Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using <scp>RNA</scp> sequencing

Lim, Kyu-Sang; Lee, K. T.; Park, Juhyeon; Chung, Won‐Hyong; Jang, Gul Won; Choi, Bong Hwan; Hong, Kyung Pyo; Kim, T. H.

doi:10.1111/age.12518

Cited by 47 publications

(46 citation statements)

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“…PLIN2 and FASN also play an important role in regulating intramuscular fat deposition [69,11]. PLIN2, an adipose differentiation-related protein (ADRP), is a kind of perilipin which can promote the biosynthesis and storage of fatty acid by coating lipid droplets [69].…”

Section: Pigsmentioning

confidence: 99%

“…FASN is a key enzyme of de novo fatty acid synthesis and can catalyze malonyl-CoA to form fatty acid [70]. The expression level of FASN was high in the longissimus dorsi muscle of Berkshire pig with high intramuscular fat content during the slaughter period [11]. In this study, FASN was highly expressed in the RNA extracted from intramuscular adipose tissue of LY pig and the intramuscular adipose tissue was separated in the part of longissimus muscle, which was inconsistent with the result of above-mentioned study.…”

Section: Pigsmentioning

confidence: 99%

“…They include stearoyl-CoA desaturase (SCD) [7][8][9], fatty acid synthase (FASN) [10,11], sterol regulatory element binding transcription factor 1 (SREBF1) [10], peroxisome proliferator-activated receptor γ (PPARγ) [12]. Some molecular events in the development of intramuscular fat have been recently revealed using longissimus dorsi muscle or adipocytes in pig [11,[13][14][15]. These studies indicate that adipocyte proliferation and differentiation is higher in subcutaneous fat than in intramuscular fat as well as in fat-type pig than in lean-type pig.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Huang

Zhang

et al. 2018

Cell Physiol Biochem

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Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

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Section: Pigsmentioning

confidence: 99%

Section: Pigsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Huang

Zhang

et al. 2018

Cell Physiol Biochem

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“…It encodes FA synthase, an important enzyme that catalyses the biosynthesis FAs. Differential expressions of FASN in muscle were reported within the same breed divergent for IMF content (in pig; Lim et al., ) and meat tenderness (in cattle; Zhao, Tian, et al., ; in pig; Zhao, Li, et al., ). Breed‐specific expression of FASN was also observed in pigs (Duran‐Montge, Theil, Lauridsen, & Esteve‐Garcia, ), cattle (Ji et al., ), and chicken (Cui et al., ).…”

Section: Discussionmentioning

confidence: 99%

Expression analyses of candidate genes related to meat quality traits in squabs from two breeds of meat‐type pigeon

Chen³

et al. 2018

Animal Physiology Nutrition

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In this study, meat quality traits were compared between squabs from two pigeon breeds: one Chinese indigenous breed, the Shiqi (SQ) meat-type pigeon, and an imported breed, the white king (WK) meat-type pigeon. Breed differences were detected in the content of intramuscular fat (IMF) in the breast muscle. SQ squabs had significantly higher IMF content than the WK birds. The shear force value (an objective measure of meat tenderness) of SQ birds was also relatively lower than that of the WK squabs. Further analysis of fatty acids profile revealed that SQ squabs exhibited significant advantage in the synthesis of polyunsaturated fatty acids, while WK squabs were significantly higher in the sum of monounsaturated fatty acids. Breast muscle in the SQ squabs was also significantly higher in the ratio of polyunsaturated fatty acids to saturated fatty acids, as well as the sum of omega 6 fatty acids. Variability of expression levels of functional genes in relation to fat accumulation and meat tenderness was analysed by qRT-PCR. Gene expression analyses showed that the hepatic expression of LPL (lipoprotein lipase), FABP4 (fatty acid-binding protein 4), and CAPN2 (calpain-2) were significantly higher in the SQ squabs. In the breast muscle tissue, the FABP3 (fatty acid-binding protein 3) and CAPN2mRNA abundance was significantly higher in SQ squabs. Our results suggested that these differentially expressed genes might be candidate genes used in the programmes of targeted selection for squabs with higher IMF content, tender meat, and more favourable fatty acids composition.

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“…To date, RNA-seq has been carried out in different livestock species, such as cattle [6], sheep [7], and pig [8], to identify genes involved in IMF content and other meat quality traits. Several studies on transcriptome profiling of porcine longissimus dorsi (LD) between breeds with different IMF content [9], or between individuals with extremely high or low IMF content in Berkshire [10] have been reported. However, studies on transcriptome profiling in Duroc for identify differentially expressed genes (DEGs) and pathways related to IMF content are still not reported.…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Muscle Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Duroc Pigs

Zhao

Wang

et al. 2019

Preprint

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Background Intramuscular fat (IMF) content plays a key role in meat quality of pork. Duroc is a common commercial pig breed, which is extensively used as the terminal male parent of DLY (Duroc × Landrace × Yorkshire) commercial pigs. For identification potential candidate genes and pathways, IMF content of 28 purebred Duroc pigs were measured, and transcriptome differences of muscles from individuals with divergent IMF content were analyzed based on RNA sequencing. Results As a result, a total of 309 DEGs were detected using edgeR and DESeq2 (p < 0.05, |log2(fold change)| ≥ 1) between the the IMF-High and -Low groups. Functional analysis of the DEGs revealed 27 Gene Ontology (GO) terms, two pathways (q < 0.05) and 23 key DEGs, which closely related to lipid metabolism and fat cell differentiation. Among these key DEGs, LEP, SFRP1, CIDEC, PNPLA3 and MT3, are potential candidate genes affecting IMF content due to their biological functions, the significant correlation between these genes’ expression with IMF content values in the 28 Duroc samples and proofs from previous studies. Meanwhile, a weighted gene co-expression network analysis (WGCNA) also revealed seven out of these key DEGs, including ADIPOQ, FABP4, PLIN1, CIDEA, ACAA1, CYP2A19 and ADIRF, were hub genes in turquoise module which may exhibit important functions in influencing IMF content. Furthermore, two pathways, regulation of lipolysis in adipocytes and PPAR signaling pathway, were potential pathways affecting IMF content because of their significant enrichment for the DEGs and co-expression genes of turquoise modules. Conclusions Our study demonstrates that some DEGs and pathways detected have essential role in regulating IMF content, and are supposed to be potential candidate genes and pathways affecting the trait in Duroc pigs. The study provides information for understanding molecular mechanism of IMF content, and would be of help for improving pork quality of Duroc pigs.

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Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing

Cited by 47 publications

References 47 publications

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Expression analyses of candidate genes related to meat quality traits in squabs from two breeds of meat‐type pigeon

Transcriptome Analysis of Muscle Reveals Potential Candidate Genes and Pathways Affecting Intramuscular Fat Content in Duroc Pigs

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