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

Zhao, Xueyan; Hu, Hongmei; Lin, Haichao; Cheng, Wang; Wang, Yanping; Wang, Jiying

doi:10.3389/fgene.2020.00877

Cited by 32 publications

(32 citation statements)

References 70 publications

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“…In the past, many studies have used low-density microsatellite markers to identify QTL associated with porcine IMF [ 5 , 6 , 7 ]. However, due to the low marker density, it is difficult to accurately locate the target genes [ 8 ].…”

Section: Introductionmentioning

confidence: 99%

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Cheng

Liang

Yang

et al. 2021

Animals

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Intramuscular fat (IMF) content is a complex trait that affects meat quality and determines pork quality. In order to explore the potential mechanisms that affect the intramuscular fat content of pigs, a Large white × Min pigs F2 resource populations were constructed, then whole-transcriptome profile analysis was carried out for five low-IMF and five high-IMF F2 individuals. In total, 218 messenger RNA (mRNAs), 213 long non-coding RNAs (lncRNAs), 18 microRNAs (miRNAs), and 59 circular RNAs (circRNAs) were found to be differentially expressed in the longissimus dorsi muscle. Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes annotations revealed that these differentially expressed (DE) genes or potential target genes (PTGs) of DE regulatory RNAs (lncRNAs, miRNAs, and circRNAs) are mainly involved in cell differentiation, fatty acid synthesis, system development, muscle fiber development, and regulating lipid metabolism. In total, 274 PTGs were found to be differentially expressed between low- and high-IMF pigs, which indicated that some DE regulatory RNAs may contribute to the deposition/metabolism of IMF by regulating their PTGs. In addition, we analyzed the quantitative trait loci (QTLs) of DE RNAs co-located in high- and low-IMF groups. A total of 97 DE regulatory RNAs could be found located in the QTLs related to IMF. Co-expression networks among different types of RNA and competing endogenous RNA (ceRNA) regulatory networks were also constructed, and some genes involved in type I diabetes mellitus were found to play an important role in the complex molecular process of intramuscular fat deposition. This study identified and analyzed some differential RNAs, regulatory RNAs, and PTGs related to IMF, and provided new insights into the study of IMF formation at the level of the genome-wide landscape.

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Section: Introductionmentioning

confidence: 99%

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Cheng

Liang

Yang

et al. 2021

Animals

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“…Adiponectin is involved in insulin sensitization, fat metabolism, immunity, and inflammation [37], and ADORA1 is responsible for anti-lipolysis [38]. Studies have reported that it is a candidate gene that affects the intramuscular fat content [39]. GNAS plays multiple important roles in cell fate determination and differentiation during osteogenic differentiation [40].…”

Section: Discussionmentioning

confidence: 99%

Comparative Transcriptomic Profiles of Differentiated Adipocytes Provide Insights into Adipogenesis Mechanisms of Subcutaneous and Intramuscular Fat Tissues in Pigs

Zhang

Shang

et al. 2022

Cells

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Subcutaneous fat thickness and intramuscular fat content are closely related to meat production and quality in the pig industry. Adipogenesis in adipocytes from subcutaneous and intramuscular fat tissues involves different genes and regulatory mechanisms. Analyzing the data of mRNA and miRNA transcriptomes during the differentiation of adipocytes from these two sources will help identify the different mechanisms of subcutaneous and intramuscular fat deposition. In this study, RNA sequencing technology was used to analyze the differential expression of genes and miRNAs in subcutaneous and intramuscular adipocytes at days 0, 2, 4, and 8 of differentiation. We mainly attributed the difference between fat depositions of the two types of adipocytes to variations in the expression patterns of related genes. Through combined weighted gene co-expression network analysis and K-MEANS, we identified 30 and 22 genes that mainly regulated the differentiation of subcutaneous adipocytes and intramuscular adipocytes, respectively. A total of 17 important candidate miRNAs were identified. This study provides valuable reference for the study of different mechanisms of adipogenesis among subcutaneous and intramuscular fat and contributes to improving pig breeding.

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“…The novel-m0170-3p was a novel miRNA identified, and there was no study on novel-m0170-3p. ADIPOQ is related to lipid metabolism and adipocyte differentiation ( 54 , 55 ). ADIPOQ was potentially regulated by the XR_003585597.1-miR-376c-3p relationship pair in this study.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Transcriptome Analysis Reveals the Role of lncRNA in Fatty Acid Metabolism in the Longissimus Thoracis Muscle of Tibetan Sheep at Different Ages

Bao

Zhao

et al. 2022

Front. Nutr.

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Long noncoding RNA (lncRNA) plays an important regulatory role in mammalian adipogenesis and lipid metabolism. However, their function in the longissimus thoracis (LT) muscle of fatty acid metabolism of Tibetan sheep remains undefined. In this study, fatty acid and fat content in LT muscle of Tibetan sheep were determined, and RNA sequencing was performed to reveal the temporal regularity of lncRNA expression and the effect of lncRNA-miRNA-mRNA ceRNA regulatory network on lipid metabolism of LT muscle in Tibetan sheep at four growth stages (4-month-old, 4 m; 1.5-year-old, 1.5 y; 3.5-year-old, 3.5 y; 6-year-old, 6 y). The results indicated that the intramuscular fat (IMF) content was highest at 1.5 y. Moreover, the monounsaturated fatty acid (MUFA) content in 1.5 y of Tibetan sheep is significantly higher than those of the other groups (P < 0.05), and it was also rich in a variety of polyunsaturated fatty acids (PUFA). A total of 360 differentially expressed lncRNAs (DE lncRNAs) were identified from contiguous period transcriptome comparative groups of 4 m vs. 1.5 y, 1.5 y vs. 3.5 y, 3.5 y vs. 6 y, and 4 m vs. 6 y, respectively. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis found that the target genes in lncRNA trans-mRNA were significantly related to the protein digestion, absorption, and fatty acid biosynthesis pathways (P < 0.05), which demonstrated that DE lncRNA trans-regulated the target genes, and further regulated the growth and development of the LT muscle and intramuscular fatty acid metabolism in Tibetan sheep. We further analyzed the role of the lncRNA-miRNA-mRNA regulatory network in the lipid metabolism of Tibetan sheep. Additionally, GPD2, LIPE (lipase E hormone-sensitive enzyme), TFDP2, CPT1A, ACACB, ADIPOQ, and other mRNA related to fatty acid and lipid metabolism and the corresponding lncRNA-miRNA regulatory pairs were identified. The enrichment analysis of mRNA in the regulatory network found that the AMPK signaling pathway was the most significantly enriched (P = 0.0000112361). Comprehensive transcriptome analysis found that the LIPE, ADIPOQ, ACACB, and CPT1A that were regulated by lncRNA might change the formation of energy metabolism in Tibetan sheep muscle through the AMPK signaling pathway, and oxidized muscle fibers are transformed into glycolytic muscle fibers, reduced IMF content, and the fatty acid profile also changed.

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

Cited by 32 publications

References 70 publications

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Systematic Identification and Comparison of the Expressed Profiles of lncRNAs, miRNAs, circRNAs, and mRNAs with Associated Co-Expression Networks in Pigs with Low and High Intramuscular Fat

Comparative Transcriptomic Profiles of Differentiated Adipocytes Provide Insights into Adipogenesis Mechanisms of Subcutaneous and Intramuscular Fat Tissues in Pigs

Comprehensive Transcriptome Analysis Reveals the Role of lncRNA in Fatty Acid Metabolism in the Longissimus Thoracis Muscle of Tibetan Sheep at Different Ages

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