Grzes M. Genetics of fat tissue accumulation in pigs: a comparative approach. J Appl Genet 2010; 51:153-68. [DOI: 10.1007/bf03195724] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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48
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Intramuscular fat content in meat-producing animals: development, genetic and nutritional control, and identification of putative markers. Animal 2010; 4:303-19. [PMID: 22443885 DOI: 10.1017/s1751731109991091] [Citation(s) in RCA: 516] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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