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Malgwi IH, Halas V, Grünvald P, Schiavon S, Jócsák I. Genes Related to Fat Metabolism in Pigs and Intramuscular Fat Content of Pork: A Focus on Nutrigenetics and Nutrigenomics. Animals (Basel) 2022; 12:ani12020150. [PMID: 35049772 PMCID: PMC8772548 DOI: 10.3390/ani12020150] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The intramuscular fat (IMF) or marbling is an essential pork sensory quality that influences the preference of the consumers and premiums for pork. IMF is the streak of visible fat intermixed with the lean within a muscle fibre and determines sensorial qualities of pork such as flavour, tenderness and juiciness. Fat metabolism and IMF development are controlled by dietary nutrients, genes, and their metabolic pathways in the pig. Nutrigenetics explains how the genetic make-up of an individual pig influences the pig’s response to dietary nutrient intake. Differently, nutrigenomics is the analysis of how the entire genome of an individual pig is affected by dietary nutrient intake. The knowledge of nutrigenetics and nutrigenomics, when harmonized, is a powerful tool in estimating nutrient requirements for swine and programming dietary nutrient supply according to an individual pig’s genetic make-up. The current paper aimed to highlight the roles of nutrigenetics and nutrigenomics in elucidating the underlying mechanisms of fat metabolism and IMF deposition in pigs. This knowledge is essential in redefining nutritional intervention for swine production and the improvement of some economically important traits such as growth performance, backfat thickness, IMF accretion, disease resistance etc., in animals. Abstract Fat metabolism and intramuscular fat (IMF) are qualitative traits in pigs whose development are influenced by several genes and metabolic pathways. Nutrigenetics and nutrigenomics offer prospects in estimating nutrients required by a pig. Application of these emerging fields in nutritional science provides an opportunity for matching nutrients based on the genetic make-up of the pig for trait improvements. Today, integration of high throughput “omics” technologies into nutritional genomic research has revealed many quantitative trait loci (QTLs) and single nucleotide polymorphisms (SNPs) for the mutation(s) of key genes directly or indirectly involved in fat metabolism and IMF deposition in pigs. Nutrient–gene interaction and the underlying molecular mechanisms involved in fatty acid synthesis and marbling in pigs is difficult to unravel. While existing knowledge on QTLs and SNPs of genes related to fat metabolism and IMF development is yet to be harmonized, the scientific explanations behind the nature of the existing correlation between the nutrients, the genes and the environment remain unclear, being inconclusive or lacking precision. This paper aimed to: (1) discuss nutrigenetics, nutrigenomics and epigenetic mechanisms controlling fat metabolism and IMF accretion in pigs; (2) highlight the potentials of these concepts in pig nutritional programming and research.
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Affiliation(s)
- Isaac Hyeladi Malgwi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
- Correspondence: ; Tel.: +39-33-17566768
| | - Veronika Halas
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Petra Grünvald
- Department of Farm Animal Nutrition, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary; (V.H.); (P.G.)
| | - Stefano Schiavon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padua, Viale dell’ Università 16, 35020 Padova, Italy;
| | - Ildikó Jócsák
- Institute of Agronomy, Kaposvár Campus, Hungarian University of Agriculture and Life Sciences, Guba Sándor Utca 40, 7400 Kaposvár, Hungary;
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Xing K, Wang K, Ao H, Chen S, Tan Z, Wang Y, Xitong Z, Yang T, Zhang F, Liu Y, Ni H, Sheng X, Qi X, Wang X, Guo Y, Wang C. Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds. Sci Rep 2019; 9:12925. [PMID: 31501489 PMCID: PMC6733950 DOI: 10.1038/s41598-019-49548-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 08/22/2019] [Indexed: 12/13/2022] Open
Abstract
Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.
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Affiliation(s)
- Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kejun Wang
- College of animal science and veterinary medicine, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Hong Ao
- State Key Laboratory for Animal Nutrition, Key Laboratory for Domestic Animal Genetic Resources and Breeding of the Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Shaokang Chen
- Beijing General Station of Animal Husbandry, Beijing, 100125, China
| | - Zhen Tan
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhao Xitong
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ting Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Hemin Ni
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xihui Sheng
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiaolong Qi
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Xiangguo Wang
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Yong Guo
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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3
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Miao Z, Wei P, Khan MA, Zhang J, Guo L, Liu D, Zhang X, Bai Y, Wang S. Transcriptome analysis reveals differential gene expression in intramuscular adipose tissues of Jinhua and Landrace pigs. J Vet Med Sci 2018; 80:953-959. [PMID: 29709900 PMCID: PMC6021883 DOI: 10.1292/jvms.18-0074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Meat is a rich source of protein, fatty acids and carbohydrates for human needs. In
addition to necessary nutrients, high fat contents in pork increase the tenderness and
juiciness of the meat, featuring diverse application in various dishes. This study
investigated the transcriptomic profiles of intramuscular adipose tissues in Jinhua and
Landrace pigs by employing advanced RNA sequencing. Results showed significant interesting
to note that there were significant differences in the expression of genes. 1,632 genes
showed significant differential expression, 837 genes were up-regulated and 195 genes were
down-regulated. Variations in genes responsible for cell aggregation, extracellular matrix
formation, cellular lipid catabolic process, and fatty acid binding strongly supported
that both pig breeds feature variable fat and muscle metabolism. Certain differentially
expressed genes are included in the pathway of mitogen-activated protein kinase signaling
pathway, Ras signaling pathway and insulin pathway. Results from real-time quantitative
polymerase chain reaction also validated the differential expression of 17 mRNAs between
meats of the two pig breeds. Overall, these findings reveal significant differences in fat
and protein metabolism of intramuscular adipose tissues of two pig breeds at the
transcriptomic level and suggest diversification at the genetic level between breeds of
the same species.
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Affiliation(s)
- Zhiguo Miao
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Panpeng Wei
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Muhammad Akram Khan
- Department of Pathobiology, Faculty of Veterinary and Animal Sciences, PMAS- Arid Agriculture University Rawalpindi, 46000, Pakistan
| | - Jinzhou Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Liping Guo
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Dongyang Liu
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Xiaojian Zhang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
| | - Yueyu Bai
- Animal Health Supervision of Henan Province, Bureau of Animal Husbandry of Henan province, Zhengzhou, 450000, P.R. China
| | - Shan Wang
- College of Animal Science and Veterinary Medicine, Henan Institute of Science and Technology, Xinxiang, Henan, 453003, P. R. China
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Yang Y, Zhou R, Mu Y, Hou X, Tang Z, Li K. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep 2016; 6:30160. [PMID: 27444743 PMCID: PMC4957084 DOI: 10.1038/srep30160] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5' and 3' flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals.
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Affiliation(s)
- Yalan Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Rong Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
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5
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Li XJ, Zhou J, Liu LQ, Qian K, Wang CL. Identification of genes in longissimus dorsi muscle differentially expressed between Wannanhua and Yorkshire pigs using RNA-sequencing. Anim Genet 2016; 47:324-33. [DOI: 10.1111/age.12421] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2015] [Indexed: 12/14/2022]
Affiliation(s)
- X.-J. Li
- Anhui Academy of Agricultural Sciences; Institute of Animal Husbandry and Veterinary Medicine; Hefei 230031 China
- College of Animal Science and Technology; Anhui Agricultural University; Hefei 230036 China
| | - J. Zhou
- College of Animal Science and Technology; Anhui Agricultural University; Hefei 230036 China
| | - L.-Q. Liu
- Anhui Academy of Agricultural Sciences; Institute of Animal Husbandry and Veterinary Medicine; Hefei 230031 China
| | - K. Qian
- Anhui Academy of Agricultural Sciences; Institute of Animal Husbandry and Veterinary Medicine; Hefei 230031 China
| | - C.-L. Wang
- Anhui Academy of Agricultural Sciences; Institute of Animal Husbandry and Veterinary Medicine; Hefei 230031 China
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6
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Zambonelli P, Gaffo E, Zappaterra M, Bortoluzzi S, Davoli R. Transcriptional profiling of subcutaneous adipose tissue in Italian Large White pigs divergent for backfat thickness. Anim Genet 2016; 47:306-23. [PMID: 26931818 DOI: 10.1111/age.12413] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2015] [Indexed: 12/30/2022]
Abstract
Fat deposition is a widely studied trait in pigs because of its implications with animal growth efficiency, technological and nutritional characteristics of meat products, but the global framework of the biological and molecular processes regulating fat deposition in pigs is still incomplete. This study describes the backfat tissue transcription profile in Italian Large White pigs and reports genes differentially expressed between fat and lean animals according to RNA-seq data. The backfat transcription profile was characterised by the expression of 23 483 genes, of which 54.1% were represented by known genes. Of 63 418 expressed transcripts, about 80% were non-previously annotated isoforms. By comparing the expression level of fat vs. lean pigs, we detected 86 robust differentially expressed transcripts, 72 more highly expressed (e.g. ACP5, BCL2A1, CCR1, CD163, CD1A, EGR2, ENPP1, GPNMB, INHBB, LYZ, MSR1, OLR1, PIK3AP1, PLIN2, SPP1, SLC11A1, STC1) and 14 lower expressed (e.g. ADSSL1, CDO1, DNAJB1, HSPA1A, HSPA1B, HSPA2, HSPB8, IGFBP5, OLFML3) in fat pigs. The main functional categories enriched in differentially expressed genes were immune system process, response to stimulus, cell activation and skeletal system development, for the overexpressed genes, and unfolded protein binding and stress response, for the underexpressed genes, which included five heat shock proteins. Adipose tissue alterations and impaired stress response are linked to inflammation and, in turn, to adipose tissue secretory activity, similar to what is observed in human obesity. Our results provide the opportunity to identify biomarkers of carcass fat traits to improve the pig production chain and to identify genetic factors that regulate the observed differential expression.
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Affiliation(s)
- P Zambonelli
- Department of Agricultural and-Food Sciences (DISTAL), Bologna University, Via Fratelli Rosselli 107, 42123, Reggio Emilia, Italy
| | - E Gaffo
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy
| | - M Zappaterra
- Department of Agricultural and-Food Sciences (DISTAL), Bologna University, Via Fratelli Rosselli 107, 42123, Reggio Emilia, Italy
| | - S Bortoluzzi
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121, Padova, Italy
| | - R Davoli
- Department of Agricultural and-Food Sciences (DISTAL), Bologna University, Via Fratelli Rosselli 107, 42123, Reggio Emilia, Italy
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7
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Xu X, Wei X, Yang Y, Niu W, Kou Q, Wang X, Chen Y. mRNA transcription and protein expression of PPARγ, FAS, and HSL in different parts of the carcass between fat-tailed and thin-tailed sheep. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Xing K, Zhu F, Zhai L, Liu H, Wang Y, Wang Z, Chen S, Hou Z, Wang C. Integration of transcriptome and whole genomic resequencing data to identify key genes affecting swine fat deposition. PLoS One 2015; 10:e0122396. [PMID: 25849573 PMCID: PMC4388518 DOI: 10.1371/journal.pone.0122396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/21/2015] [Indexed: 12/17/2022] Open
Abstract
Fat deposition is highly correlated with the growth, meat quality, reproductive performance and immunity of pigs. Fatty acid synthesis takes place mainly in the adipose tissue of pigs; therefore, in this study, a high-throughput massively parallel sequencing approach was used to generate adipose tissue transcriptomes from two groups of Songliao black pigs that had opposite backfat thickness phenotypes. The total number of paired-end reads produced for each sample was in the range of 39.29-49.36 millions. Approximately 188 genes were differentially expressed in adipose tissue and were enriched for metabolic processes, such as fatty acid biosynthesis, lipid synthesis, metabolism of fatty acids, etinol, caffeine and arachidonic acid and immunity. Additionally, many genetic variations were detected between the two groups through pooled whole-genome resequencing. Integration of transcriptome and whole-genome resequencing data revealed important genomic variations among the differentially expressed genes for fat deposition, for example, the lipogenic genes. Further studies are required to investigate the roles of candidate genes in fat deposition to improve pig breeding programs.
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Affiliation(s)
- Kai Xing
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Feng Zhu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Liwei Zhai
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Huijie Liu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuan Wang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Zhijun Wang
- Tianjin Ninghe primary pig breeding farm, Ninghe, 301500, Tianjin, China
| | - Shaokang Chen
- Animal husbandry and veterinary station of Beijing, Beijing, 100125, Beijing, China
| | - Zhuocheng Hou
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
| | - Chuduan Wang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, Department of Animal Genetics and Breeding, China Agricultural University, Beijing, 100193, China
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Xu X, Wei X, Yang Y, Niu W, Kou Q, Wang X, Chen Y. PPARγ, FAS, HSL mRNA and protein expression during Tan sheep fat-tail development. ELECTRON J BIOTECHN 2015. [DOI: 10.1016/j.ejbt.2015.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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10
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Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq. Mol Biol Rep 2014; 41:6305-15. [PMID: 25008993 DOI: 10.1007/s11033-014-3513-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/19/2014] [Indexed: 10/25/2022]
Abstract
Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.
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Sodhi SS, Song KD, Ghosh M, Sharma N, Lee SJ, Kim JH, Kim N, Mongre RK, Adhikari P, Kim JY, Hong SP, Oh SJ, Jeong DK. Comparative transcriptomic analysis by RNA-seq to discern differential expression of genes in liver and muscle tissues of adult Berkshire and Jeju Native Pig. Gene 2014; 546:233-42. [PMID: 24910116 DOI: 10.1016/j.gene.2014.06.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 05/29/2014] [Accepted: 06/04/2014] [Indexed: 12/16/2022]
Abstract
RNA-seq is being rapidly adopted for the profiling of the transcriptomes in different areas of biology, especially in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds of Sus scrofa, is of particular interest for the current study. For the better understanding of the gene expression profiles of the liver and longissimus dorsi muscle, DEGs were identified via RNA-seq. Sequence reads were obtained from Illumina HiSeq2000 and mapped to the pig reference genome (Sscrofa10.2) using Tophat2. We identified 169 and 39 DEGs in the liver and muscle of JNP respectively, by comparison with Berkshire breed. Out of all identified genes, 41 genes in the liver and 9 genes in the muscle have given significant expression. Gene ontology (GO) terms of developmental process and KEGG pathway analysis showed that metabolic, immune response and protein binding were commonly enriched pathways in the two tissues. Further the heat map analysis by ArrayStar has shown the different levels of expression in JNP with respect to the Berkshire breed. The validation through real time PCR and western blotting also confirmed the differential expression of genes in both breeds. Genes pertaining to metabolic process and inflammatory and immune system are more enriched in Berkshire breed. This comparative transcriptome analysis of two tissues suggests a subset of novel marker genes which expressed differently between the JNP and Berkshire.
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Affiliation(s)
- Simrinder Singh Sodhi
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Ki-Duk Song
- The Animal Genomics and Breeding Center, Hankyong National University, Anseong-si, Gyeonggi-do 456-749, South Korea
| | - Mrinmoy Ghosh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Neelesh Sharma
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Sung Jin Lee
- Department of Animal Biotechnology, College of Animal Bioscience and Technology, Kangwon National University, Chuncheon 200-701, South Korea
| | - Jeong Hyun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Nameun Kim
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Raj Kumar Mongre
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Pradeep Adhikari
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Jin Young Kim
- Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea
| | - Sang Pyo Hong
- Institute for Livestock Promotion, Jeju-do, Jeju 690-802, South Korea
| | - Sung Jong Oh
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea
| | - Dong Kee Jeong
- Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju 690-756, South Korea; Sustainable Agriculture Research Institute (SARI), Jeju National University, Jeju 690-756, South Korea.
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12
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Pérez-Montarelo D, Hudson NJ, Fernández AI, Ramayo-Caldas Y, Dalrymple BP, Reverter A. Porcine tissue-specific regulatory networks derived from meta-analysis of the transcriptome. PLoS One 2012; 7:e46159. [PMID: 23049964 PMCID: PMC3458843 DOI: 10.1371/journal.pone.0046159] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 08/28/2012] [Indexed: 11/19/2022] Open
Abstract
The processes that drive tissue identity and differentiation remain unclear for most tissue types. So are the gene networks and transcription factors (TF) responsible for the differential structure and function of each particular tissue, and this is particularly true for non model species with incomplete genomic resources. To better understand the regulation of genes responsible for tissue identity in pigs, we have inferred regulatory networks from a meta-analysis of 20 gene expression studies spanning 480 Porcine Affymetrix chips for 134 experimental conditions on 27 distinct tissues. We developed a mixed-model normalization approach with a covariance structure that accommodated the disparity in the origin of the individual studies, and obtained the normalized expression of 12,320 genes across the 27 tissues. Using this resource, we constructed a network, based on the co-expression patterns of 1,072 TF and 1,232 tissue specific genes. The resulting network is consistent with the known biology of tissue development. Within the network, genes clustered by tissue and tissues clustered by site of embryonic origin. These clusters were significantly enriched for genes annotated in key relevant biological processes and confirm gene functions and interactions from the literature. We implemented a Regulatory Impact Factor (RIF) metric to identify the key regulators in skeletal muscle and tissues from the central nervous systems. The normalization of the meta-analysis, the inference of the gene co-expression network and the RIF metric, operated synergistically towards a successful search for tissue-specific regulators. Novel among these findings are evidence suggesting a novel key role of ERCC3 as a muscle regulator. Together, our results recapitulate the known biology behind tissue specificity and provide new valuable insights in a less studied but valuable model species.
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Affiliation(s)
- Dafne Pérez-Montarelo
- Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Nicholas J. Hudson
- Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | - Ana I. Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Yuliaxis Ramayo-Caldas
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Brian P. Dalrymple
- Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
| | - Antonio Reverter
- Computational and Systems Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO) Animal, Food and Health Sciences, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, Australia
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Roh JG, Kim SW, Choi JS, Choi YI, Kim JJ, Choi BH, Kim TH, Kim KS. Characterization and Evaluation of Melanocortin 4 Receptor (MC4R) Gene Effect on Pork Quality Traits in Pigs. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2012. [DOI: 10.5187/jast.2012.54.1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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14
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Lim D, Lee KT, Park JE, Kim H, Kim TH, Choi BH, Kim MJ, Park HS, Jang GW. Analysis of gene expression profiles from subcutaneous adipose tissue of two pig breeds. Genes Genomics 2011. [DOI: 10.1007/s13258-011-0083-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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15
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Kim SW, Choi YI, Choi JS, Kim JJ, Choi BH, Kim TH, Kim KS. Porcine Fatty Acid Synthase Gene Polymorphisms Are Associated with Meat Quality and Fatty Acid Composition. Korean J Food Sci Anim Resour 2011. [DOI: 10.5851/kosfa.2011.31.3.356] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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16
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Differences in hepatic gene expression as a major distinguishing factor between Korean native pig and Yorkshire. Biosci Biotechnol Biochem 2011; 75:451-8. [PMID: 21389631 DOI: 10.1271/bbb.100625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
There are phenotypic differences between Korean native pig (KNP) and Yorkshire (YS) breeds due to different interests in selection. YS has been selected for industrial interests such as a growth rate and lean meat production, while KNP has been maintained as a regional breed with local interests such as disease resistance and fat content in and between muscle. A comparison of gene expression profiles from liver tissue reflected overall long-term effects of artificial selection for these two pig breeds. Based on minimum positive false discovery rate (less than 10%) and fold change (|FC|>1.5), 73 differentially expressed genes (DEGs) were identified. Functional analysis of these DEGs indicated clear distinctions in signaling capacity related to epidermal growth factor (EGF), extracellular structure, protein metabolism, and detoxification. Hepatic DEGs demonstrated the importance of hormonal and metabolic capabilities to differences between these two pig breeds.
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17
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D'Andrea M, Dal Monego S, Pallavicini A, Modonut M, Dreos R, Stefanon B, Pilla F. Muscle transcriptome profiling in divergent phenotype swine breeds during growth using microarray and RT-PCR tools. Anim Genet 2011; 42:501-9. [PMID: 21906101 DOI: 10.1111/j.1365-2052.2010.02164.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using an array consisting of 10 665 70-mer oligonucleotide probes, the longissimus dorsi muscle tissue expression during growth in nine pigs belonging to Casertana (CT), an autochthonous breed characterized by slow growth and a massive accumulation of backfat, was compared with that of two cosmopolitan breeds, Large White (LW) and a crossbreed (CB; Duroc × Landrace × Large White). The results were validated by real-time PCR. All animals were of the same age and were raised under the same environmental conditions. Muscle tissues were collected at 3, 6, 9 and 11 months of age, and a total of 173 genes showed significant differential expression between CT and the cosmopolitan genetic types at 3 months of age. Time series cluster analysis indicated that the CT breed had a different pattern of gene expression compared with that of the LW and the CB. Four of the eight clusters highlighted the gene differences between CT and the other two breeds, which were further supported by statistical analyses: clusters 4 and 5 contained a total of 71 genes that were underexpressed at 3 months of age, and cluster 3 and cluster 7 included 28 and 42 genes respectively that were overexpressed at 3 months of age. As expected, differentially expressed genes belonged to the category of genes coding for contractile fibres and transcription factors involved in muscle development and differentiation. These findings highlight muscle expression genes during pig growth and are useful to understand the genetic meaning of the different developmental rates.
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Affiliation(s)
- M D'Andrea
- University of Molise, SAVA, Campobasso, Italy.
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18
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Li X, Lee CK, Choi BH, Kim TH, Kim JJ, Kim KS. Quantitative gene expression analysis on chromosome 6 between Korean native pigs and Yorkshire breeds for fat deposition. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0009-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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19
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Kim SS, Kim JR, Moon JK, Choi BH, Kim TH, Kim KS, Kim JJ, Lee CK. Transcriptional alteration of p53 related processes as a key factor for skeletal muscle characteristics in Sus scrofa. Mol Cells 2009; 28:565-73. [PMID: 19937136 DOI: 10.1007/s10059-009-0159-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Accepted: 09/22/2009] [Indexed: 12/14/2022] Open
Abstract
The pig could be a useful model to characterize molecular aspects determining several delicate phenotypes because they have been bred for those characteristics. The Korean native pig (KNP) is a regional breed in Korea that was characterized by relatively high intramuscular fat content and reddish meat color compared to other western breeds such as Yorkshire (YS). YS grew faster and contained more lean muscle than KNP. We compared the KNP to Yorksire to find molecular clues determining muscle characteristics. The comparison of skeletal gene expression profiles between these two breeds showed molecular differences in muscle. We found 82 differentially expressed genes (DEGs) defined by fold change (more than 1.5 fold difference) and statistical significance (within 5% of false discovery rate). Functional analyses of these DEGs indicated up-regulation of most genes involved in cell cycle arrest, down-regulation of most genes involved in cellular differentiation and its inhibition, down-regulation of most genes encoding component of muscular-structural system, and up-regulation of most genes involved in diverse metabolism in KNP. Especially, DEGs in above-mentioned categories included a large number of genes encoding proteins directly or indirectly involved in p53 pathway. Our results indicated a possible role of p53 to determine muscle characteristics between these two breeds.
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Affiliation(s)
- Seung-Soo Kim
- College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
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